# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 08:38:09 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-[2-(6-carboxynaphthalen-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: OC(=O)C1=C(CCc2ccc3cc(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
 W7J  W7J  '5-[2-(6-carboxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  40  26  .  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_W7J
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
 W7J  OAJ  O  O     0  -0.396   2.1874  -2.5121   0.0377
 W7J  CAI  C  C     0   0.517   3.3212  -2.2575  -0.2643
 W7J  OAK  O  OH1   0  -0.589   4.2022  -3.1392  -0.6999
 W7J  C4   C  CR6   0   0.284   3.9252  -0.8884  -0.1762
 W7J  N3   N  NR16  0  -0.732   5.2849  -0.8662   0.0055
 W7J  C2   C  CR6   0   0.671   6.0223   0.2742   0.1381
 W7J  O2   O  O     0  -0.472   7.2223   0.2746   0.3122
 W7J  N1   N  NR16  0  -0.717   5.2755   1.4203   0.0587
 W7J  C6   C  CR6   0   0.588   3.9140   1.5178  -0.1332
 W7J  O6   O  O     0  -0.439   3.3758   2.6064  -0.1809
 W7J  C5   C  CR6   0  -0.121   3.1971   0.2459  -0.2655
 W7J  CAL  C  CH2   0  -0.500   1.7180   0.3399  -0.4782
 W7J  CAM  C  CH2   0  -0.506   0.9563   0.5055   0.8459
 W7J  CAN  C  CR6   0   0.133  -0.5199   0.6309   0.6099
 W7J  CAO  C  CR16  0  -0.383  -1.3463  -0.4612   0.6880
 W7J  CAP  C  CR66  0   0.146  -2.7309  -0.3546   0.4308
 W7J  CAT  C  CR16  0  -0.304  -3.5990  -1.4690   0.5113
 W7J  CAU  C  CR16  0  -0.267  -4.9355  -1.3396   0.2627
 W7J  CAV  C  CR6   0  -0.090  -5.4787  -0.0780  -0.0845
 W7J  CAX  C  C     0   0.536  -6.9234   0.1074  -0.3621
 W7J  OAZ  O  OH1   0  -0.595  -7.6233  -1.0090  -0.2154
 W7J  OAY  O  O     0  -0.440  -7.4204   1.1602  -0.6862
 W7J  CAW  C  CR16  0  -0.324  -4.6549   1.0180  -0.1704
 W7J  CAQ  C  CR66  0   0.122  -3.2734   0.9087   0.0836
 W7J  CAR  C  CR16  0  -0.292  -2.4076   2.0255   0.0049
 W7J  CAS  C  CR16  0  -0.297  -1.0729   1.8871   0.2594
 W7J  H1   H  HOH1  0   0.504   3.8187  -4.0303  -0.7147
 W7J  H2   H  HNR6  0   0.431   5.7846   2.2897   0.1629
 W7J  H4   H  HCH2  0   0.265   1.5200   1.2023  -1.1172
 W7J  H5   H  HCH2  0   0.267   1.3380  -0.5309  -1.0061
 W7J  H6   H  HCH2  0   0.259   1.1572  -0.3540   1.4859
 W7J  H7   H  HCH2  0   0.257   1.3245   1.3903   1.3692
 W7J  H8   H  HCR6  0   0.250  -0.9391  -1.4297   0.9578
 W7J  H9   H  HCR6  0   0.261  -3.1902  -2.4361   0.7765
 W7J  H10  H  HCR6  0   0.266  -5.5737  -2.2090   0.3327
 W7J  H11  H  HOH1  0   0.488  -8.5584  -0.8405  -0.4038
 W7J  H12  H  HCR6  0   0.265  -5.0614   1.9858  -0.4369
 W7J  H13  H  HCR6  0   0.259  -2.8173   2.9932  -0.2574
 W7J  H14  H  HCR6  0   0.254  -0.4203   2.7502   0.2005
 W7J  H15  H  HNR6  0   0.439   5.7949  -1.7358   0.0745

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
 W7J  O2   C2   double    1.213  0.020  1.213
 W7J  C2   N3   single    1.364  0.020  1.364
 W7J  C2   N1   single    1.370  0.020  1.370
 W7J  N3   C4   single    1.372  0.020  1.372
 W7J  N1   C6   single    1.378  0.020  1.378
 W7J  OAJ  CAI  double    1.201  0.020  1.201
 W7J  CAI  C4   single    1.499  0.020  1.499
 W7J  CAI  OAK  single    1.320  0.020  1.320
 W7J  C4   C5   double    1.351  0.020  1.351
 W7J  C6   C5   single    1.466  0.020  1.466
 W7J  C6   O6   double    1.215  0.020  1.215
 W7J  C5   CAL  single    1.497  0.020  1.497
 W7J  CAL  CAM  single    1.537  0.020  1.537
 W7J  CAS  CAR  aromatic  1.366  0.020  1.366
 W7J  CAS  CAN  aromatic  1.417  0.020  1.417
 W7J  CAR  CAQ  aromatic  1.415  0.020  1.415
 W7J  CAM  CAN  single    1.500  0.020  1.500
 W7J  CAN  CAO  aromatic  1.372  0.020  1.372
 W7J  OAY  CAX  double    1.208  0.020  1.208
 W7J  CAQ  CAW  aromatic  1.409  0.020  1.409
 W7J  CAQ  CAP  aromatic  1.418  0.020  1.418
 W7J  CAW  CAV  aromatic  1.374  0.020  1.374
 W7J  CAO  CAP  aromatic  1.412  0.020  1.412
 W7J  CAV  CAX  single    1.483  0.020  1.483
 W7J  CAV  CAU  aromatic  1.417  0.020  1.417
 W7J  CAP  CAT  aromatic  1.415  0.020  1.415
 W7J  CAX  OAZ  single    1.326  0.020  1.326
 W7J  CAT  CAU  aromatic  1.366  0.020  1.366
 W7J  OAK  H1   single    0.850  0.020  0.980
 W7J  N1   H2   single    0.860  0.020  1.020
 W7J  CAL  H4   single    0.970  0.020  1.090
 W7J  CAL  H5   single    0.970  0.020  1.090
 W7J  CAM  H6   single    0.970  0.020  1.090
 W7J  CAM  H7   single    0.970  0.020  1.090
 W7J  CAO  H8   single    0.930  0.020  1.080
 W7J  CAT  H9   single    0.930  0.020  1.080
 W7J  CAU  H10  single    0.930  0.020  1.080
 W7J  OAZ  H11  single    0.850  0.020  0.980
 W7J  CAW  H12  single    0.930  0.020  1.080
 W7J  CAR  H13  single    0.930  0.020  1.080
 W7J  CAS  H14  single    0.930  0.020  1.080
 W7J  N3   H15  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
 W7J  C4   CAI  OAK  111.13  3.000
 W7J  OAK  CAI  OAJ  124.86  3.000
 W7J  C4   CAI  OAJ  124.01  3.000
 W7J  H1   OAK  CAI  110.77  3.000
 W7J  C5   C4   N3   121.96  3.000
 W7J  C5   C4   CAI  123.08  3.000
 W7J  N3   C4   CAI  114.95  3.000
 W7J  H15  N3   C2   116.09  3.000
 W7J  H15  N3   C4   119.70  3.000
 W7J  C2   N3   C4   124.20  3.000
 W7J  N1   C2   O2   123.18  3.000
 W7J  N1   C2   N3   113.51  3.000
 W7J  O2   C2   N3   123.31  3.000
 W7J  H2   N1   C6   116.75  3.000
 W7J  H2   N1   C2   115.98  3.000
 W7J  C6   N1   C2   127.27  3.000
 W7J  C5   C6   O6   123.85  3.000
 W7J  O6   C6   N1   120.41  3.000
 W7J  C5   C6   N1   115.74  3.000
 W7J  CAL  C5   C6   116.19  3.000
 W7J  CAL  C5   C4   126.49  3.000
 W7J  C6   C5   C4   117.32  3.000
 W7J  H5   CAL  H4   106.57  3.000
 W7J  H5   CAL  CAM  109.36  3.000
 W7J  H4   CAL  CAM  109.24  3.000
 W7J  H5   CAL  C5   111.35  3.000
 W7J  H4   CAL  C5   108.19  3.000
 W7J  CAM  CAL  C5   111.97  3.000
 W7J  H7   CAM  H6   107.17  3.000
 W7J  H7   CAM  CAN  109.85  3.000
 W7J  H6   CAM  CAN  109.85  3.000
 W7J  H7   CAM  CAL  109.46  3.000
 W7J  H6   CAM  CAL  109.24  3.000
 W7J  CAN  CAM  CAL  111.18  3.000
 W7J  CAS  CAN  CAO  119.01  3.000
 W7J  CAO  CAN  CAM  121.15  3.000
 W7J  CAS  CAN  CAM  119.82  3.000
 W7J  H8   CAO  CAP  118.73  3.000
 W7J  H8   CAO  CAN  119.93  3.000
 W7J  CAP  CAO  CAN  121.34  3.000
 W7J  CAQ  CAP  CAT  118.74  3.000
 W7J  CAT  CAP  CAO  122.12  3.000
 W7J  CAQ  CAP  CAO  119.14  3.000
 W7J  H9   CAT  CAU  119.92  3.000
 W7J  H9   CAT  CAP  119.05  3.000
 W7J  CAU  CAT  CAP  121.03  3.000
 W7J  H10  CAU  CAV  120.38  3.000
 W7J  H10  CAU  CAT  119.33  3.000
 W7J  CAV  CAU  CAT  120.28  3.000
 W7J  CAW  CAV  CAX  118.21  3.000
 W7J  CAX  CAV  CAU  122.06  3.000
 W7J  CAW  CAV  CAU  119.72  3.000
 W7J  OAY  CAX  OAZ  123.10  3.000
 W7J  OAZ  CAX  CAV  112.85  3.000
 W7J  OAY  CAX  CAV  124.05  3.000
 W7J  H11  OAZ  CAX  109.98  3.000
 W7J  H12  CAW  CAQ  118.80  3.000
 W7J  H12  CAW  CAV  120.21  3.000
 W7J  CAQ  CAW  CAV  120.99  3.000
 W7J  CAR  CAQ  CAW  121.91  3.000
 W7J  CAW  CAQ  CAP  119.24  3.000
 W7J  CAR  CAQ  CAP  118.85  3.000
 W7J  H13  CAR  CAS  120.35  3.000
 W7J  H13  CAR  CAQ  119.15  3.000
 W7J  CAS  CAR  CAQ  120.50  3.000
 W7J  H14  CAS  CAR  119.85  3.000
 W7J  H14  CAS  CAN  118.99  3.000
 W7J  CAR  CAS  CAN  121.16  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
 W7J  CONST_01  CAQ  CAR  CAS  CAN     0.00   0.0  0
 W7J  CONST_02  CAQ  CAP  CAO  CAN     0.00   0.0  0
 W7J  CONST_03  CAT  CAP  CAO  CAN   180.00   0.0  0
 W7J  CONST_04  CAR  CAS  CAN  CAO     0.00   0.0  0
 W7J  CONST_05  CAR  CAQ  CAP  CAO     0.00   0.0  0
 W7J  CONST_06  CAW  CAQ  CAP  CAO   180.00   0.0  0
 W7J  CONST_07  CAU  CAT  CAP  CAO   180.00   0.0  0
 W7J  CONST_08  CAS  CAR  CAQ  CAP     0.00   0.0  0
 W7J  CONST_09  CAV  CAW  CAQ  CAP     0.00   0.0  0
 W7J  CONST_10  CAS  CAN  CAO  CAP     0.00   0.0  0
 W7J  CONST_11  CAV  CAU  CAT  CAP     0.00   0.0  0
 W7J  CONST_12  CAR  CAQ  CAP  CAT   180.00   0.0  0
 W7J  CONST_13  CAW  CAQ  CAP  CAT     0.00   0.0  0
 W7J  CONST_14  CAW  CAV  CAU  CAT     0.00   0.0  0
 W7J  CONST_15  CAQ  CAW  CAV  CAU     0.00   0.0  0
 W7J  CONST_16  CAQ  CAP  CAT  CAU     0.00   0.0  0
 W7J  CONST_17  CAR  CAQ  CAW  CAV   180.00   0.0  0
 W7J  CONST_18  CAS  CAR  CAQ  CAW   180.00   0.0  0
 W7J  CONST_19  N1   C2   N3   C4      0.00   0.0  0
 W7J  CONST_20  C6   N1   C2   N3      0.00   0.0  0
 W7J  CONST_21  C5   C6   N1   C2      0.00   0.0  0
 W7J  CONST_22  CAR  CAS  CAN  CAM   180.00   0.0  0
 W7J  CONST_23  CAP  CAO  CAN  CAM   180.00   0.0  0
 W7J  CONST_24  CAX  CAV  CAU  CAT   180.00   0.0  0
 W7J  CONST_25  CAQ  CAW  CAV  CAX   180.00   0.0  0
 W7J  CONST_26  O2   C2   N3   C4    180.00   0.0  0
 W7J  CONST_27  O6   C6   N1   C2    180.00   0.0  0
 W7J  CONST_28  C6   N1   C2   O2    180.00   0.0  0
 W7J  CONST_29  H13  CAR  CAS  CAN   180.00   0.0  0
 W7J  CONST_30  H14  CAS  CAN  CAO   180.00   0.0  0
 W7J  CONST_31  H9   CAT  CAP  CAO     0.00   0.0  0
 W7J  CONST_32  H12  CAW  CAQ  CAP   180.00   0.0  0
 W7J  CONST_33  H10  CAU  CAT  CAP   180.00   0.0  0
 W7J  CONST_34  H8   CAO  CAP  CAT     0.00   0.0  0
 W7J  CONST_35  H2   N1   C2   N3    180.00   0.0  0
 W7J  CONST_36  H15  N3   C2   N1    180.00   0.0  0
 W7J  CONST_37  H1   OAK  CAI  C4    180.00   0.0  0
 W7J  CONST_38  H11  OAZ  CAX  CAV   180.00   0.0  0
 W7J  Var_01    N3   C4   CAI  OAJ   153.07  30.0  2
 W7J  Var_02    CAM  CAL  C5   C4     96.02  30.0  3
 W7J  Var_03    CAN  CAM  CAL  C5    178.64  30.0  3
 W7J  Var_04    CAS  CAN  CAM  CAL   -82.63  30.0  2
 W7J  Var_05    OAY  CAX  CAV  CAU  -178.50  30.0  2

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
 W7J  plan-1  CAI  0.020
 W7J  plan-1  C4   0.020
 W7J  plan-1  N3   0.020
 W7J  plan-1  C2   0.020
 W7J  plan-1  O2   0.020
 W7J  plan-1  N1   0.020
 W7J  plan-1  C6   0.020
 W7J  plan-1  O6   0.020
 W7J  plan-1  C5   0.020
 W7J  plan-1  CAL  0.020
 W7J  plan-1  H2   0.020
 W7J  plan-1  H15  0.020
 W7J  plan-2  CAM  0.020
 W7J  plan-2  CAN  0.020
 W7J  plan-2  CAO  0.020
 W7J  plan-2  CAP  0.020
 W7J  plan-2  CAT  0.020
 W7J  plan-2  CAU  0.020
 W7J  plan-2  CAV  0.020
 W7J  plan-2  CAX  0.020
 W7J  plan-2  CAW  0.020
 W7J  plan-2  CAQ  0.020
 W7J  plan-2  CAR  0.020
 W7J  plan-2  CAS  0.020
 W7J  plan-2  H8   0.020
 W7J  plan-2  H9   0.020
 W7J  plan-2  H10  0.020
 W7J  plan-2  H12  0.020
 W7J  plan-2  H13  0.020
 W7J  plan-2  H14  0.020
 W7J  plan-3  OAJ  0.020
 W7J  plan-3  CAI  0.020
 W7J  plan-3  OAK  0.020
 W7J  plan-3  C4   0.020
 W7J  plan-3  H1   0.020
 W7J  plan-4  CAV  0.020
 W7J  plan-4  CAX  0.020
 W7J  plan-4  OAZ  0.020
 W7J  plan-4  OAY  0.020
 W7J  plan-4  H11  0.020

