# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:33:14 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (3S)-3-(4-chlorophenyl)-4-(5,7-dichloro-1H-benzimidazol-2-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](Cc1[nH]c2c(Cl)cc(Cl)cc2n1)c3ccc(Cl)cc3
#
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
 AZ7  AZ7  '(3S)-3-(4-chlorophenyl)-4-(5,7-dichloro-1H-benzimidazol-2-yl)butanoic acid'  ligand  36  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AZ7
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
 AZ7  CL6   CL  CL     0  -0.125  -6.7441  -0.9145  -1.1772
 AZ7  C5    C   CR6    0  -0.061  -5.1864  -0.3381  -0.6726
 AZ7  C6    C   CR16   0  -0.220  -5.1104   0.3662   0.5347
 AZ7  C1    C   CR6    0  -0.131  -3.8881   0.8436   0.9663
 AZ7  CL5   CL  CL     0  -0.103  -3.7369   1.7186   2.4449
 AZ7  C4    C   CR16   0  -0.296  -4.0881  -0.5881  -1.4713
 AZ7  C3    C   CR56   0   0.141  -2.8610  -0.1013  -1.0264
 AZ7  N9    N   N      0  -0.467  -1.6184  -0.1919  -1.6005
 AZ7  C8    C   CR5    0   0.444  -0.8087   0.4303  -0.7848
 AZ7  N7    N   NR15   0  -0.689  -1.4524   0.9286   0.3065
 AZ7  C2    C   CR56   0   0.458  -2.7708   0.6061   0.1830
 AZ7  C10   C   CH2    0  -0.518   0.6572   0.5943  -0.9678
 AZ7  C11   C   CH1    0  -0.339   1.4814  -0.1148   0.1253
 AZ7  C19   C   CH2    0  -0.564   1.2259  -1.6193   0.1394
 AZ7  C20   C   C      0   0.415   1.9832  -2.3625   1.2543
 AZ7  O22   O   O      0  -0.601   2.1567  -1.7448   2.3228
 AZ7  O21   O   OC    -1  -0.622   2.3304  -3.5360   1.0097
 AZ7  C12   C   C      0   0.196   2.9440   0.2026  -0.0653
 AZ7  C17   C   C1     0  -0.329   3.6136   1.0309   0.8292
 AZ7  C16   C   C1     0  -0.198   4.9538   1.3480   0.6591
 AZ7  C15   C   C      0  -0.061   5.6359   0.8226  -0.4261
 AZ7  CL9   CL  CL     0  -0.139   7.3143   1.2071  -0.6498
 AZ7  C14   C   C1     0  -0.198   4.9984  -0.0065  -1.3355
 AZ7  C13   C   C1     0  -0.317   3.6576  -0.3082  -1.1471
 AZ7  H6    H   HCR6   0   0.298  -5.9999   0.5364   1.1248
 AZ7  H4    H   HCR6   0   0.283  -4.1717  -1.1362  -2.3998
 AZ7  H7    H   HNR5   0   0.423  -1.0297   1.4489   1.0597
 AZ7  H101  H   HCH2   0   0.267   0.9154   0.2036  -1.9529
 AZ7  H102  H   HCH2   0   0.279   0.8990   1.6613  -0.9705
 AZ7  H11   H   HCH1   0   0.249   1.1876   0.2884   1.0978
 AZ7  H191  H   HCH2   0   0.245   0.1550  -1.8005   0.2911
 AZ7  H192  H   HCH2   0   0.215   1.4649  -2.0536  -0.8353
 AZ7  H17   H   H      0   0.254   3.0818   1.4387   1.6798
 AZ7  H13   H   H      0   0.258   3.1686  -0.9572  -1.8638
 AZ7  H16   H   H      0   0.275   5.4583   1.9916   1.3671
 AZ7  H14   H   H      0   0.275   5.5363  -0.4148  -2.1805

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
 AZ7  CL6  C5    single    1.736  0.020  1.736
 AZ7  C5   C6    aromatic  1.400  0.020  1.400
 AZ7  C5   C4    aromatic  1.381  0.020  1.381
 AZ7  C6   C1    aromatic  1.381  0.020  1.381
 AZ7  C1   CL5   single    1.725  0.020  1.725
 AZ7  C1   C2    aromatic  1.385  0.020  1.385
 AZ7  C4   C3    aromatic  1.393  0.020  1.393
 AZ7  C3   N9    aromatic  1.372  0.020  1.372
 AZ7  C3   C2    aromatic  1.404  0.020  1.404
 AZ7  N9   C8    aromatic  1.307  0.020  1.307
 AZ7  C8   N7    aromatic  1.362  0.020  1.362
 AZ7  C8   C10   single    1.486  0.020  1.486
 AZ7  N7   C2    aromatic  1.363  0.020  1.363
 AZ7  C10  C11   single    1.542  0.020  1.542
 AZ7  C11  C19   single    1.526  0.020  1.526
 AZ7  C11  C12   single    1.509  0.020  1.509
 AZ7  C19  C20   single    1.539  0.020  1.539
 AZ7  C20  O22   deloc     1.246  0.020  1.246
 AZ7  C20  O21   deloc     1.248  0.020  1.248
 AZ7  C12  C17   aromatic  1.391  0.020  1.391
 AZ7  C12  C13   aromatic  1.393  0.020  1.393
 AZ7  C17  C16   aromatic  1.388  0.020  1.388
 AZ7  C16  C15   aromatic  1.385  0.020  1.385
 AZ7  C15  CL9   single    1.736  0.020  1.736
 AZ7  C15  C14   aromatic  1.386  0.020  1.386
 AZ7  C14  C13   aromatic  1.387  0.020  1.387
 AZ7  C6   H6    single    0.930  0.020  1.080
 AZ7  C4   H4    single    0.930  0.020  1.080
 AZ7  N7   H7    single    0.860  0.020  1.020
 AZ7  C10  H101  single    0.970  0.020  1.090
 AZ7  C10  H102  single    0.970  0.020  1.090
 AZ7  C11  H11   single    0.970  0.020  1.090
 AZ7  C19  H191  single    0.970  0.020  1.090
 AZ7  C19  H192  single    0.970  0.020  1.090
 AZ7  C17  H17   single    0.930  0.020  1.080
 AZ7  C13  H13   single    0.930  0.020  1.080
 AZ7  C16  H16   single    0.930  0.020  1.080
 AZ7  C14  H14   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
 AZ7  C4    C5   C6    123.15  3.000
 AZ7  C4    C5   CL6   119.05  3.000
 AZ7  C6    C5   CL6   117.80  3.000
 AZ7  H6    C6   C1    120.21  3.000
 AZ7  H6    C6   C5    120.36  3.000
 AZ7  C1    C6   C5    119.43  3.000
 AZ7  C2    C1   CL5   120.07  3.000
 AZ7  C2    C1   C6    118.55  3.000
 AZ7  CL5   C1   C6    121.38  3.000
 AZ7  H4    C4   C3    121.29  3.000
 AZ7  H4    C4   C5    121.80  3.000
 AZ7  C3    C4   C5    116.91  3.000
 AZ7  C2    C3   N9    109.61  3.000
 AZ7  C2    C3   C4    120.51  3.000
 AZ7  N9    C3   C4    129.88  3.000
 AZ7  C8    N9   C3    105.58  3.000
 AZ7  C10   C8   N7    121.64  3.000
 AZ7  C10   C8   N9    125.93  3.000
 AZ7  N7    C8   N9    112.43  3.000
 AZ7  H7    N7   C2    126.54  3.000
 AZ7  H7    N7   C8    126.11  3.000
 AZ7  C2    N7   C8    107.35  3.000
 AZ7  N7    C2   C3    105.04  3.000
 AZ7  N7    C2   C1    133.52  3.000
 AZ7  C3    C2   C1    121.45  3.000
 AZ7  H102  C10  H101  107.15  3.000
 AZ7  H102  C10  C11   109.40  3.000
 AZ7  H101  C10  C11   110.43  3.000
 AZ7  H102  C10  C8    109.02  3.000
 AZ7  H101  C10  C8    107.76  3.000
 AZ7  C11   C10  C8    112.90  3.000
 AZ7  H11   C11  C12   107.18  3.000
 AZ7  H11   C11  C19   108.09  3.000
 AZ7  C12   C11  C19   111.77  3.000
 AZ7  H11   C11  C10   108.51  3.000
 AZ7  C12   C11  C10   109.38  3.000
 AZ7  C19   C11  C10   111.74  3.000
 AZ7  H192  C19  H191  105.73  3.000
 AZ7  H192  C19  C20   110.26  3.000
 AZ7  H191  C19  C20   107.48  3.000
 AZ7  H192  C19  C11   110.29  3.000
 AZ7  H191  C19  C11   109.13  3.000
 AZ7  C20   C19  C11   113.60  3.000
 AZ7  O21   C20  O22   126.54  3.000
 AZ7  O21   C20  C19   116.68  3.000
 AZ7  O22   C20  C19   116.76  3.000
 AZ7  C13   C12  C17   118.11  3.000
 AZ7  C13   C12  C11   121.17  3.000
 AZ7  C17   C12  C11   120.71  3.000
 AZ7  H17   C17  C16   118.98  3.000
 AZ7  H17   C17  C12   119.54  3.000
 AZ7  C16   C17  C12   121.48  3.000
 AZ7  H16   C16  C15   120.58  3.000
 AZ7  H16   C16  C17   120.41  3.000
 AZ7  C15   C16  C17   119.01  3.000
 AZ7  C14   C15  CL9   119.51  3.000
 AZ7  C14   C15  C16   120.96  3.000
 AZ7  CL9   C15  C16   119.53  3.000
 AZ7  H14   C14  C13   120.31  3.000
 AZ7  H14   C14  C15   120.64  3.000
 AZ7  C13   C14  C15   119.05  3.000
 AZ7  H13   C13  C14   118.47  3.000
 AZ7  H13   C13  C12   120.14  3.000
 AZ7  C14   C13  C12   121.39  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
 AZ7  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 AZ7  CONST_02  N9   C3   C4   C5    180.00   0.0  0
 AZ7  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 AZ7  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 AZ7  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 AZ7  CONST_06  N7   C2   C1   C6    180.00   0.0  0
 AZ7  CONST_07  C4   C5   C6   C1      0.00   0.0  0
 AZ7  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 AZ7  CONST_09  N9   C3   C2   C1    180.00   0.0  0
 AZ7  CONST_10  C8   N7   C2   C1    180.00   0.0  0
 AZ7  CONST_11  C8   N9   C3   C4    180.00   0.0  0
 AZ7  CONST_12  N7   C2   C3   C4    180.00   0.0  0
 AZ7  CONST_13  N7   C8   N9   C3      0.00   0.0  0
 AZ7  CONST_14  C8   N7   C2   C3      0.00   0.0  0
 AZ7  CONST_15  N7   C2   C3   N9      0.00   0.0  0
 AZ7  CONST_16  C2   N7   C8   N9      0.00   0.0  0
 AZ7  CONST_17  C2   C3   N9   C8      0.00   0.0  0
 AZ7  CONST_18  C15  C16  C17  C12     0.00   0.0  0
 AZ7  CONST_19  C15  C14  C13  C12     0.00   0.0  0
 AZ7  CONST_20  C14  C13  C12  C17     0.00   0.0  0
 AZ7  CONST_21  C14  C15  C16  C17     0.00   0.0  0
 AZ7  CONST_22  C13  C12  C17  C16     0.00   0.0  0
 AZ7  CONST_23  C13  C14  C15  C16     0.00   0.0  0
 AZ7  CONST_24  C1   C6   C5   CL6   180.00   0.0  0
 AZ7  CONST_25  C3   C4   C5   CL6   180.00   0.0  0
 AZ7  CONST_26  CL5  C1   C6   C5    180.00   0.0  0
 AZ7  CONST_27  C3   C2   C1   CL5   180.00   0.0  0
 AZ7  CONST_28  N7   C2   C1   CL5     0.00   0.0  0
 AZ7  CONST_29  C10  C8   N9   C3    180.00   0.0  0
 AZ7  CONST_30  C10  C8   N7   C2    180.00   0.0  0
 AZ7  CONST_31  C16  C17  C12  C11   180.00   0.0  0
 AZ7  CONST_32  C14  C13  C12  C11   180.00   0.0  0
 AZ7  CONST_33  CL9  C15  C16  C17   180.00   0.0  0
 AZ7  CONST_34  C13  C14  C15  CL9   180.00   0.0  0
 AZ7  CONST_35  H4   C4   C5   C6    180.00   0.0  0
 AZ7  CONST_36  H7   N7   C2   C1      0.00   0.0  0
 AZ7  CONST_37  H6   C6   C5   C4    180.00   0.0  0
 AZ7  CONST_38  H16  C16  C17  C12   180.00   0.0  0
 AZ7  CONST_39  H14  C14  C13  C12   180.00   0.0  0
 AZ7  CONST_40  H13  C13  C12  C17   180.00   0.0  0
 AZ7  CONST_41  H17  C17  C16  C15   180.00   0.0  0
 AZ7  Var_01    C11  C10  C8   N9   -115.95  30.0  2
 AZ7  Var_02    O22  C20  C19  C11    33.26  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
 AZ7  chir_01  C11  C10  C19  C12  negativ

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
 AZ7  plan-1  C11  0.020
 AZ7  plan-1  C12  0.020
 AZ7  plan-1  C17  0.020
 AZ7  plan-1  C16  0.020
 AZ7  plan-1  C15  0.020
 AZ7  plan-1  CL9  0.020
 AZ7  plan-1  C14  0.020
 AZ7  plan-1  C13  0.020
 AZ7  plan-1  H17  0.020
 AZ7  plan-1  H13  0.020
 AZ7  plan-1  H16  0.020
 AZ7  plan-1  H14  0.020
 AZ7  plan-2  CL6  0.020
 AZ7  plan-2  C5   0.020
 AZ7  plan-2  C6   0.020
 AZ7  plan-2  C1   0.020
 AZ7  plan-2  CL5  0.020
 AZ7  plan-2  C4   0.020
 AZ7  plan-2  C3   0.020
 AZ7  plan-2  N9   0.020
 AZ7  plan-2  C8   0.020
 AZ7  plan-2  N7   0.020
 AZ7  plan-2  C2   0.020
 AZ7  plan-2  C10  0.020
 AZ7  plan-2  H6   0.020
 AZ7  plan-2  H4   0.020
 AZ7  plan-2  H7   0.020
 AZ7  plan-3  C19  0.020
 AZ7  plan-3  C20  0.020
 AZ7  plan-3  O22  0.020
 AZ7  plan-3  O21  0.020

