# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:52:00 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(7-methoxynaphthalen-1-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2cccc(CCC3=C(NC(=O)NC3=O)C(O)=O)c2c1
#
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
 W7F  W7F  '5-[2-(7-methoxynaphthalen-1-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  40  25  .  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_W7F
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
 W7F  OAB  O  O      0  -0.534  -0.7820  -2.1585  -0.2951
 W7F  CAQ  C  C      0   0.422  -2.0167  -2.1887  -0.2455
 W7F  OAE  O  OC    -1  -0.584  -2.7673  -3.1702  -0.3893
 W7F  CAT  C  CR6    0   0.200  -2.7571  -0.8606   0.0040
 W7F  NAN  N  NR16   0  -0.707  -4.1075  -0.9947  -0.1741
 W7F  CAV  C  CR6    0   0.656  -5.0224  -0.0003  -0.0521
 W7F  OAC  O  O      0  -0.493  -6.2188  -0.1538  -0.2157
 W7F  NAO  N  NR16   0  -0.714  -4.4629   1.2074   0.2717
 W7F  CAW  C  CR6    0   0.564  -3.1230   1.4717   0.4854
 W7F  OAD  O  O      0  -0.465  -2.7727   2.6076   0.7613
 W7F  CAU  C  CR6    0  -0.155  -2.2190   0.3335   0.3543
 W7F  CAM  C  CH2    0  -0.478  -0.7662   0.6245   0.5874
 W7F  CAL  C  CH2    0  -0.529  -0.0650   1.1018  -0.6952
 W7F  CAS  C  CR6    0   0.103   1.3145   1.6431  -0.4410
 W7F  CAY  C  CR6    0   0.108   2.4321   0.7793  -0.2213
 W7F  CAK  C  C1     0  -0.486   2.3167  -0.6261  -0.2608
 W7F  CAR  C  C      0   0.398   3.4095  -1.4369  -0.0500
 W7F  OAP  O  O2     0  -0.471   3.1988  -2.7675  -0.1070
 W7F  CAA  C  CH3    0  -0.438   4.2902  -3.6426   0.0945
 W7F  CAH  C  C1     0  -0.382   4.6746  -0.8649   0.2125
 W7F  CAJ  C  C1     0  -0.298   4.8050   0.4967   0.2558
 W7F  CAX  C  CR6    0   0.092   3.7059   1.3550   0.0442
 W7F  CAI  C  CR16   0  -0.333   3.8511   2.7614   0.0904
 W7F  CAF  C  CR16   0  -0.253   2.7715   3.5696  -0.1216
 W7F  CAG  C  CR16   0  -0.340   1.5083   3.0004  -0.3867
 W7F  H2   H  HNR6   0   0.419  -5.1020   1.9865   0.3651
 W7F  H4   H  HCH2   0   0.242  -0.6874   1.4116   1.3388
 W7F  H5   H  HCH2   0   0.255  -0.2596  -0.2499   0.9832
 W7F  H6   H  HCH2   0   0.244  -0.0402   0.2760  -1.4096
 W7F  H7   H  HCH2   0   0.254  -0.6649   1.8921  -1.1509
 W7F  H8   H  H      0   0.290   1.3567  -1.0908  -0.4497
 W7F  H9   H  HCH3   0   0.227   4.7239  -3.5389   1.0927
 W7F  H10  H  HCH3   0   0.259   3.8979  -4.6514  -0.0088
 W7F  H11  H  HCH3   0   0.228   5.0780  -3.4955  -0.6486
 W7F  H12  H  H      0   0.280   5.5462  -1.4827   0.3803
 W7F  H13  H  H      0   0.258   5.7768   0.9299   0.4598
 W7F  H14  H  HCR6   0   0.250   4.8278   3.1836   0.2957
 W7F  H15  H  HCR6   0   0.251   2.8764   4.6463  -0.0905
 W7F  H16  H  HCR6   0   0.244   0.6624   3.6581  -0.5515
 W7F  H17  H  HNR6   0   0.417  -4.4245  -1.9314  -0.3983

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
 W7F  CAI  CAF  aromatic  1.365  0.020  1.365
 W7F  CAI  CAX  aromatic  1.415  0.020  1.415
 W7F  CAF  CAG  aromatic  1.411  0.020  1.411
 W7F  CAJ  CAX  aromatic  1.410  0.020  1.410
 W7F  CAJ  CAH  aromatic  1.369  0.020  1.369
 W7F  CAX  CAY  aromatic  1.423  0.020  1.423
 W7F  CAG  CAS  aromatic  1.372  0.020  1.372
 W7F  CAH  CAR  aromatic  1.413  0.020  1.413
 W7F  CAY  CAS  aromatic  1.429  0.020  1.429
 W7F  CAY  CAK  aromatic  1.411  0.020  1.411
 W7F  CAS  CAL  single    1.504  0.020  1.504
 W7F  CAR  CAK  aromatic  1.377  0.020  1.377
 W7F  CAR  OAP  single    1.348  0.020  1.348
 W7F  CAL  CAM  single    1.538  0.020  1.538
 W7F  OAP  CAA  single    1.413  0.020  1.413
 W7F  CAM  CAU  single    1.500  0.020  1.500
 W7F  OAD  CAW  double    1.220  0.020  1.220
 W7F  CAU  CAW  single    1.459  0.020  1.459
 W7F  CAU  CAT  double    1.356  0.020  1.356
 W7F  CAW  NAO  single    1.382  0.020  1.382
 W7F  CAQ  CAT  single    1.541  0.020  1.541
 W7F  CAQ  OAB  deloc     1.236  0.020  1.236
 W7F  CAQ  OAE  deloc     1.244  0.020  1.244
 W7F  CAT  NAN  single    1.369  0.020  1.369
 W7F  NAO  CAV  single    1.370  0.020  1.370
 W7F  NAN  CAV  single    1.357  0.020  1.357
 W7F  CAV  OAC  double    1.217  0.020  1.217
 W7F  NAO  H2   single    0.860  0.020  1.020
 W7F  CAM  H4   single    0.970  0.020  1.090
 W7F  CAM  H5   single    0.970  0.020  1.090
 W7F  CAL  H6   single    0.970  0.020  1.090
 W7F  CAL  H7   single    0.970  0.020  1.090
 W7F  CAK  H8   single    0.930  0.020  1.080
 W7F  CAA  H9   single    0.970  0.020  1.090
 W7F  CAA  H10  single    0.970  0.020  1.090
 W7F  CAA  H11  single    0.970  0.020  1.090
 W7F  CAH  H12  single    0.930  0.020  1.080
 W7F  CAJ  H13  single    0.930  0.020  1.080
 W7F  CAI  H14  single    0.930  0.020  1.080
 W7F  CAF  H15  single    0.930  0.020  1.080
 W7F  CAG  H16  single    0.930  0.020  1.080
 W7F  NAN  H17  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
 W7F  CAT  CAQ  OAE  114.13  3.000
 W7F  OAE  CAQ  OAB  128.13  3.000
 W7F  CAT  CAQ  OAB  117.74  3.000
 W7F  CAU  CAT  NAN  120.77  3.000
 W7F  NAN  CAT  CAQ  111.62  3.000
 W7F  CAU  CAT  CAQ  127.61  3.000
 W7F  H17  NAN  CAV  119.09  3.000
 W7F  H17  NAN  CAT  115.32  3.000
 W7F  CAV  NAN  CAT  125.57  3.000
 W7F  NAO  CAV  OAC  122.99  3.000
 W7F  OAC  CAV  NAN  123.93  3.000
 W7F  NAO  CAV  NAN  113.08  3.000
 W7F  H2   NAO  CAW  116.79  3.000
 W7F  H2   NAO  CAV  116.27  3.000
 W7F  CAW  NAO  CAV  126.95  3.000
 W7F  CAU  CAW  OAD  124.64  3.000
 W7F  CAU  CAW  NAO  115.94  3.000
 W7F  OAD  CAW  NAO  119.42  3.000
 W7F  CAM  CAU  CAW  115.77  3.000
 W7F  CAW  CAU  CAT  117.66  3.000
 W7F  CAM  CAU  CAT  126.55  3.000
 W7F  H5   CAM  H4   107.24  3.000
 W7F  H5   CAM  CAL  109.97  3.000
 W7F  H4   CAM  CAL  108.51  3.000
 W7F  H5   CAM  CAU  110.64  3.000
 W7F  H4   CAM  CAU  108.48  3.000
 W7F  CAL  CAM  CAU  111.85  3.000
 W7F  H7   CAL  H6   106.67  3.000
 W7F  H7   CAL  CAS  108.31  3.000
 W7F  H6   CAL  CAS  111.22  3.000
 W7F  H7   CAL  CAM  108.80  3.000
 W7F  H6   CAL  CAM  108.73  3.000
 W7F  CAS  CAL  CAM  112.90  3.000
 W7F  CAG  CAS  CAY  118.76  3.000
 W7F  CAY  CAS  CAL  121.72  3.000
 W7F  CAG  CAS  CAL  119.50  3.000
 W7F  CAX  CAY  CAK  118.79  3.000
 W7F  CAK  CAY  CAS  122.25  3.000
 W7F  CAX  CAY  CAS  118.96  3.000
 W7F  H8   CAK  CAR  118.52  3.000
 W7F  H8   CAK  CAY  120.32  3.000
 W7F  CAR  CAK  CAY  121.15  3.000
 W7F  CAH  CAR  OAP  123.18  3.000
 W7F  OAP  CAR  CAK  116.78  3.000
 W7F  CAH  CAR  CAK  120.04  3.000
 W7F  CAA  OAP  CAR  118.97  3.000
 W7F  H11  CAA  H10  108.68  3.000
 W7F  H11  CAA  H9   108.79  3.000
 W7F  H10  CAA  H9   108.54  3.000
 W7F  H11  CAA  OAP  112.11  3.000
 W7F  H10  CAA  OAP  106.40  3.000
 W7F  H9   CAA  OAP  112.20  3.000
 W7F  H12  CAH  CAJ  119.13  3.000
 W7F  H12  CAH  CAR  121.28  3.000
 W7F  CAJ  CAH  CAR  119.60  3.000
 W7F  H13  CAJ  CAX  118.94  3.000
 W7F  H13  CAJ  CAH  119.29  3.000
 W7F  CAX  CAJ  CAH  121.77  3.000
 W7F  CAI  CAX  CAJ  121.34  3.000
 W7F  CAJ  CAX  CAY  118.65  3.000
 W7F  CAI  CAX  CAY  120.01  3.000
 W7F  H14  CAI  CAF  120.77  3.000
 W7F  H14  CAI  CAX  119.08  3.000
 W7F  CAF  CAI  CAX  120.15  3.000
 W7F  H15  CAF  CAG  119.58  3.000
 W7F  H15  CAF  CAI  120.52  3.000
 W7F  CAG  CAF  CAI  119.90  3.000
 W7F  H16  CAG  CAF  118.85  3.000
 W7F  H16  CAG  CAS  118.94  3.000
 W7F  CAF  CAG  CAS  122.21  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
 W7F  CONST_01  CAI  CAF  CAG  CAS     0.00   0.0  0
 W7F  CONST_02  CAI  CAX  CAY  CAS     0.00   0.0  0
 W7F  CONST_03  CAJ  CAX  CAY  CAS   180.00   0.0  0
 W7F  CONST_04  CAR  CAK  CAY  CAS   180.00   0.0  0
 W7F  CONST_05  CAF  CAI  CAX  CAY     0.00   0.0  0
 W7F  CONST_06  CAH  CAJ  CAX  CAY     0.00   0.0  0
 W7F  CONST_07  CAF  CAG  CAS  CAY     0.00   0.0  0
 W7F  CONST_08  CAH  CAR  CAK  CAY     0.00   0.0  0
 W7F  CONST_09  CAI  CAX  CAY  CAK   180.00   0.0  0
 W7F  CONST_10  CAJ  CAX  CAY  CAK     0.00   0.0  0
 W7F  CONST_11  CAG  CAS  CAY  CAK   180.00   0.0  0
 W7F  CONST_12  CAJ  CAH  CAR  CAK     0.00   0.0  0
 W7F  CONST_13  CAX  CAJ  CAH  CAR     0.00   0.0  0
 W7F  CONST_14  CAX  CAY  CAK  CAR     0.00   0.0  0
 W7F  CONST_15  CAI  CAX  CAJ  CAH   180.00   0.0  0
 W7F  CONST_16  CAF  CAI  CAX  CAJ   180.00   0.0  0
 W7F  CONST_17  CAG  CAF  CAI  CAX     0.00   0.0  0
 W7F  CONST_18  CAG  CAS  CAY  CAX     0.00   0.0  0
 W7F  CONST_19  NAO  CAV  NAN  CAT     0.00   0.0  0
 W7F  CONST_20  CAW  NAO  CAV  NAN     0.00   0.0  0
 W7F  CONST_21  CAU  CAW  NAO  CAV     0.00   0.0  0
 W7F  CONST_22  CAF  CAG  CAS  CAL   180.00   0.0  0
 W7F  CONST_23  CAX  CAY  CAS  CAL   180.00   0.0  0
 W7F  CONST_24  CAK  CAY  CAS  CAL     0.00   0.0  0
 W7F  CONST_25  OAP  CAR  CAK  CAY   180.00   0.0  0
 W7F  CONST_26  CAJ  CAH  CAR  OAP   180.00   0.0  0
 W7F  CONST_27  OAC  CAV  NAN  CAT   180.00   0.0  0
 W7F  CONST_28  OAD  CAW  NAO  CAV   180.00   0.0  0
 W7F  CONST_29  CAW  NAO  CAV  OAC   180.00   0.0  0
 W7F  CONST_30  H15  CAF  CAG  CAS   180.00   0.0  0
 W7F  CONST_31  H8   CAK  CAY  CAS     0.00   0.0  0
 W7F  CONST_32  H14  CAI  CAX  CAY   180.00   0.0  0
 W7F  CONST_33  H13  CAJ  CAX  CAY   180.00   0.0  0
 W7F  CONST_34  H16  CAG  CAS  CAY   180.00   0.0  0
 W7F  CONST_35  H12  CAH  CAR  CAK   180.00   0.0  0
 W7F  CONST_36  H2   NAO  CAV  NAN   180.00   0.0  0
 W7F  CONST_37  H17  NAN  CAV  NAO   180.00   0.0  0
 W7F  Var_01    CAU  CAT  CAQ  OAB    -9.46  30.0  2
 W7F  Var_02    CAL  CAM  CAU  CAT    91.33  30.0  2
 W7F  Var_03    CAS  CAL  CAM  CAU   169.25  30.0  1
 W7F  Var_04    CAG  CAS  CAL  CAM  -100.56  30.0  2
 W7F  Var_05    CAH  CAR  OAP  CAA    -0.46  30.0  1
 W7F  Var_06    H9   CAA  OAP  CAR    62.25  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
 W7F  plan-1  CAQ  0.020
 W7F  plan-1  CAT  0.020
 W7F  plan-1  NAN  0.020
 W7F  plan-1  CAV  0.020
 W7F  plan-1  OAC  0.020
 W7F  plan-1  NAO  0.020
 W7F  plan-1  CAW  0.020
 W7F  plan-1  OAD  0.020
 W7F  plan-1  CAU  0.020
 W7F  plan-1  CAM  0.020
 W7F  plan-1  H2   0.020
 W7F  plan-1  H17  0.020
 W7F  plan-2  CAL  0.020
 W7F  plan-2  CAS  0.020
 W7F  plan-2  CAY  0.020
 W7F  plan-2  CAK  0.020
 W7F  plan-2  CAR  0.020
 W7F  plan-2  OAP  0.020
 W7F  plan-2  CAH  0.020
 W7F  plan-2  CAJ  0.020
 W7F  plan-2  CAX  0.020
 W7F  plan-2  CAI  0.020
 W7F  plan-2  CAF  0.020
 W7F  plan-2  CAG  0.020
 W7F  plan-2  H8   0.020
 W7F  plan-2  H12  0.020
 W7F  plan-2  H13  0.020
 W7F  plan-2  H14  0.020
 W7F  plan-2  H15  0.020
 W7F  plan-2  H16  0.020
 W7F  plan-3  OAB  0.020
 W7F  plan-3  CAQ  0.020
 W7F  plan-3  OAE  0.020
 W7F  plan-3  CAT  0.020

