# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 03:03:59 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-[3-(benzyloxy)benzyl]-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCN1C=C(Cc2cccc(OCc3ccccc3)c2)C(=O)NC1=O
#
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
 183  183  5-[3-(benzyloxy)benzyl]-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione  ligand  50  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_183
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
 183  OAC   O  OH1   0  -0.670  -0.8250  -3.0538   0.9330
 183  CAN   C  CH2   0  -0.187  -0.9223  -2.8496  -0.4571
 183  CAO   C  CH2   0  -0.183   0.2742  -2.0715  -0.9417
 183  OAT   O  O2    0  -0.463   1.4563  -2.8282  -0.7580
 183  CAR   C  CH2   0  -0.062   2.5838  -2.2903  -1.3587
 183  NBC   N  NR6   0  -0.543   3.0189  -1.0487  -0.7274
 183  CBB   C  CR6   0   0.733   3.6547  -1.1195   0.4937
 183  OAB   O  OC    0  -0.477   4.0141  -2.1637   0.9939
 183  NAS   N  NR16  0  -0.732   3.8549   0.0942   1.0980
 183  CBA   C  CR6   0   0.571   3.4367   1.3418   0.6652
 183  OAA   O  OC    0  -0.447   3.6314   2.3310   1.3455
 183  CAY   C  CR16  0   0.026   2.6216   0.1538  -1.2479
 183  CAZ   C  CR6   0  -0.149   2.7788   1.3345  -0.6266
 183  CAQ   C  CH2   0  -0.591   2.1703   2.6033  -1.1446
 183  CAW   C  CR6   0   0.157   0.8356   2.8420  -0.4721
 183  CAK   C  CR16  0  -0.344   0.5949   3.9540   0.3301
 183  CAH   C  CR16  0  -0.228  -0.6326   4.0906   0.9628
 183  CAL   C  CR16  0  -0.398  -1.6279   3.1280   0.8323
 183  CAM   C  CR16  0  -0.376  -0.1629   1.8927  -0.6226
 183  CAX   C  CR6   0   0.405  -1.3829   2.0108   0.0363
 183  OAU   O  O2    0  -0.467  -2.2395   0.9883  -0.1539
 183  CAP   C  CH2   0  -0.262  -3.4259   0.9092   0.6228
 183  CAV   C  CR6   0   0.100  -3.9564  -0.4815   0.4428
 183  CAJ   C  CR16  0  -0.300  -3.7950  -1.4342   1.4429
 183  CAG   C  CR16  0  -0.277  -4.2312  -2.7399   1.2511
 183  CAE   C  CR16  0  -0.257  -4.8190  -3.1053   0.0473
 183  CAF   C  CR16  0  -0.242  -4.9855  -2.1580  -0.9558
 183  CAI   C  CR16  0  -0.278  -4.5590  -0.8532  -0.7565
 183  HAC   H  HOH1  0   0.457  -1.6984  -3.2928   1.2558
 183  HAN1  H  HCH2  0   0.201  -0.9895  -3.7983  -1.0060
 183  HAN2  H  HCH2  0   0.218  -1.8107  -2.2629  -0.7190
 183  HAO1  H  HCH2  0   0.218   0.1258  -1.8385  -2.0048
 183  HAO2  H  HCH2  0   0.214   0.3257  -1.1212  -0.3948
 183  HAR1  H  HCH2  0   0.273   3.3802  -3.0249  -1.2802
 183  HAR2  H  HCH2  0   0.251   2.4187  -2.0604  -2.4164
 183  HAS   H  HNR6  0   0.427   4.3328   0.0596   1.9907
 183  HAY   H  HCR6  0   0.321   2.1437   0.0939  -2.2177
 183  HAQ1  H  HCH2  0   0.272   2.8381   3.4479  -0.9737
 183  HAQ2  H  HCH2  0   0.278   2.0304   2.5226  -2.2248
 183  HAK   H  HCR6  0   0.246   1.3642   4.7032   0.4674
 183  HAH   H  HCR6  0   0.257  -0.8216   4.9560   1.5852
 183  HAL   H  HCR6  0   0.278  -2.5678   3.2603   1.3518
 183  HAM   H  HCR6  0   0.241   0.0025   1.0223  -1.2467
 183  HAP1  H  HCH2  0   0.243  -3.2116   1.0990   1.6793
 183  HAP2  H  HCH2  0   0.239  -4.1518   1.6579   0.2874
 183  HAJ   H  HCR6  0   0.258  -3.3325  -1.1526   2.3814
 183  HAG   H  HCR6  0   0.271  -4.1166  -3.4705   2.0423
 183  HAE   H  HCR6  0   0.261  -5.1521  -4.1235  -0.1070
 183  HAF   H  HCR6  0   0.259  -5.4517  -2.4371  -1.8919
 183  HAI   H  HCR6  0   0.256  -4.6946  -0.1177  -1.5407

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
 183  OAC  CAN   single    1.408  0.020  1.408
 183  OAC  HAC   single    0.850  0.020  0.980
 183  CAN  CAO   single    1.507  0.020  1.507
 183  CAN  HAN1  single    0.970  0.020  1.090
 183  CAN  HAN2  single    0.970  0.020  1.090
 183  CAO  OAT   single    1.415  0.020  1.415
 183  CAO  HAO1  single    0.970  0.020  1.090
 183  CAO  HAO2  single    0.970  0.020  1.090
 183  OAT  CAR   single    1.386  0.020  1.386
 183  CAR  NBC   single    1.459  0.020  1.459
 183  CAR  HAR1  single    0.970  0.020  1.090
 183  CAR  HAR2  single    0.970  0.020  1.090
 183  NBC  CBB   aromatic  1.379  0.020  1.379
 183  NBC  CAY   aromatic  1.369  0.020  1.369
 183  CBB  OAB   double    1.212  0.020  1.212
 183  CBB  NAS   aromatic  1.370  0.020  1.370
 183  NAS  CBA   aromatic  1.385  0.020  1.385
 183  NAS  HAS   single    0.860  0.020  1.020
 183  CBA  OAA   double    1.216  0.020  1.216
 183  CBA  CAZ   aromatic  1.450  0.020  1.450
 183  CAY  CAZ   aromatic  1.343  0.020  1.343
 183  CAY  HAY   single    0.930  0.020  1.080
 183  CAZ  CAQ   single    1.500  0.020  1.500
 183  CAQ  CAW   single    1.513  0.020  1.513
 183  CAQ  HAQ1  single    0.970  0.020  1.090
 183  CAQ  HAQ2  single    0.970  0.020  1.090
 183  CAW  CAK   aromatic  1.392  0.020  1.392
 183  CAW  CAM   aromatic  1.386  0.020  1.386
 183  CAK  CAH   aromatic  1.388  0.020  1.388
 183  CAK  HAK   single    0.930  0.020  1.080
 183  CAH  CAL   aromatic  1.391  0.020  1.391
 183  CAH  HAH   single    0.930  0.020  1.080
 183  CAL  CAX   aromatic  1.393  0.020  1.393
 183  CAL  HAL   single    0.930  0.020  1.080
 183  CAM  CAX   aromatic  1.392  0.020  1.392
 183  CAM  HAM   single    0.930  0.020  1.080
 183  CAX  OAU   single    1.347  0.020  1.347
 183  OAU  CAP   single    1.420  0.020  1.420
 183  CAP  CAV   single    1.499  0.020  1.499
 183  CAP  HAP1  single    0.970  0.020  1.090
 183  CAP  HAP2  single    0.970  0.020  1.090
 183  CAV  CAJ   aromatic  1.391  0.020  1.391
 183  CAV  CAI   aromatic  1.393  0.020  1.393
 183  CAJ  CAG   aromatic  1.390  0.020  1.390
 183  CAJ  HAJ   single    0.930  0.020  1.080
 183  CAG  CAE   aromatic  1.389  0.020  1.389
 183  CAG  HAG   single    0.930  0.020  1.080
 183  CAE  CAF   aromatic  1.390  0.020  1.390
 183  CAE  HAE   single    0.930  0.020  1.080
 183  CAF  CAI   aromatic  1.387  0.020  1.387
 183  CAF  HAF   single    0.930  0.020  1.080
 183  CAI  HAI   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
 183  HAC   OAC  CAN   107.74  3.000
 183  HAN2  CAN  HAN1  107.06  3.000
 183  HAN2  CAN  CAO   106.87  3.000
 183  HAN1  CAN  CAO   109.51  3.000
 183  HAN2  CAN  OAC   111.67  3.000
 183  HAN1  CAN  OAC   111.86  3.000
 183  CAO   CAN  OAC   109.72  3.000
 183  HAO2  CAO  HAO1  107.75  3.000
 183  HAO2  CAO  OAT   111.04  3.000
 183  HAO1  CAO  OAT   110.60  3.000
 183  HAO2  CAO  CAN   108.91  3.000
 183  HAO1  CAO  CAN   108.26  3.000
 183  OAT   CAO  CAN   110.19  3.000
 183  CAR   OAT  CAO   114.56  3.000
 183  HAR2  CAR  HAR1  108.81  3.000
 183  HAR2  CAR  NBC   106.51  3.000
 183  HAR1  CAR  NBC   109.00  3.000
 183  HAR2  CAR  OAT   112.18  3.000
 183  HAR1  CAR  OAT   107.62  3.000
 183  NBC   CAR  OAT   112.66  3.000
 183  CAY   NBC  CBB   121.04  3.000
 183  CAY   NBC  CAR   119.75  3.000
 183  CBB   NBC  CAR   118.49  3.000
 183  NAS   CBB  OAB   122.51  3.000
 183  NAS   CBB  NBC   114.36  3.000
 183  OAB   CBB  NBC   123.13  3.000
 183  HAS   NAS  CBA   116.64  3.000
 183  HAS   NAS  CBB   115.29  3.000
 183  CBA   NAS  CBB   128.01  3.000
 183  CAZ   CBA  OAA   125.11  3.000
 183  CAZ   CBA  NAS   114.26  3.000
 183  OAA   CBA  NAS   120.63  3.000
 183  HAY   CAY  CAZ   120.97  3.000
 183  HAY   CAY  NBC   114.83  3.000
 183  CAZ   CAY  NBC   124.20  3.000
 183  CAQ   CAZ  CAY   122.44  3.000
 183  CAQ   CAZ  CBA   119.19  3.000
 183  CAY   CAZ  CBA   118.01  3.000
 183  HAQ2  CAQ  HAQ1  106.90  3.000
 183  HAQ2  CAQ  CAW   109.76  3.000
 183  HAQ1  CAQ  CAW   110.39  3.000
 183  HAQ2  CAQ  CAZ   109.34  3.000
 183  HAQ1  CAQ  CAZ   110.66  3.000
 183  CAW   CAQ  CAZ   109.74  3.000
 183  CAM   CAW  CAK   119.02  3.000
 183  CAM   CAW  CAQ   118.63  3.000
 183  CAK   CAW  CAQ   122.31  3.000
 183  HAK   CAK  CAH   120.18  3.000
 183  HAK   CAK  CAW   120.20  3.000
 183  CAH   CAK  CAW   119.63  3.000
 183  HAH   CAH  CAL   118.83  3.000
 183  HAH   CAH  CAK   119.69  3.000
 183  CAL   CAH  CAK   121.47  3.000
 183  HAL   CAL  CAX   121.66  3.000
 183  HAL   CAL  CAH   119.47  3.000
 183  CAX   CAL  CAH   118.86  3.000
 183  HAM   CAM  CAX   118.34  3.000
 183  HAM   CAM  CAW   120.18  3.000
 183  CAX   CAM  CAW   121.47  3.000
 183  OAU   CAX  CAM   115.22  3.000
 183  OAU   CAX  CAL   125.26  3.000
 183  CAM   CAX  CAL   119.51  3.000
 183  CAP   OAU  CAX   119.74  3.000
 183  HAP2  CAP  HAP1  107.87  3.000
 183  HAP2  CAP  CAV   111.27  3.000
 183  HAP1  CAP  CAV   110.24  3.000
 183  HAP2  CAP  OAU   110.36  3.000
 183  HAP1  CAP  OAU   110.77  3.000
 183  CAV   CAP  OAU   106.35  3.000
 183  CAI   CAV  CAJ   119.12  3.000
 183  CAI   CAV  CAP   120.26  3.000
 183  CAJ   CAV  CAP   120.53  3.000
 183  HAJ   CAJ  CAG   119.85  3.000
 183  HAJ   CAJ  CAV   119.63  3.000
 183  CAG   CAJ  CAV   120.52  3.000
 183  HAG   CAG  CAE   120.04  3.000
 183  HAG   CAG  CAJ   119.98  3.000
 183  CAE   CAG  CAJ   119.98  3.000
 183  HAE   CAE  CAF   120.10  3.000
 183  HAE   CAE  CAG   120.10  3.000
 183  CAF   CAE  CAG   119.81  3.000
 183  HAF   CAF  CAI   119.96  3.000
 183  HAF   CAF  CAE   120.00  3.000
 183  CAI   CAF  CAE   120.04  3.000
 183  HAI   CAI  CAF   119.73  3.000
 183  HAI   CAI  CAV   119.75  3.000
 183  CAF   CAI  CAV   120.52  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
 183  CONST_01  CBA  NAS  CBB  NBC     0.00   0.0  0
 183  CONST_02  CBA  CAZ  CAY  NBC     0.00   0.0  0
 183  CONST_03  CAZ  CAY  NBC  CBB     0.00   0.0  0
 183  CONST_04  CAZ  CBA  NAS  CBB     0.00   0.0  0
 183  CONST_05  CAY  NBC  CBB  NAS     0.00   0.0  0
 183  CONST_06  CAY  CAZ  CBA  NAS     0.00   0.0  0
 183  CONST_07  CAL  CAH  CAK  CAW     0.00   0.0  0
 183  CONST_08  CAL  CAX  CAM  CAW     0.00   0.0  0
 183  CONST_09  CAX  CAM  CAW  CAK     0.00   0.0  0
 183  CONST_10  CAX  CAL  CAH  CAK     0.00   0.0  0
 183  CONST_11  CAM  CAW  CAK  CAH     0.00   0.0  0
 183  CONST_12  CAM  CAX  CAL  CAH     0.00   0.0  0
 183  CONST_13  CAE  CAG  CAJ  CAV     0.00   0.0  0
 183  CONST_14  CAE  CAF  CAI  CAV     0.00   0.0  0
 183  CONST_15  CAF  CAI  CAV  CAJ     0.00   0.0  0
 183  CONST_16  CAF  CAE  CAG  CAJ     0.00   0.0  0
 183  CONST_17  CAI  CAV  CAJ  CAG     0.00   0.0  0
 183  CONST_18  CAI  CAF  CAE  CAG     0.00   0.0  0
 183  CONST_19  NAS  CBB  NBC  CAR   180.00   0.0  0
 183  CONST_20  CAZ  CAY  NBC  CAR   180.00   0.0  0
 183  CONST_21  CAQ  CAZ  CAY  NBC   180.00   0.0  0
 183  CONST_22  OAA  CBA  NAS  CBB   180.00   0.0  0
 183  CONST_23  CAY  NBC  CBB  OAB   180.00   0.0  0
 183  CONST_24  CBA  NAS  CBB  OAB   180.00   0.0  0
 183  CONST_25  CAQ  CAZ  CBA  NAS   180.00   0.0  0
 183  CONST_26  CAY  CAZ  CBA  OAA   180.00   0.0  0
 183  CONST_27  CAH  CAK  CAW  CAQ   180.00   0.0  0
 183  CONST_28  CAX  CAM  CAW  CAQ   180.00   0.0  0
 183  CONST_29  OAU  CAX  CAM  CAW   180.00   0.0  0
 183  CONST_30  OAU  CAX  CAL  CAH   180.00   0.0  0
 183  CONST_31  CAG  CAJ  CAV  CAP   180.00   0.0  0
 183  CONST_32  CAF  CAI  CAV  CAP   180.00   0.0  0
 183  CONST_33  HAS  NAS  CBB  NBC   180.00   0.0  0
 183  CONST_34  HAY  CAY  NBC  CBB   180.00   0.0  0
 183  CONST_35  HAH  CAH  CAK  CAW   180.00   0.0  0
 183  CONST_36  HAM  CAM  CAW  CAK   180.00   0.0  0
 183  CONST_37  HAL  CAL  CAH  CAK   180.00   0.0  0
 183  CONST_38  HAK  CAK  CAH  CAL   180.00   0.0  0
 183  CONST_39  HAG  CAG  CAJ  CAV   180.00   0.0  0
 183  CONST_40  HAF  CAF  CAI  CAV   180.00   0.0  0
 183  CONST_41  HAI  CAI  CAV  CAJ   180.00   0.0  0
 183  CONST_42  HAE  CAE  CAG  CAJ   180.00   0.0  0
 183  CONST_43  HAJ  CAJ  CAG  CAE   180.00   0.0  0
 183  CONST_44  OAB  CBB  NBC  CAR     0.00   0.0  0
 183  Var_01    CAW  CAQ  CAZ  CBA   -78.68  30.0  2
 183  Var_02    CAK  CAW  CAQ  CAZ   117.43  30.0  2
 183  Var_03    CBB  NBC  CAR  OAT    74.82  30.0  2
 183  Var_04    CAV  CAP  OAU  CAX  -165.37  30.0  3
 183  Var_05    CAJ  CAV  CAP  OAU   103.39  30.0  2
 183  Var_06    NBC  CAR  OAT  CAO    68.34  30.0  3
 183  Var_07    OAT  CAO  CAN  OAC    64.55  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
 183  plan-1  CAR  0.020
 183  plan-1  NBC  0.020
 183  plan-1  CBB  0.020
 183  plan-1  OAB  0.020
 183  plan-1  NAS  0.020
 183  plan-1  CBA  0.020
 183  plan-1  OAA  0.020
 183  plan-1  CAY  0.020
 183  plan-1  CAZ  0.020
 183  plan-1  CAQ  0.020
 183  plan-1  HAS  0.020
 183  plan-1  HAY  0.020
 183  plan-2  CAQ  0.020
 183  plan-2  CAW  0.020
 183  plan-2  CAK  0.020
 183  plan-2  CAH  0.020
 183  plan-2  CAL  0.020
 183  plan-2  CAM  0.020
 183  plan-2  CAX  0.020
 183  plan-2  OAU  0.020
 183  plan-2  HAK  0.020
 183  plan-2  HAH  0.020
 183  plan-2  HAL  0.020
 183  plan-2  HAM  0.020
 183  plan-3  CAP  0.020
 183  plan-3  CAV  0.020
 183  plan-3  CAJ  0.020
 183  plan-3  CAG  0.020
 183  plan-3  CAE  0.020
 183  plan-3  CAF  0.020
 183  plan-3  CAI  0.020
 183  plan-3  HAJ  0.020
 183  plan-3  HAG  0.020
 183  plan-3  HAE  0.020
 183  plan-3  HAF  0.020
 183  plan-3  HAI  0.020

