# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:07:47 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5-[methyl(pyridin-3-ylmethyl)amino]-2-(propanoylamino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccc(cc1C(O)=O)N(C)Cc2cccnc2
#
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
 7Z5  7Z5  '5-[methyl(pyridin-3-ylmethyl)amino]-2-(propanoylamino)benzoic acid'  ligand  42  23  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7Z5
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
 7Z5  CAA   C  CR6   0  -0.150  -1.3806   1.2114  -0.2178
 7Z5  CAB   C  CR6   0   0.328  -1.7455  -0.0962   0.1655
 7Z5  CAC   C  CR16  0  -0.400  -0.0950   1.6918   0.0481
 7Z5  CAD   C  C     0   0.582  -2.3327   2.1030  -0.9205
 7Z5  CAE   C  CR16  0  -0.306  -0.7677  -0.8709   0.7953
 7Z5  NAF   N  NH1   0  -0.765  -3.0274  -0.5763  -0.0990
 7Z5  CAG   C  CR6   0   0.424   0.8719   0.9240   0.6970
 7Z5  OAH   O  O     0  -0.466  -3.4424   1.7750  -1.2949
 7Z5  OAI   O  OH1   0  -0.587  -1.8691   3.3251  -1.1204
 7Z5  CAJ   C  CR16  0  -0.310   0.4966  -0.3824   1.0486
 7Z5  CAK   C  C     0   0.550  -3.6494  -1.6867   0.3805
 7Z5  NAL   N  NT    0  -0.519   2.1215   1.4255   0.9780
 7Z5  CAM   C  CH2   0  -0.589  -5.0953  -1.7903  -0.0615
 7Z5  OAN   O  O     0  -0.471  -3.1252  -2.5140   1.1045
 7Z5  CAO   C  CH2   0  -0.395   3.1537   0.5492   1.4674
 7Z5  CAP   C  CH3   0  -0.552   2.4750   2.7554   0.5395
 7Z5  CAQ   C  CH3   0  -0.658  -5.7119  -3.1524   0.2004
 7Z5  CAR   C  CR6   0  -0.000   3.6536  -0.4646   0.4633
 7Z5  CAS   C  CR16  0  -0.172   3.5717  -0.2630  -0.9080
 7Z5  CAT   C  CR16  0  -0.096   4.2441  -1.6469   0.8982
 7Z5  CAU   C  CR16  0  -0.315   4.0833  -1.2251  -1.7650
 7Z5  NAV   N  N     0  -0.400   4.7405  -2.5737   0.0892
 7Z5  CAW   C  CR16  0  -0.075   4.6610  -2.3613  -1.2194
 7Z5  HAC   H  HCR6  0   0.285   0.1501   2.6924  -0.2709
 7Z5  HAE   H  HCR6  0   0.286  -0.9897  -1.8813   1.0933
 7Z5  HNAF  H  HNH1  0   0.425  -3.5880   0.0514  -0.6634
 7Z5  HOAI  H  HOH1  0   0.492  -2.5319   3.8533  -1.5903
 7Z5  HAJ   H  HCR6  0   0.273   1.1946  -1.0502   1.5338
 7Z5  HAM   H  HCH2  0   0.275  -5.6594  -1.0157   0.4682
 7Z5  HAMA  H  HCH2  0   0.262  -5.1696  -1.5365  -1.1222
 7Z5  HAO   H  HCH2  0   0.289   3.9913   1.1698   1.7899
 7Z5  HAOA  H  HCH2  0   0.264   2.8209   0.0296   2.3718
 7Z5  HAP   H  HCH3  0   0.245   1.8078   3.5086   0.9659
 7Z5  HAPA  H  HCH3  0   0.264   3.4820   2.9849   0.8765
 7Z5  HAPB  H  HCH3  0   0.231   2.4534   2.8683  -0.5501
 7Z5  HAQ   H  HCH3  0   0.230  -5.6891  -3.4078   1.2588
 7Z5  HAQA  H  HCH3  0   0.236  -6.7534  -3.1549  -0.1186
 7Z5  HAQB  H  HCH3  0   0.229  -5.1951  -3.9402  -0.3470
 7Z5  HAS   H  HCR6  0   0.266   3.1130   0.6312  -1.3108
 7Z5  HAT   H  HCR6  0   0.258   4.3132  -1.8526   1.9628
 7Z5  HAU   H  HCR6  0   0.271   4.0352  -1.0985  -2.8379
 7Z5  HAW   H  HCR6  0   0.263   5.0710  -3.1312  -1.8634

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
 7Z5  CAD  CAA   single    1.482  0.020  1.482
 7Z5  CAC  CAA   aromatic  1.398  0.020  1.398
 7Z5  CAA  CAB   aromatic  1.411  0.020  1.411
 7Z5  CAB  NAF   single    1.394  0.020  1.394
 7Z5  CAB  CAE   aromatic  1.397  0.020  1.397
 7Z5  CAC  CAG   aromatic  1.395  0.020  1.395
 7Z5  CAC  HAC   single    0.930  0.020  1.080
 7Z5  OAH  CAD   double    1.216  0.020  1.216
 7Z5  CAD  OAI   single    1.322  0.020  1.322
 7Z5  CAJ  CAE   aromatic  1.379  0.020  1.379
 7Z5  CAE  HAE   single    0.930  0.020  1.080
 7Z5  NAF  CAK   single    1.360  0.020  1.360
 7Z5  NAF  HNAF  single    0.860  0.020  1.020
 7Z5  NAL  CAG   single    1.375  0.020  1.375
 7Z5  CAG  CAJ   aromatic  1.404  0.020  1.404
 7Z5  OAI  HOAI  single    0.850  0.020  0.980
 7Z5  CAJ  HAJ   single    0.930  0.020  1.080
 7Z5  CAM  CAK   single    1.516  0.020  1.516
 7Z5  CAK  OAN   double    1.218  0.020  1.218
 7Z5  CAP  NAL   single    1.444  0.020  1.444
 7Z5  NAL  CAO   single    1.440  0.020  1.440
 7Z5  CAQ  CAM   single    1.518  0.020  1.518
 7Z5  CAM  HAM   single    0.970  0.020  1.090
 7Z5  CAM  HAMA  single    0.970  0.020  1.090
 7Z5  CAO  CAR   single    1.512  0.020  1.512
 7Z5  CAO  HAO   single    0.970  0.020  1.090
 7Z5  CAO  HAOA  single    0.970  0.020  1.090
 7Z5  CAP  HAP   single    0.970  0.020  1.090
 7Z5  CAP  HAPA  single    0.970  0.020  1.090
 7Z5  CAP  HAPB  single    0.970  0.020  1.090
 7Z5  CAQ  HAQ   single    0.970  0.020  1.090
 7Z5  CAQ  HAQA  single    0.970  0.020  1.090
 7Z5  CAQ  HAQB  single    0.970  0.020  1.090
 7Z5  CAS  CAR   aromatic  1.389  0.020  1.389
 7Z5  CAR  CAT   aromatic  1.391  0.020  1.391
 7Z5  CAS  CAU   aromatic  1.386  0.020  1.386
 7Z5  CAS  HAS   single    0.930  0.020  1.080
 7Z5  CAT  NAV   aromatic  1.327  0.020  1.327
 7Z5  CAT  HAT   single    0.930  0.020  1.080
 7Z5  CAU  CAW   aromatic  1.386  0.020  1.386
 7Z5  CAU  HAU   single    0.930  0.020  1.080
 7Z5  CAW  NAV   aromatic  1.328  0.020  1.328
 7Z5  CAW  HAW   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
 7Z5  CAD   CAA  CAC   118.32  3.000
 7Z5  CAC   CAA  CAB   120.32  3.000
 7Z5  CAD   CAA  CAB   121.36  3.000
 7Z5  NAF   CAB  CAE   122.55  3.000
 7Z5  CAE   CAB  CAA   117.08  3.000
 7Z5  NAF   CAB  CAA   120.36  3.000
 7Z5  HAC   CAC  CAG   119.39  3.000
 7Z5  HAC   CAC  CAA   118.14  3.000
 7Z5  CAG   CAC  CAA   122.47  3.000
 7Z5  OAI   CAD  OAH   121.51  3.000
 7Z5  OAI   CAD  CAA   113.74  3.000
 7Z5  OAH   CAD  CAA   124.75  3.000
 7Z5  HAE   CAE  CAJ   118.08  3.000
 7Z5  HAE   CAE  CAB   120.05  3.000
 7Z5  CAJ   CAE  CAB   121.87  3.000
 7Z5  HNAF  NAF  CAK   116.68  3.000
 7Z5  HNAF  NAF  CAB   113.65  3.000
 7Z5  CAK   NAF  CAB   129.40  3.000
 7Z5  NAL   CAG  CAJ   122.07  3.000
 7Z5  CAJ   CAG  CAC   116.32  3.000
 7Z5  NAL   CAG  CAC   121.61  3.000
 7Z5  HOAI  OAI  CAD   109.71  3.000
 7Z5  HAJ   CAJ  CAG   120.98  3.000
 7Z5  HAJ   CAJ  CAE   117.10  3.000
 7Z5  CAG   CAJ  CAE   121.92  3.000
 7Z5  OAN   CAK  CAM   122.52  3.000
 7Z5  OAN   CAK  NAF   124.57  3.000
 7Z5  CAM   CAK  NAF   112.91  3.000
 7Z5  CAP   NAL  CAO   119.22  3.000
 7Z5  CAO   NAL  CAG   119.93  3.000
 7Z5  CAP   NAL  CAG   119.74  3.000
 7Z5  HAMA  CAM  HAM   105.67  3.000
 7Z5  HAMA  CAM  CAQ   110.37  3.000
 7Z5  HAM   CAM  CAQ   110.01  3.000
 7Z5  HAMA  CAM  CAK   109.39  3.000
 7Z5  HAM   CAM  CAK   107.58  3.000
 7Z5  CAQ   CAM  CAK   113.49  3.000
 7Z5  HAOA  CAO  HAO   105.02  3.000
 7Z5  HAOA  CAO  CAR   109.32  3.000
 7Z5  HAO   CAO  CAR   108.90  3.000
 7Z5  HAOA  CAO  NAL   110.59  3.000
 7Z5  HAO   CAO  NAL   107.74  3.000
 7Z5  CAR   CAO  NAL   114.80  3.000
 7Z5  HAPB  CAP  HAPA  107.76  3.000
 7Z5  HAPB  CAP  HAP   107.75  3.000
 7Z5  HAPA  CAP  HAP   107.41  3.000
 7Z5  HAPB  CAP  NAL   113.08  3.000
 7Z5  HAPA  CAP  NAL   109.10  3.000
 7Z5  HAP   CAP  NAL   111.52  3.000
 7Z5  HAQB  CAQ  HAQA  107.74  3.000
 7Z5  HAQB  CAQ  HAQ   107.99  3.000
 7Z5  HAQA  CAQ  HAQ   107.70  3.000
 7Z5  HAQB  CAQ  CAM   111.68  3.000
 7Z5  HAQA  CAQ  CAM   109.87  3.000
 7Z5  HAQ   CAQ  CAM   111.69  3.000
 7Z5  CAT   CAR  CAS   117.20  3.000
 7Z5  CAT   CAR  CAO   120.18  3.000
 7Z5  CAS   CAR  CAO   122.62  3.000
 7Z5  HAS   CAS  CAU   119.97  3.000
 7Z5  HAS   CAS  CAR   120.82  3.000
 7Z5  CAU   CAS  CAR   119.21  3.000
 7Z5  HAT   CAT  NAV   116.20  3.000
 7Z5  HAT   CAT  CAR   119.61  3.000
 7Z5  NAV   CAT  CAR   124.19  3.000
 7Z5  HAU   CAU  CAW   120.32  3.000
 7Z5  HAU   CAU  CAS   121.05  3.000
 7Z5  CAW   CAU  CAS   118.64  3.000
 7Z5  CAW   NAV  CAT   117.82  3.000
 7Z5  HAW   CAW  NAV   116.68  3.000
 7Z5  HAW   CAW  CAU   120.38  3.000
 7Z5  NAV   CAW  CAU   122.94  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
 7Z5  CONST_01  CAJ   CAG  CAC  CAA    0.00   0.0  0
 7Z5  CONST_02  CAJ   CAE  CAB  CAA    0.00   0.0  0
 7Z5  CONST_03  CAG   CAC  CAA  CAB    0.00   0.0  0
 7Z5  CONST_04  CAG   CAJ  CAE  CAB    0.00   0.0  0
 7Z5  CONST_05  CAE   CAB  CAA  CAC    0.00   0.0  0
 7Z5  CONST_06  CAE   CAJ  CAG  CAC    0.00   0.0  0
 7Z5  CONST_07  CAW   CAU  CAS  CAR    0.00   0.0  0
 7Z5  CONST_08  CAW   NAV  CAT  CAR    0.00   0.0  0
 7Z5  CONST_09  NAV   CAT  CAR  CAS    0.00   0.0  0
 7Z5  CONST_10  NAV   CAW  CAU  CAS    0.00   0.0  0
 7Z5  CONST_11  CAU   CAS  CAR  CAT    0.00   0.0  0
 7Z5  CONST_12  CAU   CAW  NAV  CAT    0.00   0.0  0
 7Z5  CONST_13  NAL   CAG  CAC  CAA  180.00   0.0  0
 7Z5  CONST_14  NAF   CAB  CAA  CAC  180.00   0.0  0
 7Z5  CONST_15  CAG   CAC  CAA  CAD  180.00   0.0  0
 7Z5  CONST_16  CAE   CAB  CAA  CAD  180.00   0.0  0
 7Z5  CONST_17  NAL   CAG  CAJ  CAE  180.00   0.0  0
 7Z5  CONST_18  CAJ   CAE  CAB  NAF  180.00   0.0  0
 7Z5  CONST_19  CAU   CAS  CAR  CAO  180.00   0.0  0
 7Z5  CONST_20  NAV   CAT  CAR  CAO  180.00   0.0  0
 7Z5  CONST_21  HAE   CAE  CAB  CAA  180.00   0.0  0
 7Z5  CONST_22  HAC   CAC  CAA  CAB  180.00   0.0  0
 7Z5  CONST_23  HAJ   CAJ  CAE  CAB  180.00   0.0  0
 7Z5  CONST_24  HAU   CAU  CAS  CAR  180.00   0.0  0
 7Z5  CONST_25  HAT   CAT  CAR  CAS  180.00   0.0  0
 7Z5  CONST_26  HAW   CAW  CAU  CAS  180.00   0.0  0
 7Z5  CONST_27  HAS   CAS  CAR  CAT  180.00   0.0  0
 7Z5  CONST_28  CAK   NAF  CAB  CAA  180.00   0.0  0
 7Z5  CONST_29  CAP   NAL  CAG  CAC    0.00   0.0  0
 7Z5  CONST_30  CAO   NAL  CAG  CAC  180.00   0.0  0
 7Z5  CONST_31  CAK   NAF  CAB  CAE    0.00   0.0  0
 7Z5  CONST_32  CAP   NAL  CAG  CAJ  180.00   0.0  0
 7Z5  CONST_33  CAO   NAL  CAG  CAJ    0.00   0.0  0
 7Z5  CONST_34  HNAF  NAF  CAB  CAA    0.00   0.0  0
 7Z5  CONST_35  CAM   CAK  NAF  CAB  180.00   0.0  0
 7Z5  CONST_36  OAN   CAK  NAF  CAB    0.00   0.0  0
 7Z5  CONST_37  HOAI  OAI  CAD  CAA  180.00   0.0  0
 7Z5  Var_01    OAH   CAD  CAA  CAB   -4.87  30.0  2
 7Z5  Var_02    CAR   CAO  NAL  CAG   68.45  30.0  3
 7Z5  Var_03    CAS   CAR  CAO  NAL   25.09  30.0  2
 7Z5  Var_04    HAP   CAP  NAL  CAG   59.86  30.0  3
 7Z5  Var_05    CAQ   CAM  CAK  NAF  167.28  30.0  2
 7Z5  Var_06    HAQ   CAQ  CAM  CAK   59.33  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
 7Z5  plan-1  CAA   0.020
 7Z5  plan-1  CAB   0.020
 7Z5  plan-1  CAC   0.020
 7Z5  plan-1  CAD   0.020
 7Z5  plan-1  CAE   0.020
 7Z5  plan-1  NAF   0.020
 7Z5  plan-1  CAG   0.020
 7Z5  plan-1  CAJ   0.020
 7Z5  plan-1  NAL   0.020
 7Z5  plan-1  HAC   0.020
 7Z5  plan-1  HAE   0.020
 7Z5  plan-1  HAJ   0.020
 7Z5  plan-2  CAO   0.020
 7Z5  plan-2  CAR   0.020
 7Z5  plan-2  CAS   0.020
 7Z5  plan-2  CAT   0.020
 7Z5  plan-2  CAU   0.020
 7Z5  plan-2  NAV   0.020
 7Z5  plan-2  CAW   0.020
 7Z5  plan-2  HAS   0.020
 7Z5  plan-2  HAT   0.020
 7Z5  plan-2  HAU   0.020
 7Z5  plan-2  HAW   0.020
 7Z5  plan-3  CAB   0.020
 7Z5  plan-3  NAF   0.020
 7Z5  plan-3  CAK   0.020
 7Z5  plan-3  CAM   0.020
 7Z5  plan-3  OAN   0.020
 7Z5  plan-3  HNAF  0.020
 7Z5  plan-4  CAG   0.020
 7Z5  plan-4  NAL   0.020
 7Z5  plan-4  CAO   0.020
 7Z5  plan-4  CAP   0.020
 7Z5  plan-5  CAA   0.020
 7Z5  plan-5  CAD   0.020
 7Z5  plan-5  OAH   0.020
 7Z5  plan-5  OAI   0.020
 7Z5  plan-5  HOAI  0.020

