better SO autobonding

CHANGELOG.md

@@ -6,6 +6,7 @@ Note that since we don't clearly distinguish between a public and private interf
 ## [Unreleased]
 
 - Add glTF (GLB) and STL support to ``geo-export`` extension.
+- Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
 
 ## [v2.0.5] - 2021-04-26
 

src/mol-model/structure/structure/unit/bonds/common.ts

 /**
- * Copyright (c) 2017-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -23,6 +23,10 @@ const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D
 const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 2.0, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
 
 /**
+ * Added O-S (316) as 1.8
+ * N-O-S bridge (e.g. LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
+ * (https://www.nature.com/articles/s41586-021-03513-3?s=09)
+ *
  * Increased N-N (112) threshold from 1.55 to 1.6 (e.g. for 0QH in 1BMA)
  *
  * More experimentally observed bond length here (https://cccbdb.nist.gov/expbondlengths1x.asp)
@@ -51,8 +55,8 @@ const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42,
  * Added P-H (135) as 1.47
  * P-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rPH)
  * - Average    1.423 ((+/- 0.007)
- * - Min        0.912
- * - Max        1.033
+ * - Min        1.414
+ * - Max        1.435
  *
  * Added S-H (152) as 1.45
  * S-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rSH)
@@ -63,7 +67,7 @@ const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42,
  * Added Si-Si (420) as 2.37
  * (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rSiSi)
  */
-const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.2, 35: 1.15, 44: 1.1, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.6, 113: 1.59, 114: 1.36, 129: 1.45, 135: 1.47, 144: 1.6, 152: 1.45, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 420: 2.37, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
+const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.2, 35: 1.15, 44: 1.1, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.6, 113: 1.59, 114: 1.36, 129: 1.45, 135: 1.47, 144: 1.6, 152: 1.45, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 316: 1.8, 420: 2.37, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
 
 const __DefaultBondingRadius = 2.001;