# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:52:09 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: {(1R,2R,3S,4R)-4-[(5-{4-[(1S)-1-(6-bromopyridin-2-yl)-1-hydroxyethyl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2,3-dihydroxycyclopentyl}methyl sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(c1csc(c1)C(=O)c2cncnc2N[C@@H]3C[C@H](CO[S](N)(=O)=O)[C@@H](O)[C@H]3O)c4cccc(Br)n4
#
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
 VAY  VAY  '{(1R,2R,3S,4R)-4-[(5-{4-[(1S)-1-(6-bromopyridin-2-yl)-1-hydroxyethyl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2,3-dihydroxycyclopentyl}methyl sulfamate'  ligand  61  37  .  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_VAY
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
 VAY  C4    C   CH2   0  -0.468  34.4910   -2.7759  26.0710
 VAY  C5    C   CH1   0  -0.292  33.4632   -3.1342  24.9735
 VAY  C6    C   CH2   0  -0.193  32.0551   -2.9373  25.4937
 VAY  C8    C   CR6   0   0.582  37.5541   -3.9011  27.4205
 VAY  C10   C   CR16  0   0.078  39.5607   -3.3269  26.5090
 VAY  C13   C   CR6   0  -0.241  38.2071   -4.0703  28.6837
 VAY  C15   C   CR5   0  -0.294  38.2149   -5.0167  31.0440
 VAY  C20   C   CR15  0  -0.245  39.3838   -5.7235  31.1304
 VAY  C21   C   CT    0   0.121  40.9268   -6.9234  32.7996
 VAY  C22   C   CR6   0   0.244  40.7613   -8.3699  32.3317
 VAY  C24   C   CR6   0   0.095  41.8054  -10.1575  31.3898
 VAY  C26   C   CR16  0  -0.134  39.5820  -10.4280  32.1276
 VAY  C27   C   CR16  0  -0.311  39.6014   -9.1041  32.5342
 VAY  C25   C   CR16  0  -0.284  40.7063  -10.9855  31.5363
 VAY  BR28  BR  BR    0  -0.028  43.3836  -10.8390  30.5991
 VAY  N23   N   N     0  -0.449  41.8390   -8.9023  31.7691
 VAY  O30   O   OH1   0  -0.667  41.9990   -6.3266  32.1189
 VAY  C29   C   CH3   0  -0.673  41.1996   -6.9495  34.3069
 VAY  C19   C   CR5   0   0.211  39.6880   -6.1305  32.4562
 VAY  C18   C   CR15  0  -0.536  38.7305   -5.7197  33.3402
 VAY  S17   S   S2    0   0.284  37.4577   -4.8750  32.5877
 VAY  C14   C   C     0   0.429  37.4827   -4.4720  29.8942
 VAY  O16   O   O     0  -0.426  36.2656   -4.3591  29.9840
 VAY  C12   C   CR16  0  -0.060  39.5541   -3.7379  28.7079
 VAY  N11   N   N     0  -0.428  40.2504   -3.3626  27.6438
 VAY  N9    N   N     0  -0.459  38.2804   -3.5609  26.3447
 VAY  N7    N   NH1   0  -0.676  36.2438   -4.0769  27.2636
 VAY  C3    C   CH1   0  -0.119  35.5115   -3.9132  26.0329
 VAY  C2    C   CH1   0   0.051  34.6314   -5.1170  25.6978
 VAY  O32   O   OH1   0  -0.663  35.3089   -6.2783  25.3147
 VAY  C1    C   CH1   0   0.016  33.7629   -4.5883  24.5570
 VAY  O31   O   OH1   0  -0.670  34.4711   -4.5541  23.3401
 VAY  O33   O   OC2   0  -0.575  31.1342   -3.1249  24.3984
 VAY  S34   S   S     0   1.564  29.7694   -3.9271  24.6259
 VAY  O35   O   OS    0  -0.638  29.1964   -3.9747  23.3050
 VAY  O36   O   OS    0  -0.648  30.0499   -5.1381  25.3639
 VAY  N37   N   NC2   0  -0.892  28.8029   -3.0115  25.5675
 VAY  H1    H   HCH2  0   0.266  34.9463   -1.7992  25.9156
 VAY  H2    H   HCH2  0   0.246  34.0117   -2.7538  27.0553
 VAY  H3    H   HCH1  0   0.273  33.6017   -2.4884  24.1034
 VAY  H4    H   HCH2  0   0.268  31.9186   -1.9238  25.8755
 VAY  H5    H   HCH2  0   0.250  31.8466   -3.6388  26.3057
 VAY  H6    H   HCR6  0   0.263  40.1154   -3.0586  25.6154
 VAY  H7    H   HCR5  0   0.291  39.9972   -5.9784  30.2775
 VAY  H8    H   HCR6  0   0.289  38.6941  -11.0303  32.2655
 VAY  H9    H   HCR6  0   0.284  38.7307   -8.6542  32.9913
 VAY  H10   H   HCR6  0   0.294  40.7191  -12.0145  31.2072
 VAY  H11   H   HOH1  0   0.449  42.6048   -7.0405  31.8665
 VAY  H12   H   HCH3  0   0.238  40.3928   -7.4257  34.8643
 VAY  H13   H   HCH3  0   0.253  42.1136   -7.5105  34.5056
 VAY  H14   H   HCH3  0   0.250  41.3305   -5.9358  34.6872
 VAY  H15   H   HCR5  0   0.306  38.7072   -5.8745  34.4086
 VAY  H16   H   HCR6  0   0.287  40.0951   -3.7462  29.6472
 VAY  H17   H   HNH1  0   0.419  35.7101   -4.2353  28.1089
 VAY  H18   H   HCH1  0   0.275  36.2281   -3.7552  25.2285
 VAY  H19   H   HCH1  0   0.210  33.9713   -5.3024  26.5616
 VAY  H20   H   HOH1  0   0.456  35.8563   -6.5765  26.0484
 VAY  H21   H   HCH1  0   0.227  32.8480   -5.1867  24.4581
 VAY  H22   H   HOH1  0   0.447  34.7898   -5.4433  23.1514
 VAY  H23   H   HNC2  0   0.426  29.0751   -2.9674  26.5429
 VAY  H24   H   HNC2  0   0.424  28.5837   -2.0974  25.1871

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
 VAY  O31   C1   single    1.408  0.020  1.408
 VAY  O35   S34  deloc     1.441  0.020  1.441
 VAY  O33   S34  single    1.599  0.020  1.599
 VAY  O33   C6   single    1.443  0.020  1.443
 VAY  S34   O36  deloc     1.446  0.020  1.446
 VAY  S34   N37  single    1.631  0.020  1.631
 VAY  C1    C5   single    1.542  0.020  1.542
 VAY  C1    C2   single    1.528  0.020  1.528
 VAY  C5    C6   single    1.514  0.020  1.514
 VAY  C5    C4   single    1.546  0.020  1.546
 VAY  O32   C2   single    1.398  0.020  1.398
 VAY  C2    C3   single    1.528  0.020  1.528
 VAY  C3    C4   single    1.529  0.020  1.529
 VAY  C3    N7   single    1.441  0.020  1.441
 VAY  N9    C10  aromatic  1.312  0.020  1.312
 VAY  N9    C8   aromatic  1.342  0.020  1.342
 VAY  C10   N11  aromatic  1.328  0.020  1.328
 VAY  N7    C8   single    1.331  0.020  1.331
 VAY  C8    C13  aromatic  1.432  0.020  1.432
 VAY  N11   C12  aromatic  1.326  0.020  1.326
 VAY  C13   C12  aromatic  1.388  0.020  1.388
 VAY  C13   C14  single    1.467  0.020  1.467
 VAY  BR28  C24  single    1.892  0.020  1.892
 VAY  C14   O16  double    1.226  0.020  1.226
 VAY  C14   C15  single    1.468  0.020  1.468
 VAY  C24   N23  aromatic  1.312  0.020  1.312
 VAY  C24   C25  aromatic  1.384  0.020  1.384
 VAY  C15   C20  aromatic  1.369  0.020  1.369
 VAY  C15   S17  aromatic  1.725  0.020  1.725
 VAY  C20   C19  aromatic  1.420  0.020  1.420
 VAY  N23   C22  aromatic  1.327  0.020  1.327
 VAY  C25   C26  aromatic  1.387  0.020  1.387
 VAY  O30   C21  single    1.403  0.020  1.403
 VAY  C19   C21  single    1.510  0.020  1.510
 VAY  C19   C18  aromatic  1.366  0.020  1.366
 VAY  C22   C21  single    1.529  0.020  1.529
 VAY  C22   C27  aromatic  1.388  0.020  1.388
 VAY  S17   C18  aromatic  1.703  0.020  1.703
 VAY  C21   C29  single    1.532  0.020  1.532
 VAY  C26   C27  aromatic  1.385  0.020  1.385
 VAY  C4    H1   single    0.970  0.020  1.090
 VAY  C4    H2   single    0.970  0.020  1.090
 VAY  C5    H3   single    0.970  0.020  1.090
 VAY  C6    H4   single    0.970  0.020  1.090
 VAY  C6    H5   single    0.970  0.020  1.090
 VAY  C10   H6   single    0.930  0.020  1.080
 VAY  C20   H7   single    0.930  0.020  1.080
 VAY  C26   H8   single    0.930  0.020  1.080
 VAY  C27   H9   single    0.930  0.020  1.080
 VAY  C25   H10  single    0.930  0.020  1.080
 VAY  O30   H11  single    0.850  0.020  0.980
 VAY  C29   H12  single    0.970  0.020  1.090
 VAY  C29   H13  single    0.970  0.020  1.090
 VAY  C29   H14  single    0.970  0.020  1.090
 VAY  C18   H15  single    0.930  0.020  1.080
 VAY  C12   H16  single    0.930  0.020  1.080
 VAY  N7    H17  single    0.860  0.020  1.020
 VAY  C3    H18  single    0.970  0.020  1.090
 VAY  C2    H19  single    0.970  0.020  1.090
 VAY  O32   H20  single    0.850  0.020  0.980
 VAY  C1    H21  single    0.970  0.020  1.090
 VAY  O31   H22  single    0.850  0.020  0.980
 VAY  N37   H23  single    0.890  0.020  1.040
 VAY  N37   H24  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
 VAY  H2    C4   H1    107.05  3.000
 VAY  H2    C4   C3    109.25  3.000
 VAY  H1    C4   C3    112.63  3.000
 VAY  H2    C4   C5    110.60  3.000
 VAY  H1    C4   C5    112.62  3.000
 VAY  C3    C4   C5    104.70  3.000
 VAY  H3    C5   C1    108.52  3.000
 VAY  H3    C5   C6    108.34  3.000
 VAY  C1    C5   C6    113.34  3.000
 VAY  H3    C5   C4    110.13  3.000
 VAY  C6    C5   C4    110.14  3.000
 VAY  C1    C5   C4    106.33  3.000
 VAY  H5    C6   H4    108.19  3.000
 VAY  H5    C6   O33   111.02  3.000
 VAY  H4    C6   O33   107.84  3.000
 VAY  H5    C6   C5    110.43  3.000
 VAY  H4    C6   C5    110.93  3.000
 VAY  O33   C6   C5    108.41  3.000
 VAY  N7    C8   N9    118.14  3.000
 VAY  N7    C8   C13   122.49  3.000
 VAY  N9    C8   C13   119.37  3.000
 VAY  H6    C10  N9    116.09  3.000
 VAY  H6    C10  N11   116.40  3.000
 VAY  N9    C10  N11   127.51  3.000
 VAY  C12   C13  C14   122.05  3.000
 VAY  C14   C13  C8    122.36  3.000
 VAY  C12   C13  C8    115.45  3.000
 VAY  C14   C15  S17   116.84  3.000
 VAY  S17   C15  C20   111.15  3.000
 VAY  C14   C15  C20   131.84  3.000
 VAY  H7    C20  C19   123.20  3.000
 VAY  H7    C20  C15   123.82  3.000
 VAY  C19   C20  C15   112.94  3.000
 VAY  C19   C21  C29   112.25  3.000
 VAY  C29   C21  O30   110.39  3.000
 VAY  C19   C21  O30   107.05  3.000
 VAY  C29   C21  C22   107.70  3.000
 VAY  C19   C21  C22   109.77  3.000
 VAY  O30   C21  C22   109.67  3.000
 VAY  N23   C22  C27   121.90  3.000
 VAY  C27   C22  C21   123.12  3.000
 VAY  N23   C22  C21   114.91  3.000
 VAY  N23   C24  BR28  116.37  3.000
 VAY  N23   C24  C25   124.22  3.000
 VAY  BR28  C24  C25   119.42  3.000
 VAY  H8    C26  C25   119.72  3.000
 VAY  H8    C26  C27   120.41  3.000
 VAY  C25   C26  C27   119.86  3.000
 VAY  H9    C27  C26   120.70  3.000
 VAY  H9    C27  C22   120.97  3.000
 VAY  C26   C27  C22   118.33  3.000
 VAY  H10   C25  C26   121.48  3.000
 VAY  H10   C25  C24   121.89  3.000
 VAY  C26   C25  C24   116.63  3.000
 VAY  C24   N23  C22   119.05  3.000
 VAY  H11   O30  C21   106.89  3.000
 VAY  H14   C29  H13   108.30  3.000
 VAY  H14   C29  H12   108.46  3.000
 VAY  H13   C29  H12   107.60  3.000
 VAY  H14   C29  C21   110.40  3.000
 VAY  H13   C29  C21   109.71  3.000
 VAY  H12   C29  C21   112.25  3.000
 VAY  C18   C19  C21   125.84  3.000
 VAY  C18   C19  C20   111.59  3.000
 VAY  C21   C19  C20   122.58  3.000
 VAY  H15   C18  S17   119.49  3.000
 VAY  H15   C18  C19   127.75  3.000
 VAY  S17   C18  C19   112.76  3.000
 VAY  C18   S17  C15    91.53  3.000
 VAY  O16   C14  C15   118.17  3.000
 VAY  C15   C14  C13   120.11  3.000
 VAY  O16   C14  C13   121.71  3.000
 VAY  H16   C12  N11   115.82  3.000
 VAY  H16   C12  C13   119.85  3.000
 VAY  N11   C12  C13   124.31  3.000
 VAY  C12   N11  C10   114.87  3.000
 VAY  C10   N9   C8    118.23  3.000
 VAY  H17   N7   C3    117.58  3.000
 VAY  H17   N7   C8    116.18  3.000
 VAY  C3    N7   C8    125.85  3.000
 VAY  H18   C3   C2    109.35  3.000
 VAY  H18   C3   N7    108.23  3.000
 VAY  C2    C3   N7    112.98  3.000
 VAY  H18   C3   C4    110.48  3.000
 VAY  N7    C3   C4    113.73  3.000
 VAY  C2    C3   C4    101.95  3.000
 VAY  H19   C2   C1    107.62  3.000
 VAY  H19   C2   O32   111.41  3.000
 VAY  C1    C2   O32   111.00  3.000
 VAY  H19   C2   C3    107.78  3.000
 VAY  O32   C2   C3    115.80  3.000
 VAY  C1    C2   C3    102.62  3.000
 VAY  H20   O32  C2    108.91  3.000
 VAY  H21   C1   O31   110.77  3.000
 VAY  H21   C1   C2    110.63  3.000
 VAY  O31   C1   C2    111.57  3.000
 VAY  H21   C1   C5    112.11  3.000
 VAY  C2    C1   C5    103.60  3.000
 VAY  O31   C1   C5    107.95  3.000
 VAY  H22   O31  C1    108.25  3.000
 VAY  S34   O33  C6    120.12  3.000
 VAY  N37   S34  O36   106.89  3.000
 VAY  N37   S34  O35   108.20  3.000
 VAY  O36   S34  O35   121.17  3.000
 VAY  N37   S34  O33   107.83  3.000
 VAY  O36   S34  O33   109.10  3.000
 VAY  O35   S34  O33   103.04  3.000
 VAY  H24   N37  H23   112.32  3.000
 VAY  H24   N37  S34   114.69  3.000
 VAY  H23   N37  S34   114.89  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
 VAY  CONST_01  N11   C10  N9   C8      0.00   0.0  0
 VAY  CONST_02  N11   C12  C13  C8      0.00   0.0  0
 VAY  CONST_03  C13   C8   N9   C10     0.00   0.0  0
 VAY  CONST_04  C13   C12  N11  C10     0.00   0.0  0
 VAY  CONST_05  C18   C19  C20  C15     0.00   0.0  0
 VAY  CONST_06  C19   C18  S17  C15     0.00   0.0  0
 VAY  CONST_07  C18   S17  C15  C20     0.00   0.0  0
 VAY  CONST_08  S17   C18  C19  C20     0.00   0.0  0
 VAY  CONST_09  C25   C24  N23  C22     0.00   0.0  0
 VAY  CONST_10  C25   C26  C27  C22     0.00   0.0  0
 VAY  CONST_11  C27   C22  N23  C24     0.00   0.0  0
 VAY  CONST_12  C27   C26  C25  C24     0.00   0.0  0
 VAY  CONST_13  N23   C24  C25  C26     0.00   0.0  0
 VAY  CONST_14  N23   C22  C27  C26     0.00   0.0  0
 VAY  CONST_15  S17   C15  C20  C19     0.00   0.0  0
 VAY  CONST_16  N9    C10  N11  C12     0.00   0.0  0
 VAY  CONST_17  N9    C8   C13  C12     0.00   0.0  0
 VAY  CONST_18  N7    C8   N9   C10   180.00   0.0  0
 VAY  CONST_19  C21   C19  C20  C15   180.00   0.0  0
 VAY  CONST_20  S17   C18  C19  C21   180.00   0.0  0
 VAY  CONST_21  C24   N23  C22  C21   180.00   0.0  0
 VAY  CONST_22  C26   C27  C22  C21   180.00   0.0  0
 VAY  CONST_23  BR28  C24  N23  C22   180.00   0.0  0
 VAY  CONST_24  BR28  C24  C25  C26   180.00   0.0  0
 VAY  CONST_25  C14   C15  C20  C19   180.00   0.0  0
 VAY  CONST_26  C14   C15  S17  C18   180.00   0.0  0
 VAY  CONST_27  N9    C8   C13  C14   180.00   0.0  0
 VAY  CONST_28  N11   C12  C13  C14   180.00   0.0  0
 VAY  CONST_29  N7    C8   C13  C12   180.00   0.0  0
 VAY  CONST_30  C3    N7   C8   C13   180.00   0.0  0
 VAY  CONST_31  C3    N7   C8   N9      0.00   0.0  0
 VAY  CONST_32  H6    C10  N9   C8    180.00   0.0  0
 VAY  CONST_33  H16   C12  C13  C8    180.00   0.0  0
 VAY  CONST_34  H15   C18  S17  C15   180.00   0.0  0
 VAY  CONST_35  H8    C26  C27  C22   180.00   0.0  0
 VAY  CONST_36  H10   C25  C26  C27   180.00   0.0  0
 VAY  CONST_37  H9    C27  C26  C25   180.00   0.0  0
 VAY  CONST_38  H7    C20  C19  C18   180.00   0.0  0
 VAY  CONST_39  H17   N7   C8   C13     0.00   0.0  0
 VAY  Var_01    C15   C14  C13  C8    161.69  30.0  2
 VAY  Var_02    C20   C15  C14  C13   -29.13  30.0  2
 VAY  Var_03    O35   S34  O33  C6   -176.10  30.0  3
 VAY  Var_04    H23   N37  S34  O33   -73.66  30.0  3
 VAY  Var_05    H4    C6   O33  S34  -100.89  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
 VAY  chir_01  C5   C1   C6   C4   negativ
 VAY  chir_02  C21  C19  C22  C29  positiv
 VAY  chir_03  C3   C2   C4   N7   negativ
 VAY  chir_04  C2   O32  C1   C3   positiv
 VAY  chir_05  C1   O31  C5   C2   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
 VAY  plan-1  C15   0.020
 VAY  plan-1  C20   0.020
 VAY  plan-1  C21   0.020
 VAY  plan-1  C19   0.020
 VAY  plan-1  C18   0.020
 VAY  plan-1  S17   0.020
 VAY  plan-1  C14   0.020
 VAY  plan-1  H7    0.020
 VAY  plan-1  H15   0.020
 VAY  plan-2  C21   0.020
 VAY  plan-2  C22   0.020
 VAY  plan-2  C24   0.020
 VAY  plan-2  C26   0.020
 VAY  plan-2  C27   0.020
 VAY  plan-2  C25   0.020
 VAY  plan-2  BR28  0.020
 VAY  plan-2  N23   0.020
 VAY  plan-2  H8    0.020
 VAY  plan-2  H9    0.020
 VAY  plan-2  H10   0.020
 VAY  plan-3  C8    0.020
 VAY  plan-3  C10   0.020
 VAY  plan-3  C13   0.020
 VAY  plan-3  C14   0.020
 VAY  plan-3  C12   0.020
 VAY  plan-3  N11   0.020
 VAY  plan-3  N9    0.020
 VAY  plan-3  N7    0.020
 VAY  plan-3  H6    0.020
 VAY  plan-3  H16   0.020
 VAY  plan-4  C8    0.020
 VAY  plan-4  N7    0.020
 VAY  plan-4  C3    0.020
 VAY  plan-4  H17   0.020
 VAY  plan-5  C13   0.020
 VAY  plan-5  C15   0.020
 VAY  plan-5  C14   0.020
 VAY  plan-5  O16   0.020

