# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 09:47:18 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-{2-[6-(methoxycarbonyl)naphthalen-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: COC(=O)c1ccc2cc(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
 W7M  W7M  '5-{2-[6-(methoxycarbonyl)naphthalen-2-yl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  43  27  .  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_W7M
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
 W7M  OAB  O  OH1   0  -0.589  -4.5581   3.1380  -0.6735
 W7M  CAR  C  C     0   0.518  -3.6786   2.2471  -0.2542
 W7M  OAF  O  O     0  -0.396  -2.5464   2.4955   0.0591
 W7M  CAV  C  CR6   0   0.284  -4.2812   0.8756  -0.2021
 W7M  NAO  N  NR16  0  -0.731  -5.6426   0.8476  -0.0342
 W7M  CAX  C  CR6   0   0.671  -6.3791  -0.2962   0.0669
 W7M  OAD  O  O     0  -0.472  -7.5806  -0.3024   0.2309
 W7M  NAP  N  NR16  0  -0.716  -5.6300  -1.4394  -0.0321
 W7M  CAY  C  CR6   0   0.588  -4.2665  -1.5310  -0.2121
 W7M  OAE  O  O     0  -0.439  -3.7262  -2.6175  -0.2782
 W7M  CAW  C  CR6   0  -0.121  -3.5503  -0.2554  -0.3089
 W7M  CAN  C  CH2   0  -0.499  -2.0687  -0.3437  -0.5065
 W7M  CAM  C  CH2   0  -0.506  -1.3233  -0.5311   0.8238
 W7M  CAT  C  CR6   0   0.133   0.1533  -0.6788   0.6036
 W7M  CAK  C  CR16  0  -0.385   1.0003   0.3941   0.7179
 W7M  CAG  C  CR16  0  -0.297   0.6863  -1.9382   0.2335
 W7M  CAI  C  CR16  0  -0.293   2.0216  -2.0982  -0.0040
 W7M  CBA  C  CR66  0   0.124   2.9085  -1.0016   0.1127
 W7M  CAL  C  CR16  0  -0.325   4.2914  -1.1340  -0.1223
 W7M  CAZ  C  CR66  0   0.146   2.3865   0.2647   0.4793
 W7M  CAJ  C  CR16  0  -0.304   3.2763   1.3587   0.5967
 W7M  CAH  C  CR16  0  -0.273   4.6136   1.2072   0.3645
 W7M  CAU  C  CR6   0  -0.092   5.1364  -0.0577  -0.0014
 W7M  CAS  C  C     0   0.600   6.5813  -0.2714  -0.2637
 W7M  OAC  O  O     0  -0.449   7.0577  -1.3317  -0.5938
 W7M  OAQ  O  O2    0  -0.458   7.2966   0.8288  -0.0958
 W7M  CAA  C  CH3   0  -0.423   8.7042   0.7425  -0.3177
 W7M  H1   H  HOH1  0   0.504  -4.1766   4.0300  -0.6629
 W7M  H2   H  HNR6  0   0.431  -6.1387  -2.3115   0.0493
 W7M  H4   H  HCH2  0   0.265  -1.8625  -1.1950  -1.1575
 W7M  H5   H  HCH2  0   0.267  -1.6837   0.5366  -1.0151
 W7M  H6   H  HCH2  0   0.259  -1.5177   0.3261   1.4688
 W7M  H7   H  HCH2  0   0.257  -1.7095  -1.4145   1.3365
 W7M  H8   H  HCR6  0   0.250   0.6083   1.3646   1.0027
 W7M  H9   H  HCR6  0   0.254   0.0175  -2.7863   0.1458
 W7M  H10  H  HCR6  0   0.259   2.4157  -3.0682  -0.2812
 W7M  H11  H  HCR6  0   0.262   4.6817  -2.1042  -0.4037
 W7M  H12  H  HCR6  0   0.260   2.8836   2.3283   0.8764
 W7M  H13  H  HCR6  0   0.263   5.2685   2.0611   0.4625
 W7M  H14  H  HCH3  0   0.241   8.9271   0.4535  -1.3442
 W7M  H15  H  HCH3  0   0.254   9.0962   1.7371  -0.1290
 W7M  H16  H  HCH3  0   0.241   9.1707   0.0339   0.3659
 W7M  H17  H  HNR6  0   0.439  -6.1544   1.7147   0.0501

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
 W7M  OAD  CAX  double    1.213  0.020  1.213
 W7M  CAX  NAO  single    1.364  0.020  1.364
 W7M  CAX  NAP  single    1.370  0.020  1.370
 W7M  NAO  CAV  single    1.372  0.020  1.372
 W7M  NAP  CAY  single    1.378  0.020  1.378
 W7M  OAF  CAR  double    1.201  0.020  1.201
 W7M  OAB  CAR  single    1.320  0.020  1.320
 W7M  CAV  CAR  single    1.499  0.020  1.499
 W7M  CAV  CAW  double    1.351  0.020  1.351
 W7M  CAY  CAW  single    1.466  0.020  1.466
 W7M  CAY  OAE  double    1.215  0.020  1.215
 W7M  CAW  CAN  single    1.497  0.020  1.497
 W7M  CAN  CAM  single    1.536  0.020  1.536
 W7M  CAG  CAI  aromatic  1.366  0.020  1.366
 W7M  CAG  CAT  aromatic  1.417  0.020  1.417
 W7M  CAI  CBA  aromatic  1.415  0.020  1.415
 W7M  CAA  OAQ  single    1.428  0.020  1.428
 W7M  CAM  CAT  single    1.500  0.020  1.500
 W7M  CAT  CAK  aromatic  1.372  0.020  1.372
 W7M  CBA  CAL  aromatic  1.409  0.020  1.409
 W7M  CBA  CAZ  aromatic  1.418  0.020  1.418
 W7M  CAL  CAU  aromatic  1.374  0.020  1.374
 W7M  CAK  CAZ  aromatic  1.412  0.020  1.412
 W7M  CAZ  CAJ  aromatic  1.415  0.020  1.415
 W7M  OAQ  CAS  single    1.323  0.020  1.323
 W7M  CAU  CAS  single    1.484  0.020  1.484
 W7M  CAU  CAH  aromatic  1.417  0.020  1.417
 W7M  CAS  OAC  double    1.208  0.020  1.208
 W7M  CAJ  CAH  aromatic  1.366  0.020  1.366
 W7M  OAB  H1   single    0.850  0.020  0.980
 W7M  NAP  H2   single    0.860  0.020  1.020
 W7M  CAN  H4   single    0.970  0.020  1.090
 W7M  CAN  H5   single    0.970  0.020  1.090
 W7M  CAM  H6   single    0.970  0.020  1.090
 W7M  CAM  H7   single    0.970  0.020  1.090
 W7M  CAK  H8   single    0.930  0.020  1.080
 W7M  CAG  H9   single    0.930  0.020  1.080
 W7M  CAI  H10  single    0.930  0.020  1.080
 W7M  CAL  H11  single    0.930  0.020  1.080
 W7M  CAJ  H12  single    0.930  0.020  1.080
 W7M  CAH  H13  single    0.930  0.020  1.080
 W7M  CAA  H14  single    0.970  0.020  1.090
 W7M  CAA  H15  single    0.970  0.020  1.090
 W7M  CAA  H16  single    0.970  0.020  1.090
 W7M  NAO  H17  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
 W7M  H1   OAB  CAR  110.79  3.000
 W7M  CAV  CAR  OAF  124.00  3.000
 W7M  CAV  CAR  OAB  111.14  3.000
 W7M  OAF  CAR  OAB  124.85  3.000
 W7M  CAW  CAV  NAO  121.97  3.000
 W7M  CAW  CAV  CAR  123.08  3.000
 W7M  NAO  CAV  CAR  114.95  3.000
 W7M  H17  NAO  CAX  116.10  3.000
 W7M  H17  NAO  CAV  119.69  3.000
 W7M  CAX  NAO  CAV  124.19  3.000
 W7M  NAP  CAX  OAD  123.17  3.000
 W7M  NAP  CAX  NAO  113.52  3.000
 W7M  OAD  CAX  NAO  123.31  3.000
 W7M  H2   NAP  CAY  116.75  3.000
 W7M  H2   NAP  CAX  115.98  3.000
 W7M  CAY  NAP  CAX  127.27  3.000
 W7M  CAW  CAY  OAE  123.85  3.000
 W7M  OAE  CAY  NAP  120.42  3.000
 W7M  CAW  CAY  NAP  115.72  3.000
 W7M  CAN  CAW  CAY  116.15  3.000
 W7M  CAN  CAW  CAV  126.53  3.000
 W7M  CAY  CAW  CAV  117.32  3.000
 W7M  H5   CAN  H4   106.60  3.000
 W7M  H5   CAN  CAM  109.39  3.000
 W7M  H4   CAN  CAM  109.25  3.000
 W7M  H5   CAN  CAW  111.37  3.000
 W7M  H4   CAN  CAW  108.16  3.000
 W7M  CAM  CAN  CAW  111.90  3.000
 W7M  H7   CAM  H6   107.17  3.000
 W7M  H7   CAM  CAT  109.72  3.000
 W7M  H6   CAM  CAT  109.87  3.000
 W7M  H7   CAM  CAN  109.48  3.000
 W7M  H6   CAM  CAN  109.26  3.000
 W7M  CAT  CAM  CAN  111.26  3.000
 W7M  CAG  CAT  CAK  119.00  3.000
 W7M  CAK  CAT  CAM  121.23  3.000
 W7M  CAG  CAT  CAM  119.75  3.000
 W7M  H8   CAK  CAZ  118.75  3.000
 W7M  H8   CAK  CAT  119.91  3.000
 W7M  CAZ  CAK  CAT  121.35  3.000
 W7M  H9   CAG  CAI  119.85  3.000
 W7M  H9   CAG  CAT  118.99  3.000
 W7M  CAI  CAG  CAT  121.16  3.000
 W7M  H10  CAI  CBA  119.14  3.000
 W7M  H10  CAI  CAG  120.35  3.000
 W7M  CBA  CAI  CAG  120.51  3.000
 W7M  CAZ  CBA  CAL  119.24  3.000
 W7M  CAZ  CBA  CAI  118.86  3.000
 W7M  CAL  CBA  CAI  121.91  3.000
 W7M  H11  CAL  CAU  120.20  3.000
 W7M  H11  CAL  CBA  118.77  3.000
 W7M  CAU  CAL  CBA  121.03  3.000
 W7M  CAJ  CAZ  CBA  118.71  3.000
 W7M  CAJ  CAZ  CAK  122.16  3.000
 W7M  CBA  CAZ  CAK  119.13  3.000
 W7M  H12  CAJ  CAH  119.90  3.000
 W7M  H12  CAJ  CAZ  119.05  3.000
 W7M  CAH  CAJ  CAZ  121.06  3.000
 W7M  H13  CAH  CAU  120.35  3.000
 W7M  H13  CAH  CAJ  119.36  3.000
 W7M  CAU  CAH  CAJ  120.29  3.000
 W7M  CAS  CAU  CAH  122.25  3.000
 W7M  CAH  CAU  CAL  119.68  3.000
 W7M  CAS  CAU  CAL  118.07  3.000
 W7M  OAQ  CAS  OAC  123.45  3.000
 W7M  OAC  CAS  CAU  123.96  3.000
 W7M  OAQ  CAS  CAU  112.59  3.000
 W7M  CAA  OAQ  CAS  117.58  3.000
 W7M  H16  CAA  H15  109.40  3.000
 W7M  H16  CAA  H14  109.33  3.000
 W7M  H15  CAA  H14  109.44  3.000
 W7M  H16  CAA  OAQ  111.35  3.000
 W7M  H15  CAA  OAQ  105.88  3.000
 W7M  H14  CAA  OAQ  111.36  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
 W7M  CONST_01  CBA  CAI  CAG  CAT     0.00   0.0  0
 W7M  CONST_02  CBA  CAZ  CAK  CAT     0.00   0.0  0
 W7M  CONST_03  CAJ  CAZ  CAK  CAT   180.00   0.0  0
 W7M  CONST_04  CAI  CAG  CAT  CAK     0.00   0.0  0
 W7M  CONST_05  CAI  CBA  CAZ  CAK     0.00   0.0  0
 W7M  CONST_06  CAL  CBA  CAZ  CAK   180.00   0.0  0
 W7M  CONST_07  CAH  CAJ  CAZ  CAK   180.00   0.0  0
 W7M  CONST_08  CAL  CBA  CAI  CAG   180.00   0.0  0
 W7M  CONST_09  CAZ  CBA  CAI  CAG     0.00   0.0  0
 W7M  CONST_10  CAZ  CAK  CAT  CAG     0.00   0.0  0
 W7M  CONST_11  CAU  CAL  CBA  CAI   180.00   0.0  0
 W7M  CONST_12  CAJ  CAZ  CBA  CAI   180.00   0.0  0
 W7M  CONST_13  CAH  CAU  CAL  CBA     0.00   0.0  0
 W7M  CONST_14  CAH  CAJ  CAZ  CBA     0.00   0.0  0
 W7M  CONST_15  CAJ  CAZ  CBA  CAL     0.00   0.0  0
 W7M  CONST_16  CAJ  CAH  CAU  CAL     0.00   0.0  0
 W7M  CONST_17  CAU  CAL  CBA  CAZ     0.00   0.0  0
 W7M  CONST_18  CAU  CAH  CAJ  CAZ     0.00   0.0  0
 W7M  CONST_19  NAP  CAX  NAO  CAV     0.00   0.0  0
 W7M  CONST_20  CAY  NAP  CAX  NAO     0.00   0.0  0
 W7M  CONST_21  CAW  CAY  NAP  CAX     0.00   0.0  0
 W7M  CONST_22  CAI  CAG  CAT  CAM   180.00   0.0  0
 W7M  CONST_23  CAZ  CAK  CAT  CAM   180.00   0.0  0
 W7M  CONST_24  CAS  CAU  CAL  CBA   180.00   0.0  0
 W7M  CONST_25  CAS  CAU  CAH  CAJ   180.00   0.0  0
 W7M  CONST_26  OAD  CAX  NAO  CAV   180.00   0.0  0
 W7M  CONST_27  OAE  CAY  NAP  CAX   180.00   0.0  0
 W7M  CONST_28  CAY  NAP  CAX  OAD   180.00   0.0  0
 W7M  CONST_29  H10  CAI  CAG  CAT   180.00   0.0  0
 W7M  CONST_30  H9   CAG  CAT  CAK   180.00   0.0  0
 W7M  CONST_31  H12  CAJ  CAZ  CAK     0.00   0.0  0
 W7M  CONST_32  H8   CAK  CAT  CAG   180.00   0.0  0
 W7M  CONST_33  H11  CAL  CBA  CAI     0.00   0.0  0
 W7M  CONST_34  H13  CAH  CAU  CAL   180.00   0.0  0
 W7M  CONST_35  H2   NAP  CAX  NAO   180.00   0.0  0
 W7M  CONST_36  H17  NAO  CAX  NAP   180.00   0.0  0
 W7M  CONST_37  H1   OAB  CAR  CAV   180.00   0.0  0
 W7M  Var_01    NAO  CAV  CAR  OAB   -25.93  30.0  3
 W7M  Var_02    CAM  CAN  CAW  CAV    95.71  30.0  3
 W7M  Var_03    CAT  CAM  CAN  CAW   177.47  30.0  3
 W7M  Var_04    CAG  CAT  CAM  CAN   -81.82  30.0  2
 W7M  Var_05    OAQ  CAS  CAU  CAL  -178.99  30.0  2
 W7M  Var_06    H14  CAA  OAQ  CAS    61.16  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
 W7M  plan-1  CAR  0.020
 W7M  plan-1  CAV  0.020
 W7M  plan-1  NAO  0.020
 W7M  plan-1  CAX  0.020
 W7M  plan-1  OAD  0.020
 W7M  plan-1  NAP  0.020
 W7M  plan-1  CAY  0.020
 W7M  plan-1  OAE  0.020
 W7M  plan-1  CAW  0.020
 W7M  plan-1  CAN  0.020
 W7M  plan-1  H2   0.020
 W7M  plan-1  H17  0.020
 W7M  plan-2  CAU  0.020
 W7M  plan-2  CAS  0.020
 W7M  plan-2  OAC  0.020
 W7M  plan-2  OAQ  0.020
 W7M  plan-3  CAM  0.020
 W7M  plan-3  CAT  0.020
 W7M  plan-3  CAK  0.020
 W7M  plan-3  CAG  0.020
 W7M  plan-3  CAI  0.020
 W7M  plan-3  CBA  0.020
 W7M  plan-3  CAL  0.020
 W7M  plan-3  CAZ  0.020
 W7M  plan-3  CAJ  0.020
 W7M  plan-3  CAH  0.020
 W7M  plan-3  CAU  0.020
 W7M  plan-3  CAS  0.020
 W7M  plan-3  H8   0.020
 W7M  plan-3  H9   0.020
 W7M  plan-3  H10  0.020
 W7M  plan-3  H11  0.020
 W7M  plan-3  H12  0.020
 W7M  plan-3  H13  0.020
 W7M  plan-4  OAB  0.020
 W7M  plan-4  CAR  0.020
 W7M  plan-4  OAF  0.020
 W7M  plan-4  CAV  0.020
 W7M  plan-4  H1   0.020

