# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 17:01:28 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1n2c(nnc2c3ccncn3)[C@@H]4C[C@H](C4)N5C(=O)Nc6cc(ccc56)C#N
#
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
 92T  92T  1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile  ligand  51  34  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_92T
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
 92T  C2   C   CR16  0   0.058  -6.3985  -0.2825   1.0923
 92T  C4   C   CR6   0   0.212  -4.7650   1.1684   0.5220
 92T  CAY  C   CR5   0   0.673   3.2818  -0.8285  -1.1733
 92T  NAX  N   NR15  0  -0.752   4.6019  -1.1889  -1.2256
 92T  CAW  C   CR56  0   0.333   5.3693  -0.3332  -0.4755
 92T  CBC  C   CR16  0  -0.294   6.7208  -0.2939  -0.2301
 92T  CBB  C   CR6   0  -0.022   7.1847   0.7366   0.5976
 92T  CBE  C   CSP   0   0.049   8.5773   0.8218   0.8843
 92T  NBF  N   NS    0  -0.260   9.7032   0.8868   1.1247
 92T  CBA  C   CR16  0  -0.253   6.3152   1.6818   1.1487
 92T  CAZ  C   CR16  0  -0.306   4.9534   1.6283   0.8924
 92T  CAV  C   CR56  0   0.362   4.4898   0.6123   0.0749
 92T  NAU  N   NR5   0  -0.603   3.2273   0.2918  -0.3620
 92T  CAN  C   C     0  -0.103   2.0111   0.9974  -0.0363
 92T  CBH  C   C     0  -0.435   0.8405   0.1634   0.5267
 92T  CBG  C   C     0  -0.430   1.1192   1.4606  -1.2085
 92T  CAH  C   C     0  -0.403  -0.0078   0.5280  -0.7213
 92T  CAE  C   CR5   0   0.467  -1.3198   1.1613  -0.4690
 92T  NAD  N   N     0  -0.319  -1.6402   2.4151  -0.6382
 92T  NAC  N   N     0  -0.308  -2.9329   2.5670  -0.2902
 92T  CAB  C   CR5   0   0.414  -3.3935   1.4083   0.0867
 92T  N3   N   N     0  -0.410  -5.1495  -0.0892   0.7030
 92T  N1   N   N     0  -0.394  -7.3079   0.6526   1.3175
 92T  C6   C   CR16  0  -0.024  -6.9151   1.9092   1.1309
 92T  C5   C   CR16  0  -0.314  -5.6342   2.2340   0.7277
 92T  NAA  N   NR5   0  -0.589  -2.3997   0.4788  -0.0019
 92T  CAG  C   CR6   0   0.366  -2.4152  -0.9078   0.2882
 92T  CAI  C   CR6   0  -0.044  -2.7397  -1.8195  -0.7078
 92T  CL1  CL  CL    0  -0.097  -3.1891  -1.2411  -2.2686
 92T  CAJ  C   CR16  0  -0.233  -2.7180  -3.1787  -0.4476
 92T  CAK  C   CR16  0  -0.245  -2.3671  -3.6222   0.8198
 92T  CAL  C   CR16  0  -0.260  -2.0391  -2.7157   1.8178
 92T  CAM  C   CR16  0  -0.247  -2.0618  -1.3561   1.5493
 92T  H1   H   HCR6  0   0.267  -6.7049  -1.3120   1.2395
 92T  H2   H   HNR5  0   0.427   4.9367  -1.9859  -1.7439
 92T  H3   H   HCR6  0   0.293   7.3977  -1.0221  -0.6552
 92T  H4   H   HCR6  0   0.283   6.7074   2.4657   1.7814
 92T  H5   H   HCR6  0   0.289   4.2918   2.3645   1.3267
 92T  H6   H   H     0   0.285   2.2961   1.8157   0.6206
 92T  H7   H   H     0   0.270   1.0258  -0.8994   0.6644
 92T  H8   H   H     0   0.262   0.4582   0.5702   1.4623
 92T  H9   H   H     0   0.264   0.8763   2.5196  -1.1467
 92T  H10  H   H     0   0.268   1.4892   1.2485  -2.2090
 92T  H11  H   H     0   0.289  -0.1348  -0.3314  -1.3819
 92T  H12  H   HCR6  0   0.288  -7.6478   2.6866   1.3124
 92T  H13  H   HCR6  0   0.287  -5.3282   3.2594   0.5838
 92T  H14  H   HCR6  0   0.288  -2.9734  -3.8842  -1.2263
 92T  H15  H   HCR6  0   0.276  -2.3499  -4.6845   1.0226
 92T  H16  H   HCR6  0   0.274  -1.7630  -3.0637   2.8034
 92T  H17  H   HCR6  0   0.283  -1.8118  -0.6355   2.3166
 92T  OBD  O   O     0  -0.483   2.3434  -1.3721  -1.7208

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
 92T  NBF  CBE  triple    1.153  0.020  1.153
 92T  CL1  CAI  single    1.724  0.020  1.724
 92T  CBE  CBB  single    1.424  0.020  1.424
 92T  CAJ  CAI  aromatic  1.384  0.020  1.384
 92T  CAJ  CAK  aromatic  1.388  0.020  1.388
 92T  CBB  CBA  aromatic  1.398  0.020  1.398
 92T  CBB  CBC  aromatic  1.401  0.020  1.401
 92T  CBA  CAZ  aromatic  1.387  0.020  1.387
 92T  CAI  CAG  aromatic  1.389  0.020  1.389
 92T  CAK  CAL  aromatic  1.388  0.020  1.388
 92T  CBC  CAW  aromatic  1.374  0.020  1.374
 92T  CAZ  CAV  aromatic  1.384  0.020  1.384
 92T  CBH  CAH  single    1.552  0.020  1.552
 92T  CBH  CAN  single    1.544  0.020  1.544
 92T  CAW  CAV  aromatic  1.404  0.020  1.404
 92T  CAW  NAX  single    1.372  0.020  1.372
 92T  CAV  NAU  single    1.374  0.020  1.374
 92T  CAG  NAA  single    1.417  0.020  1.417
 92T  CAG  CAM  aromatic  1.384  0.020  1.384
 92T  CAH  CAE  single    1.479  0.020  1.479
 92T  CAH  CBG  single    1.542  0.020  1.542
 92T  CAL  CAM  aromatic  1.386  0.020  1.386
 92T  C5   C6   aromatic  1.382  0.020  1.382
 92T  C5   C4   aromatic  1.390  0.020  1.390
 92T  NAA  CAE  aromatic  1.360  0.020  1.360
 92T  NAA  CAB  aromatic  1.364  0.020  1.364
 92T  NAX  CAY  single    1.369  0.020  1.369
 92T  CAE  NAD  aromatic  1.305  0.020  1.305
 92T  NAU  CAY  single    1.384  0.020  1.384
 92T  NAU  CAN  single    1.443  0.020  1.443
 92T  C6   N1   aromatic  1.330  0.020  1.330
 92T  CAY  OBD  double    1.215  0.020  1.215
 92T  CAB  C4   single    1.459  0.020  1.459
 92T  CAB  NAC  aromatic  1.303  0.020  1.303
 92T  CAN  CBG  single    1.544  0.020  1.544
 92T  NAD  NAC  aromatic  1.347  0.020  1.347
 92T  C4   N3   aromatic  1.327  0.020  1.327
 92T  N1   C2   aromatic  1.324  0.020  1.324
 92T  N3   C2   aromatic  1.322  0.020  1.322
 92T  C2   H1   single    0.930  0.020  1.080
 92T  NAX  H2   single    0.860  0.020  1.020
 92T  CBC  H3   single    0.930  0.020  1.080
 92T  CBA  H4   single    0.930  0.020  1.080
 92T  CAZ  H5   single    0.930  0.020  1.080
 92T  CAN  H6   single    0.970  0.020  1.090
 92T  CBH  H7   single    0.970  0.020  1.090
 92T  CBH  H8   single    0.970  0.020  1.090
 92T  CBG  H9   single    0.970  0.020  1.090
 92T  CBG  H10  single    0.970  0.020  1.090
 92T  CAH  H11  single    0.970  0.020  1.090
 92T  C6   H12  single    0.930  0.020  1.080
 92T  C5   H13  single    0.930  0.020  1.080
 92T  CAJ  H14  single    0.930  0.020  1.080
 92T  CAK  H15  single    0.930  0.020  1.080
 92T  CAL  H16  single    0.930  0.020  1.080
 92T  CAM  H17  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
 92T  H1   C2   N1   116.97  3.000
 92T  H1   C2   N3   116.47  3.000
 92T  N1   C2   N3   126.56  3.000
 92T  C5   C4   N3   121.65  3.000
 92T  N3   C4   CAB  117.96  3.000
 92T  C5   C4   CAB  120.39  3.000
 92T  NAU  CAY  NAX  105.86  3.000
 92T  NAU  CAY  OBD  126.58  3.000
 92T  NAX  CAY  OBD  127.56  3.000
 92T  H2   NAX  CAW  126.04  3.000
 92T  H2   NAX  CAY  123.22  3.000
 92T  CAW  NAX  CAY  110.73  3.000
 92T  CAV  CAW  CBC  121.79  3.000
 92T  CAV  CAW  NAX  106.50  3.000
 92T  CBC  CAW  NAX  131.71  3.000
 92T  H3   CBC  CBB  121.36  3.000
 92T  H3   CBC  CAW  121.75  3.000
 92T  CBB  CBC  CAW  116.89  3.000
 92T  CBA  CBB  CBE  119.24  3.000
 92T  CBA  CBB  CBC  121.64  3.000
 92T  CBE  CBB  CBC  119.13  3.000
 92T  NBF  CBE  CBB  180.00  3.000
 92T  H4   CBA  CAZ  119.50  3.000
 92T  H4   CBA  CBB  119.70  3.000
 92T  CAZ  CBA  CBB  120.79  3.000
 92T  H5   CAZ  CAV  122.16  3.000
 92T  H5   CAZ  CBA  120.03  3.000
 92T  CAV  CAZ  CBA  117.81  3.000
 92T  NAU  CAV  CAZ  131.83  3.000
 92T  NAU  CAV  CAW  107.09  3.000
 92T  CAZ  CAV  CAW  121.08  3.000
 92T  CAN  NAU  CAV  126.05  3.000
 92T  CAN  NAU  CAY  124.13  3.000
 92T  CAV  NAU  CAY  109.82  3.000
 92T  H6   CAN  CBG  112.60  3.000
 92T  H6   CAN  CBH  112.65  3.000
 92T  CBG  CAN  CBH   90.05  3.000
 92T  H6   CAN  NAU  106.46  3.000
 92T  CBG  CAN  NAU  117.52  3.000
 92T  CBH  CAN  NAU  117.21  3.000
 92T  H8   CBH  H7   108.42  3.000
 92T  H8   CBH  CAH  114.26  3.000
 92T  H7   CBH  CAH  115.11  3.000
 92T  H8   CBH  CAN  112.18  3.000
 92T  H7   CBH  CAN  116.42  3.000
 92T  CAH  CBH  CAN   89.67  3.000
 92T  H10  CBG  H9   108.54  3.000
 92T  H10  CBG  CAH  114.92  3.000
 92T  H9   CBG  CAH  114.05  3.000
 92T  H10  CBG  CAN  116.32  3.000
 92T  H9   CBG  CAN  112.20  3.000
 92T  CAH  CBG  CAN   90.05  3.000
 92T  H11  CAH  CAE  109.71  3.000
 92T  H11  CAH  CBG  111.72  3.000
 92T  CAE  CAH  CBG  116.33  3.000
 92T  H11  CAH  CBH  111.42  3.000
 92T  CBG  CAH  CBH   89.81  3.000
 92T  CAE  CAH  CBH  116.64  3.000
 92T  NAA  CAE  NAD  109.37  3.000
 92T  NAD  CAE  CAH  127.39  3.000
 92T  NAA  CAE  CAH  123.24  3.000
 92T  NAC  NAD  CAE  108.08  3.000
 92T  CAB  NAC  NAD  108.29  3.000
 92T  NAA  CAB  NAC  109.26  3.000
 92T  NAC  CAB  C4   124.41  3.000
 92T  NAA  CAB  C4   126.33  3.000
 92T  C4   N3   C2   116.89  3.000
 92T  C6   N1   C2   116.15  3.000
 92T  H12  C6   C5   120.47  3.000
 92T  H12  C6   N1   117.05  3.000
 92T  C5   C6   N1   122.48  3.000
 92T  H13  C5   C6   121.67  3.000
 92T  H13  C5   C4   122.06  3.000
 92T  C6   C5   C4   116.27  3.000
 92T  CAG  NAA  CAB  130.23  3.000
 92T  CAB  NAA  CAE  105.01  3.000
 92T  CAG  NAA  CAE  124.75  3.000
 92T  CAM  CAG  CAI  120.03  3.000
 92T  CAM  CAG  NAA  120.05  3.000
 92T  CAI  CAG  NAA  119.88  3.000
 92T  CAJ  CAI  CL1  120.25  3.000
 92T  CAJ  CAI  CAG  120.41  3.000
 92T  CL1  CAI  CAG  119.34  3.000
 92T  H14  CAJ  CAK  120.58  3.000
 92T  H14  CAJ  CAI  120.11  3.000
 92T  CAK  CAJ  CAI  119.31  3.000
 92T  H15  CAK  CAL  120.20  3.000
 92T  H15  CAK  CAJ  119.29  3.000
 92T  CAL  CAK  CAJ  120.51  3.000
 92T  H16  CAL  CAM  119.77  3.000
 92T  H16  CAL  CAK  120.38  3.000
 92T  CAM  CAL  CAK  119.85  3.000
 92T  H17  CAM  CAL  120.81  3.000
 92T  H17  CAM  CAG  119.30  3.000
 92T  CAL  CAM  CAG  119.89  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
 92T  CONST_01  C5   C6   N1   C2     0.00  0.0  0
 92T  CONST_02  C5   C4   N3   C2     0.00  0.0  0
 92T  CONST_03  CAB  C4   N3   C2   180.00  0.0  0
 92T  CONST_04  N1   C6   C5   C4     0.00  0.0  0
 92T  CONST_05  CAG  NAA  CAB  C4     0.00  0.0  0
 92T  CONST_06  CAE  NAA  CAB  C4   180.00  0.0  0
 92T  CONST_07  NAD  NAC  CAB  C4   180.00  0.0  0
 92T  CONST_08  N1   C2   N3   C4     0.00  0.0  0
 92T  CONST_09  CBA  CBB  CBC  CAW    0.00  0.0  0
 92T  CONST_10  CBA  CAZ  CAV  CAW    0.00  0.0  0
 92T  CONST_11  CAZ  CBA  CBB  CBC    0.00  0.0  0
 92T  CONST_12  CAZ  CAV  CAW  CBC    0.00  0.0  0
 92T  CONST_13  CAV  CAZ  CBA  CBB    0.00  0.0  0
 92T  CONST_14  CAV  CAW  CBC  CBB    0.00  0.0  0
 92T  CONST_17  NAC  CAB  NAA  CAE    0.00  0.0  0
 92T  CONST_18  CAB  NAC  NAD  CAE    0.00  0.0  0
 92T  CONST_19  CAG  NAA  CAE  NAD  180.00  0.0  0
 92T  CONST_20  CAB  NAA  CAE  NAD    0.00  0.0  0
 92T  CONST_21  NAA  CAB  NAC  NAD    0.00  0.0  0
 92T  CONST_22  CAG  NAA  CAB  NAC  180.00  0.0  0
 92T  CONST_23  C5   C4   CAB  NAC    0.00  0.0  0
 92T  CONST_24  N3   C4   CAB  NAC  180.00  0.0  0
 92T  CONST_25  NAA  CAE  NAD  NAC    0.00  0.0  0
 92T  CONST_28  C6   C5   C4   CAB  180.00  0.0  0
 92T  CONST_29  C6   C5   C4   N3     0.00  0.0  0
 92T  CONST_30  NAA  CAB  C4   N3     0.00  0.0  0
 92T  CONST_31  C6   N1   C2   N3     0.00  0.0  0
 92T  CONST_32  NAA  CAB  C4   C5   180.00  0.0  0
 92T  CONST_33  CAJ  CAI  CAG  NAA  180.00  0.0  0
 92T  CONST_34  CAL  CAM  CAG  NAA  180.00  0.0  0
 92T  CONST_35  CAK  CAJ  CAI  CAG    0.00  0.0  0
 92T  CONST_36  CAK  CAL  CAM  CAG    0.00  0.0  0
 92T  CONST_37  CAL  CAK  CAJ  CAI    0.00  0.0  0
 92T  CONST_38  CAL  CAM  CAG  CAI    0.00  0.0  0
 92T  CONST_39  CAM  CAG  CAI  CAJ    0.00  0.0  0
 92T  CONST_40  CAM  CAL  CAK  CAJ    0.00  0.0  0
 92T  CONST_41  CAG  NAA  CAE  CAH    0.00  0.0  0
 92T  CONST_42  CAB  NAA  CAE  CAH  180.00  0.0  0
 92T  CONST_43  NAC  NAD  CAE  CAH  180.00  0.0  0
 92T  CONST_44  CAV  CAW  NAX  CAY    0.00  0.0  0
 92T  CONST_45  CAW  CAV  NAU  CAY    0.00  0.0  0
 92T  CONST_46  NAU  CAV  CAW  NAX    0.00  0.0  0
 92T  CONST_47  CAV  NAU  CAY  NAX    0.00  0.0  0
 92T  CONST_48  CAN  NAU  CAY  NAX  180.00  0.0  0
 92T  CONST_49  CAN  NAU  CAV  CAW  180.00  0.0  0
 92T  CONST_50  NAU  CAY  NAX  CAW    0.00  0.0  0
 92T  CONST_51  CBE  CBB  CBC  CAW  180.00  0.0  0
 92T  CONST_52  CAZ  CBA  CBB  CBE  180.00  0.0  0
 92T  CONST_53  CL1  CAI  CAG  NAA    0.00  0.0  0
 92T  CONST_54  CAK  CAJ  CAI  CL1  180.00  0.0  0
 92T  CONST_55  CAM  CAG  CAI  CL1  180.00  0.0  0
 92T  CONST_56  CAW  NAX  CAY  OBD  180.00  0.0  0
 92T  CONST_57  CAV  NAU  CAY  OBD  180.00  0.0  0
 92T  CONST_58  CAN  NAU  CAY  OBD    0.00  0.0  0
 92T  CONST_59  H12  C6   N1   C2   180.00  0.0  0
 92T  CONST_60  H1   C2   N3   C4   180.00  0.0  0
 92T  CONST_61  H3   CBC  CAW  NAX    0.00  0.0  0
 92T  CONST_62  H5   CAZ  CAV  CAW  180.00  0.0  0
 92T  CONST_63  H4   CBA  CBB  CBC  180.00  0.0  0
 92T  CONST_64  H13  C5   C4   CAB    0.00  0.0  0
 92T  CONST_65  H17  CAM  CAG  NAA    0.00  0.0  0
 92T  CONST_66  H14  CAJ  CAI  CAG  180.00  0.0  0
 92T  CONST_67  H16  CAL  CAM  CAG  180.00  0.0  0
 92T  CONST_68  H15  CAK  CAJ  CAI  180.00  0.0  0
 92T  CONST_69  H2   NAX  CAW  CAV  180.00  0.0  0

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
 92T  chir_01  CAN  CBH  NAU  CBG  negativ
 92T  chir_02  CAH  CBH  CAE  CBG  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
 92T  plan-1  C4   0.020
 92T  plan-1  CAH  0.020
 92T  plan-1  CAE  0.020
 92T  plan-1  NAD  0.020
 92T  plan-1  NAC  0.020
 92T  plan-1  CAB  0.020
 92T  plan-1  NAA  0.020
 92T  plan-1  CAG  0.020
 92T  plan-2  C2   0.020
 92T  plan-2  C4   0.020
 92T  plan-2  CAB  0.020
 92T  plan-2  N3   0.020
 92T  plan-2  N1   0.020
 92T  plan-2  C6   0.020
 92T  plan-2  C5   0.020
 92T  plan-2  H1   0.020
 92T  plan-2  H12  0.020
 92T  plan-2  H13  0.020
 92T  plan-3  NAA  0.020
 92T  plan-3  CAG  0.020
 92T  plan-3  CAI  0.020
 92T  plan-3  CL1  0.020
 92T  plan-3  CAJ  0.020
 92T  plan-3  CAK  0.020
 92T  plan-3  CAL  0.020
 92T  plan-3  CAM  0.020
 92T  plan-3  H14  0.020
 92T  plan-3  H15  0.020
 92T  plan-3  H16  0.020
 92T  plan-3  H17  0.020
 92T  plan-4  CAY  0.020
 92T  plan-4  NAX  0.020
 92T  plan-4  CAW  0.020
 92T  plan-4  CBC  0.020
 92T  plan-4  CBB  0.020
 92T  plan-4  CBE  0.020
 92T  plan-4  NBF  0.020
 92T  plan-4  CBA  0.020
 92T  plan-4  CAZ  0.020
 92T  plan-4  CAV  0.020
 92T  plan-4  NAU  0.020
 92T  plan-4  CAN  0.020
 92T  plan-4  H2   0.020
 92T  plan-4  H3   0.020
 92T  plan-4  H4   0.020
 92T  plan-4  H5   0.020
 92T  plan-4  OBD  0.020

