# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 14:00:54 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-{2-[3-(methoxymethoxy)naphthalen-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: COCOc1cc2ccccc2cc1CCC3=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
 W8Z  W8Z  '5-{2-[3-(methoxymethoxy)naphthalen-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_W8Z
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
 W8Z  OAB  O  O     0  -0.384   1.9895  -2.2775   0.6904
 W8Z  CAS  C  C     0   0.508   3.0171  -1.8657   0.2294
 W8Z  OAE  O  OH1   0  -0.590   4.0382  -2.6193  -0.1403
 W8Z  CAV  C  CR6   0   0.285   3.3140  -0.4119   0.0144
 W8Z  NAO  N  NR16  0  -0.730   4.6403  -0.0731   0.1095
 W8Z  CAX  C  CR6   0   0.670   5.1188   1.1971  -0.0282
 W8Z  OAC  O  O     0  -0.473   6.2937   1.4807   0.0719
 W8Z  NAP  N  NR16  0  -0.716   4.1432   2.1227  -0.2898
 W8Z  CAY  C  CR6   0   0.586   2.7892   1.8952  -0.4175
 W8Z  OAD  O  O     0  -0.440   2.0330   2.8167  -0.6552
 W8Z  CAW  C  CR6   0  -0.119   2.3576   0.5044  -0.2494
 W8Z  CAM  C  CH2   0  -0.507   0.8904   0.2485  -0.4070
 W8Z  CAL  C  CH2   0  -0.490   0.0996   0.5574   0.8756
 W8Z  CAT  C  CR6   0   0.030  -1.3817   0.5001   0.6314
 W8Z  CAJ  C  CR16  0  -0.369  -2.0994   1.6473   0.4345
 W8Z  CAZ  C  CR66  0   0.111  -3.4825   1.6336   0.1394
 W8Z  CAH  C  CR16  0  -0.312  -4.2227   2.8204  -0.0621
 W8Z  CAF  C  CR16  0  -0.268  -5.5585   2.7681  -0.3594
 W8Z  CAG  C  CR16  0  -0.259  -6.2092   1.5217  -0.4663
 W8Z  CAI  C  CR16  0  -0.321  -5.5150   0.3568  -0.2746
 W8Z  CBA  C  CR66  0   0.132  -4.1350   0.3816   0.0357
 W8Z  CAK  C  CR16  0  -0.457  -3.3955  -0.8076   0.2379
 W8Z  CAU  C  CR6   0   0.364  -2.0594  -0.7520   0.5441
 W8Z  OAR  O  O2    0  -0.479  -1.2758  -1.8237   0.7921
 W8Z  CAN  C  CH2   0   0.022  -1.8096  -3.1245   0.7457
 W8Z  OAQ  O  O2    0  -0.482  -2.1067  -3.5464  -0.5343
 W8Z  CAA  C  CH3   0  -0.410  -0.9798  -3.7077  -1.3738
 W8Z  H1   H  HOH1  0   0.502   3.8585  -3.5547   0.0444
 W8Z  H2   H  HNR6  0   0.438   5.3269  -0.7867   0.3103
 W8Z  H3   H  HNR6  0   0.430   4.4571   3.0793  -0.4027
 W8Z  H4   H  HCH2  0   0.260   0.5220   0.8949  -1.2058
 W8Z  H5   H  HCH2  0   0.274   0.7001  -0.7751  -0.7193
 W8Z  H6   H  HCH2  0   0.256   0.4017  -0.1377   1.6595
 W8Z  H7   H  HCH2  0   0.254   0.3527   1.5605   1.2231
 W8Z  H8   H  HCR6  0   0.247  -1.5919   2.6036   0.5041
 W8Z  H9   H  HCR6  0   0.252  -3.7168   3.7750   0.0231
 W8Z  H10  H  HCR6  0   0.254  -6.1185   3.6810  -0.5149
 W8Z  H11  H  HCR6  0   0.255  -7.2653   1.4882  -0.7008
 W8Z  H12  H  HCR6  0   0.251  -6.0192  -0.5986  -0.3601
 W8Z  H13  H  HCR6  0   0.275  -3.9192  -1.7488   0.1339
 W8Z  H14  H  HCH2  0   0.241  -1.0380  -3.7479   1.2089
 W8Z  H15  H  HCH2  0   0.237  -2.7322  -3.1893   1.3298
 W8Z  H16  H  HCH3  0   0.222  -0.5702  -2.7516  -1.7092
 W8Z  H17  H  HCH3  0   0.212  -0.1811  -4.2668  -0.8754
 W8Z  H18  H  HCH3  0   0.238  -1.3039  -4.2687  -2.2483

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
 W8Z  CAF  CAH  aromatic  1.370  0.020  1.370
 W8Z  CAF  CAG  aromatic  1.410  0.020  1.410
 W8Z  CAA  OAQ  single    1.414  0.020  1.414
 W8Z  CAH  CAZ  aromatic  1.413  0.020  1.413
 W8Z  CAG  CAI  aromatic  1.370  0.020  1.370
 W8Z  CAZ  CAJ  aromatic  1.414  0.020  1.414
 W8Z  CAZ  CBA  aromatic  1.416  0.020  1.416
 W8Z  CAJ  CAT  aromatic  1.367  0.020  1.367
 W8Z  CAI  CBA  aromatic  1.415  0.020  1.415
 W8Z  CBA  CAK  aromatic  1.415  0.020  1.415
 W8Z  OAQ  CAN  single    1.380  0.020  1.380
 W8Z  CAT  CAL  single    1.502  0.020  1.502
 W8Z  CAT  CAU  aromatic  1.426  0.020  1.426
 W8Z  CAK  CAU  aromatic  1.372  0.020  1.372
 W8Z  CAL  CAM  single    1.538  0.020  1.538
 W8Z  CAU  OAR  single    1.351  0.020  1.351
 W8Z  CAN  OAR  single    1.407  0.020  1.407
 W8Z  CAM  CAW  single    1.498  0.020  1.498
 W8Z  OAD  CAY  double    1.215  0.020  1.215
 W8Z  CAW  CAY  single    1.466  0.020  1.466
 W8Z  CAW  CAV  double    1.350  0.020  1.350
 W8Z  CAY  NAP  single    1.379  0.020  1.379
 W8Z  OAB  CAS  double    1.199  0.020  1.199
 W8Z  CAS  CAV  single    1.499  0.020  1.499
 W8Z  CAS  OAE  single    1.322  0.020  1.322
 W8Z  CAV  NAO  single    1.372  0.020  1.372
 W8Z  NAP  CAX  single    1.370  0.020  1.370
 W8Z  NAO  CAX  single    1.364  0.020  1.364
 W8Z  CAX  OAC  double    1.213  0.020  1.213
 W8Z  OAE  H1   single    0.850  0.020  0.980
 W8Z  NAO  H2   single    0.860  0.020  1.020
 W8Z  NAP  H3   single    0.860  0.020  1.020
 W8Z  CAM  H4   single    0.970  0.020  1.090
 W8Z  CAM  H5   single    0.970  0.020  1.090
 W8Z  CAL  H6   single    0.970  0.020  1.090
 W8Z  CAL  H7   single    0.970  0.020  1.090
 W8Z  CAJ  H8   single    0.930  0.020  1.080
 W8Z  CAH  H9   single    0.930  0.020  1.080
 W8Z  CAF  H10  single    0.930  0.020  1.080
 W8Z  CAG  H11  single    0.930  0.020  1.080
 W8Z  CAI  H12  single    0.930  0.020  1.080
 W8Z  CAK  H13  single    0.930  0.020  1.080
 W8Z  CAN  H14  single    0.970  0.020  1.090
 W8Z  CAN  H15  single    0.970  0.020  1.090
 W8Z  CAA  H16  single    0.970  0.020  1.090
 W8Z  CAA  H17  single    0.970  0.020  1.090
 W8Z  CAA  H18  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
 W8Z  CAV  CAS  OAE  111.08  3.000
 W8Z  OAE  CAS  OAB  125.01  3.000
 W8Z  CAV  CAS  OAB  123.90  3.000
 W8Z  H1   OAE  CAS  110.69  3.000
 W8Z  CAW  CAV  NAO  122.04  3.000
 W8Z  NAO  CAV  CAS  114.89  3.000
 W8Z  CAW  CAV  CAS  123.07  3.000
 W8Z  H2   NAO  CAX  116.05  3.000
 W8Z  H2   NAO  CAV  119.75  3.000
 W8Z  CAX  NAO  CAV  124.18  3.000
 W8Z  NAP  CAX  OAC  123.20  3.000
 W8Z  OAC  CAX  NAO  123.31  3.000
 W8Z  NAP  CAX  NAO  113.49  3.000
 W8Z  H3   NAP  CAY  116.72  3.000
 W8Z  H3   NAP  CAX  116.02  3.000
 W8Z  CAY  NAP  CAX  127.26  3.000
 W8Z  CAW  CAY  OAD  123.95  3.000
 W8Z  CAW  CAY  NAP  115.78  3.000
 W8Z  OAD  CAY  NAP  120.26  3.000
 W8Z  CAM  CAW  CAY  116.00  3.000
 W8Z  CAY  CAW  CAV  117.23  3.000
 W8Z  CAM  CAW  CAV  126.76  3.000
 W8Z  H5   CAM  H4   106.75  3.000
 W8Z  H5   CAM  CAL  109.80  3.000
 W8Z  H4   CAM  CAL  108.53  3.000
 W8Z  H5   CAM  CAW  111.26  3.000
 W8Z  H4   CAM  CAW  107.85  3.000
 W8Z  CAL  CAM  CAW  112.43  3.000
 W8Z  H7   CAL  H6   107.03  3.000
 W8Z  H7   CAL  CAT  108.39  3.000
 W8Z  H6   CAL  CAT  111.45  3.000
 W8Z  H7   CAL  CAM  109.32  3.000
 W8Z  H6   CAL  CAM  109.20  3.000
 W8Z  CAT  CAL  CAM  111.33  3.000
 W8Z  CAU  CAT  CAJ  118.57  3.000
 W8Z  CAU  CAT  CAL  120.79  3.000
 W8Z  CAJ  CAT  CAL  120.59  3.000
 W8Z  H8   CAJ  CAZ  118.65  3.000
 W8Z  H8   CAJ  CAT  119.00  3.000
 W8Z  CAZ  CAJ  CAT  122.35  3.000
 W8Z  CBA  CAZ  CAH  119.40  3.000
 W8Z  CBA  CAZ  CAJ  118.33  3.000
 W8Z  CAH  CAZ  CAJ  122.27  3.000
 W8Z  H9   CAH  CAF  120.40  3.000
 W8Z  H9   CAH  CAZ  118.95  3.000
 W8Z  CAF  CAH  CAZ  120.65  3.000
 W8Z  H10  CAF  CAG  119.73  3.000
 W8Z  H10  CAF  CAH  120.25  3.000
 W8Z  CAG  CAF  CAH  120.02  3.000
 W8Z  H11  CAG  CAI  119.91  3.000
 W8Z  H11  CAG  CAF  119.60  3.000
 W8Z  CAI  CAG  CAF  120.49  3.000
 W8Z  H12  CAI  CBA  119.12  3.000
 W8Z  H12  CAI  CAG  120.20  3.000
 W8Z  CBA  CAI  CAG  120.68  3.000
 W8Z  CAK  CBA  CAI  121.77  3.000
 W8Z  CAK  CBA  CAZ  119.47  3.000
 W8Z  CAI  CBA  CAZ  118.76  3.000
 W8Z  H13  CAK  CAU  121.88  3.000
 W8Z  H13  CAK  CBA  117.67  3.000
 W8Z  CAU  CAK  CBA  120.46  3.000
 W8Z  OAR  CAU  CAK  125.02  3.000
 W8Z  OAR  CAU  CAT  114.18  3.000
 W8Z  CAK  CAU  CAT  120.80  3.000
 W8Z  CAN  OAR  CAU  120.49  3.000
 W8Z  H15  CAN  H14  109.56  3.000
 W8Z  H15  CAN  OAQ  107.19  3.000
 W8Z  H14  CAN  OAQ  111.72  3.000
 W8Z  H15  CAN  OAR  110.93  3.000
 W8Z  H14  CAN  OAR  104.19  3.000
 W8Z  OAQ  CAN  OAR  113.26  3.000
 W8Z  CAA  OAQ  CAN  114.44  3.000
 W8Z  H18  CAA  H17  108.64  3.000
 W8Z  H18  CAA  H16  108.42  3.000
 W8Z  H17  CAA  H16  108.24  3.000
 W8Z  H18  CAA  OAQ  107.36  3.000
 W8Z  H17  CAA  OAQ  111.67  3.000
 W8Z  H16  CAA  OAQ  112.40  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
 W8Z  CONST_01  CAH  CAZ  CAJ  CAT  180.00   0.0  0
 W8Z  CONST_02  CBA  CAZ  CAJ  CAT    0.00   0.0  0
 W8Z  CONST_03  CBA  CAK  CAU  CAT    0.00   0.0  0
 W8Z  CONST_04  CAF  CAH  CAZ  CAJ  180.00   0.0  0
 W8Z  CONST_05  CAI  CBA  CAZ  CAJ  180.00   0.0  0
 W8Z  CONST_06  CAK  CBA  CAZ  CAJ    0.00   0.0  0
 W8Z  CONST_07  CAK  CAU  CAT  CAJ    0.00   0.0  0
 W8Z  CONST_08  CAG  CAF  CAH  CAZ    0.00   0.0  0
 W8Z  CONST_09  CAU  CAT  CAJ  CAZ    0.00   0.0  0
 W8Z  CONST_10  CAG  CAI  CBA  CAZ    0.00   0.0  0
 W8Z  CONST_11  CAU  CAK  CBA  CAZ    0.00   0.0  0
 W8Z  CONST_12  CAI  CAG  CAF  CAH    0.00   0.0  0
 W8Z  CONST_13  CAI  CBA  CAZ  CAH    0.00   0.0  0
 W8Z  CONST_14  CAK  CBA  CAZ  CAH  180.00   0.0  0
 W8Z  CONST_15  CBA  CAZ  CAH  CAF    0.00   0.0  0
 W8Z  CONST_16  CBA  CAI  CAG  CAF    0.00   0.0  0
 W8Z  CONST_17  CAK  CBA  CAI  CAG  180.00   0.0  0
 W8Z  CONST_18  CAU  CAK  CBA  CAI  180.00   0.0  0
 W8Z  CONST_19  NAP  CAX  NAO  CAV    0.00   0.0  0
 W8Z  CONST_20  CAY  NAP  CAX  NAO    0.00   0.0  0
 W8Z  CONST_21  CAW  CAY  NAP  CAX    0.00   0.0  0
 W8Z  CONST_22  CAZ  CAJ  CAT  CAL  180.00   0.0  0
 W8Z  CONST_23  CAK  CAU  CAT  CAL  180.00   0.0  0
 W8Z  CONST_24  OAR  CAU  CAT  CAJ  180.00   0.0  0
 W8Z  CONST_25  OAR  CAU  CAK  CBA  180.00   0.0  0
 W8Z  CONST_26  OAC  CAX  NAO  CAV  180.00   0.0  0
 W8Z  CONST_27  OAD  CAY  NAP  CAX  180.00   0.0  0
 W8Z  CONST_28  CAY  NAP  CAX  OAC  180.00   0.0  0
 W8Z  CONST_29  H13  CAK  CAU  CAT  180.00   0.0  0
 W8Z  CONST_30  H9   CAH  CAZ  CAJ    0.00   0.0  0
 W8Z  CONST_31  H10  CAF  CAH  CAZ  180.00   0.0  0
 W8Z  CONST_32  H12  CAI  CBA  CAZ  180.00   0.0  0
 W8Z  CONST_33  H11  CAG  CAF  CAH  180.00   0.0  0
 W8Z  CONST_34  H8   CAJ  CAZ  CAH    0.00   0.0  0
 W8Z  CONST_35  H3   NAP  CAX  NAO  180.00   0.0  0
 W8Z  CONST_36  H2   NAO  CAX  NAP  180.00   0.0  0
 W8Z  CONST_37  H1   OAE  CAS  CAV  180.00   0.0  0
 W8Z  Var_01    CAW  CAV  CAS  OAB  -29.88  30.0  2
 W8Z  Var_02    CAL  CAM  CAW  CAV   98.47  30.0  1
 W8Z  Var_03    CAT  CAL  CAM  CAW  171.14  30.0  2
 W8Z  Var_04    CAJ  CAT  CAL  CAM  -99.57  30.0  2
 W8Z  Var_05    OAQ  CAN  OAR  CAU   71.36  30.0  2
 W8Z  Var_06    H16  CAA  OAQ  CAN  -74.77  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
 W8Z  plan-1  CAS  0.020
 W8Z  plan-1  CAV  0.020
 W8Z  plan-1  NAO  0.020
 W8Z  plan-1  CAX  0.020
 W8Z  plan-1  OAC  0.020
 W8Z  plan-1  NAP  0.020
 W8Z  plan-1  CAY  0.020
 W8Z  plan-1  OAD  0.020
 W8Z  plan-1  CAW  0.020
 W8Z  plan-1  CAM  0.020
 W8Z  plan-1  H2   0.020
 W8Z  plan-1  H3   0.020
 W8Z  plan-2  CAL  0.020
 W8Z  plan-2  CAT  0.020
 W8Z  plan-2  CAJ  0.020
 W8Z  plan-2  CAZ  0.020
 W8Z  plan-2  CAH  0.020
 W8Z  plan-2  CAF  0.020
 W8Z  plan-2  CAG  0.020
 W8Z  plan-2  CAI  0.020
 W8Z  plan-2  CBA  0.020
 W8Z  plan-2  CAK  0.020
 W8Z  plan-2  CAU  0.020
 W8Z  plan-2  OAR  0.020
 W8Z  plan-2  H8   0.020
 W8Z  plan-2  H9   0.020
 W8Z  plan-2  H10  0.020
 W8Z  plan-2  H11  0.020
 W8Z  plan-2  H12  0.020
 W8Z  plan-2  H13  0.020
 W8Z  plan-3  OAB  0.020
 W8Z  plan-3  CAS  0.020
 W8Z  plan-3  OAE  0.020
 W8Z  plan-3  CAV  0.020
 W8Z  plan-3  H1   0.020

