# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 17:50:24 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-fluoro-N-[3-[6-(1-oxa-4$l^{4}-azacyclohex-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)C(=O)Nc2c[nH]nc2c3[nH]c4cc(C[NH]5CCOCC5)ccc4n3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 L0C  L0C  4-fluoro-N-[3-[6-(1-oxa-4$l^{4}-azacyclohex-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl]benzamide  ligand  53  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L0C
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
 L0C  F1   F  F     0  -0.306   7.7383  27.8101   0.8821
 L0C  C2   C  CR6   0   0.536   7.3805  28.1885   2.1145
 L0C  C3   C  CR16  0  -0.396   6.7010  29.3807   2.2761
 L0C  C4   C  CR16  0  -0.277   6.3352  29.7672   3.5552
 L0C  C5   C  CR6   0  -0.061   6.6468  28.9730   4.6588
 L0C  C6   C  CR16  0  -0.245   7.3436  27.7826   4.4567
 L0C  C7   C  CR16  0  -0.398   7.7095  27.3778   3.1848
 L0C  C8   C  C     0   0.535   6.3098  29.3539   6.0599
 L0C  O9   O  O     0  -0.466   6.8882  28.8642   7.0174
 L0C  N10  N  NH1   0  -0.767   5.3243  30.2666   6.1990
 L0C  C11  C  CR5   0   0.112   4.9145  30.8202   7.3989
 L0C  C12  C  CR15  0  -0.006   5.2968  30.5862   8.7028
 L0C  N13  N  NR15  0  -0.415   4.5627  31.4369   9.4507
 L0C  N15  N  N     0  -0.269   3.7449  32.1948   8.7583
 L0C  C16  C  CR5   0   0.112   3.9397  31.8381   7.4971
 L0C  C17  C  CR5   0   0.528   3.2290  32.4410   6.3964
 L0C  N18  N  N     0  -0.549   3.3774  32.0629   5.1484
 L0C  C19  C  CR56  0   0.195   2.5410  32.8709   4.4247
 L0C  C20  C  CR16  0  -0.325   2.2813  32.9059   3.0568
 L0C  C21  C  CR16  0  -0.291   1.3688  33.8360   2.5968
 L0C  C22  C  CR6   0   0.055   0.7160  34.7267   3.4664
 L0C  C23  C  CH2   0  -0.400  -0.2539  35.7274   2.9199
 L0C  N24  N  NT1   1  -0.532   0.3627  37.0887   2.7644
 L0C  C26  C  CH2   0  -0.338  -0.6665  38.0947   2.3648
 L0C  C27  C  CH2   0  -0.211  -0.0265  39.4563   2.1861
 L0C  O28  O  O2    0  -0.464   1.0141  39.4168   1.2418
 L0C  C29  C  CH2   0  -0.205   2.0223  38.5260   1.6484
 L0C  C30  C  CH2   0  -0.340   1.4989  37.1110   1.7969
 L0C  C31  C  CR16  0  -0.347   0.9599  34.6952   4.8333
 L0C  C32  C  CR56  0   0.344   1.8764  33.7609   5.2881
 L0C  N33  N  NR15  0  -0.708   2.3411  33.4538   6.5379
 L0C  H14  H  HNR5  0   0.434   4.5963  31.5254  10.4544
 L0C  H25  H  HNT1  0   0.461   0.7267  37.3637   3.6813
 L0C  H34  H  HNR5  0   0.428   2.0881  33.8997   7.4064
 L0C  H35  H  HCR6  0   0.291   6.4690  30.0026   1.4219
 L0C  H36  H  HCR6  0   0.260   5.8264  30.7169   3.6644
 L0C  H37  H  HCR6  0   0.273   7.6012  27.1591   5.3020
 L0C  H38  H  HCR6  0   0.288   8.2448  26.4508   3.0288
 L0C  H39  H  HNH1  0   0.441   4.8020  30.6052   5.3966
 L0C  H40  H  HCR5  0   0.305   6.0033  29.9086   9.1452
 L0C  H41  H  HCR6  0   0.264   2.7743  32.2231   2.3777
 L0C  H42  H  HCR6  0   0.266   1.1449  33.8785   1.5382
 L0C  H43  H  HCH2  0   0.321  -0.6266  35.4417   1.9374
 L0C  H44  H  HCH2  0   0.322  -1.1067  35.8606   3.5847
 L0C  H45  H  HCH2  0   0.304  -1.1147  37.7397   1.4370
 L0C  H46  H  HCH2  0   0.315  -1.4281  38.1240   3.1417
 L0C  H47  H  HCH2  0   0.280  -0.7870  40.1494   1.8273
 L0C  H48  H  HCH2  0   0.237   0.3340  39.8281   3.1549
 L0C  H49  H  HCH2  0   0.280   2.8027  38.5251   0.8885
 L0C  H50  H  HCH2  0   0.236   2.4771  38.8522   2.5940
 L0C  H51  H  HCH2  0   0.302   1.1227  36.7197   0.8517
 L0C  H52  H  HCH2  0   0.315   2.2839  36.4559   2.1690
 L0C  H53  H  HCR6  0   0.279   0.4477  35.3639   5.5146

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
 L0C  F1   C2   single    1.338  0.020  1.338
 L0C  C2   C3   aromatic  1.382  0.020  1.382
 L0C  C2   C7   aromatic  1.382  0.020  1.382
 L0C  H35  C3   single    0.930  0.020  1.080
 L0C  C3   C4   aromatic  1.385  0.020  1.385
 L0C  C4   H36  single    0.930  0.020  1.080
 L0C  C4   C5   aromatic  1.395  0.020  1.395
 L0C  C6   C5   aromatic  1.394  0.020  1.394
 L0C  C5   C8   single    1.491  0.020  1.491
 L0C  C7   C6   aromatic  1.384  0.020  1.384
 L0C  C6   H37  single    0.930  0.020  1.080
 L0C  H38  C7   single    0.930  0.020  1.080
 L0C  C8   N10  single    1.350  0.020  1.350
 L0C  C8   O9   double    1.221  0.020  1.221
 L0C  H39  N10  single    0.860  0.020  1.020
 L0C  N10  C11  single    1.384  0.020  1.384
 L0C  C11  C16  aromatic  1.413  0.020  1.413
 L0C  C11  C12  aromatic  1.379  0.020  1.379
 L0C  C12  H40  single    0.930  0.020  1.080
 L0C  C12  N13  aromatic  1.350  0.020  1.350
 L0C  N15  N13  aromatic  1.312  0.020  1.312
 L0C  N13  H14  single    0.860  0.020  1.020
 L0C  C16  N15  aromatic  1.325  0.020  1.325
 L0C  C17  C16  single    1.442  0.020  1.442
 L0C  N18  C17  aromatic  1.312  0.020  1.312
 L0C  C17  N33  aromatic  1.354  0.020  1.354
 L0C  C19  N18  aromatic  1.370  0.020  1.370
 L0C  C20  C19  aromatic  1.393  0.020  1.393
 L0C  C19  C32  aromatic  1.407  0.020  1.407
 L0C  H41  C20  single    0.930  0.020  1.080
 L0C  C21  C20  aromatic  1.382  0.020  1.382
 L0C  H42  C21  single    0.930  0.020  1.080
 L0C  C21  C22  aromatic  1.406  0.020  1.406
 L0C  C23  C22  single    1.497  0.020  1.497
 L0C  C22  C31  aromatic  1.389  0.020  1.389
 L0C  N24  C23  single    1.502  0.020  1.502
 L0C  H43  C23  single    0.970  0.020  1.090
 L0C  C23  H44  single    0.970  0.020  1.090
 L0C  C30  N24  single    1.493  0.020  1.493
 L0C  C26  N24  single    1.494  0.020  1.494
 L0C  N24  H25  single    0.890  0.020  1.040
 L0C  C27  C26  single    1.515  0.020  1.515
 L0C  H45  C26  single    0.970  0.020  1.090
 L0C  C26  H46  single    0.970  0.020  1.090
 L0C  O28  C27  single    1.406  0.020  1.406
 L0C  H47  C27  single    0.970  0.020  1.090
 L0C  C27  H48  single    0.970  0.020  1.090
 L0C  O28  C29  single    1.406  0.020  1.406
 L0C  H49  C29  single    0.970  0.020  1.090
 L0C  C29  C30  single    1.516  0.020  1.516
 L0C  C29  H50  single    0.970  0.020  1.090
 L0C  H52  C30  single    0.970  0.020  1.090
 L0C  C30  H51  single    0.970  0.020  1.090
 L0C  C31  C32  aromatic  1.386  0.020  1.386
 L0C  C31  H53  single    0.930  0.020  1.080
 L0C  C32  N33  aromatic  1.368  0.020  1.368
 L0C  N33  H34  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
 L0C  C7   C2   C3   122.18  3.000
 L0C  C7   C2   F1   118.92  3.000
 L0C  C3   C2   F1   118.90  3.000
 L0C  H35  C3   C4   120.80  3.000
 L0C  C4   C3   C2   118.59  3.000
 L0C  H35  C3   C2   120.61  3.000
 L0C  H36  C4   C5   121.64  3.000
 L0C  C5   C4   C3   120.84  3.000
 L0C  H36  C4   C3   117.50  3.000
 L0C  C8   C5   C6   117.87  3.000
 L0C  C8   C5   C4   123.21  3.000
 L0C  C6   C5   C4   118.89  3.000
 L0C  H37  C6   C7   119.12  3.000
 L0C  H37  C6   C5   119.87  3.000
 L0C  C7   C6   C5   121.00  3.000
 L0C  H38  C7   C6   120.92  3.000
 L0C  H38  C7   C2   120.58  3.000
 L0C  C6   C7   C2   118.50  3.000
 L0C  N10  C8   O9   122.41  3.000
 L0C  O9   C8   C5   121.84  3.000
 L0C  N10  C8   C5   115.75  3.000
 L0C  H39  N10  C11  113.55  3.000
 L0C  C11  N10  C8   125.16  3.000
 L0C  H39  N10  C8   121.29  3.000
 L0C  C16  C11  C12  104.35  3.000
 L0C  C12  C11  N10  132.07  3.000
 L0C  C16  C11  N10  123.57  3.000
 L0C  H40  C12  N13  121.81  3.000
 L0C  N13  C12  C11  105.44  3.000
 L0C  H40  C12  C11  132.75  3.000
 L0C  H14  N13  N15  119.69  3.000
 L0C  H14  N13  C12  126.07  3.000
 L0C  N15  N13  C12  114.24  3.000
 L0C  C16  N15  N13  104.78  3.000
 L0C  C17  C16  N15  122.78  3.000
 L0C  C17  C16  C11  126.03  3.000
 L0C  N15  C16  C11  111.19  3.000
 L0C  N33  C17  N18  112.89  3.000
 L0C  N33  C17  C16  123.78  3.000
 L0C  N18  C17  C16  123.33  3.000
 L0C  C19  N18  C17  105.27  3.000
 L0C  C32  C19  C20  119.92  3.000
 L0C  C32  C19  N18  109.72  3.000
 L0C  C20  C19  N18  130.37  3.000
 L0C  H41  C20  C21  121.12  3.000
 L0C  C21  C20  C19  117.84  3.000
 L0C  H41  C20  C19  121.04  3.000
 L0C  H42  C21  C22  118.95  3.000
 L0C  C22  C21  C20  121.82  3.000
 L0C  H42  C21  C20  119.23  3.000
 L0C  C31  C22  C23  119.22  3.000
 L0C  C31  C22  C21  120.87  3.000
 L0C  C23  C22  C21  119.91  3.000
 L0C  H44  C23  H43  108.35  3.000
 L0C  H44  C23  N24  105.88  3.000
 L0C  H43  C23  N24  106.55  3.000
 L0C  H44  C23  C22  111.47  3.000
 L0C  H43  C23  C22  112.07  3.000
 L0C  N24  C23  C22  112.18  3.000
 L0C  H25  N24  C30  107.80  3.000
 L0C  H25  N24  C26  107.68  3.000
 L0C  C30  N24  C26  109.94  3.000
 L0C  H25  N24  C23  107.25  3.000
 L0C  C26  N24  C23  110.80  3.000
 L0C  C30  N24  C23  113.14  3.000
 L0C  H46  C26  H45  109.19  3.000
 L0C  H46  C26  C27  110.83  3.000
 L0C  H45  C26  C27  111.47  3.000
 L0C  H46  C26  N24  108.02  3.000
 L0C  H45  C26  N24  106.97  3.000
 L0C  C27  C26  N24  110.23  3.000
 L0C  H48  C27  H47  107.70  3.000
 L0C  H48  C27  O28  111.04  3.000
 L0C  H47  C27  O28  108.26  3.000
 L0C  H48  C27  C26  109.80  3.000
 L0C  H47  C27  C26  108.40  3.000
 L0C  O28  C27  C26  111.51  3.000
 L0C  C29  O28  C27  110.76  3.000
 L0C  H50  C29  H49  107.70  3.000
 L0C  H50  C29  C30  109.62  3.000
 L0C  H49  C29  C30  108.36  3.000
 L0C  H50  C29  O28  110.96  3.000
 L0C  C30  C29  O28  111.85  3.000
 L0C  H49  C29  O28  108.22  3.000
 L0C  H52  C30  H51  109.24  3.000
 L0C  H51  C30  C29  111.67  3.000
 L0C  H52  C30  C29  110.26  3.000
 L0C  H51  C30  N24  107.10  3.000
 L0C  H52  C30  N24  108.57  3.000
 L0C  C29  C30  N24  109.89  3.000
 L0C  H53  C31  C32  121.50  3.000
 L0C  H53  C31  C22  121.47  3.000
 L0C  C32  C31  C22  117.03  3.000
 L0C  N33  C32  C31  132.51  3.000
 L0C  N33  C32  C19  104.96  3.000
 L0C  C31  C32  C19  122.53  3.000
 L0C  H34  N33  C32  127.03  3.000
 L0C  H34  N33  C17  125.80  3.000
 L0C  C32  N33  C17  107.17  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
 L0C  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 L0C  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 L0C  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 L0C  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 L0C  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 L0C  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 L0C  CONST_07  N13  N15  C16  C11    0.00   0.0  0
 L0C  CONST_08  N18  C17  C16  C11    0.00   0.0  0
 L0C  CONST_09  N33  C17  C16  C11  180.00   0.0  0
 L0C  CONST_10  N15  N13  C12  C11    0.00   0.0  0
 L0C  CONST_11  N15  C16  C11  C12    0.00   0.0  0
 L0C  CONST_12  C17  C16  C11  C12  180.00   0.0  0
 L0C  CONST_13  C16  N15  N13  C12    0.00   0.0  0
 L0C  CONST_14  C16  C11  C12  N13    0.00   0.0  0
 L0C  CONST_15  C17  C16  N15  N13  180.00   0.0  0
 L0C  CONST_16  N18  C17  C16  N15  180.00   0.0  0
 L0C  CONST_17  N33  C17  C16  N15    0.00   0.0  0
 L0C  CONST_18  C19  N18  C17  C16  180.00   0.0  0
 L0C  CONST_19  C32  N33  C17  C16  180.00   0.0  0
 L0C  CONST_20  C20  C19  N18  C17  180.00   0.0  0
 L0C  CONST_21  C32  C19  N18  C17    0.00   0.0  0
 L0C  CONST_22  C19  C32  N33  C17    0.00   0.0  0
 L0C  CONST_23  C31  C32  N33  C17  180.00   0.0  0
 L0C  CONST_24  C32  N33  C17  N18    0.00   0.0  0
 L0C  CONST_25  C21  C20  C19  N18  180.00   0.0  0
 L0C  CONST_26  C31  C32  C19  N18  180.00   0.0  0
 L0C  CONST_27  N33  C32  C19  N18    0.00   0.0  0
 L0C  CONST_28  N33  C17  N18  C19    0.00   0.0  0
 L0C  CONST_29  C22  C21  C20  C19    0.00   0.0  0
 L0C  CONST_30  C22  C31  C32  C19    0.00   0.0  0
 L0C  CONST_31  C31  C32  C19  C20    0.00   0.0  0
 L0C  CONST_32  N33  C32  C19  C20  180.00   0.0  0
 L0C  CONST_33  C31  C22  C21  C20    0.00   0.0  0
 L0C  CONST_34  C32  C19  C20  C21    0.00   0.0  0
 L0C  CONST_35  C32  C31  C22  C21    0.00   0.0  0
 L0C  CONST_36  N33  C32  C31  C22  180.00   0.0  0
 L0C  CONST_37  C4   C3   C2   F1   180.00   0.0  0
 L0C  CONST_38  C6   C7   C2   F1   180.00   0.0  0
 L0C  CONST_39  C8   C5   C4   C3   180.00   0.0  0
 L0C  CONST_40  C8   C5   C6   C7   180.00   0.0  0
 L0C  CONST_41  N15  C16  C11  N10  180.00   0.0  0
 L0C  CONST_42  C17  C16  C11  N10    0.00   0.0  0
 L0C  CONST_43  N13  C12  C11  N10  180.00   0.0  0
 L0C  CONST_44  C23  C22  C21  C20  180.00   0.0  0
 L0C  CONST_45  C32  C31  C22  C23  180.00   0.0  0
 L0C  CONST_46  H36  C4   C3   C2   180.00   0.0  0
 L0C  CONST_47  H37  C6   C7   C2   180.00   0.0  0
 L0C  CONST_48  H38  C7   C2   C3   180.00   0.0  0
 L0C  CONST_49  H35  C3   C4   C5   180.00   0.0  0
 L0C  CONST_50  H14  N13  C12  C11  180.00   0.0  0
 L0C  CONST_51  H40  C12  N13  N15  180.00   0.0  0
 L0C  CONST_52  H34  N33  C17  C16    0.00   0.0  0
 L0C  CONST_53  H41  C20  C19  N18    0.00   0.0  0
 L0C  CONST_54  H42  C21  C20  C19  180.00   0.0  0
 L0C  CONST_55  H53  C31  C32  C19  180.00   0.0  0
 L0C  CONST_56  C11  N10  C8   C5   180.00   0.0  0
 L0C  CONST_57  C16  C11  N10  C8   180.00   0.0  0
 L0C  CONST_58  C12  C11  N10  C8     0.00   0.0  0
 L0C  CONST_59  H39  N10  C11  C12  180.00   0.0  0
 L0C  CONST_60  C11  N10  C8   O9     0.00   0.0  0
 L0C  Var_01    O28  C29  C30  N24  -56.97  30.0  1
 L0C  Var_02    O28  C27  C26  N24   56.96  30.0  1
 L0C  Var_03    C30  C29  O28  C27   60.52  30.0  1
 L0C  Var_04    N24  C23  C22  C21  -99.41  30.0  1
 L0C  Var_05    N10  C8   C5   C4    20.83  30.0  2

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
 L0C  chir_01  N24  C23  C30  C26  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
 L0C  plan-1  N10  0.020
 L0C  plan-1  C11  0.020
 L0C  plan-1  C12  0.020
 L0C  plan-1  N13  0.020
 L0C  plan-1  N15  0.020
 L0C  plan-1  C16  0.020
 L0C  plan-1  C17  0.020
 L0C  plan-1  H14  0.020
 L0C  plan-1  H40  0.020
 L0C  plan-2  F1   0.020
 L0C  plan-2  C2   0.020
 L0C  plan-2  C3   0.020
 L0C  plan-2  C4   0.020
 L0C  plan-2  C5   0.020
 L0C  plan-2  C6   0.020
 L0C  plan-2  C7   0.020
 L0C  plan-2  C8   0.020
 L0C  plan-2  H35  0.020
 L0C  plan-2  H36  0.020
 L0C  plan-2  H37  0.020
 L0C  plan-2  H38  0.020
 L0C  plan-3  C16  0.020
 L0C  plan-3  C17  0.020
 L0C  plan-3  N18  0.020
 L0C  plan-3  C19  0.020
 L0C  plan-3  C20  0.020
 L0C  plan-3  C21  0.020
 L0C  plan-3  C22  0.020
 L0C  plan-3  C23  0.020
 L0C  plan-3  C31  0.020
 L0C  plan-3  C32  0.020
 L0C  plan-3  N33  0.020
 L0C  plan-3  H34  0.020
 L0C  plan-3  H41  0.020
 L0C  plan-3  H42  0.020
 L0C  plan-3  H53  0.020
 L0C  plan-4  C5   0.020
 L0C  plan-4  C8   0.020
 L0C  plan-4  O9   0.020
 L0C  plan-4  N10  0.020
 L0C  plan-4  C11  0.020
 L0C  plan-4  H39  0.020

