# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:05:01 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[(3S)-5-phenyl-3-thiophen-2-yl-3H-1,4-benzodiazepin-2-yl]azetidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CN(C1)C2=Nc3ccccc3C(=N[C@@H]2c4sccc4)c5ccccc5
#
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
 VGA  VGA  1-[(3S)-5-phenyl-3-thiophen-2-yl-3H-1,4-benzodiazepin-2-yl]azetidin-3-ol  ligand  46  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VGA
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
 VGA  N1    N  N     0  -0.481  -1.2379  -0.0474  -1.3778
 VGA  C2    C  C     0   0.461  -1.5886   0.4785  -0.2542
 VGA  C3    C  CH1   0  -0.317  -0.8930   0.1862   1.0636
 VGA  C4    C  C     0   0.220   1.2764   0.3841   0.1717
 VGA  N5    N  N     0  -0.360   0.4071   0.8145   1.0050
 VGA  C6    C  CR6   0   0.013   1.0816  -0.6943  -0.8073
 VGA  C7    C  CR6   0   0.234  -0.1396  -0.8633  -1.4947
 VGA  C8    C  CR16  0  -0.307  -0.2239  -1.8923  -2.4489
 VGA  C9    C  CR16  0  -0.252   0.8265  -2.7530  -2.6763
 VGA  C10   C  CR16  0  -0.269   2.0253  -2.5988  -1.9786
 VGA  C11   C  CR16  0  -0.283   2.1466  -1.5650  -1.0754
 VGA  C12   C  CR6   0   0.022   2.5996   1.0587   0.2117
 VGA  N13   N  N     0  -0.472  -2.5981   1.3417  -0.2235
 VGA  C14   C  C     0  -0.268  -3.3446   1.9306  -1.3173
 VGA  C15   C  C     0  -0.031  -4.1437   2.7398  -0.2795
 VGA  C16   C  C     0  -0.288  -3.2369   2.1285   0.8202
 VGA  C17   C  CR16  0  -0.284   3.3002   1.3372  -0.9615
 VGA  C18   C  CR16  0  -0.240   4.5086   2.0176  -0.9152
 VGA  C19   C  CR16  0  -0.258   5.0394   2.4127   0.3054
 VGA  C20   C  CR16  0  -0.244   4.3513   2.1320   1.4798
 VGA  C21   C  CR16  0  -0.287   3.1354   1.4679   1.4325
 VGA  C22   C  CR5   0  -0.143  -0.8684  -1.2823   1.4001
 VGA  S23   S  S2    0   0.222  -2.1691  -2.3164   0.9508
 VGA  C24   C  CR15  0  -0.471  -1.4828  -3.6505   1.7797
 VGA  C25   C  CR15  0  -0.177  -0.3062  -3.3122   2.3725
 VGA  C26   C  CR15  0  -0.226   0.0425  -1.9503   2.1604
 VGA  O27   O  OH1   0  -0.660  -4.0545   4.1144  -0.4848
 VGA  H3    H  HCH1  0   0.305  -1.4408   0.6856   1.8678
 VGA  H11   H  HCR6  0   0.256   3.0800  -1.4344  -0.5422
 VGA  H8    H  HCR6  0   0.248  -1.1516  -2.0002  -2.9968
 VGA  H9    H  HCR6  0   0.256   0.7203  -3.5491  -3.4023
 VGA  H10   H  HCR6  0   0.253   2.8532  -3.2734  -2.1508
 VGA  H17   H  HCR6  0   0.260   2.8943   1.0360  -1.9188
 VGA  H21   H  HCR6  0   0.254   2.6003   1.2521   2.3480
 VGA  H141  H  H     0   0.250  -2.7287   2.5390  -1.9847
 VGA  H142  H  H     0   0.256  -3.9150   1.2136  -1.9096
 VGA  H161  H  H     0   0.257  -3.7473   1.5387   1.5832
 VGA  H162  H  H     0   0.255  -2.5719   2.8506   1.3004
 VGA  H15   H  H     0   0.243  -5.1801   2.4031  -0.1875
 VGA  H27   H  HOH1  0   0.459  -4.5805   4.5595   0.1871
 VGA  H18   H  HCR6  0   0.260   5.0356   2.2367  -1.8346
 VGA  H19   H  HCR6  0   0.260   5.9862   2.9361   0.3425
 VGA  H20   H  HCR6  0   0.260   4.7646   2.4286   2.4350
 VGA  H26   H  HCR5  0   0.258   0.9407  -1.4932   2.5506
 VGA  H24   H  HCR5  0   0.293  -1.9767  -4.6097   1.7718
 VGA  H25   H  HCR5  0   0.264   0.2953  -4.0066   2.9416

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
 VGA  N1   C2    double    1.289  0.020  1.289
 VGA  N1   C7    single    1.373  0.020  1.373
 VGA  C2   C3    single    1.519  0.020  1.519
 VGA  C2   N13   single    1.329  0.020  1.329
 VGA  C3   N5    single    1.445  0.020  1.445
 VGA  C3   C22   single    1.507  0.020  1.507
 VGA  C4   N5    double    1.279  0.020  1.279
 VGA  C4   C6    single    1.469  0.020  1.469
 VGA  C4   C12   single    1.486  0.020  1.486
 VGA  C6   C7    aromatic  1.412  0.020  1.412
 VGA  C6   C11   aromatic  1.401  0.020  1.401
 VGA  C7   C8    aromatic  1.406  0.020  1.406
 VGA  C8   C9    aromatic  1.377  0.020  1.377
 VGA  C9   C10   aromatic  1.396  0.020  1.396
 VGA  C10  C11   aromatic  1.378  0.020  1.378
 VGA  C12  C17   aromatic  1.394  0.020  1.394
 VGA  C12  C21   aromatic  1.395  0.020  1.395
 VGA  N13  C14   single    1.449  0.020  1.449
 VGA  N13  C16   single    1.455  0.020  1.455
 VGA  C14  C15   single    1.540  0.020  1.540
 VGA  C15  C16   single    1.551  0.020  1.551
 VGA  C15  O27   single    1.393  0.020  1.393
 VGA  C17  C18   aromatic  1.388  0.020  1.388
 VGA  C18  C19   aromatic  1.388  0.020  1.388
 VGA  C19  C20   aromatic  1.390  0.020  1.390
 VGA  C20  C21   aromatic  1.386  0.020  1.386
 VGA  C22  S23   aromatic  1.721  0.020  1.721
 VGA  C22  C26   aromatic  1.362  0.020  1.362
 VGA  S23  C24   aromatic  1.714  0.020  1.714
 VGA  C24  C25   aromatic  1.360  0.020  1.360
 VGA  C25  C26   aromatic  1.422  0.020  1.422
 VGA  C3   H3    single    0.970  0.020  1.090
 VGA  C11  H11   single    0.930  0.020  1.080
 VGA  C8   H8    single    0.930  0.020  1.080
 VGA  C9   H9    single    0.930  0.020  1.080
 VGA  C10  H10   single    0.930  0.020  1.080
 VGA  C17  H17   single    0.930  0.020  1.080
 VGA  C21  H21   single    0.930  0.020  1.080
 VGA  C14  H141  single    0.970  0.020  1.090
 VGA  C14  H142  single    0.970  0.020  1.090
 VGA  C16  H161  single    0.970  0.020  1.090
 VGA  C16  H162  single    0.970  0.020  1.090
 VGA  C15  H15   single    0.970  0.020  1.090
 VGA  O27  H27   single    0.850  0.020  0.980
 VGA  C18  H18   single    0.930  0.020  1.080
 VGA  C19  H19   single    0.930  0.020  1.080
 VGA  C20  H20   single    0.930  0.020  1.080
 VGA  C26  H26   single    0.930  0.020  1.080
 VGA  C24  H24   single    0.930  0.020  1.080
 VGA  C25  H25   single    0.930  0.020  1.080

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
 VGA  C7    N1   C2    122.29  3.000
 VGA  N13   C2   C3    116.94  3.000
 VGA  N13   C2   N1    119.46  3.000
 VGA  C3    C2   N1    123.59  3.000
 VGA  H3    C3   C22   106.80  3.000
 VGA  H3    C3   N5    106.38  3.000
 VGA  C22   C3   N5    114.71  3.000
 VGA  H3    C3   C2    108.71  3.000
 VGA  C22   C3   C2    112.88  3.000
 VGA  N5    C3   C2    107.05  3.000
 VGA  C12   C4   C6    117.98  3.000
 VGA  C12   C4   N5    115.79  3.000
 VGA  C6    C4   N5    126.23  3.000
 VGA  C4    N5   C3    119.45  3.000
 VGA  C11   C6   C7    119.34  3.000
 VGA  C11   C6   C4    118.86  3.000
 VGA  C7    C6   C4    121.80  3.000
 VGA  C8    C7   C6    118.03  3.000
 VGA  C8    C7   N1    116.41  3.000
 VGA  C6    C7   N1    125.41  3.000
 VGA  H8    C8   C9    120.52  3.000
 VGA  H8    C8   C7    117.88  3.000
 VGA  C9    C8   C7    121.59  3.000
 VGA  H9    C9   C10   120.05  3.000
 VGA  H9    C9   C8    119.71  3.000
 VGA  C10   C9   C8    120.24  3.000
 VGA  H10   C10  C11   120.32  3.000
 VGA  H10   C10  C9    120.59  3.000
 VGA  C11   C10  C9    119.09  3.000
 VGA  H11   C11  C10   119.27  3.000
 VGA  H11   C11  C6    119.07  3.000
 VGA  C10   C11  C6    121.64  3.000
 VGA  C21   C12  C17   119.00  3.000
 VGA  C21   C12  C4    119.93  3.000
 VGA  C17   C12  C4    121.03  3.000
 VGA  C16   N13  C14    95.48  3.000
 VGA  C16   N13  C2    134.55  3.000
 VGA  C14   N13  C2    129.64  3.000
 VGA  H142  C14  H141  109.20  3.000
 VGA  H142  C14  C15   116.10  3.000
 VGA  H141  C14  C15   114.29  3.000
 VGA  H142  C14  N13   114.33  3.000
 VGA  H141  C14  N13   113.37  3.000
 VGA  C15   C14  N13    88.41  3.000
 VGA  H15   C15  O27   112.15  3.000
 VGA  H15   C15  C16   111.91  3.000
 VGA  O27   C15  C16   117.14  3.000
 VGA  H15   C15  C14   112.75  3.000
 VGA  O27   C15  C14   112.72  3.000
 VGA  C16   C15  C14    88.13  3.000
 VGA  H162  C16  H161  109.55  3.000
 VGA  H162  C16  C15   114.01  3.000
 VGA  H161  C16  C15   115.81  3.000
 VGA  H162  C16  N13   113.92  3.000
 VGA  H161  C16  N13   114.50  3.000
 VGA  C15   C16  N13    87.78  3.000
 VGA  H17   C17  C18   119.50  3.000
 VGA  H17   C17  C12   120.00  3.000
 VGA  C18   C17  C12   120.49  3.000
 VGA  H18   C18  C19   120.21  3.000
 VGA  H18   C18  C17   119.67  3.000
 VGA  C19   C18  C17   120.12  3.000
 VGA  H19   C19  C20   120.12  3.000
 VGA  H19   C19  C18   120.14  3.000
 VGA  C20   C19  C18   119.74  3.000
 VGA  H20   C20  C21   119.76  3.000
 VGA  H20   C20  C19   120.09  3.000
 VGA  C21   C20  C19   120.15  3.000
 VGA  H21   C21  C20   120.02  3.000
 VGA  H21   C21  C12   119.48  3.000
 VGA  C20   C21  C12   120.49  3.000
 VGA  C26   C22  S23   110.89  3.000
 VGA  C26   C22  C3    127.86  3.000
 VGA  S23   C22  C3    120.99  3.000
 VGA  C24   S23  C22    92.22  3.000
 VGA  H24   C24  C25   128.34  3.000
 VGA  H24   C24  S23   120.34  3.000
 VGA  C25   C24  S23   111.32  3.000
 VGA  H25   C25  C26   123.88  3.000
 VGA  H25   C25  C24   123.45  3.000
 VGA  C26   C25  C24   112.67  3.000
 VGA  H26   C26  C25   123.72  3.000
 VGA  H26   C26  C22   123.37  3.000
 VGA  C25   C26  C22   112.90  3.000
 VGA  H27   O27  C15   108.58  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
 VGA  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 VGA  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 VGA  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 VGA  CONST_04  C19  C18  C17  C12     0.00   0.0  0
 VGA  CONST_05  C19  C20  C21  C12     0.00   0.0  0
 VGA  CONST_06  C20  C21  C12  C17     0.00   0.0  0
 VGA  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 VGA  CONST_08  C21  C12  C17  C18     0.00   0.0  0
 VGA  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 VGA  CONST_10  C25  C24  S23  C22     0.00   0.0  0
 VGA  CONST_11  C24  C25  C26  C22     0.00   0.0  0
 VGA  CONST_12  C25  C26  C22  S23     0.00   0.0  0
 VGA  CONST_13  C26  C25  C24  S23     0.00   0.0  0
 VGA  CONST_14  C26  C22  S23  C24     0.00   0.0  0
 VGA  CONST_15  C24  S23  C22  C3    180.00   0.0  0
 VGA  CONST_16  C25  C26  C22  C3    180.00   0.0  0
 VGA  CONST_17  C18  C17  C12  C4    180.00   0.0  0
 VGA  CONST_18  C20  C21  C12  C4    180.00   0.0  0
 VGA  CONST_19  H26  C26  C22  C3      0.00   0.0  0
 VGA  CONST_20  H17  C17  C12  C4      0.00   0.0  0
 VGA  CONST_21  H21  C21  C12  C4      0.00   0.0  0
 VGA  CONST_22  H10  C10  C11  C6    180.00   0.0  0
 VGA  CONST_23  H9   C9   C8   C7    180.00   0.0  0
 VGA  CONST_24  H11  C11  C10  C9    180.00   0.0  0
 VGA  CONST_25  H8   C8   C9   C10   180.00   0.0  0
 VGA  CONST_26  H18  C18  C17  C12   180.00   0.0  0
 VGA  CONST_27  H20  C20  C21  C12   180.00   0.0  0
 VGA  CONST_28  H19  C19  C18  C17   180.00   0.0  0
 VGA  CONST_29  H24  C24  S23  C22   180.00   0.0  0
 VGA  CONST_30  H25  C25  C26  C22   180.00   0.0  0
 VGA  Var_01    C15  C14  N13  C2   -177.71  30.0  1
 VGA  Var_02    C15  C16  N13  C2    177.21  30.0  1

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
 VGA  chir_01  C3   C2   N5   C22  positiv
 VGA  chir_02  C15  O27  C16  C14  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
 VGA  plan-1  C3   0.020
 VGA  plan-1  C22  0.020
 VGA  plan-1  S23  0.020
 VGA  plan-1  C24  0.020
 VGA  plan-1  C25  0.020
 VGA  plan-1  C26  0.020
 VGA  plan-1  H26  0.020
 VGA  plan-1  H24  0.020
 VGA  plan-1  H25  0.020
 VGA  plan-2  N1   0.020
 VGA  plan-2  C4   0.020
 VGA  plan-2  C6   0.020
 VGA  plan-2  C7   0.020
 VGA  plan-2  C8   0.020
 VGA  plan-2  C9   0.020
 VGA  plan-2  C10  0.020
 VGA  plan-2  C11  0.020
 VGA  plan-2  H11  0.020
 VGA  plan-2  H8   0.020
 VGA  plan-2  H9   0.020
 VGA  plan-2  H10  0.020
 VGA  plan-3  C4   0.020
 VGA  plan-3  C12  0.020
 VGA  plan-3  C17  0.020
 VGA  plan-3  C18  0.020
 VGA  plan-3  C19  0.020
 VGA  plan-3  C20  0.020
 VGA  plan-3  C21  0.020
 VGA  plan-3  H17  0.020
 VGA  plan-3  H21  0.020
 VGA  plan-3  H18  0.020
 VGA  plan-3  H19  0.020
 VGA  plan-3  H20  0.020
 VGA  plan-4  N1   0.020
 VGA  plan-4  C2   0.020
 VGA  plan-4  C3   0.020
 VGA  plan-4  C7   0.020
 VGA  plan-4  N13  0.020
 VGA  plan-4  C14  0.020
 VGA  plan-4  C16  0.020

