# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 12:13:12 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-[2-(3,6-dimethoxynaphthalen-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: COc1ccc2cc(CCC3=C(NC(=O)NC3=O)C(O)=O)c(OC)cc2c1
#
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
 W7K  W7K  '5-[2-(3,6-dimethoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  45  27  .  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_W7K
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
 W7K  OAC  O  O     0  -0.387   2.8210   2.4660  -0.4197
 W7K  CAR  C  C     0   0.504   3.7823   1.9145   0.0387
 W7K  OAF  O  OH1   0  -0.588   4.8534   2.5240   0.5156
 W7K  CAV  C  CR6   0   0.289   3.9277   0.4252   0.1241
 W7K  NAN  N  NR16  0  -0.729   5.2128  -0.0358  -0.0135
 W7K  CAX  C  CR6   0   0.670   5.5590  -1.3554   0.0050
 W7K  OAD  O  O     0  -0.473   6.6981  -1.7470  -0.1357
 W7K  NAO  N  NR16  0  -0.717   4.4946  -2.1965   0.1964
 W7K  CAY  C  CR6   0   0.585   3.1706  -1.8452   0.3568
 W7K  OAE  O  O     0  -0.439   2.3237  -2.7022   0.5162
 W7K  CAW  C  CR6   0  -0.124   2.8829  -0.4081   0.3173
 W7K  CAM  C  CH2   0  -0.498   1.4491  -0.0155   0.5055
 W7K  CAL  C  CH2   0  -0.492   0.6399  -0.1387  -0.7964
 W7K  CAT  C  CR6   0   0.033  -0.8343   0.0496  -0.5731
 W7K  CAJ  C  CR16  0  -0.368  -1.6853  -1.0189  -0.5671
 W7K  CAZ  C  CR66  0   0.093  -3.0736  -0.8833  -0.3235
 W7K  CAH  C  CR16  0  -0.298  -3.9541  -1.9819  -0.3207
 W7K  CAG  C  CR16  0  -0.389  -5.2951  -1.8262  -0.0807
 W7K  CAS  C  CR6   0   0.393  -5.8164  -0.5367   0.1701
 W7K  OAP  O  O2    0  -0.474  -7.1207  -0.2992   0.4125
 W7K  CAA  C  CH3   0  -0.438  -8.0328  -1.3788   0.3825
 W7K  CAI  C  CR16  0  -0.443  -4.9766   0.5557   0.1749
 W7K  CBA  C  CR66  0   0.166  -3.5986   0.4077  -0.0709
 W7K  CAK  C  CR16  0  -0.484  -2.7185   1.5186  -0.0774
 W7K  CAU  C  CR6   0   0.362  -1.3801   1.3477  -0.3246
 W7K  OAQ  O  O2    0  -0.454  -0.4849   2.3478  -0.3560
 W7K  CAB  C  CH3   0  -0.436  -0.9192   3.6622  -0.0797
 W7K  H1   H  HOH1  0   0.502   4.7762   3.4857   0.4122
 W7K  H2   H  HNR6  0   0.430   4.7085  -3.1865   0.2172
 W7K  H4   H  HCH2  0   0.258   1.0131  -0.6821   1.2518
 W7K  H5   H  HCH2  0   0.267   1.3659   0.9937   0.8983
 W7K  H6   H  HCH2  0   0.254   1.0251   0.5802  -1.5208
 W7K  H7   H  HCH2  0   0.252   0.7978  -1.1320  -1.2194
 W7K  H8   H  HCR6  0   0.246  -1.2893  -2.0107  -0.7579
 W7K  H9   H  HCR6  0   0.257  -3.5623  -2.9734  -0.5140
 W7K  H10  H  HCR6  0   0.279  -5.9364  -2.6967  -0.0865
 W7K  H11  H  HCH3  0   0.260  -9.0153  -0.9560   0.5774
 W7K  H12  H  HCH3  0   0.228  -8.0524  -1.8730  -0.5922
 W7K  H13  H  HCH3  0   0.228  -7.8143  -2.1245   1.1513
 W7K  H14  H  HCR6  0   0.252  -5.3830   1.5415   0.3701
 W7K  H15  H  HCR6  0   0.272  -3.1327   2.4999   0.1158
 W7K  H16  H  HCH3  0   0.259  -0.0395   4.2972  -0.1466
 W7K  H17  H  HCH3  0   0.228  -1.6613   4.0085  -0.8039
 W7K  H18  H  HCH3  0   0.228  -1.3429   3.7479   0.9245
 W7K  H19  H  HNR6  0   0.438   5.9677   0.6184  -0.1658

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
 W7K  CAH  CAG  aromatic  1.371  0.020  1.371
 W7K  CAH  CAZ  aromatic  1.408  0.020  1.408
 W7K  CAG  CAS  aromatic  1.413  0.020  1.413
 W7K  CAJ  CAZ  aromatic  1.416  0.020  1.416
 W7K  CAJ  CAT  aromatic  1.366  0.020  1.366
 W7K  CAZ  CBA  aromatic  1.416  0.020  1.416
 W7K  CAS  OAP  single    1.348  0.020  1.348
 W7K  CAS  CAI  aromatic  1.378  0.020  1.378
 W7K  CAT  CAL  single    1.503  0.020  1.503
 W7K  CAT  CAU  aromatic  1.430  0.020  1.430
 W7K  CAL  CAM  single    1.538  0.020  1.538
 W7K  OAP  CAA  single    1.414  0.020  1.414
 W7K  CBA  CAI  aromatic  1.407  0.020  1.407
 W7K  CBA  CAK  aromatic  1.417  0.020  1.417
 W7K  CAU  CAK  aromatic  1.372  0.020  1.372
 W7K  CAU  OAQ  single    1.343  0.020  1.343
 W7K  OAQ  CAB  single    1.412  0.020  1.412
 W7K  CAM  CAW  single    1.498  0.020  1.498
 W7K  OAE  CAY  double    1.215  0.020  1.215
 W7K  CAW  CAY  single    1.466  0.020  1.466
 W7K  CAW  CAV  double    1.350  0.020  1.350
 W7K  CAY  NAO  single    1.379  0.020  1.379
 W7K  CAV  CAR  single    1.499  0.020  1.499
 W7K  CAV  NAN  single    1.372  0.020  1.372
 W7K  OAC  CAR  double    1.199  0.020  1.199
 W7K  CAR  OAF  single    1.321  0.020  1.321
 W7K  NAO  CAX  single    1.370  0.020  1.370
 W7K  NAN  CAX  single    1.364  0.020  1.364
 W7K  CAX  OAD  double    1.213  0.020  1.213
 W7K  OAF  H1   single    0.850  0.020  0.980
 W7K  NAO  H2   single    0.860  0.020  1.020
 W7K  CAM  H4   single    0.970  0.020  1.090
 W7K  CAM  H5   single    0.970  0.020  1.090
 W7K  CAL  H6   single    0.970  0.020  1.090
 W7K  CAL  H7   single    0.970  0.020  1.090
 W7K  CAJ  H8   single    0.930  0.020  1.080
 W7K  CAH  H9   single    0.930  0.020  1.080
 W7K  CAG  H10  single    0.930  0.020  1.080
 W7K  CAA  H11  single    0.970  0.020  1.090
 W7K  CAA  H12  single    0.970  0.020  1.090
 W7K  CAA  H13  single    0.970  0.020  1.090
 W7K  CAI  H14  single    0.930  0.020  1.080
 W7K  CAK  H15  single    0.930  0.020  1.080
 W7K  CAB  H16  single    0.970  0.020  1.090
 W7K  CAB  H17  single    0.970  0.020  1.090
 W7K  CAB  H18  single    0.970  0.020  1.090
 W7K  NAN  H19  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
 W7K  CAV  CAR  OAF  111.04  3.000
 W7K  OAF  CAR  OAC  125.13  3.000
 W7K  CAV  CAR  OAC  123.82  3.000
 W7K  H1   OAF  CAR  110.75  3.000
 W7K  CAW  CAV  NAN  122.12  3.000
 W7K  NAN  CAV  CAR  114.77  3.000
 W7K  CAW  CAV  CAR  123.11  3.000
 W7K  H19  NAN  CAX  116.02  3.000
 W7K  H19  NAN  CAV  119.81  3.000
 W7K  CAX  NAN  CAV  124.14  3.000
 W7K  NAO  CAX  OAD  123.21  3.000
 W7K  OAD  CAX  NAN  123.30  3.000
 W7K  NAO  CAX  NAN  113.49  3.000
 W7K  H2   NAO  CAY  116.69  3.000
 W7K  H2   NAO  CAX  116.02  3.000
 W7K  CAY  NAO  CAX  127.28  3.000
 W7K  CAW  CAY  OAE  123.92  3.000
 W7K  CAW  CAY  NAO  115.78  3.000
 W7K  OAE  CAY  NAO  120.30  3.000
 W7K  CAM  CAW  CAY  116.18  3.000
 W7K  CAY  CAW  CAV  117.19  3.000
 W7K  CAM  CAW  CAV  126.64  3.000
 W7K  H5   CAM  H4   106.84  3.000
 W7K  H5   CAM  CAL  109.89  3.000
 W7K  H4   CAM  CAL  108.64  3.000
 W7K  H5   CAM  CAW  111.23  3.000
 W7K  H4   CAM  CAW  107.95  3.000
 W7K  CAL  CAM  CAW  112.10  3.000
 W7K  H7   CAL  H6   106.94  3.000
 W7K  H7   CAL  CAT  108.28  3.000
 W7K  H6   CAL  CAT  111.25  3.000
 W7K  H7   CAL  CAM  108.97  3.000
 W7K  H6   CAL  CAM  108.88  3.000
 W7K  CAT  CAL  CAM  112.35  3.000
 W7K  CAU  CAT  CAJ  118.13  3.000
 W7K  CAU  CAT  CAL  120.93  3.000
 W7K  CAJ  CAT  CAL  120.91  3.000
 W7K  H8   CAJ  CAZ  118.40  3.000
 W7K  H8   CAJ  CAT  119.14  3.000
 W7K  CAZ  CAJ  CAT  122.46  3.000
 W7K  CBA  CAZ  CAH  118.62  3.000
 W7K  CBA  CAZ  CAJ  118.77  3.000
 W7K  CAH  CAZ  CAJ  122.60  3.000
 W7K  H9   CAH  CAG  119.26  3.000
 W7K  H9   CAH  CAZ  119.18  3.000
 W7K  CAG  CAH  CAZ  121.56  3.000
 W7K  H10  CAG  CAS  121.12  3.000
 W7K  H10  CAG  CAH  119.19  3.000
 W7K  CAS  CAG  CAH  119.70  3.000
 W7K  CAI  CAS  OAP  116.71  3.000
 W7K  CAI  CAS  CAG  119.94  3.000
 W7K  OAP  CAS  CAG  123.35  3.000
 W7K  CAA  OAP  CAS  119.08  3.000
 W7K  H13  CAA  H12  108.80  3.000
 W7K  H13  CAA  H11  108.65  3.000
 W7K  H12  CAA  H11  108.63  3.000
 W7K  H13  CAA  OAP  112.15  3.000
 W7K  H12  CAA  OAP  112.07  3.000
 W7K  H11  CAA  OAP  106.40  3.000
 W7K  H14  CAI  CBA  119.61  3.000
 W7K  H14  CAI  CAS  119.54  3.000
 W7K  CBA  CAI  CAS  120.85  3.000
 W7K  CAK  CBA  CAI  121.76  3.000
 W7K  CAK  CBA  CAZ  118.91  3.000
 W7K  CAI  CBA  CAZ  119.33  3.000
 W7K  H15  CAK  CAU  121.22  3.000
 W7K  H15  CAK  CBA  118.17  3.000
 W7K  CAU  CAK  CBA  120.61  3.000
 W7K  OAQ  CAU  CAK  124.20  3.000
 W7K  OAQ  CAU  CAT  114.69  3.000
 W7K  CAK  CAU  CAT  121.12  3.000
 W7K  CAB  OAQ  CAU  118.94  3.000
 W7K  H18  CAB  H17  108.70  3.000
 W7K  H18  CAB  H16  108.93  3.000
 W7K  H17  CAB  H16  108.88  3.000
 W7K  H18  CAB  OAQ  111.84  3.000
 W7K  H17  CAB  OAQ  111.97  3.000
 W7K  H16  CAB  OAQ  106.44  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
 W7K  CONST_01  CAH  CAZ  CAJ  CAT   180.00   0.0  0
 W7K  CONST_02  CBA  CAZ  CAJ  CAT     0.00   0.0  0
 W7K  CONST_03  CBA  CAK  CAU  CAT     0.00   0.0  0
 W7K  CONST_04  CAG  CAH  CAZ  CAJ   180.00   0.0  0
 W7K  CONST_05  CAI  CBA  CAZ  CAJ   180.00   0.0  0
 W7K  CONST_06  CAK  CBA  CAZ  CAJ     0.00   0.0  0
 W7K  CONST_07  CAK  CAU  CAT  CAJ     0.00   0.0  0
 W7K  CONST_08  CAS  CAG  CAH  CAZ     0.00   0.0  0
 W7K  CONST_09  CAU  CAT  CAJ  CAZ     0.00   0.0  0
 W7K  CONST_10  CAS  CAI  CBA  CAZ     0.00   0.0  0
 W7K  CONST_11  CAU  CAK  CBA  CAZ     0.00   0.0  0
 W7K  CONST_12  CAI  CAS  CAG  CAH     0.00   0.0  0
 W7K  CONST_13  CAI  CBA  CAZ  CAH     0.00   0.0  0
 W7K  CONST_14  CAK  CBA  CAZ  CAH   180.00   0.0  0
 W7K  CONST_15  CBA  CAZ  CAH  CAG     0.00   0.0  0
 W7K  CONST_16  CBA  CAI  CAS  CAG     0.00   0.0  0
 W7K  CONST_17  CAK  CBA  CAI  CAS   180.00   0.0  0
 W7K  CONST_18  CAU  CAK  CBA  CAI   180.00   0.0  0
 W7K  CONST_19  NAO  CAX  NAN  CAV     0.00   0.0  0
 W7K  CONST_20  CAY  NAO  CAX  NAN     0.00   0.0  0
 W7K  CONST_21  CAW  CAY  NAO  CAX     0.00   0.0  0
 W7K  CONST_22  CAZ  CAJ  CAT  CAL   180.00   0.0  0
 W7K  CONST_23  CAK  CAU  CAT  CAL   180.00   0.0  0
 W7K  CONST_24  OAQ  CAU  CAT  CAJ   180.00   0.0  0
 W7K  CONST_25  OAP  CAS  CAG  CAH   180.00   0.0  0
 W7K  CONST_26  CBA  CAI  CAS  OAP   180.00   0.0  0
 W7K  CONST_27  OAQ  CAU  CAK  CBA   180.00   0.0  0
 W7K  CONST_28  OAD  CAX  NAN  CAV   180.00   0.0  0
 W7K  CONST_29  OAE  CAY  NAO  CAX   180.00   0.0  0
 W7K  CONST_30  CAY  NAO  CAX  OAD   180.00   0.0  0
 W7K  CONST_31  H15  CAK  CAU  CAT   180.00   0.0  0
 W7K  CONST_32  H9   CAH  CAZ  CAJ     0.00   0.0  0
 W7K  CONST_33  H10  CAG  CAH  CAZ   180.00   0.0  0
 W7K  CONST_34  H14  CAI  CBA  CAZ   180.00   0.0  0
 W7K  CONST_35  H8   CAJ  CAZ  CAH     0.00   0.0  0
 W7K  CONST_36  H2   NAO  CAX  NAN   180.00   0.0  0
 W7K  CONST_37  H19  NAN  CAX  NAO   180.00   0.0  0
 W7K  CONST_38  H1   OAF  CAR  CAV   180.00   0.0  0
 W7K  Var_01    CAW  CAV  CAR  OAC   -32.69  30.0  2
 W7K  Var_02    CAL  CAM  CAW  CAV    98.59  30.0  3
 W7K  Var_03    CAT  CAL  CAM  CAW   171.29  30.0  1
 W7K  Var_04    CAJ  CAT  CAL  CAM  -103.96  30.0  2
 W7K  Var_05    CAI  CAS  OAP  CAA   178.25  30.0  3
 W7K  Var_06    H11  CAA  OAP  CAS  -178.57  30.0  3
 W7K  Var_07    H16  CAB  OAQ  CAU   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
 W7K  plan-1  CAR  0.020
 W7K  plan-1  CAV  0.020
 W7K  plan-1  NAN  0.020
 W7K  plan-1  CAX  0.020
 W7K  plan-1  OAD  0.020
 W7K  plan-1  NAO  0.020
 W7K  plan-1  CAY  0.020
 W7K  plan-1  OAE  0.020
 W7K  plan-1  CAW  0.020
 W7K  plan-1  CAM  0.020
 W7K  plan-1  H2   0.020
 W7K  plan-1  H19  0.020
 W7K  plan-2  CAL  0.020
 W7K  plan-2  CAT  0.020
 W7K  plan-2  CAJ  0.020
 W7K  plan-2  CAZ  0.020
 W7K  plan-2  CAH  0.020
 W7K  plan-2  CAG  0.020
 W7K  plan-2  CAS  0.020
 W7K  plan-2  OAP  0.020
 W7K  plan-2  CAI  0.020
 W7K  plan-2  CBA  0.020
 W7K  plan-2  CAK  0.020
 W7K  plan-2  CAU  0.020
 W7K  plan-2  OAQ  0.020
 W7K  plan-2  H8   0.020
 W7K  plan-2  H9   0.020
 W7K  plan-2  H10  0.020
 W7K  plan-2  H14  0.020
 W7K  plan-2  H15  0.020
 W7K  plan-3  OAC  0.020
 W7K  plan-3  CAR  0.020
 W7K  plan-3  OAF  0.020
 W7K  plan-3  CAV  0.020
 W7K  plan-3  H1   0.020

