# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:52:27 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  38  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 OK
;

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  -0.541   2.0922  -2.3984  -0.1908
 W7J  CAI  C  C      0   0.414   3.3194  -2.2609  -0.2382
 W7J  OAK  O  OC    -1  -0.586   4.1935  -3.1458  -0.2822
 W7J  C4   C  C      0   0.200   3.8823  -0.8246  -0.2202
 W7J  N3   N  NH1    0  -0.707   5.2418  -0.8162  -0.0662
 W7J  C2   C  C      0   0.656   6.0193   0.2929   0.0138
 W7J  O2   O  O      0  -0.493   7.2285   0.2668   0.1515
 W7J  N1   N  NH1    0  -0.715   5.3039   1.4583  -0.0720
 W7J  C6   C  C      0   0.565   3.9368   1.5842  -0.2357
 W7J  O6   O  O      0  -0.466   3.4375   2.6969  -0.2862
 W7J  C5   C  C      0  -0.158   3.1903   0.3359  -0.3323
 W7J  CAL  C  CH2    0  -0.473   1.7065   0.4616  -0.5061
 W7J  CAM  C  CH2    0  -0.497   0.9727   0.5776   0.8371
 W7J  CAN  C  CR6    0   0.123  -0.5109   0.6891   0.6412
 W7J  CAO  C  CR16   0  -0.385  -1.3143  -0.4231   0.6521
 W7J  CAP  C  CR66   0   0.130  -2.7048  -0.3333   0.4128
 W7J  CAT  C  CR16   0  -0.309  -3.5497  -1.4687   0.4202
 W7J  CAU  C  CR16   0  -0.293  -4.8895  -1.3459   0.1765
 W7J  CAV  C  CR6    0  -0.104  -5.4751  -0.0850  -0.0898
 W7J  CAX  C  C      0   0.399  -6.9686   0.0281  -0.3669
 W7J  OAZ  O  OC    -1  -0.593  -7.6197  -1.0342  -0.3380
 W7J  OAY  O  O      0  -0.593  -7.4125   1.1690  -0.5996
 W7J  CAW  C  CR16   0  -0.365  -4.6704   1.0261  -0.0954
 W7J  CAQ  C  CR66   0   0.123  -3.2820   0.9357   0.1518
 W7J  CAR  C  CR16   0  -0.302  -2.4397   2.0730   0.1461
 W7J  CAS  C  CR16   0  -0.305  -1.0988   1.9513   0.3824
 W7J  H2   H  HNH1   0   0.420   5.8361   2.3163   0.0003
 W7J  H4   H  HCH2   0   0.239   1.4969   1.3498  -1.1055
 W7J  H5   H  HCH2   0   0.254   1.3132  -0.3935  -1.0462
 W7J  H6   H  HCH2   0   0.246   1.2030  -0.3036   1.4367
 W7J  H7   H  HCH2   0   0.239   1.3456   1.4477   1.3826
 W7J  H8   H  HCR6   0   0.240  -0.8791  -1.3983   0.8461
 W7J  H9   H  HCR6   0   0.244  -3.1186  -2.4424   0.6227
 W7J  H10  H  HCR6   0   0.243  -5.5226  -2.2230   0.1838
 W7J  H12  H  HCR6   0   0.239  -5.1022   1.9989  -0.2975
 W7J  H13  H  HCR6   0   0.248  -2.8726   3.0470  -0.0496
 W7J  H14  H  HCR6   0   0.245  -0.4675   2.8326   0.3765
 W7J  H15  H  HNH1   0   0.416   5.6773  -1.7308  -0.0219

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    1.217  0.020  1.217
 W7J  C2   N3   single    1.357  0.020  1.357
 W7J  C2   N1   single    1.370  0.020  1.370
 W7J  N3   C4   single    1.368  0.020  1.368
 W7J  N1   C6   single    1.383  0.020  1.383
 W7J  OAJ  CAI  deloc     1.236  0.020  1.236
 W7J  CAI  C4   single    1.543  0.020  1.543
 W7J  CAI  OAK  deloc     1.245  0.020  1.245
 W7J  C4   C5   double    1.356  0.020  1.356
 W7J  C6   C5   single    1.458  0.020  1.458
 W7J  C6   O6   double    1.221  0.020  1.221
 W7J  C5   CAL  single    1.499  0.020  1.499
 W7J  CAL  CAM  single    1.535  0.020  1.535
 W7J  CAS  CAR  aromatic  1.367  0.020  1.367
 W7J  CAS  CAN  aromatic  1.416  0.020  1.416
 W7J  CAR  CAQ  aromatic  1.415  0.020  1.415
 W7J  CAM  CAN  single    1.501  0.020  1.501
 W7J  CAN  CAO  aromatic  1.372  0.020  1.372
 W7J  OAY  CAX  deloc     1.246  0.020  1.246
 W7J  CAQ  CAW  aromatic  1.413  0.020  1.413
 W7J  CAQ  CAP  aromatic  1.418  0.020  1.418
 W7J  CAW  CAV  aromatic  1.372  0.020  1.372
 W7J  CAO  CAP  aromatic  1.414  0.020  1.414
 W7J  CAV  CAX  single    1.523  0.020  1.523
 W7J  CAV  CAU  aromatic  1.415  0.020  1.415
 W7J  CAP  CAT  aromatic  1.415  0.020  1.415
 W7J  CAX  OAZ  deloc     1.246  0.020  1.246
 W7J  CAT  CAU  aromatic  1.367  0.020  1.367
 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  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  113.96  3.000
 W7J  OAK  CAI  OAJ  128.29  3.000
 W7J  C4   CAI  OAJ  117.74  3.000
 W7J  C5   C4   N3   120.75  3.000
 W7J  C5   C4   CAI  127.57  3.000
 W7J  N3   C4   CAI  111.69  3.000
 W7J  H15  N3   C2   119.25  3.000
 W7J  H15  N3   C4   115.22  3.000
 W7J  C2   N3   C4   125.52  3.000
 W7J  N1   C2   O2   122.95  3.000
 W7J  N1   C2   N3   113.10  3.000
 W7J  O2   C2   N3   123.95  3.000
 W7J  H2   N1   C6   116.81  3.000
 W7J  H2   N1   C2   116.23  3.000
 W7J  C6   N1   C2   126.96  3.000
 W7J  C5   C6   O6   124.64  3.000
 W7J  O6   C6   N1   119.50  3.000
 W7J  C5   C6   N1   115.86  3.000
 W7J  CAL  C5   C6   116.28  3.000
 W7J  CAL  C5   C4   125.91  3.000
 W7J  C6   C5   C4   117.78  3.000
 W7J  H5   CAL  H4   107.35  3.000
 W7J  H5   CAL  CAM  108.77  3.000
 W7J  H4   CAL  CAM  109.10  3.000
 W7J  H5   CAL  C5   110.51  3.000
 W7J  H4   CAL  C5   108.78  3.000
 W7J  CAM  CAL  C5   112.21  3.000
 W7J  H7   CAM  H6   107.28  3.000
 W7J  H7   CAM  CAN  110.08  3.000
 W7J  H6   CAM  CAN  109.92  3.000
 W7J  H7   CAM  CAL  109.50  3.000
 W7J  H6   CAM  CAL  108.61  3.000
 W7J  CAN  CAM  CAL  111.35  3.000
 W7J  CAS  CAN  CAO  118.74  3.000
 W7J  CAO  CAN  CAM  121.17  3.000
 W7J  CAS  CAN  CAM  120.03  3.000
 W7J  H8   CAO  CAP  118.80  3.000
 W7J  H8   CAO  CAN  119.67  3.000
 W7J  CAP  CAO  CAN  121.53  3.000
 W7J  CAQ  CAP  CAT  118.41  3.000
 W7J  CAT  CAP  CAO  122.36  3.000
 W7J  CAQ  CAP  CAO  119.23  3.000
 W7J  H9   CAT  CAU  120.25  3.000
 W7J  H9   CAT  CAP  118.96  3.000
 W7J  CAU  CAT  CAP  120.80  3.000
 W7J  H10  CAU  CAV  118.78  3.000
 W7J  H10  CAU  CAT  119.96  3.000
 W7J  CAV  CAU  CAT  121.26  3.000
 W7J  CAW  CAV  CAX  120.95  3.000
 W7J  CAX  CAV  CAU  120.40  3.000
 W7J  CAW  CAV  CAU  118.65  3.000
 W7J  OAY  CAX  OAZ  126.77  3.000
 W7J  OAZ  CAX  CAV  116.40  3.000
 W7J  OAY  CAX  CAV  116.82  3.000
 W7J  H12  CAW  CAQ  118.79  3.000
 W7J  H12  CAW  CAV  119.62  3.000
 W7J  CAQ  CAW  CAV  121.59  3.000
 W7J  CAR  CAQ  CAW  122.18  3.000
 W7J  CAW  CAQ  CAP  119.29  3.000
 W7J  CAR  CAQ  CAP  118.53  3.000
 W7J  H13  CAR  CAS  120.20  3.000
 W7J  H13  CAR  CAQ  119.04  3.000
 W7J  CAS  CAR  CAQ  120.76  3.000
 W7J  H14  CAS  CAR  119.86  3.000
 W7J  H14  CAS  CAN  118.94  3.000
 W7J  CAR  CAS  CAN  121.21  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  Var_01    N3   C4   CAI  OAJ   170.47  30.0  2
 W7J  Var_02    CAM  CAL  C5   C4     91.12  30.0  3
 W7J  Var_03    CAN  CAM  CAL  C5   -179.45  30.0  3
 W7J  Var_04    CAS  CAN  CAM  CAL   -84.57  30.0  2
 W7J  Var_05    OAY  CAX  CAV  CAU  -179.66  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-4  CAV  0.020
 W7J  plan-4  CAX  0.020
 W7J  plan-4  OAZ  0.020
 W7J  plan-4  OAY  0.020

