# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:14:13 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1cnc2cc(ccc12)C(O)=O
#
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
 549  549  '1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid'  ligand  26  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_549
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
 549  C10  C  CH1    0  -0.136  -3.1738  -0.8046   0.0023
 549  C01  C  CR6    0  -0.125   2.0549  -0.1351  -0.0090
 549  C02  C  CR16   0  -0.305   1.3493  -1.3543   0.0042
 549  C03  C  CR16   0  -0.300  -0.0312  -1.4132   0.0075
 549  C04  C  CR56   0   0.336  -0.7124  -0.1990  -0.0020
 549  C05  C  CR56   0   0.142  -0.0355   1.0316  -0.0127
 549  C06  C  CR16   0  -0.374   1.3574   1.0631  -0.0165
 549  N07  N  NR5    0  -0.502  -2.0452   0.1216  -0.0035
 549  C08  C  CR15   0   0.099  -2.1095   1.4782  -0.0142
 549  N09  N  N      0  -0.474  -0.9458   2.0643  -0.0199
 549  C11  C  CH3    0  -0.649  -4.0087  -0.6314   1.2632
 549  C12  C  CH3    0  -0.648  -4.0028  -0.6532  -1.2653
 549  O14  O  OC    -1  -0.597   4.1391  -1.2489  -0.0061
 549  O15  O  O      0  -0.597   4.1393   0.9775  -0.0356
 549  H20  H  HCH1   0   0.268  -2.7346  -1.8029   0.0117
 549  H16  H  HCR6   0   0.242   1.9151  -2.2762   0.0112
 549  H17  H  HCR6   0   0.262  -0.5485  -2.3644   0.0169
 549  H18  H  HCR6   0   0.240   1.8883   2.0063  -0.0276
 549  H19  H  HCR5   0   0.286  -3.0564   1.9994  -0.0169
 549  H23  H  HCH3   0   0.245  -3.3973  -0.7337   2.1595
 549  H21  H  HCH3   0   0.229  -4.4945   0.3456   1.2876
 549  H22  H  HCH3   0   0.243  -4.7906  -1.3897   1.2972
 549  H24  H  HCH3   0   0.245  -3.3873  -0.7727  -2.1568
 549  H25  H  HCH3   0   0.243  -4.7857  -1.4112  -1.2891
 549  H26  H  HCH3   0   0.229  -4.4873   0.3237  -1.3100
 549  C13  C  C      0   0.400   3.5777  -0.1355  -0.0175

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
 549  O15  C13  deloc     1.247  0.020  1.247
 549  O14  C13  deloc     1.247  0.020  1.247
 549  C13  C01  single    1.523  0.020  1.523
 549  C01  C02  aromatic  1.409  0.020  1.409
 549  C01  C06  aromatic  1.386  0.020  1.386
 549  C02  C03  aromatic  1.382  0.020  1.382
 549  C06  C05  aromatic  1.393  0.020  1.393
 549  C03  C04  aromatic  1.392  0.020  1.392
 549  C05  C04  aromatic  1.405  0.020  1.405
 549  C05  N09  aromatic  1.377  0.020  1.377
 549  C04  N07  aromatic  1.371  0.020  1.371
 549  N09  C08  aromatic  1.303  0.020  1.303
 549  C12  C10  single    1.522  0.020  1.522
 549  N07  C10  single    1.460  0.020  1.460
 549  N07  C08  aromatic  1.358  0.020  1.358
 549  C11  C10  single    1.522  0.020  1.522
 549  C10  H20  single    0.970  0.020  1.090
 549  C02  H16  single    0.930  0.020  1.080
 549  C03  H17  single    0.930  0.020  1.080
 549  C06  H18  single    0.930  0.020  1.080
 549  C08  H19  single    0.930  0.020  1.080
 549  C11  H23  single    0.970  0.020  1.090
 549  C11  H21  single    0.970  0.020  1.090
 549  C11  H22  single    0.970  0.020  1.090
 549  C12  H24  single    0.970  0.020  1.090
 549  C12  H25  single    0.970  0.020  1.090
 549  C12  H26  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
 549  H20  C10  C12  108.52  3.000
 549  H20  C10  C11  108.53  3.000
 549  C12  C10  C11  112.32  3.000
 549  H20  C10  N07  105.63  3.000
 549  C11  C10  N07  110.80  3.000
 549  C12  C10  N07  110.77  3.000
 549  C06  C01  C02  119.74  3.000
 549  C06  C01  C13  120.21  3.000
 549  C02  C01  C13  120.05  3.000
 549  H16  C02  C03  119.10  3.000
 549  H16  C02  C01  118.40  3.000
 549  C03  C02  C01  122.50  3.000
 549  H17  C03  C04  122.17  3.000
 549  H17  C03  C02  120.98  3.000
 549  C04  C03  C02  116.85  3.000
 549  N07  C04  C05  105.29  3.000
 549  N07  C04  C03  132.82  3.000
 549  C05  C04  C03  121.89  3.000
 549  N09  C05  C06  130.10  3.000
 549  N09  C05  C04  109.79  3.000
 549  C06  C05  C04  120.11  3.000
 549  H18  C06  C05  120.67  3.000
 549  H18  C06  C01  120.42  3.000
 549  C05  C06  C01  118.91  3.000
 549  C08  N07  C04  106.24  3.000
 549  C08  N07  C10  126.66  3.000
 549  C04  N07  C10  127.10  3.000
 549  H19  C08  N09  124.43  3.000
 549  H19  C08  N07  121.55  3.000
 549  N09  C08  N07  114.02  3.000
 549  C08  N09  C05  104.66  3.000
 549  H22  C11  H21  107.63  3.000
 549  H22  C11  H23  108.15  3.000
 549  H21  C11  H23  108.39  3.000
 549  H22  C11  C10  109.89  3.000
 549  H21  C11  C10  111.38  3.000
 549  H23  C11  C10  111.27  3.000
 549  H26  C12  H25  107.63  3.000
 549  H26  C12  H24  108.38  3.000
 549  H25  C12  H24  108.15  3.000
 549  H26  C12  C10  111.40  3.000
 549  H25  C12  C10  109.88  3.000
 549  H24  C12  C10  111.26  3.000
 549  O15  C13  O14  126.47  3.000
 549  O14  C13  C01  116.77  3.000
 549  O15  C13  C01  116.76  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
 549  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 549  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 549  CONST_03  N09  C05  C06  C01   180.00   0.0  0
 549  CONST_04  C05  C06  C01  C02     0.00   0.0  0
 549  CONST_05  C05  C04  C03  C02     0.00   0.0  0
 549  CONST_06  N07  C04  C03  C02   180.00   0.0  0
 549  CONST_07  C06  C01  C02  C03     0.00   0.0  0
 549  CONST_08  C06  C05  C04  C03     0.00   0.0  0
 549  CONST_09  N09  C05  C04  C03   180.00   0.0  0
 549  CONST_10  C08  N07  C04  C03   180.00   0.0  0
 549  CONST_11  C08  N09  C05  C04     0.00   0.0  0
 549  CONST_12  N09  C08  N07  C04     0.00   0.0  0
 549  CONST_13  C08  N07  C04  C05     0.00   0.0  0
 549  CONST_14  N07  C08  N09  C05     0.00   0.0  0
 549  CONST_15  N07  C04  C05  C06   180.00   0.0  0
 549  CONST_16  C08  N09  C05  C06   180.00   0.0  0
 549  CONST_17  N09  C05  C04  N07     0.00   0.0  0
 549  CONST_18  C03  C04  N07  C10     0.00   0.0  0
 549  CONST_19  C05  C04  N07  C10   180.00   0.0  0
 549  CONST_20  N09  C08  N07  C10   180.00   0.0  0
 549  CONST_21  C03  C02  C01  C13   180.00   0.0  0
 549  CONST_22  C05  C06  C01  C13   180.00   0.0  0
 549  CONST_23  H17  C03  C02  C01   180.00   0.0  0
 549  CONST_24  H18  C06  C01  C02   180.00   0.0  0
 549  CONST_25  H16  C02  C03  C04   180.00   0.0  0
 549  CONST_26  H19  C08  N07  C04   180.00   0.0  0
 549  Var_01    O15  C13  C01  C02   179.66  30.0  3
 549  Var_02    C12  C10  N07  C04  -117.11  30.0  2
 549  Var_03    H24  C12  C10  N07    55.08  30.0  3
 549  Var_04    H23  C11  C10  N07   -54.99  30.0  3

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
 549  plan-1  C10  0.020
 549  plan-1  C01  0.020
 549  plan-1  C02  0.020
 549  plan-1  C03  0.020
 549  plan-1  C04  0.020
 549  plan-1  C05  0.020
 549  plan-1  C06  0.020
 549  plan-1  N07  0.020
 549  plan-1  C08  0.020
 549  plan-1  N09  0.020
 549  plan-1  H16  0.020
 549  plan-1  H17  0.020
 549  plan-1  H18  0.020
 549  plan-1  H19  0.020
 549  plan-1  C13  0.020
 549  plan-2  C01  0.020
 549  plan-2  O14  0.020
 549  plan-2  O15  0.020
 549  plan-2  C13  0.020

