Trying a 3D scene with 2D overlays

.gitignore

.idea
*.iml

2d_overlay_3d.js

const canvas = document.getElementById('3d')
const svg = document.getElementById('2d')
const xmlns = svg.getAttribute('xmlns')
const xlinkns = 'http://www.w3.org/1999/xlink';
const renderer = new THREE.WebGLRenderer({
  canvas,
  alpha: true,
  antialias: true
})
const camera = new THREE.PerspectiveCamera(
  45,
  window.innerWidth / window.innerHeight,
  0.1,
  10000
)
const scene = new THREE.Scene()
const group = new THREE.Group()
scene.add(group)

const directionalLight = new THREE.DirectionalLight(0xffffff, .5)
directionalLight.position.set(-2, 2, 2)
directionalLight.castShadow = true
scene.add(directionalLight)

const directionalLight2 = new THREE.DirectionalLight(0xffffff, .5)
directionalLight2.position.set(1, 2, 1)
directionalLight2.castShadow = true
scene.add( directionalLight2 )

const ambientLight = new THREE.AmbientLight(0x808080, .5)
scene.add(ambientLight)

const light = new THREE.HemisphereLight( 0xcefeff, 0xb3eaf0, .5 )
scene.add( light )
scene.fog = new THREE.Fog('#262626', 7, 9)

camera.position.set(0, 0, 8)
camera.lookAt(new THREE.Vector3(0,0,0))
camera.rotation.z = Math.PI
renderer.shadowMap.enabled = true
renderer.shadowMap.type = THREE.PCFSoftShadowMap

let width
let height
let square
let center = new THREE.Vector2()
const deg = Math.PI / 180
const resize = () => {
  const clientWidth = canvas.clientWidth
  const clientHeight = canvas.clientHeight
  const dpr = window.devicePixelRatio
  width = clientWidth * dpr
  height = clientHeight * dpr
  square = Math.min(width, height)
  if (
    canvas.width !== width ||
    canvas.height !== height
  ) {
    const aspect = width / height
    const desiredMinimumFov = Math.PI / 4 //90 deg
    // this ensures that I always have a 90deg square in the center of both landscape and portrait viewports
    camera.fov = (
      aspect >= 1 ? desiredMinimumFov : 2 * Math.atan(Math.tan(desiredMinimumFov / 2) / aspect)
    ) / deg
    camera.aspect = aspect
    camera.updateProjectionMatrix()
    renderer.setPixelRatio(dpr)
    renderer.setSize(
      clientWidth,
      clientHeight,
      false
    )
    svg.setAttribute('viewBox', `0 0 ${width} ${height}`)
    center.set(width / 2, height / 2)
    reziseDefs()
  }
}

let go = true
const loop = (time) => {
  if (go) {
    requestAnimationFrame(loop)
    resize()
    animate(time)
  }
}
const start = async () => {
  await makeObjects()
  requestAnimationFrame(loop)
}

const vector = new THREE.Vector3()
const getScreenXY = (object) => {
  vector.setFromMatrixPosition(object.matrixWorld)
  vector.project(camera);

  return new THREE.Vector3(
    ((( vector.x + 1 ) * 0.5)) * width,
    (1 - (( vector.y + 1 ) * 0.5)) * height,
    (( vector.z + 1 ) * 0.5) * square
  )
}

// now to get creative

const defs = document.createElementNS(xmlns, 'defs')
const overlayDef = document.createElementNS(xmlns, 'g')
const circle = document.createElementNS(xmlns, 'circle')
const line = document.createElementNS(xmlns, 'path')
overlayDef.setAttributeNS(null, 'id', 'overlay')
circle.setAttributeNS(null, 'class', 'stroke')
line.setAttributeNS(null, 'class', 'stroke')
overlayDef.appendChild(circle)
overlayDef.appendChild(line)
defs.appendChild(overlayDef)
svg.appendChild(defs)

let circleRadius
let fontSize
const reziseDefs = () => {
  const strokeWidth = '' + (square / 300)
  circleRadius = square / 15
  fontSize = (circleRadius * 0.35) + 'px'
  const lsa = circleRadius * 0.575
  const lsb = circleRadius * 0.525
  circle.setAttributeNS(null, 'r', circleRadius)
  line.setAttributeNS(null, 'd', `
    M-${lsa},-${lsa} L-${lsb},-${lsb}Z
    M${lsa},-${lsa} L${lsb},-${lsb}Z
    M-${lsa},${lsa} L-${lsb},${lsb}Z
    M${lsa},${lsa} L${lsb},${lsb}Z
  `)
  document.querySelectorAll('.stroke').forEach((element) => {
    element.setAttributeNS(null, 'stroke-width', strokeWidth)
  })
}

const materialBase = {metalness: 0.1, roughness: 0.5}
const atomDataMap = {
  h: {scale: 0.5, material: new THREE.MeshStandardMaterial(Object.assign({color: '#b1cbbf'}, materialBase))},
  c: {scale: 1.0, material: new THREE.MeshStandardMaterial(Object.assign({color: '#425d61'}, materialBase))},
  o: {scale: 1.1, material: new THREE.MeshStandardMaterial(Object.assign({color: '#c41715'}, materialBase))},
  n: {scale: 1.1, material: new THREE.MeshStandardMaterial(Object.assign({color: '#0b5366'}, materialBase))},
  cl: {scale: 1.2, material: new THREE.MeshStandardMaterial(Object.assign({color: '#216359'}, materialBase))},
  na: {scale: 1.2, material: new THREE.MeshStandardMaterial(Object.assign({color: '#474a9c'}, materialBase))},
}
const molecules = [
  {name: 'Sucrose', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/5988/sdf?record_type=3d'},
  {name: 'Nicotine', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/89594/sdf?record_type=3d'},
  {name: 'Cholesterol', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/5997/sdf?record_type=3d', rotation: new THREE.Euler(0, 0, -Math.PI / 2)},
  {name: 'Methylphenidate', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/4158/sdf?record_type=3d'},
  {name: 'Salt', path: 'https://cactus.nci.nih.gov/chemical/structure/[Cl-][Na+]/file?format=sdf&get3d=True'},
  {name: 'Alcohol', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/5798/sdf?record_type=3d'},
  {name: 'THC', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/16078/sdf?record_type=3d'},
  {name: 'Caffeine', path: 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2519/sdf?record_type=3d'}
]

let objects = []
const completeSets = 2
const makeObjects = () => {
  molecules.forEach((molecule) => {
    molecule.sdfText = sdfData[molecule.path]
    const parsedMolecule = sdfTextToThreeSnatom(molecule.sdfText, atomDataMap, molecule.rotation)
    molecule.data = parsedMolecule.data
    molecule.model = parsedMolecule.model
  })
  let moleculeScale = -Infinity
  let moleculeScaleVector = new THREE.Vector3()
  molecules.forEach((molecule) => {
    molecule.data.bounds.getSize(moleculeScaleVector)
    moleculeScale = Math.max(moleculeScale, moleculeScaleVector.length())
    molecule.model.children[0].position.sub(
      molecule.data.bounds.getCenter(moleculeScaleVector)
    )
  })
  for (let i = 0; i < molecules.length * completeSets; i++) {
    const moleculeIndex = i % molecules.length
    const pivotA = new THREE.Group()
    const pivotB = new THREE.Group()
    const molecule = molecules[moleculeIndex].model.clone(true)
    const overlay = document.createElementNS(xmlns, 'g')
    const use = document.createElementNS(xmlns, 'use')
    const text = document.createElementNS(xmlns, 'text')
    const line = document.createElementNS(xmlns, 'path')
    pivotA.position.x = 1.25
    molecule.scale.multiplyScalar(1 / moleculeScale)
    molecule.position.x = 0.75
    pivotA.add(molecule)
    pivotB.add(pivotA)
    group.add(pivotB)
    use.setAttributeNS(xlinkns, 'xlink:href', '#overlay')
    text.setAttributeNS(null, 'class', 'text')
    text.setAttributeNS(null, 'text-anchor', 'middle')
    text.setAttributeNS(null, 'alignment-baseline', 'central')
    line.setAttributeNS(null, 'class', 'stroke')
    text.textContent = molecules[moleculeIndex].name
    overlay.appendChild(use)
    overlay.appendChild(text)
    overlay.appendChild(line)
    svg.appendChild(overlay)

    objects.push({
      pivotA,
      pivotB,
      molecule,
      line,
      use,
      text,
      overlay
    })
  }
}

const loopDuration = 20
const tau = Math.PI * 2
const diff = new THREE.Vector2()
const pointA = new THREE.Vector2()
const pointB = new THREE.Vector2()
const pointC = new THREE.Vector2()
const rotatedRadius = new THREE.Vector2()
const circleRadiusVector = new THREE.Vector2()
const emptyVector = new THREE.Vector2(0, 0)
const clamp = (n) => { return Math.min(Math.max(0, n), 1) }
const animate = (time) => {
  const phase = time / 1000 / loopDuration / completeSets
  const objectFrac = 1 / objects.length
  // 3D loop
  objects.forEach((object, index) => {
    const frac = index * objectFrac
    object.pivotB.rotation.z = ((phase * completeSets) + 0.5 + frac) * tau
    object.pivotA.rotation.y = (phase + frac) * tau * 4
    object.molecule.rotation.z = (phase + frac) * tau * -2
  })
  renderer.render(scene, camera)
  // 2D loop needs to be run after the 3D render so all matrices are "baked"
  circleRadiusVector.set(circleRadius, 0)
  objects.forEach((object) => {
    const position = getScreenXY(object.molecule)
    diff.copy(position).sub(center)
    const angle = diff.angle()
    rotatedRadius.copy(circleRadiusVector).rotateAround(emptyVector, angle)
    pointA.copy(rotatedRadius).multiplyScalar(1.000)
    pointB.copy(rotatedRadius).multiplyScalar(1.500)
    pointC.copy(rotatedRadius).multiplyScalar(2.000)
    object.line.setAttributeNS(null, 'd', `M${pointA.x},${pointA.y} L${pointB.x},${pointB.y}Z`)
    object.use.setAttributeNS(null, 'transform', `rotate(${-(angle / deg) * 2})`)
    object.overlay.setAttributeNS(null, 'opacity', `${1 - clamp(((position.z / square) - 0.9863) * 1000) }`)
    object.overlay.setAttributeNS(null, 'transform', `translate(${position.x}, ${position.y})`)
    object.text.setAttributeNS(null, 'x', pointC.x)
    object.text.setAttributeNS(null, 'y', pointC.y)
    object.text.setAttributeNS(null, 'font-size', fontSize)
  })
}

start()

README.md

Trying a 3D scene with 2D overlays

Inspirations:

1. https://twitter.com/thespite/status/1024719405354287105
2. https://codepen.io/chrisgannon/pen/djjZBq
3. http://dvdp.tumblr.com/post/176088143808/180720-one-of-those-days-again
4. https://snatoms.com/

Resources:

1. http://alteredqualia.com/canvasmol/
2. http://molview.org/

index.html

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no" />
    <link href="https://fonts.googleapis.com/css?family=Exo+2" rel="stylesheet">
    <link rel="stylesheet" href="./styles.css" />
    <title>2D Overlay on to 3D</title>
</head>
<body>
    <canvas id="3d"></canvas>
    <svg id="2d" xmlns="http://www.w3.org/2000/svg"></svg>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/three.js/95/three.js"></script>
    <script src="./sdf_data.js"></script>
    <script src="./sdf_to_three.js"></script>
    <script src="./2d_overlay_3d.js"></script>
</body>
</html>

sdf_data.js

const sdfData = {
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/5988/sdf?record_type=3d": "5988\n  -OEChem-10052106453D\n\n 45 46  0     1  0  0  0  0  0999 V2000\n   -1.4680    0.4385   -0.9184 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6033   -0.8919    0.8122 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.9285    0.4834   -0.3053 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.0702   -2.0054    1.1933 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.6200    0.6319    0.7326 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2231    0.2156    2.5658 O   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6108   -1.7286    0.6379 O   0  0  0  0  0  0  0  0  0  0  0  0\n    3.1500    1.8347    1.1537 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9582   -1.8480   -2.4300 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.3845    3.2450   -0.8933 O   0  0  0  0  0  0  0  0  0  0  0  0\n    3.8369    0.2057   -2.5044 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4947   -0.8632   -0.3037 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -2.9301   -1.0229    0.1866 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -3.2290    0.3737    0.6887 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -2.5505    1.2243   -0.3791 C   0  0  1  0  0  0  0  0  0  0  0  0\n    0.7534   -0.7453    0.3971 C   0  0  1  0  0  0  0  0  0  0  0  0\n    1.6462   -0.7853    1.6390 C   0  0  1  0  0  0  0  0  0  0  0  0\n    3.1147   -0.5553    1.2746 C   0  0  2  0  0  0  0  0  0  0  0  0\n    3.2915    0.6577    0.3521 C   0  0  1  0  0  0  0  0  0  0  0  0\n    2.2579    0.7203   -0.7858 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -1.0903   -1.9271   -1.3122 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.0027    2.5323    0.1653 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.5886   -0.1903   -1.9666 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.6217   -1.2732   -0.6273 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.8148    0.5301    1.6917 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.2289    1.4361   -1.2150 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0588   -1.5992   -0.2109 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.5257   -1.7530    2.1409 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6908   -0.4029    2.1956 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.3100    0.6750   -0.0511 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2441    1.7505   -1.1644 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1311   -2.9324   -0.8803 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0995   -1.7686   -1.7400 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.2448    2.3605    0.9369 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7990    3.1543    0.5841 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8210   -0.1132   -2.7443 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.6532   -1.2446   -1.6891 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.9800   -1.9485    1.5318 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.7364    1.5664    0.9746 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.2787    0.0666    2.7433 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.5490   -1.5769    0.4327 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.3427    2.6011    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.6962   -2.5508   -3.0488 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6790    2.6806   -1.2535 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7489    1.1234   -2.8135 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1 12  1  0  0  0  0\n  1 15  1  0  0  0  0\n  2 12  1  0  0  0  0\n  2 16  1  0  0  0  0\n  3 16  1  0  0  0  0\n  3 20  1  0  0  0  0\n  4 13  1  0  0  0  0\n  4 38  1  0  0  0  0\n  5 14  1  0  0  0  0\n  5 39  1  0  0  0  0\n  6 17  1  0  0  0  0\n  6 40  1  0  0  0  0\n  7 18  1  0  0  0  0\n  7 41  1  0  0  0  0\n  8 19  1  0  0  0  0\n  8 42  1  0  0  0  0\n  9 21  1  0  0  0  0\n  9 43  1  0  0  0  0\n 10 22  1  0  0  0  0\n 10 44  1  0  0  0  0\n 11 23  1  0  0  0  0\n 11 45  1  0  0  0  0\n 12 13  1  0  0  0  0\n 12 21  1  0  0  0  0\n 13 14  1  0  0  0  0\n 13 24  1  0  0  0  0\n 14 15  1  0  0  0  0\n 14 25  1  0  0  0  0\n 15 22  1  0  0  0  0\n 15 26  1  0  0  0  0\n 16 17  1  0  0  0  0\n 16 27  1  0  0  0  0\n 17 18  1  0  0  0  0\n 17 28  1  0  0  0  0\n 18 19  1  0  0  0  0\n 18 29  1  0  0  0  0\n 19 20  1  0  0  0  0\n 19 30  1  0  0  0  0\n 20 23  1  0  0  0  0\n 20 31  1  0  0  0  0\n 21 32  1  0  0  0  0\n 21 33  1  0  0  0  0\n 22 34  1  0  0  0  0\n 22 35  1  0  0  0  0\n 23 36  1  0  0  0  0\n 23 37  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n5988\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.8\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n5\n7\n3\n6\n2\n4\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n31\n1 -0.56\n10 -0.68\n11 -0.68\n12 0.56\n13 0.28\n14 0.28\n15 0.28\n16 0.56\n17 0.28\n18 0.28\n19 0.28\n2 -0.56\n20 0.28\n21 0.28\n22 0.28\n23 0.28\n3 -0.56\n38 0.4\n39 0.4\n4 -0.68\n40 0.4\n41 0.4\n42 0.4\n43 0.4\n44 0.4\n45 0.4\n5 -0.68\n6 -0.68\n7 -0.68\n8 -0.68\n9 -0.68\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n7.2\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n21\n1 1 acceptor\n1 10 acceptor\n1 10 donor\n1 11 acceptor\n1 11 donor\n1 2 acceptor\n1 3 acceptor\n1 4 acceptor\n1 4 donor\n1 5 acceptor\n1 5 donor\n1 6 acceptor\n1 6 donor\n1 7 acceptor\n1 7 donor\n1 8 acceptor\n1 8 donor\n1 9 acceptor\n1 9 donor\n5 1 12 13 14 15 rings\n6 3 16 17 18 19 20 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n23\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n9\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n0000176400000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n77.6043\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n106.726\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n10498660 4 18408044026397964117\n10922523 26 18270957947412558034\n12173636 292 18187639206870113283\n13224815 77 17458622358473311570\n13538477 17 18113339708453955071\n14787075 74 16953691508025939297\n16752209 62 18263631888762839941\n16945 1 18335425621479279865\n18186145 218 17274547520514330359\n18981168 100 18268423530044661341\n21069387 34 14261360128088530127\n21486144 27 17060339638598854669\n21524375 3 18051681158311593581\n23557571 272 18058448883949780938\n23598288 3 18263344932996233811\n3286 77 13046208503433749912\n3797600 57 17024331783845889456\n45790113 50 17748831773987668583\n474 4 16660656180029715844\n5161694 15 17275108284303089140\n5845 1 17700395143258406769\n7097593 13 17606669223978608523\n81228 2 17772737510739799175\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n408.77\n6.87\n2.31\n2.04\n0.35\n1.13\n-0.51\n0.41\n0.45\n-1.56\n-0.45\n1.48\n-0.52\n-0.16\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n844.863\n\n> <PUBCHEM_SHAPE_VOLUME>\n231.2\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n",
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/89594/sdf?record_type=3d": "89594\n  -OEChem-10052106453D\n\n 26 27  0     1  0  0  0  0  0999 V2000\n   -1.7023   -0.7962   -0.0339 N   0  0  1  0  0  0  0  0  0  0  0  0\n    2.2968   -0.7091    1.2171 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8846    0.3095   -0.5713 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -1.4955    1.5824    0.0436 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6857    1.0984    0.8596 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.0281   -0.2382    0.2329 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.5872    0.1544   -0.2513 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.7618   -1.9503   -0.9217 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.5569    0.7025   -1.0791 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0008   -0.5357    0.8738 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9009    0.5451   -0.7593 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.2156   -0.1627    0.3895 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0084    0.3665   -1.6624 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8454    2.2456   -0.7571 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8018    2.1528    0.6709 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3896    0.9650    1.9076 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.5220    1.8029    0.8293 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.6094   -0.8662    0.9151 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.6021   -0.0880   -0.6903 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3643   -2.7460   -0.4698 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7627   -2.3668   -1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1975   -1.7036   -1.8965 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2798    1.2544   -1.9728 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3027   -0.9778    1.5770 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6775    0.9638   -1.3890 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.2491   -0.3134    0.6833 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  3  1  0  0  0  0\n  1  6  1  0  0  0  0\n  1  8  1  0  0  0  0\n  2 10  1  0  0  0  0\n  2 12  2  0  0  0  0\n  3  4  1  0  0  0  0\n  3  7  1  0  0  0  0\n  3 13  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4 14  1  0  0  0  0\n  4 15  1  0  0  0  0\n  5  6  1  0  0  0  0\n  5 16  1  0  0  0  0\n  5 17  1  0  0  0  0\n  6 18  1  0  0  0  0\n  6 19  1  0  0  0  0\n  7  9  1  0  0  0  0\n  7 10  2  0  0  0  0\n  8 20  1  0  0  0  0\n  8 21  1  0  0  0  0\n  8 22  1  0  0  0  0\n  9 11  2  0  0  0  0\n  9 23  1  0  0  0  0\n 10 24  1  0  0  0  0\n 11 12  1  0  0  0  0\n 11 25  1  0  0  0  0\n 12 26  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n89594\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.6\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n3\n8\n5\n2\n1\n4\n6\n7\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n14\n1 -0.81\n10 0.16\n11 -0.15\n12 0.16\n2 -0.62\n23 0.15\n24 0.15\n25 0.15\n26 0.15\n3 0.41\n6 0.27\n7 -0.14\n8 0.27\n9 -0.15\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n2\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n4\n1 1 cation\n1 2 acceptor\n5 1 3 4 5 6 rings\n6 2 7 9 10 11 12 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n12\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n1\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n00015DFA00000003\n\n> <PUBCHEM_MMFF94_ENERGY>\n28.7208\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n20.297\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n10857977 72 17775003526630995877\n11031198 65 15195570112767051744\n124424 183 16630243602600998766\n12716758 59 17917438587693076950\n12932764 1 18260546727622590676\n13024252 1 16226046682879912029\n13538477 17 18408885174204472783\n13581323 91 18343582940815744751\n14144814 61 18408043996021716112\n15669948 3 18342177807847078535\n15775835 57 18335709325059071392\n16945 1 18272369771797619637\n17844478 74 16200440186260247257\n19422 9 18261119568669312802\n20645464 45 17275099513985106371\n20871998 184 18059580243045283455\n21061003 4 15791740684565994036\n21930827 45 17775288257134836167\n22445834 79 18114461171538339858\n23236772 104 18187931711079941641\n23402539 116 17917418822849705989\n23552423 10 18046347710651554349\n2748010 2 17832141619578997365\n276578 36 17986406502870703379\n3248919 1 18131066030632652660\n369184 2 17385724686165187853\n63268167 104 17603863420775935508\n77492 1 18260548934961214197\n8030462 33 18186801408873701612\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n236.99\n5.05\n1.44\n1.11\n1.12\n0.29\n-0.05\n-0.19\n-0.59\n-1.11\n0.21\n0.41\n0.08\n-0.79\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n494.786\n\n> <PUBCHEM_SHAPE_VOLUME>\n134.9\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n",
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/5997/sdf?record_type=3d": "5997\n  -OEChem-10052106453D\n\n 74 77  0     1  0  0  0  0  0999 V2000\n    7.4996    1.5828   -0.3199 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8177   -1.1082   -0.2032 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -0.1192   -0.4371    0.9962 C   0  0  2  0  0  0  0  0  0  0  0  0\n    1.4069   -0.5652    0.9577 C   0  0  1  0  0  0  0  0  0  0  0  0\n    1.9478    0.0601   -0.3611 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -2.2919   -0.8444    0.1890 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -0.3507   -0.3835   -1.4733 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5192   -0.0819   -0.4669 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -0.8724   -0.9821    2.2059 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1802   -0.4327   -1.6188 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3228   -1.1293    1.7092 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0419    0.1295    2.1715 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.3507   -1.6209   -0.5805 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -0.5360   -2.6262   -0.3284 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.1902    0.2693    0.8685 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.0250    0.9005   -1.5654 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5099    0.3709    2.0236 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.9298   -1.5261   -0.8427 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.6816    0.5131    0.8483 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5422    1.0788   -1.6005 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.7871   -1.2758   -0.1342 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.0799    1.5067   -0.2396 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -3.2110   -1.3511   -2.0841 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.1857    0.2026   -0.2341 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -6.5950    0.4923    0.2927 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -7.0210    1.9641    0.1265 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -6.9608    2.4322   -1.3284 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -6.1320    2.8612    0.9919 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.3420    0.6430    0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.6832   -1.6247    1.0013 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7287    1.1384   -0.2924 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4681    0.2316    0.0536 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6679    0.6670   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7587   -0.8152   -2.3872 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8128   -0.3057    3.0646 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4762   -1.9538    2.5211 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4682   -1.4584   -1.8669 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4577    0.1809   -2.4834 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6868   -2.1380    1.9354 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.9829   -0.4196    2.2204 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8749   -0.4861    3.0637 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.5596    1.0968    2.3598 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.2280   -2.6991   -0.4184 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.9839   -3.0472   -1.2333 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.5324   -2.8514   -0.3834 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.9299   -3.1942    0.5205 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5741    1.8900   -1.4087 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6971    0.5660   -2.5568 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.0374    0.6439    2.9344 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6098   -1.7868   -1.8567 H   0  0  0  0  0  0  0  0  0  0  0  0\n    5.0153   -1.6694   -0.8217 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5014   -2.2625   -0.1550 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.0427    0.8850    1.8160 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.2092   -0.4372    0.6979 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.0327    0.1540   -1.9285 H   0  0  0  0  0  0  0  0  0  0  0  0\n    5.8095    1.8311   -2.3531 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.4968   -1.8725   -0.7224 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.9223   -1.6028    0.9045 H   0  0  0  0  0  0  0  0  0  0  0  0\n    5.7045    2.5078    0.0055 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.0371   -0.2938   -2.3068 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.1284   -1.6408   -2.6111 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4266   -1.9624   -2.5342 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.4754    0.8060    0.3359 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.1073    0.5076   -1.2817 H   0  0  0  0  0  0  0  0  0  0  0  0\n    7.8276    1.8603    0.5525 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -6.6571    0.2080    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -7.3119   -0.1425   -0.2432 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -8.0556    2.0552    0.4799 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -7.5096    1.7460   -1.9817 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -7.4214    3.4218   -1.4250 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.9346    2.5173   -1.6989 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -6.1070    2.5091    2.0285 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -6.5260    3.8837    1.0014 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.1039    2.9156    0.6205 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1 22  1  0  0  0  0\n  1 65  1  0  0  0  0\n  2  3  1  0  0  0  0\n  2  6  1  0  0  0  0\n  2  7  1  0  0  0  0\n  2 14  1  0  0  0  0\n  3  4  1  0  0  0  0\n  3  9  1  0  0  0  0\n  3 29  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4 12  1  0  0  0  0\n  4 30  1  0  0  0  0\n  5  8  1  0  0  0  0\n  5 10  1  0  0  0  0\n  5 31  1  0  0  0  0\n  6 11  1  0  0  0  0\n  6 13  1  0  0  0  0\n  6 32  1  0  0  0  0\n  7 10  1  0  0  0  0\n  7 33  1  0  0  0  0\n  7 34  1  0  0  0  0\n  8 15  1  0  0  0  0\n  8 16  1  0  0  0  0\n  8 18  1  0  0  0  0\n  9 11  1  0  0  0  0\n  9 35  1  0  0  0  0\n  9 36  1  0  0  0  0\n 10 37  1  0  0  0  0\n 10 38  1  0  0  0  0\n 11 39  1  0  0  0  0\n 11 40  1  0  0  0  0\n 12 17  1  0  0  0  0\n 12 41  1  0  0  0  0\n 12 42  1  0  0  0  0\n 13 21  1  0  0  0  0\n 13 23  1  0  0  0  0\n 13 43  1  0  0  0  0\n 14 44  1  0  0  0  0\n 14 45  1  0  0  0  0\n 14 46  1  0  0  0  0\n 15 17  2  0  0  0  0\n 15 19  1  0  0  0  0\n 16 20  1  0  0  0  0\n 16 47  1  0  0  0  0\n 16 48  1  0  0  0  0\n 17 49  1  0  0  0  0\n 18 50  1  0  0  0  0\n 18 51  1  0  0  0  0\n 18 52  1  0  0  0  0\n 19 22  1  0  0  0  0\n 19 53  1  0  0  0  0\n 19 54  1  0  0  0  0\n 20 22  1  0  0  0  0\n 20 55  1  0  0  0  0\n 20 56  1  0  0  0  0\n 21 24  1  0  0  0  0\n 21 57  1  0  0  0  0\n 21 58  1  0  0  0  0\n 22 59  1  0  0  0  0\n 23 60  1  0  0  0  0\n 23 61  1  0  0  0  0\n 23 62  1  0  0  0  0\n 24 25  1  0  0  0  0\n 24 63  1  0  0  0  0\n 24 64  1  0  0  0  0\n 25 26  1  0  0  0  0\n 25 66  1  0  0  0  0\n 25 67  1  0  0  0  0\n 26 27  1  0  0  0  0\n 26 28  1  0  0  0  0\n 26 68  1  0  0  0  0\n 27 69  1  0  0  0  0\n 27 70  1  0  0  0  0\n 27 71  1  0  0  0  0\n 28 72  1  0  0  0  0\n 28 73  1  0  0  0  0\n 28 74  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n5997\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.8\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n7\n5\n8\n4\n3\n2\n6\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n9\n1 -0.68\n12 0.14\n15 -0.28\n17 -0.29\n19 0.14\n22 0.28\n49 0.15\n65 0.4\n8 0.14\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n7\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n9\n1 1 acceptor\n1 1 donor\n1 23 hydrophobe\n3 26 27 28 hydrophobe\n5 13 21 24 25 26 hydrophobe\n5 2 3 6 9 11 rings\n6 2 3 4 5 7 10 rings\n6 4 5 8 12 15 17 rings\n6 8 15 16 19 20 22 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n28\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n8\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n0000176D00000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n82.553\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n45.771\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n10 15 14201398317544894844\n10554248 39 18199174101953245359\n10674148 151 18114187432842097806\n10693767 8 14548746058220655756\n10763959 59 17846497071130424904\n10906281 52 17676499366678374398\n11456790 92 17530959199002116096\n11578080 2 18129671794048770365\n11646440 116 15791729715594053676\n12011746 2 16702310087321501690\n12035758 1 14490475287696122777\n12236239 1 17967809478914911594\n12596602 18 17530688727435562617\n12788726 201 18040703771474481796\n12838862 33 15913321408802949984\n13140716 1 15431175757926876262\n13540713 4 16055169497864760667\n13690498 29 16987705965868870375\n13914758 101 18342460322649070642\n14251764 18 17386006217161245607\n14251764 30 8502655891874380677\n14765038 42 16950288428821426101\n14849402 71 17168435985638482997\n14931854 50 16988575610561587846\n15183329 4 16630528406409440099\n15196674 1 15625960754516932474\n15238133 3 18333725836347762376\n15840311 113 17822853057797274213\n17349148 13 13038919857996304966\n17980427 23 17967535700941478639\n18222031 100 14405187257277350666\n20105231 36 15068620466676381880\n20511986 3 17917986187750276934\n20775438 99 12676311884408373973\n21033648 29 18200865270647027048\n21267235 1 15625393462087966950\n21279426 13 16487252213924147391\n21424621 283 18407760322496464899\n21521239 73 14476956787811061861\n21623969 137 14345793842346874809\n21756936 100 18113336432095723219\n21781055 127 17458634398395783884\n21792961 116 17274830168344647799\n21859007 373 17560505236312641768\n22122407 14 18042137586055571521\n221357 26 15410623592460290010\n2215653 11 15913331307642354906\n22393880 68 16773787139040921655\n23559900 14 16056880286053780946\n23569914 152 15836511509965455149\n23576562 1 16844434098215242269\n2838139 119 18336546109696149021\n3004659 81 16415479384839559866\n312425 54 12974155234818435261\n3178227 256 15068343419394461636\n3633792 109 18059303063262761046\n3882209 13 16194826947298677463\n392239 28 15719396157206857359\n4058900 60 18343027649132611883\n4093350 32 18187080646932444458\n4098825 35 18412826850544501902\n4340502 62 14996282517783219032\n465052 167 11169916086851966654\n474113 269 17131275628731627422\n5104073 3 14635410659827713573\n5385378 56 17022899021542622650\n59755656 215 16988847167741490984\n999808 66 12612750220459161881\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n570.36\n18.22\n2.24\n2.01\n9.38\n0.64\n-0.38\n16.13\n3.09\n3.43\n0.33\n-0.76\n-0.09\n-0.4\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n1181.228\n\n> <PUBCHEM_SHAPE_VOLUME>\n325.9\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n",
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/4158/sdf?record_type=3d": "4158\n  -OEChem-10052106453D\n\n 36 37  0     1  0  0  0  0  0999 V2000\n    0.2042   -2.1333    0.9271 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1037   -2.7833   -1.2609 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.3120    1.6427   -0.3159 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.2425    0.2183    0.0339 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -2.5386   -0.5031   -0.3606 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0430   -0.4113   -0.6720 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -3.7572    0.1638    0.2717 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.7666    1.6585   -0.0300 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4360    2.3066    0.3450 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2688    0.2663   -0.3052 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0026   -1.9122   -0.4071 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4350    0.7493    0.9768 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2536    0.3781   -1.2657 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.6376    1.3708    1.3130 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.4563    0.9995   -0.9295 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6483    1.4958    0.3598 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.2932   -3.5068    1.3197 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1596    0.1181    1.1229 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5234   -1.5509   -0.0405 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6558   -0.5040   -1.4525 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1887   -0.3014   -1.7576 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.7372    0.0096    1.3575 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.6763   -0.3004   -0.1025 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.9644    1.8142   -1.0982 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.5822    2.1416    0.5195 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4173    1.7366   -1.3264 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4476    3.3617    0.0505 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.2936    2.2862    1.4322 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.6947    0.6496    1.7611 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1138   -0.0075   -2.2711 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.7907    1.7511    2.3188 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.2437    1.0961   -1.6713 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.5855    1.9781    0.6221 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1404   -3.9885    0.8224 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6404   -4.0278    1.0870 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4545   -3.5413    2.4004 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1 11  1  0  0  0  0\n  1 17  1  0  0  0  0\n  2 11  2  0  0  0  0\n  3  4  1  0  0  0  0\n  3  9  1  0  0  0  0\n  3 26  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4  6  1  0  0  0  0\n  4 18  1  0  0  0  0\n  5  7  1  0  0  0  0\n  5 19  1  0  0  0  0\n  5 20  1  0  0  0  0\n  6 10  1  0  0  0  0\n  6 11  1  0  0  0  0\n  6 21  1  0  0  0  0\n  7  8  1  0  0  0  0\n  7 22  1  0  0  0  0\n  7 23  1  0  0  0  0\n  8  9  1  0  0  0  0\n  8 24  1  0  0  0  0\n  8 25  1  0  0  0  0\n  9 27  1  0  0  0  0\n  9 28  1  0  0  0  0\n 10 12  2  0  0  0  0\n 10 13  1  0  0  0  0\n 12 14  1  0  0  0  0\n 12 29  1  0  0  0  0\n 13 15  2  0  0  0  0\n 13 30  1  0  0  0  0\n 14 16  2  0  0  0  0\n 14 31  1  0  0  0  0\n 15 16  1  0  0  0  0\n 15 32  1  0  0  0  0\n 16 33  1  0  0  0  0\n 17 34  1  0  0  0  0\n 17 35  1  0  0  0  0\n 17 36  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n4158\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.6\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n5\n32\n24\n31\n14\n49\n17\n30\n39\n19\n51\n34\n45\n13\n9\n11\n41\n42\n26\n7\n20\n37\n27\n4\n36\n33\n44\n16\n35\n40\n18\n38\n6\n48\n10\n8\n29\n21\n25\n52\n50\n12\n2\n3\n15\n23\n22\n46\n28\n43\n47\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n20\n1 -0.43\n10 -0.14\n11 0.66\n12 -0.15\n13 -0.15\n14 -0.15\n15 -0.15\n16 -0.15\n17 0.28\n2 -0.57\n26 0.36\n29 0.15\n3 -0.9\n30 0.15\n31 0.15\n32 0.15\n33 0.15\n4 0.27\n6 0.2\n9 0.27\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n5.2\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n5\n1 2 acceptor\n1 3 cation\n1 3 donor\n6 10 12 13 14 15 16 rings\n6 3 4 5 7 8 9 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n17\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n2\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n0000103E00000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n33.3157\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n25.371\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n10498660 4 18412540999017839093\n10922049 32 18411707586034940766\n11578080 2 11983202641268361197\n12532896 13 18338514243904318222\n12788726 201 17537733465812068146\n13132413 78 17617090313793228182\n13294875 104 18128802071998635144\n13538477 17 17751638990603554108\n13878862 14 17689429391989729989\n14178342 30 18334585611944736097\n14787075 74 18057318612178083833\n15309172 13 18261109690323776661\n15490181 7 18343010090967974591\n15775835 57 18413388734939903649\n15906896 17 18192433193299426270\n16945 1 18129089198862150316\n17980427 23 17407924749437572813\n18186145 218 17846227656374206768\n201361 129 18266183824848416361\n20510252 161 18267872863745140281\n20600515 1 16820750759296398752\n20645476 183 17968100888330046412\n20671657 1 18124032334564486137\n20711985 344 18050561047851860866\n21069387 34 13695874765958571177\n21501502 16 18124594185402113369\n21524375 3 18412263917417352822\n23402539 116 18271796969289812164\n23419403 2 17402674705631994618\n23526113 38 17774183244049625830\n23557571 272 17908151228376174388\n23558518 356 17980185706298501080\n25 1 17988371390089469268\n2748010 2 18340215115230311997\n276578 36 18334293167230804136\n305870 269 18336821992181971121\n3071541 236 18190173684003282602\n43471831 8 18335135380274163523\n5104073 3 18049735023406131881\n57177213 63 18335425608357261021\n6138700 20 18050858719725790774\n633830 44 18273215278991471405\n68419 9 17485323921139529391\n7364860 26 18054508006642727527\n77492 1 17459182040104515044\n81228 2 17978780538969920742\n81539 233 18334573491214392669\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n333.13\n5.83\n3.14\n1.21\n1.08\n3.21\n0.07\n-4.87\n0.04\n0.54\n0.84\n-0.77\n0.38\n-0.01\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n691.966\n\n> <PUBCHEM_SHAPE_VOLUME>\n188.4\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n",
  "https://cactus.nci.nih.gov/chemical/structure/[Cl-][Na+]/file?format=sdf&get3d=True": "ClNa\nAPtclcactv10042123193D 0   0.00000     0.00000\n \n  2  1  0  0  0  0  0  0  0  0999 V2000\n   -0.9245    0.0000    0.0000 Cl  0  4  0  0  0  0  0  0  0  0  0  0\n    1.4255    0.0000    0.0000 Na  0  4  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\nM  CHG  2   1  -1   2   1\nM  RAD  2   1   2   2   2\nM  END\n$$$$\n",
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/5798/sdf?record_type=3d": "5798\n  -OEChem-10052106453D\n\n 15 16  0     0  0  0  0  0  0999 V2000\n    1.5466    1.1309   -0.0001 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.6283   -1.0902    0.0001 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.2393    0.7166   -0.0001 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3170   -0.6734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.9675    1.4168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8699   -1.4256   -0.0001 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1388    0.6524    0.0002 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.3379    0.0161    0.0001 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.0930   -0.7436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8680    2.0898   -0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0004    2.5004    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8451   -2.5106   -0.0001 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.4166    0.0792    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.1028    1.1552    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.0205   -1.3105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  3  1  0  0  0  0\n  1  8  1  0  0  0  0\n  1 10  1  0  0  0  0\n  2  4  1  0  0  0  0\n  2  8  2  0  0  0  0\n  3  4  1  0  0  0  0\n  3  5  2  0  0  0  0\n  4  6  2  0  0  0  0\n  5  7  1  0  0  0  0\n  5 11  1  0  0  0  0\n  6  9  1  0  0  0  0\n  6 12  1  0  0  0  0\n  7  9  2  0  0  0  0\n  7 14  1  0  0  0  0\n  8 13  1  0  0  0  0\n  9 15  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n5798\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.4\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n15\n1 0.03\n10 0.27\n11 0.15\n12 0.15\n13 0.15\n14 0.15\n15 0.15\n2 -0.57\n3 -0.15\n4 0.23\n5 -0.15\n6 -0.15\n7 -0.15\n8 0.04\n9 -0.15\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n0\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n4\n1 1 donor\n3 1 2 8 cation\n5 1 2 3 4 8 rings\n6 3 4 5 6 7 9 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n9\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n000016A600000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n14.039\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n20.404\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n16945 1 18410573985162007143\n18185500 45 18194681690298610967\n21040471 1 18338517430527374272\n23552423 10 18260832609146004622\n2748010 2 18410855503220253223\n29004967 10 18261960759488928083\n369184 2 18410849962585860283\n5084963 1 18272367538303765043\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n175.25\n2.95\n1.52\n0.6\n0.35\n0\n0\n-0.01\n0\n-0.25\n0\n-0.03\n0\n0\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n387.656\n\n> <PUBCHEM_SHAPE_VOLUME>\n96.5\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n",
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/16078/sdf?record_type=3d": "16078\n  -OEChem-10052106453D\n\n 53 55  0     1  0  0  0  0  0999 V2000\n   -0.5787   -1.9919    0.4990 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.3951    2.6957   -0.8292 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7626   -0.9279    0.1684 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -2.1208    0.3156   -0.4942 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -1.8900   -2.1827   -0.0737 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.2255   -1.0355   -0.2831 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6628    0.3922   -0.0810 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.0238    0.1842    0.1928 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.9653    1.5429   -0.2199 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.2731    1.4881    0.0931 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0013   -0.7572    0.3763 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4784   -3.4921    0.4747 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.6307   -2.3886   -1.5769 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0890    1.5706   -0.2281 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.3498   -0.7035    0.7501 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.0789    2.7258    0.3636 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0651    0.4844    0.6346 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4370    1.6193    0.1358 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5035    0.5330    1.0232 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.4822    0.1832   -0.1131 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.9447    0.1800    0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.8816   -0.1965   -0.8055 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.3316   -0.2391   -0.3500 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7678   -0.7687    1.2599 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1239    0.2077   -1.5874 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.7027   -1.9361    0.1170 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.2831   -1.1023   -1.3765 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.3102    0.0339    1.2415 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.9523    0.2416   -0.3877 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5384    2.5337   -0.2992 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7071   -3.3855    1.5409 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.3910   -3.7904   -0.0496 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.7529   -4.3100    0.3960 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0447   -3.3038   -1.7339 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5631   -2.5009   -2.1391 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0362   -1.5994   -2.0459 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8418   -1.6018    1.1174 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.5017    2.6890    1.3728 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -5.9006    2.8083   -0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.4775    3.6379    0.2882 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0084    2.5365    0.0105 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7439    1.5317    1.4116 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6714   -0.1492    1.8673 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.3559    0.8995   -0.9348 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.2275   -0.8046   -0.5182 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.2871    3.3882   -0.8427 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.2111    1.1713    0.7286 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.0679   -0.5326    1.1673 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.7804    0.5287   -1.6213 H   0  0  0  0  0  0  0  0  0  0  0  0\n    6.6037   -1.1779   -1.2071 H   0  0  0  0  0  0  0  0  0  0  0  0\n    8.4722   -0.9806    0.4429 H   0  0  0  0  0  0  0  0  0  0  0  0\n    8.9839   -0.5086   -1.1865 H   0  0  0  0  0  0  0  0  0  0  0  0\n    8.6519    0.7361    0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  5  1  0  0  0  0\n  1 11  1  0  0  0  0\n  2 14  1  0  0  0  0\n  2 46  1  0  0  0  0\n  3  4  1  0  0  0  0\n  3  5  1  0  0  0  0\n  3  6  1  0  0  0  0\n  3 24  1  0  0  0  0\n  4  7  1  0  0  0  0\n  4  9  1  0  0  0  0\n  4 25  1  0  0  0  0\n  5 12  1  0  0  0  0\n  5 13  1  0  0  0  0\n  6  8  1  0  0  0  0\n  6 26  1  0  0  0  0\n  6 27  1  0  0  0  0\n  7 11  1  0  0  0  0\n  7 14  2  0  0  0  0\n  8 10  1  0  0  0  0\n  8 28  1  0  0  0  0\n  8 29  1  0  0  0  0\n  9 10  2  0  0  0  0\n  9 30  1  0  0  0  0\n 10 16  1  0  0  0  0\n 11 15  2  0  0  0  0\n 12 31  1  0  0  0  0\n 12 32  1  0  0  0  0\n 12 33  1  0  0  0  0\n 13 34  1  0  0  0  0\n 13 35  1  0  0  0  0\n 13 36  1  0  0  0  0\n 14 18  1  0  0  0  0\n 15 17  1  0  0  0  0\n 15 37  1  0  0  0  0\n 16 38  1  0  0  0  0\n 16 39  1  0  0  0  0\n 16 40  1  0  0  0  0\n 17 18  2  0  0  0  0\n 17 19  1  0  0  0  0\n 18 41  1  0  0  0  0\n 19 20  1  0  0  0  0\n 19 42  1  0  0  0  0\n 19 43  1  0  0  0  0\n 20 21  1  0  0  0  0\n 20 44  1  0  0  0  0\n 20 45  1  0  0  0  0\n 21 22  1  0  0  0  0\n 21 47  1  0  0  0  0\n 21 48  1  0  0  0  0\n 22 23  1  0  0  0  0\n 22 49  1  0  0  0  0\n 22 50  1  0  0  0  0\n 23 51  1  0  0  0  0\n 23 52  1  0  0  0  0\n 23 53  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n16078\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.8\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n10\n9\n2\n4\n3\n7\n8\n6\n5\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n19\n1 -0.36\n10 -0.28\n11 0.08\n14 0.08\n15 -0.15\n16 0.14\n17 -0.14\n18 -0.15\n19 0.14\n2 -0.53\n30 0.15\n37 0.15\n4 0.28\n41 0.15\n46 0.45\n5 0.28\n7 -0.14\n8 0.14\n9 -0.29\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n4.8\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n8\n1 1 acceptor\n1 2 donor\n1 23 hydrophobe\n3 5 12 13 hydrophobe\n4 19 20 21 22 hydrophobe\n6 1 3 4 5 7 11 rings\n6 3 4 6 8 9 10 rings\n6 7 11 14 15 17 18 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n23\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n2\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n9\n\n> <PUBCHEM_CONFORMER_ID>\n00003ECE00000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n60.7777\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n40.642\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n10165383 225 18339924806171102705\n10382601 240 18048040671259510633\n10411042 1 18049443948729322315\n10493431 412 18338516344554984201\n10730089 173 18334013874440565932\n10835480 77 18202277035968949360\n11036077 3 18411421670394297057\n11524674 6 17275099527418953630\n12011746 2 18336536179836846437\n12236239 1 17603303739767393064\n12390115 104 18270967847644556561\n12553582 1 18188753037897430376\n12643181 29 18341892975166310846\n13140716 1 18264760133252392913\n13288520 33 18411701010766986748\n13583140 156 15911906448163276298\n13914758 101 14548747161958230154\n14251752 14 18408886231404717962\n14617045 38 18412829071243300558\n14790565 3 18193840344755048457\n14856354 85 16443358575671451651\n15042514 8 18193839469489042379\n15183329 4 18408036304458040506\n15230672 131 18337954472976587790\n15927050 60 18411416177095358427\n16945 1 18335988674812882451\n17093844 174 18273210920189873138\n17492 89 17978228592760089778\n17804303 29 18340201994142308193\n19141452 34 18201999979727277718\n19591789 44 18121495748270077939\n20681677 155 18410007732753327432\n21033648 29 17774988120435619441\n21236236 1 18411980277750718648\n21267235 1 18335986466941132195\n21279426 13 18198909102027632254\n21781055 127 17772781358050478273\n23035841 295 18335137584109136624\n23402539 116 18341888597697746596\n23557571 272 18342462551831867566\n23559900 14 18272363214037070088\n2748010 2 18265048029938174023\n293599 30 18338796715176564465\n3004659 81 18334858329989337400\n335352 9 18408600383887400349\n34934 24 18334853879300769874\n350125 39 18409447003841680561\n4073 2 18262238932696286386\n437815 12 17847063281586398968\n484989 97 18191013712016142463\n5104073 3 18337379561169391800\n5265222 85 18270405022524488798\n559249 180 18412544306152485390\n59755656 215 18271528607417779894\n6328613 192 18408888460124116068\n7226269 152 18059859432677601073\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n461.59\n14.6\n2.92\n0.92\n33.68\n1.08\n0.12\n-2.36\n1.41\n-4.78\n0.15\n0.21\n0.22\n0\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n968.897\n\n> <PUBCHEM_SHAPE_VOLUME>\n260.6\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n",
  "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2519/sdf?record_type=3d": "2519\n  -OEChem-10052106453D\n\n 24 25  0     0  0  0  0  0  0999 V2000\n    0.4700    2.5688    0.0006 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.1271   -0.4436   -0.0003 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.9686   -1.3125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2182    0.1412   -0.0003 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.3477    1.0797   -0.0001 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4119   -1.9372    0.0002 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8579    0.2592   -0.0008 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3897   -1.0264   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0307    1.4220   -0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9061   -0.2495   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.5032   -1.1998    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4276   -2.6960    0.0008 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.1926    1.2061    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.2969    2.1881    0.0007 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5163   -1.5787    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0451   -3.1973   -0.8937 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5186   -2.7596    0.0011 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0447   -3.1963    0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.1992    0.7801    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0468    1.8092   -0.8992 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0466    1.8083    0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8087    3.1651   -0.0003 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.9322    2.1027    0.8881 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.9346    2.1021   -0.8849 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  9  2  0  0  0  0\n  2 10  2  0  0  0  0\n  3  8  1  0  0  0  0\n  3 10  1  0  0  0  0\n  3 12  1  0  0  0  0\n  4  7  1  0  0  0  0\n  4 11  1  0  0  0  0\n  4 13  1  0  0  0  0\n  5  9  1  0  0  0  0\n  5 10  1  0  0  0  0\n  5 14  1  0  0  0  0\n  6  8  1  0  0  0  0\n  6 11  2  0  0  0  0\n  7  8  2  0  0  0  0\n  7  9  1  0  0  0  0\n 11 15  1  0  0  0  0\n 12 16  1  0  0  0  0\n 12 17  1  0  0  0  0\n 12 18  1  0  0  0  0\n 13 19  1  0  0  0  0\n 13 20  1  0  0  0  0\n 13 21  1  0  0  0  0\n 14 22  1  0  0  0  0\n 14 23  1  0  0  0  0\n 14 24  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n2519\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.4\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n15\n1 -0.57\n10 0.69\n11 0.04\n12 0.3\n13 0.26\n14 0.3\n15 0.15\n2 -0.57\n3 -0.42\n4 0.05\n5 -0.42\n6 -0.57\n7 -0.24\n8 0.29\n9 0.71\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n0\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n5\n1 1 acceptor\n1 2 acceptor\n3 4 6 11 cation\n5 4 6 7 8 11 rings\n6 3 5 7 8 9 10 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n14\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n000009D700000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n22.901\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n25.487\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n10967382 1 18338799025773621285\n11132069 177 18339075025094499008\n12524768 44 18342463625094026902\n13140716 1 17978511158789908153\n16945 1 18338517550775811621\n193761 8 15816500986559935910\n20588541 1 18339082691204868851\n21501502 16 18338796715286957384\n22802520 49 18128840606503503494\n2334 1 18338516344016692929\n23402539 116 18270382932679789735\n23552423 10 18262240993325675966\n23559900 14 18199193898169584358\n241688 4 18266458702623303353\n2748010 2 18266180539182415717\n5084963 1 17698433339235542986\n528886 8 18267580380709240570\n53812653 166 18198902694142226312\n66348 1 18339079396917369615\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n256.45\n4.01\n2.83\n0.58\n0.71\n0.08\n0\n-0.48\n0\n-0.81\n0\n0.01\n0\n0\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n550.88\n\n> <PUBCHEM_SHAPE_VOLUME>\n143.9\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n"
}

sdf_to_three.js

const atomGeometry = new THREE.IcosahedronGeometry(1, 1)
const instructionHandlers = {
  // atom
  '16': (args, data) => {
    if(args[0] !== 'M'){
      data.atoms.push({
        vector: new THREE.Vector3(
          parseFloat(args[0]),
          parseFloat(args[1]),
          parseFloat(args[2])
        ),
        symbol: args[3]
      })
    }
  },
  // bond
  '7': (args, data) => {
    if(args[0] !== 'M'){
      data.bonds.push({
        a: parseInt(args[0]) - 1,
        b: parseInt(args[1]) - 1,
        bonds: parseInt(args[2])
      })
    }
  }
}

const sdfTextToThreeSnatom = (sdfText, atomDataMap, rotation) => {
  let data = {
    atoms: [],
    bonds: [],
    maxBondLength: -Infinity,
    minBondLength: Infinity,
    bounds: new THREE.Box3()
  }
  let model = new THREE.Group()
  let molecule = new THREE.Group()
  const instructions = sdfText.split('M  END').shift().split('\n')
  instructions.forEach((instructionLine) => {
    const args = instructionLine
      .replace(/[ \t]+/g, ' ')
      .replace(/^ /, '')
      .split(' ')
    const instrunctionHandler = instructionHandlers[args.length.toString()]
    if (instrunctionHandler) {
      instrunctionHandler(args, data)
    }
  })
  data.bonds.forEach((bond) => {
    const atomA = data.atoms[bond.a]
    const atomB = data.atoms[bond.b]
    bond.length = atomA.vector.distanceTo(atomB.vector)
    data.maxBondLength = Math.max(data.maxBondLength, bond.length)
    data.minBondLength = Math.min(data.minBondLength, bond.length)
  })
  const baseAtomScale = ((data.maxBondLength - data.minBondLength) * 0.5) + data.minBondLength * 0.6
  data.atoms.forEach((atom) => {
    const atomData = atomDataMap[atom.symbol.toLocaleLowerCase()]
    if(!atomData) {
      console.error('Could not find material for: ', atom.symbol)
    }
    let ball = new THREE.Mesh(atomGeometry, atomData.material)
    ball.position.add(atom.vector)
    ball.castShadow = ball.receiveShadow = true
    ball.scale.multiplyScalar(baseAtomScale * atomData.scale)
    molecule.add(ball)
  })
  data.bounds.expandByObject(molecule)
  molecule.scale.multiplyScalar(1 / baseAtomScale)
  if (rotation) {
    molecule.rotation.copy(rotation)
  }
  // console.log(data)
  model.add(molecule)
  return {
    data,
    model
  }
}

styles.css

* {
    margin: 0;
    padding: 0;
    border: 0;
    outline: 0;
    vertical-align: inherit;
    font-size: inherit;
    line-height: inherit;
    font-weight: inherit;
    font-style: inherit;
    font-family: inherit;
    text-align: inherit;
    text-decoration: inherit;
    color: inherit;
    background-color: transparent;
}

html, body{
    height: 100%;
}

html {
    font-size: 16px;
    -webkit-text-size-adjust: 100%;
}

body {
    background-color: #262626;
    font-size: 1rem;
    line-height: 1.5rem;
    font-weight: 400;
    font-style: normal;
    vertical-align: top;
    font-family: 'Exo 2', sans-serif;
    text-align: left;
    text-decoration: none;
    color: #ccc;
    position: relative;
}

canvas,
svg {
    display: block;
    position: absolute;
    top: 0;
    left: 0;
    width: 100%;
    height: 100%;
}

.stroke{
    stroke-linecap: round;
    stroke-linejoin: round;
    stroke: #888;
    fill: transparent;
}

.text{
    stroke: none;
    fill: #888;
}