# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 07:10:02 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-[3-(benzyloxy)benzyl]-6-hydroxy-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCN1C(=O)NC(=O)C(=C1O)Cc2cccc(OCc3ccccc3)c2
#
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
 BBB  BBB  5-[3-(benzyloxy)benzyl]-6-hydroxy-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione  ligand  51  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BBB
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
 BBB  OAC   O  OH1   0  -0.661   6.6526   0.8752   0.9563
 BBB  CAN   C  CH2   0  -0.189   7.0250   1.1407   2.2901
 BBB  CAO   C  CH2   0  -0.196   6.1381   2.1800   2.9384
 BBB  OAT   O  O2    0  -0.489   4.8357   1.6299   3.0233
 BBB  CAR   C  CH2   0  -0.028   3.8042   2.5728   3.0500
 BBB  NBC   N  NR6   0  -0.609   2.5615   1.8395   2.9305
 BBB  CBB   C  CR6   0   0.728   1.8615   1.5396   4.0893
 BBB  OAB   O  OC    0  -0.473   2.1656   1.9877   5.1737
 BBB  NAS   N  NR16  0  -0.733   0.7939   0.7123   3.9148
 BBB  CBA   C  CR6   0   0.567   0.4074   0.0694   2.7490
 BBB  OAA   O  OC    0  -0.457  -0.5381  -0.6990   2.7633
 BBB  CAY   C  CR6   0   0.631   2.2273   1.2555   1.7279
 BBB  CAZ   C  CR6   0  -0.234   1.1958   0.3842   1.5892
 BBB  CAQ   C  CH2   0  -0.623   0.9018  -0.3705   0.3239
 BBB  CAW   C  CR6   0   0.195   1.4862  -1.7650   0.3655
 BBB  CAK   C  CR16  0  -0.354   0.6759  -2.8842   0.2611
 BBB  CAH   C  CR16  0  -0.226   1.2405  -4.1556   0.3266
 BBB  CAL   C  CR16  0  -0.358   2.6004  -4.3211   0.5071
 BBB  CAM   C  CR16  0  -0.417   2.8614  -1.9277   0.5383
 BBB  CAX   C  CR6   0   0.405   3.4226  -3.1963   0.6165
 BBB  OAU   O  O2    0  -0.469   4.7396  -3.4293   0.8002
 BBB  CAP   C  CH2   0  -0.277   5.6047  -2.3127   0.9611
 BBB  CAV   C  CR6   0   0.112   6.9873  -2.8410   1.1897
 BBB  CAJ   C  CR16  0  -0.296   7.4820  -2.9963   2.4804
 BBB  CAG   C  CR16  0  -0.243   8.7542  -3.5125   2.6902
 BBB  CAE   C  CR16  0  -0.261   9.5410  -3.8822   1.6076
 BBB  CAF   C  CR16  0  -0.243   9.0536  -3.7303   0.3151
 BBB  CAI   C  CR16  0  -0.290   7.7829  -3.2125   0.1095
 BBB  OAD   O  OH1   0  -0.596   3.0339   1.6341   0.7493
 BBB  HAC   H  HOH1  0   0.436   5.6954   0.7798   0.9326
 BBB  HAN1  H  HCH2  0   0.203   7.0222   0.2277   2.9007
 BBB  HAN2  H  HCH2  0   0.233   8.0509   1.5126   2.2776
 BBB  HAO1  H  HCH2  0   0.221   6.1354   3.0953   2.3328
 BBB  HAO2  H  HCH2  0   0.227   6.5212   2.4406   3.9316
 BBB  HAR1  H  HCH2  0   0.261   3.7752   3.1316   3.9855
 BBB  HAR2  H  HCH2  0   0.252   3.8899   3.2897   2.2303
 BBB  HAS   H  HNR6  0   0.427   0.2608   0.5046   4.7503
 BBB  HAQ1  H  HCH2  0   0.265   1.2712   0.1546  -0.5631
 BBB  HAQ2  H  HCH2  0   0.289  -0.1772  -0.4315   0.1818
 BBB  HAK   H  HCR6  0   0.247  -0.3932  -2.7691   0.1377
 BBB  HAH   H  HCR6  0   0.257   0.6065  -5.0292   0.2455
 BBB  HAL   H  HCR6  0   0.261   3.0343  -5.3112   0.5701
 BBB  HAM   H  HCR6  0   0.250   3.4892  -1.0501   0.6116
 BBB  HAP1  H  HCH2  0   0.228   5.2833  -1.7061   1.8155
 BBB  HAP2  H  HCH2  0   0.240   5.5803  -1.6833   0.0654
 BBB  HAJ   H  HCR6  0   0.253   6.8722  -2.7096   3.3294
 BBB  HAG   H  HCR6  0   0.259   9.1303  -3.6259   3.6986
 BBB  HAE   H  HCR6  0   0.259  10.5324  -4.2846   1.7708
 BBB  HAF   H  HCR6  0   0.258   9.6651  -4.0108  -0.5328
 BBB  HAI   H  HCR6  0   0.255   7.4097  -3.0878  -0.9002
 BBB  HAD   H  HOH1  0   0.503   2.7100   1.3340  -0.1098

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
 BBB  OAC  CAN   single    1.410  0.020  1.410
 BBB  OAC  HAC   single    0.850  0.020  0.980
 BBB  CAN  CAO   single    1.512  0.020  1.512
 BBB  CAN  HAN1  single    0.970  0.020  1.090
 BBB  CAN  HAN2  single    0.970  0.020  1.090
 BBB  CAO  OAT   single    1.416  0.020  1.416
 BBB  CAO  HAO1  single    0.970  0.020  1.090
 BBB  CAO  HAO2  single    0.970  0.020  1.090
 BBB  OAT  CAR   single    1.398  0.020  1.398
 BBB  CAR  NBC   single    1.448  0.020  1.448
 BBB  CAR  HAR1  single    0.970  0.020  1.090
 BBB  CAR  HAR2  single    0.970  0.020  1.090
 BBB  NBC  CBB   aromatic  1.387  0.020  1.387
 BBB  NBC  CAY   aromatic  1.378  0.020  1.378
 BBB  CBB  OAB   double    1.212  0.020  1.212
 BBB  CBB  NAS   aromatic  1.362  0.020  1.362
 BBB  NAS  CBA   aromatic  1.386  0.020  1.386
 BBB  NAS  HAS   single    0.860  0.020  1.020
 BBB  CBA  OAA   double    1.218  0.020  1.218
 BBB  CBA  CAZ   aromatic  1.437  0.020  1.437
 BBB  CAY  CAZ   aromatic  1.357  0.020  1.357
 BBB  CAY  OAD   single    1.323  0.020  1.323
 BBB  CAZ  CAQ   single    1.502  0.020  1.502
 BBB  CAQ  CAW   single    1.513  0.020  1.513
 BBB  CAQ  HAQ1  single    0.970  0.020  1.090
 BBB  CAQ  HAQ2  single    0.970  0.020  1.090
 BBB  CAW  CAK   aromatic  1.386  0.020  1.386
 BBB  CAW  CAM   aromatic  1.396  0.020  1.396
 BBB  CAK  CAH   aromatic  1.393  0.020  1.393
 BBB  CAK  HAK   single    0.930  0.020  1.080
 BBB  CAH  CAL   aromatic  1.382  0.020  1.382
 BBB  CAH  HAH   single    0.930  0.020  1.080
 BBB  CAL  CAX   aromatic  1.398  0.020  1.398
 BBB  CAL  HAL   single    0.930  0.020  1.080
 BBB  CAM  CAX   aromatic  1.389  0.020  1.389
 BBB  CAM  HAM   single    0.930  0.020  1.080
 BBB  CAX  OAU   single    1.350  0.020  1.350
 BBB  OAU  CAP   single    1.422  0.020  1.422
 BBB  CAP  CAV   single    1.498  0.020  1.498
 BBB  CAP  HAP1  single    0.970  0.020  1.090
 BBB  CAP  HAP2  single    0.970  0.020  1.090
 BBB  CAV  CAJ   aromatic  1.391  0.020  1.391
 BBB  CAV  CAI   aromatic  1.392  0.020  1.392
 BBB  CAJ  CAG   aromatic  1.389  0.020  1.389
 BBB  CAJ  HAJ   single    0.930  0.020  1.080
 BBB  CAG  CAE   aromatic  1.388  0.020  1.388
 BBB  CAG  HAG   single    0.930  0.020  1.080
 BBB  CAE  CAF   aromatic  1.390  0.020  1.390
 BBB  CAE  HAE   single    0.930  0.020  1.080
 BBB  CAF  CAI   aromatic  1.387  0.020  1.387
 BBB  CAF  HAF   single    0.930  0.020  1.080
 BBB  CAI  HAI   single    0.930  0.020  1.080
 BBB  OAD  HAD   single    0.850  0.020  0.980

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
 BBB  HAC   OAC  CAN   107.75  3.000
 BBB  HAN2  CAN  HAN1  106.98  3.000
 BBB  HAN2  CAN  CAO   108.78  3.000
 BBB  HAN1  CAN  CAO   109.35  3.000
 BBB  HAN2  CAN  OAC   107.56  3.000
 BBB  HAN1  CAN  OAC   111.63  3.000
 BBB  CAO   CAN  OAC   112.33  3.000
 BBB  HAO2  CAO  HAO1  107.61  3.000
 BBB  HAO2  CAO  OAT   111.07  3.000
 BBB  HAO1  CAO  OAT   110.78  3.000
 BBB  HAO2  CAO  CAN   110.30  3.000
 BBB  HAO1  CAO  CAN   109.76  3.000
 BBB  OAT   CAO  CAN   107.34  3.000
 BBB  CAR   OAT  CAO   114.69  3.000
 BBB  HAR2  CAR  HAR1  108.04  3.000
 BBB  HAR2  CAR  NBC   109.75  3.000
 BBB  HAR1  CAR  NBC   107.92  3.000
 BBB  HAR2  CAR  OAT   111.75  3.000
 BBB  HAR1  CAR  OAT   112.44  3.000
 BBB  NBC   CAR  OAT   106.87  3.000
 BBB  CAY   NBC  CBB   121.01  3.000
 BBB  CAY   NBC  CAR   119.65  3.000
 BBB  CBB   NBC  CAR   118.29  3.000
 BBB  NAS   CBB  OAB   122.41  3.000
 BBB  NAS   CBB  NBC   114.84  3.000
 BBB  OAB   CBB  NBC   122.75  3.000
 BBB  HAS   NAS  CBA   116.87  3.000
 BBB  HAS   NAS  CBB   115.57  3.000
 BBB  CBA   NAS  CBB   127.45  3.000
 BBB  CAZ   CBA  OAA   124.98  3.000
 BBB  CAZ   CBA  NAS   115.09  3.000
 BBB  OAA   CBA  NAS   119.93  3.000
 BBB  OAD   CAY  CAZ   124.83  3.000
 BBB  OAD   CAY  NBC   112.10  3.000
 BBB  CAZ   CAY  NBC   123.06  3.000
 BBB  CAQ   CAZ  CAY   123.86  3.000
 BBB  CAQ   CAZ  CBA   117.54  3.000
 BBB  CAY   CAZ  CBA   118.36  3.000
 BBB  HAQ2  CAQ  HAQ1  104.78  3.000
 BBB  HAQ2  CAQ  CAW   109.54  3.000
 BBB  HAQ1  CAQ  CAW   109.52  3.000
 BBB  HAQ2  CAQ  CAZ   109.36  3.000
 BBB  HAQ1  CAQ  CAZ   112.05  3.000
 BBB  CAW   CAQ  CAZ   111.37  3.000
 BBB  CAM   CAW  CAK   119.44  3.000
 BBB  CAM   CAW  CAQ   119.44  3.000
 BBB  CAK   CAW  CAQ   121.11  3.000
 BBB  HAK   CAK  CAH   120.19  3.000
 BBB  HAK   CAK  CAW   120.02  3.000
 BBB  CAH   CAK  CAW   119.79  3.000
 BBB  HAH   CAH  CAL   119.32  3.000
 BBB  HAH   CAH  CAK   119.72  3.000
 BBB  CAL   CAH  CAK   120.96  3.000
 BBB  HAL   CAL  CAX   119.71  3.000
 BBB  HAL   CAL  CAH   120.76  3.000
 BBB  CAX   CAL  CAH   119.53  3.000
 BBB  HAM   CAM  CAX   120.17  3.000
 BBB  HAM   CAM  CAW   119.07  3.000
 BBB  CAX   CAM  CAW   120.76  3.000
 BBB  OAU   CAX  CAM   124.01  3.000
 BBB  OAU   CAX  CAL   116.46  3.000
 BBB  CAM   CAX  CAL   119.53  3.000
 BBB  CAP   OAU  CAX   118.26  3.000
 BBB  HAP2  CAP  HAP1  108.24  3.000
 BBB  HAP2  CAP  CAV   110.38  3.000
 BBB  HAP1  CAP  CAV   110.30  3.000
 BBB  HAP2  CAP  OAU   110.19  3.000
 BBB  HAP1  CAP  OAU   110.14  3.000
 BBB  CAV   CAP  OAU   107.58  3.000
 BBB  CAI   CAV  CAJ   119.14  3.000
 BBB  CAI   CAV  CAP   120.22  3.000
 BBB  CAJ   CAV  CAP   120.62  3.000
 BBB  HAJ   CAJ  CAG   119.69  3.000
 BBB  HAJ   CAJ  CAV   119.81  3.000
 BBB  CAG   CAJ  CAV   120.49  3.000
 BBB  HAG   CAG  CAE   120.11  3.000
 BBB  HAG   CAG  CAJ   119.87  3.000
 BBB  CAE   CAG  CAJ   120.02  3.000
 BBB  HAE   CAE  CAF   120.14  3.000
 BBB  HAE   CAE  CAG   120.03  3.000
 BBB  CAF   CAE  CAG   119.83  3.000
 BBB  HAF   CAF  CAI   119.87  3.000
 BBB  HAF   CAF  CAE   120.14  3.000
 BBB  CAI   CAF  CAE   119.99  3.000
 BBB  HAI   CAI  CAF   119.77  3.000
 BBB  HAI   CAI  CAV   119.70  3.000
 BBB  CAF   CAI  CAV   120.53  3.000
 BBB  HAD   OAD  CAY   111.37  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
 BBB  CONST_01  CBA  NAS  CBB  NBC    0.00   0.0  0
 BBB  CONST_02  CBA  CAZ  CAY  NBC    0.00   0.0  0
 BBB  CONST_03  CAZ  CAY  NBC  CBB    0.00   0.0  0
 BBB  CONST_04  CAZ  CBA  NAS  CBB    0.00   0.0  0
 BBB  CONST_05  CAY  NBC  CBB  NAS    0.00   0.0  0
 BBB  CONST_06  CAY  CAZ  CBA  NAS    0.00   0.0  0
 BBB  CONST_07  CAL  CAH  CAK  CAW    0.00   0.0  0
 BBB  CONST_08  CAL  CAX  CAM  CAW    0.00   0.0  0
 BBB  CONST_09  CAX  CAM  CAW  CAK    0.00   0.0  0
 BBB  CONST_10  CAX  CAL  CAH  CAK    0.00   0.0  0
 BBB  CONST_11  CAM  CAW  CAK  CAH    0.00   0.0  0
 BBB  CONST_12  CAM  CAX  CAL  CAH    0.00   0.0  0
 BBB  CONST_13  CAE  CAG  CAJ  CAV    0.00   0.0  0
 BBB  CONST_14  CAE  CAF  CAI  CAV    0.00   0.0  0
 BBB  CONST_15  CAF  CAI  CAV  CAJ    0.00   0.0  0
 BBB  CONST_16  CAF  CAE  CAG  CAJ    0.00   0.0  0
 BBB  CONST_17  CAI  CAV  CAJ  CAG    0.00   0.0  0
 BBB  CONST_18  CAI  CAF  CAE  CAG    0.00   0.0  0
 BBB  CONST_19  NAS  CBB  NBC  CAR  180.00   0.0  0
 BBB  CONST_20  CAZ  CAY  NBC  CAR  180.00   0.0  0
 BBB  CONST_21  CAQ  CAZ  CAY  NBC  180.00   0.0  0
 BBB  CONST_22  OAD  CAY  NBC  CBB  180.00   0.0  0
 BBB  CONST_23  OAA  CBA  NAS  CBB  180.00   0.0  0
 BBB  CONST_24  CAY  NBC  CBB  OAB  180.00   0.0  0
 BBB  CONST_25  CBA  NAS  CBB  OAB  180.00   0.0  0
 BBB  CONST_26  CAQ  CAZ  CBA  NAS  180.00   0.0  0
 BBB  CONST_27  OAD  CAY  CAZ  CBA  180.00   0.0  0
 BBB  CONST_28  CAY  CAZ  CBA  OAA  180.00   0.0  0
 BBB  CONST_29  CAH  CAK  CAW  CAQ  180.00   0.0  0
 BBB  CONST_30  CAX  CAM  CAW  CAQ  180.00   0.0  0
 BBB  CONST_31  OAU  CAX  CAM  CAW  180.00   0.0  0
 BBB  CONST_32  OAU  CAX  CAL  CAH  180.00   0.0  0
 BBB  CONST_33  CAG  CAJ  CAV  CAP  180.00   0.0  0
 BBB  CONST_34  CAF  CAI  CAV  CAP  180.00   0.0  0
 BBB  CONST_35  HAS  NAS  CBB  NBC  180.00   0.0  0
 BBB  CONST_36  HAH  CAH  CAK  CAW  180.00   0.0  0
 BBB  CONST_37  HAM  CAM  CAW  CAK  180.00   0.0  0
 BBB  CONST_38  HAL  CAL  CAH  CAK  180.00   0.0  0
 BBB  CONST_39  HAK  CAK  CAH  CAL  180.00   0.0  0
 BBB  CONST_40  HAG  CAG  CAJ  CAV  180.00   0.0  0
 BBB  CONST_41  HAF  CAF  CAI  CAV  180.00   0.0  0
 BBB  CONST_42  HAI  CAI  CAV  CAJ  180.00   0.0  0
 BBB  CONST_43  HAE  CAE  CAG  CAJ  180.00   0.0  0
 BBB  CONST_44  HAJ  CAJ  CAG  CAE  180.00   0.0  0
 BBB  CONST_45  OAB  CBB  NBC  CAR    0.00   0.0  0
 BBB  Var_01    CAW  CAQ  CAZ  CBA  -77.36  30.0  2
 BBB  Var_02    CAK  CAW  CAQ  CAZ  119.73  30.0  2
 BBB  Var_03    CBB  NBC  CAR  OAT   97.16  30.0  2
 BBB  Var_04    CAV  CAP  OAU  CAX  178.22  30.0  3
 BBB  Var_05    CAJ  CAV  CAP  OAU  -95.60  30.0  2
 BBB  Var_06    NBC  CAR  OAT  CAO  171.44  30.0  3
 BBB  Var_07    OAT  CAO  CAN  OAC   65.04  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
 BBB  plan-1  CAR  0.020
 BBB  plan-1  NBC  0.020
 BBB  plan-1  CBB  0.020
 BBB  plan-1  OAB  0.020
 BBB  plan-1  NAS  0.020
 BBB  plan-1  CBA  0.020
 BBB  plan-1  OAA  0.020
 BBB  plan-1  CAY  0.020
 BBB  plan-1  CAZ  0.020
 BBB  plan-1  CAQ  0.020
 BBB  plan-1  OAD  0.020
 BBB  plan-1  HAS  0.020
 BBB  plan-2  CAQ  0.020
 BBB  plan-2  CAW  0.020
 BBB  plan-2  CAK  0.020
 BBB  plan-2  CAH  0.020
 BBB  plan-2  CAL  0.020
 BBB  plan-2  CAM  0.020
 BBB  plan-2  CAX  0.020
 BBB  plan-2  OAU  0.020
 BBB  plan-2  HAK  0.020
 BBB  plan-2  HAH  0.020
 BBB  plan-2  HAL  0.020
 BBB  plan-2  HAM  0.020
 BBB  plan-3  CAP  0.020
 BBB  plan-3  CAV  0.020
 BBB  plan-3  CAJ  0.020
 BBB  plan-3  CAG  0.020
 BBB  plan-3  CAE  0.020
 BBB  plan-3  CAF  0.020
 BBB  plan-3  CAI  0.020
 BBB  plan-3  HAJ  0.020
 BBB  plan-3  HAG  0.020
 BBB  plan-3  HAE  0.020
 BBB  plan-3  HAF  0.020
 BBB  plan-3  HAI  0.020

