# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:26:37 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 6-amino-1-butyl-5-(cyclopentylamino)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1C(=O)NC(=O)C(=C1N)NC2CCCC2
#
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
 NIQ  NIQ  6-amino-1-butyl-5-(cyclopentylamino)pyrimidine-2,4(1H,3H)-dione  ligand  41  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NIQ
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
 NIQ  NAM   N  NH1   0  -0.663   1.8377  -0.3272  -1.4450
 NIQ  CAL   C  CR6   0  -0.086   0.6958   0.4877  -1.2765
 NIQ  CAH   C  CR6   0   0.654  -0.5356  -0.1369  -1.1917
 NIQ  NAI   N  NH2   0  -0.840  -0.6205  -1.4636  -1.3278
 NIQ  CAK   C  CR6   0   0.529   0.7718   1.9032  -1.2116
 NIQ  OAQ   O  O     0  -0.499   1.7841   2.5852  -1.3323
 NIQ  NAJ   N  NR16  0  -0.736  -0.4523   2.5374  -1.0053
 NIQ  CAF   C  CR6   0   0.710  -1.6693   1.9544  -0.8398
 NIQ  OAE   O  O     0  -0.492  -2.6717   2.6025  -0.6018
 NIQ  NAG   N  NR6   0  -0.591  -1.6913   0.5791  -0.9734
 NIQ  CAD   C  CH2   0  -0.353  -2.9809  -0.0929  -0.8130
 NIQ  CAC   C  CH2   0  -0.427  -3.1981  -0.6279   0.5966
 NIQ  CAB   C  CH2   0  -0.427  -4.5544  -1.3081   0.7359
 NIQ  CAA   C  CH3   0  -0.661  -4.7918  -1.8509   2.1379
 NIQ  CAO   C  CH2   0  -0.447   3.5248  -1.8496  -0.4481
 NIQ  CAP   C  CH2   0  -0.453   4.3082  -1.9132   0.8650
 NIQ  CAS   C  CH2   0  -0.450   4.2489  -0.4812   1.4565
 NIQ  CAR   C  CH2   0  -0.436   3.3561   0.3307   0.5072
 NIQ  CAN   C  CR15  0  -0.079   2.5183  -0.7259  -0.2208
 NIQ  HAN   H  HCR5  0   0.226   1.7451  -1.0914   0.4659
 NIQ  HAI1  H  HNH2  0   0.415   0.2376  -1.9528  -1.5245
 NIQ  HAI2  H  HNH2  0   0.421  -1.4465  -2.0047  -1.1539
 NIQ  HAJ   H  HNR6  0   0.416  -0.4370   3.5463  -0.9370
 NIQ  HAD1  H  HCH2  0   0.285  -3.7554   0.6275  -1.0615
 NIQ  HAD2  H  HCH2  0   0.262  -3.0602  -0.8833  -1.5608
 NIQ  HAC1  H  HCH2  0   0.226  -2.4050  -1.3342   0.8603
 NIQ  HAC2  H  HCH2  0   0.238  -3.1256   0.2009   1.3066
 NIQ  HAB1  H  HCH2  0   0.222  -5.3433  -0.5940   0.4820
 NIQ  HAB2  H  HCH2  0   0.221  -4.6329  -2.1219   0.0090
 NIQ  HAA1  H  HCH3  0   0.230  -5.7758  -2.3128   2.2220
 NIQ  HAA2  H  HCH3  0   0.220  -4.0489  -2.6055   2.4020
 NIQ  HAA3  H  HCH3  0   0.220  -4.7335  -1.0559   2.8830
 NIQ  HAO1  H  HCH2  0   0.216   4.1877  -1.5783  -1.2771
 NIQ  HAO2  H  HCH2  0   0.231   3.0474  -2.7952  -0.7111
 NIQ  HAP1  H  HCH2  0   0.225   3.8364  -2.6224   1.5478
 NIQ  HAP2  H  HCH2  0   0.229   5.3320  -2.2568   0.7144
 NIQ  HAS1  H  HCH2  0   0.225   3.8270  -0.5036   2.4624
 NIQ  HAS2  H  HCH2  0   0.228   5.2411  -0.0382   1.5486
 NIQ  HAR1  H  HCH2  0   0.228   2.7476   1.0708   1.0277
 NIQ  HAR2  H  HCH2  0   0.214   3.9604   0.8687  -0.2285
 NIQ  HNAM  H  HNH1  0   0.348   2.4903   0.0875  -2.0991

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
 NIQ  NAM  CAL   single  1.413  0.020  1.413
 NIQ  NAM  CAN   single  1.456  0.020  1.456
 NIQ  CAL  CAH   double  1.383  0.020  1.383
 NIQ  CAL  CAK   single  1.419  0.020  1.419
 NIQ  CAH  NAI   single  1.336  0.020  1.336
 NIQ  CAH  NAG   single  1.377  0.020  1.377
 NIQ  CAK  OAQ   double  1.227  0.020  1.227
 NIQ  CAK  NAJ   single  1.394  0.020  1.394
 NIQ  NAJ  CAF   single  1.360  0.020  1.360
 NIQ  CAF  OAE   double  1.217  0.020  1.217
 NIQ  CAF  NAG   single  1.382  0.020  1.382
 NIQ  NAG  CAD   single  1.463  0.020  1.463
 NIQ  CAD  CAC   single  1.523  0.020  1.523
 NIQ  CAC  CAB   single  1.524  0.020  1.524
 NIQ  CAB  CAA   single  1.522  0.020  1.522
 NIQ  CAO  CAP   single  1.530  0.020  1.530
 NIQ  CAO  CAN   single  1.526  0.020  1.526
 NIQ  CAP  CAS   single  1.551  0.020  1.551
 NIQ  CAS  CAR   single  1.535  0.020  1.535
 NIQ  CAR  CAN   single  1.532  0.020  1.532
 NIQ  CAN  HAN   single  0.970  0.020  1.090
 NIQ  NAI  HAI1  single  0.860  0.020  1.020
 NIQ  NAI  HAI2  single  0.860  0.020  1.020
 NIQ  NAJ  HAJ   single  0.860  0.020  1.020
 NIQ  CAD  HAD1  single  0.970  0.020  1.090
 NIQ  CAD  HAD2  single  0.970  0.020  1.090
 NIQ  CAC  HAC1  single  0.970  0.020  1.090
 NIQ  CAC  HAC2  single  0.970  0.020  1.090
 NIQ  CAB  HAB1  single  0.970  0.020  1.090
 NIQ  CAB  HAB2  single  0.970  0.020  1.090
 NIQ  CAA  HAA1  single  0.970  0.020  1.090
 NIQ  CAA  HAA2  single  0.970  0.020  1.090
 NIQ  CAA  HAA3  single  0.970  0.020  1.090
 NIQ  CAO  HAO1  single  0.970  0.020  1.090
 NIQ  CAO  HAO2  single  0.970  0.020  1.090
 NIQ  CAP  HAP1  single  0.970  0.020  1.090
 NIQ  CAP  HAP2  single  0.970  0.020  1.090
 NIQ  CAS  HAS1  single  0.970  0.020  1.090
 NIQ  CAS  HAS2  single  0.970  0.020  1.090
 NIQ  CAR  HAR1  single  0.970  0.020  1.090
 NIQ  CAR  HAR2  single  0.970  0.020  1.090
 NIQ  NAM  HNAM  single  0.890  0.020  1.040

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
 NIQ  HNAM  NAM  CAN   110.73  3.000
 NIQ  HNAM  NAM  CAL   111.20  3.000
 NIQ  CAN   NAM  CAL   115.80  3.000
 NIQ  CAK   CAL  CAH   119.68  3.000
 NIQ  CAK   CAL  NAM   122.52  3.000
 NIQ  CAH   CAL  NAM   117.80  3.000
 NIQ  NAG   CAH  NAI   118.63  3.000
 NIQ  NAG   CAH  CAL   121.47  3.000
 NIQ  NAI   CAH  CAL   119.90  3.000
 NIQ  HAI2  NAI  HAI1  118.27  3.000
 NIQ  HAI2  NAI  CAH   124.78  3.000
 NIQ  HAI1  NAI  CAH   116.62  3.000
 NIQ  NAJ   CAK  OAQ   119.10  3.000
 NIQ  NAJ   CAK  CAL   114.43  3.000
 NIQ  OAQ   CAK  CAL   126.46  3.000
 NIQ  HAJ   NAJ  CAF   115.66  3.000
 NIQ  HAJ   NAJ  CAK   116.78  3.000
 NIQ  CAF   NAJ  CAK   127.52  3.000
 NIQ  NAG   CAF  OAE   122.39  3.000
 NIQ  NAG   CAF  NAJ   115.42  3.000
 NIQ  OAE   CAF  NAJ   122.19  3.000
 NIQ  CAD   NAG  CAF   117.42  3.000
 NIQ  CAD   NAG  CAH   121.23  3.000
 NIQ  CAF   NAG  CAH   121.30  3.000
 NIQ  HAD2  CAD  HAD1  105.77  3.000
 NIQ  HAD2  CAD  CAC   111.68  3.000
 NIQ  HAD1  CAD  CAC   110.05  3.000
 NIQ  HAD2  CAD  NAG   108.76  3.000
 NIQ  HAD1  CAD  NAG   107.38  3.000
 NIQ  CAC   CAD  NAG   112.86  3.000
 NIQ  HAC2  CAC  HAC1  106.54  3.000
 NIQ  HAC2  CAC  CAB   109.75  3.000
 NIQ  HAC1  CAC  CAB   109.57  3.000
 NIQ  HAC2  CAC  CAD   108.97  3.000
 NIQ  HAC1  CAC  CAD   110.26  3.000
 NIQ  CAB   CAC  CAD   111.61  3.000
 NIQ  HAB2  CAB  HAB1  106.23  3.000
 NIQ  HAB2  CAB  CAA   109.60  3.000
 NIQ  HAB1  CAB  CAA   109.52  3.000
 NIQ  HAB2  CAB  CAC   109.59  3.000
 NIQ  HAB1  CAB  CAC   109.23  3.000
 NIQ  CAA   CAB  CAC   112.48  3.000
 NIQ  HAA3  CAA  HAA2  107.59  3.000
 NIQ  HAA3  CAA  HAA1  107.71  3.000
 NIQ  HAA2  CAA  HAA1  107.63  3.000
 NIQ  HAA3  CAA  CAB   111.15  3.000
 NIQ  HAA2  CAA  CAB   111.30  3.000
 NIQ  HAA1  CAA  CAB   111.28  3.000
 NIQ  HAO2  CAO  HAO1  107.27  3.000
 NIQ  HAO2  CAO  CAN   112.67  3.000
 NIQ  HAO1  CAO  CAN   109.24  3.000
 NIQ  HAO2  CAO  CAP   113.25  3.000
 NIQ  HAO1  CAO  CAP   110.48  3.000
 NIQ  CAN   CAO  CAP   103.92  3.000
 NIQ  HAP2  CAP  HAP1  106.71  3.000
 NIQ  HAP2  CAP  CAS   112.31  3.000
 NIQ  HAP1  CAP  CAS   110.17  3.000
 NIQ  HAP2  CAP  CAO   112.04  3.000
 NIQ  HAP1  CAP  CAO   110.02  3.000
 NIQ  CAS   CAP  CAO   105.62  3.000
 NIQ  HAS2  CAS  HAS1  106.40  3.000
 NIQ  HAS2  CAS  CAR   111.50  3.000
 NIQ  HAS1  CAS  CAR   110.86  3.000
 NIQ  HAS2  CAS  CAP   111.87  3.000
 NIQ  HAS1  CAS  CAP   110.34  3.000
 NIQ  CAR   CAS  CAP   105.95  3.000
 NIQ  HAR2  CAR  HAR1  107.19  3.000
 NIQ  HAR2  CAR  CAN   108.76  3.000
 NIQ  HAR1  CAR  CAN   112.94  3.000
 NIQ  HAR2  CAR  CAS   110.78  3.000
 NIQ  HAR1  CAR  CAS   112.85  3.000
 NIQ  CAN   CAR  CAS   104.30  3.000
 NIQ  HAN   CAN  CAR   108.53  3.000
 NIQ  HAN   CAN  CAO   108.23  3.000
 NIQ  CAR   CAN  CAO   102.59  3.000
 NIQ  HAN   CAN  NAM   106.75  3.000
 NIQ  CAR   CAN  NAM   117.78  3.000
 NIQ  CAO   CAN  NAM   112.63  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
 NIQ  CONST_01  CAF   NAG  CAH  CAL    0.00   0.0  0
 NIQ  CONST_02  CAF   NAJ  CAK  CAL    0.00   0.0  0
 NIQ  CONST_03  NAJ   CAF  NAG  CAH    0.00   0.0  0
 NIQ  CONST_04  NAG   CAF  NAJ  CAK    0.00   0.0  0
 NIQ  CONST_05  CAD   NAG  CAH  CAL  180.00   0.0  0
 NIQ  CONST_06  OAE   CAF  NAG  CAH  180.00   0.0  0
 NIQ  CONST_07  CAF   NAG  CAH  NAI  180.00   0.0  0
 NIQ  CONST_08  OAE   CAF  NAJ  CAK  180.00   0.0  0
 NIQ  CONST_09  CAF   NAJ  CAK  OAQ  180.00   0.0  0
 NIQ  CONST_10  CAD   NAG  CAF  NAJ  180.00   0.0  0
 NIQ  CONST_11  HAJ   NAJ  CAK  CAL  180.00   0.0  0
 NIQ  CONST_12  CAD   NAG  CAH  NAI    0.00   0.0  0
 NIQ  CONST_13  CAD   NAG  CAF  OAE    0.00   0.0  0
 NIQ  CONST_14  HAI1  NAI  CAH  CAL    0.00   0.0  0
 NIQ  CONST_15  HAI2  NAI  CAH  CAL  180.00   0.0  0
 NIQ  Var_01    CAR   CAS  CAP  CAO    3.60  30.0  1
 NIQ  Var_02    CAN   CAR  CAS  CAP   21.81  30.0  1
 NIQ  Var_03    CAN   CAO  CAP  CAS  -27.76  30.0  1
 NIQ  Var_04    CAN   NAM  CAL  CAH  -92.73  30.0  1
 NIQ  Var_05    CAC   CAD  NAG  CAH   81.41  30.0  3
 NIQ  Var_06    CAB   CAC  CAD  NAG  179.38  30.0  3
 NIQ  Var_07    CAA   CAB  CAC  CAD  179.98  30.0  3
 NIQ  Var_08    HAA1  CAA  CAB  CAC  178.71  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
 NIQ  chir_01  CAN  NAM  CAO  CAR  negativ

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
 NIQ  plan-1  NAM   0.020
 NIQ  plan-1  CAL   0.020
 NIQ  plan-1  CAH   0.020
 NIQ  plan-1  NAI   0.020
 NIQ  plan-1  CAK   0.020
 NIQ  plan-1  OAQ   0.020
 NIQ  plan-1  NAJ   0.020
 NIQ  plan-1  CAF   0.020
 NIQ  plan-1  OAE   0.020
 NIQ  plan-1  NAG   0.020
 NIQ  plan-1  CAD   0.020
 NIQ  plan-1  HAI1  0.020
 NIQ  plan-1  HAI2  0.020
 NIQ  plan-1  HAJ   0.020

