# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 12:29:33 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-{4-[5-(methoxycarbonyl)naphthalen-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: COC(=O)c1cccc2cc(CCCCC3=C(NC(=O)NC3=O)C(O)=O)ccc12
#
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
 W87  W87  '5-{4-[5-(methoxycarbonyl)naphthalen-2-yl]butyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  49  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 PERFECT
;

data_comp_W87
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
 W87  OAB  O  OH1   0  -0.593  -5.8946  -2.6854   1.2081
 W87  CAT  C  C     0   0.523  -4.8670  -1.9555   0.8121
 W87  OAF  O  O     0  -0.396  -3.7352  -2.3509   0.7466
 W87  CAX  C  CR6   0   0.276  -5.2973  -0.5695   0.4374
 W87  NAQ  N  NR16  0  -0.733  -6.6295  -0.4411   0.1281
 W87  CAZ  C  CR6   0   0.669  -7.2184   0.7249  -0.2606
 W87  OAD  O  O     0  -0.474  -8.3952   0.8172  -0.5404
 W87  NAR  N  NR16  0  -0.715  -6.3519   1.7853  -0.3075
 W87  CBA  C  CR6   0   0.584  -5.0054   1.7761  -0.0151
 W87  OAE  O  O     0  -0.441  -4.3512   2.7961  -0.1100
 W87  CAY  C  CR6   0  -0.113  -4.4500   0.4828   0.3999
 W87  CAP  C  CH2   0  -0.500  -2.9876   0.4656   0.7252
 W87  CAN  C  CH2   0  -0.415  -2.1141   0.2335  -0.5100
 W87  CAM  C  CH2   0  -0.423  -0.6339   0.1934  -0.1577
 W87  CAO  C  CH2   0  -0.507   0.2522  -0.0303  -1.3846
 W87  CAV  C  CR6   0   0.147   1.7087  -0.0818  -1.0265
 W87  CAL  C  CR16  0  -0.396   2.4085  -1.2575  -0.9997
 W87  CAI  C  CR16  0  -0.284   2.3937   1.1034  -0.6711
 W87  CAK  C  CR16  0  -0.320   3.7055   1.0948  -0.2860
 W87  CBC  C  CR66  0   0.119   4.4433  -0.1149  -0.2317
 W87  CBB  C  CR66  0   0.129   3.7703  -1.3058  -0.6190
 W87  CAJ  C  CR16  0  -0.307   4.4657  -2.5360  -0.6261
 W87  CAG  C  CR16  0  -0.250   5.7859  -2.5945  -0.2805
 W87  CAH  C  CR16  0  -0.279   6.4646  -1.4233   0.0945
 W87  CAW  C  CR6   0  -0.082   5.8203  -0.2077   0.1373
 W87  CAU  C  C     0   0.542   6.5716   0.9748   0.6374
 W87  OAC  O  O     0  -0.446   6.0875   1.8822   1.2705
 W87  OAS  O  O2    0  -0.451   7.8583   0.9120   0.3297
 W87  CAA  C  CH3   0  -0.423   8.7063   1.9470   0.8286
 W87  H1   H  HOH1  0   0.503  -5.6141  -3.5914   1.4122
 W87  H2   H  HNR6  0   0.430  -6.7493   2.6713  -0.5953
 W87  H4   H  HCH2  0   0.251  -2.7280   1.4286   1.1684
 W87  H5   H  HCH2  0   0.252  -2.7663  -0.2898   1.4759
 W87  H6   H  HCH2  0   0.230  -2.4032  -0.7079  -0.9821
 W87  H7   H  HCH2  0   0.226  -2.2955   1.0242  -1.2435
 W87  H8   H  HCH2  0   0.226  -0.3469   1.1291   0.3320
 W87  H9   H  HCH2  0   0.227  -0.4523  -0.6049   0.5685
 W87  H10  H  HCH2  0   0.241  -0.0398  -0.9612  -1.8767
 W87  H11  H  HCH2  0   0.241   0.0785   0.7748  -2.1050
 W87  H12  H  HCR6  0   0.249   1.9226  -2.1857  -1.2806
 W87  H13  H  HCR6  0   0.253   1.8641   2.0485  -0.7106
 W87  H14  H  HCR6  0   0.256   4.1736   2.0320  -0.0303
 W87  H15  H  HCR6  0   0.263   3.9349  -3.4350  -0.9148
 W87  H16  H  HCR6  0   0.266   6.3154  -3.5376  -0.2864
 W87  H17  H  HCR6  0   0.271   7.5065  -1.4992   0.3736
 W87  H18  H  HCH3  0   0.241   8.7031   1.9737   1.9179
 W87  H19  H  HCH3  0   0.254   9.7050   1.7078   0.4763
 W87  H20  H  HCH3  0   0.241   8.4107   2.9223   0.4437
 W87  H21  H  HNR6  0   0.438  -7.2319  -1.2511   0.1667

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
 W87  OAD  CAZ  double    1.213  0.020  1.213
 W87  CAZ  NAQ  single    1.363  0.020  1.363
 W87  CAZ  NAR  single    1.370  0.020  1.370
 W87  NAQ  CAX  single    1.374  0.020  1.374
 W87  NAR  CBA  single    1.378  0.020  1.378
 W87  CAX  CAT  single    1.499  0.020  1.499
 W87  CAX  CAY  double    1.352  0.020  1.352
 W87  CAT  OAF  double    1.201  0.020  1.201
 W87  CAT  OAB  single    1.321  0.020  1.321
 W87  CBA  CAY  single    1.467  0.020  1.467
 W87  CBA  OAE  double    1.215  0.020  1.215
 W87  CAY  CAP  single    1.498  0.020  1.498
 W87  CAP  CAN  single    1.531  0.020  1.531
 W87  CAN  CAM  single    1.522  0.020  1.522
 W87  CAM  CAO  single    1.530  0.020  1.530
 W87  OAC  CAU  double    1.208  0.020  1.208
 W87  CAA  OAS  single    1.428  0.020  1.428
 W87  CAI  CAK  aromatic  1.367  0.020  1.367
 W87  CAI  CAV  aromatic  1.414  0.020  1.414
 W87  CAK  CBC  aromatic  1.418  0.020  1.418
 W87  CAU  OAS  single    1.325  0.020  1.325
 W87  CAU  CAW  single    1.488  0.020  1.488
 W87  CAO  CAV  single    1.501  0.020  1.501
 W87  CAV  CAL  aromatic  1.368  0.020  1.368
 W87  CBC  CAW  aromatic  1.429  0.020  1.429
 W87  CBC  CBB  aromatic  1.422  0.020  1.422
 W87  CAW  CAH  aromatic  1.376  0.020  1.376
 W87  CAL  CBB  aromatic  1.415  0.020  1.415
 W87  CBB  CAJ  aromatic  1.413  0.020  1.413
 W87  CAH  CAG  aromatic  1.405  0.020  1.405
 W87  CAJ  CAG  aromatic  1.366  0.020  1.366
 W87  OAB  H1   single    0.850  0.020  0.980
 W87  NAR  H2   single    0.860  0.020  1.020
 W87  CAP  H4   single    0.970  0.020  1.090
 W87  CAP  H5   single    0.970  0.020  1.090
 W87  CAN  H6   single    0.970  0.020  1.090
 W87  CAN  H7   single    0.970  0.020  1.090
 W87  CAM  H8   single    0.970  0.020  1.090
 W87  CAM  H9   single    0.970  0.020  1.090
 W87  CAO  H10  single    0.970  0.020  1.090
 W87  CAO  H11  single    0.970  0.020  1.090
 W87  CAL  H12  single    0.930  0.020  1.080
 W87  CAI  H13  single    0.930  0.020  1.080
 W87  CAK  H14  single    0.930  0.020  1.080
 W87  CAJ  H15  single    0.930  0.020  1.080
 W87  CAG  H16  single    0.930  0.020  1.080
 W87  CAH  H17  single    0.930  0.020  1.080
 W87  CAA  H18  single    0.970  0.020  1.090
 W87  CAA  H19  single    0.970  0.020  1.090
 W87  CAA  H20  single    0.970  0.020  1.090
 W87  NAQ  H21  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
 W87  H1   OAB  CAT  110.75  3.000
 W87  CAX  CAT  OAF  124.16  3.000
 W87  OAF  CAT  OAB  124.58  3.000
 W87  CAX  CAT  OAB  111.26  3.000
 W87  CAY  CAX  NAQ  121.94  3.000
 W87  CAY  CAX  CAT  123.15  3.000
 W87  NAQ  CAX  CAT  114.91  3.000
 W87  H21  NAQ  CAZ  116.06  3.000
 W87  H21  NAQ  CAX  119.65  3.000
 W87  CAZ  NAQ  CAX  124.28  3.000
 W87  NAR  CAZ  OAD  123.14  3.000
 W87  NAR  CAZ  NAQ  113.49  3.000
 W87  OAD  CAZ  NAQ  123.37  3.000
 W87  H2   NAR  CBA  116.72  3.000
 W87  H2   NAR  CAZ  116.01  3.000
 W87  CBA  NAR  CAZ  127.27  3.000
 W87  CAY  CBA  OAE  123.92  3.000
 W87  OAE  CBA  NAR  120.25  3.000
 W87  CAY  CBA  NAR  115.84  3.000
 W87  CAP  CAY  CBA  116.16  3.000
 W87  CAP  CAY  CAX  126.66  3.000
 W87  CBA  CAY  CAX  117.18  3.000
 W87  H5   CAP  H4   106.50  3.000
 W87  H5   CAP  CAN  109.61  3.000
 W87  H4   CAP  CAN  109.01  3.000
 W87  H5   CAP  CAY  110.88  3.000
 W87  H4   CAP  CAY  108.07  3.000
 W87  CAN  CAP  CAY  112.56  3.000
 W87  H7   CAN  H6   106.82  3.000
 W87  H7   CAN  CAM  109.61  3.000
 W87  H6   CAN  CAM  109.56  3.000
 W87  H7   CAN  CAP  109.69  3.000
 W87  H6   CAN  CAP  109.18  3.000
 W87  CAM  CAN  CAP  111.85  3.000
 W87  H9   CAM  H8   106.46  3.000
 W87  H9   CAM  CAO  109.23  3.000
 W87  H8   CAM  CAO  109.39  3.000
 W87  H9   CAM  CAN  109.53  3.000
 W87  H8   CAM  CAN  109.64  3.000
 W87  CAO  CAM  CAN  112.42  3.000
 W87  H11  CAO  H10  106.73  3.000
 W87  H11  CAO  CAV  109.66  3.000
 W87  H10  CAO  CAV  109.73  3.000
 W87  H11  CAO  CAM  109.18  3.000
 W87  H10  CAO  CAM  109.33  3.000
 W87  CAV  CAO  CAM  112.07  3.000
 W87  CAI  CAV  CAL  117.86  3.000
 W87  CAL  CAV  CAO  122.04  3.000
 W87  CAI  CAV  CAO  120.08  3.000
 W87  H12  CAL  CBB  118.14  3.000
 W87  H12  CAL  CAV  120.07  3.000
 W87  CBB  CAL  CAV  121.79  3.000
 W87  H13  CAI  CAK  118.97  3.000
 W87  H13  CAI  CAV  119.00  3.000
 W87  CAK  CAI  CAV  122.02  3.000
 W87  H14  CAK  CBC  120.43  3.000
 W87  H14  CAK  CAI  118.54  3.000
 W87  CBC  CAK  CAI  121.02  3.000
 W87  CAW  CBC  CBB  118.18  3.000
 W87  CBB  CBC  CAK  117.25  3.000
 W87  CAW  CBC  CAK  124.53  3.000
 W87  CAJ  CBB  CBC  119.84  3.000
 W87  CAJ  CBB  CAL  120.13  3.000
 W87  CBC  CBB  CAL  120.03  3.000
 W87  H15  CAJ  CAG  120.36  3.000
 W87  H15  CAJ  CBB  118.86  3.000
 W87  CAG  CAJ  CBB  120.78  3.000
 W87  H16  CAG  CAH  119.47  3.000
 W87  H16  CAG  CAJ  120.61  3.000
 W87  CAH  CAG  CAJ  119.92  3.000
 W87  H17  CAH  CAW  120.33  3.000
 W87  H17  CAH  CAG  118.42  3.000
 W87  CAW  CAH  CAG  121.23  3.000
 W87  CAU  CAW  CAH  118.43  3.000
 W87  CAH  CAW  CBC  120.04  3.000
 W87  CAU  CAW  CBC  121.46  3.000
 W87  OAS  CAU  OAC  123.15  3.000
 W87  OAS  CAU  CAW  112.02  3.000
 W87  OAC  CAU  CAW  124.83  3.000
 W87  CAA  OAS  CAU  117.48  3.000
 W87  H20  CAA  H19  109.41  3.000
 W87  H20  CAA  H18  109.30  3.000
 W87  H19  CAA  H18  109.42  3.000
 W87  H20  CAA  OAS  111.36  3.000
 W87  H19  CAA  OAS  105.85  3.000
 W87  H18  CAA  OAS  111.42  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
 W87  CONST_01  CBC  CAK  CAI  CAV     0.00   0.0  0
 W87  CONST_02  CBC  CBB  CAL  CAV     0.00   0.0  0
 W87  CONST_03  CAJ  CBB  CAL  CAV   180.00   0.0  0
 W87  CONST_04  CAK  CAI  CAV  CAL     0.00   0.0  0
 W87  CONST_05  CAK  CBC  CBB  CAL     0.00   0.0  0
 W87  CONST_06  CAW  CBC  CBB  CAL   180.00   0.0  0
 W87  CONST_07  CAG  CAJ  CBB  CAL   180.00   0.0  0
 W87  CONST_08  CAW  CBC  CAK  CAI   180.00   0.0  0
 W87  CONST_09  CBB  CBC  CAK  CAI     0.00   0.0  0
 W87  CONST_10  CBB  CAL  CAV  CAI     0.00   0.0  0
 W87  CONST_11  CAH  CAW  CBC  CAK   180.00   0.0  0
 W87  CONST_12  CAJ  CBB  CBC  CAK   180.00   0.0  0
 W87  CONST_13  CAG  CAH  CAW  CBC     0.00   0.0  0
 W87  CONST_14  CAG  CAJ  CBB  CBC     0.00   0.0  0
 W87  CONST_15  CAH  CAW  CBC  CBB     0.00   0.0  0
 W87  CONST_16  CAH  CAG  CAJ  CBB     0.00   0.0  0
 W87  CONST_17  CAW  CBC  CBB  CAJ     0.00   0.0  0
 W87  CONST_18  CAW  CAH  CAG  CAJ     0.00   0.0  0
 W87  CONST_19  NAR  CAZ  NAQ  CAX     0.00   0.0  0
 W87  CONST_20  CBA  NAR  CAZ  NAQ     0.00   0.0  0
 W87  CONST_21  CAY  CBA  NAR  CAZ     0.00   0.0  0
 W87  CONST_22  CAK  CAI  CAV  CAO   180.00   0.0  0
 W87  CONST_23  CBB  CAL  CAV  CAO   180.00   0.0  0
 W87  CONST_24  CAU  CAW  CBC  CAK     0.00   0.0  0
 W87  CONST_25  CAU  CAW  CBC  CBB   180.00   0.0  0
 W87  CONST_26  CAU  CAW  CAH  CAG   180.00   0.0  0
 W87  CONST_27  OAD  CAZ  NAQ  CAX   180.00   0.0  0
 W87  CONST_28  OAE  CBA  NAR  CAZ   180.00   0.0  0
 W87  CONST_29  CBA  NAR  CAZ  OAD   180.00   0.0  0
 W87  CONST_30  H14  CAK  CAI  CAV   180.00   0.0  0
 W87  CONST_31  H13  CAI  CAV  CAL   180.00   0.0  0
 W87  CONST_32  H15  CAJ  CBB  CAL     0.00   0.0  0
 W87  CONST_33  H12  CAL  CAV  CAI   180.00   0.0  0
 W87  CONST_34  H17  CAH  CAW  CBC   180.00   0.0  0
 W87  CONST_35  H16  CAG  CAJ  CBB   180.00   0.0  0
 W87  CONST_36  H2   NAR  CAZ  NAQ   180.00   0.0  0
 W87  CONST_37  H21  NAQ  CAZ  NAR   180.00   0.0  0
 W87  CONST_38  H1   OAB  CAT  CAX   180.00   0.0  0
 W87  Var_01    NAQ  CAX  CAT  OAB   -21.25  30.0  2
 W87  Var_02    CAN  CAP  CAY  CAX    92.56  30.0  3
 W87  Var_03    CAI  CAV  CAO  CAM   -73.19  30.0  2
 W87  Var_04    OAC  CAU  CAW  CBC    31.37  30.0  2
 W87  Var_05    CAM  CAN  CAP  CAY  -178.95  30.0  3
 W87  Var_06    CAV  CAO  CAM  CAN  -179.44  30.0  3
 W87  Var_07    CAO  CAM  CAN  CAP  -179.68  30.0  3
 W87  Var_08    H18  CAA  OAS  CAU    60.65  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
 W87  plan-1  CAT  0.020
 W87  plan-1  CAX  0.020
 W87  plan-1  NAQ  0.020
 W87  plan-1  CAZ  0.020
 W87  plan-1  OAD  0.020
 W87  plan-1  NAR  0.020
 W87  plan-1  CBA  0.020
 W87  plan-1  OAE  0.020
 W87  plan-1  CAY  0.020
 W87  plan-1  CAP  0.020
 W87  plan-1  H2   0.020
 W87  plan-1  H21  0.020
 W87  plan-2  CAW  0.020
 W87  plan-2  CAU  0.020
 W87  plan-2  OAC  0.020
 W87  plan-2  OAS  0.020
 W87  plan-3  CAO  0.020
 W87  plan-3  CAV  0.020
 W87  plan-3  CAL  0.020
 W87  plan-3  CAI  0.020
 W87  plan-3  CAK  0.020
 W87  plan-3  CBC  0.020
 W87  plan-3  CBB  0.020
 W87  plan-3  CAJ  0.020
 W87  plan-3  CAG  0.020
 W87  plan-3  CAH  0.020
 W87  plan-3  CAW  0.020
 W87  plan-3  CAU  0.020
 W87  plan-3  H12  0.020
 W87  plan-3  H13  0.020
 W87  plan-3  H14  0.020
 W87  plan-3  H15  0.020
 W87  plan-3  H16  0.020
 W87  plan-3  H17  0.020
 W87  plan-4  OAB  0.020
 W87  plan-4  CAT  0.020
 W87  plan-4  OAF  0.020
 W87  plan-4  CAX  0.020
 W87  plan-4  H1   0.020

