# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 09:52:55 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(3-methoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ccccc2cc1CCC3=C(NC(=O)NC3=O)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
 W7I  W7I  '5-[2-(3-methoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  41  25  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W7I
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
 W7I  OAB  O  OH1   0  -0.590  -4.0979  -2.6893   0.4157
 W7I  CAQ  C  C     0   0.508  -3.0289  -2.0259   0.0114
 W7I  OAE  O  O     0  -0.387  -2.0211  -2.5293  -0.4003
 W7I  CAT  C  CR6   0   0.284  -3.2422  -0.5456   0.1116
 W7I  NAN  N  NR16  0  -0.730  -4.5449  -0.1391  -0.0327
 W7I  CAV  C  CR6   0   0.670  -4.9489   1.1638  -0.0071
 W7I  OAC  O  O     0  -0.473  -6.1041   1.5055  -0.1474
 W7I  NAO  N  NR16  0  -0.716  -3.9227   2.0498   0.1899
 W7I  CAW  C  CR6   0   0.586  -2.5864   1.7551   0.3597
 W7I  OAD  O  O     0  -0.440  -1.7784   2.6479   0.5258
 W7I  CAU  C  CR6   0  -0.121  -2.2367   0.3317   0.3203
 W7I  CAM  C  CH2   0  -0.499  -0.7895   0.0045   0.5272
 W7I  CAL  C  CH2   0  -0.492   0.0323   0.1664  -0.7626
 W7I  CAR  C  CR6   0   0.041   1.5099   0.0654  -0.5091
 W7I  CAJ  C  CR16  0  -0.373   2.2954   1.1838  -0.4933
 W7I  CAX  C  CR66  0   0.110   3.6835   1.1338  -0.2189
 W7I  CAH  C  CR16  0  -0.313   4.4909   2.2929  -0.2066
 W7I  CAF  C  CR16  0  -0.269   5.8304   2.2086   0.0683
 W7I  CAG  C  CR16  0  -0.259   6.4165   0.9562   0.3418
 W7I  CAI  C  CR16  0  -0.323   5.6560  -0.1833   0.3351
 W7I  CAY  C  CR66  0   0.135   4.2712  -0.1247   0.0540
 W7I  CAK  C  CR16  0  -0.472   3.4620  -1.2856   0.0366
 W7I  CAS  C  CR6   0   0.361   2.1209  -1.1978  -0.2410
 W7I  OAP  O  O2    0  -0.455   1.2851  -2.2479  -0.2850
 W7I  CAA  C  CH3   0  -0.437   1.7936  -3.5358  -0.0108
 W7I  H1   H  HOH1  0   0.503  -3.9733  -3.6448   0.3018
 W7I  H2   H  HNR6  0   0.438  -5.2703  -0.8255  -0.1856
 W7I  H3   H  HNR6  0   0.430  -4.1781   3.0300   0.2087
 W7I  H4   H  HCH2  0   0.259  -0.3958   0.6903   1.2796
 W7I  H5   H  HCH2  0   0.269  -0.6646  -0.9997   0.9211
 W7I  H6   H  HCH2  0   0.255  -0.2941  -0.5800  -1.4879
 W7I  H7   H  HCH2  0   0.254  -0.1758   1.1457  -1.1961
 W7I  H8   H  HCR6  0   0.247   1.8441   2.1484  -0.6999
 W7I  H9   H  HCR6  0   0.252   4.0352   3.2526  -0.4200
 W7I  H10  H  HCR6  0   0.254   6.4428   3.1007   0.0777
 W7I  H11  H  HCR6  0   0.255   7.4757   0.8972   0.5566
 W7I  H12  H  HCR6  0   0.250   6.1104  -1.1440   0.5467
 W7I  H13  H  HCR6  0   0.274   3.9318  -2.2378   0.2479
 W7I  H14  H  HCH3  0   0.227   2.5712  -3.8284  -0.7214
 W7I  H15  H  HCH3  0   0.228   2.2004  -3.6054   1.0017
 W7I  H16  H  HCH3  0   0.260   0.9561  -4.2225  -0.1026

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
 W7I  CAH  CAF  aromatic  1.370  0.020  1.370
 W7I  CAH  CAX  aromatic  1.413  0.020  1.413
 W7I  CAF  CAG  aromatic  1.410  0.020  1.410
 W7I  CAJ  CAX  aromatic  1.416  0.020  1.416
 W7I  CAJ  CAR  aromatic  1.367  0.020  1.367
 W7I  CAX  CAY  aromatic  1.416  0.020  1.416
 W7I  CAL  CAR  single    1.503  0.020  1.503
 W7I  CAL  CAM  single    1.538  0.020  1.538
 W7I  CAG  CAI  aromatic  1.370  0.020  1.370
 W7I  CAR  CAS  aromatic  1.429  0.020  1.429
 W7I  CAY  CAI  aromatic  1.414  0.020  1.414
 W7I  CAY  CAK  aromatic  1.415  0.020  1.415
 W7I  CAS  CAK  aromatic  1.372  0.020  1.372
 W7I  CAS  OAP  single    1.343  0.020  1.343
 W7I  OAP  CAA  single    1.412  0.020  1.412
 W7I  CAM  CAU  single    1.498  0.020  1.498
 W7I  OAD  CAW  double    1.215  0.020  1.215
 W7I  CAU  CAW  single    1.466  0.020  1.466
 W7I  CAU  CAT  double    1.351  0.020  1.351
 W7I  CAW  NAO  single    1.379  0.020  1.379
 W7I  CAT  CAQ  single    1.499  0.020  1.499
 W7I  CAT  NAN  single    1.372  0.020  1.372
 W7I  OAE  CAQ  double    1.199  0.020  1.199
 W7I  CAQ  OAB  single    1.322  0.020  1.322
 W7I  NAO  CAV  single    1.370  0.020  1.370
 W7I  NAN  CAV  single    1.364  0.020  1.364
 W7I  CAV  OAC  double    1.213  0.020  1.213
 W7I  OAB  H1   single    0.850  0.020  0.980
 W7I  NAN  H2   single    0.860  0.020  1.020
 W7I  NAO  H3   single    0.860  0.020  1.020
 W7I  CAM  H4   single    0.970  0.020  1.090
 W7I  CAM  H5   single    0.970  0.020  1.090
 W7I  CAL  H6   single    0.970  0.020  1.090
 W7I  CAL  H7   single    0.970  0.020  1.090
 W7I  CAJ  H8   single    0.930  0.020  1.080
 W7I  CAH  H9   single    0.930  0.020  1.080
 W7I  CAF  H10  single    0.930  0.020  1.080
 W7I  CAG  H11  single    0.930  0.020  1.080
 W7I  CAI  H12  single    0.930  0.020  1.080
 W7I  CAK  H13  single    0.930  0.020  1.080
 W7I  CAA  H14  single    0.970  0.020  1.090
 W7I  CAA  H15  single    0.970  0.020  1.090
 W7I  CAA  H16  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
 W7I  H1   OAB  CAQ  110.76  3.000
 W7I  CAT  CAQ  OAE  123.85  3.000
 W7I  OAE  CAQ  OAB  125.03  3.000
 W7I  CAT  CAQ  OAB  111.11  3.000
 W7I  CAU  CAT  NAN  122.04  3.000
 W7I  NAN  CAT  CAQ  114.87  3.000
 W7I  CAU  CAT  CAQ  123.08  3.000
 W7I  H2   NAN  CAV  116.04  3.000
 W7I  H2   NAN  CAT  119.76  3.000
 W7I  CAV  NAN  CAT  124.20  3.000
 W7I  NAO  CAV  OAC  123.22  3.000
 W7I  OAC  CAV  NAN  123.29  3.000
 W7I  NAO  CAV  NAN  113.48  3.000
 W7I  H3   NAO  CAW  116.66  3.000
 W7I  H3   NAO  CAV  116.08  3.000
 W7I  CAW  NAO  CAV  127.26  3.000
 W7I  CAU  CAW  OAD  123.93  3.000
 W7I  CAU  CAW  NAO  115.80  3.000
 W7I  OAD  CAW  NAO  120.27  3.000
 W7I  CAM  CAU  CAW  116.02  3.000
 W7I  CAW  CAU  CAT  117.21  3.000
 W7I  CAM  CAU  CAT  126.77  3.000
 W7I  H5   CAM  H4   106.83  3.000
 W7I  H5   CAM  CAL  109.88  3.000
 W7I  H4   CAM  CAL  108.61  3.000
 W7I  H5   CAM  CAU  111.30  3.000
 W7I  H4   CAM  CAU  107.84  3.000
 W7I  CAL  CAM  CAU  112.17  3.000
 W7I  H7   CAL  H6   107.03  3.000
 W7I  H7   CAL  CAR  108.36  3.000
 W7I  H6   CAL  CAR  111.13  3.000
 W7I  H7   CAL  CAM  109.02  3.000
 W7I  H6   CAL  CAM  109.01  3.000
 W7I  CAR  CAL  CAM  112.14  3.000
 W7I  CAS  CAR  CAJ  118.40  3.000
 W7I  CAS  CAR  CAL  120.78  3.000
 W7I  CAJ  CAR  CAL  120.80  3.000
 W7I  H8   CAJ  CAX  118.44  3.000
 W7I  H8   CAJ  CAR  119.10  3.000
 W7I  CAX  CAJ  CAR  122.46  3.000
 W7I  CAY  CAX  CAH  119.37  3.000
 W7I  CAY  CAX  CAJ  118.41  3.000
 W7I  CAH  CAX  CAJ  122.21  3.000
 W7I  H9   CAH  CAF  120.34  3.000
 W7I  H9   CAH  CAX  118.98  3.000
 W7I  CAF  CAH  CAX  120.67  3.000
 W7I  H10  CAF  CAG  119.70  3.000
 W7I  H10  CAF  CAH  120.29  3.000
 W7I  CAG  CAF  CAH  120.01  3.000
 W7I  H11  CAG  CAI  119.93  3.000
 W7I  H11  CAG  CAF  119.59  3.000
 W7I  CAI  CAG  CAF  120.48  3.000
 W7I  H12  CAI  CAY  119.09  3.000
 W7I  H12  CAI  CAG  120.24  3.000
 W7I  CAY  CAI  CAG  120.67  3.000
 W7I  CAK  CAY  CAI  121.90  3.000
 W7I  CAK  CAY  CAX  119.31  3.000
 W7I  CAI  CAY  CAX  118.79  3.000
 W7I  H13  CAK  CAS  121.32  3.000
 W7I  H13  CAK  CAY  118.10  3.000
 W7I  CAS  CAK  CAY  120.59  3.000
 W7I  OAP  CAS  CAK  124.39  3.000
 W7I  OAP  CAS  CAR  114.78  3.000
 W7I  CAK  CAS  CAR  120.83  3.000
 W7I  CAA  OAP  CAS  118.88  3.000
 W7I  H16  CAA  H15  108.95  3.000
 W7I  H16  CAA  H14  108.91  3.000
 W7I  H15  CAA  H14  108.67  3.000
 W7I  H16  CAA  OAP  106.41  3.000
 W7I  H15  CAA  OAP  111.84  3.000
 W7I  H14  CAA  OAP  111.97  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
 W7I  CONST_01  CAH  CAX  CAJ  CAR   180.00   0.0  0
 W7I  CONST_02  CAY  CAX  CAJ  CAR     0.00   0.0  0
 W7I  CONST_03  CAY  CAK  CAS  CAR     0.00   0.0  0
 W7I  CONST_04  CAF  CAH  CAX  CAJ   180.00   0.0  0
 W7I  CONST_05  CAI  CAY  CAX  CAJ   180.00   0.0  0
 W7I  CONST_06  CAK  CAY  CAX  CAJ     0.00   0.0  0
 W7I  CONST_07  CAK  CAS  CAR  CAJ     0.00   0.0  0
 W7I  CONST_08  CAG  CAF  CAH  CAX     0.00   0.0  0
 W7I  CONST_09  CAS  CAR  CAJ  CAX     0.00   0.0  0
 W7I  CONST_10  CAG  CAI  CAY  CAX     0.00   0.0  0
 W7I  CONST_11  CAS  CAK  CAY  CAX     0.00   0.0  0
 W7I  CONST_12  CAI  CAG  CAF  CAH     0.00   0.0  0
 W7I  CONST_13  CAI  CAY  CAX  CAH     0.00   0.0  0
 W7I  CONST_14  CAK  CAY  CAX  CAH   180.00   0.0  0
 W7I  CONST_15  CAY  CAX  CAH  CAF     0.00   0.0  0
 W7I  CONST_16  CAY  CAI  CAG  CAF     0.00   0.0  0
 W7I  CONST_17  CAK  CAY  CAI  CAG   180.00   0.0  0
 W7I  CONST_18  CAS  CAK  CAY  CAI   180.00   0.0  0
 W7I  CONST_19  NAO  CAV  NAN  CAT     0.00   0.0  0
 W7I  CONST_20  CAW  NAO  CAV  NAN     0.00   0.0  0
 W7I  CONST_21  CAU  CAW  NAO  CAV     0.00   0.0  0
 W7I  CONST_22  CAX  CAJ  CAR  CAL   180.00   0.0  0
 W7I  CONST_23  CAK  CAS  CAR  CAL   180.00   0.0  0
 W7I  CONST_24  OAP  CAS  CAR  CAJ   180.00   0.0  0
 W7I  CONST_25  OAP  CAS  CAK  CAY   180.00   0.0  0
 W7I  CONST_26  OAC  CAV  NAN  CAT   180.00   0.0  0
 W7I  CONST_27  OAD  CAW  NAO  CAV   180.00   0.0  0
 W7I  CONST_28  CAW  NAO  CAV  OAC   180.00   0.0  0
 W7I  CONST_29  H13  CAK  CAS  CAR   180.00   0.0  0
 W7I  CONST_30  H9   CAH  CAX  CAJ     0.00   0.0  0
 W7I  CONST_31  H10  CAF  CAH  CAX   180.00   0.0  0
 W7I  CONST_32  H12  CAI  CAY  CAX   180.00   0.0  0
 W7I  CONST_33  H11  CAG  CAF  CAH   180.00   0.0  0
 W7I  CONST_34  H8   CAJ  CAX  CAH     0.00   0.0  0
 W7I  CONST_35  H3   NAO  CAV  NAN   180.00   0.0  0
 W7I  CONST_36  H2   NAN  CAV  NAO   180.00   0.0  0
 W7I  CONST_37  H1   OAB  CAQ  CAT   180.00   0.0  0
 W7I  Var_01    CAU  CAT  CAQ  OAB   151.12  30.0  2
 W7I  Var_02    CAL  CAM  CAU  CAT    98.59  30.0  2
 W7I  Var_03    CAR  CAL  CAM  CAU   170.39  30.0  2
 W7I  Var_04    CAJ  CAR  CAL  CAM  -103.86  30.0  2
 W7I  Var_05    H14  CAA  OAP  CAS   -61.07  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
 W7I  plan-1  CAQ  0.020
 W7I  plan-1  CAT  0.020
 W7I  plan-1  NAN  0.020
 W7I  plan-1  CAV  0.020
 W7I  plan-1  OAC  0.020
 W7I  plan-1  NAO  0.020
 W7I  plan-1  CAW  0.020
 W7I  plan-1  OAD  0.020
 W7I  plan-1  CAU  0.020
 W7I  plan-1  CAM  0.020
 W7I  plan-1  H2   0.020
 W7I  plan-1  H3   0.020
 W7I  plan-2  CAL  0.020
 W7I  plan-2  CAR  0.020
 W7I  plan-2  CAJ  0.020
 W7I  plan-2  CAX  0.020
 W7I  plan-2  CAH  0.020
 W7I  plan-2  CAF  0.020
 W7I  plan-2  CAG  0.020
 W7I  plan-2  CAI  0.020
 W7I  plan-2  CAY  0.020
 W7I  plan-2  CAK  0.020
 W7I  plan-2  CAS  0.020
 W7I  plan-2  OAP  0.020
 W7I  plan-2  H8   0.020
 W7I  plan-2  H9   0.020
 W7I  plan-2  H10  0.020
 W7I  plan-2  H11  0.020
 W7I  plan-2  H12  0.020
 W7I  plan-2  H13  0.020
 W7I  plan-3  OAB  0.020
 W7I  plan-3  CAQ  0.020
 W7I  plan-3  OAE  0.020
 W7I  plan-3  CAT  0.020
 W7I  plan-3  H1   0.020

