# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 05:23:23 2022
#   Inital geometry file: a 152 line input string
#   Ligand name: {(1R,2S,4R)-4-[(5-{4-[(1R)-3,4-dihydro-1H-2-benzopyran-1-yl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2-hydroxycyclopentyl}methyl sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)OC[C@H]1C[C@H](C[C@@H]1O)Nc2ncncc2C(=O)c3scc(c3)[C@@H]4OCCc5ccccc45
#
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
 VB7  VB7  '{(1R,2S,4R)-4-[(5-{4-[(1R)-3,4-dihydro-1H-2-benzopyran-1-yl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2-hydroxycyclopentyl}methyl sulfamate'  ligand  62  36  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VB7
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
 VB7  C5   C  CR16  0   0.072  39.7166   -2.4728  26.9845
 VB7  C7   C  CR16  0  -0.059  39.3503   -3.3639  29.0049
 VB7  C8   C  CR6   0  -0.226  38.2116   -4.0137  28.5568
 VB7  C13  C  CR5   0   0.192  39.3921   -6.6222  32.0596
 VB7  C17  C  CR66  0   0.008  41.1168   -8.3340  31.5520
 VB7  C20  C  C     0  -0.199  42.9429   -6.6656  32.7813
 VB7  C22  C  CR16  0  -0.265  40.2121   -9.3238  31.1717
 VB7  C24  C  CR16  0  -0.253  41.8841  -10.3543  29.7938
 VB7  C26  C  CH2   0  -0.466  35.5061   -2.6759  25.1534
 VB7  C28  C  CH1   0   0.046  34.3174   -4.3866  23.9599
 VB7  C23  C  CR16  0  -0.257  40.5880  -10.3286  30.2969
 VB7  C25  C  CR16  0  -0.299  42.7895   -9.3812  30.1812
 VB7  C18  C  CR66  0   0.067  42.4211   -8.3673  31.0646
 VB7  C19  C  C     0  -0.512  43.4141   -7.3277  31.5032
 VB7  O21  O  O     0  -0.486  41.6166   -6.2042  32.6240
 VB7  C16  C  CR16  0  -0.018  40.6775   -7.2444  32.5154
 VB7  C12  C  CR15  0  -0.242  39.2574   -5.9163  30.8370
 VB7  C14  C  CR15  0  -0.535  38.2125   -6.6872  32.7420
 VB7  S15  S  S2    0   0.277  36.9294   -5.9368  31.9084
 VB7  C11  C  CR5   0  -0.298  37.9816   -5.4713  30.6212
 VB7  C9   C  C     0   0.424  37.3764   -4.8238  29.4536
 VB7  O10  O  O     0  -0.421  36.1789   -4.9804  29.2517
 VB7  N6   N  N     0  -0.428  40.1177   -2.5926  28.2440
 VB7  N4   N  N     0  -0.463  38.6426   -2.9908  26.4333
 VB7  C3   C  CR6   0   0.570  37.8491   -3.7585  27.1960
 VB7  N2   N  NH1   0  -0.669  36.7588   -4.2733  26.6344
 VB7  C1   C  CH1   0  -0.056  36.3205   -3.9908  25.2819
 VB7  C29  C  CH2   0  -0.522  35.3854   -5.1036  24.7780
 VB7  O32  O  OH1   0  -0.669  34.7993   -4.0005  22.6891
 VB7  C27  C  CH1   0  -0.322  34.0850   -3.0922  24.7434
 VB7  C30  C  CH2   0  -0.182  33.2273   -3.2909  25.9797
 VB7  O31  O  OC2   0  -0.574  31.9213   -3.7201  25.5496
 VB7  S33  S  S     0   1.573  30.8013   -4.0559  26.6449
 VB7  O35  O  OS    0  -0.639  29.6459   -4.3714  25.8439
 VB7  O36  O  OS    0  -0.651  31.3350   -5.0072  27.5925
 VB7  N34  N  NC2   0  -0.897  30.4858   -2.6855  27.4689
 VB7  H1   H  HCR6  0   0.262  40.3392   -1.8646  26.3357
 VB7  H2   H  HCR6  0   0.286  39.6436   -3.4454  30.0455
 VB7  H4   H  H     0   0.246  43.5538   -5.7963  33.0254
 VB7  H5   H  HCR6  0   0.252  39.1995   -9.3018  31.5578
 VB7  H6   H  HCR6  0   0.252  42.1870  -11.1349  29.1078
 VB7  H7   H  HCH2  0   0.261  35.9435   -2.0432  24.3820
 VB7  H8   H  HCH2  0   0.253  35.5240   -2.0970  26.0788
 VB7  H9   H  HCH1  0   0.231  33.4096   -4.9935  23.8641
 VB7  H10  H  HCR6  0   0.252  39.8734  -11.0879  30.0066
 VB7  H11  H  HCR6  0   0.247  43.8044   -9.4070  29.8011
 VB7  H12  H  H     0   0.251  44.3953   -7.7824  31.6569
 VB7  H13  H  H     0   0.253  43.5395   -6.5727  30.7210
 VB7  H14  H  HCR6  0   0.250  40.5121   -7.7084  33.5011
 VB7  H15  H  HCR5  0   0.291  40.0655   -5.7842  30.1306
 VB7  H16  H  HCR5  0   0.306  38.0415   -7.1499  33.7033
 VB7  H17  H  HNH1  0   0.418  36.1133   -4.7426  27.2530
 VB7  H18  H  HCH1  0   0.269  37.2071   -3.9318  24.6546
 VB7  H19  H  HCH2  0   0.247  34.9125   -5.6235  25.6161
 VB7  H20  H  HCH2  0   0.267  35.9134   -5.8672  24.2041
 VB7  H21  H  HOH1  0   0.448  35.0639   -4.7938  22.2130
 VB7  H22  H  HCH1  0   0.267  33.6098   -2.3345  24.1146
 VB7  H23  H  HCH2  0   0.259  33.1432   -2.3411  26.5155
 VB7  H24  H  HCH2  0   0.249  33.6562   -4.0285  26.6622
 VB7  H25  H  HNC2  0   0.427  31.1925   -2.4083  28.1401
 VB7  H26  H  HNC2  0   0.425  30.1630   -1.9093  26.9015
 VB7  H3   H  H     0   0.212  43.0123   -7.3679  33.6229

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
 VB7  O32  C28  single    1.413  0.020  1.413
 VB7  O35  S33  deloc     1.441  0.020  1.441
 VB7  O31  S33  single    1.602  0.020  1.602
 VB7  O31  C30  single    1.440  0.020  1.440
 VB7  S33  O36  deloc     1.445  0.020  1.445
 VB7  S33  N34  single    1.630  0.020  1.630
 VB7  C28  C27  single    1.531  0.020  1.531
 VB7  C28  C29  single    1.525  0.020  1.525
 VB7  C27  C30  single    1.518  0.020  1.518
 VB7  C27  C26  single    1.537  0.020  1.537
 VB7  C29  C1   single    1.538  0.020  1.538
 VB7  C1   C26  single    1.552  0.020  1.552
 VB7  C1   N2   single    1.449  0.020  1.449
 VB7  N4   C5   aromatic  1.314  0.020  1.314
 VB7  N4   C3   aromatic  1.342  0.020  1.342
 VB7  C5   N6   aromatic  1.327  0.020  1.327
 VB7  N2   C3   single    1.330  0.020  1.330
 VB7  C3   C8   aromatic  1.431  0.020  1.431
 VB7  N6   C7   aromatic  1.328  0.020  1.328
 VB7  C8   C7   aromatic  1.386  0.020  1.386
 VB7  C8   C9   single    1.469  0.020  1.469
 VB7  O10  C9   double    1.224  0.020  1.224
 VB7  C9   C11  single    1.466  0.020  1.466
 VB7  C25  C24  aromatic  1.385  0.020  1.385
 VB7  C25  C18  aromatic  1.394  0.020  1.394
 VB7  C24  C23  aromatic  1.391  0.020  1.391
 VB7  C11  C12  aromatic  1.368  0.020  1.368
 VB7  C11  S15  aromatic  1.726  0.020  1.726
 VB7  C12  C13  aromatic  1.418  0.020  1.418
 VB7  C19  C18  single    1.503  0.020  1.503
 VB7  C19  C20  single    1.515  0.020  1.515
 VB7  C18  C17  aromatic  1.393  0.020  1.393
 VB7  C23  C22  aromatic  1.384  0.020  1.384
 VB7  C17  C22  aromatic  1.394  0.020  1.394
 VB7  C17  C16  single    1.519  0.020  1.519
 VB7  O21  C20  single    1.413  0.020  1.413
 VB7  O21  C16  single    1.406  0.020  1.406
 VB7  C13  C16  single    1.499  0.020  1.499
 VB7  C13  C14  aromatic  1.364  0.020  1.364
 VB7  S15  C14  aromatic  1.704  0.020  1.704
 VB7  C5   H1   single    0.930  0.020  1.080
 VB7  C7   H2   single    0.930  0.020  1.080
 VB7  C20  H3   single    0.970  0.020  1.090
 VB7  C20  H4   single    0.970  0.020  1.090
 VB7  C22  H5   single    0.930  0.020  1.080
 VB7  C24  H6   single    0.930  0.020  1.080
 VB7  C26  H7   single    0.970  0.020  1.090
 VB7  C26  H8   single    0.970  0.020  1.090
 VB7  C28  H9   single    0.970  0.020  1.090
 VB7  C23  H10  single    0.930  0.020  1.080
 VB7  C25  H11  single    0.930  0.020  1.080
 VB7  C19  H12  single    0.970  0.020  1.090
 VB7  C19  H13  single    0.970  0.020  1.090
 VB7  C16  H14  single    0.970  0.020  1.090
 VB7  C12  H15  single    0.930  0.020  1.080
 VB7  C14  H16  single    0.930  0.020  1.080
 VB7  N2   H17  single    0.860  0.020  1.020
 VB7  C1   H18  single    0.970  0.020  1.090
 VB7  C29  H19  single    0.970  0.020  1.090
 VB7  C29  H20  single    0.970  0.020  1.090
 VB7  O32  H21  single    0.850  0.020  0.980
 VB7  C27  H22  single    0.970  0.020  1.090
 VB7  C30  H23  single    0.970  0.020  1.090
 VB7  C30  H24  single    0.970  0.020  1.090
 VB7  N34  H25  single    0.890  0.020  1.040
 VB7  N34  H26  single    0.890  0.020  1.040

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
 VB7  H1   C5   N4   116.04  3.000
 VB7  H1   C5   N6   116.39  3.000
 VB7  N4   C5   N6   127.57  3.000
 VB7  H2   C7   N6   115.94  3.000
 VB7  H2   C7   C8   119.83  3.000
 VB7  N6   C7   C8   124.20  3.000
 VB7  C3   C8   C9   122.33  3.000
 VB7  C9   C8   C7   121.90  3.000
 VB7  C3   C8   C7   115.60  3.000
 VB7  C14  C13  C12  111.89  3.000
 VB7  C14  C13  C16  124.72  3.000
 VB7  C12  C13  C16  123.38  3.000
 VB7  C16  C17  C18  120.65  3.000
 VB7  C16  C17  C22  119.65  3.000
 VB7  C18  C17  C22  119.70  3.000
 VB7  H4   C20  H3   107.63  3.000
 VB7  H4   C20  O21  106.89  3.000
 VB7  H3   C20  O21  110.70  3.000
 VB7  H4   C20  C19  111.29  3.000
 VB7  H3   C20  C19  110.33  3.000
 VB7  O21  C20  C19  109.93  3.000
 VB7  H5   C22  C23  119.57  3.000
 VB7  H5   C22  C17  119.65  3.000
 VB7  C23  C22  C17  120.77  3.000
 VB7  H6   C24  C25  120.08  3.000
 VB7  H6   C24  C23  120.23  3.000
 VB7  C25  C24  C23  119.69  3.000
 VB7  H8   C26  H7   106.60  3.000
 VB7  H8   C26  C27  112.64  3.000
 VB7  H7   C26  C27  109.86  3.000
 VB7  H8   C26  C1   111.74  3.000
 VB7  H7   C26  C1   109.88  3.000
 VB7  C27  C26  C1   106.13  3.000
 VB7  H9   C28  C27  112.78  3.000
 VB7  H9   C28  O32  110.80  3.000
 VB7  C27  C28  O32  106.33  3.000
 VB7  H9   C28  C29  111.51  3.000
 VB7  C27  C28  C29  103.26  3.000
 VB7  O32  C28  C29  111.86  3.000
 VB7  H10  C23  C24  120.36  3.000
 VB7  H10  C23  C22  119.96  3.000
 VB7  C24  C23  C22  119.68  3.000
 VB7  H11  C25  C18  119.13  3.000
 VB7  H11  C25  C24  119.83  3.000
 VB7  C18  C25  C24  121.04  3.000
 VB7  C19  C18  C25  120.88  3.000
 VB7  C19  C18  C17  120.00  3.000
 VB7  C25  C18  C17  119.11  3.000
 VB7  H13  C19  H12  106.55  3.000
 VB7  H13  C19  C18  110.14  3.000
 VB7  H12  C19  C18  110.28  3.000
 VB7  H13  C19  C20  109.71  3.000
 VB7  H12  C19  C20  110.04  3.000
 VB7  C18  C19  C20  110.06  3.000
 VB7  C16  O21  C20  113.21  3.000
 VB7  H14  C16  O21  110.04  3.000
 VB7  H14  C16  C17  107.98  3.000
 VB7  O21  C16  C17  112.74  3.000
 VB7  H14  C16  C13  108.55  3.000
 VB7  O21  C16  C13  106.81  3.000
 VB7  C17  C16  C13  110.66  3.000
 VB7  H15  C12  C11  123.64  3.000
 VB7  H15  C12  C13  123.57  3.000
 VB7  C11  C12  C13  112.73  3.000
 VB7  H16  C14  S15  120.30  3.000
 VB7  H16  C14  C13  127.03  3.000
 VB7  S15  C14  C13  112.66  3.000
 VB7  C11  S15  C14   91.41  3.000
 VB7  C9   C11  S15  117.47  3.000
 VB7  S15  C11  C12  111.28  3.000
 VB7  C9   C11  C12  130.86  3.000
 VB7  O10  C9   C11  118.60  3.000
 VB7  C11  C9   C8   119.68  3.000
 VB7  O10  C9   C8   121.73  3.000
 VB7  C7   N6   C5   114.94  3.000
 VB7  C3   N4   C5   118.07  3.000
 VB7  N2   C3   N4   117.79  3.000
 VB7  N2   C3   C8   122.69  3.000
 VB7  N4   C3   C8   119.52  3.000
 VB7  H17  N2   C1   117.96  3.000
 VB7  H17  N2   C3   116.44  3.000
 VB7  C1   N2   C3   124.50  3.000
 VB7  H18  C1   C29  110.23  3.000
 VB7  H18  C1   N2   107.59  3.000
 VB7  C29  C1   N2   110.39  3.000
 VB7  H18  C1   C26  109.51  3.000
 VB7  N2   C1   C26  113.65  3.000
 VB7  C29  C1   C26  105.47  3.000
 VB7  H20  C29  H19  106.23  3.000
 VB7  H20  C29  C1   112.60  3.000
 VB7  H19  C29  C1   110.83  3.000
 VB7  H20  C29  C28  112.69  3.000
 VB7  H19  C29  C28  109.38  3.000
 VB7  C1   C29  C28  105.15  3.000
 VB7  H21  O32  C28  108.27  3.000
 VB7  H22  C27  C30  108.28  3.000
 VB7  H22  C27  C28  110.95  3.000
 VB7  C30  C27  C28  113.08  3.000
 VB7  H22  C27  C26  111.57  3.000
 VB7  C30  C27  C26  109.93  3.000
 VB7  C28  C27  C26  103.02  3.000
 VB7  H24  C30  H23  108.08  3.000
 VB7  H24  C30  O31  109.95  3.000
 VB7  H23  C30  O31  109.59  3.000
 VB7  H24  C30  C27  112.05  3.000
 VB7  H23  C30  C27  109.19  3.000
 VB7  O31  C30  C27  107.95  3.000
 VB7  S33  O31  C30  119.48  3.000
 VB7  N34  S33  O36  107.07  3.000
 VB7  N34  S33  O35  108.05  3.000
 VB7  O36  S33  O35  121.10  3.000
 VB7  N34  S33  O31  107.74  3.000
 VB7  O36  S33  O31  109.15  3.000
 VB7  O35  S33  O31  103.08  3.000
 VB7  H26  N34  H25  112.53  3.000
 VB7  H26  N34  S33  114.98  3.000
 VB7  H25  N34  S33  115.46  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
 VB7  CONST_01  C8   C3   N4   C5     0.00   0.0  0
 VB7  CONST_02  C8   C7   N6   C5     0.00   0.0  0
 VB7  CONST_03  N4   C5   N6   C7     0.00   0.0  0
 VB7  CONST_04  N4   C3   C8   C7     0.00   0.0  0
 VB7  CONST_05  S15  C11  C12  C13    0.00   0.0  0
 VB7  CONST_06  C11  S15  C14  C13    0.00   0.0  0
 VB7  CONST_07  C24  C25  C18  C17    0.00   0.0  0
 VB7  CONST_08  C24  C23  C22  C17    0.00   0.0  0
 VB7  CONST_09  C25  C24  C23  C22    0.00   0.0  0
 VB7  CONST_10  C25  C18  C17  C22    0.00   0.0  0
 VB7  CONST_11  C18  C25  C24  C23    0.00   0.0  0
 VB7  CONST_12  C18  C17  C22  C23    0.00   0.0  0
 VB7  CONST_13  C14  S15  C11  C12    0.00   0.0  0
 VB7  CONST_14  S15  C14  C13  C12    0.00   0.0  0
 VB7  CONST_15  C11  C12  C13  C14    0.00   0.0  0
 VB7  CONST_16  C3   N4   C5   N6     0.00   0.0  0
 VB7  CONST_17  C3   C8   C7   N6     0.00   0.0  0
 VB7  CONST_18  C11  C12  C13  C16  180.00   0.0  0
 VB7  CONST_19  S15  C14  C13  C16  180.00   0.0  0
 VB7  CONST_20  N2   C3   N4   C5   180.00   0.0  0
 VB7  CONST_21  N2   C3   C8   C7   180.00   0.0  0
 VB7  CONST_22  C9   C11  C12  C13  180.00   0.0  0
 VB7  CONST_23  C9   C11  S15  C14  180.00   0.0  0
 VB7  CONST_24  N4   C3   C8   C9   180.00   0.0  0
 VB7  CONST_25  N6   C7   C8   C9   180.00   0.0  0
 VB7  CONST_26  C1   N2   C3   C8   180.00   0.0  0
 VB7  CONST_27  C1   N2   C3   N4     0.00   0.0  0
 VB7  CONST_28  H2   C7   N6   C5   180.00   0.0  0
 VB7  CONST_29  H1   C5   N6   C7   180.00   0.0  0
 VB7  CONST_30  H11  C25  C18  C17  180.00   0.0  0
 VB7  CONST_31  H10  C23  C22  C17  180.00   0.0  0
 VB7  CONST_32  H6   C24  C23  C22  180.00   0.0  0
 VB7  CONST_33  H5   C22  C23  C24  180.00   0.0  0
 VB7  CONST_34  H15  C12  C13  C16    0.00   0.0  0
 VB7  CONST_35  H16  C14  C13  C16    0.00   0.0  0
 VB7  CONST_36  H17  N2   C3   C8     0.00   0.0  0
 VB7  Var_01    C20  C19  C18  C17   19.11  30.0  1
 VB7  Var_02    O21  C20  C19  C18  -52.00  30.0  1
 VB7  Var_03    C11  C9   C8   C7   -27.98  30.0  2
 VB7  Var_04    C12  C11  C9   C8   -28.32  30.0  2
 VB7  Var_05    O35  S33  O31  C30  177.14  30.0  3
 VB7  Var_06    H25  N34  S33  O31  -74.97  30.0  3
 VB7  Var_07    H23  C30  O31  S33  -63.05  30.0  3

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
 VB7  chir_01  C28  O32  C27  C29  positiv
 VB7  chir_02  C16  C17  O21  C13  negativ
 VB7  chir_03  C1   C29  C26  N2   negativ
 VB7  chir_04  C27  C26  C30  C28  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
 VB7  plan-1  C13  0.020
 VB7  plan-1  C16  0.020
 VB7  plan-1  C12  0.020
 VB7  plan-1  C14  0.020
 VB7  plan-1  S15  0.020
 VB7  plan-1  C11  0.020
 VB7  plan-1  C9   0.020
 VB7  plan-1  H15  0.020
 VB7  plan-1  H16  0.020
 VB7  plan-2  C17  0.020
 VB7  plan-2  C22  0.020
 VB7  plan-2  C24  0.020
 VB7  plan-2  C23  0.020
 VB7  plan-2  C25  0.020
 VB7  plan-2  C18  0.020
 VB7  plan-2  C19  0.020
 VB7  plan-2  C16  0.020
 VB7  plan-2  H5   0.020
 VB7  plan-2  H6   0.020
 VB7  plan-2  H10  0.020
 VB7  plan-2  H11  0.020
 VB7  plan-3  C5   0.020
 VB7  plan-3  C7   0.020
 VB7  plan-3  C8   0.020
 VB7  plan-3  C9   0.020
 VB7  plan-3  N6   0.020
 VB7  plan-3  N4   0.020
 VB7  plan-3  C3   0.020
 VB7  plan-3  N2   0.020
 VB7  plan-3  H1   0.020
 VB7  plan-3  H2   0.020
 VB7  plan-4  C3   0.020
 VB7  plan-4  N2   0.020
 VB7  plan-4  C1   0.020
 VB7  plan-4  H17  0.020
 VB7  plan-5  C8   0.020
 VB7  plan-5  C11  0.020
 VB7  plan-5  C9   0.020
 VB7  plan-5  O10  0.020

