# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:23:29 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  43  24  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.331  -1.5184   0.2148   0.1892
 1X5  CAB   C  CR6   0  -0.157  -1.1283   1.5304  -0.1399
 1X5  CAC   C  CR16  0  -0.309  -0.5439  -0.6175   0.7462
 1X5  NAD   N  NH1   0  -0.781  -2.8254  -0.2065  -0.0499
 1X5  CAE   C  CR16  0  -0.397   0.1788   1.9601   0.1045
 1X5  CAF   C  C     0   0.585  -2.0782   2.4868  -0.7556
 1X5  CAG   C  CR16  0  -0.312   0.7423  -0.1780   0.9797
 1X5  CAH   C  CR6   0   0.425   1.1440   1.1334   0.6805
 1X5  OAI   O  OH1   0  -0.586  -1.5666   3.6883  -0.9608
 1X5  OAJ   O  O     0  -0.466  -3.2268   2.2247  -1.0587
 1X5  CAK   C  CR6   0  -0.002   3.9156  -0.3222   0.3756
 1X5  CAL   C  CR16  0  -0.183   4.5718  -1.4823   0.7707
 1X5  CAM   C  CR16  0  -0.083   3.7558  -0.1166  -0.9900
 1X5  CAN   C  CH2   0  -0.394   3.4252   0.6711   1.4050
 1X5  CAO   C  CR16  0  -0.317   5.0384  -2.3619  -0.1914
 1X5  NAP   N  N     0  -0.400   4.1960  -0.9543  -1.9224
 1X5  NAQ   N  NT    0  -0.519   2.4159   1.5863   0.9415
 1X5  CAR   C  CR16  0  -0.075   4.8255  -2.0533  -1.5273
 1X5  CAS   C  CH3   0  -0.551   2.8073   2.9103   0.5173
 1X5  CAT   C  CH1   0  -0.439  -4.8614  -1.4308  -0.1281
 1X5  CAU   C  C     0   0.592  -3.4296  -1.3791   0.2720
 1X5  CAV   C  CH2   0  -0.463  -5.8022  -2.2395   0.7266
 1X5  CAW   C  CH2   0  -0.464  -5.4086  -2.7508  -0.6092
 1X5  OAX   O  O     0  -0.482  -2.8797  -2.3142   0.8331
 1X5  HAC   H  HCR6  0   0.289  -0.7869  -1.6343   1.0029
 1X5  HNAD  H  HNH1  0   0.428  -3.3967   0.4940  -0.5081
 1X5  HAE   H  HCR6  0   0.286   0.4422   2.9696  -0.1680
 1X5  HAG   H  HCR6  0   0.274   1.4360  -0.8899   1.4048
 1X5  HOAI  H  HOH1  0   0.492  -2.2335   4.2622  -1.3667
 1X5  HAL   H  HCR6  0   0.269   4.7131  -1.6987   1.8234
 1X5  HAM   H  HCR6  0   0.254   3.2436   0.7683  -1.3529
 1X5  HAN   H  HCH2  0   0.265   3.0725   0.1276   2.2875
 1X5  HANA  H  HCH2  0   0.290   4.2734   1.2600   1.7576
 1X5  HAO   H  HCR6  0   0.271   5.5513  -3.2731   0.0844
 1X5  HAR   H  HCR6  0   0.263   5.1735  -2.7220  -2.3068
 1X5  HAS   H  HCH3  0   0.245   2.1883   3.6820   0.9815
 1X5  HASA  H  HCH3  0   0.264   3.8350   3.0911   0.8199
 1X5  HASB  H  HCH3  0   0.231   2.7509   3.0436  -0.5684
 1X5  HAT   H  HCH1  0   0.280  -5.2725  -0.5404  -0.5891
 1X5  HAV   H  HCH2  0   0.258  -5.3861  -2.7215   1.6016
 1X5  HAVA  H  HCH2  0   0.265  -6.8004  -1.8437   0.8575
 1X5  HAW   H  HCH2  0   0.265  -6.1302  -2.7122  -1.4139
 1X5  HAWA  H  HCH2  0   0.259  -4.7203  -3.5846  -0.6555

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  1.411  0.020  1.411
 1X5  NAD  CAA   single    1.394  0.020  1.394
 1X5  CAA  CAC   aromatic  1.397  0.020  1.397
 1X5  CAF  CAB   single    1.482  0.020  1.482
 1X5  CAE  CAB   aromatic  1.397  0.020  1.397
 1X5  CAG  CAC   aromatic  1.379  0.020  1.379
 1X5  CAC  HAC   single    0.930  0.020  1.080
 1X5  NAD  CAU   single    1.358  0.020  1.358
 1X5  NAD  HNAD  single    0.860  0.020  1.020
 1X5  CAE  CAH   aromatic  1.395  0.020  1.395
 1X5  CAE  HAE   single    0.930  0.020  1.080
 1X5  OAJ  CAF   double    1.216  0.020  1.216
 1X5  CAF  OAI   single    1.322  0.020  1.322
 1X5  CAH  CAG   aromatic  1.404  0.020  1.404
 1X5  CAG  HAG   single    0.930  0.020  1.080
 1X5  NAQ  CAH   single    1.375  0.020  1.375
 1X5  OAI  HOAI  single    0.850  0.020  0.980
 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    1.439  0.020  1.439
 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    1.444  0.020  1.444
 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    1.487  0.020  1.487
 1X5  CAT  CAW   single    1.508  0.020  1.508
 1X5  CAT  CAV   single    1.507  0.020  1.507
 1X5  CAT  HAT   single    0.970  0.020  1.090
 1X5  CAU  OAX   double    1.221  0.020  1.221
 1X5  CAW  CAV   single    1.484  0.020  1.484
 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   122.84  3.000
 1X5  CAC   CAA  CAB   117.10  3.000
 1X5  NAD   CAA  CAB   120.06  3.000
 1X5  CAF   CAB  CAE   118.29  3.000
 1X5  CAE   CAB  CAA   120.29  3.000
 1X5  CAF   CAB  CAA   121.42  3.000
 1X5  HAC   CAC  CAG   118.11  3.000
 1X5  HAC   CAC  CAA   120.02  3.000
 1X5  CAG   CAC  CAA   121.87  3.000
 1X5  HNAD  NAD  CAU   116.95  3.000
 1X5  HNAD  NAD  CAA   113.41  3.000
 1X5  CAU   NAD  CAA   129.61  3.000
 1X5  HAE   CAE  CAH   119.34  3.000
 1X5  HAE   CAE  CAB   118.17  3.000
 1X5  CAH   CAE  CAB   122.49  3.000
 1X5  OAJ   CAF  OAI   121.50  3.000
 1X5  OAI   CAF  CAB   113.76  3.000
 1X5  OAJ   CAF  CAB   124.73  3.000
 1X5  HAG   CAG  CAH   121.02  3.000
 1X5  HAG   CAG  CAC   117.07  3.000
 1X5  CAH   CAG  CAC   121.90  3.000
 1X5  NAQ   CAH  CAG   122.13  3.000
 1X5  NAQ   CAH  CAE   121.54  3.000
 1X5  CAG   CAH  CAE   116.32  3.000
 1X5  HOAI  OAI  CAF   109.69  3.000
 1X5  CAN   CAK  CAM   122.30  3.000
 1X5  CAM   CAK  CAL   117.18  3.000
 1X5  CAN   CAK  CAL   120.51  3.000
 1X5  HAL   CAL  CAO   120.27  3.000
 1X5  HAL   CAL  CAK   120.28  3.000
 1X5  CAO   CAL  CAK   119.45  3.000
 1X5  HAM   CAM  NAP   115.85  3.000
 1X5  HAM   CAM  CAK   120.23  3.000
 1X5  NAP   CAM  CAK   123.93  3.000
 1X5  HANA  CAN  HAN   104.94  3.000
 1X5  HANA  CAN  NAQ   107.82  3.000
 1X5  HAN   CAN  NAQ   110.45  3.000
 1X5  HANA  CAN  CAK   108.81  3.000
 1X5  HAN   CAN  CAK   109.10  3.000
 1X5  NAQ   CAN  CAK   115.21  3.000
 1X5  HAO   CAO  CAR   120.38  3.000
 1X5  HAO   CAO  CAL   121.19  3.000
 1X5  CAR   CAO  CAL   118.42  3.000
 1X5  CAR   NAP  CAM   118.07  3.000
 1X5  CAS   NAQ  CAN   119.17  3.000
 1X5  CAS   NAQ  CAH   119.79  3.000
 1X5  CAN   NAQ  CAH   120.02  3.000
 1X5  HAR   CAR  NAP   116.68  3.000
 1X5  HAR   CAR  CAO   120.37  3.000
 1X5  NAP   CAR  CAO   122.94  3.000
 1X5  HASB  CAS  HASA  107.73  3.000
 1X5  HASB  CAS  HAS   107.81  3.000
 1X5  HASA  CAS  HAS   107.46  3.000
 1X5  HASB  CAS  NAQ   112.88  3.000
 1X5  HASA  CAS  NAQ   109.09  3.000
 1X5  HAS   CAS  NAQ   111.65  3.000
 1X5  HAT   CAT  CAW   116.48  3.000
 1X5  HAT   CAT  CAV   116.45  3.000
 1X5  CAW   CAT  CAV    58.97  3.000
 1X5  HAT   CAT  CAU   116.80  3.000
 1X5  CAV   CAT  CAU   117.85  3.000
 1X5  CAW   CAT  CAU   117.75  3.000
 1X5  OAX   CAU  CAT   122.02  3.000
 1X5  OAX   CAU  NAD   124.74  3.000
 1X5  CAT   CAU  NAD   113.24  3.000
 1X5  HAVA  CAV  HAV   114.84  3.000
 1X5  HAVA  CAV  CAW   118.68  3.000
 1X5  HAV   CAV  CAW   118.19  3.000
 1X5  HAVA  CAV  CAT   116.65  3.000
 1X5  HAV   CAV  CAT   117.23  3.000
 1X5  CAW   CAV  CAT    60.56  3.000
 1X5  HAWA  CAW  HAW   114.84  3.000
 1X5  HAWA  CAW  CAV   118.22  3.000
 1X5  HAW   CAW  CAV   118.72  3.000
 1X5  HAWA  CAW  CAT   117.21  3.000
 1X5  HAW   CAW  CAT   116.64  3.000
 1X5  CAV   CAW  CAT    60.48  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  CONST_37  HOAI  OAI  CAF  CAB   180.00   0.0  0
 1X5  Var_01    CAV   CAW  CAT  CAU   107.43  30.0  1
 1X5  Var_02    HAV   CAV  CAW  CAT  -107.08  30.0  1
 1X5  Var_03    OAJ   CAF  CAB  CAA    -2.18  30.0  3
 1X5  Var_04    CAW   CAT  CAU  NAD   144.03  30.0  1
 1X5  Var_05    CAK   CAN  NAQ  CAH    70.71  30.0  3
 1X5  Var_06    NAQ   CAN  CAK  CAL  -161.01  30.0  3
 1X5  Var_07    HAS   CAS  NAQ  CAH    60.75  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
 1X5  plan-5  HOAI  0.020

