# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 04:38:56 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: 6-[[methyl-[(1-phenylpyrazol-3-yl)methyl]amino]methyl]-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC1=CC(=O)NC(=O)N1)Cc2ccn(n2)c3ccccc3
#
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
 P0W  P0W  6-[[methyl-[(1-phenylpyrazol-3-yl)methyl]amino]methyl]-1~{H}-pyrimidine-2,4-dione  ligand  40  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P0W
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
 P0W  CAA  C  CH3   0  -0.526   0.0517  -4.0054  5.7570
 P0W  CAD  C  CR16  0  -0.261   1.5067   5.0898  7.5951
 P0W  CAE  C  CR16  0  -0.249   0.3823   5.2064  6.7897
 P0W  CAF  C  CR16  0  -0.248   2.0161   3.8294  7.8802
 P0W  CAG  C  CR16  0  -0.315  -0.2341   4.0757  6.2742
 P0W  CAH  C  CR16  0  -0.291   1.4179   2.6925  7.3597
 P0W  CAI  C  CR15  0  -0.524  -1.3633   0.2519  4.7246
 P0W  CAJ  C  CR15  0   0.035  -1.0052   1.5665  4.8533
 P0W  CAK  C  CR16  0  -0.527   2.4461   0.1015  4.6293
 P0W  CAL  C  CH2   0  -0.333  -0.8265  -1.8279  6.2165
 P0W  CAM  C  CH2   0  -0.345   1.4594  -2.0670  5.4563
 P0W  CAQ  C  CR5   0   0.261  -0.8239  -0.3783  5.8648
 P0W  CAR  C  CR6   0   0.440   1.6675  -0.9818  4.4368
 P0W  CAS  C  CR6   0   0.377   0.2915   2.8197  6.5544
 P0W  CAT  C  CR6   0   0.578   2.6098   1.0644  3.5725
 P0W  CAU  C  CR6   0   0.661   1.1077  -0.3287  2.1886
 P0W  NAN  N  N     0  -0.280  -0.2025   0.4951  6.6333
 P0W  NAO  N  NR16  0  -0.695   1.0544  -1.1975  3.2416
 P0W  NAP  N  NR16  0  -0.719   1.9107   0.7591  2.4102
 P0W  NAV  N  NT    0  -0.431   0.1117  -2.5993  5.4039
 P0W  NAW  N  NR5   0  -0.398  -0.3131   1.6680  6.0143
 P0W  OAB  O  O     0  -0.474   3.2824   2.0792  3.6315
 P0W  OAC  O  O     0  -0.481   0.5031  -0.5063  1.1496
 P0W  H1   H  HCH3  0   0.241  -0.9646  -4.3738  5.6153
 P0W  H2   H  HCH3  0   0.246   0.7091  -4.5822  5.1072
 P0W  H3   H  HCH3  0   0.207   0.3388  -4.2033  6.7987
 P0W  H5   H  HCR6  0   0.265  -0.0307   6.1818  6.5697
 P0W  H6   H  HCR6  0   0.263   2.8933   3.7275  8.5055
 P0W  H7   H  HCR6  0   0.277  -1.1251   4.1780  5.6687
 P0W  H8   H  HCR6  0   0.272   1.8241   1.7133  7.5702
 P0W  H9   H  HCR5  0   0.267  -1.9156  -0.2001  3.9173
 P0W  H10  H  HCR5  0   0.300  -1.1759   2.4143  4.2104
 P0W  H11  H  HCR6  0   0.272   2.9287   0.2759  5.5793
 P0W  H13  H  HCH2  0   0.259  -1.8241  -2.2427  6.0583
 P0W  H14  H  HCH2  0   0.225  -0.5979  -1.9288  7.2880
 P0W  H15  H  HCH2  0   0.292   2.1591  -2.8700  5.2078
 P0W  H16  H  HCH2  0   0.256   1.7466  -1.6937  6.4471
 P0W  H17  H  HNR6  0   0.422   1.9839   1.4187  1.6457
 P0W  H12  H  HNR6  0   0.418   0.3984  -1.9686  3.1936
 P0W  H4   H  HCR6  0   0.261   1.9815   5.9741  7.9987

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
 P0W  OAC  CAU  double    1.215  0.020  1.215
 P0W  CAU  NAP  single    1.370  0.020  1.370
 P0W  CAU  NAO  single    1.366  0.020  1.366
 P0W  NAP  CAT  single    1.390  0.020  1.390
 P0W  NAO  CAR  single    1.360  0.020  1.360
 P0W  CAT  OAB  double    1.219  0.020  1.219
 P0W  CAT  CAK  single    1.439  0.020  1.439
 P0W  CAR  CAK  double    1.348  0.020  1.348
 P0W  CAR  CAM  single    1.503  0.020  1.503
 P0W  CAI  CAJ  aromatic  1.369  0.020  1.369
 P0W  CAI  CAQ  aromatic  1.410  0.020  1.410
 P0W  CAJ  NAW  aromatic  1.355  0.020  1.355
 P0W  CAM  NAV  single    1.450  0.020  1.450
 P0W  NAV  CAA  single    1.451  0.020  1.451
 P0W  NAV  CAL  single    1.461  0.020  1.461
 P0W  CAG  CAE  aromatic  1.387  0.020  1.387
 P0W  CAG  CAS  aromatic  1.390  0.020  1.390
 P0W  CAQ  CAL  single    1.492  0.020  1.492
 P0W  CAQ  NAN  aromatic  1.319  0.020  1.319
 P0W  NAW  CAS  single    1.408  0.020  1.408
 P0W  NAW  NAN  aromatic  1.331  0.020  1.331
 P0W  CAE  CAD  aromatic  1.388  0.020  1.388
 P0W  CAS  CAH  aromatic  1.391  0.020  1.391
 P0W  CAD  CAF  aromatic  1.389  0.020  1.389
 P0W  CAH  CAF  aromatic  1.386  0.020  1.386
 P0W  CAA  H1   single    0.970  0.020  1.090
 P0W  CAA  H2   single    0.970  0.020  1.090
 P0W  CAA  H3   single    0.970  0.020  1.090
 P0W  CAD  H4   single    0.930  0.020  1.080
 P0W  CAE  H5   single    0.930  0.020  1.080
 P0W  CAF  H6   single    0.930  0.020  1.080
 P0W  CAG  H7   single    0.930  0.020  1.080
 P0W  CAH  H8   single    0.930  0.020  1.080
 P0W  CAI  H9   single    0.930  0.020  1.080
 P0W  CAJ  H10  single    0.930  0.020  1.080
 P0W  CAK  H11  single    0.930  0.020  1.080
 P0W  CAL  H13  single    0.970  0.020  1.090
 P0W  CAL  H14  single    0.970  0.020  1.090
 P0W  CAM  H15  single    0.970  0.020  1.090
 P0W  CAM  H16  single    0.970  0.020  1.090
 P0W  NAP  H17  single    0.860  0.020  1.020
 P0W  NAO  H12  single    0.860  0.020  1.020

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
 P0W  H3   CAA  H2   108.21  3.000
 P0W  H3   CAA  H1   107.82  3.000
 P0W  H2   CAA  H1   107.82  3.000
 P0W  H3   CAA  NAV  113.23  3.000
 P0W  H2   CAA  NAV  110.05  3.000
 P0W  H1   CAA  NAV  109.53  3.000
 P0W  H4   CAD  CAF  120.28  3.000
 P0W  H4   CAD  CAE  120.22  3.000
 P0W  CAF  CAD  CAE  119.50  3.000
 P0W  H5   CAE  CAG  119.32  3.000
 P0W  H5   CAE  CAD  120.20  3.000
 P0W  CAG  CAE  CAD  120.47  3.000
 P0W  H6   CAF  CAH  119.32  3.000
 P0W  H6   CAF  CAD  120.09  3.000
 P0W  CAH  CAF  CAD  120.59  3.000
 P0W  H7   CAG  CAS  120.63  3.000
 P0W  H7   CAG  CAE  119.78  3.000
 P0W  CAS  CAG  CAE  119.58  3.000
 P0W  H8   CAH  CAS  120.00  3.000
 P0W  H8   CAH  CAF  120.52  3.000
 P0W  CAS  CAH  CAF  119.48  3.000
 P0W  H9   CAI  CAQ  127.91  3.000
 P0W  H9   CAI  CAJ  127.41  3.000
 P0W  CAQ  CAI  CAJ  104.66  3.000
 P0W  H10  CAJ  NAW  122.21  3.000
 P0W  H10  CAJ  CAI  131.16  3.000
 P0W  NAW  CAJ  CAI  106.62  3.000
 P0W  H11  CAK  CAT  119.15  3.000
 P0W  H11  CAK  CAR  120.91  3.000
 P0W  CAT  CAK  CAR  119.91  3.000
 P0W  H14  CAL  H13  107.22  3.000
 P0W  H14  CAL  NAV  111.08  3.000
 P0W  H13  CAL  NAV  107.78  3.000
 P0W  H14  CAL  CAQ  108.57  3.000
 P0W  H13  CAL  CAQ  109.67  3.000
 P0W  NAV  CAL  CAQ  112.39  3.000
 P0W  H16  CAM  H15  106.71  3.000
 P0W  H16  CAM  NAV  113.64  3.000
 P0W  H15  CAM  NAV  108.48  3.000
 P0W  H16  CAM  CAR  109.30  3.000
 P0W  H15  CAM  CAR  106.69  3.000
 P0W  NAV  CAM  CAR  111.66  3.000
 P0W  NAN  CAQ  CAL  120.46  3.000
 P0W  NAN  CAQ  CAI  110.82  3.000
 P0W  CAL  CAQ  CAI  128.63  3.000
 P0W  NAO  CAR  CAM  114.77  3.000
 P0W  CAM  CAR  CAK  124.28  3.000
 P0W  NAO  CAR  CAK  120.87  3.000
 P0W  NAW  CAS  CAH  119.67  3.000
 P0W  CAH  CAS  CAG  120.37  3.000
 P0W  NAW  CAS  CAG  119.95  3.000
 P0W  OAB  CAT  NAP  120.05  3.000
 P0W  OAB  CAT  CAK  125.76  3.000
 P0W  NAP  CAT  CAK  114.19  3.000
 P0W  OAC  CAU  NAP  123.09  3.000
 P0W  NAP  CAU  NAO  113.78  3.000
 P0W  OAC  CAU  NAO  123.13  3.000
 P0W  NAW  NAN  CAQ  105.87  3.000
 P0W  H12  NAO  CAU  118.20  3.000
 P0W  H12  NAO  CAR  116.99  3.000
 P0W  CAU  NAO  CAR  123.97  3.000
 P0W  H17  NAP  CAU  115.95  3.000
 P0W  H17  NAP  CAT  116.87  3.000
 P0W  CAU  NAP  CAT  127.18  3.000
 P0W  CAM  NAV  CAL  112.51  3.000
 P0W  CAL  NAV  CAA  110.47  3.000
 P0W  CAM  NAV  CAA  112.67  3.000
 P0W  NAN  NAW  CAS  120.44  3.000
 P0W  NAN  NAW  CAJ  112.02  3.000
 P0W  CAS  NAW  CAJ  127.50  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
 P0W  CONST_01  CAS  CAG  CAE  CAD     0.00   0.0  0
 P0W  CONST_02  CAS  CAH  CAF  CAD     0.00   0.0  0
 P0W  CONST_03  NAW  CAS  CAG  CAE   180.00   0.0  0
 P0W  CONST_04  CAH  CAS  CAG  CAE     0.00   0.0  0
 P0W  CONST_05  CAH  CAF  CAD  CAE     0.00   0.0  0
 P0W  CONST_06  CAG  CAE  CAD  CAF     0.00   0.0  0
 P0W  CONST_07  CAG  CAS  CAH  CAF     0.00   0.0  0
 P0W  CONST_08  NAW  CAS  CAH  CAF   180.00   0.0  0
 P0W  CONST_13  CAS  NAW  CAJ  CAI   180.00   0.0  0
 P0W  CONST_14  NAN  NAW  CAJ  CAI     0.00   0.0  0
 P0W  CONST_15  NAW  NAN  CAQ  CAI     0.00   0.0  0
 P0W  CONST_16  NAN  CAQ  CAI  CAJ     0.00   0.0  0
 P0W  CONST_17  CAQ  NAN  NAW  CAJ     0.00   0.0  0
 P0W  CONST_18  NAW  CAJ  CAI  CAQ     0.00   0.0  0
 P0W  CONST_19  CAS  NAW  NAN  CAQ   180.00   0.0  0
 P0W  CONST_20  CAU  NAP  CAT  CAK     0.00   0.0  0
 P0W  CONST_21  NAP  CAU  NAO  CAR     0.00   0.0  0
 P0W  CONST_22  NAO  CAU  NAP  CAT     0.00   0.0  0
 P0W  CONST_23  CAL  CAQ  CAI  CAJ   180.00   0.0  0
 P0W  CONST_24  NAW  NAN  CAQ  CAL   180.00   0.0  0
 P0W  CONST_25  OAC  CAU  NAO  CAR   180.00   0.0  0
 P0W  CONST_26  OAC  CAU  NAP  CAT   180.00   0.0  0
 P0W  CONST_27  OAB  CAT  NAP  CAU   180.00   0.0  0
 P0W  CONST_28  H7   CAG  CAE  CAD   180.00   0.0  0
 P0W  CONST_29  H8   CAH  CAF  CAD   180.00   0.0  0
 P0W  CONST_30  H6   CAF  CAD  CAE   180.00   0.0  0
 P0W  CONST_31  H5   CAE  CAD  CAF   180.00   0.0  0
 P0W  CONST_32  H4   CAD  CAE  CAG   180.00   0.0  0
 P0W  CONST_33  H10  CAJ  CAI  CAQ   180.00   0.0  0
 P0W  CONST_34  H9   CAI  CAQ  NAN   180.00   0.0  0
 P0W  CONST_35  H17  NAP  CAT  CAK   180.00   0.0  0
 P0W  CONST_36  H12  NAO  CAU  NAP   180.00   0.0  0
 P0W  Var_01    NAV  CAL  CAQ  CAI    73.44  30.0  2
 P0W  Var_02    NAV  CAM  CAR  CAK   145.02  30.0  3
 P0W  Var_03    CAR  CAM  NAV  CAA   148.08  30.0  1
 P0W  Var_04    CAQ  CAL  NAV  CAA  -178.60  30.0  3
 P0W  Var_05    H1   CAA  NAV  CAL    58.24  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
 P0W  plan-1  CAI  0.020
 P0W  plan-1  CAJ  0.020
 P0W  plan-1  CAL  0.020
 P0W  plan-1  CAQ  0.020
 P0W  plan-1  CAS  0.020
 P0W  plan-1  NAN  0.020
 P0W  plan-1  NAW  0.020
 P0W  plan-1  H9   0.020
 P0W  plan-1  H10  0.020
 P0W  plan-2  CAD  0.020
 P0W  plan-2  CAE  0.020
 P0W  plan-2  CAF  0.020
 P0W  plan-2  CAG  0.020
 P0W  plan-2  CAH  0.020
 P0W  plan-2  CAS  0.020
 P0W  plan-2  NAW  0.020
 P0W  plan-2  H5   0.020
 P0W  plan-2  H6   0.020
 P0W  plan-2  H7   0.020
 P0W  plan-2  H8   0.020
 P0W  plan-2  H4   0.020
 P0W  plan-3  CAK  0.020
 P0W  plan-3  CAM  0.020
 P0W  plan-3  CAR  0.020
 P0W  plan-3  CAT  0.020
 P0W  plan-3  CAU  0.020
 P0W  plan-3  NAO  0.020
 P0W  plan-3  NAP  0.020
 P0W  plan-3  OAB  0.020
 P0W  plan-3  OAC  0.020
 P0W  plan-3  H11  0.020
 P0W  plan-3  H17  0.020
 P0W  plan-3  H12  0.020

