# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 23:52:47 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(NC(=O)c2ccccc2)C(=O)NC(=O)N1Cc3ccccc3
#
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
 BZ0  BZ0  N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)benzamide  ligand  41  25  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BZ0
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
 BZ0  CAW   C  CR16  0  -0.282   3.9542  -0.6525  -0.7057
 BZ0  CAX   C  CR16  0  -0.239   4.6399  -1.6797  -1.3375
 BZ0  CBA   C  CR16  0  -0.263   5.0904  -2.7737  -0.6089
 BZ0  CAZ   C  CR16  0  -0.241   4.8486  -2.8354   0.7560
 BZ0  CAY   C  CR16  0  -0.307   4.1571  -1.8089   1.3867
 BZ0  CAV   C  CR6   0   0.086   3.7064  -0.7099   0.6630
 BZ0  CAU   C  CH2   0  -0.426   3.0060   0.4164   1.3814
 BZ0  NAN   N  NR6   0  -0.601   1.8842   0.9761   0.6346
 BZ0  CAO   C  CR6   0   0.675   0.7194   0.2595   0.4818
 BZ0  NAP   N  NH2   0  -0.831   0.6479  -0.9523   1.0286
 BZ0  CAM   C  CR6   0   0.723   2.0330   2.2458   0.0940
 BZ0  OAL   O  O     0  -0.477   3.0643   2.8773   0.2041
 BZ0  NAD   N  NR16  0  -0.741   0.9489   2.7338  -0.5640
 BZ0  CAE   C  CR6   0   0.542  -0.2696   2.0960  -0.7792
 BZ0  OAA   O  O     0  -0.479  -1.1545   2.6685  -1.3964
 BZ0  CAF   C  CR6   0  -0.043  -0.3402   0.7881  -0.2294
 BZ0  NAG   N  NH1   0  -0.736  -1.5245   0.0471  -0.3690
 BZ0  OAC   O  O     0  -0.461  -2.5838   1.0605   1.3485
 BZ0  CA0   C  C     0   0.522  -2.6182   0.3102   0.3899
 BZ0  CAT   C  CR6   0  -0.037  -3.8699  -0.4037  -0.0001
 BZ0  CAS   C  CR16  0  -0.270  -4.8009  -0.6914   0.9963
 BZ0  CAR   C  CR16  0  -0.242  -5.9839  -1.3417   0.6829
 BZ0  CAI   C  CR16  0  -0.250  -6.2592  -1.6908  -0.6336
 BZ0  CAJ   C  CR16  0  -0.240  -5.3458  -1.3889  -1.6338
 BZ0  CAK   C  CR16  0  -0.292  -4.1536  -0.7520  -1.3193
 BZ0  HAY   H  HCR6  0   0.262   3.9659  -1.8671   2.4525
 BZ0  HAZ   H  HCR6  0   0.261   5.1928  -3.6848   1.3315
 BZ0  HBA   H  HCR6  0   0.260   5.6241  -3.5742  -1.1039
 BZ0  HAX   H  HCR6  0   0.261   4.8250  -1.6238  -2.4024
 BZ0  HAW   H  HCR6  0   0.254   3.6122   0.1920  -1.2914
 BZ0  HAU1  H  HCH2  0   0.291   2.6602   0.0989   2.3670
 BZ0  HAU2  H  HCH2  0   0.319   3.7052   1.2296   1.5598
 BZ0  HAP1  H  HNH2  0   0.431   1.3982  -1.3926   1.5286
 BZ0  HAP2  H  HNH2  0   0.422  -0.2046  -1.4784   0.9377
 BZ0  HAD   H  HNR6  0   0.423   1.0570   3.6602  -0.9559
 BZ0  HAG   H  HNH1  0   0.410  -1.6053  -0.5945  -1.1435
 BZ0  HAS   H  HCR6  0   0.263  -4.5938  -0.4161   2.0219
 BZ0  HAK   H  HCR6  0   0.262  -3.4673  -0.5072  -2.1203
 BZ0  HAR   H  HCR6  0   0.264  -6.6935  -1.5738   1.4662
 BZ0  HAI   H  HCR6  0   0.265  -7.1855  -2.1932  -0.8801
 BZ0  HAJ   H  HCR6  0   0.266  -5.5624  -1.6431  -2.6628

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
 BZ0  CAY  CAZ   aromatic  1.389  0.020  1.389
 BZ0  CAY  CAV   aromatic  1.391  0.020  1.391
 BZ0  CAZ  CBA   aromatic  1.387  0.020  1.387
 BZ0  CBA  CAX   aromatic  1.389  0.020  1.389
 BZ0  CAX  CAW   aromatic  1.387  0.020  1.387
 BZ0  CAW  CAV   aromatic  1.392  0.020  1.392
 BZ0  CAV  CAU   single    1.508  0.020  1.508
 BZ0  CAU  NAN   single    1.459  0.020  1.459
 BZ0  NAN  CAO   single    1.376  0.020  1.376
 BZ0  NAN  CAM   single    1.388  0.020  1.388
 BZ0  CAO  NAP   single    1.331  0.020  1.331
 BZ0  CAO  CAF   double    1.381  0.020  1.381
 BZ0  CAM  OAL   double    1.214  0.020  1.214
 BZ0  CAM  NAD   single    1.359  0.020  1.359
 BZ0  NAD  CAE   single    1.392  0.020  1.392
 BZ0  CAE  OAA   double    1.221  0.020  1.221
 BZ0  CAE  CAF   single    1.421  0.020  1.421
 BZ0  CAF  NAG   single    1.404  0.020  1.404
 BZ0  NAG  CA0   single    1.357  0.020  1.357
 BZ0  OAC  CA0   double    1.218  0.020  1.218
 BZ0  CA0  CAT   single    1.493  0.020  1.493
 BZ0  CAT  CAS   aromatic  1.394  0.020  1.394
 BZ0  CAT  CAK   aromatic  1.394  0.020  1.394
 BZ0  CAS  CAR   aromatic  1.386  0.020  1.386
 BZ0  CAR  CAI   aromatic  1.390  0.020  1.390
 BZ0  CAI  CAJ   aromatic  1.388  0.020  1.388
 BZ0  CAJ  CAK   aromatic  1.388  0.020  1.388
 BZ0  CAY  HAY   single    0.930  0.020  1.080
 BZ0  CAZ  HAZ   single    0.930  0.020  1.080
 BZ0  CBA  HBA   single    0.930  0.020  1.080
 BZ0  CAX  HAX   single    0.930  0.020  1.080
 BZ0  CAW  HAW   single    0.930  0.020  1.080
 BZ0  CAU  HAU1  single    0.970  0.020  1.090
 BZ0  CAU  HAU2  single    0.970  0.020  1.090
 BZ0  NAP  HAP1  single    0.860  0.020  1.020
 BZ0  NAP  HAP2  single    0.860  0.020  1.020
 BZ0  NAD  HAD   single    0.860  0.020  1.020
 BZ0  NAG  HAG   single    0.860  0.020  1.020
 BZ0  CAS  HAS   single    0.930  0.020  1.080
 BZ0  CAK  HAK   single    0.930  0.020  1.080
 BZ0  CAR  HAR   single    0.930  0.020  1.080
 BZ0  CAI  HAI   single    0.930  0.020  1.080
 BZ0  CAJ  HAJ   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
 BZ0  HAW   CAW  CAV   120.50  3.000
 BZ0  HAW   CAW  CAX   119.15  3.000
 BZ0  CAV   CAW  CAX   120.35  3.000
 BZ0  HAX   CAX  CBA   120.08  3.000
 BZ0  HAX   CAX  CAW   119.63  3.000
 BZ0  CBA   CAX  CAW   120.29  3.000
 BZ0  HBA   CBA  CAZ   120.20  3.000
 BZ0  HBA   CBA  CAX   120.16  3.000
 BZ0  CAZ   CBA  CAX   119.63  3.000
 BZ0  HAZ   CAZ  CAY   119.79  3.000
 BZ0  HAZ   CAZ  CBA   120.18  3.000
 BZ0  CAY   CAZ  CBA   120.03  3.000
 BZ0  HAY   CAY  CAV   119.78  3.000
 BZ0  HAY   CAY  CAZ   119.63  3.000
 BZ0  CAV   CAY  CAZ   120.59  3.000
 BZ0  CAU   CAV  CAY   119.52  3.000
 BZ0  CAU   CAV  CAW   121.34  3.000
 BZ0  CAY   CAV  CAW   119.10  3.000
 BZ0  HAU2  CAU  HAU1  105.84  3.000
 BZ0  HAU2  CAU  NAN   106.95  3.000
 BZ0  HAU1  CAU  NAN   109.27  3.000
 BZ0  HAU2  CAU  CAV   109.76  3.000
 BZ0  HAU1  CAU  CAV   111.09  3.000
 BZ0  NAN   CAU  CAV   113.56  3.000
 BZ0  CAM   NAN  CAO   121.59  3.000
 BZ0  CAM   NAN  CAU   117.89  3.000
 BZ0  CAO   NAN  CAU   120.52  3.000
 BZ0  CAF   CAO  NAP   121.24  3.000
 BZ0  CAF   CAO  NAN   120.48  3.000
 BZ0  NAP   CAO  NAN   118.28  3.000
 BZ0  HAP2  NAP  HAP1  116.70  3.000
 BZ0  HAP2  NAP  CAO   118.98  3.000
 BZ0  HAP1  NAP  CAO   124.32  3.000
 BZ0  NAD   CAM  OAL   122.32  3.000
 BZ0  NAD   CAM  NAN   115.57  3.000
 BZ0  OAL   CAM  NAN   122.11  3.000
 BZ0  HAD   NAD  CAE   116.95  3.000
 BZ0  HAD   NAD  CAM   115.55  3.000
 BZ0  CAE   NAD  CAM   127.49  3.000
 BZ0  CAF   CAE  OAA   126.24  3.000
 BZ0  CAF   CAE  NAD   113.92  3.000
 BZ0  OAA   CAE  NAD   119.83  3.000
 BZ0  NAG   CAF  CAE   119.29  3.000
 BZ0  NAG   CAF  CAO   119.76  3.000
 BZ0  CAE   CAF  CAO   120.90  3.000
 BZ0  HAG   NAG  CA0   119.21  3.000
 BZ0  HAG   NAG  CAF   118.65  3.000
 BZ0  CA0   NAG  CAF   121.46  3.000
 BZ0  CAT   CA0  OAC   121.60  3.000
 BZ0  CAT   CA0  NAG   115.91  3.000
 BZ0  OAC   CA0  NAG   122.47  3.000
 BZ0  CAK   CAT  CAS   119.28  3.000
 BZ0  CAK   CAT  CA0   122.51  3.000
 BZ0  CAS   CAT  CA0   118.17  3.000
 BZ0  HAS   CAS  CAR   119.81  3.000
 BZ0  HAS   CAS  CAT   119.82  3.000
 BZ0  CAR   CAS  CAT   120.36  3.000
 BZ0  HAR   CAR  CAI   120.13  3.000
 BZ0  HAR   CAR  CAS   119.79  3.000
 BZ0  CAI   CAR  CAS   120.08  3.000
 BZ0  HAI   CAI  CAJ   120.01  3.000
 BZ0  HAI   CAI  CAR   120.14  3.000
 BZ0  CAJ   CAI  CAR   119.85  3.000
 BZ0  HAJ   CAJ  CAK   119.70  3.000
 BZ0  HAJ   CAJ  CAI   120.17  3.000
 BZ0  CAK   CAJ  CAI   120.13  3.000
 BZ0  HAK   CAK  CAJ   118.72  3.000
 BZ0  HAK   CAK  CAT   120.98  3.000
 BZ0  CAJ   CAK  CAT   120.28  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
 BZ0  CONST_01  CAZ   CBA  CAX  CAW    0.00   0.0  0
 BZ0  CONST_02  CAZ   CAY  CAV  CAW    0.00   0.0  0
 BZ0  CONST_03  CAY   CAZ  CBA  CAX    0.00   0.0  0
 BZ0  CONST_04  CAY   CAV  CAW  CAX    0.00   0.0  0
 BZ0  CONST_05  CAV   CAY  CAZ  CBA    0.00   0.0  0
 BZ0  CONST_06  CAV   CAW  CAX  CBA    0.00   0.0  0
 BZ0  CONST_07  CAI   CAR  CAS  CAT    0.00   0.0  0
 BZ0  CONST_08  CAI   CAJ  CAK  CAT    0.00   0.0  0
 BZ0  CONST_09  CAJ   CAK  CAT  CAS    0.00   0.0  0
 BZ0  CONST_10  CAJ   CAI  CAR  CAS    0.00   0.0  0
 BZ0  CONST_11  CAK   CAT  CAS  CAR    0.00   0.0  0
 BZ0  CONST_12  CAK   CAJ  CAI  CAR    0.00   0.0  0
 BZ0  CONST_13  CAE   NAD  CAM  NAN    0.00   0.0  0
 BZ0  CONST_14  NAD   CAM  NAN  CAO    0.00   0.0  0
 BZ0  CONST_15  CAF   CAO  NAN  CAM    0.00   0.0  0
 BZ0  CONST_16  CAF   CAE  NAD  CAM    0.00   0.0  0
 BZ0  CONST_17  CAU   CAV  CAW  CAX  180.00   0.0  0
 BZ0  CONST_18  CAU   CAV  CAY  CAZ  180.00   0.0  0
 BZ0  CONST_19  CAR   CAS  CAT  CA0  180.00   0.0  0
 BZ0  CONST_20  CAJ   CAK  CAT  CA0  180.00   0.0  0
 BZ0  CONST_21  CAF   CAO  NAN  CAU  180.00   0.0  0
 BZ0  CONST_22  NAD   CAM  NAN  CAU  180.00   0.0  0
 BZ0  CONST_23  OAL   CAM  NAN  CAO  180.00   0.0  0
 BZ0  CONST_24  CAM   NAN  CAO  NAP  180.00   0.0  0
 BZ0  CONST_25  OAA   CAE  NAD  CAM  180.00   0.0  0
 BZ0  CONST_26  CAE   NAD  CAM  OAL  180.00   0.0  0
 BZ0  CONST_27  HBA   CBA  CAX  CAW  180.00   0.0  0
 BZ0  CONST_28  HAY   CAY  CAV  CAW  180.00   0.0  0
 BZ0  CONST_29  HAZ   CAZ  CBA  CAX  180.00   0.0  0
 BZ0  CONST_30  HAW   CAW  CAX  CBA  180.00   0.0  0
 BZ0  CONST_31  HAX   CAX  CBA  CAZ  180.00   0.0  0
 BZ0  CONST_32  HAR   CAR  CAS  CAT  180.00   0.0  0
 BZ0  CONST_33  HAJ   CAJ  CAK  CAT  180.00   0.0  0
 BZ0  CONST_34  HAK   CAK  CAT  CAS  180.00   0.0  0
 BZ0  CONST_35  HAI   CAI  CAR  CAS  180.00   0.0  0
 BZ0  CONST_36  HAS   CAS  CAR  CAI  180.00   0.0  0
 BZ0  CONST_37  HAD   NAD  CAM  NAN  180.00   0.0  0
 BZ0  CONST_38  CAT   CA0  NAG  CAF  180.00   0.0  0
 BZ0  CONST_39  NAP   CAO  NAN  CAU    0.00   0.0  0
 BZ0  CONST_40  OAL   CAM  NAN  CAU    0.00   0.0  0
 BZ0  CONST_41  HAP1  NAP  CAO  NAN    0.00   0.0  0
 BZ0  CONST_42  HAP2  NAP  CAO  NAN  180.00   0.0  0
 BZ0  CONST_43  OAC   CA0  NAG  CAF    0.00   0.0  0
 BZ0  CONST_44  HAG   NAG  CA0  CAT    0.00   0.0  0
 BZ0  Var_01    NAN   CAU  CAV  CAW   41.10  30.0  2
 BZ0  Var_02    CAO   NAN  CAU  CAV   71.42  30.0  3
 BZ0  Var_03    CA0   NAG  CAF  CAO  101.33  30.0  2
 BZ0  Var_04    CAS   CAT  CA0  NAG  150.77  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
 BZ0  plan-1  CAW   0.020
 BZ0  plan-1  CAX   0.020
 BZ0  plan-1  CBA   0.020
 BZ0  plan-1  CAZ   0.020
 BZ0  plan-1  CAY   0.020
 BZ0  plan-1  CAV   0.020
 BZ0  plan-1  CAU   0.020
 BZ0  plan-1  HAY   0.020
 BZ0  plan-1  HAZ   0.020
 BZ0  plan-1  HBA   0.020
 BZ0  plan-1  HAX   0.020
 BZ0  plan-1  HAW   0.020
 BZ0  plan-2  CAU   0.020
 BZ0  plan-2  NAN   0.020
 BZ0  plan-2  CAO   0.020
 BZ0  plan-2  NAP   0.020
 BZ0  plan-2  CAM   0.020
 BZ0  plan-2  OAL   0.020
 BZ0  plan-2  NAD   0.020
 BZ0  plan-2  CAE   0.020
 BZ0  plan-2  OAA   0.020
 BZ0  plan-2  CAF   0.020
 BZ0  plan-2  NAG   0.020
 BZ0  plan-2  HAP1  0.020
 BZ0  plan-2  HAP2  0.020
 BZ0  plan-2  HAD   0.020
 BZ0  plan-3  CA0   0.020
 BZ0  plan-3  CAT   0.020
 BZ0  plan-3  CAS   0.020
 BZ0  plan-3  CAR   0.020
 BZ0  plan-3  CAI   0.020
 BZ0  plan-3  CAJ   0.020
 BZ0  plan-3  CAK   0.020
 BZ0  plan-3  HAS   0.020
 BZ0  plan-3  HAK   0.020
 BZ0  plan-3  HAR   0.020
 BZ0  plan-3  HAI   0.020
 BZ0  plan-3  HAJ   0.020
 BZ0  plan-4  CAF   0.020
 BZ0  plan-4  NAG   0.020
 BZ0  plan-4  OAC   0.020
 BZ0  plan-4  CA0   0.020
 BZ0  plan-4  CAT   0.020
 BZ0  plan-4  HAG   0.020

