# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 03:20:15 2022
#   Inital geometry file: a 165 line input string
#   Ligand name: (2~{S})-2-azanyl-5-[[(2~{R})-3-[(2~{R},5~{R})-5-(hydroxymethyl)-3,6-bis(oxidanylidene)-2-(phenylmethyl)-5-sulfanyl-piperazin-2-yl]sulfanyl-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CS[C@@]1(Cc2ccccc2)NC(=O)[C@](S)(CO)NC1=O)C(=O)NCC(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 U8B  U8B  '(2~{S})-2-azanyl-5-[[(2~{R})-3-[(2~{R},5~{R})-5-(hydroxymethyl)-3,6-bis(oxidanylidene)-2-(phenylmethyl)-5-sulfanyl-piperazin-2-yl]sulfanyl-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid'  ligand  65  38  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U8B
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 U8B  C4   C  CH2    0  -0.500  -12.4830   1.8284  56.4970
 U8B  C5   C  CR6    0  -0.186  -13.6364   2.8546  56.3756
 U8B  C7   C  CH2    0  -0.629  -16.4252   3.1252  55.7917
 U8B  C8   C  CH1    0  -0.165  -17.0304   3.7781  57.0342
 U8B  C13  C  CH2    0  -0.416  -18.4442   2.1568  61.4728
 U8B  C21  C  CH2    0  -0.411  -18.8519   6.9288  55.9351
 U8B  C22  C  C      0   0.400  -18.2656   8.3562  56.0130
 U8B  C16  C  C      0   0.383  -18.4445  -0.3059  62.0226
 U8B  O17  O  OC    -1  -0.607  -17.4126  -0.5430  62.6856
 U8B  C14  C  CH1    0  -0.192  -19.1277   1.0574  62.2905
 U8B  N15  N  NH2    0  -0.793  -19.1248   1.4658  63.6930
 U8B  C12  C  CH2    0  -0.594  -18.5161   1.9387  59.9689
 U8B  O11  O  O      0  -0.492  -18.0129   4.2621  59.5575
 U8B  N9   N  NH1    0  -0.636  -17.4795   2.7791  57.9611
 U8B  C19  C  C      0   0.545  -18.2081   4.6553  56.5749
 U8B  O25  O  O      0  -0.496  -19.3058   4.1632  56.3530
 U8B  N20  N  NH1    0  -0.635  -17.9134   5.9418  56.4046
 U8B  O23  O  O      0  -0.599  -19.0093   9.2486  55.5735
 U8B  O24  O  OC    -1  -0.589  -17.1277   8.4831  56.5071
 U8B  S6   S  S2     0   0.079  -15.1548   1.8670  56.0892
 U8B  C3   C  CR6    0   0.110  -11.1637   2.5152  56.7225
 U8B  C55  C  CR16   0  -0.289  -10.7049   2.7793  58.0115
 U8B  C56  C  CR16   0  -0.241   -9.5170   3.4688  58.2144
 U8B  C57  C  CR16   0  -0.264   -8.7672   3.9010  57.1286
 U8B  C1   C  CR16   0  -0.240   -9.2077   3.6309  55.8396
 U8B  C2   C  CR16   0  -0.302  -10.3969   2.9434  55.6403
 U8B  C53  C  CR6    0   0.611  -13.7430   3.6079  57.6945
 U8B  O54  O  O      0  -0.449  -14.0022   3.0069  58.7193
 U8B  N52  N  NR16   0  -0.620  -13.4940   4.9241  57.6716
 U8B  N26  N  NR16   0  -0.605  -13.4112   3.7130  55.2490
 U8B  C27  C  CR6    0   0.582  -13.1362   5.0239  55.2325
 U8B  O28  O  O      0  -0.446  -12.8812   5.6341  54.2112
 U8B  C29  C  CR6    0  -0.206  -13.1846   5.7677  56.5531
 U8B  C50  C  CH2    0  -0.116  -11.8319   6.4683  56.7787
 U8B  O51  O  OH1    0  -0.650  -11.8465   7.2494  57.9404
 U8B  S30  S  S2     0  -0.145  -14.5361   6.9971  56.2807
 U8B  H1   H  HCH2   0   0.287  -12.4573   1.2486  55.5713
 U8B  H2   H  HCH2   0   0.287  -12.7074   1.1351  57.3082
 U8B  H3   H  HCH2   0   0.307  -16.0270   3.8931  55.1270
 U8B  H4   H  HCH2   0   0.310  -17.2009   2.5926  55.2363
 U8B  H5   H  HCH1   0   0.270  -16.2811   4.4150  57.5115
 U8B  H6   H  HCH2   0   0.213  -17.3975   2.2340  61.7869
 U8B  H7   H  HCH2   0   0.224  -18.9154   3.1085  61.7261
 U8B  H8   H  HCH2   0   0.238  -19.7687   6.8960  56.5315
 U8B  H9   H  HCH2   0   0.235  -19.1503   6.7233  54.9023
 U8B  H11  H  HCH1   0   0.198  -20.1716   0.9981  61.9643
 U8B  H12  H  HNH2   0   0.333  -19.6914   0.8129  64.2224
 U8B  H13  H  HNH2   0   0.322  -18.1829   1.3261  64.0436
 U8B  H15  H  HCH2   0   0.263  -19.5616   1.8020  59.6687
 U8B  H16  H  HCH2   0   0.255  -18.0028   1.0213  59.6764
 U8B  H17  H  HNH1   0   0.399  -17.4834   1.8137  57.6738
 U8B  H18  H  HNH1   0   0.407  -16.9878   6.2908  56.6207
 U8B  H20  H  HCR6   0   0.256  -11.2776   2.4395  58.8658
 U8B  H21  H  HCR6   0   0.256   -9.1766   3.6654  59.2229
 U8B  H22  H  HCR6   0   0.256   -7.8414   4.4393  57.2856
 U8B  H23  H  HCR6   0   0.256   -8.6248   3.9545  54.9870
 U8B  H24  H  HCR6   0   0.255  -10.7294   2.7316  54.6309
 U8B  H25  H  HNR6   0   0.411  -13.5467   5.3830  58.5734
 U8B  H26  H  HNR6   0   0.416  -13.3575   3.2477  54.3501
 U8B  H27  H  HCH2   0   0.244  -11.0483   5.7017  56.8084
 U8B  H28  H  HCH2   0   0.241  -11.6359   7.1193  55.9272
 U8B  H29  H  HOH1   0   0.461  -11.4827   6.7394  58.6700
 U8B  H30  H  HSH1   0   0.243  -14.6193   7.4107  57.5496
 U8B  C10  C  C      0   0.572  -17.9793   3.1034  59.1681
 U8B  O18  O  O      0  -0.611  -18.9549  -1.0378  61.1494

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 U8B  O23  C22  deloc     1.242  0.020  1.242
 U8B  C22  C21  single    1.545  0.020  1.545
 U8B  C22  O24  deloc     1.247  0.020  1.247
 U8B  C21  N20  single    1.441  0.020  1.441
 U8B  O28  C27  double    1.217  0.020  1.217
 U8B  N20  C19  single    1.331  0.020  1.331
 U8B  C2   C1   aromatic  1.388  0.020  1.388
 U8B  C2   C3   aromatic  1.394  0.020  1.394
 U8B  N26  C27  single    1.340  0.020  1.340
 U8B  N26  C5   single    1.434  0.020  1.434
 U8B  C7   S6   single    1.813  0.020  1.813
 U8B  C7   C8   single    1.529  0.020  1.529
 U8B  C1   C57  aromatic  1.389  0.020  1.389
 U8B  C27  C29  single    1.516  0.020  1.516
 U8B  S6   C5   single    1.834  0.020  1.834
 U8B  C19  O25  double    1.223  0.020  1.223
 U8B  C19  C8   single    1.539  0.020  1.539
 U8B  C4   C3   single    1.504  0.020  1.504
 U8B  C4   C5   single    1.549  0.020  1.549
 U8B  C3   C55  aromatic  1.394  0.020  1.394
 U8B  C5   C53  single    1.523  0.020  1.523
 U8B  C8   N9   single    1.435  0.020  1.435
 U8B  C57  C56  aromatic  1.389  0.020  1.389
 U8B  S30  C29  single    1.847  0.020  1.847
 U8B  C29  C50  single    1.540  0.020  1.540
 U8B  C29  N52  single    1.435  0.020  1.435
 U8B  N9   C10  single    1.346  0.020  1.346
 U8B  C50  O51  single    1.400  0.020  1.400
 U8B  C55  C56  aromatic  1.388  0.020  1.388
 U8B  C53  N52  single    1.340  0.020  1.340
 U8B  C53  O54  double    1.216  0.020  1.216
 U8B  C10  O11  double    1.223  0.020  1.223
 U8B  C10  C12  single    1.512  0.020  1.512
 U8B  C12  C13  single    1.521  0.020  1.521
 U8B  O18  C16  deloc     1.248  0.020  1.248
 U8B  C13  C14  single    1.531  0.020  1.531
 U8B  C16  O17  deloc     1.249  0.020  1.249
 U8B  C16  C14  single    1.548  0.020  1.548
 U8B  C14  N15  single    1.461  0.020  1.461
 U8B  C4   H1   single    0.970  0.020  1.090
 U8B  C4   H2   single    0.970  0.020  1.090
 U8B  C7   H3   single    0.970  0.020  1.090
 U8B  C7   H4   single    0.970  0.020  1.090
 U8B  C8   H5   single    0.970  0.020  1.090
 U8B  C13  H6   single    0.970  0.020  1.090
 U8B  C13  H7   single    0.970  0.020  1.090
 U8B  C21  H8   single    0.970  0.020  1.090
 U8B  C21  H9   single    0.970  0.020  1.090
 U8B  C14  H11  single    0.970  0.020  1.090
 U8B  N15  H12  single    0.890  0.020  1.040
 U8B  N15  H13  single    0.890  0.020  1.040
 U8B  C12  H15  single    0.970  0.020  1.090
 U8B  C12  H16  single    0.970  0.020  1.090
 U8B  N9   H17  single    0.860  0.020  1.020
 U8B  N20  H18  single    0.860  0.020  1.020
 U8B  C55  H20  single    0.930  0.020  1.080
 U8B  C56  H21  single    0.930  0.020  1.080
 U8B  C57  H22  single    0.930  0.020  1.080
 U8B  C1   H23  single    0.930  0.020  1.080
 U8B  C2   H24  single    0.930  0.020  1.080
 U8B  N52  H25  single    0.860  0.020  1.020
 U8B  N26  H26  single    0.860  0.020  1.020
 U8B  C50  H27  single    0.970  0.020  1.090
 U8B  C50  H28  single    0.970  0.020  1.090
 U8B  O51  H29  single    0.850  0.020  0.980
 U8B  S30  H30  single    1.200  0.020  1.300

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 U8B  H2   C4   H1   107.32  3.000
 U8B  H2   C4   C3   111.06  3.000
 U8B  H1   C4   C3   110.41  3.000
 U8B  H2   C4   C5   109.05  3.000
 U8B  H1   C4   C5   107.62  3.000
 U8B  C3   C4   C5   111.25  3.000
 U8B  N26  C5   C53  113.29  3.000
 U8B  C53  C5   S6   110.10  3.000
 U8B  N26  C5   S6   109.25  3.000
 U8B  C53  C5   C4   108.18  3.000
 U8B  S6   C5   C4   105.79  3.000
 U8B  N26  C5   C4   109.95  3.000
 U8B  H4   C7   H3   107.01  3.000
 U8B  H4   C7   S6   104.04  3.000
 U8B  H3   C7   S6   109.44  3.000
 U8B  H4   C7   C8   109.89  3.000
 U8B  H3   C7   C8   109.83  3.000
 U8B  S6   C7   C8   116.14  3.000
 U8B  H5   C8   C19  108.83  3.000
 U8B  H5   C8   N9   109.76  3.000
 U8B  C19  C8   N9   110.50  3.000
 U8B  H5   C8   C7   109.41  3.000
 U8B  N9   C8   C7   110.59  3.000
 U8B  C19  C8   C7   107.69  3.000
 U8B  H7   C13  H6   106.52  3.000
 U8B  H7   C13  C12  109.51  3.000
 U8B  H6   C13  C12  109.79  3.000
 U8B  H7   C13  C14  108.02  3.000
 U8B  H6   C13  C14  108.90  3.000
 U8B  C12  C13  C14  113.82  3.000
 U8B  H9   C21  H8   106.28  3.000
 U8B  H9   C21  N20  110.88  3.000
 U8B  H8   C21  N20  110.35  3.000
 U8B  H9   C21  C22  108.94  3.000
 U8B  H8   C21  C22  108.55  3.000
 U8B  N20  C21  C22  111.67  3.000
 U8B  O24  C22  O23  127.85  3.000
 U8B  O24  C22  C21  117.40  3.000
 U8B  O23  C22  C21  114.75  3.000
 U8B  C14  C16  O17  116.09  3.000
 U8B  C14  C16  O18  117.18  3.000
 U8B  O17  C16  O18  126.70  3.000
 U8B  H11  C14  N15  107.63  3.000
 U8B  H11  C14  C16  108.74  3.000
 U8B  N15  C14  C16  114.29  3.000
 U8B  H11  C14  C13  107.78  3.000
 U8B  N15  C14  C13  108.13  3.000
 U8B  C16  C14  C13  110.06  3.000
 U8B  H13  N15  H12  104.46  3.000
 U8B  H13  N15  C14  107.16  3.000
 U8B  H12  N15  C14  108.68  3.000
 U8B  H16  C12  H15  105.69  3.000
 U8B  H16  C12  C13  111.31  3.000
 U8B  H15  C12  C13  109.49  3.000
 U8B  H16  C12  C10  109.80  3.000
 U8B  H15  C12  C10  106.83  3.000
 U8B  C13  C12  C10  113.35  3.000
 U8B  H17  N9   C10  119.03  3.000
 U8B  H17  N9   C8   118.97  3.000
 U8B  C10  N9   C8   121.85  3.000
 U8B  N20  C19  O25  124.37  3.000
 U8B  O25  C19  C8   120.77  3.000
 U8B  N20  C19  C8   114.82  3.000
 U8B  H18  N20  C19  120.56  3.000
 U8B  H18  N20  C21  115.40  3.000
 U8B  C19  N20  C21  124.04  3.000
 U8B  C7   S6   C5   103.42  3.000
 U8B  C2   C3   C55  118.62  3.000
 U8B  C55  C3   C4   120.92  3.000
 U8B  C2   C3   C4   120.42  3.000
 U8B  H20  C55  C56  119.53  3.000
 U8B  H20  C55  C3   119.74  3.000
 U8B  C56  C55  C3   120.73  3.000
 U8B  H21  C56  C57  120.15  3.000
 U8B  H21  C56  C55  119.70  3.000
 U8B  C57  C56  C55  120.15  3.000
 U8B  H22  C57  C1   120.18  3.000
 U8B  H22  C57  C56  120.22  3.000
 U8B  C1   C57  C56  119.60  3.000
 U8B  H23  C1   C2   119.76  3.000
 U8B  H23  C1   C57  120.14  3.000
 U8B  C2   C1   C57  120.10  3.000
 U8B  H24  C2   C1   119.57  3.000
 U8B  H24  C2   C3   119.63  3.000
 U8B  C1   C2   C3   120.80  3.000
 U8B  N52  C53  O54  122.66  3.000
 U8B  O54  C53  C5   120.03  3.000
 U8B  N52  C53  C5   117.27  3.000
 U8B  H25  N52  C29  116.03  3.000
 U8B  H25  N52  C53  114.84  3.000
 U8B  C29  N52  C53  129.13  3.000
 U8B  H26  N26  C27  115.30  3.000
 U8B  H26  N26  C5   115.48  3.000
 U8B  C27  N26  C5   128.88  3.000
 U8B  C29  C27  O28  119.46  3.000
 U8B  C29  C27  N26  117.56  3.000
 U8B  O28  C27  N26  122.97  3.000
 U8B  S30  C29  C50  111.19  3.000
 U8B  C50  C29  C27  108.82  3.000
 U8B  S30  C29  C27  102.79  3.000
 U8B  C50  C29  N52  110.04  3.000
 U8B  S30  C29  N52  110.40  3.000
 U8B  C27  C29  N52  113.42  3.000
 U8B  H28  C50  H27  108.08  3.000
 U8B  H28  C50  O51  108.48  3.000
 U8B  H27  C50  O51  112.02  3.000
 U8B  H28  C50  C29  108.38  3.000
 U8B  H27  C50  C29  108.28  3.000
 U8B  O51  C50  C29  111.48  3.000
 U8B  H29  O51  C50  109.25  3.000
 U8B  H30  S30  C29   96.40  3.000
 U8B  N9   C10  O11  121.60  3.000
 U8B  O11  C10  C12  123.47  3.000
 U8B  N9   C10  C12  114.91  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 U8B  CONST_01  C57  C1   C2   C3     0.00   0.0  0
 U8B  CONST_02  C57  C56  C55  C3     0.00   0.0  0
 U8B  CONST_03  C1   C2   C3   C55    0.00   0.0  0
 U8B  CONST_04  C1   C57  C56  C55    0.00   0.0  0
 U8B  CONST_05  C2   C1   C57  C56    0.00   0.0  0
 U8B  CONST_06  C2   C3   C55  C56    0.00   0.0  0
 U8B  CONST_07  C29  C27  N26  C5     0.00   0.0  0
 U8B  CONST_08  C29  N52  C53  C5     0.00   0.0  0
 U8B  CONST_09  C1   C2   C3   C4   180.00   0.0  0
 U8B  CONST_10  C56  C55  C3   C4   180.00   0.0  0
 U8B  CONST_11  O28  C27  N26  C5   180.00   0.0  0
 U8B  CONST_12  C29  N52  C53  O54  180.00   0.0  0
 U8B  CONST_13  H23  C1   C2   C3   180.00   0.0  0
 U8B  CONST_14  H21  C56  C55  C3   180.00   0.0  0
 U8B  CONST_15  H24  C2   C3   C55  180.00   0.0  0
 U8B  CONST_16  H22  C57  C56  C55  180.00   0.0  0
 U8B  CONST_17  H20  C55  C56  C57  180.00   0.0  0
 U8B  CONST_18  H25  N52  C53  C5   180.00   0.0  0
 U8B  CONST_19  H26  N26  C27  C29  180.00   0.0  0
 U8B  CONST_20  C21  N20  C19  C8   180.00   0.0  0
 U8B  CONST_21  O11  C10  N9   C8     0.00   0.0  0
 U8B  CONST_22  C12  C10  N9   C8   180.00   0.0  0
 U8B  CONST_23  O25  C19  N20  C21    0.00   0.0  0
 U8B  CONST_24  H18  N20  C19  C8     0.00   0.0  0
 U8B  CONST_25  H17  N9   C10  C12    0.00   0.0  0
 U8B  Var_01    C2   C3   C4   C5   -87.28  30.0  2
 U8B  Var_02    C8   C7   S6   C5   -81.35  30.0  1
 U8B  Var_03    C14  C13  C12  C10  173.43  30.0  3
 U8B  Var_04    N9   C10  C12  C13  152.19  30.0  1
 U8B  Var_05    C19  N20  C21  C22  172.78  30.0  3
 U8B  Var_06    O23  C22  C21  N20  177.37  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 U8B  chir_01  C5   N26  C4   C53  negativ
 U8B  chir_02  C8   N9   C7   C19  negativ
 U8B  chir_03  C14  N15  C13  C16  negativ
 U8B  chir_04  C29  N52  C27  C50  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 U8B  plan-1  C4   0.020
 U8B  plan-1  C3   0.020
 U8B  plan-1  C55  0.020
 U8B  plan-1  C56  0.020
 U8B  plan-1  C57  0.020
 U8B  plan-1  C1   0.020
 U8B  plan-1  C2   0.020
 U8B  plan-1  H20  0.020
 U8B  plan-1  H21  0.020
 U8B  plan-1  H22  0.020
 U8B  plan-1  H23  0.020
 U8B  plan-1  H24  0.020
 U8B  plan-2  C8   0.020
 U8B  plan-2  C21  0.020
 U8B  plan-2  C19  0.020
 U8B  plan-2  O25  0.020
 U8B  plan-2  N20  0.020
 U8B  plan-2  H18  0.020
 U8B  plan-3  C8   0.020
 U8B  plan-3  C12  0.020
 U8B  plan-3  O11  0.020
 U8B  plan-3  N9   0.020
 U8B  plan-3  H17  0.020
 U8B  plan-3  C10  0.020
 U8B  plan-4  C5   0.020
 U8B  plan-4  C53  0.020
 U8B  plan-4  O54  0.020
 U8B  plan-4  N52  0.020
 U8B  plan-4  C29  0.020
 U8B  plan-4  H25  0.020
 U8B  plan-5  C5   0.020
 U8B  plan-5  N26  0.020
 U8B  plan-5  C27  0.020
 U8B  plan-5  O28  0.020
 U8B  plan-5  C29  0.020
 U8B  plan-5  H26  0.020
 U8B  plan-6  C21  0.020
 U8B  plan-6  C22  0.020
 U8B  plan-6  O23  0.020
 U8B  plan-6  O24  0.020
 U8B  plan-7  C16  0.020
 U8B  plan-7  O17  0.020
 U8B  plan-7  C14  0.020
 U8B  plan-7  O18  0.020

