# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 14:22:19 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-(cyclopropylcarbonylamino)-5-[methyl(pyridin-3-ylmethyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1cccnc1)c2ccc(NC(=O)C3CC3)c(c2)C(O)=O
#
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
 1X5  1X5  '2-(cyclopropylcarbonylamino)-5-[methyl(pyridin-3-ylmethyl)amino]benzoic acid'  ligand  42  24  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1X5
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
 1X5  CAA   C  CR6    0   0.290  -1.5288   0.1865   0.2277
 1X5  CAB   C  CR6    0  -0.198  -1.1634   1.4600  -0.2539
 1X5  CAC   C  CR16   0  -0.315  -0.5506  -0.5846   0.8578
 1X5  NAD   N  NH1    0  -0.775  -2.8497  -0.2329   0.0459
 1X5  CAE   C  CR16   0  -0.411   0.1438   1.9031  -0.0832
 1X5  CAF   C  C      0   0.465  -2.1336   2.4024  -0.9668
 1X5  CAG   C  CR16   0  -0.330   0.7435  -0.1235   1.0158
 1X5  CAH   C  CR6    0   0.411   1.1291   1.1436   0.5568
 1X5  OAI   O  OC    -1  -0.561  -1.6895   3.4885  -1.3625
 1X5  OAJ   O  O      0  -0.604  -3.3247   2.0155  -1.1063
 1X5  CAK   C  CR6    0  -0.000   3.9127  -0.3300   0.3610
 1X5  CAL   C  CR16   0  -0.184   4.6318  -1.4048   0.8716
 1X5  CAM   C  CR16   0  -0.084   3.6840  -0.3141  -1.0101
 1X5  CAN   C  CH2    0  -0.389   3.4332   0.7764   1.2739
 1X5  CAO   C  CR16   0  -0.317   5.0885  -2.3894   0.0117
 1X5  NAP   N  N      0  -0.401   4.1158  -1.2529  -1.8453
 1X5  NAQ   N  NT     0  -0.517   2.4102   1.6268   0.7297
 1X5  CAR   C  CR16   0  -0.077   4.8054  -2.2680  -1.3411
 1X5  CAS   C  CH3    0  -0.543   2.7895   2.8842   0.1314
 1X5  CAT   C  CH1    0  -0.428  -4.8862  -1.4472   0.0096
 1X5  CAU   C  C      0   0.571  -3.4436  -1.3929   0.3819
 1X5  CAV   C  CH2    0  -0.466  -5.8138  -2.2440   0.8879
 1X5  CAW   C  CH2    0  -0.467  -5.4463  -2.7672  -0.4526
 1X5  OAX   O  O      0  -0.504  -2.8902  -2.3364   0.9377
 1X5  HAC   H  HCR6   0   0.272  -0.7932  -1.5655   1.2322
 1X5  HNAD  H  HNH1   0   0.423  -3.3876   0.5064  -0.4359
 1X5  HAE   H  HCR6   0   0.261   0.3784   2.8823  -0.4735
 1X5  HAG   H  HCR6   0   0.257   1.4478  -0.7803   1.5077
 1X5  HAL   H  HCR6   0   0.267   4.8309  -1.4729   1.9351
 1X5  HAM   H  HCR6   0   0.254   3.1194   0.4964  -1.4587
 1X5  HAN   H  HCH2   0   0.260   3.1027   0.3390   2.2216
 1X5  HANA  H  HCH2   0   0.284   4.2871   1.4041   1.5361
 1X5  HAO   H  HCR6   0   0.270   5.6482  -3.2387   0.3792
 1X5  HAR   H  HCR6   0   0.262   5.1465  -3.0215  -2.0425
 1X5  HAS   H  HCH3   0   0.239   2.1965   3.7147   0.5233
 1X5  HASA  H  HCH3   0   0.257   3.8316   3.0883   0.3629
 1X5  HASB  H  HCH3   0   0.227   2.6849   2.8885  -0.9592
 1X5  HAT   H  HCH1   0   0.274  -5.3017  -0.5584  -0.4509
 1X5  HAV   H  HCH2   0   0.254  -5.3824  -2.7223   1.7575
 1X5  HAVA  H  HCH2   0   0.260  -6.8098  -1.8482   1.0353
 1X5  HAW   H  HCH2   0   0.260  -6.1845  -2.7352  -1.2425
 1X5  HAWA  H  HCH2   0   0.254  -4.7629  -3.6048  -0.5040

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
 1X5  CAB  CAA   aromatic  1.410  0.020  1.410
 1X5  NAD  CAA   single    1.398  0.020  1.398
 1X5  CAA  CAC   aromatic  1.396  0.020  1.396
 1X5  CAF  CAB   single    1.529  0.020  1.529
 1X5  CAE  CAB   aromatic  1.391  0.020  1.391
 1X5  CAG  CAC   aromatic  1.383  0.020  1.383
 1X5  CAC  HAC   single    0.930  0.020  1.080
 1X5  NAD  CAU   single    1.346  0.020  1.346
 1X5  NAD  HNAD  single    0.860  0.020  1.020
 1X5  CAE  CAH   aromatic  1.399  0.020  1.399
 1X5  CAE  HAE   single    0.930  0.020  1.080
 1X5  OAJ  CAF   deloc     1.260  0.020  1.260
 1X5  CAF  OAI   deloc     1.238  0.020  1.238
 1X5  CAH  CAG   aromatic  1.402  0.020  1.402
 1X5  CAG  HAG   single    0.930  0.020  1.080
 1X5  NAQ  CAH   single    1.380  0.020  1.380
 1X5  CAN  CAK   single    1.512  0.020  1.512
 1X5  CAM  CAK   aromatic  1.390  0.020  1.390
 1X5  CAK  CAL   aromatic  1.390  0.020  1.390
 1X5  CAL  CAO   aromatic  1.385  0.020  1.385
 1X5  CAL  HAL   single    0.930  0.020  1.080
 1X5  CAM  NAP   aromatic  1.329  0.020  1.329
 1X5  CAM  HAM   single    0.930  0.020  1.080
 1X5  NAQ  CAN   single    1.437  0.020  1.437
 1X5  CAN  HAN   single    0.970  0.020  1.090
 1X5  CAN  HANA  single    0.970  0.020  1.090
 1X5  CAR  CAO   aromatic  1.387  0.020  1.387
 1X5  CAO  HAO   single    0.930  0.020  1.080
 1X5  NAP  CAR   aromatic  1.327  0.020  1.327
 1X5  CAS  NAQ   single    1.443  0.020  1.443
 1X5  CAR  HAR   single    0.930  0.020  1.080
 1X5  CAS  HAS   single    0.970  0.020  1.090
 1X5  CAS  HASA  single    0.970  0.020  1.090
 1X5  CAS  HASB  single    0.970  0.020  1.090
 1X5  CAT  CAU   single    1.491  0.020  1.491
 1X5  CAT  CAW   single    1.507  0.020  1.507
 1X5  CAT  CAV   single    1.506  0.020  1.506
 1X5  CAT  HAT   single    0.970  0.020  1.090
 1X5  CAU  OAX   double    1.227  0.020  1.227
 1X5  CAW  CAV   single    1.485  0.020  1.485
 1X5  CAV  HAV   single    0.970  0.020  1.090
 1X5  CAV  HAVA  single    0.970  0.020  1.090
 1X5  CAW  HAW   single    0.970  0.020  1.090
 1X5  CAW  HAWA  single    0.970  0.020  1.090

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
 1X5  NAD   CAA  CAC   123.72  3.000
 1X5  CAC   CAA  CAB   118.14  3.000
 1X5  NAD   CAA  CAB   118.14  3.000
 1X5  CAF   CAB  CAE   117.21  3.000
 1X5  CAE   CAB  CAA   119.31  3.000
 1X5  CAF   CAB  CAA   123.48  3.000
 1X5  HAC   CAC  CAG   118.33  3.000
 1X5  HAC   CAC  CAA   120.13  3.000
 1X5  CAG   CAC  CAA   121.54  3.000
 1X5  HNAD  NAD  CAU   120.22  3.000
 1X5  HNAD  NAD  CAA   109.75  3.000
 1X5  CAU   NAD  CAA   130.03  3.000
 1X5  HAE   CAE  CAH   120.30  3.000
 1X5  HAE   CAE  CAB   116.66  3.000
 1X5  CAH   CAE  CAB   123.03  3.000
 1X5  OAJ   CAF  OAI   124.95  3.000
 1X5  OAI   CAF  CAB   117.52  3.000
 1X5  OAJ   CAF  CAB   117.53  3.000
 1X5  HAG   CAG  CAH   121.25  3.000
 1X5  HAG   CAG  CAC   117.32  3.000
 1X5  CAH   CAG  CAC   121.43  3.000
 1X5  NAQ   CAH  CAG   122.06  3.000
 1X5  NAQ   CAH  CAE   121.40  3.000
 1X5  CAG   CAH  CAE   116.54  3.000
 1X5  CAN   CAK  CAM   122.33  3.000
 1X5  CAM   CAK  CAL   117.14  3.000
 1X5  CAN   CAK  CAL   120.52  3.000
 1X5  HAL   CAL  CAO   120.27  3.000
 1X5  HAL   CAL  CAK   120.25  3.000
 1X5  CAO   CAL  CAK   119.48  3.000
 1X5  HAM   CAM  NAP   115.92  3.000
 1X5  HAM   CAM  CAK   120.13  3.000
 1X5  NAP   CAM  CAK   123.95  3.000
 1X5  HANA  CAN  HAN   104.94  3.000
 1X5  HANA  CAN  NAQ   107.90  3.000
 1X5  HAN   CAN  NAQ   110.44  3.000
 1X5  HANA  CAN  CAK   108.52  3.000
 1X5  HAN   CAN  CAK   109.02  3.000
 1X5  NAQ   CAN  CAK   115.46  3.000
 1X5  HAO   CAO  CAR   120.37  3.000
 1X5  HAO   CAO  CAL   121.20  3.000
 1X5  CAR   CAO  CAL   118.42  3.000
 1X5  CAR   NAP  CAM   118.07  3.000
 1X5  CAS   NAQ  CAN   119.04  3.000
 1X5  CAS   NAQ  CAH   119.81  3.000
 1X5  CAN   NAQ  CAH   120.06  3.000
 1X5  HAR   CAR  NAP   116.70  3.000
 1X5  HAR   CAR  CAO   120.37  3.000
 1X5  NAP   CAR  CAO   122.93  3.000
 1X5  HASB  CAS  HASA  107.63  3.000
 1X5  HASB  CAS  HAS   107.58  3.000
 1X5  HASA  CAS  HAS   107.52  3.000
 1X5  HASB  CAS  NAQ   113.02  3.000
 1X5  HASA  CAS  NAQ   109.10  3.000
 1X5  HAS   CAS  NAQ   111.76  3.000
 1X5  HAT   CAT  CAW   116.46  3.000
 1X5  HAT   CAT  CAV   116.47  3.000
 1X5  CAW   CAT  CAV    59.08  3.000
 1X5  HAT   CAT  CAU   116.57  3.000
 1X5  CAV   CAT  CAU   118.02  3.000
 1X5  CAW   CAT  CAU   117.92  3.000
 1X5  OAX   CAU  CAT   121.43  3.000
 1X5  OAX   CAU  NAD   125.23  3.000
 1X5  CAT   CAU  NAD   113.33  3.000
 1X5  HAVA  CAV  HAV   114.79  3.000
 1X5  HAVA  CAV  CAW   118.66  3.000
 1X5  HAV   CAV  CAW   118.09  3.000
 1X5  HAVA  CAV  CAT   116.94  3.000
 1X5  HAV   CAV  CAT   117.20  3.000
 1X5  CAW   CAV  CAT    60.49  3.000
 1X5  HAWA  CAW  HAW   114.78  3.000
 1X5  HAWA  CAW  CAV   118.15  3.000
 1X5  HAW   CAW  CAV   118.67  3.000
 1X5  HAWA  CAW  CAT   117.25  3.000
 1X5  HAW   CAW  CAT   116.86  3.000
 1X5  CAV   CAW  CAT    60.43  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
 1X5  CONST_01  CAH   CAE  CAB  CAA     0.00   0.0  0
 1X5  CONST_02  CAH   CAG  CAC  CAA     0.00   0.0  0
 1X5  CONST_03  CAG   CAC  CAA  CAB     0.00   0.0  0
 1X5  CONST_04  CAG   CAH  CAE  CAB     0.00   0.0  0
 1X5  CONST_05  CAE   CAB  CAA  CAC     0.00   0.0  0
 1X5  CONST_06  CAE   CAH  CAG  CAC     0.00   0.0  0
 1X5  CONST_07  CAR   NAP  CAM  CAK     0.00   0.0  0
 1X5  CONST_08  CAR   CAO  CAL  CAK     0.00   0.0  0
 1X5  CONST_09  NAP   CAM  CAK  CAL     0.00   0.0  0
 1X5  CONST_10  NAP   CAR  CAO  CAL     0.00   0.0  0
 1X5  CONST_11  CAO   CAL  CAK  CAM     0.00   0.0  0
 1X5  CONST_12  CAO   CAR  NAP  CAM     0.00   0.0  0
 1X5  CONST_13  NAQ   CAH  CAE  CAB   180.00   0.0  0
 1X5  CONST_14  CAF   CAB  CAA  CAC   180.00   0.0  0
 1X5  CONST_15  NAQ   CAH  CAG  CAC   180.00   0.0  0
 1X5  CONST_16  CAE   CAB  CAA  NAD   180.00   0.0  0
 1X5  CONST_17  CAG   CAC  CAA  NAD   180.00   0.0  0
 1X5  CONST_18  CAH   CAE  CAB  CAF   180.00   0.0  0
 1X5  CONST_19  NAP   CAM  CAK  CAN   180.00   0.0  0
 1X5  CONST_20  CAO   CAL  CAK  CAN   180.00   0.0  0
 1X5  CONST_21  HAE   CAE  CAB  CAA   180.00   0.0  0
 1X5  CONST_22  HAG   CAG  CAC  CAA   180.00   0.0  0
 1X5  CONST_23  HAC   CAC  CAA  CAB   180.00   0.0  0
 1X5  CONST_24  HAO   CAO  CAL  CAK   180.00   0.0  0
 1X5  CONST_25  HAM   CAM  CAK  CAL   180.00   0.0  0
 1X5  CONST_26  HAR   CAR  CAO  CAL   180.00   0.0  0
 1X5  CONST_27  HAL   CAL  CAK  CAM   180.00   0.0  0
 1X5  CONST_28  CAT   CAU  NAD  CAA   180.00   0.0  0
 1X5  CONST_29  CAU   NAD  CAA  CAB   180.00   0.0  0
 1X5  CONST_30  CAU   NAD  CAA  CAC     0.00   0.0  0
 1X5  CONST_31  CAN   NAQ  CAH  CAE   180.00   0.0  0
 1X5  CONST_32  CAS   NAQ  CAH  CAE     0.00   0.0  0
 1X5  CONST_33  CAN   NAQ  CAH  CAG     0.00   0.0  0
 1X5  CONST_34  CAS   NAQ  CAH  CAG   180.00   0.0  0
 1X5  CONST_35  HNAD  NAD  CAA  CAB     0.00   0.0  0
 1X5  CONST_36  OAX   CAU  NAD  CAA     0.00   0.0  0
 1X5  Var_01    CAV   CAW  CAT  CAU   107.60  30.0  1
 1X5  Var_02    HAV   CAV  CAW  CAT  -107.05  30.0  1
 1X5  Var_03    OAJ   CAF  CAB  CAA     1.11  30.0  3
 1X5  Var_04    CAW   CAT  CAU  NAD   144.10  30.0  1
 1X5  Var_05    CAK   CAN  NAQ  CAH    71.12  30.0  3
 1X5  Var_06    NAQ   CAN  CAK  CAL  -163.63  30.0  3
 1X5  Var_07    HAS   CAS  NAQ  CAH    62.12  30.0  3

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
 1X5  chir_01  CAT  CAU  CAW  CAV  both

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
 1X5  plan-1  CAA   0.020
 1X5  plan-1  CAB   0.020
 1X5  plan-1  CAC   0.020
 1X5  plan-1  NAD   0.020
 1X5  plan-1  CAE   0.020
 1X5  plan-1  CAF   0.020
 1X5  plan-1  CAG   0.020
 1X5  plan-1  CAH   0.020
 1X5  plan-1  NAQ   0.020
 1X5  plan-1  HAC   0.020
 1X5  plan-1  HAE   0.020
 1X5  plan-1  HAG   0.020
 1X5  plan-2  CAK   0.020
 1X5  plan-2  CAL   0.020
 1X5  plan-2  CAM   0.020
 1X5  plan-2  CAN   0.020
 1X5  plan-2  CAO   0.020
 1X5  plan-2  NAP   0.020
 1X5  plan-2  CAR   0.020
 1X5  plan-2  HAL   0.020
 1X5  plan-2  HAM   0.020
 1X5  plan-2  HAO   0.020
 1X5  plan-2  HAR   0.020
 1X5  plan-3  CAH   0.020
 1X5  plan-3  CAN   0.020
 1X5  plan-3  NAQ   0.020
 1X5  plan-3  CAS   0.020
 1X5  plan-4  CAA   0.020
 1X5  plan-4  NAD   0.020
 1X5  plan-4  CAT   0.020
 1X5  plan-4  CAU   0.020
 1X5  plan-4  OAX   0.020
 1X5  plan-4  HNAD  0.020
 1X5  plan-5  CAB   0.020
 1X5  plan-5  CAF   0.020
 1X5  plan-5  OAI   0.020
 1X5  plan-5  OAJ   0.020

