# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:35:33 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-(6-amino-1-butyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1C(=O)NC(=O)C(=C1N)N(C)C(=O)c2ccccc2
#
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
 942  942  N-(6-amino-1-butyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzamide  ligand  43  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_942
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
 942  CAW   C  CH3   0  -0.662   5.9302   0.8423   2.1113
 942  CAX   C  CH2   0  -0.427   4.8763   1.3764   1.1525
 942  CAV   C  CH2   0  -0.428   3.7433   0.3827   0.9276
 942  CAU   C  CH2   0  -0.360   2.6998   0.9345  -0.0334
 942  NAQ   N  NR6   0  -0.595   1.6168  -0.0130  -0.3096
 942  CAR   C  CR6   0   0.697   0.5147  -0.1010   0.5052
 942  NAS   N  NH2   0  -0.839   0.4412   0.7177   1.5584
 942  CAP   C  CR6   0   0.721   1.7924  -0.8657  -1.3878
 942  OAO   O  O     0  -0.479   2.7860  -0.8295  -2.0842
 942  NAG   N  NR16  0  -0.737   0.7781  -1.7438  -1.6166
 942  CAH   C  CR6   0   0.567  -0.3977  -1.8762  -0.8911
 942  OAA   O  O     0  -0.484  -1.2270  -2.7145  -1.2174
 942  CAI   C  CR6   0  -0.091  -0.5078  -0.9816   0.2063
 942  NAJ   N  NT    0  -0.498  -1.6386  -1.0665   1.0420
 942  CAB   C  CH3   0  -0.533  -1.7134  -2.1303   2.0364
 942  OAT   O  O     0  -0.468  -3.6063  -0.2184   1.7386
 942  CAE   C  CR16  0  -0.245  -2.6639   1.4918  -2.4379
 942  CAD   C  CR16  0  -0.257  -2.6225   2.8308  -2.0700
 942  CAL   C  CR16  0  -0.246  -2.5822   3.1775  -0.7264
 942  CAM   C  CR16  0  -0.279  -2.5856   2.1885   0.2476
 942  CAK   C  C     0   0.485  -2.6700  -0.1904   0.9564
 942  CAN   C  CR6   0  -0.052  -2.6015   0.8469  -0.1197
 942  CAF   C  CR16  0  -0.256  -2.6472   0.5014  -1.4672
 942  HAW1  H  HCH3  0   0.231   6.7399   1.5587   2.2510
 942  HAW2  H  HCH3  0   0.220   5.4995   0.6335   3.0921
 942  HAW3  H  HCH3  0   0.220   6.3694  -0.0853   1.7396
 942  HAX1  H  HCH2  0   0.223   4.4699   2.3147   1.5416
 942  HAX2  H  HCH2  0   0.224   5.3396   1.6196   0.1918
 942  HAV1  H  HCH2  0   0.240   4.1465  -0.5488   0.5207
 942  HAV2  H  HCH2  0   0.228   3.2858   0.1269   1.8885
 942  HAU1  H  HCH2  0   0.268   2.2644   1.8658   0.3317
 942  HAU2  H  HCH2  0   0.289   3.1635   1.1853  -0.9839
 942  HAS1  H  HNH2  0   0.429   1.2275   1.2409   1.8991
 942  HAS2  H  HNH2  0   0.421  -0.3074   0.5921   2.2175
 942  HAG   H  HNR6  0   0.423   0.9046  -2.3663  -2.4040
 942  HAB1  H  HCH3  0   0.247  -1.7179  -1.7303   3.0509
 942  HAB2  H  HCH3  0   0.250  -2.6086  -2.7361   1.9021
 942  HAB3  H  HCH3  0   0.254  -0.8433  -2.7691   1.9222
 942  HAL   H  HCR6  0   0.259  -2.5545   4.2194  -0.4350
 942  HAM   H  HCR6  0   0.259  -2.5654   2.4647   1.2946
 942  HAD   H  HCR6  0   0.260  -2.6268   3.6019  -2.8292
 942  HAF   H  HCR6  0   0.260  -2.6841  -0.5393  -1.7630
 942  HAE   H  HCR6  0   0.259  -2.7083   1.2173  -3.4838

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
 942  CAW  CAX   single    1.522  0.020  1.522
 942  CAX  CAV   single    1.524  0.020  1.524
 942  CAV  CAU   single    1.522  0.020  1.522
 942  CAU  NAQ   single    1.465  0.020  1.465
 942  NAQ  CAR   single    1.373  0.020  1.373
 942  NAQ  CAP   single    1.386  0.020  1.386
 942  CAR  NAS   single    1.336  0.020  1.336
 942  CAR  CAI   double    1.382  0.020  1.382
 942  CAP  OAO   double    1.214  0.020  1.214
 942  CAP  NAG   single    1.361  0.020  1.361
 942  NAG  CAH   single    1.388  0.020  1.388
 942  CAH  OAA   double    1.224  0.020  1.224
 942  CAH  CAI   single    1.420  0.020  1.420
 942  CAI  NAJ   single    1.409  0.020  1.409
 942  NAJ  CAB   single    1.458  0.020  1.458
 942  NAJ  CAK   single    1.356  0.020  1.356
 942  CAL  CAM   aromatic  1.388  0.020  1.388
 942  CAL  CAD   aromatic  1.388  0.020  1.388
 942  CAM  CAN   aromatic  1.391  0.020  1.391
 942  CAN  CAF   aromatic  1.392  0.020  1.392
 942  CAN  CAK   single    1.496  0.020  1.496
 942  CAF  CAE   aromatic  1.387  0.020  1.387
 942  CAE  CAD   aromatic  1.389  0.020  1.389
 942  CAK  OAT   double    1.220  0.020  1.220
 942  CAW  HAW1  single    0.970  0.020  1.090
 942  CAW  HAW2  single    0.970  0.020  1.090
 942  CAW  HAW3  single    0.970  0.020  1.090
 942  CAX  HAX1  single    0.970  0.020  1.090
 942  CAX  HAX2  single    0.970  0.020  1.090
 942  CAV  HAV1  single    0.970  0.020  1.090
 942  CAV  HAV2  single    0.970  0.020  1.090
 942  CAU  HAU1  single    0.970  0.020  1.090
 942  CAU  HAU2  single    0.970  0.020  1.090
 942  NAS  HAS1  single    0.890  0.020  1.040
 942  NAS  HAS2  single    0.890  0.020  1.040
 942  NAG  HAG   single    0.860  0.020  1.020
 942  CAB  HAB1  single    0.970  0.020  1.090
 942  CAB  HAB2  single    0.970  0.020  1.090
 942  CAB  HAB3  single    0.970  0.020  1.090
 942  CAL  HAL   single    0.930  0.020  1.080
 942  CAM  HAM   single    0.930  0.020  1.080
 942  CAD  HAD   single    0.930  0.020  1.080
 942  CAF  HAF   single    0.930  0.020  1.080
 942  CAE  HAE   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
 942  HAW3  CAW  HAW2  107.60  3.000
 942  HAW3  CAW  HAW1  107.65  3.000
 942  HAW2  CAW  HAW1  107.68  3.000
 942  HAW3  CAW  CAX   111.25  3.000
 942  HAW2  CAW  CAX   111.10  3.000
 942  HAW1  CAW  CAX   111.38  3.000
 942  HAX2  CAX  HAX1  106.20  3.000
 942  HAX2  CAX  CAV   109.28  3.000
 942  HAX1  CAX  CAV   109.60  3.000
 942  HAX2  CAX  CAW   109.76  3.000
 942  HAX1  CAX  CAW   109.53  3.000
 942  CAV   CAX  CAW   112.28  3.000
 942  HAV2  CAV  HAV1  106.36  3.000
 942  HAV2  CAV  CAU   110.64  3.000
 942  HAV1  CAV  CAU   109.06  3.000
 942  HAV2  CAV  CAX   109.49  3.000
 942  HAV1  CAV  CAX   109.65  3.000
 942  CAU   CAV  CAX   111.50  3.000
 942  HAU2  CAU  HAU1  105.42  3.000
 942  HAU2  CAU  NAQ   107.43  3.000
 942  HAU1  CAU  NAQ   108.67  3.000
 942  HAU2  CAU  CAV   110.08  3.000
 942  HAU1  CAU  CAV   111.82  3.000
 942  NAQ   CAU  CAV   113.03  3.000
 942  CAP   NAQ  CAR   121.59  3.000
 942  CAP   NAQ  CAU   116.80  3.000
 942  CAR   NAQ  CAU   121.51  3.000
 942  CAI   CAR  NAS   121.35  3.000
 942  CAI   CAR  NAQ   120.41  3.000
 942  NAS   CAR  NAQ   118.20  3.000
 942  HAS2  NAS  HAS1  115.20  3.000
 942  HAS2  NAS  CAR   118.77  3.000
 942  HAS1  NAS  CAR   122.94  3.000
 942  NAG   CAP  OAO   122.19  3.000
 942  NAG   CAP  NAQ   115.68  3.000
 942  OAO   CAP  NAQ   122.13  3.000
 942  HAG   NAG  CAH   117.01  3.000
 942  HAG   NAG  CAP   115.76  3.000
 942  CAH   NAG  CAP   127.23  3.000
 942  CAI   CAH  OAA   125.81  3.000
 942  CAI   CAH  NAG   114.18  3.000
 942  OAA   CAH  NAG   120.01  3.000
 942  NAJ   CAI  CAH   118.86  3.000
 942  NAJ   CAI  CAR   120.27  3.000
 942  CAH   CAI  CAR   120.73  3.000
 942  CAK   NAJ  CAB   118.39  3.000
 942  CAK   NAJ  CAI   122.29  3.000
 942  CAB   NAJ  CAI   119.32  3.000
 942  HAB3  CAB  HAB2  108.58  3.000
 942  HAB3  CAB  HAB1  108.48  3.000
 942  HAB2  CAB  HAB1  108.38  3.000
 942  HAB3  CAB  NAJ   108.45  3.000
 942  HAB2  CAB  NAJ   111.33  3.000
 942  HAB1  CAB  NAJ   111.54  3.000
 942  HAE   CAE  CAF   119.73  3.000
 942  HAE   CAE  CAD   120.10  3.000
 942  CAF   CAE  CAD   120.17  3.000
 942  HAD   CAD  CAL   120.08  3.000
 942  HAD   CAD  CAE   120.06  3.000
 942  CAL   CAD  CAE   119.86  3.000
 942  HAL   CAL  CAM   119.81  3.000
 942  HAL   CAL  CAD   120.11  3.000
 942  CAM   CAL  CAD   120.08  3.000
 942  HAM   CAM  CAN   120.10  3.000
 942  HAM   CAM  CAL   119.77  3.000
 942  CAN   CAM  CAL   120.13  3.000
 942  CAN   CAK  OAT   120.80  3.000
 942  OAT   CAK  NAJ   121.89  3.000
 942  CAN   CAK  NAJ   117.29  3.000
 942  CAF   CAN  CAK   121.52  3.000
 942  CAK   CAN  CAM   118.64  3.000
 942  CAF   CAN  CAM   119.70  3.000
 942  HAF   CAF  CAN   120.29  3.000
 942  HAF   CAF  CAE   119.66  3.000
 942  CAN   CAF  CAE   120.05  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
 942  CONST_01  CAM   CAN  CAF  CAE     0.00   0.0  0
 942  CONST_02  CAM   CAL  CAD  CAE     0.00   0.0  0
 942  CONST_03  CAN   CAM  CAL  CAD     0.00   0.0  0
 942  CONST_04  CAN   CAF  CAE  CAD     0.00   0.0  0
 942  CONST_05  CAF   CAN  CAM  CAL     0.00   0.0  0
 942  CONST_06  CAF   CAE  CAD  CAL     0.00   0.0  0
 942  CONST_07  CAH   NAG  CAP  NAQ     0.00   0.0  0
 942  CONST_08  NAG   CAP  NAQ  CAR     0.00   0.0  0
 942  CONST_09  CAI   CAR  NAQ  CAP     0.00   0.0  0
 942  CONST_10  CAI   CAH  NAG  CAP     0.00   0.0  0
 942  CONST_11  CAK   CAN  CAF  CAE   180.00   0.0  0
 942  CONST_12  CAK   CAN  CAM  CAL   180.00   0.0  0
 942  CONST_13  CAI   CAR  NAQ  CAU   180.00   0.0  0
 942  CONST_14  NAG   CAP  NAQ  CAU   180.00   0.0  0
 942  CONST_15  OAO   CAP  NAQ  CAR   180.00   0.0  0
 942  CONST_16  CAP   NAQ  CAR  NAS   180.00   0.0  0
 942  CONST_17  OAA   CAH  NAG  CAP   180.00   0.0  0
 942  CONST_18  CAH   NAG  CAP  OAO   180.00   0.0  0
 942  CONST_19  HAL   CAL  CAD  CAE   180.00   0.0  0
 942  CONST_20  HAM   CAM  CAL  CAD   180.00   0.0  0
 942  CONST_21  HAF   CAF  CAE  CAD   180.00   0.0  0
 942  CONST_22  HAE   CAE  CAD  CAL   180.00   0.0  0
 942  CONST_23  HAD   CAD  CAL  CAM   180.00   0.0  0
 942  CONST_24  HAG   NAG  CAP  NAQ   180.00   0.0  0
 942  CONST_25  CAN   CAK  NAJ  CAI     0.00   0.0  0
 942  CONST_26  NAS   CAR  NAQ  CAU     0.00   0.0  0
 942  CONST_27  OAO   CAP  NAQ  CAU     0.00   0.0  0
 942  CONST_28  HAS1  NAS  CAR  NAQ     0.00   0.0  0
 942  CONST_29  HAS2  NAS  CAR  NAQ   180.00   0.0  0
 942  CONST_30  OAT   CAK  NAJ  CAI   180.00   0.0  0
 942  CONST_31  CAN   CAK  NAJ  CAB   180.00   0.0  0
 942  CONST_32  OAT   CAK  NAJ  CAB     0.00   0.0  0
 942  Var_01    CAR   NAQ  CAU  CAV    86.19  30.0  3
 942  Var_02    CAB   NAJ  CAI  CAR   -98.28  30.0  2
 942  Var_03    CAM   CAN  CAK  NAJ  -119.00  30.0  2
 942  Var_04    NAQ   CAU  CAV  CAX   178.03  30.0  3
 942  Var_05    HAB1  CAB  NAJ  CAI   115.83  30.0  3
 942  Var_06    CAU   CAV  CAX  CAW   180.00  30.0  3
 942  Var_07    HAW1  CAW  CAX  CAV   179.23  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
 942  plan-1  CAU   0.020
 942  plan-1  NAQ   0.020
 942  plan-1  CAR   0.020
 942  plan-1  NAS   0.020
 942  plan-1  CAP   0.020
 942  plan-1  OAO   0.020
 942  plan-1  NAG   0.020
 942  plan-1  CAH   0.020
 942  plan-1  OAA   0.020
 942  plan-1  CAI   0.020
 942  plan-1  NAJ   0.020
 942  plan-1  HAS1  0.020
 942  plan-1  HAS2  0.020
 942  plan-1  HAG   0.020
 942  plan-2  CAE   0.020
 942  plan-2  CAD   0.020
 942  plan-2  CAL   0.020
 942  plan-2  CAM   0.020
 942  plan-2  CAK   0.020
 942  plan-2  CAN   0.020
 942  plan-2  CAF   0.020
 942  plan-2  HAL   0.020
 942  plan-2  HAM   0.020
 942  plan-2  HAD   0.020
 942  plan-2  HAF   0.020
 942  plan-2  HAE   0.020
 942  plan-3  CAI   0.020
 942  plan-3  NAJ   0.020
 942  plan-3  CAB   0.020
 942  plan-3  OAT   0.020
 942  plan-3  CAK   0.020
 942  plan-3  CAN   0.020

