# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 07:59:35 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: ~{N}-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]-1-bicyclo[1.1.1]pentanyl]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1n2c(nnc2C34CC(C3)(C4)NC(=O)c5ccccn5)c6ccncn6
#
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
 NJH  NJH  ~{N}-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]-1-bicyclo[1.1.1]pentanyl]pyridine-2-carboxamide  ligand  50  32  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NJH
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
 NJH  C4   C   CR6   0   0.194   -4.3456   5.8094  26.9760
 NJH  C5   C   CR16  0  -0.312   -2.9663   5.8479  26.8035
 NJH  C6   C   CR16  0  -0.024   -2.3896   7.1028  26.7673
 NJH  N1   N   N     0  -0.394   -3.1010   8.2196  26.8890
 NJH  N3   N   N     0  -0.410   -5.0634   6.9193  27.0965
 NJH  CAB  C   CR6   0  -0.042   -7.4899   5.7154  28.9443
 NJH  CAC  C   CR16  0  -0.233   -8.4892   6.6024  29.3044
 NJH  CAD  C   CR16  0  -0.245   -9.3765   7.0544  28.3377
 NJH  CAE  C   CR16  0  -0.260   -9.2656   6.6236  27.0232
 NJH  CAF  C   CR16  0  -0.252   -8.2596   5.7384  26.6692
 NJH  CAG  C   CR6   0   0.360   -7.3713   5.2865  27.6288
 NJH  NAH  N   NR5   0  -0.597   -6.3716   4.3432  27.2850
 NJH  CAI  C   CR5   0   0.420   -5.0451   4.5301  27.0302
 NJH  C2   C   CR16  0   0.059   -4.4062   8.0657  27.0466
 NJH  NAJ  N   N     0  -0.312   -4.4754   3.3729  26.8413
 NJH  NAK  N   N     0  -0.311   -5.4078   2.4140  26.9831
 NJH  CAL  C   CR5   0   0.358   -6.5453   2.9955  27.2553
 NJH  CAM  C   CT    0  -0.010   -7.8118   2.3058  27.5072
 NJH  CAP  C   CH2   0  -0.445   -9.0516   2.2071  26.5817
 NJH  CAQ  C   CH2   0  -0.469   -8.7954   2.5159  28.6844
 NJH  CAN  C   CH2   0  -0.439   -7.9402   0.7916  27.7491
 NJH  CAO  C   CT    0   0.304   -9.3693   1.3698  27.8396
 NJH  NAR  N   NH1   0  -0.742  -10.5733   0.6922  28.1537
 NJH  CAS  C   C     0   0.499  -11.0386  -0.3405  27.4266
 NJH  OAT  O   O     0  -0.461  -10.4555  -0.7935  26.4583
 NJH  CAU  C   CR6   0   0.103  -12.3486  -0.9131  27.8917
 NJH  NAZ  N   N     0  -0.407  -12.4809  -2.2240  27.7198
 NJH  CAY  C   CR16  0  -0.075  -13.6180  -2.7911  28.0920
 NJH  CAX  C   CR16  0  -0.313  -14.6838  -2.0827  28.6335
 NJH  CAW  C   CR16  0  -0.146  -14.5489  -0.7145  28.7923
 NJH  CAV  C   CR16  0  -0.318  -13.3548  -0.1137  28.4199
 NJH  H5   H   HCR6  0   0.287   -2.3741   4.9503  26.7062
 NJH  H6   H   HCR6  0   0.288   -1.3191   7.2124  26.6390
 NJH  HAC  H   HCR6  0   0.289   -8.5768   6.9332  30.3300
 NJH  HAD  H   HCR6  0   0.276  -10.1606   7.7443  28.6191
 NJH  HAE  H   HCR6  0   0.274   -9.9596   6.9763  26.2730
 NJH  HAF  H   HCR6  0   0.285   -8.1569   5.3969  25.6476
 NJH  H2   H   HCR6  0   0.268   -4.9983   8.9682  27.1488
 NJH  HAP  H   HCH2  0   0.250   -9.6330   3.1194  26.4443
 NJH  HAQ  H   HCH2  0   0.256   -8.9133   1.6638  25.6477
 NJH  HAR  H   HCH2  0   0.259   -8.4230   2.2569  29.6765
 NJH  HAS  H   HCH2  0   0.254   -9.3665   3.4453  28.6918
 NJH  HAN  H   HCH2  0   0.253   -7.7253   0.1411  26.9027
 NJH  HAO  H   HCH2  0   0.250   -7.5049   0.4165  28.6763
 NJH  H6L  H   HNH1  0   0.413  -11.0498   0.9619  28.9996
 NJH  HAY  H   HCR6  0   0.271  -13.6921  -3.8636  27.9516
 NJH  HAX  H   HCR6  0   0.279  -15.5927  -2.5957  28.9154
 NJH  HAW  H   HCR6  0   0.282  -15.3580  -0.1210  29.1962
 NJH  HAV  H   HCR6  0   0.281  -13.2288   0.9561  28.5203
 NJH  CL1  CL  CL    0  -0.095   -6.3854   5.1243  30.1295

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
 NJH  C4   C5   aromatic  1.391  0.020  1.391
 NJH  C4   N3   aromatic  1.327  0.020  1.327
 NJH  C4   CAI  single    1.459  0.020  1.459
 NJH  C5   C6   aromatic  1.382  0.020  1.382
 NJH  C6   N1   aromatic  1.330  0.020  1.330
 NJH  N1   C2   aromatic  1.324  0.020  1.324
 NJH  N3   C2   aromatic  1.322  0.020  1.322
 NJH  CL1  CAB  single    1.725  0.020  1.725
 NJH  CAB  CAC  aromatic  1.384  0.020  1.384
 NJH  CAB  CAG  aromatic  1.389  0.020  1.389
 NJH  CAC  CAD  aromatic  1.388  0.020  1.388
 NJH  CAD  CAE  aromatic  1.388  0.020  1.388
 NJH  CAE  CAF  aromatic  1.386  0.020  1.386
 NJH  CAF  CAG  aromatic  1.384  0.020  1.384
 NJH  CAG  NAH  single    1.417  0.020  1.417
 NJH  NAH  CAI  aromatic  1.364  0.020  1.364
 NJH  NAH  CAL  aromatic  1.359  0.020  1.359
 NJH  CAI  NAJ  aromatic  1.304  0.020  1.304
 NJH  NAJ  NAK  aromatic  1.345  0.020  1.345
 NJH  NAK  CAL  aromatic  1.306  0.020  1.306
 NJH  CAL  CAM  single    1.464  0.020  1.464
 NJH  CAM  CAP  single    1.550  0.020  1.550
 NJH  CAM  CAQ  single    1.548  0.020  1.548
 NJH  CAM  CAN  single    1.539  0.020  1.539
 NJH  CAP  CAO  single    1.544  0.020  1.544
 NJH  CAQ  CAO  single    1.535  0.020  1.535
 NJH  CAN  CAO  single    1.544  0.020  1.544
 NJH  CAO  NAR  single    1.417  0.020  1.417
 NJH  NAR  CAS  single    1.346  0.020  1.346
 NJH  CAS  OAT  double    1.218  0.020  1.218
 NJH  CAS  CAU  single    1.503  0.020  1.503
 NJH  CAU  NAZ  aromatic  1.329  0.020  1.329
 NJH  CAU  CAV  aromatic  1.389  0.020  1.389
 NJH  NAZ  CAY  aromatic  1.324  0.020  1.324
 NJH  CAY  CAX  aromatic  1.390  0.020  1.390
 NJH  CAX  CAW  aromatic  1.384  0.020  1.384
 NJH  CAW  CAV  aromatic  1.388  0.020  1.388
 NJH  C5   H5   single    0.930  0.020  1.080
 NJH  C6   H6   single    0.930  0.020  1.080
 NJH  CAC  HAC  single    0.930  0.020  1.080
 NJH  CAD  HAD  single    0.930  0.020  1.080
 NJH  CAE  HAE  single    0.930  0.020  1.080
 NJH  CAF  HAF  single    0.930  0.020  1.080
 NJH  C2   H2   single    0.930  0.020  1.080
 NJH  CAP  HAP  single    0.970  0.020  1.090
 NJH  CAP  HAQ  single    0.970  0.020  1.090
 NJH  CAQ  HAR  single    0.970  0.020  1.090
 NJH  CAQ  HAS  single    0.970  0.020  1.090
 NJH  CAN  HAN  single    0.970  0.020  1.090
 NJH  CAN  HAO  single    0.970  0.020  1.090
 NJH  NAR  H6L  single    0.860  0.020  1.020
 NJH  CAY  HAY  single    0.930  0.020  1.080
 NJH  CAX  HAX  single    0.930  0.020  1.080
 NJH  CAW  HAW  single    0.930  0.020  1.080
 NJH  CAV  HAV  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
 NJH  CAI  C4   N3   118.07  3.000
 NJH  CAI  C4   C5   120.30  3.000
 NJH  N3   C4   C5   121.64  3.000
 NJH  H5   C5   C6   121.59  3.000
 NJH  H5   C5   C4   122.15  3.000
 NJH  C6   C5   C4   116.26  3.000
 NJH  H6   C6   N1   117.02  3.000
 NJH  H6   C6   C5   120.49  3.000
 NJH  N1   C6   C5   122.49  3.000
 NJH  C2   N1   C6   116.15  3.000
 NJH  C2   N3   C4   116.92  3.000
 NJH  CAG  CAB  CAC  120.41  3.000
 NJH  CAG  CAB  CL1  119.37  3.000
 NJH  CAC  CAB  CL1  120.22  3.000
 NJH  HAC  CAC  CAD  120.62  3.000
 NJH  HAC  CAC  CAB  120.10  3.000
 NJH  CAD  CAC  CAB  119.28  3.000
 NJH  HAD  CAD  CAE  120.16  3.000
 NJH  HAD  CAD  CAC  119.34  3.000
 NJH  CAE  CAD  CAC  120.50  3.000
 NJH  HAE  CAE  CAF  119.81  3.000
 NJH  HAE  CAE  CAD  120.31  3.000
 NJH  CAF  CAE  CAD  119.88  3.000
 NJH  HAF  CAF  CAG  119.40  3.000
 NJH  HAF  CAF  CAE  120.77  3.000
 NJH  CAG  CAF  CAE  119.83  3.000
 NJH  NAH  CAG  CAF  120.14  3.000
 NJH  NAH  CAG  CAB  119.72  3.000
 NJH  CAF  CAG  CAB  120.09  3.000
 NJH  CAL  NAH  CAI  104.84  3.000
 NJH  CAL  NAH  CAG  125.12  3.000
 NJH  CAI  NAH  CAG  129.83  3.000
 NJH  NAJ  CAI  NAH  109.30  3.000
 NJH  NAJ  CAI  C4   124.29  3.000
 NJH  NAH  CAI  C4   126.41  3.000
 NJH  H2   C2   N3   116.53  3.000
 NJH  H2   C2   N1   116.93  3.000
 NJH  N3   C2   N1   126.54  3.000
 NJH  NAK  NAJ  CAI  108.34  3.000
 NJH  CAL  NAK  NAJ  107.95  3.000
 NJH  CAM  CAL  NAK  125.41  3.000
 NJH  CAM  CAL  NAH  125.03  3.000
 NJH  NAK  CAL  NAH  109.56  3.000
 NJH  CAN  CAM  CAQ   87.76  3.000
 NJH  CAN  CAM  CAP   87.96  3.000
 NJH  CAQ  CAM  CAP   87.39  3.000
 NJH  CAN  CAM  CAL  124.25  3.000
 NJH  CAQ  CAM  CAL  128.06  3.000
 NJH  CAP  CAM  CAL  128.25  3.000
 NJH  HAQ  CAP  HAP  112.14  3.000
 NJH  HAQ  CAP  CAO  117.01  3.000
 NJH  HAP  CAP  CAO  116.53  3.000
 NJH  HAQ  CAP  CAM  116.24  3.000
 NJH  HAP  CAP  CAM  116.64  3.000
 NJH  CAO  CAP  CAM   73.31  3.000
 NJH  HAS  CAQ  HAR  112.01  3.000
 NJH  HAS  CAQ  CAO  116.37  3.000
 NJH  HAR  CAQ  CAO  116.80  3.000
 NJH  HAS  CAQ  CAM  116.96  3.000
 NJH  HAR  CAQ  CAM  116.26  3.000
 NJH  CAO  CAQ  CAM   73.61  3.000
 NJH  HAO  CAN  HAN  112.11  3.000
 NJH  HAO  CAN  CAO  116.63  3.000
 NJH  HAN  CAN  CAO  116.87  3.000
 NJH  HAO  CAN  CAM  116.02  3.000
 NJH  HAN  CAN  CAM  116.69  3.000
 NJH  CAO  CAN  CAM   73.62  3.000
 NJH  NAR  CAO  CAN  128.34  3.000
 NJH  NAR  CAO  CAQ  123.56  3.000
 NJH  CAN  CAO  CAQ   88.04  3.000
 NJH  NAR  CAO  CAP  127.93  3.000
 NJH  CAN  CAO  CAP   87.99  3.000
 NJH  CAQ  CAO  CAP   88.08  3.000
 NJH  H6L  NAR  CAS  119.69  3.000
 NJH  H6L  NAR  CAO  117.38  3.000
 NJH  CAS  NAR  CAO  122.75  3.000
 NJH  CAU  CAS  OAT  121.44  3.000
 NJH  CAU  CAS  NAR  115.23  3.000
 NJH  OAT  CAS  NAR  123.33  3.000
 NJH  CAV  CAU  NAZ  123.00  3.000
 NJH  CAV  CAU  CAS  121.97  3.000
 NJH  NAZ  CAU  CAS  114.99  3.000
 NJH  CAY  NAZ  CAU  118.14  3.000
 NJH  HAY  CAY  CAX  120.15  3.000
 NJH  HAY  CAY  NAZ  116.49  3.000
 NJH  CAX  CAY  NAZ  123.36  3.000
 NJH  HAX  CAX  CAW  121.41  3.000
 NJH  HAX  CAX  CAY  120.30  3.000
 NJH  CAW  CAX  CAY  118.29  3.000
 NJH  HAW  CAW  CAV  120.43  3.000
 NJH  HAW  CAW  CAX  120.82  3.000
 NJH  CAV  CAW  CAX  118.75  3.000
 NJH  HAV  CAV  CAW  120.23  3.000
 NJH  HAV  CAV  CAU  121.32  3.000
 NJH  CAW  CAV  CAU  118.44  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
 NJH  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 NJH  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 NJH  CONST_03  CAG  NAH  CAI  C4      0.00   0.0  0
 NJH  CONST_04  CAL  NAH  CAI  C4    180.00   0.0  0
 NJH  CONST_05  NAK  NAJ  CAI  C4    180.00   0.0  0
 NJH  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 NJH  CONST_07  NAH  CAI  C4   C5    180.00   0.0  0
 NJH  CONST_08  NAJ  CAI  C4   C5      0.00   0.0  0
 NJH  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 NJH  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 NJH  CONST_11  CAI  C4   C5   C6    180.00   0.0  0
 NJH  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 NJH  CONST_13  NAH  CAI  C4   N3      0.00   0.0  0
 NJH  CONST_14  NAJ  CAI  C4   N3    180.00   0.0  0
 NJH  CONST_15  CAE  CAD  CAC  CAB     0.00   0.0  0
 NJH  CONST_16  CAE  CAF  CAG  CAB     0.00   0.0  0
 NJH  CONST_19  CAF  CAG  CAB  CAC     0.00   0.0  0
 NJH  CONST_20  NAH  CAG  CAB  CAC   180.00   0.0  0
 NJH  CONST_21  CAF  CAE  CAD  CAC     0.00   0.0  0
 NJH  CONST_22  CAG  CAB  CAC  CAD     0.00   0.0  0
 NJH  CONST_23  CAG  CAF  CAE  CAD     0.00   0.0  0
 NJH  CONST_24  NAH  CAG  CAF  CAE   180.00   0.0  0
 NJH  CONST_27  NAJ  CAI  NAH  CAG   180.00   0.0  0
 NJH  CONST_28  NAK  CAL  NAH  CAG   180.00   0.0  0
 NJH  CONST_29  NAK  NAJ  CAI  NAH     0.00   0.0  0
 NJH  CONST_30  NAJ  NAK  CAL  NAH     0.00   0.0  0
 NJH  CONST_31  C2   N3   C4   CAI   180.00   0.0  0
 NJH  CONST_32  NAK  CAL  NAH  CAI     0.00   0.0  0
 NJH  CONST_33  CAL  NAK  NAJ  CAI     0.00   0.0  0
 NJH  CONST_34  CAL  NAH  CAI  NAJ     0.00   0.0  0
 NJH  CONST_35  CAX  CAY  NAZ  CAU     0.00   0.0  0
 NJH  CONST_36  CAX  CAW  CAV  CAU     0.00   0.0  0
 NJH  CONST_37  CAW  CAV  CAU  NAZ     0.00   0.0  0
 NJH  CONST_38  CAW  CAX  CAY  NAZ     0.00   0.0  0
 NJH  CONST_39  CAV  CAU  NAZ  CAY     0.00   0.0  0
 NJH  CONST_40  CAV  CAW  CAX  CAY     0.00   0.0  0
 NJH  CONST_41  CAM  CAL  NAH  CAG     0.00   0.0  0
 NJH  CONST_42  CAM  CAL  NAH  CAI   180.00   0.0  0
 NJH  CONST_43  CAM  CAL  NAK  NAJ   180.00   0.0  0
 NJH  CONST_44  CAD  CAC  CAB  CL1   180.00   0.0  0
 NJH  CONST_45  CAF  CAG  CAB  CL1   180.00   0.0  0
 NJH  CONST_46  NAH  CAG  CAB  CL1     0.00   0.0  0
 NJH  CONST_47  CAY  NAZ  CAU  CAS   180.00   0.0  0
 NJH  CONST_48  CAW  CAV  CAU  CAS   180.00   0.0  0
 NJH  CONST_49  H6   C6   C5   C4    180.00   0.0  0
 NJH  CONST_50  H2   C2   N3   C4    180.00   0.0  0
 NJH  CONST_51  H5   C5   C6   N1    180.00   0.0  0
 NJH  CONST_52  HAD  CAD  CAC  CAB   180.00   0.0  0
 NJH  CONST_53  HAF  CAF  CAG  CAB   180.00   0.0  0
 NJH  CONST_54  HAE  CAE  CAD  CAC   180.00   0.0  0
 NJH  CONST_55  HAC  CAC  CAD  CAE   180.00   0.0  0
 NJH  CONST_56  HAY  CAY  NAZ  CAU   180.00   0.0  0
 NJH  CONST_57  HAW  CAW  CAV  CAU   180.00   0.0  0
 NJH  CONST_58  HAV  CAV  CAU  NAZ   180.00   0.0  0
 NJH  CONST_59  HAX  CAX  CAY  NAZ   180.00   0.0  0
 NJH  CONST_60  CAU  CAS  NAR  CAO   180.00   0.0  0
 NJH  CONST_61  OAT  CAS  NAR  CAO     0.00   0.0  0
 NJH  CONST_62  H6L  NAR  CAS  CAU     0.00   0.0  0
 NJH  Var_01    CAP  CAM  CAL  NAH    74.03  30.0  2
 NJH  Var_02    CAO  CAP  CAM  CAL   177.52  30.0  3
 NJH  Var_03    CAO  CAQ  CAM  CAL  -177.15  30.0  3
 NJH  Var_04    CAO  CAN  CAM  CAL   179.64  30.0  3
 NJH  Var_05    NAZ  CAU  CAS  NAR  -146.18  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
 NJH  chir_01  CAO  CAQ  CAN  NAR  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
 NJH  plan-1  C4   0.020
 NJH  plan-1  CAG  0.020
 NJH  plan-1  NAH  0.020
 NJH  plan-1  CAI  0.020
 NJH  plan-1  NAJ  0.020
 NJH  plan-1  NAK  0.020
 NJH  plan-1  CAL  0.020
 NJH  plan-1  CAM  0.020
 NJH  plan-2  C4   0.020
 NJH  plan-2  C5   0.020
 NJH  plan-2  C6   0.020
 NJH  plan-2  N1   0.020
 NJH  plan-2  N3   0.020
 NJH  plan-2  CAI  0.020
 NJH  plan-2  C2   0.020
 NJH  plan-2  H5   0.020
 NJH  plan-2  H6   0.020
 NJH  plan-2  H2   0.020
 NJH  plan-3  CAB  0.020
 NJH  plan-3  CAC  0.020
 NJH  plan-3  CAD  0.020
 NJH  plan-3  CAE  0.020
 NJH  plan-3  CAF  0.020
 NJH  plan-3  CAG  0.020
 NJH  plan-3  NAH  0.020
 NJH  plan-3  HAC  0.020
 NJH  plan-3  HAD  0.020
 NJH  plan-3  HAE  0.020
 NJH  plan-3  HAF  0.020
 NJH  plan-3  CL1  0.020
 NJH  plan-4  CAS  0.020
 NJH  plan-4  CAU  0.020
 NJH  plan-4  NAZ  0.020
 NJH  plan-4  CAY  0.020
 NJH  plan-4  CAX  0.020
 NJH  plan-4  CAW  0.020
 NJH  plan-4  CAV  0.020
 NJH  plan-4  HAY  0.020
 NJH  plan-4  HAX  0.020
 NJH  plan-4  HAW  0.020
 NJH  plan-4  HAV  0.020
 NJH  plan-5  CAO  0.020
 NJH  plan-5  NAR  0.020
 NJH  plan-5  CAS  0.020
 NJH  plan-5  OAT  0.020
 NJH  plan-5  CAU  0.020
 NJH  plan-5  H6L  0.020

