# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 13:05:49 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5-[4-(6-carboxynaphthalen-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: OC(=O)C1=C(CCCCc2ccc3cc(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
 W88  W88  '5-[4-(6-carboxynaphthalen-2-yl)butyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  46  28  .  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_W88
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
 W88  OAB  O  O     0  -0.397   3.3148   2.5429   0.0876
 W88  CAT  C  C     0   0.514   4.4651   2.2871   0.3169
 W88  OAF  O  OH1   0  -0.589   5.3829   3.1770   0.6498
 W88  CAX  C  CR6   0   0.282   5.0496   0.9096   0.2422
 W88  NAQ  N  NR16  0  -0.731   6.3877   0.8664  -0.0632
 W88  CAY  C  CR6   0   0.670   7.1021  -0.2852  -0.2125
 W88  OAC  O  O     0  -0.474   8.2800  -0.3067  -0.5013
 W88  NAR  N  NR16  0  -0.716   6.3602  -1.4187  -0.0058
 W88  CAZ  C  CR6   0   0.586   5.0220  -1.4940   0.3173
 W88  OAD  O  O     0  -0.441   4.4878  -2.5752   0.4688
 W88  CAW  C  CR6   0  -0.115   4.3256  -0.2108   0.4530
 W88  CAP  C  CH2   0  -0.500   2.8706  -0.2773   0.8028
 W88  CAN  C  CH2   0  -0.416   1.9838  -0.5065  -0.4235
 W88  CAM  C  CH2   0  -0.421   0.5082  -0.5636  -0.0551
 W88  CAO  C  CH2   0  -0.509  -0.3872  -0.7846  -1.2765
 W88  CAU  C  CR6   0   0.146  -1.8416  -0.8033  -0.9069
 W88  CAK  C  CR16  0  -0.390  -2.6198   0.3213  -1.0156
 W88  CBA  C  CR66  0   0.148  -3.9768   0.3189  -0.6240
 W88  CAJ  C  CR16  0  -0.305  -4.7921   1.4705  -0.7285
 W88  CAH  C  CR16  0  -0.267  -6.1024   1.4429  -0.3445
 W88  CAV  C  CR6   0  -0.091  -6.6715   0.2515   0.1693
 W88  CAS  C  C     0   0.535  -8.0886   0.1775   0.5982
 W88  OAE  O  OH1   0  -0.595  -8.7421   1.3174   0.4194
 W88  OAA  O  O     0  -0.441  -8.6044  -0.8119   1.0627
 W88  CAL  C  CR16  0  -0.325  -5.8990  -0.8793   0.2804
 W88  CBB  C  CR66  0   0.121  -4.5453  -0.8738  -0.1092
 W88  CAI  C  CR16  0  -0.291  -3.7313  -2.0267  -0.0040
 W88  CAG  C  CR16  0  -0.301  -2.4216  -1.9885  -0.3895
 W88  H1   H  HOH1  0   0.503   5.0082   4.0720   0.6489
 W88  H2   H  HNR6  0   0.430   6.8515  -2.2973  -0.1171
 W88  H4   H  HCH2  0   0.251   2.7264  -1.0995   1.5066
 W88  H5   H  HCH2  0   0.252   2.5533   0.6268   1.3177
 W88  H6   H  HCH2  0   0.230   2.1494   0.2974  -1.1448
 W88  H7   H  HCH2  0   0.227   2.2758  -1.4380  -0.9154
 W88  H8   H  HCH2  0   0.227   0.3386  -1.3626   0.6738
 W88  H9   H  HCH2  0   0.227   0.2161   0.3705   0.4339
 W88  H10  H  HCH2  0   0.243  -0.2020   0.0075  -2.0063
 W88  H11  H  HCH2  0   0.242  -0.1155  -1.7285  -1.7574
 W88  H12  H  HCR6  0   0.249  -2.1942   1.2379  -1.4097
 W88  H13  H  HCR6  0   0.260  -4.3624   2.3849  -1.1186
 W88  H14  H  HCR6  0   0.266  -6.6999   2.3391  -0.4350
 W88  H15  H  HOH1  0   0.487  -9.6601   1.2199   0.7123
 W88  H16  H  HCR6  0   0.265  -6.3256  -1.7949   0.6710
 W88  H17  H  HCR6  0   0.259  -4.1614  -2.9422   0.3837
 W88  H18  H  HCR6  0   0.254  -1.8095  -2.8788  -0.3054
 W88  H19  H  HNR6  0   0.438   6.8941   1.7269  -0.2181

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
 W88  OAC  CAY  double    1.213  0.020  1.213
 W88  CAY  NAQ  single    1.363  0.020  1.363
 W88  CAY  NAR  single    1.370  0.020  1.370
 W88  NAQ  CAX  single    1.373  0.020  1.373
 W88  NAR  CAZ  single    1.379  0.020  1.379
 W88  OAB  CAT  double    1.201  0.020  1.201
 W88  OAF  CAT  single    1.321  0.020  1.321
 W88  CAX  CAT  single    1.498  0.020  1.498
 W88  CAX  CAW  double    1.351  0.020  1.351
 W88  CAZ  CAW  single    1.466  0.020  1.466
 W88  CAZ  OAD  double    1.215  0.020  1.215
 W88  CAW  CAP  single    1.498  0.020  1.498
 W88  CAP  CAN  single    1.531  0.020  1.531
 W88  CAN  CAM  single    1.522  0.020  1.522
 W88  CAM  CAO  single    1.530  0.020  1.530
 W88  CAG  CAI  aromatic  1.366  0.020  1.366
 W88  CAG  CAU  aromatic  1.417  0.020  1.417
 W88  CAI  CBB  aromatic  1.415  0.020  1.415
 W88  CAO  CAU  single    1.501  0.020  1.501
 W88  CAU  CAK  aromatic  1.372  0.020  1.372
 W88  CBB  CAL  aromatic  1.409  0.020  1.409
 W88  CBB  CBA  aromatic  1.418  0.020  1.418
 W88  CAL  CAV  aromatic  1.374  0.020  1.374
 W88  CAK  CBA  aromatic  1.412  0.020  1.412
 W88  CBA  CAJ  aromatic  1.415  0.020  1.415
 W88  OAA  CAS  double    1.209  0.020  1.209
 W88  CAV  CAS  single    1.482  0.020  1.482
 W88  CAV  CAH  aromatic  1.417  0.020  1.417
 W88  CAS  OAE  single    1.326  0.020  1.326
 W88  CAJ  CAH  aromatic  1.366  0.020  1.366
 W88  OAF  H1   single    0.850  0.020  0.980
 W88  NAR  H2   single    0.860  0.020  1.020
 W88  CAP  H4   single    0.970  0.020  1.090
 W88  CAP  H5   single    0.970  0.020  1.090
 W88  CAN  H6   single    0.970  0.020  1.090
 W88  CAN  H7   single    0.970  0.020  1.090
 W88  CAM  H8   single    0.970  0.020  1.090
 W88  CAM  H9   single    0.970  0.020  1.090
 W88  CAO  H10  single    0.970  0.020  1.090
 W88  CAO  H11  single    0.970  0.020  1.090
 W88  CAK  H12  single    0.930  0.020  1.080
 W88  CAJ  H13  single    0.930  0.020  1.080
 W88  CAH  H14  single    0.930  0.020  1.080
 W88  OAE  H15  single    0.850  0.020  0.980
 W88  CAL  H16  single    0.930  0.020  1.080
 W88  CAI  H17  single    0.930  0.020  1.080
 W88  CAG  H18  single    0.930  0.020  1.080
 W88  NAQ  H19  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
 W88  CAX  CAT  OAF  111.15  3.000
 W88  CAX  CAT  OAB  124.07  3.000
 W88  OAF  CAT  OAB  124.77  3.000
 W88  H1   OAF  CAT  110.66  3.000
 W88  CAW  CAX  NAQ  122.07  3.000
 W88  CAW  CAX  CAT  123.08  3.000
 W88  NAQ  CAX  CAT  114.85  3.000
 W88  H19  NAQ  CAY  116.10  3.000
 W88  H19  NAQ  CAX  119.72  3.000
 W88  CAY  NAQ  CAX  124.16  3.000
 W88  NAR  CAY  OAC  123.16  3.000
 W88  NAR  CAY  NAQ  113.48  3.000
 W88  OAC  CAY  NAQ  123.36  3.000
 W88  H2   NAR  CAZ  116.70  3.000
 W88  H2   NAR  CAY  115.99  3.000
 W88  CAZ  NAR  CAY  127.30  3.000
 W88  CAW  CAZ  OAD  123.93  3.000
 W88  OAD  CAZ  NAR  120.29  3.000
 W88  CAW  CAZ  NAR  115.78  3.000
 W88  CAP  CAW  CAZ  116.37  3.000
 W88  CAP  CAW  CAX  126.44  3.000
 W88  CAZ  CAW  CAX  117.19  3.000
 W88  H5   CAP  H4   106.39  3.000
 W88  H5   CAP  CAN  109.56  3.000
 W88  H4   CAP  CAN  109.10  3.000
 W88  H5   CAP  CAW  110.92  3.000
 W88  H4   CAP  CAW  108.19  3.000
 W88  CAN  CAP  CAW  112.48  3.000
 W88  H7   CAN  H6   106.82  3.000
 W88  H7   CAN  CAM  109.63  3.000
 W88  H6   CAN  CAM  109.53  3.000
 W88  H7   CAN  CAP  109.48  3.000
 W88  H6   CAN  CAP  109.32  3.000
 W88  CAM  CAN  CAP  111.93  3.000
 W88  H9   CAM  H8   106.51  3.000
 W88  H9   CAM  CAO  108.89  3.000
 W88  H8   CAM  CAO  109.59  3.000
 W88  H9   CAM  CAN  109.57  3.000
 W88  H8   CAM  CAN  109.80  3.000
 W88  CAO  CAM  CAN  112.30  3.000
 W88  H11  CAO  H10  106.85  3.000
 W88  H11  CAO  CAU  109.77  3.000
 W88  H10  CAO  CAU  109.74  3.000
 W88  H11  CAO  CAM  109.28  3.000
 W88  H10  CAO  CAM  109.22  3.000
 W88  CAU  CAO  CAM  111.85  3.000
 W88  CAG  CAU  CAK  118.84  3.000
 W88  CAK  CAU  CAO  121.33  3.000
 W88  CAG  CAU  CAO  119.80  3.000
 W88  H12  CAK  CBA  118.63  3.000
 W88  H12  CAK  CAU  119.93  3.000
 W88  CBA  CAK  CAU  121.44  3.000
 W88  CBB  CBA  CAJ  118.72  3.000
 W88  CAJ  CBA  CAK  122.12  3.000
 W88  CBB  CBA  CAK  119.16  3.000
 W88  H13  CAJ  CAH  119.93  3.000
 W88  H13  CAJ  CBA  119.03  3.000
 W88  CAH  CAJ  CBA  121.04  3.000
 W88  H14  CAH  CAV  120.37  3.000
 W88  H14  CAH  CAJ  119.35  3.000
 W88  CAV  CAH  CAJ  120.29  3.000
 W88  CAL  CAV  CAS  118.23  3.000
 W88  CAS  CAV  CAH  122.06  3.000
 W88  CAL  CAV  CAH  119.71  3.000
 W88  OAA  CAS  OAE  123.04  3.000
 W88  OAE  CAS  CAV  112.91  3.000
 W88  OAA  CAS  CAV  124.06  3.000
 W88  H15  OAE  CAS  109.86  3.000
 W88  H16  CAL  CBB  118.79  3.000
 W88  H16  CAL  CAV  120.24  3.000
 W88  CBB  CAL  CAV  120.98  3.000
 W88  CAI  CBB  CAL  121.94  3.000
 W88  CAL  CBB  CBA  119.27  3.000
 W88  CAI  CBB  CBA  118.79  3.000
 W88  H17  CAI  CAG  120.36  3.000
 W88  H17  CAI  CBB  119.12  3.000
 W88  CAG  CAI  CBB  120.51  3.000
 W88  H18  CAG  CAI  119.79  3.000
 W88  H18  CAG  CAU  118.96  3.000
 W88  CAI  CAG  CAU  121.26  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
 W88  CONST_01  CBB  CAI  CAG  CAU     0.00   0.0  0
 W88  CONST_02  CBB  CBA  CAK  CAU     0.00   0.0  0
 W88  CONST_03  CAJ  CBA  CAK  CAU   180.00   0.0  0
 W88  CONST_04  CAI  CAG  CAU  CAK     0.00   0.0  0
 W88  CONST_05  CAI  CBB  CBA  CAK     0.00   0.0  0
 W88  CONST_06  CAL  CBB  CBA  CAK   180.00   0.0  0
 W88  CONST_07  CAH  CAJ  CBA  CAK   180.00   0.0  0
 W88  CONST_08  CAG  CAI  CBB  CBA     0.00   0.0  0
 W88  CONST_09  CAV  CAL  CBB  CBA     0.00   0.0  0
 W88  CONST_10  CAG  CAU  CAK  CBA     0.00   0.0  0
 W88  CONST_11  CAV  CAH  CAJ  CBA     0.00   0.0  0
 W88  CONST_12  CAI  CBB  CBA  CAJ   180.00   0.0  0
 W88  CONST_13  CAL  CBB  CBA  CAJ     0.00   0.0  0
 W88  CONST_14  CAL  CAV  CAH  CAJ     0.00   0.0  0
 W88  CONST_15  CBB  CAL  CAV  CAH     0.00   0.0  0
 W88  CONST_16  CBB  CBA  CAJ  CAH     0.00   0.0  0
 W88  CONST_17  CAI  CBB  CAL  CAV   180.00   0.0  0
 W88  CONST_18  CAG  CAI  CBB  CAL   180.00   0.0  0
 W88  CONST_19  NAR  CAY  NAQ  CAX     0.00   0.0  0
 W88  CONST_20  CAZ  NAR  CAY  NAQ     0.00   0.0  0
 W88  CONST_21  CAW  CAZ  NAR  CAY     0.00   0.0  0
 W88  CONST_22  CAI  CAG  CAU  CAO   180.00   0.0  0
 W88  CONST_23  CBA  CAK  CAU  CAO   180.00   0.0  0
 W88  CONST_24  CAS  CAV  CAH  CAJ   180.00   0.0  0
 W88  CONST_25  CBB  CAL  CAV  CAS   180.00   0.0  0
 W88  CONST_26  OAC  CAY  NAQ  CAX   180.00   0.0  0
 W88  CONST_27  OAD  CAZ  NAR  CAY   180.00   0.0  0
 W88  CONST_28  CAZ  NAR  CAY  OAC   180.00   0.0  0
 W88  CONST_29  H17  CAI  CAG  CAU   180.00   0.0  0
 W88  CONST_30  H18  CAG  CAU  CAK   180.00   0.0  0
 W88  CONST_31  H13  CAJ  CBA  CAK     0.00   0.0  0
 W88  CONST_32  H16  CAL  CBB  CBA   180.00   0.0  0
 W88  CONST_33  H14  CAH  CAJ  CBA   180.00   0.0  0
 W88  CONST_34  H12  CAK  CBA  CAJ     0.00   0.0  0
 W88  CONST_35  H2   NAR  CAY  NAQ   180.00   0.0  0
 W88  CONST_36  H19  NAQ  CAY  NAR   180.00   0.0  0
 W88  CONST_37  H1   OAF  CAT  CAX   180.00   0.0  0
 W88  CONST_38  H15  OAE  CAS  CAV   180.00   0.0  0
 W88  Var_01    NAQ  CAX  CAT  OAB   151.82  30.0  2
 W88  Var_02    CAN  CAP  CAW  CAX    96.39  30.0  3
 W88  Var_03    CAG  CAU  CAO  CAM   -81.70  30.0  2
 W88  Var_04    OAA  CAS  CAV  CAH  -178.66  30.0  2
 W88  Var_05    CAM  CAN  CAP  CAW  -179.66  30.0  3
 W88  Var_06    CAU  CAO  CAM  CAN  -178.51  30.0  3
 W88  Var_07    CAO  CAM  CAN  CAP   179.67  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
 W88  plan-1  CAT  0.020
 W88  plan-1  CAX  0.020
 W88  plan-1  NAQ  0.020
 W88  plan-1  CAY  0.020
 W88  plan-1  OAC  0.020
 W88  plan-1  NAR  0.020
 W88  plan-1  CAZ  0.020
 W88  plan-1  OAD  0.020
 W88  plan-1  CAW  0.020
 W88  plan-1  CAP  0.020
 W88  plan-1  H2   0.020
 W88  plan-1  H19  0.020
 W88  plan-2  CAO  0.020
 W88  plan-2  CAU  0.020
 W88  plan-2  CAK  0.020
 W88  plan-2  CBA  0.020
 W88  plan-2  CAJ  0.020
 W88  plan-2  CAH  0.020
 W88  plan-2  CAV  0.020
 W88  plan-2  CAS  0.020
 W88  plan-2  CAL  0.020
 W88  plan-2  CBB  0.020
 W88  plan-2  CAI  0.020
 W88  plan-2  CAG  0.020
 W88  plan-2  H12  0.020
 W88  plan-2  H13  0.020
 W88  plan-2  H14  0.020
 W88  plan-2  H16  0.020
 W88  plan-2  H17  0.020
 W88  plan-2  H18  0.020
 W88  plan-3  OAB  0.020
 W88  plan-3  CAT  0.020
 W88  plan-3  OAF  0.020
 W88  plan-3  CAX  0.020
 W88  plan-3  H1   0.020
 W88  plan-4  CAV  0.020
 W88  plan-4  CAS  0.020
 W88  plan-4  OAE  0.020
 W88  plan-4  OAA  0.020
 W88  plan-4  H15  0.020

