# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:02:03 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-(ethylcarbamoylamino)-4-pyrazol-1-yl-~{N}-pyridin-3-yl-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1cc(n2cccn2)c(cn1)C(=O)Nc3cccnc3
#
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
 CZ5  CZ5  6-(ethylcarbamoylamino)-4-pyrazol-1-yl-~{N}-pyridin-3-yl-pyridine-3-carboxamide  ligand  43  26  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CZ5
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
 CZ5  CAF  C  CR16  0  -0.210  -4.7556   0.9078  -0.8659
 CZ5  CAA  C  CR16  0  -0.312  -6.0524   1.3947  -0.8017
 CZ5  CAB  C  CR16  0  -0.084  -6.3993   2.2967   0.1893
 CZ5  NAC  N  N     0  -0.388  -5.5282   2.7233   1.0980
 CZ5  CAD  C  CR16  0  -0.143  -4.2915   2.2653   1.0427
 CZ5  CAE  C  CR6   0   0.287  -3.8386   1.3536   0.0834
 CZ5  NAH  N  NH1   0  -0.728  -2.5026   0.9665   0.1623
 CZ5  CAK  C  C     0   0.514  -1.8116   0.1442  -0.6640
 CZ5  OAL  O  O     0  -0.439  -2.2753  -0.4094  -1.6409
 CZ5  CAM  C  CR6   0  -0.211  -0.3619   0.0288  -0.3195
 CZ5  CAN  C  CR16  0  -0.066   0.4550   1.1450  -0.3833
 CZ5  NAO  N  N     0  -0.427   1.7774   1.1236  -0.2893
 CZ5  CAP  C  CR6   0   0.556   2.3647  -0.0459  -0.0968
 CZ5  NAX  N  NH1   0  -0.775   3.7368  -0.1271  -0.0325
 CZ5  CAY  C  C     0   0.729   4.6417   0.8997   0.2115
 CZ5  OBA  O  O     0  -0.497   4.3180   2.0196   0.5583
 CZ5  NAZ  N  NH1   0  -0.675   5.9240   0.5034   0.0595
 CZ5  CBB  C  CH2   0  -0.261   7.0344   1.4195   0.2274
 CZ5  CBC  C  CH3   0  -0.692   8.3357   0.6494   0.3541
 CZ5  CAQ  C  CR16  0  -0.484   1.6416  -1.2407   0.0309
 CZ5  CAR  C  CR6   0   0.508   0.2712  -1.1980  -0.0942
 CZ5  NAS  N  NR5   0  -0.406  -0.4788  -2.3676   0.0547
 CZ5  NAT  N  N     0  -0.277  -1.6801  -2.3169   0.6396
 CZ5  CAU  C  CR15  0  -0.022  -2.1064  -3.5585   0.6577
 CZ5  CAV  C  CR15  0  -0.511  -1.1691  -4.4375   0.0758
 CZ5  CAW  C  CR15  0   0.045  -0.1300  -3.6306  -0.2974
 CZ5  H1   H  HCR6  0   0.295  -4.4811   0.2051  -1.6352
 CZ5  H2   H  HCR6  0   0.275  -6.7897   1.0681  -1.5221
 CZ5  H3   H  HCR6  0   0.265  -7.4071   2.6895   0.2540
 CZ5  H4   H  HCR6  0   0.273  -3.6009   2.6356   1.7961
 CZ5  H5   H  HNH1  0   0.423  -1.9980   1.3201   0.9620
 CZ5  H6   H  HCR6  0   0.281   0.0132   2.1208  -0.5579
 CZ5  H7   H  HNH1  0   0.419   4.1118  -1.0624  -0.0791
 CZ5  H8   H  HNH1  0   0.398   6.1170  -0.3614  -0.4216
 CZ5  H9   H  HCH2  0   0.231   7.0941   2.1170  -0.6139
 CZ5  H10  H  HCH2  0   0.240   6.8683   2.0159   1.1244
 CZ5  H11  H  HCH3  0   0.234   8.3230  -0.0079   1.2236
 CZ5  H12  H  HCH3  0   0.231   8.5277   0.0412  -0.5317
 CZ5  H13  H  HCH3  0   0.243   9.1694   1.3415   0.4644
 CZ5  H14  H  HCR6  0   0.305   2.1525  -2.1663   0.2618
 CZ5  H15  H  HCR5  0   0.274  -3.0656  -3.7967   1.0911
 CZ5  H16  H  HCR5  0   0.275  -1.2501  -5.5030  -0.0564
 CZ5  H17  H  HCR5  0   0.307   0.7994  -3.8512  -0.7960

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
 CZ5  CBC  CBB  single    1.517  0.020  1.517
 CZ5  CBB  NAZ  single    1.449  0.020  1.449
 CZ5  NAZ  CAY  single    1.351  0.020  1.351
 CZ5  OBA  CAY  double    1.216  0.020  1.216
 CZ5  CAY  NAX  single    1.390  0.020  1.390
 CZ5  NAX  CAP  single    1.376  0.020  1.376
 CZ5  CAW  CAV  aromatic  1.368  0.020  1.368
 CZ5  CAW  NAS  aromatic  1.357  0.020  1.357
 CZ5  CAV  CAU  aromatic  1.411  0.020  1.411
 CZ5  CAQ  CAP  aromatic  1.402  0.020  1.402
 CZ5  CAQ  CAR  aromatic  1.377  0.020  1.377
 CZ5  CAP  NAO  aromatic  1.323  0.020  1.323
 CZ5  NAS  CAR  single    1.397  0.020  1.397
 CZ5  NAS  NAT  aromatic  1.337  0.020  1.337
 CZ5  CAU  NAT  aromatic  1.313  0.020  1.313
 CZ5  CAR  CAM  aromatic  1.399  0.020  1.399
 CZ5  NAO  CAN  aromatic  1.326  0.020  1.326
 CZ5  CAM  CAN  aromatic  1.385  0.020  1.385
 CZ5  CAM  CAK  single    1.494  0.020  1.494
 CZ5  OAL  CAK  double    1.215  0.020  1.215
 CZ5  CAK  NAH  single    1.355  0.020  1.355
 CZ5  NAH  CAE  single    1.393  0.020  1.393
 CZ5  CAE  CAF  aromatic  1.393  0.020  1.393
 CZ5  CAE  CAD  aromatic  1.399  0.020  1.399
 CZ5  CAF  CAA  aromatic  1.387  0.020  1.387
 CZ5  CAD  NAC  aromatic  1.320  0.020  1.320
 CZ5  CAA  CAB  aromatic  1.384  0.020  1.384
 CZ5  NAC  CAB  aromatic  1.329  0.020  1.329
 CZ5  CAF  H1   single    0.930  0.020  1.080
 CZ5  CAA  H2   single    0.930  0.020  1.080
 CZ5  CAB  H3   single    0.930  0.020  1.080
 CZ5  CAD  H4   single    0.930  0.020  1.080
 CZ5  NAH  H5   single    0.860  0.020  1.020
 CZ5  CAN  H6   single    0.930  0.020  1.080
 CZ5  NAX  H7   single    0.860  0.020  1.020
 CZ5  NAZ  H8   single    0.860  0.020  1.020
 CZ5  CBB  H9   single    0.970  0.020  1.090
 CZ5  CBB  H10  single    0.970  0.020  1.090
 CZ5  CBC  H11  single    0.970  0.020  1.090
 CZ5  CBC  H12  single    0.970  0.020  1.090
 CZ5  CBC  H13  single    0.970  0.020  1.090
 CZ5  CAQ  H14  single    0.930  0.020  1.080
 CZ5  CAU  H15  single    0.930  0.020  1.080
 CZ5  CAV  H16  single    0.930  0.020  1.080
 CZ5  CAW  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
 CZ5  H1   CAF  CAE  121.84  3.000
 CZ5  H1   CAF  CAA  120.03  3.000
 CZ5  CAE  CAF  CAA  118.14  3.000
 CZ5  H2   CAA  CAB  120.19  3.000
 CZ5  H2   CAA  CAF  120.05  3.000
 CZ5  CAB  CAA  CAF  119.76  3.000
 CZ5  H3   CAB  NAC  116.90  3.000
 CZ5  H3   CAB  CAA  120.80  3.000
 CZ5  NAC  CAB  CAA  122.30  3.000
 CZ5  CAD  NAC  CAB  118.30  3.000
 CZ5  H4   CAD  CAE  119.45  3.000
 CZ5  H4   CAD  NAC  116.62  3.000
 CZ5  CAE  CAD  NAC  123.93  3.000
 CZ5  NAH  CAE  CAD  116.92  3.000
 CZ5  CAD  CAE  CAF  117.57  3.000
 CZ5  NAH  CAE  CAF  125.51  3.000
 CZ5  H5   NAH  CAK  116.14  3.000
 CZ5  H5   NAH  CAE  115.27  3.000
 CZ5  CAK  NAH  CAE  128.54  3.000
 CZ5  CAM  CAK  OAL  121.36  3.000
 CZ5  OAL  CAK  NAH  124.90  3.000
 CZ5  CAM  CAK  NAH  113.64  3.000
 CZ5  CAR  CAM  CAN  116.58  3.000
 CZ5  CAN  CAM  CAK  119.96  3.000
 CZ5  CAR  CAM  CAK  122.95  3.000
 CZ5  H6   CAN  NAO  115.59  3.000
 CZ5  H6   CAN  CAM  119.48  3.000
 CZ5  NAO  CAN  CAM  124.90  3.000
 CZ5  CAP  NAO  CAN  117.87  3.000
 CZ5  CAQ  CAP  NAX  117.37  3.000
 CZ5  CAQ  CAP  NAO  122.52  3.000
 CZ5  NAX  CAP  NAO  120.11  3.000
 CZ5  H7   NAX  CAY  116.81  3.000
 CZ5  H7   NAX  CAP  115.03  3.000
 CZ5  CAY  NAX  CAP  127.86  3.000
 CZ5  NAZ  CAY  OBA  123.71  3.000
 CZ5  OBA  CAY  NAX  123.84  3.000
 CZ5  NAZ  CAY  NAX  112.43  3.000
 CZ5  H8   NAZ  CBB  116.79  3.000
 CZ5  H8   NAZ  CAY  119.15  3.000
 CZ5  CBB  NAZ  CAY  121.93  3.000
 CZ5  H10  CBB  H9   106.99  3.000
 CZ5  H10  CBB  CBC  109.86  3.000
 CZ5  H9   CBB  CBC  109.92  3.000
 CZ5  H10  CBB  NAZ  108.94  3.000
 CZ5  H9   CBB  NAZ  110.83  3.000
 CZ5  CBC  CBB  NAZ  110.24  3.000
 CZ5  H13  CBC  H12  107.56  3.000
 CZ5  H13  CBC  H11  108.14  3.000
 CZ5  H12  CBC  H11  108.26  3.000
 CZ5  H13  CBC  CBB  110.02  3.000
 CZ5  H12  CBC  CBB  111.46  3.000
 CZ5  H11  CBC  CBB  111.26  3.000
 CZ5  H14  CAQ  CAR  121.06  3.000
 CZ5  H14  CAQ  CAP  120.31  3.000
 CZ5  CAR  CAQ  CAP  118.59  3.000
 CZ5  NAS  CAR  CAQ  119.91  3.000
 CZ5  NAS  CAR  CAM  120.55  3.000
 CZ5  CAQ  CAR  CAM  119.50  3.000
 CZ5  CAW  NAS  NAT  112.32  3.000
 CZ5  NAT  NAS  CAR  119.81  3.000
 CZ5  CAW  NAS  CAR  127.84  3.000
 CZ5  CAU  NAT  NAS  105.18  3.000
 CZ5  H15  CAU  CAV  128.23  3.000
 CZ5  H15  CAU  NAT  120.19  3.000
 CZ5  CAV  CAU  NAT  111.59  3.000
 CZ5  H16  CAV  CAW  127.42  3.000
 CZ5  H16  CAV  CAU  128.12  3.000
 CZ5  CAW  CAV  CAU  104.46  3.000
 CZ5  H17  CAW  CAV  131.36  3.000
 CZ5  H17  CAW  NAS  122.17  3.000
 CZ5  CAV  CAW  NAS  106.45  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
 CZ5  CONST_01  NAC  CAD  CAE  CAF    0.00   0.0  0
 CZ5  CONST_02  NAC  CAB  CAA  CAF    0.00   0.0  0
 CZ5  CONST_03  CAD  CAE  CAF  CAA    0.00   0.0  0
 CZ5  CONST_04  CAD  NAC  CAB  CAA    0.00   0.0  0
 CZ5  CONST_05  CAE  CAF  CAA  CAB    0.00   0.0  0
 CZ5  CONST_06  CAE  CAD  NAC  CAB    0.00   0.0  0
 CZ5  CONST_07  CAP  CAQ  CAR  CAM    0.00   0.0  0
 CZ5  CONST_10  CAP  NAO  CAN  CAM    0.00   0.0  0
 CZ5  CONST_11  CAQ  CAP  NAO  CAN    0.00   0.0  0
 CZ5  CONST_12  CAQ  CAR  CAM  CAN    0.00   0.0  0
 CZ5  CONST_13  NAS  CAR  CAM  CAN  180.00   0.0  0
 CZ5  CONST_14  CAR  CAQ  CAP  NAO    0.00   0.0  0
 CZ5  CONST_15  CAR  CAM  CAN  NAO    0.00   0.0  0
 CZ5  CONST_16  NAS  CAR  CAQ  CAP  180.00   0.0  0
 CZ5  CONST_19  CAV  CAW  NAS  CAR  180.00   0.0  0
 CZ5  CONST_20  CAU  NAT  NAS  CAR  180.00   0.0  0
 CZ5  CONST_21  CAU  CAV  CAW  NAS    0.00   0.0  0
 CZ5  CONST_22  CAV  CAU  NAT  NAS    0.00   0.0  0
 CZ5  CONST_23  CAV  CAW  NAS  NAT    0.00   0.0  0
 CZ5  CONST_24  CAW  CAV  CAU  NAT    0.00   0.0  0
 CZ5  CONST_25  CAW  NAS  NAT  CAU    0.00   0.0  0
 CZ5  CONST_26  NAH  CAE  CAF  CAA  180.00   0.0  0
 CZ5  CONST_27  NAH  CAE  CAD  NAC  180.00   0.0  0
 CZ5  CONST_28  CAQ  CAR  CAM  CAK  180.00   0.0  0
 CZ5  CONST_29  NAS  CAR  CAM  CAK    0.00   0.0  0
 CZ5  CONST_30  NAO  CAN  CAM  CAK  180.00   0.0  0
 CZ5  CONST_31  NAX  CAP  NAO  CAN  180.00   0.0  0
 CZ5  CONST_32  CAR  CAQ  CAP  NAX  180.00   0.0  0
 CZ5  CONST_33  H4   CAD  CAE  CAF  180.00   0.0  0
 CZ5  CONST_34  H3   CAB  CAA  CAF  180.00   0.0  0
 CZ5  CONST_35  H1   CAF  CAA  CAB  180.00   0.0  0
 CZ5  CONST_36  H2   CAA  CAB  NAC  180.00   0.0  0
 CZ5  CONST_37  H14  CAQ  CAR  CAM  180.00   0.0  0
 CZ5  CONST_38  H6   CAN  NAO  CAP  180.00   0.0  0
 CZ5  CONST_39  H17  CAW  NAS  CAR    0.00   0.0  0
 CZ5  CONST_40  H16  CAV  CAW  NAS  180.00   0.0  0
 CZ5  CONST_41  H15  CAU  NAT  NAS  180.00   0.0  0
 CZ5  CONST_42  CAM  CAK  NAH  CAE  180.00   0.0  0
 CZ5  CONST_43  CAK  NAH  CAE  CAF    0.00   0.0  0
 CZ5  CONST_44  CAK  NAH  CAE  CAD  180.00   0.0  0
 CZ5  CONST_47  H5   NAH  CAE  CAF  180.00   0.0  0
 CZ5  CONST_48  H7   NAX  CAP  NAO  180.00   0.0  0
 CZ5  CONST_49  OAL  CAK  NAH  CAE    0.00   0.0  0
 CZ5  CONST_50  OBA  CAY  NAX  CAP    0.00   0.0  0
 CZ5  CONST_51  NAZ  CAY  NAX  CAP  180.00   0.0  0
 CZ5  CONST_52  CBB  NAZ  CAY  OBA    0.00   0.0  0
 CZ5  CONST_53  CBB  NAZ  CAY  NAX  180.00   0.0  0
 CZ5  CONST_54  H8   NAZ  CAY  OBA  180.00   0.0  0
 CZ5  Var_01    CAR  CAM  CAK  NAH  125.53  30.0  2
 CZ5  Var_02    CBC  CBB  NAZ  CAY  165.43  30.0  2
 CZ5  Var_03    H11  CBC  CBB  NAZ  -61.06  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
 CZ5  plan-1  CAR  0.020
 CZ5  plan-1  NAS  0.020
 CZ5  plan-1  NAT  0.020
 CZ5  plan-1  CAU  0.020
 CZ5  plan-1  CAV  0.020
 CZ5  plan-1  CAW  0.020
 CZ5  plan-1  H15  0.020
 CZ5  plan-1  H16  0.020
 CZ5  plan-1  H17  0.020
 CZ5  plan-2  CAF  0.020
 CZ5  plan-2  CAA  0.020
 CZ5  plan-2  CAB  0.020
 CZ5  plan-2  NAC  0.020
 CZ5  plan-2  CAD  0.020
 CZ5  plan-2  CAE  0.020
 CZ5  plan-2  NAH  0.020
 CZ5  plan-2  H1   0.020
 CZ5  plan-2  H2   0.020
 CZ5  plan-2  H3   0.020
 CZ5  plan-2  H4   0.020
 CZ5  plan-3  CAK  0.020
 CZ5  plan-3  CAM  0.020
 CZ5  plan-3  CAN  0.020
 CZ5  plan-3  NAO  0.020
 CZ5  plan-3  CAP  0.020
 CZ5  plan-3  NAX  0.020
 CZ5  plan-3  CAQ  0.020
 CZ5  plan-3  CAR  0.020
 CZ5  plan-3  NAS  0.020
 CZ5  plan-3  H6   0.020
 CZ5  plan-3  H14  0.020
 CZ5  plan-4  CAE  0.020
 CZ5  plan-4  NAH  0.020
 CZ5  plan-4  CAK  0.020
 CZ5  plan-4  OAL  0.020
 CZ5  plan-4  CAM  0.020
 CZ5  plan-4  H5   0.020
 CZ5  plan-5  CAP  0.020
 CZ5  plan-5  NAX  0.020
 CZ5  plan-5  CAY  0.020
 CZ5  plan-5  OBA  0.020
 CZ5  plan-5  NAZ  0.020
 CZ5  plan-5  CBB  0.020
 CZ5  plan-5  H7   0.020
 CZ5  plan-5  H8   0.020

