# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:57:05 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (3S)-4-(5-chloro-1H-benzimidazol-2-yl)-3-(4-chlorophenyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](Cc1[nH]c2ccc(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
 A06  A06  '(3S)-4-(5-chloro-1H-benzimidazol-2-yl)-3-(4-chlorophenyl)butanoic acid'  ligand  36  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A06
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
 A06  C1    C   CR6    0   0.195   2.5359   0.2445   0.0108
 A06  C6    C   CR16   0  -0.328   3.2863   0.8411   1.0186
 A06  C5    C   CR16   0  -0.199   4.6485   1.0627   0.8760
 A06  C4    C   CR6    0  -0.062   5.2726   0.6764  -0.2989
 A06  C3    C   CR16   0  -0.197   4.5541   0.0816  -1.3235
 A06  C2    C   CR16   0  -0.318   3.1922  -0.1270  -1.1607
 A06  C8    C   CR56   0   0.344  -3.1271   1.1847   0.5011
 A06  C9    C   CR16   0  -0.308  -4.2148   1.4063   1.3341
 A06  C10   C   CR16   0  -0.241  -5.4636   1.0629   0.8466
 A06  C11   C   CR6    0  -0.051  -5.5989   0.5171  -0.4355
 A06  C12   C   CR16   0  -0.301  -4.5233   0.2967  -1.2733
 A06  C13   C   CR56   0   0.136  -3.2634   0.6428  -0.7881
 A06  N14   N   N      0  -0.470  -2.0334   0.5420  -1.3892
 A06  C15   C   CR5    0   0.439  -1.1800   0.9991  -0.5102
 A06  C14   C   CH1    0  -0.331   1.0507   0.0355   0.1777
 A06  C16   C   CH2    0  -0.515   0.2947   1.0667  -0.6869
 A06  C17   C   CH2    0  -0.566   0.6349  -1.3939  -0.1542
 A06  C18   C   C      0   0.415   1.3553  -2.4607   0.6880
 A06  O1    O   OC    -1  -0.623   1.5470  -3.5666   0.1422
 A06  O2    O   O      0  -0.601   1.6563  -2.1464   1.8559
 A06  N9    N   NR15   0  -0.691  -1.7833   1.3965   0.6419
 A06  CL2   CL  CL     0  -0.140   6.9781   0.9412  -0.4908
 A06  H6    H   HCR6   0   0.254   2.8009   1.1412   1.9391
 A06  H2    H   HCR6   0   0.256   2.6456  -0.5928  -1.9719
 A06  H5    H   HCR6   0   0.275   5.2133   1.5256   1.6741
 A06  H3    H   HCR6   0   0.275   5.0456  -0.2196  -2.2388
 A06  HA    H   HNR5   0   0.421  -1.3226   1.7945   1.4451
 A06  H10   H   HCR6   0   0.277  -6.3406   1.2164   1.4601
 A06  H12   H   HCR6   0   0.276  -4.6476  -0.1269  -2.2609
 A06  H14   H   HCH1   0   0.249   0.8090   0.2226   1.2271
 A06  H161  H   HCH2   0   0.263   0.5125   0.9039  -1.7436
 A06  H162  H   HCH2   0   0.274   0.6433   2.0724  -0.4359
 A06  H171  H   HCH2   0   0.246  -0.4412  -1.5020   0.0265
 A06  H172  H   HCH2   0   0.213   0.7725  -1.5948  -1.2200
 A06  CL1   CL  CL     0  -0.141  -7.1948   0.0999  -0.9885
 A06  H9    H   HCR6   0   0.276  -4.1053   1.8291   2.3237

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
 A06  C1   C6    aromatic  1.391  0.020  1.391
 A06  C1   C2    aromatic  1.393  0.020  1.393
 A06  C1   C14   single    1.509  0.020  1.509
 A06  C6   C5    aromatic  1.388  0.020  1.388
 A06  C5   C4    aromatic  1.385  0.020  1.385
 A06  C4   C3    aromatic  1.386  0.020  1.386
 A06  C4   CL2   single    1.737  0.020  1.737
 A06  C3   C2    aromatic  1.387  0.020  1.387
 A06  C8   C9    aromatic  1.388  0.020  1.388
 A06  C8   C13   aromatic  1.405  0.020  1.405
 A06  C8   N9    aromatic  1.368  0.020  1.368
 A06  C9   C10   aromatic  1.384  0.020  1.384
 A06  C10  C11   aromatic  1.400  0.020  1.400
 A06  C11  C12   aromatic  1.381  0.020  1.381
 A06  C11  CL1   single    1.740  0.020  1.740
 A06  C12  C13   aromatic  1.394  0.020  1.394
 A06  C13  N14   aromatic  1.373  0.020  1.373
 A06  N14  C15   aromatic  1.308  0.020  1.308
 A06  C15  C16   single    1.487  0.020  1.487
 A06  C15  N9    aromatic  1.360  0.020  1.360
 A06  C14  C16   single    1.544  0.020  1.544
 A06  C14  C17   single    1.525  0.020  1.525
 A06  C17  C18   single    1.538  0.020  1.538
 A06  C18  O1    deloc     1.248  0.020  1.248
 A06  C18  O2    deloc     1.246  0.020  1.246
 A06  C14  H14   single    0.970  0.020  1.090
 A06  C6   H6    single    0.930  0.020  1.080
 A06  C2   H2    single    0.930  0.020  1.080
 A06  C5   H5    single    0.930  0.020  1.080
 A06  C3   H3    single    0.930  0.020  1.080
 A06  C9   H9    single    0.930  0.020  1.080
 A06  N9   HA    single    0.860  0.020  1.020
 A06  C10  H10   single    0.930  0.020  1.080
 A06  C12  H12   single    0.930  0.020  1.080
 A06  C16  H161  single    0.970  0.020  1.090
 A06  C16  H162  single    0.970  0.020  1.090
 A06  C17  H171  single    0.970  0.020  1.090
 A06  C17  H172  single    0.970  0.020  1.090

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
 A06  C14   C1   C2    121.31  3.000
 A06  C14   C1   C6    120.68  3.000
 A06  C2    C1   C6    118.00  3.000
 A06  H6    C6   C5    118.89  3.000
 A06  H6    C6   C1    119.53  3.000
 A06  C5    C6   C1    121.58  3.000
 A06  H5    C5   C4    120.65  3.000
 A06  H5    C5   C6    120.34  3.000
 A06  C4    C5   C6    119.00  3.000
 A06  CL2   C4   C3    119.53  3.000
 A06  CL2   C4   C5    119.58  3.000
 A06  C3    C4   C5    120.89  3.000
 A06  H3    C3   C2    120.23  3.000
 A06  H3    C3   C4    120.64  3.000
 A06  C2    C3   C4    119.13  3.000
 A06  H2    C2   C3    118.17  3.000
 A06  H2    C2   C1    120.44  3.000
 A06  C3    C2   C1    121.40  3.000
 A06  N9    C8   C13   104.45  3.000
 A06  N9    C8   C9    133.12  3.000
 A06  C13   C8   C9    122.43  3.000
 A06  H9    C9   C10   120.71  3.000
 A06  H9    C9   C8    122.15  3.000
 A06  C10   C9   C8    117.14  3.000
 A06  H10   C10  C11   119.78  3.000
 A06  H10   C10  C9    119.79  3.000
 A06  C11   C10  C9    120.43  3.000
 A06  CL1   C11  C12   118.91  3.000
 A06  CL1   C11  C10   118.24  3.000
 A06  C12   C11  C10   122.85  3.000
 A06  H12   C12  C13   121.26  3.000
 A06  H12   C12  C11   121.79  3.000
 A06  C13   C12  C11   116.95  3.000
 A06  N14   C13  C12   129.74  3.000
 A06  N14   C13  C8    110.07  3.000
 A06  C12   C13  C8    120.19  3.000
 A06  C15   N14  C13   105.35  3.000
 A06  N9    C15  C16   121.84  3.000
 A06  N9    C15  N14   112.47  3.000
 A06  C16   C15  N14   125.68  3.000
 A06  H14   C14  C17   108.00  3.000
 A06  H14   C14  C16   108.37  3.000
 A06  C17   C14  C16   111.75  3.000
 A06  H14   C14  C1    107.47  3.000
 A06  C17   C14  C1    111.97  3.000
 A06  C16   C14  C1    109.12  3.000
 A06  H162  C16  H161  107.21  3.000
 A06  H162  C16  C14   109.25  3.000
 A06  H161  C16  C14   110.18  3.000
 A06  H162  C16  C15   109.31  3.000
 A06  H161  C16  C15   107.84  3.000
 A06  C14   C16  C15   112.88  3.000
 A06  H172  C17  H171  105.44  3.000
 A06  H172  C17  C18   110.32  3.000
 A06  H171  C17  C18   107.51  3.000
 A06  H172  C17  C14   110.49  3.000
 A06  H171  C17  C14   108.91  3.000
 A06  C18   C17  C14   113.77  3.000
 A06  O2    C18  O1    126.60  3.000
 A06  O2    C18  C17   116.82  3.000
 A06  O1    C18  C17   116.55  3.000
 A06  HA    N9   C15   126.00  3.000
 A06  HA    N9   C8    126.32  3.000
 A06  C15   N9   C8    107.66  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
 A06  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 A06  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 A06  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 A06  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 A06  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 A06  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 A06  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 A06  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 A06  CONST_09  C15  N14  C13  C8      0.00   0.0  0
 A06  CONST_10  N14  C15  N9   C8      0.00   0.0  0
 A06  CONST_11  C12  C13  C8   C9      0.00   0.0  0
 A06  CONST_12  N14  C13  C8   C9    180.00   0.0  0
 A06  CONST_13  C15  N9   C8   C9    180.00   0.0  0
 A06  CONST_14  C12  C11  C10  C9      0.00   0.0  0
 A06  CONST_15  C13  C8   C9   C10     0.00   0.0  0
 A06  CONST_16  N9   C8   C9   C10   180.00   0.0  0
 A06  CONST_17  C13  C12  C11  C10     0.00   0.0  0
 A06  CONST_18  N14  C13  C12  C11   180.00   0.0  0
 A06  CONST_19  N9   C8   C13  C12   180.00   0.0  0
 A06  CONST_20  C15  N14  C13  C12   180.00   0.0  0
 A06  CONST_21  C15  N9   C8   C13     0.00   0.0  0
 A06  CONST_22  N9   C15  N14  C13     0.00   0.0  0
 A06  CONST_23  N9   C8   C13  N14     0.00   0.0  0
 A06  CONST_24  CL2  C4   C5   C6    180.00   0.0  0
 A06  CONST_25  C14  C1   C6   C5    180.00   0.0  0
 A06  CONST_26  C14  C1   C2   C3    180.00   0.0  0
 A06  CONST_27  CL2  C4   C3   C2    180.00   0.0  0
 A06  CONST_28  C16  C15  N9   C8    180.00   0.0  0
 A06  CONST_29  CL1  C11  C10  C9    180.00   0.0  0
 A06  CONST_30  CL1  C11  C12  C13   180.00   0.0  0
 A06  CONST_31  C16  C15  N14  C13   180.00   0.0  0
 A06  CONST_32  H5   C5   C6   C1    180.00   0.0  0
 A06  CONST_33  H3   C3   C2   C1    180.00   0.0  0
 A06  CONST_34  H2   C2   C1   C6    180.00   0.0  0
 A06  CONST_35  H6   C6   C5   C4    180.00   0.0  0
 A06  CONST_36  H10  C10  C9   C8    180.00   0.0  0
 A06  CONST_37  H12  C12  C13  C8    180.00   0.0  0
 A06  CONST_38  HA   N9   C8   C9      0.00   0.0  0
 A06  CONST_39  H9   C9   C10  C11   180.00   0.0  0
 A06  Var_01    C14  C16  C15  N14  -108.37  30.0  2
 A06  Var_02    O1   C18  C17  C14  -149.25  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
 A06  chir_01  C14  C1  C16  C17  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
 A06  plan-1  C1   0.020
 A06  plan-1  C6   0.020
 A06  plan-1  C5   0.020
 A06  plan-1  C4   0.020
 A06  plan-1  C3   0.020
 A06  plan-1  C2   0.020
 A06  plan-1  C14  0.020
 A06  plan-1  CL2  0.020
 A06  plan-1  H6   0.020
 A06  plan-1  H2   0.020
 A06  plan-1  H5   0.020
 A06  plan-1  H3   0.020
 A06  plan-2  C8   0.020
 A06  plan-2  C9   0.020
 A06  plan-2  C10  0.020
 A06  plan-2  C11  0.020
 A06  plan-2  C12  0.020
 A06  plan-2  C13  0.020
 A06  plan-2  N14  0.020
 A06  plan-2  C15  0.020
 A06  plan-2  C16  0.020
 A06  plan-2  N9   0.020
 A06  plan-2  HA   0.020
 A06  plan-2  H10  0.020
 A06  plan-2  H12  0.020
 A06  plan-2  CL1  0.020
 A06  plan-2  H9   0.020
 A06  plan-3  C17  0.020
 A06  plan-3  C18  0.020
 A06  plan-3  O1   0.020
 A06  plan-3  O2   0.020

