# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:11:27 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 5-(2-{6-[(2-hydroxyethyl)carbamoyl]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: OCCNC(=O)c1ccc2cc(CCC3=C(NC(=O)NC3=O)C(O)=O)ccc2c1
#
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
 W7N  W7N  '5-(2-{6-[(2-hydroxyethyl)carbamoyl]naphthalen-2-yl}ethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  47  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W7N
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
 W7N  OAA  O  OC    -1  -0.585  -6.1124  -2.6437   0.2122
 W7N  CAT  C  C      0   0.418  -5.0275  -2.0343   0.2115
 W7N  OAF  O  O      0  -0.540  -3.8848  -2.5044   0.1758
 W7N  CAY  C  CR6    0   0.202  -5.1715  -0.4988   0.2447
 W7N  NAR  N  NR16   0  -0.706  -6.4776  -0.1115   0.1260
 W7N  CAZ  C  CR6    0   0.657  -6.9212   1.1708   0.1035
 W7N  OAC  O  O      0  -0.492  -8.0933   1.4819   0.0006
 W7N  NAS  N  NR16   0  -0.715  -5.9109   2.0908   0.2045
 W7N  CBA  C  CR6    0   0.562  -4.5585   1.8298   0.3265
 W7N  OAD  O  O      0  -0.467  -3.7709   2.7602   0.3868
 W7N  CAX  C  CR6    0  -0.159  -4.1840   0.4215   0.3704
 W7N  CAP  C  CH2    0  -0.477  -2.7199   0.1257   0.5032
 W7N  CAO  C  CH2    0  -0.497  -2.0319  -0.0054  -0.8615
 W7N  CAV  C  C      0   0.129  -0.5758  -0.3356  -0.7188
 W7N  CAK  C  C1     0  -0.392   0.3957   0.6238  -0.8452
 W7N  CAG  C  C1     0  -0.298  -0.1884  -1.6646  -0.4113
 W7N  CAI  C  C1     0  -0.296   1.1256  -2.0000  -0.2497
 W7N  CBC  C  CR6    0   0.122   2.1402  -1.0210  -0.3802
 W7N  CAL  C  CR16   0  -0.341   3.5065  -1.3356  -0.2294
 W7N  CBB  C  CR6    0   0.139   1.7645   0.3129  -0.6792
 W7N  CAJ  C  CR16   0  -0.304   2.7791   1.2889  -0.8110
 W7N  CAH  C  CR16   0  -0.294   4.0952   0.9611  -0.6436
 W7N  CAW  C  CR6    0  -0.042   4.4754  -0.3695  -0.3434
 W7N  CAU  C  C      0   0.535   5.9034  -0.7772  -0.1691
 W7N  OAB  O  O      0  -0.493   6.2612  -1.9330  -0.3601
 W7N  NAQ  N  NH1    0  -0.650   6.7496   0.1953   0.2056
 W7N  CAN  C  CH2    0  -0.293   8.1609  -0.0238   0.4324
 W7N  CAM  C  CH2    0  -0.178   8.9435   1.2471   0.1883
 W7N  OAE  O  OH1    0  -0.673   8.4798   2.2351   1.0835
 W7N  H2   H  HNR6   0   0.417  -7.1477  -0.8700   0.0651
 W7N  H3   H  HNR6   0   0.420  -6.1867   3.0645   0.1790
 W7N  H4   H  HCH2   0   0.242  -2.2444   0.9348   1.0598
 W7N  H5   H  HCH2   0   0.255  -2.5712  -0.7872   1.0724
 W7N  H6   H  HCH2   0   0.250  -2.5330  -0.7902  -1.4308
 W7N  H7   H  HCH2   0   0.243  -2.1476   0.9251  -1.4209
 W7N  H8   H  H      0   0.247   0.1185   1.6455  -1.0818
 W7N  H9   H  H      0   0.255  -0.9575  -2.4215  -0.3116
 W7N  H10  H  H      0   0.255   1.4056  -3.0215  -0.0225
 W7N  H11  H  HCR6   0   0.257   3.7862  -2.3586  -0.0096
 W7N  H12  H  HCR6   0   0.259   2.5022   2.3071  -1.0554
 W7N  H13  H  HCR6   0   0.254   4.8439   1.7311  -0.7774
 W7N  H14  H  HNH1   0   0.400   6.3783   1.0778   0.5200
 W7N  H15  H  HCH2   0   0.241   8.3409  -0.3850   1.4505
 W7N  H16  H  HCH2   0   0.253   8.5195  -0.7940  -0.2490
 W7N  H17  H  HCH2   0   0.213  10.0078   1.0292   0.3370
 W7N  H18  H  HCH2   0   0.210   8.8147   1.5556  -0.8557
 W7N  H19  H  HOH1   0   0.460   8.8518   3.0821   0.8228

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
 W7N  OAE  CAM  single    1.412  0.020  1.412
 W7N  OAB  CAU  double    1.225  0.020  1.225
 W7N  CAH  CAJ  aromatic  1.367  0.020  1.367
 W7N  CAH  CAW  aromatic  1.416  0.020  1.416
 W7N  CAJ  CBB  aromatic  1.414  0.020  1.414
 W7N  CAM  CAN  single    1.512  0.020  1.512
 W7N  CAU  CAW  single    1.495  0.020  1.495
 W7N  CAU  NAQ  single    1.343  0.020  1.343
 W7N  CAW  CAL  aromatic  1.373  0.020  1.373
 W7N  CBB  CAK  aromatic  1.413  0.020  1.413
 W7N  CBB  CBC  aromatic  1.418  0.020  1.418
 W7N  CAK  CAV  aromatic  1.371  0.020  1.371
 W7N  CAL  CBC  aromatic  1.410  0.020  1.410
 W7N  NAQ  CAN  single    1.446  0.020  1.446
 W7N  CBC  CAI  aromatic  1.416  0.020  1.416
 W7N  CAV  CAO  single    1.500  0.020  1.500
 W7N  CAV  CAG  aromatic  1.418  0.020  1.418
 W7N  CAO  CAP  single    1.534  0.020  1.534
 W7N  CAI  CAG  aromatic  1.366  0.020  1.366
 W7N  CAP  CAX  single    1.500  0.020  1.500
 W7N  OAD  CBA  double    1.221  0.020  1.221
 W7N  CAX  CBA  single    1.458  0.020  1.458
 W7N  CAX  CAY  double    1.356  0.020  1.356
 W7N  CBA  NAS  single    1.383  0.020  1.383
 W7N  OAF  CAT  deloc     1.236  0.020  1.236
 W7N  CAY  CAT  single    1.543  0.020  1.543
 W7N  CAY  NAR  single    1.367  0.020  1.367
 W7N  CAT  OAA  deloc     1.244  0.020  1.244
 W7N  NAS  CAZ  single    1.370  0.020  1.370
 W7N  NAR  CAZ  single    1.357  0.020  1.357
 W7N  CAZ  OAC  double    1.217  0.020  1.217
 W7N  NAR  H2   single    0.860  0.020  1.020
 W7N  NAS  H3   single    0.860  0.020  1.020
 W7N  CAP  H4   single    0.970  0.020  1.090
 W7N  CAP  H5   single    0.970  0.020  1.090
 W7N  CAO  H6   single    0.970  0.020  1.090
 W7N  CAO  H7   single    0.970  0.020  1.090
 W7N  CAK  H8   single    0.930  0.020  1.080
 W7N  CAG  H9   single    0.930  0.020  1.080
 W7N  CAI  H10  single    0.930  0.020  1.080
 W7N  CAL  H11  single    0.930  0.020  1.080
 W7N  CAJ  H12  single    0.930  0.020  1.080
 W7N  CAH  H13  single    0.930  0.020  1.080
 W7N  NAQ  H14  single    0.860  0.020  1.020
 W7N  CAN  H15  single    0.970  0.020  1.090
 W7N  CAN  H16  single    0.970  0.020  1.090
 W7N  CAM  H17  single    0.970  0.020  1.090
 W7N  CAM  H18  single    0.970  0.020  1.090
 W7N  OAE  H19  single    0.850  0.020  0.980

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
 W7N  CAY  CAT  OAF  117.74  3.000
 W7N  CAY  CAT  OAA  113.96  3.000
 W7N  OAF  CAT  OAA  128.29  3.000
 W7N  CAX  CAY  NAR  120.77  3.000
 W7N  NAR  CAY  CAT  111.67  3.000
 W7N  CAX  CAY  CAT  127.57  3.000
 W7N  H2   NAR  CAZ  119.33  3.000
 W7N  H2   NAR  CAY  115.13  3.000
 W7N  CAZ  NAR  CAY  125.54  3.000
 W7N  NAS  CAZ  OAC  123.00  3.000
 W7N  OAC  CAZ  NAR  123.90  3.000
 W7N  NAS  CAZ  NAR  113.09  3.000
 W7N  H3   NAS  CBA  116.76  3.000
 W7N  H3   NAS  CAZ  116.30  3.000
 W7N  CBA  NAS  CAZ  126.94  3.000
 W7N  CAX  CBA  OAD  124.69  3.000
 W7N  CAX  CBA  NAS  115.86  3.000
 W7N  OAD  CBA  NAS  119.45  3.000
 W7N  CAP  CAX  CBA  116.36  3.000
 W7N  CBA  CAX  CAY  117.76  3.000
 W7N  CAP  CAX  CAY  125.84  3.000
 W7N  H5   CAP  H4   107.24  3.000
 W7N  H5   CAP  CAO  109.45  3.000
 W7N  H4   CAP  CAO  108.77  3.000
 W7N  H5   CAP  CAX  110.24  3.000
 W7N  H4   CAP  CAX  108.93  3.000
 W7N  CAO  CAP  CAX  112.09  3.000
 W7N  H7   CAO  H6   107.27  3.000
 W7N  H7   CAO  CAV  109.83  3.000
 W7N  H6   CAO  CAV  109.70  3.000
 W7N  H7   CAO  CAP  109.60  3.000
 W7N  H6   CAO  CAP  108.64  3.000
 W7N  CAV  CAO  CAP  111.69  3.000
 W7N  CAG  CAV  CAK  118.83  3.000
 W7N  CAG  CAV  CAO  119.48  3.000
 W7N  CAK  CAV  CAO  121.67  3.000
 W7N  H8   CAK  CBB  118.70  3.000
 W7N  H8   CAK  CAV  119.87  3.000
 W7N  CBB  CAK  CAV  121.43  3.000
 W7N  H9   CAG  CAI  120.03  3.000
 W7N  H9   CAG  CAV  118.73  3.000
 W7N  CAI  CAG  CAV  121.24  3.000
 W7N  H10  CAI  CBC  119.08  3.000
 W7N  H10  CAI  CAG  120.34  3.000
 W7N  CBC  CAI  CAG  120.58  3.000
 W7N  CBB  CBC  CAL  119.29  3.000
 W7N  CAL  CBC  CAI  122.02  3.000
 W7N  CBB  CBC  CAI  118.69  3.000
 W7N  H11  CAL  CAW  119.95  3.000
 W7N  H11  CAL  CBC  118.85  3.000
 W7N  CAW  CAL  CBC  121.19  3.000
 W7N  CAJ  CBB  CBC  118.62  3.000
 W7N  CBC  CBB  CAK  119.23  3.000
 W7N  CAJ  CBB  CAK  122.15  3.000
 W7N  H12  CAJ  CAH  119.96  3.000
 W7N  H12  CAJ  CBB  119.11  3.000
 W7N  CAH  CAJ  CBB  120.93  3.000
 W7N  H13  CAH  CAW  120.60  3.000
 W7N  H13  CAH  CAJ  118.71  3.000
 W7N  CAW  CAH  CAJ  120.66  3.000
 W7N  CAU  CAW  CAH  122.51  3.000
 W7N  CAU  CAW  CAL  118.19  3.000
 W7N  CAH  CAW  CAL  119.30  3.000
 W7N  NAQ  CAU  OAB  122.88  3.000
 W7N  NAQ  CAU  CAW  115.91  3.000
 W7N  OAB  CAU  CAW  121.21  3.000
 W7N  H14  NAQ  CAN  116.32  3.000
 W7N  H14  NAQ  CAU  119.29  3.000
 W7N  CAN  NAQ  CAU  123.31  3.000
 W7N  H16  CAN  H15  107.11  3.000
 W7N  H16  CAN  CAM  108.84  3.000
 W7N  H15  CAN  CAM  110.00  3.000
 W7N  H16  CAN  NAQ  109.30  3.000
 W7N  H15  CAN  NAQ  110.86  3.000
 W7N  CAM  CAN  NAQ  110.63  3.000
 W7N  H18  CAM  H17  107.40  3.000
 W7N  H18  CAM  OAE  111.62  3.000
 W7N  H17  CAM  OAE  111.84  3.000
 W7N  H18  CAM  CAN  109.23  3.000
 W7N  H17  CAM  CAN  108.26  3.000
 W7N  OAE  CAM  CAN  108.41  3.000
 W7N  H19  OAE  CAM  108.52  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
 W7N  CONST_01  CAJ  CBB  CAK  CAV   180.00   0.0  0
 W7N  CONST_02  CBC  CBB  CAK  CAV     0.00   0.0  0
 W7N  CONST_03  CBC  CAI  CAG  CAV     0.00   0.0  0
 W7N  CONST_04  CAH  CAJ  CBB  CAK   180.00   0.0  0
 W7N  CONST_05  CAL  CBC  CBB  CAK   180.00   0.0  0
 W7N  CONST_06  CAI  CBC  CBB  CAK     0.00   0.0  0
 W7N  CONST_07  CAI  CAG  CAV  CAK     0.00   0.0  0
 W7N  CONST_08  CBB  CAK  CAV  CAG     0.00   0.0  0
 W7N  CONST_09  CBB  CBC  CAI  CAG     0.00   0.0  0
 W7N  CONST_10  CAL  CBC  CAI  CAG   180.00   0.0  0
 W7N  CONST_11  CAJ  CBB  CBC  CAI   180.00   0.0  0
 W7N  CONST_12  CAW  CAL  CBC  CAI   180.00   0.0  0
 W7N  CONST_13  CAH  CAJ  CBB  CBC     0.00   0.0  0
 W7N  CONST_14  CAH  CAW  CAL  CBC     0.00   0.0  0
 W7N  CONST_15  CAJ  CAH  CAW  CAL     0.00   0.0  0
 W7N  CONST_16  CAJ  CBB  CBC  CAL     0.00   0.0  0
 W7N  CONST_17  CAW  CAH  CAJ  CBB     0.00   0.0  0
 W7N  CONST_18  CAW  CAL  CBC  CBB     0.00   0.0  0
 W7N  CONST_19  NAS  CAZ  NAR  CAY     0.00   0.0  0
 W7N  CONST_20  CBA  NAS  CAZ  NAR     0.00   0.0  0
 W7N  CONST_21  CAX  CBA  NAS  CAZ     0.00   0.0  0
 W7N  CONST_22  CBB  CAK  CAV  CAO   180.00   0.0  0
 W7N  CONST_23  CAI  CAG  CAV  CAO   180.00   0.0  0
 W7N  CONST_24  CAU  CAW  CAL  CBC   180.00   0.0  0
 W7N  CONST_25  CAU  CAW  CAH  CAJ   180.00   0.0  0
 W7N  CONST_26  OAC  CAZ  NAR  CAY   180.00   0.0  0
 W7N  CONST_27  OAD  CBA  NAS  CAZ   180.00   0.0  0
 W7N  CONST_28  CBA  NAS  CAZ  OAC   180.00   0.0  0
 W7N  CONST_29  H10  CAI  CAG  CAV   180.00   0.0  0
 W7N  CONST_30  H12  CAJ  CBB  CAK     0.00   0.0  0
 W7N  CONST_31  H9   CAG  CAV  CAK   180.00   0.0  0
 W7N  CONST_32  H8   CAK  CAV  CAG   180.00   0.0  0
 W7N  CONST_33  H11  CAL  CBC  CAI     0.00   0.0  0
 W7N  CONST_34  H13  CAH  CAW  CAL   180.00   0.0  0
 W7N  CONST_35  H3   NAS  CAZ  NAR   180.00   0.0  0
 W7N  CONST_36  H2   NAR  CAZ  NAS   180.00   0.0  0
 W7N  CONST_37  CAN  NAQ  CAU  CAW   180.00   0.0  0
 W7N  CONST_38  H14  NAQ  CAU  CAW     0.00   0.0  0
 W7N  CONST_39  CAN  NAQ  CAU  OAB     0.00   0.0  0
 W7N  Var_01    CAX  CAY  CAT  OAA   173.65  30.0  2
 W7N  Var_02    CAO  CAP  CAX  CAY    87.41  30.0  2
 W7N  Var_03    CAV  CAO  CAP  CAX  -178.56  30.0  2
 W7N  Var_04    CAK  CAV  CAO  CAP  -100.64  30.0  1
 W7N  Var_05    OAB  CAU  CAW  CAL    23.83  30.0  2
 W7N  Var_06    CAM  CAN  NAQ  CAU   152.92  30.0  3
 W7N  Var_07    OAE  CAM  CAN  NAQ    60.40  30.0  2

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
 W7N  plan-1  CAT  0.020
 W7N  plan-1  CAY  0.020
 W7N  plan-1  NAR  0.020
 W7N  plan-1  CAZ  0.020
 W7N  plan-1  OAC  0.020
 W7N  plan-1  NAS  0.020
 W7N  plan-1  CBA  0.020
 W7N  plan-1  OAD  0.020
 W7N  plan-1  CAX  0.020
 W7N  plan-1  CAP  0.020
 W7N  plan-1  H2   0.020
 W7N  plan-1  H3   0.020
 W7N  plan-2  CAO  0.020
 W7N  plan-2  CAV  0.020
 W7N  plan-2  CAK  0.020
 W7N  plan-2  CAG  0.020
 W7N  plan-2  CAI  0.020
 W7N  plan-2  CBC  0.020
 W7N  plan-2  CAL  0.020
 W7N  plan-2  CBB  0.020
 W7N  plan-2  CAJ  0.020
 W7N  plan-2  CAH  0.020
 W7N  plan-2  CAW  0.020
 W7N  plan-2  CAU  0.020
 W7N  plan-2  H8   0.020
 W7N  plan-2  H9   0.020
 W7N  plan-2  H10  0.020
 W7N  plan-2  H11  0.020
 W7N  plan-2  H12  0.020
 W7N  plan-2  H13  0.020
 W7N  plan-3  CAW  0.020
 W7N  plan-3  CAU  0.020
 W7N  plan-3  OAB  0.020
 W7N  plan-3  NAQ  0.020
 W7N  plan-3  CAN  0.020
 W7N  plan-3  H14  0.020
 W7N  plan-4  OAA  0.020
 W7N  plan-4  CAT  0.020
 W7N  plan-4  OAF  0.020
 W7N  plan-4  CAY  0.020

