# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 01:43:00 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(6-methoxynaphthalen-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: COc1ccc2cc(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
 ROE  ROE  '5-[2-(6-methoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  41  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ROE
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
 ROE  OAB  O  OH1   0  -0.589  -3.9153  -3.1559   0.5853
 ROE  CAQ  C  C     0   0.517  -3.0285  -2.2614   0.1891
 ROE  OAE  O  O     0  -0.396  -1.8918  -2.5079  -0.1089
 ROE  CAT  C  CR6   0   0.283  -3.6295  -0.8890   0.1417
 ROE  NAN  N  NR16  0  -0.731  -4.9875  -0.8588  -0.0533
 ROE  CAV  C  CR6   0   0.670  -5.7218   0.2864  -0.1543
 ROE  OAC  O  O     0  -0.472  -6.9196   0.2951  -0.3436
 ROE  NAO  N  NR16  0  -0.717  -4.9752   1.4279  -0.0230
 ROE  CAW  C  CR6   0   0.588  -3.6152   1.5169   0.1843
 ROE  OAD  O  O     0  -0.439  -3.0768   2.6026   0.2754
 ROE  CAU  C  CR6   0  -0.121  -2.9008   0.2400   0.2786
 ROE  CAM  C  CH2   0  -0.497  -1.4232   0.3247   0.5065
 ROE  CAL  C  CH2   0  -0.504  -0.6482   0.5228  -0.8049
 ROE  CAR  C  CR6   0   0.119   0.8249   0.6692  -0.5570
 ROE  CAJ  C  CR16  0  -0.381   1.6740  -0.4026  -0.6409
 ROE  CAX  C  CR66  0   0.119   3.0579  -0.2722  -0.3761
 ROE  CAI  C  CR16  0  -0.301   3.9475  -1.3640  -0.4594
 ROE  CAG  C  CR16  0  -0.378   5.2855  -1.2188  -0.2055
 ROE  CAS  C  CR6   0   0.391   5.8061   0.0487   0.1471
 ROE  OAP  O  O2    0  -0.474   7.1105   0.2681   0.4047
 ROE  CAA  C  CH3   0  -0.438   8.0191  -0.8117   0.3190
 ROE  CAK  C  CR16  0  -0.428   4.9617   1.1317   0.2392
 ROE  CAY  C  CR66  0   0.123   3.5836   0.9955  -0.0161
 ROE  CAH  C  CR16  0  -0.307   2.6899   2.0925   0.0705
 ROE  CAF  C  CR16  0  -0.299   1.3590   1.9299  -0.1893
 ROE  H1   H  HOH1  0   0.503  -3.5332  -4.0476   0.5735
 ROE  H2   H  HNR6  0   0.438  -5.4968  -1.7245  -0.1635
 ROE  H3   H  HNR6  0   0.431  -5.4829   2.3011  -0.0985
 ROE  H4   H  HCH2  0   0.262  -1.2291   1.1696   1.1698
 ROE  H5   H  HCH2  0   0.264  -1.0497  -0.5610   1.0147
 ROE  H6   H  HCH2  0   0.255  -0.8310  -0.3295  -1.4601
 ROE  H7   H  HCH2  0   0.251  -1.0268   1.4087  -1.3198
 ROE  H8   H  HCR6  0   0.244   1.2886  -1.3775  -0.9213
 ROE  H9   H  HCR6  0   0.259   3.5620  -2.3391  -0.7315
 ROE  H10  H  HCR6  0   0.282   5.9305  -2.0838  -0.2790
 ROE  H11  H  HCH3  0   0.260   9.0010  -0.4051   0.5478
 ROE  H12  H  HCH3  0   0.229   7.7902  -1.6000   1.0408
 ROE  H13  H  HCH3  0   0.229   8.0469  -1.2480  -0.6828
 ROE  H14  H  HCR6  0   0.257   5.3600   2.1019   0.5130
 ROE  H15  H  HCR6  0   0.250   3.0765   3.0668   0.3442
 ROE  H16  H  HCR6  0   0.247   0.6917   2.7816  -0.1214

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
 ROE  CAH  CAF  aromatic  1.366  0.020  1.366
 ROE  CAH  CAY  aromatic  1.418  0.020  1.418
 ROE  CAF  CAR  aromatic  1.418  0.020  1.418
 ROE  CAK  CAY  aromatic  1.408  0.020  1.408
 ROE  CAK  CAS  aromatic  1.376  0.020  1.376
 ROE  CAY  CAX  aromatic  1.419  0.020  1.419
 ROE  OAP  CAS  single    1.348  0.020  1.348
 ROE  OAP  CAA  single    1.414  0.020  1.414
 ROE  CAS  CAG  aromatic  1.415  0.020  1.415
 ROE  CAR  CAL  single    1.501  0.020  1.501
 ROE  CAR  CAJ  aromatic  1.370  0.020  1.370
 ROE  CAL  CAM  single    1.536  0.020  1.536
 ROE  CAX  CAJ  aromatic  1.415  0.020  1.415
 ROE  CAX  CAI  aromatic  1.411  0.020  1.411
 ROE  CAG  CAI  aromatic  1.370  0.020  1.370
 ROE  CAM  CAU  single    1.498  0.020  1.498
 ROE  OAD  CAW  double    1.215  0.020  1.215
 ROE  CAU  CAW  single    1.466  0.020  1.466
 ROE  CAU  CAT  double    1.351  0.020  1.351
 ROE  CAW  NAO  single    1.379  0.020  1.379
 ROE  OAE  CAQ  double    1.201  0.020  1.201
 ROE  CAT  CAQ  single    1.499  0.020  1.499
 ROE  CAT  NAN  single    1.372  0.020  1.372
 ROE  CAQ  OAB  single    1.320  0.020  1.320
 ROE  NAO  CAV  single    1.370  0.020  1.370
 ROE  NAN  CAV  single    1.364  0.020  1.364
 ROE  CAV  OAC  double    1.213  0.020  1.213
 ROE  OAB  H1   single    0.850  0.020  0.980
 ROE  NAN  H2   single    0.860  0.020  1.020
 ROE  NAO  H3   single    0.860  0.020  1.020
 ROE  CAM  H4   single    0.970  0.020  1.090
 ROE  CAM  H5   single    0.970  0.020  1.090
 ROE  CAL  H6   single    0.970  0.020  1.090
 ROE  CAL  H7   single    0.970  0.020  1.090
 ROE  CAJ  H8   single    0.930  0.020  1.080
 ROE  CAI  H9   single    0.930  0.020  1.080
 ROE  CAG  H10  single    0.930  0.020  1.080
 ROE  CAA  H11  single    0.970  0.020  1.090
 ROE  CAA  H12  single    0.970  0.020  1.090
 ROE  CAA  H13  single    0.970  0.020  1.090
 ROE  CAK  H14  single    0.930  0.020  1.080
 ROE  CAH  H15  single    0.930  0.020  1.080
 ROE  CAF  H16  single    0.930  0.020  1.080

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
 ROE  H1   OAB  CAQ  110.76  3.000
 ROE  CAT  CAQ  OAE  124.04  3.000
 ROE  CAT  CAQ  OAB  111.12  3.000
 ROE  OAE  CAQ  OAB  124.83  3.000
 ROE  CAU  CAT  NAN  121.99  3.000
 ROE  NAN  CAT  CAQ  114.93  3.000
 ROE  CAU  CAT  CAQ  123.08  3.000
 ROE  H2   NAN  CAV  116.10  3.000
 ROE  H2   NAN  CAT  119.69  3.000
 ROE  CAV  NAN  CAT  124.18  3.000
 ROE  NAO  CAV  OAC  123.17  3.000
 ROE  OAC  CAV  NAN  123.32  3.000
 ROE  NAO  CAV  NAN  113.51  3.000
 ROE  H3   NAO  CAW  116.75  3.000
 ROE  H3   NAO  CAV  115.97  3.000
 ROE  CAW  NAO  CAV  127.28  3.000
 ROE  CAU  CAW  OAD  123.88  3.000
 ROE  CAU  CAW  NAO  115.73  3.000
 ROE  OAD  CAW  NAO  120.40  3.000
 ROE  CAM  CAU  CAW  116.19  3.000
 ROE  CAW  CAU  CAT  117.30  3.000
 ROE  CAM  CAU  CAT  126.51  3.000
 ROE  H5   CAM  H4   106.59  3.000
 ROE  H5   CAM  CAL  109.32  3.000
 ROE  H4   CAM  CAL  109.22  3.000
 ROE  H5   CAM  CAU  111.35  3.000
 ROE  H4   CAM  CAU  108.17  3.000
 ROE  CAL  CAM  CAU  112.03  3.000
 ROE  H7   CAL  H6   107.01  3.000
 ROE  H7   CAL  CAR  109.81  3.000
 ROE  H6   CAL  CAR  109.88  3.000
 ROE  H7   CAL  CAM  109.40  3.000
 ROE  H6   CAL  CAM  109.12  3.000
 ROE  CAR  CAL  CAM  111.51  3.000
 ROE  CAF  CAR  CAJ  118.56  3.000
 ROE  CAJ  CAR  CAL  121.46  3.000
 ROE  CAF  CAR  CAL  119.95  3.000
 ROE  H8   CAJ  CAX  118.58  3.000
 ROE  H8   CAJ  CAR  119.91  3.000
 ROE  CAX  CAJ  CAR  121.51  3.000
 ROE  CAY  CAX  CAI  118.22  3.000
 ROE  CAI  CAX  CAJ  122.30  3.000
 ROE  CAY  CAX  CAJ  119.48  3.000
 ROE  H9   CAI  CAG  119.32  3.000
 ROE  H9   CAI  CAX  119.14  3.000
 ROE  CAG  CAI  CAX  121.54  3.000
 ROE  H10  CAG  CAS  120.93  3.000
 ROE  H10  CAG  CAI  119.03  3.000
 ROE  CAS  CAG  CAI  120.04  3.000
 ROE  CAK  CAS  OAP  116.94  3.000
 ROE  OAP  CAS  CAG  123.34  3.000
 ROE  CAK  CAS  CAG  119.72  3.000
 ROE  CAA  OAP  CAS  119.09  3.000
 ROE  H13  CAA  H12  108.83  3.000
 ROE  H13  CAA  H11  108.61  3.000
 ROE  H12  CAA  H11  108.66  3.000
 ROE  H13  CAA  OAP  112.13  3.000
 ROE  H12  CAA  OAP  112.10  3.000
 ROE  H11  CAA  OAP  106.38  3.000
 ROE  H14  CAK  CAY  119.48  3.000
 ROE  H14  CAK  CAS  119.71  3.000
 ROE  CAY  CAK  CAS  120.81  3.000
 ROE  CAH  CAY  CAK  122.07  3.000
 ROE  CAK  CAY  CAX  119.67  3.000
 ROE  CAH  CAY  CAX  118.25  3.000
 ROE  H15  CAH  CAF  120.19  3.000
 ROE  H15  CAH  CAY  119.11  3.000
 ROE  CAF  CAH  CAY  120.70  3.000
 ROE  H16  CAF  CAH  119.63  3.000
 ROE  H16  CAF  CAR  118.88  3.000
 ROE  CAH  CAF  CAR  121.49  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
 ROE  CONST_01  CAY  CAH  CAF  CAR     0.00   0.0  0
 ROE  CONST_02  CAY  CAX  CAJ  CAR     0.00   0.0  0
 ROE  CONST_03  CAI  CAX  CAJ  CAR   180.00   0.0  0
 ROE  CONST_04  CAH  CAF  CAR  CAJ     0.00   0.0  0
 ROE  CONST_05  CAH  CAY  CAX  CAJ     0.00   0.0  0
 ROE  CONST_06  CAK  CAY  CAX  CAJ   180.00   0.0  0
 ROE  CONST_07  CAG  CAI  CAX  CAJ   180.00   0.0  0
 ROE  CONST_08  CAF  CAH  CAY  CAX     0.00   0.0  0
 ROE  CONST_09  CAS  CAK  CAY  CAX     0.00   0.0  0
 ROE  CONST_10  CAF  CAR  CAJ  CAX     0.00   0.0  0
 ROE  CONST_11  CAS  CAG  CAI  CAX     0.00   0.0  0
 ROE  CONST_12  CAH  CAY  CAX  CAI   180.00   0.0  0
 ROE  CONST_13  CAK  CAY  CAX  CAI     0.00   0.0  0
 ROE  CONST_14  CAK  CAS  CAG  CAI     0.00   0.0  0
 ROE  CONST_15  CAY  CAK  CAS  CAG     0.00   0.0  0
 ROE  CONST_16  CAY  CAX  CAI  CAG     0.00   0.0  0
 ROE  CONST_17  CAH  CAY  CAK  CAS   180.00   0.0  0
 ROE  CONST_18  CAF  CAH  CAY  CAK   180.00   0.0  0
 ROE  CONST_19  NAO  CAV  NAN  CAT     0.00   0.0  0
 ROE  CONST_20  CAW  NAO  CAV  NAN     0.00   0.0  0
 ROE  CONST_21  CAU  CAW  NAO  CAV     0.00   0.0  0
 ROE  CONST_22  CAH  CAF  CAR  CAL   180.00   0.0  0
 ROE  CONST_23  CAX  CAJ  CAR  CAL   180.00   0.0  0
 ROE  CONST_24  OAP  CAS  CAG  CAI   180.00   0.0  0
 ROE  CONST_25  CAY  CAK  CAS  OAP   180.00   0.0  0
 ROE  CONST_26  OAC  CAV  NAN  CAT   180.00   0.0  0
 ROE  CONST_27  OAD  CAW  NAO  CAV   180.00   0.0  0
 ROE  CONST_28  CAW  NAO  CAV  OAC   180.00   0.0  0
 ROE  CONST_29  H15  CAH  CAF  CAR   180.00   0.0  0
 ROE  CONST_30  H16  CAF  CAR  CAJ   180.00   0.0  0
 ROE  CONST_31  H9   CAI  CAX  CAJ     0.00   0.0  0
 ROE  CONST_32  H14  CAK  CAY  CAX   180.00   0.0  0
 ROE  CONST_33  H10  CAG  CAI  CAX   180.00   0.0  0
 ROE  CONST_34  H8   CAJ  CAX  CAI     0.00   0.0  0
 ROE  CONST_35  H3   NAO  CAV  NAN   180.00   0.0  0
 ROE  CONST_36  H2   NAN  CAV  NAO   180.00   0.0  0
 ROE  CONST_37  H1   OAB  CAQ  CAT   180.00   0.0  0
 ROE  Var_01    CAU  CAT  CAQ  OAB   153.82  30.0  2
 ROE  Var_02    CAL  CAM  CAU  CAT    95.41  30.0  2
 ROE  Var_03    CAR  CAL  CAM  CAU   177.39  30.0  1
 ROE  Var_04    CAF  CAR  CAL  CAM   -82.89  30.0  2
 ROE  Var_05    CAK  CAS  OAP  CAA  -179.79  30.0  2
 ROE  Var_06    H11  CAA  OAP  CAS   179.09  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
 ROE  plan-1  CAQ  0.020
 ROE  plan-1  CAT  0.020
 ROE  plan-1  NAN  0.020
 ROE  plan-1  CAV  0.020
 ROE  plan-1  OAC  0.020
 ROE  plan-1  NAO  0.020
 ROE  plan-1  CAW  0.020
 ROE  plan-1  OAD  0.020
 ROE  plan-1  CAU  0.020
 ROE  plan-1  CAM  0.020
 ROE  plan-1  H2   0.020
 ROE  plan-1  H3   0.020
 ROE  plan-2  CAL  0.020
 ROE  plan-2  CAR  0.020
 ROE  plan-2  CAJ  0.020
 ROE  plan-2  CAX  0.020
 ROE  plan-2  CAI  0.020
 ROE  plan-2  CAG  0.020
 ROE  plan-2  CAS  0.020
 ROE  plan-2  OAP  0.020
 ROE  plan-2  CAK  0.020
 ROE  plan-2  CAY  0.020
 ROE  plan-2  CAH  0.020
 ROE  plan-2  CAF  0.020
 ROE  plan-2  H8   0.020
 ROE  plan-2  H9   0.020
 ROE  plan-2  H10  0.020
 ROE  plan-2  H14  0.020
 ROE  plan-2  H15  0.020
 ROE  plan-2  H16  0.020
 ROE  plan-3  OAB  0.020
 ROE  plan-3  CAQ  0.020
 ROE  plan-3  OAE  0.020
 ROE  plan-3  CAT  0.020
 ROE  plan-3  H1   0.020

