# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 10:34:35 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 5-{4-[4-(methoxycarbonyl)phenyl]butyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccc(CCCCC2=C(NC(=O)NC2=O)C(O)=O)cc1
#
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
 W86  W86  '5-{4-[4-(methoxycarbonyl)phenyl]butyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  43  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 PERFECT
;

data_comp_W86
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
 W86  OAB  O  O     0  -0.397   2.6303   2.5876  -0.0407
 W86  CAR  C  C     0   0.517   3.7725   2.2953   0.1858
 W86  OAF  O  OH1   0  -0.590   4.7350   3.1625   0.4434
 W86  CAV  C  CR6   0   0.280   4.2941   0.8906   0.1942
 W86  NAO  N  NR16  0  -0.732   5.6314   0.7701  -0.0934
 W86  CAX  C  CR6   0   0.670   6.2947  -0.4185  -0.1701
 W86  OAD  O  O     0  -0.474   7.4736  -0.5081  -0.4415
 W86  NAP  N  NR16  0  -0.716   5.4998  -1.5047   0.0872
 W86  CAY  C  CR6   0   0.585   4.1580  -1.5019   0.4033
 W86  OAE  O  O     0  -0.441   3.5751  -2.5480   0.6118
 W86  CAW  C  CR6   0  -0.115   3.5185  -0.1831   0.4594
 W86  CAN  C  CH2   0  -0.500   2.0588  -0.1669   0.7953
 W86  CAL  C  CH2   0  -0.417   1.1728  -0.4066  -0.4295
 W86  CAK  C  CH2   0  -0.421  -0.3065  -0.3684  -0.0744
 W86  CAM  C  CH2   0  -0.509  -1.2052  -0.6126  -1.2894
 W86  CAT  C  CR6   0   0.142  -2.6578  -0.5203  -0.9260
 W86  CAH  C  CR16  0  -0.300  -3.3822  -1.6555  -0.5678
 W86  CAJ  C  CR16  0  -0.240  -4.7075  -1.5618  -0.1792
 W86  CAG  C  CR16  0  -0.294  -3.3028   0.7149  -0.8848
 W86  CAI  C  CR16  0  -0.250  -4.6270   0.8191  -0.4948
 W86  CAU  C  CR6   0  -0.101  -5.3436  -0.3226  -0.1360
 W86  CAS  C  C     0   0.592  -6.7632  -0.2720   0.2877
 W86  OAC  O  O     0  -0.452  -7.4147  -1.2471   0.5801
 W86  OAQ  O  O2    0  -0.457  -7.2461   0.9604   0.3139
 W86  CAA  C  CH3   0  -0.423  -8.6060   1.1301   0.7109
 W86  H1   H  HOH1  0   0.503   4.4009   4.0719   0.3927
 W86  H2   H  HNR6  0   0.430   5.9519  -2.4093   0.0315
 W86  H4   H  HCH2  0   0.251   1.8708  -0.9515   1.5308
 W86  H5   H  HCH2  0   0.252   1.7797   0.7719   1.2689
 W86  H6   H  HCH2  0   0.230   1.3856   0.3528  -1.1858
 W86  H7   H  HCH2  0   0.227   1.4196  -1.3740  -0.8750
 W86  H8   H  HCH2  0   0.228  -0.5244  -1.1179   0.6931
 W86  H9   H  HCH2  0   0.228  -0.5512   0.6045   0.3629
 W86  H10  H  HCH2  0   0.244  -0.9697   0.1216  -2.0645
 W86  H11  H  HCH2  0   0.244  -0.9884  -1.5987  -1.7076
 W86  H12  H  HCR6  0   0.253  -2.9032  -2.6269  -0.5984
 W86  H13  H  HCR6  0   0.260  -5.2492  -2.4585   0.0906
 W86  H14  H  HCR6  0   0.254  -2.7607   1.6110  -1.1624
 W86  H15  H  HCR6  0   0.261  -5.0929   1.7946  -0.4741
 W86  H16  H  HCH3  0   0.240  -8.7696   0.7821   1.7304
 W86  H17  H  HCH3  0   0.253  -8.7992   2.1974   0.6600
 W86  H18  H  HCH3  0   0.240  -9.2858   0.6076   0.0384
 W86  H19  H  HNR6  0   0.438   6.1783   1.5981  -0.2828

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
 W86  OAD  CAX  double    1.213  0.020  1.213
 W86  CAX  NAO  single    1.363  0.020  1.363
 W86  CAX  NAP  single    1.370  0.020  1.370
 W86  NAO  CAV  single    1.373  0.020  1.373
 W86  NAP  CAY  single    1.378  0.020  1.378
 W86  CAV  CAR  single    1.498  0.020  1.498
 W86  CAV  CAW  double    1.351  0.020  1.351
 W86  OAB  CAR  double    1.201  0.020  1.201
 W86  OAF  CAR  single    1.321  0.020  1.321
 W86  CAY  CAW  single    1.467  0.020  1.467
 W86  CAY  OAE  double    1.216  0.020  1.216
 W86  CAW  CAN  single    1.498  0.020  1.498
 W86  CAN  CAL  single    1.531  0.020  1.531
 W86  CAL  CAK  single    1.522  0.020  1.522
 W86  CAK  CAM  single    1.531  0.020  1.531
 W86  CAA  OAQ  single    1.427  0.020  1.427
 W86  CAJ  CAH  aromatic  1.384  0.020  1.384
 W86  CAJ  CAU  aromatic  1.394  0.020  1.394
 W86  CAH  CAT  aromatic  1.393  0.020  1.393
 W86  OAQ  CAS  single    1.324  0.020  1.324
 W86  CAS  CAU  single    1.482  0.020  1.482
 W86  CAS  OAC  double    1.209  0.020  1.209
 W86  CAU  CAI  aromatic  1.395  0.020  1.395
 W86  CAT  CAM  single    1.500  0.020  1.500
 W86  CAT  CAG  aromatic  1.394  0.020  1.394
 W86  CAI  CAG  aromatic  1.384  0.020  1.384
 W86  OAF  H1   single    0.850  0.020  0.980
 W86  NAP  H2   single    0.860  0.020  1.020
 W86  CAN  H4   single    0.970  0.020  1.090
 W86  CAN  H5   single    0.970  0.020  1.090
 W86  CAL  H6   single    0.970  0.020  1.090
 W86  CAL  H7   single    0.970  0.020  1.090
 W86  CAK  H8   single    0.970  0.020  1.090
 W86  CAK  H9   single    0.970  0.020  1.090
 W86  CAM  H10  single    0.970  0.020  1.090
 W86  CAM  H11  single    0.970  0.020  1.090
 W86  CAH  H12  single    0.930  0.020  1.080
 W86  CAJ  H13  single    0.930  0.020  1.080
 W86  CAG  H14  single    0.930  0.020  1.080
 W86  CAI  H15  single    0.930  0.020  1.080
 W86  CAA  H16  single    0.970  0.020  1.090
 W86  CAA  H17  single    0.970  0.020  1.090
 W86  CAA  H18  single    0.970  0.020  1.090
 W86  NAO  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
 W86  CAV  CAR  OAF  111.15  3.000
 W86  OAF  CAR  OAB  124.76  3.000
 W86  CAV  CAR  OAB  124.09  3.000
 W86  H1   OAF  CAR  110.74  3.000
 W86  CAW  CAV  NAO  122.04  3.000
 W86  CAW  CAV  CAR  123.12  3.000
 W86  NAO  CAV  CAR  114.84  3.000
 W86  H19  NAO  CAX  116.14  3.000
 W86  H19  NAO  CAV  119.64  3.000
 W86  CAX  NAO  CAV  124.20  3.000
 W86  NAP  CAX  OAD  123.17  3.000
 W86  NAP  CAX  NAO  113.47  3.000
 W86  OAD  CAX  NAO  123.36  3.000
 W86  H2   NAP  CAY  116.67  3.000
 W86  H2   NAP  CAX  116.02  3.000
 W86  CAY  NAP  CAX  127.31  3.000
 W86  CAW  CAY  OAE  123.92  3.000
 W86  OAE  CAY  NAP  120.29  3.000
 W86  CAW  CAY  NAP  115.79  3.000
 W86  CAN  CAW  CAY  116.31  3.000
 W86  CAN  CAW  CAV  126.51  3.000
 W86  CAY  CAW  CAV  117.18  3.000
 W86  H5   CAN  H4   106.42  3.000
 W86  H5   CAN  CAL  109.57  3.000
 W86  H4   CAN  CAL  109.08  3.000
 W86  H5   CAN  CAW  110.92  3.000
 W86  H4   CAN  CAW  108.13  3.000
 W86  CAL  CAN  CAW  112.51  3.000
 W86  H7   CAL  H6   106.80  3.000
 W86  H7   CAL  CAK  109.67  3.000
 W86  H6   CAL  CAK  109.47  3.000
 W86  H7   CAL  CAN  109.51  3.000
 W86  H6   CAL  CAN  109.41  3.000
 W86  CAK  CAL  CAN  111.84  3.000
 W86  H9   CAK  H8   106.50  3.000
 W86  H9   CAK  CAM  109.13  3.000
 W86  H8   CAK  CAM  109.30  3.000
 W86  H9   CAK  CAL  109.45  3.000
 W86  H8   CAK  CAL  109.87  3.000
 W86  CAM  CAK  CAL  112.42  3.000
 W86  H11  CAM  H10  106.97  3.000
 W86  H11  CAM  CAT  109.90  3.000
 W86  H10  CAM  CAT  109.82  3.000
 W86  H11  CAM  CAK  109.34  3.000
 W86  H10  CAM  CAK  109.21  3.000
 W86  CAT  CAM  CAK  111.49  3.000
 W86  CAG  CAT  CAH  118.28  3.000
 W86  CAG  CAT  CAM  120.64  3.000
 W86  CAH  CAT  CAM  121.03  3.000
 W86  H12  CAH  CAJ  119.47  3.000
 W86  H12  CAH  CAT  119.56  3.000
 W86  CAJ  CAH  CAT  120.98  3.000
 W86  H13  CAJ  CAU  120.05  3.000
 W86  H13  CAJ  CAH  119.56  3.000
 W86  CAU  CAJ  CAH  120.39  3.000
 W86  H14  CAG  CAI  119.24  3.000
 W86  H14  CAG  CAT  119.59  3.000
 W86  CAI  CAG  CAT  121.17  3.000
 W86  H15  CAI  CAU  120.81  3.000
 W86  H15  CAI  CAG  119.05  3.000
 W86  CAU  CAI  CAG  120.15  3.000
 W86  CAS  CAU  CAI  122.52  3.000
 W86  CAI  CAU  CAJ  119.04  3.000
 W86  CAS  CAU  CAJ  118.45  3.000
 W86  OAQ  CAS  OAC  123.34  3.000
 W86  OAC  CAS  CAU  123.90  3.000
 W86  OAQ  CAS  CAU  112.75  3.000
 W86  CAA  OAQ  CAS  117.64  3.000
 W86  H18  CAA  H17  109.35  3.000
 W86  H18  CAA  H16  109.31  3.000
 W86  H17  CAA  H16  109.34  3.000
 W86  H18  CAA  OAQ  111.46  3.000
 W86  H17  CAA  OAQ  105.87  3.000
 W86  H16  CAA  OAQ  111.43  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
 W86  CONST_01  CAU  CAJ  CAH  CAT     0.00   0.0  0
 W86  CONST_02  CAU  CAI  CAG  CAT     0.00   0.0  0
 W86  CONST_03  CAI  CAU  CAJ  CAH     0.00   0.0  0
 W86  CONST_04  CAI  CAG  CAT  CAH     0.00   0.0  0
 W86  CONST_05  CAG  CAT  CAH  CAJ     0.00   0.0  0
 W86  CONST_06  CAG  CAI  CAU  CAJ     0.00   0.0  0
 W86  CONST_07  NAP  CAX  NAO  CAV     0.00   0.0  0
 W86  CONST_08  CAY  NAP  CAX  NAO     0.00   0.0  0
 W86  CONST_09  CAW  CAY  NAP  CAX     0.00   0.0  0
 W86  CONST_10  CAJ  CAH  CAT  CAM   180.00   0.0  0
 W86  CONST_11  CAI  CAG  CAT  CAM   180.00   0.0  0
 W86  CONST_12  CAS  CAU  CAJ  CAH   180.00   0.0  0
 W86  CONST_13  CAS  CAU  CAI  CAG   180.00   0.0  0
 W86  CONST_14  OAD  CAX  NAO  CAV   180.00   0.0  0
 W86  CONST_15  OAE  CAY  NAP  CAX   180.00   0.0  0
 W86  CONST_16  CAY  NAP  CAX  OAD   180.00   0.0  0
 W86  CONST_17  H13  CAJ  CAH  CAT   180.00   0.0  0
 W86  CONST_18  H15  CAI  CAG  CAT   180.00   0.0  0
 W86  CONST_19  H14  CAG  CAT  CAH   180.00   0.0  0
 W86  CONST_20  H12  CAH  CAT  CAG   180.00   0.0  0
 W86  CONST_21  H2   NAP  CAX  NAO   180.00   0.0  0
 W86  CONST_22  H19  NAO  CAX  NAP   180.00   0.0  0
 W86  CONST_23  H1   OAF  CAR  CAV   180.00   0.0  0
 W86  Var_01    NAO  CAV  CAR  OAB   153.56  30.0  2
 W86  Var_02    CAL  CAN  CAW  CAV    95.56  30.0  3
 W86  Var_03    CAH  CAT  CAM  CAK   -93.04  30.0  2
 W86  Var_04    OAQ  CAS  CAU  CAJ   178.73  30.0  3
 W86  Var_05    CAK  CAL  CAN  CAW  -179.23  30.0  3
 W86  Var_06    CAT  CAM  CAK  CAL  -177.90  30.0  3
 W86  Var_07    CAM  CAK  CAL  CAN  -179.76  30.0  3
 W86  Var_08    H16  CAA  OAQ  CAS    61.49  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
 W86  plan-1  CAR  0.020
 W86  plan-1  CAV  0.020
 W86  plan-1  NAO  0.020
 W86  plan-1  CAX  0.020
 W86  plan-1  OAD  0.020
 W86  plan-1  NAP  0.020
 W86  plan-1  CAY  0.020
 W86  plan-1  OAE  0.020
 W86  plan-1  CAW  0.020
 W86  plan-1  CAN  0.020
 W86  plan-1  H2   0.020
 W86  plan-1  H19  0.020
 W86  plan-2  CAU  0.020
 W86  plan-2  CAS  0.020
 W86  plan-2  OAC  0.020
 W86  plan-2  OAQ  0.020
 W86  plan-3  CAM  0.020
 W86  plan-3  CAT  0.020
 W86  plan-3  CAH  0.020
 W86  plan-3  CAJ  0.020
 W86  plan-3  CAG  0.020
 W86  plan-3  CAI  0.020
 W86  plan-3  CAU  0.020
 W86  plan-3  CAS  0.020
 W86  plan-3  H12  0.020
 W86  plan-3  H13  0.020
 W86  plan-3  H14  0.020
 W86  plan-3  H15  0.020
 W86  plan-4  OAB  0.020
 W86  plan-4  CAR  0.020
 W86  plan-4  OAF  0.020
 W86  plan-4  CAV  0.020
 W86  plan-4  H1   0.020

