# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:50:10 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5-[4-(6-carboxynaphthalen-2-yl)butyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCCCc2ccc3cc(ccc3c2)C(O)=O)C(=O)NC(=O)N1
#
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
 W88  W88  '5-[4-(6-carboxynaphthalen-2-yl)butyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  44  28  .  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_W88
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
 W88  OAB  O  O      0  -0.543   3.3844   2.5437   0.3675
 W88  CAT  C  C      0   0.411   4.6029   2.3443   0.3208
 W88  OAF  O  OC    -1  -0.587   5.5201   3.1847   0.2739
 W88  CAX  C  CR6    0   0.198   5.0901   0.8820   0.2930
 W88  NAQ  N  NR16   0  -0.707   6.4224   0.8017  -0.0124
 W88  CAY  C  CR6    0   0.655   7.1320  -0.3457  -0.1493
 W88  OAC  O  O      0  -0.494   8.3146  -0.3843  -0.4367
 W88  NAR  N  NR16   0  -0.714   6.3808  -1.4706   0.0691
 W88  CAZ  C  CR6    0   0.564   5.0396  -1.5230   0.4017
 W88  OAD  O  O      0  -0.468   4.5054  -2.6081   0.5665
 W88  CAW  C  CR6    0  -0.154   4.3630  -0.2374   0.5285
 W88  CAP  C  CH2    0  -0.474   2.9031  -0.2890   0.8706
 W88  CAN  C  CH2    0  -0.412   2.0206  -0.4753  -0.3638
 W88  CAM  C  CH2    0  -0.417   0.5400  -0.5409  -0.0160
 W88  CAO  C  CH2    0  -0.506  -0.3437  -0.7260  -1.2512
 W88  CAU  C  CR6    0   0.140  -1.8042  -0.7669  -0.9037
 W88  CAK  C  CR16   0  -0.394  -2.5870   0.3576  -0.9690
 W88  CBA  C  CR66   0   0.132  -3.9510   0.3334  -0.5969
 W88  CAJ  C  CR16   0  -0.310  -4.7716   1.4847  -0.6558
 W88  CAH  C  CR16   0  -0.292  -6.0870   1.4257  -0.2875
 W88  CAV  C  CR6    0  -0.104  -6.6700   0.2180   0.1649
 W88  CAS  C  C      0   0.400  -8.1360   0.1790   0.5776
 W88  OAE  O  OC    -1  -0.593  -8.7736   1.2430   0.4556
 W88  OAA  O  O      0  -0.593  -8.5718  -0.9074   1.0040
 W88  CAL  C  CR16   0  -0.367  -5.8880  -0.9079   0.2255
 W88  CBB  C  CR66   0   0.122  -4.5253  -0.8826  -0.1476
 W88  CAI  C  CR16   0  -0.301  -3.7053  -2.0348  -0.0885
 W88  CAG  C  CR16   0  -0.308  -2.3890  -1.9760  -0.4527
 W88  H2   H  HNR6   0   0.419   6.8596  -2.3560  -0.0343
 W88  H4   H  HCH2   0   0.226   2.7358  -1.1222   1.5573
 W88  H5   H  HCH2   0   0.241   2.6057   0.6177   1.3888
 W88  H6   H  HCH2   0   0.220   2.1959   0.3545  -1.0534
 W88  H7   H  HCH2   0   0.215   2.3136  -1.3896  -0.8880
 W88  H8   H  HCH2   0   0.220   0.3613  -1.3594   0.6895
 W88  H9   H  HCH2   0   0.221   0.2438   0.3795   0.4963
 W88  H10  H  HCH2   0   0.237  -0.1543   0.0905  -1.9528
 W88  H11  H  HCH2   0   0.235  -0.0586  -1.6504  -1.7619
 W88  H12  H  HCR6   0   0.241  -2.1600   1.2936  -1.3143
 W88  H13  H  HCR6   0   0.245  -4.3405   2.4192  -0.9960
 W88  H14  H  HCR6   0   0.243  -6.7023   2.3142  -0.3355
 W88  H16  H  HCR6   0   0.239  -6.3173  -1.8414   0.5684
 W88  H17  H  HCR6   0   0.249  -4.1365  -2.9702   0.2484
 W88  H18  H  HCR6   0   0.245  -1.7760  -2.8687  -0.4027
 W88  H19  H  HNR6   0   0.416   6.8889   1.6918  -0.1463

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
 W88  OAC  CAY  double    1.218  0.020  1.218
 W88  CAY  NAQ  single    1.356  0.020  1.356
 W88  CAY  NAR  single    1.370  0.020  1.370
 W88  NAQ  CAX  single    1.369  0.020  1.369
 W88  NAR  CAZ  single    1.383  0.020  1.383
 W88  OAB  CAT  deloc     1.236  0.020  1.236
 W88  OAF  CAT  deloc     1.245  0.020  1.245
 W88  CAX  CAT  single    1.542  0.020  1.542
 W88  CAX  CAW  double    1.355  0.020  1.355
 W88  CAZ  CAW  single    1.458  0.020  1.458
 W88  CAZ  OAD  double    1.221  0.020  1.221
 W88  CAW  CAP  single    1.500  0.020  1.500
 W88  CAP  CAN  single    1.529  0.020  1.529
 W88  CAN  CAM  single    1.522  0.020  1.522
 W88  CAM  CAO  single    1.530  0.020  1.530
 W88  CAG  CAI  aromatic  1.367  0.020  1.367
 W88  CAG  CAU  aromatic  1.417  0.020  1.417
 W88  CAI  CBB  aromatic  1.415  0.020  1.415
 W88  CAO  CAU  single    1.502  0.020  1.502
 W88  CAU  CAK  aromatic  1.372  0.020  1.372
 W88  CBB  CAL  aromatic  1.413  0.020  1.413
 W88  CBB  CBA  aromatic  1.418  0.020  1.418
 W88  CAL  CAV  aromatic  1.372  0.020  1.372
 W88  CAK  CBA  aromatic  1.414  0.020  1.414
 W88  CBA  CAJ  aromatic  1.415  0.020  1.415
 W88  OAA  CAS  deloc     1.246  0.020  1.246
 W88  CAV  CAS  single    1.523  0.020  1.523
 W88  CAV  CAH  aromatic  1.415  0.020  1.415
 W88  CAS  OAE  deloc     1.246  0.020  1.246
 W88  CAJ  CAH  aromatic  1.367  0.020  1.367
 W88  NAR  H2   single    0.860  0.020  1.020
 W88  CAP  H4   single    0.970  0.020  1.090
 W88  CAP  H5   single    0.970  0.020  1.090
 W88  CAN  H6   single    0.970  0.020  1.090
 W88  CAN  H7   single    0.970  0.020  1.090
 W88  CAM  H8   single    0.970  0.020  1.090
 W88  CAM  H9   single    0.970  0.020  1.090
 W88  CAO  H10  single    0.970  0.020  1.090
 W88  CAO  H11  single    0.970  0.020  1.090
 W88  CAK  H12  single    0.930  0.020  1.080
 W88  CAJ  H13  single    0.930  0.020  1.080
 W88  CAH  H14  single    0.930  0.020  1.080
 W88  CAL  H16  single    0.930  0.020  1.080
 W88  CAI  H17  single    0.930  0.020  1.080
 W88  CAG  H18  single    0.930  0.020  1.080
 W88  NAQ  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
 W88  CAX  CAT  OAF  114.01  3.000
 W88  CAX  CAT  OAB  117.74  3.000
 W88  OAF  CAT  OAB  128.25  3.000
 W88  CAW  CAX  NAQ  120.82  3.000
 W88  CAW  CAX  CAT  127.64  3.000
 W88  NAQ  CAX  CAT  111.54  3.000
 W88  H19  NAQ  CAY  119.26  3.000
 W88  H19  NAQ  CAX  115.20  3.000
 W88  CAY  NAQ  CAX  125.54  3.000
 W88  NAR  CAY  OAC  122.96  3.000
 W88  NAR  CAY  NAQ  113.06  3.000
 W88  OAC  CAY  NAQ  123.98  3.000
 W88  H2   NAR  CAZ  116.76  3.000
 W88  H2   NAR  CAY  116.27  3.000
 W88  CAZ  NAR  CAY  126.96  3.000
 W88  CAW  CAZ  OAD  124.67  3.000
 W88  OAD  CAZ  NAR  119.38  3.000
 W88  CAW  CAZ  NAR  115.94  3.000
 W88  CAP  CAW  CAZ  116.17  3.000
 W88  CAP  CAW  CAX  126.16  3.000
 W88  CAZ  CAW  CAX  117.65  3.000
 W88  H5   CAP  H4   107.15  3.000
 W88  H5   CAP  CAN  109.21  3.000
 W88  H4   CAP  CAN  109.04  3.000
 W88  H5   CAP  CAW  110.28  3.000
 W88  H4   CAP  CAW  108.57  3.000
 W88  CAN  CAP  CAW  112.44  3.000
 W88  H7   CAN  H6   106.82  3.000
 W88  H7   CAN  CAM  109.51  3.000
 W88  H6   CAN  CAM  109.44  3.000
 W88  H7   CAN  CAP  109.52  3.000
 W88  H6   CAN  CAP  108.93  3.000
 W88  CAM  CAN  CAP  112.47  3.000
 W88  H9   CAM  H8   106.43  3.000
 W88  H9   CAM  CAO  108.87  3.000
 W88  H8   CAM  CAO  109.59  3.000
 W88  H9   CAM  CAN  109.52  3.000
 W88  H8   CAM  CAN  109.76  3.000
 W88  CAO  CAM  CAN  112.49  3.000
 W88  H11  CAO  H10  106.64  3.000
 W88  H11  CAO  CAU  109.79  3.000
 W88  H10  CAO  CAU  109.72  3.000
 W88  H11  CAO  CAM  109.18  3.000
 W88  H10  CAO  CAM  109.13  3.000
 W88  CAU  CAO  CAM  112.22  3.000
 W88  CAG  CAU  CAK  118.63  3.000
 W88  CAK  CAU  CAO  121.45  3.000
 W88  CAG  CAU  CAO  119.89  3.000
 W88  H12  CAK  CBA  118.55  3.000
 W88  H12  CAK  CAU  119.84  3.000
 W88  CBA  CAK  CAU  121.60  3.000
 W88  CBB  CBA  CAJ  118.43  3.000
 W88  CAJ  CBA  CAK  122.31  3.000
 W88  CBB  CBA  CAK  119.26  3.000
 W88  H13  CAJ  CAH  120.29  3.000
 W88  H13  CAJ  CBA  118.94  3.000
 W88  CAH  CAJ  CBA  120.77  3.000
 W88  H14  CAH  CAV  118.74  3.000
 W88  H14  CAH  CAJ  119.98  3.000
 W88  CAV  CAH  CAJ  121.28  3.000
 W88  CAL  CAV  CAS  121.03  3.000
 W88  CAS  CAV  CAH  120.32  3.000
 W88  CAL  CAV  CAH  118.65  3.000
 W88  OAA  CAS  OAE  126.80  3.000
 W88  OAE  CAS  CAV  116.36  3.000
 W88  OAA  CAS  CAV  116.85  3.000
 W88  H16  CAL  CBB  118.77  3.000
 W88  H16  CAL  CAV  119.68  3.000
 W88  CBB  CAL  CAV  121.55  3.000
 W88  CAI  CBB  CAL  122.21  3.000
 W88  CAL  CBB  CBA  119.32  3.000
 W88  CAI  CBB  CBA  118.47  3.000
 W88  H17  CAI  CAG  120.20  3.000
 W88  H17  CAI  CBB  119.02  3.000
 W88  CAG  CAI  CBB  120.78  3.000
 W88  H18  CAG  CAI  119.79  3.000
 W88  H18  CAG  CAU  118.95  3.000
 W88  CAI  CAG  CAU  121.26  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
 W88  CONST_01  CBB  CAI  CAG  CAU     0.00   0.0  0
 W88  CONST_02  CBB  CBA  CAK  CAU     0.00   0.0  0
 W88  CONST_03  CAJ  CBA  CAK  CAU   180.00   0.0  0
 W88  CONST_04  CAI  CAG  CAU  CAK     0.00   0.0  0
 W88  CONST_05  CAI  CBB  CBA  CAK     0.00   0.0  0
 W88  CONST_06  CAL  CBB  CBA  CAK   180.00   0.0  0
 W88  CONST_07  CAH  CAJ  CBA  CAK   180.00   0.0  0
 W88  CONST_08  CAG  CAI  CBB  CBA     0.00   0.0  0
 W88  CONST_09  CAV  CAL  CBB  CBA     0.00   0.0  0
 W88  CONST_10  CAG  CAU  CAK  CBA     0.00   0.0  0
 W88  CONST_11  CAV  CAH  CAJ  CBA     0.00   0.0  0
 W88  CONST_12  CAI  CBB  CBA  CAJ   180.00   0.0  0
 W88  CONST_13  CAL  CBB  CBA  CAJ     0.00   0.0  0
 W88  CONST_14  CAL  CAV  CAH  CAJ     0.00   0.0  0
 W88  CONST_15  CBB  CAL  CAV  CAH     0.00   0.0  0
 W88  CONST_16  CBB  CBA  CAJ  CAH     0.00   0.0  0
 W88  CONST_17  CAI  CBB  CAL  CAV   180.00   0.0  0
 W88  CONST_18  CAG  CAI  CBB  CAL   180.00   0.0  0
 W88  CONST_19  NAR  CAY  NAQ  CAX     0.00   0.0  0
 W88  CONST_20  CAZ  NAR  CAY  NAQ     0.00   0.0  0
 W88  CONST_21  CAW  CAZ  NAR  CAY     0.00   0.0  0
 W88  CONST_22  CAI  CAG  CAU  CAO   180.00   0.0  0
 W88  CONST_23  CBA  CAK  CAU  CAO   180.00   0.0  0
 W88  CONST_24  CAS  CAV  CAH  CAJ   180.00   0.0  0
 W88  CONST_25  CBB  CAL  CAV  CAS   180.00   0.0  0
 W88  CONST_26  OAC  CAY  NAQ  CAX   180.00   0.0  0
 W88  CONST_27  OAD  CAZ  NAR  CAY   180.00   0.0  0
 W88  CONST_28  CAZ  NAR  CAY  OAC   180.00   0.0  0
 W88  CONST_29  H17  CAI  CAG  CAU   180.00   0.0  0
 W88  CONST_30  H18  CAG  CAU  CAK   180.00   0.0  0
 W88  CONST_31  H13  CAJ  CBA  CAK     0.00   0.0  0
 W88  CONST_32  H16  CAL  CBB  CBA   180.00   0.0  0
 W88  CONST_33  H14  CAH  CAJ  CBA   180.00   0.0  0
 W88  CONST_34  H12  CAK  CBA  CAJ     0.00   0.0  0
 W88  CONST_35  H2   NAR  CAY  NAQ   180.00   0.0  0
 W88  CONST_36  H19  NAQ  CAY  NAR   180.00   0.0  0
 W88  Var_01    NAQ  CAX  CAT  OAB   168.44  30.0  2
 W88  Var_02    CAN  CAP  CAW  CAX    93.44  30.0  3
 W88  Var_03    CAG  CAU  CAO  CAM   -82.57  30.0  2
 W88  Var_04    OAA  CAS  CAV  CAH  -177.88  30.0  2
 W88  Var_05    CAM  CAN  CAP  CAW   179.46  30.0  3
 W88  Var_06    CAU  CAO  CAM  CAN  -179.04  30.0  3
 W88  Var_07    CAO  CAM  CAN  CAP   179.95  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
 W88  plan-1  CAT  0.020
 W88  plan-1  CAX  0.020
 W88  plan-1  NAQ  0.020
 W88  plan-1  CAY  0.020
 W88  plan-1  OAC  0.020
 W88  plan-1  NAR  0.020
 W88  plan-1  CAZ  0.020
 W88  plan-1  OAD  0.020
 W88  plan-1  CAW  0.020
 W88  plan-1  CAP  0.020
 W88  plan-1  H2   0.020
 W88  plan-1  H19  0.020
 W88  plan-2  CAO  0.020
 W88  plan-2  CAU  0.020
 W88  plan-2  CAK  0.020
 W88  plan-2  CBA  0.020
 W88  plan-2  CAJ  0.020
 W88  plan-2  CAH  0.020
 W88  plan-2  CAV  0.020
 W88  plan-2  CAS  0.020
 W88  plan-2  CAL  0.020
 W88  plan-2  CBB  0.020
 W88  plan-2  CAI  0.020
 W88  plan-2  CAG  0.020
 W88  plan-2  H12  0.020
 W88  plan-2  H13  0.020
 W88  plan-2  H14  0.020
 W88  plan-2  H16  0.020
 W88  plan-2  H17  0.020
 W88  plan-2  H18  0.020
 W88  plan-3  OAB  0.020
 W88  plan-3  CAT  0.020
 W88  plan-3  OAF  0.020
 W88  plan-3  CAX  0.020
 W88  plan-4  CAV  0.020
 W88  plan-4  CAS  0.020
 W88  plan-4  OAE  0.020
 W88  plan-4  OAA  0.020

