# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:29:27 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [(2~{S})-2-(6-chloranyl-7-methyl-1~{H}-benzimidazol-2-yl)-2-methyl-pyrrolidin-1-yl]-[5-methoxy-2-(1,2,3-triazol-2-yl)phenyl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(n2nccn2)c(c1)C(=O)N3CCC[C@@]3(C)c4[nH]c5c(C)c(Cl)ccc5n4
#
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
 NS2  NS2  '[(2~{S})-2-(6-chloranyl-7-methyl-1~{H}-benzimidazol-2-yl)-2-methyl-pyrrolidin-1-yl]-[5-methoxy-2-(1,2,3-triazol-2-yl)phenyl]methanone'  ligand  55  32  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NS2
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
 NS2  C01   C   CH3   0  -0.440   4.7401   4.4185  -0.8801
 NS2  C03   C   CR6   0   0.403   3.6620   2.3329  -0.5499
 NS2  C04   C   CR16  0  -0.386   4.7152   1.6178  -1.1161
 NS2  C05   C   CR16  0  -0.277   4.6471   0.2352  -1.1942
 NS2  C06   C   CR6   0   0.349   3.5306  -0.4405  -0.7350
 NS2  C07   C   CR6   0  -0.066   2.4643   0.2660  -0.1843
 NS2  C08   C   CR16  0  -0.350   2.5410   1.6429  -0.0840
 NS2  C09   C   C     0   0.530   1.1665  -0.3998   0.1729
 NS2  C12   C   CH2   0  -0.254   1.8093  -0.1756   2.5599
 NS2  C13   C   CH2   0  -0.496   1.1375  -0.7926   3.7788
 NS2  C14   C   CH2   0  -0.451  -0.3438  -0.6702   3.4470
 NS2  C15   C   CT    0  -0.002  -0.4016  -1.0094   1.9448
 NS2  C16   C   CH3   0  -0.676  -0.4940  -2.5210   1.7366
 NS2  C17   C   CR5   0   0.539  -1.5216  -0.2617   1.2738
 NS2  C19   C   CR56  0   0.143  -2.7617   1.3037   0.5426
 NS2  C20   C   CR16  0  -0.364  -3.3388   2.5207   0.1864
 NS2  C21   C   CR16  0  -0.223  -4.5401   2.4902  -0.4937
 NS2  C22   C   CR6   0  -0.152  -5.1513   1.2709  -0.8123
 NS2  C23   C   CR6   0   0.126  -4.6215   0.0319  -0.4776
 NS2  C24   C   CR56  0   0.300  -3.4093   0.1027   0.2070
 NS2  C26   C   CH3   0  -0.723  -5.2784  -1.2665  -0.8289
 NS2  C30   C   CR15  0  -0.152   3.7586  -3.7895  -1.4908
 NS2  C31   C   CR15  0  -0.134   3.1161  -3.8181  -0.2493
 NS2  N11   N   NT    0  -0.459   0.8809  -0.4794   1.4743
 NS2  N18   N   N     0  -0.456  -1.5940   1.0383   1.2107
 NS2  N25   N   NR15  0  -0.729  -2.5857  -0.8748   0.6995
 NS2  N28   N   NR5   0  -0.208   3.4836  -1.8483  -0.8027
 NS2  N29   N   N     0  -0.243   3.9752  -2.5267  -1.8140
 NS2  N32   N   N     0  -0.241   2.9635  -2.5723   0.1612
 NS2  O02   O   O2    0  -0.466   3.6342   3.6663  -0.4154
 NS2  O10   O   O     0  -0.475   0.4114  -0.7650  -0.7165
 NS2  CL1   CL  CL    0  -0.134  -6.6582   1.3246  -1.6801
 NS2  H013  H   HCH3  0   0.264   4.5129   5.4604  -0.6708
 NS2  H011  H   HCH3  0   0.233   5.6622   4.1476  -0.3603
 NS2  H012  H   HCH3  0   0.233   4.8893   4.2985  -1.9559
 NS2  H041  H   HCR6  0   0.293   5.6008   2.1117  -1.4898
 NS2  H051  H   HCR6  0   0.285   5.4794  -0.3135  -1.6134
 NS2  H081  H   HCR6  0   0.277   1.7135   2.1999   0.3404
 NS2  H121  H   HCH2  0   0.249   1.9211   0.9040   2.6849
 NS2  H122  H   HCH2  0   0.258   2.7933  -0.5986   2.3594
 NS2  H131  H   HCH2  0   0.245   1.4270  -1.8386   3.8928
 NS2  H132  H   HCH2  0   0.263   1.4078  -0.2743   4.6976
 NS2  H141  H   HCH2  0   0.263  -0.9838  -1.3307   4.0313
 NS2  H142  H   HCH2  0   0.258  -0.6783   0.3564   3.6061
 NS2  H162  H   HCH3  0   0.241  -1.4200  -2.9130   2.1598
 NS2  H161  H   HCH3  0   0.255  -0.4458  -2.7956   0.6843
 NS2  H163  H   HCH3  0   0.257   0.3316  -3.0152   2.2469
 NS2  H201  H   HCR6  0   0.261  -2.8648   3.4619   0.4305
 NS2  H211  H   HCR6  0   0.272  -5.0188   3.4148  -0.7860
 NS2  H261  H   HCH3  0   0.260  -5.3081  -1.4129  -1.9096
 NS2  H263  H   HCH3  0   0.245  -4.7533  -2.1167  -0.3976
 NS2  H262  H   HCH3  0   0.258  -6.3066  -1.3028  -0.4693
 NS2  H301  H   HCR5  0   0.285   4.0526  -4.5993  -2.1375
 NS2  H311  H   HCR5  0   0.284   2.7826  -4.6555   0.3403
 NS2  H251  H   HNR5  0   0.426  -2.7202  -1.8696   0.6160

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
 NS2  N32  C31   aromatic  1.321  0.020  1.321
 NS2  N32  N28   aromatic  1.313  0.020  1.313
 NS2  C31  C30   aromatic  1.398  0.020  1.398
 NS2  C05  C04   aromatic  1.386  0.020  1.386
 NS2  C05  C06   aromatic  1.383  0.020  1.383
 NS2  C04  C03   aromatic  1.393  0.020  1.393
 NS2  C01  O02   single    1.416  0.020  1.416
 NS2  N28  C06   single    1.410  0.020  1.410
 NS2  N28  N29   aromatic  1.313  0.020  1.313
 NS2  C06  C07   aromatic  1.393  0.020  1.393
 NS2  C30  N29   aromatic  1.321  0.020  1.321
 NS2  C03  O02   single    1.340  0.020  1.340
 NS2  C03  C08   aromatic  1.396  0.020  1.396
 NS2  C21  C20   aromatic  1.381  0.020  1.381
 NS2  C21  C22   aromatic  1.401  0.020  1.401
 NS2  C20  C19   aromatic  1.393  0.020  1.393
 NS2  CL1  C22   single    1.740  0.020  1.740
 NS2  C22  C23   aromatic  1.388  0.020  1.388
 NS2  C08  C07   aromatic  1.383  0.020  1.383
 NS2  C07  C09   single    1.502  0.020  1.502
 NS2  C19  N18   aromatic  1.371  0.020  1.371
 NS2  C19  C24   aromatic  1.405  0.020  1.405
 NS2  N18  C17   aromatic  1.304  0.020  1.304
 NS2  C23  C24   aromatic  1.394  0.020  1.394
 NS2  C23  C26   single    1.497  0.020  1.497
 NS2  C24  N25   aromatic  1.370  0.020  1.370
 NS2  C09  O10   double    1.223  0.020  1.223
 NS2  C09  N11   single    1.335  0.020  1.335
 NS2  C16  C15   single    1.529  0.020  1.529
 NS2  C17  N25   aromatic  1.356  0.020  1.356
 NS2  C17  C15   single    1.504  0.020  1.504
 NS2  N11  C15   single    1.465  0.020  1.465
 NS2  N11  C12   single    1.460  0.020  1.460
 NS2  C15  C14   single    1.541  0.020  1.541
 NS2  C12  C13   single    1.522  0.020  1.522
 NS2  C14  C13   single    1.523  0.020  1.523
 NS2  C01  H013  single    0.970  0.020  1.090
 NS2  C01  H011  single    0.970  0.020  1.090
 NS2  C01  H012  single    0.970  0.020  1.090
 NS2  C04  H041  single    0.930  0.020  1.080
 NS2  C05  H051  single    0.930  0.020  1.080
 NS2  C08  H081  single    0.930  0.020  1.080
 NS2  C12  H121  single    0.970  0.020  1.090
 NS2  C12  H122  single    0.970  0.020  1.090
 NS2  C13  H131  single    0.970  0.020  1.090
 NS2  C13  H132  single    0.970  0.020  1.090
 NS2  C14  H141  single    0.970  0.020  1.090
 NS2  C14  H142  single    0.970  0.020  1.090
 NS2  C16  H162  single    0.970  0.020  1.090
 NS2  C16  H161  single    0.970  0.020  1.090
 NS2  C16  H163  single    0.970  0.020  1.090
 NS2  C20  H201  single    0.930  0.020  1.080
 NS2  C21  H211  single    0.930  0.020  1.080
 NS2  C26  H261  single    0.970  0.020  1.090
 NS2  C26  H263  single    0.970  0.020  1.090
 NS2  C26  H262  single    0.970  0.020  1.090
 NS2  C30  H301  single    0.930  0.020  1.080
 NS2  C31  H311  single    0.930  0.020  1.080
 NS2  N25  H251  single    0.860  0.020  1.020

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
 NS2  H012  C01  H011  109.02  3.000
 NS2  H012  C01  H013  108.87  3.000
 NS2  H011  C01  H013  108.82  3.000
 NS2  H012  C01  O02   111.80  3.000
 NS2  H011  C01  O02   111.80  3.000
 NS2  H013  C01  O02   106.42  3.000
 NS2  O02   C03  C08   116.20  3.000
 NS2  C08   C03  C04   119.26  3.000
 NS2  O02   C03  C04   124.54  3.000
 NS2  H041  C04  C05   118.46  3.000
 NS2  H041  C04  C03   121.70  3.000
 NS2  C05   C04  C03   119.84  3.000
 NS2  H051  C05  C06   120.13  3.000
 NS2  H051  C05  C04   119.34  3.000
 NS2  C06   C05  C04   120.53  3.000
 NS2  N28   C06  C07   119.99  3.000
 NS2  C07   C06  C05   120.10  3.000
 NS2  N28   C06  C05   119.90  3.000
 NS2  C09   C07  C08   118.18  3.000
 NS2  C09   C07  C06   122.06  3.000
 NS2  C08   C07  C06   119.43  3.000
 NS2  H081  C08  C07   119.85  3.000
 NS2  H081  C08  C03   119.31  3.000
 NS2  C07   C08  C03   120.82  3.000
 NS2  O10   C09  N11   124.01  3.000
 NS2  N11   C09  C07   116.32  3.000
 NS2  O10   C09  C07   119.55  3.000
 NS2  H122  C12  H121  108.20  3.000
 NS2  H122  C12  N11   110.89  3.000
 NS2  H121  C12  N11   110.83  3.000
 NS2  H122  C12  C13   112.86  3.000
 NS2  H121  C12  C13   110.73  3.000
 NS2  N11   C12  C13   103.32  3.000
 NS2  H132  C13  H131  107.59  3.000
 NS2  H132  C13  C14   112.77  3.000
 NS2  H131  C13  C14   110.96  3.000
 NS2  H132  C13  C12   111.91  3.000
 NS2  H131  C13  C12   110.79  3.000
 NS2  C14   C13  C12   102.84  3.000
 NS2  H142  C14  H141  108.18  3.000
 NS2  H142  C14  C15   109.73  3.000
 NS2  H141  C14  C15   111.55  3.000
 NS2  H142  C14  C13   109.99  3.000
 NS2  H141  C14  C13   113.94  3.000
 NS2  C15   C14  C13   103.37  3.000
 NS2  N11   C15  C17   109.18  3.000
 NS2  N11   C15  C16   111.52  3.000
 NS2  C17   C15  C16   112.69  3.000
 NS2  N11   C15  C14   101.56  3.000
 NS2  C17   C15  C14   110.69  3.000
 NS2  C16   C15  C14   110.65  3.000
 NS2  H163  C16  H161  107.75  3.000
 NS2  H163  C16  H162  107.37  3.000
 NS2  H161  C16  H162  108.78  3.000
 NS2  H163  C16  C15   109.82  3.000
 NS2  H161  C16  C15   112.24  3.000
 NS2  H162  C16  C15   110.72  3.000
 NS2  N25   C17  N18   112.76  3.000
 NS2  N25   C17  C15   123.26  3.000
 NS2  N18   C17  C15   123.96  3.000
 NS2  N18   C19  C24   110.09  3.000
 NS2  C24   C19  C20   119.65  3.000
 NS2  N18   C19  C20   130.27  3.000
 NS2  H201  C20  C21   120.77  3.000
 NS2  H201  C20  C19   121.39  3.000
 NS2  C21   C20  C19   117.84  3.000
 NS2  H211  C21  C22   119.32  3.000
 NS2  H211  C21  C20   119.96  3.000
 NS2  C22   C21  C20   120.72  3.000
 NS2  CL1   C22  C23   118.57  3.000
 NS2  C23   C22  C21   123.75  3.000
 NS2  CL1   C22  C21   117.68  3.000
 NS2  C26   C23  C24   122.75  3.000
 NS2  C26   C23  C22   123.37  3.000
 NS2  C24   C23  C22   113.88  3.000
 NS2  N25   C24  C23   131.54  3.000
 NS2  N25   C24  C19   104.30  3.000
 NS2  C23   C24  C19   124.16  3.000
 NS2  H262  C26  H263  107.36  3.000
 NS2  H262  C26  H261  107.26  3.000
 NS2  H263  C26  H261  107.51  3.000
 NS2  H262  C26  C23   111.43  3.000
 NS2  H263  C26  C23   111.89  3.000
 NS2  H261  C26  C23   111.15  3.000
 NS2  H301  C30  N29   121.79  3.000
 NS2  H301  C30  C31   130.02  3.000
 NS2  N29   C30  C31   108.19  3.000
 NS2  H311  C31  N32   121.84  3.000
 NS2  H311  C31  C30   130.11  3.000
 NS2  N32   C31  C30   108.05  3.000
 NS2  C15   N11  C12   113.14  3.000
 NS2  C12   N11  C09   125.19  3.000
 NS2  C15   N11  C09   121.46  3.000
 NS2  C19   N18  C17   105.30  3.000
 NS2  H251  N25  C24   126.49  3.000
 NS2  H251  N25  C17   125.91  3.000
 NS2  C24   N25  C17   107.54  3.000
 NS2  N32   N28  N29   115.40  3.000
 NS2  N29   N28  C06   122.70  3.000
 NS2  N32   N28  C06   121.90  3.000
 NS2  N28   N29  C30   104.12  3.000
 NS2  N28   N32  C31   104.25  3.000
 NS2  C03   O02  C01   118.64  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
 NS2  CONST_01  C06   C05  C04  C03     0.00   0.0  0
 NS2  CONST_02  C06   C07  C08  C03     0.00   0.0  0
 NS2  CONST_03  N28   C06  C05  C04   180.00   0.0  0
 NS2  CONST_04  C07   C06  C05  C04     0.00   0.0  0
 NS2  CONST_05  C07   C08  C03  C04     0.00   0.0  0
 NS2  CONST_06  C08   C03  C04  C05     0.00   0.0  0
 NS2  CONST_09  C08   C07  C06  C05     0.00   0.0  0
 NS2  CONST_10  C31   N32  N28  C06   180.00   0.0  0
 NS2  CONST_11  C30   N29  N28  C06   180.00   0.0  0
 NS2  CONST_14  N28   C06  C07  C08   180.00   0.0  0
 NS2  CONST_15  C20   C19  N18  C17   180.00   0.0  0
 NS2  CONST_16  C24   C19  N18  C17     0.00   0.0  0
 NS2  CONST_17  C19   C24  N25  C17     0.00   0.0  0
 NS2  CONST_18  C23   C24  N25  C17   180.00   0.0  0
 NS2  CONST_19  C22   C21  C20  C19     0.00   0.0  0
 NS2  CONST_20  N25   C17  N18  C19     0.00   0.0  0
 NS2  CONST_21  C22   C23  C24  C19     0.00   0.0  0
 NS2  CONST_22  C23   C22  C21  C20     0.00   0.0  0
 NS2  CONST_23  C23   C24  C19  C20     0.00   0.0  0
 NS2  CONST_24  N25   C24  C19  C20   180.00   0.0  0
 NS2  CONST_25  N18   C19  C20  C21   180.00   0.0  0
 NS2  CONST_26  C24   C19  C20  C21     0.00   0.0  0
 NS2  CONST_27  C24   C23  C22  C21     0.00   0.0  0
 NS2  CONST_28  N25   C24  C23  C22   180.00   0.0  0
 NS2  CONST_29  N18   C19  C24  C23   180.00   0.0  0
 NS2  CONST_30  N18   C17  N25  C24     0.00   0.0  0
 NS2  CONST_31  N28   N32  C31  C30     0.00   0.0  0
 NS2  CONST_32  N32   N28  N29  C30     0.00   0.0  0
 NS2  CONST_33  N29   N28  N32  C31     0.00   0.0  0
 NS2  CONST_34  N28   N29  C30  C31     0.00   0.0  0
 NS2  CONST_35  N25   C24  C19  N18     0.00   0.0  0
 NS2  CONST_36  N32   C31  C30  N29     0.00   0.0  0
 NS2  CONST_37  C19   N18  C17  C15   180.00   0.0  0
 NS2  CONST_38  C24   N25  C17  C15   180.00   0.0  0
 NS2  CONST_39  C09   C07  C08  C03   180.00   0.0  0
 NS2  CONST_40  O02   C03  C04  C05   180.00   0.0  0
 NS2  CONST_41  C09   C07  C06  C05   180.00   0.0  0
 NS2  CONST_42  O02   C03  C08  C07   180.00   0.0  0
 NS2  CONST_43  N28   C06  C07  C09     0.00   0.0  0
 NS2  CONST_44  C26   C23  C24  C19   180.00   0.0  0
 NS2  CONST_45  CL1   C22  C21  C20   180.00   0.0  0
 NS2  CONST_46  C26   C23  C22  C21   180.00   0.0  0
 NS2  CONST_47  CL1   C22  C23  C24   180.00   0.0  0
 NS2  CONST_48  N25   C24  C23  C26     0.00   0.0  0
 NS2  CONST_49  C15   N11  C09  C07   180.00   0.0  0
 NS2  CONST_50  C12   N11  C09  C07     0.00   0.0  0
 NS2  CONST_51  H051  C05  C04  C03   180.00   0.0  0
 NS2  CONST_52  H081  C08  C03  C04   180.00   0.0  0
 NS2  CONST_53  H041  C04  C05  C06   180.00   0.0  0
 NS2  CONST_54  H251  N25  C17  C15     0.00   0.0  0
 NS2  CONST_55  H211  C21  C20  C19   180.00   0.0  0
 NS2  CONST_56  H201  C20  C21  C22   180.00   0.0  0
 NS2  CONST_57  H311  C31  N32  N28   180.00   0.0  0
 NS2  CONST_58  H301  C30  N29  N28   180.00   0.0  0
 NS2  CONST_59  O10   C09  N11  C12   180.00   0.0  0
 NS2  CONST_60  O10   C09  N11  C15     0.00   0.0  0
 NS2  Var_01    C15   C14  C13  C12    40.06  30.0  1
 NS2  Var_02    C15   N11  C12  C13    10.29  30.0  1
 NS2  Var_03    N11   C12  C13  C14   -30.82  30.0  1
 NS2  Var_04    N11   C09  C07  C06   111.94  30.0  2
 NS2  Var_05    C04   C03  O02  C01     0.28  30.0  2
 NS2  Var_06    H261  C26  C23  C22    65.11  30.0  2
 NS2  Var_07    H013  C01  O02  C03  -179.75  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
 NS2  chir_01  C15  C17  N11  C14  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
 NS2  plan-1  C06   0.020
 NS2  plan-1  C30   0.020
 NS2  plan-1  C31   0.020
 NS2  plan-1  N28   0.020
 NS2  plan-1  N29   0.020
 NS2  plan-1  N32   0.020
 NS2  plan-1  H301  0.020
 NS2  plan-1  H311  0.020
 NS2  plan-2  C03   0.020
 NS2  plan-2  C04   0.020
 NS2  plan-2  C05   0.020
 NS2  plan-2  C06   0.020
 NS2  plan-2  C07   0.020
 NS2  plan-2  C08   0.020
 NS2  plan-2  C09   0.020
 NS2  plan-2  N28   0.020
 NS2  plan-2  O02   0.020
 NS2  plan-2  H041  0.020
 NS2  plan-2  H051  0.020
 NS2  plan-2  H081  0.020
 NS2  plan-3  C15   0.020
 NS2  plan-3  C17   0.020
 NS2  plan-3  C19   0.020
 NS2  plan-3  C20   0.020
 NS2  plan-3  C21   0.020
 NS2  plan-3  C22   0.020
 NS2  plan-3  C23   0.020
 NS2  plan-3  C24   0.020
 NS2  plan-3  C26   0.020
 NS2  plan-3  N18   0.020
 NS2  plan-3  N25   0.020
 NS2  plan-3  CL1   0.020
 NS2  plan-3  H201  0.020
 NS2  plan-3  H211  0.020
 NS2  plan-3  H251  0.020
 NS2  plan-4  C07   0.020
 NS2  plan-4  C09   0.020
 NS2  plan-4  C12   0.020
 NS2  plan-4  C15   0.020
 NS2  plan-4  N11   0.020
 NS2  plan-4  O10   0.020

