# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 13:19:21 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-{3-[(2-amino-5-nitroso-6-oxo-1,6-dihydropyrimidin-4-yl)amino]propoxy}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=C(N=O)C(=O)N1)NCCCOc2ccc(cc2)C(O)=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
 B54  B54  '4-{3-[(2-amino-5-nitroso-6-oxo-1,6-dihydropyrimidin-4-yl)amino]propoxy}benzoic acid'  ligand  38  24  .  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_B54
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
 B54  O22   O  OC    -1  -0.598  -8.0335  -1.5711   0.0541
 B54  C21   C  C      0   0.391  -7.7603  -0.3542   0.0479
 B54  O23   O  O      0  -0.598  -8.5758   0.5893   0.0491
 B54  C18   C  CR6    0  -0.122  -6.2868   0.0151   0.0379
 B54  C19   C  CR16   0  -0.275  -5.8733   1.3478   0.0538
 B54  C20   C  CR16   0  -0.338  -4.5334   1.6888   0.0469
 B54  C17   C  CR16   0  -0.276  -5.3011  -0.9635   0.0126
 B54  C16   C  CR16   0  -0.371  -3.9484  -0.6448   0.0041
 B54  C15   C  CR6    0   0.375  -3.5558   0.6915   0.0231
 B54  O14   O  O2     0  -0.476  -2.2730   1.1089   0.0203
 B54  C13   C  CH2    0  -0.169  -1.2420   0.1389   0.0091
 B54  C12   C  CH2    0  -0.513   0.0874   0.8651   0.0365
 B54  C11   C  CH2    0  -0.246   1.2280  -0.1401   0.0292
 B54  N10   N  NH1    0  -0.642   2.4995   0.5512   0.0527
 B54  C4    C  CR6    0   0.555   3.6746  -0.0580   0.0444
 B54  C5    C  CR6    0  -0.118   4.8834   0.7175   0.0739
 B54  N9    N  N      0  -0.057   4.7115   2.0571   0.1037
 B54  O24   O  O      0  -0.419   5.6825   2.8047   0.1302
 B54  C2    C  CR6    0   0.533   6.1470   0.0235   0.0708
 B54  O8    O  O      0  -0.448   7.2615   0.5075   0.0960
 B54  N2    N  NR16   0  -0.724   6.0153  -1.3660   0.0338
 B54  C1    C  CR6    0   0.728   4.8288  -2.0146   0.0010
 B54  N1    N  N      0  -0.533   3.6681  -1.3906   0.0080
 B54  N7    N  NH2    0  -0.805   4.8463  -3.3369  -0.0380
 B54  H19   H  HCR6   0   0.243  -6.6158   2.1347   0.0723
 B54  H20   H  HCR6   0   0.253  -4.2309   2.7292   0.0608
 B54  H17   H  HCR6   0   0.244  -5.5901  -2.0062  -0.0007
 B54  H16   H  HCR6   0   0.272  -3.2247  -1.4479  -0.0160
 B54  H13   H  HCH2   0   0.226  -1.3275  -0.5234   0.8786
 B54  H13A  H  HCH2   0   0.226  -1.3113  -0.4868  -0.8886
 B54  H12   H  HCH2   0   0.253   0.1668   1.5231  -0.8330
 B54  H12A  H  HCH2   0   0.253   0.1478   1.4890   0.9324
 B54  H11   H  HCH2   0   0.246   1.1508  -0.8027   0.8947
 B54  H11A  H  HCH2   0   0.245   1.1668  -0.7727  -0.8597
 B54  HN10  H  HNH1   0   0.405   2.5143   1.5601   0.0793
 B54  HN7   H  HNH2   0   0.428   5.6999  -3.8689  -0.0567
 B54  HN7A  H  HNH2   0   0.425   3.9747  -3.8376  -0.0777
 B54  H15   H  HNR6   0   0.427   6.8760  -1.8987   0.0291

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
 B54  C21  O22   deloc     1.247  0.020  1.247
 B54  C21  O23   deloc     1.247  0.020  1.247
 B54  C18  C21   single    1.519  0.020  1.519
 B54  C19  C18   aromatic  1.395  0.020  1.395
 B54  C19  H19   single    0.930  0.020  1.080
 B54  C20  C19   aromatic  1.383  0.020  1.383
 B54  C20  H20   single    0.930  0.020  1.080
 B54  C17  C18   aromatic  1.389  0.020  1.389
 B54  C17  H17   single    0.930  0.020  1.080
 B54  C16  C17   aromatic  1.390  0.020  1.390
 B54  C16  H16   single    0.930  0.020  1.080
 B54  C15  C20   aromatic  1.397  0.020  1.397
 B54  C15  C16   aromatic  1.393  0.020  1.393
 B54  O14  C15   single    1.349  0.020  1.349
 B54  O14  C13   single    1.416  0.020  1.416
 B54  C13  C12   single    1.515  0.020  1.515
 B54  C13  H13   single    0.970  0.020  1.090
 B54  C13  H13A  single    0.970  0.020  1.090
 B54  C12  C11   single    1.520  0.020  1.520
 B54  C12  H12   single    0.970  0.020  1.090
 B54  C12  H12A  single    0.970  0.020  1.090
 B54  C11  N10   single    1.447  0.020  1.447
 B54  C11  H11   single    0.970  0.020  1.090
 B54  C11  H11A  single    0.970  0.020  1.090
 B54  N10  C4    single    1.324  0.020  1.324
 B54  N10  HN10  single    0.860  0.020  1.020
 B54  C4   C5    double    1.436  0.020  1.436
 B54  C4   N1    single    1.333  0.020  1.333
 B54  C5   C2    single    1.442  0.020  1.442
 B54  N9   C5    single    1.351  0.020  1.351
 B54  O24  N9    double    1.226  0.020  1.226
 B54  C2   O8    double    1.215  0.020  1.215
 B54  C2   N2    single    1.396  0.020  1.396
 B54  C1   N2    single    1.353  0.020  1.353
 B54  C1   N7    single    1.323  0.020  1.323
 B54  N1   C1    double    1.318  0.020  1.318
 B54  N7   HN7   single    0.860  0.020  1.020
 B54  N7   HN7A  single    0.860  0.020  1.020
 B54  N2   H15   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
 B54  C18   C21  O23  116.77  3.000
 B54  C18   C21  O22  116.72  3.000
 B54  O23   C21  O22  126.51  3.000
 B54  C17   C18  C19  117.56  3.000
 B54  C17   C18  C21  121.14  3.000
 B54  C19   C18  C21  121.30  3.000
 B54  H19   C19  C20  119.06  3.000
 B54  C20   C19  C18  121.51  3.000
 B54  H19   C19  C18  119.43  3.000
 B54  H20   C20  C15  119.37  3.000
 B54  C15   C20  C19  120.15  3.000
 B54  H20   C20  C19  120.48  3.000
 B54  H17   C17  C16  118.74  3.000
 B54  C16   C17  C18  121.95  3.000
 B54  H17   C17  C18  119.31  3.000
 B54  H16   C16  C15  121.61  3.000
 B54  C15   C16  C17  119.62  3.000
 B54  H16   C16  C17  118.77  3.000
 B54  O14   C15  C16  124.39  3.000
 B54  O14   C15  C20  116.40  3.000
 B54  C16   C15  C20  119.21  3.000
 B54  C13   O14  C15  118.72  3.000
 B54  H13A  C13  H13  107.43  3.000
 B54  H13A  C13  C12  110.11  3.000
 B54  H13   C13  C12  110.10  3.000
 B54  H13A  C13  O14  110.58  3.000
 B54  H13   C13  O14  110.54  3.000
 B54  C12   C13  O14  108.09  3.000
 B54  H12A  C12  H12  107.71  3.000
 B54  H12A  C12  C11  109.86  3.000
 B54  H12   C12  C11  109.85  3.000
 B54  H12A  C12  C13  109.68  3.000
 B54  H12   C12  C13  109.74  3.000
 B54  C11   C12  C13  109.95  3.000
 B54  H11A  C11  H11  106.82  3.000
 B54  H11A  C11  N10  109.81  3.000
 B54  H11   C11  N10  109.80  3.000
 B54  H11A  C11  C12  110.16  3.000
 B54  H11   C11  C12  110.13  3.000
 B54  N10   C11  C12  110.07  3.000
 B54  HN10  N10  C4   116.56  3.000
 B54  HN10  N10  C11  119.39  3.000
 B54  C4    N10  C11  124.05  3.000
 B54  N1    C4   C5   122.98  3.000
 B54  N1    C4   N10  117.12  3.000
 B54  C5    C4   N10  119.90  3.000
 B54  C2    C5   N9   126.08  3.000
 B54  N9    C5   C4   115.39  3.000
 B54  C2    C5   C4   118.53  3.000
 B54  O24   N9   C5   120.30  3.000
 B54  N2    C2   O8   118.91  3.000
 B54  N2    C2   C5   113.36  3.000
 B54  O8    C2   C5   127.73  3.000
 B54  H15   N2   C1   119.57  3.000
 B54  H15   N2   C2   116.34  3.000
 B54  C1    N2   C2   124.09  3.000
 B54  N7    C1   N1   119.01  3.000
 B54  N1    C1   N2   123.06  3.000
 B54  N7    C1   N2   117.93  3.000
 B54  C1    N1   C4   117.98  3.000
 B54  HN7A  N7   HN7  118.11  3.000
 B54  HN7A  N7   C1   119.15  3.000
 B54  HN7   N7   C1   122.71  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
 B54  CONST_01  C15   C20  C19  C18     0.00   0.0  0
 B54  CONST_02  C15   C16  C17  C18     0.00   0.0  0
 B54  CONST_03  C16   C17  C18  C19     0.00   0.0  0
 B54  CONST_04  C16   C15  C20  C19     0.00   0.0  0
 B54  CONST_05  C17   C18  C19  C20     0.00   0.0  0
 B54  CONST_06  C17   C16  C15  C20     0.00   0.0  0
 B54  CONST_07  N2    C1   N1   C4      0.00   0.0  0
 B54  CONST_08  C1    N1   C4   C5      0.00   0.0  0
 B54  CONST_09  C1    N2   C2   C5      0.00   0.0  0
 B54  CONST_10  N1    C1   N2   C2      0.00   0.0  0
 B54  CONST_11  C20   C19  C18  C21   180.00   0.0  0
 B54  CONST_12  C16   C17  C18  C21   180.00   0.0  0
 B54  CONST_13  O14   C15  C20  C19   180.00   0.0  0
 B54  CONST_14  O14   C15  C16  C17   180.00   0.0  0
 B54  CONST_15  C1    N1   C4   N10   180.00   0.0  0
 B54  CONST_16  N7    C1   N1   C4    180.00   0.0  0
 B54  CONST_17  N7    C1   N2   C2    180.00   0.0  0
 B54  CONST_18  C1    N2   C2   O8    180.00   0.0  0
 B54  CONST_19  H20   C20  C19  C18   180.00   0.0  0
 B54  CONST_20  H16   C16  C17  C18   180.00   0.0  0
 B54  CONST_21  H17   C17  C18  C19   180.00   0.0  0
 B54  CONST_22  H19   C19  C18  C17   180.00   0.0  0
 B54  CONST_23  H15   N2   C2   C5    180.00   0.0  0
 B54  CONST_24  C5    C4   N10  C11   180.00   0.0  0
 B54  CONST_25  N1    C4   N10  C11     0.00   0.0  0
 B54  CONST_26  HN10  N10  C4   C5      0.00   0.0  0
 B54  CONST_27  HN7   N7   C1   N2      0.00   0.0  0
 B54  CONST_28  HN7A  N7   C1   N2    180.00   0.0  0
 B54  Var_01    C19   C18  C21  O22  -178.88  30.0  2
 B54  Var_02    C2    C5   N9   O24     0.08  30.0  3
 B54  Var_03    C12   C13  O14  C15  -178.87  30.0  3
 B54  Var_04    C4    N10  C11  C12  -179.57  30.0  3
 B54  Var_05    C11   C12  C13  O14   179.86  30.0  3
 B54  Var_06    N10   C11  C12  C13   179.89  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
 B54  plan-1  C21   0.020
 B54  plan-1  C18   0.020
 B54  plan-1  C19   0.020
 B54  plan-1  C20   0.020
 B54  plan-1  C17   0.020
 B54  plan-1  C16   0.020
 B54  plan-1  C15   0.020
 B54  plan-1  O14   0.020
 B54  plan-1  H19   0.020
 B54  plan-1  H20   0.020
 B54  plan-1  H17   0.020
 B54  plan-1  H16   0.020
 B54  plan-2  C11   0.020
 B54  plan-2  N10   0.020
 B54  plan-2  C4    0.020
 B54  plan-2  C5    0.020
 B54  plan-2  N9    0.020
 B54  plan-2  C2    0.020
 B54  plan-2  O8    0.020
 B54  plan-2  N2    0.020
 B54  plan-2  C1    0.020
 B54  plan-2  N1    0.020
 B54  plan-2  N7    0.020
 B54  plan-2  HN10  0.020
 B54  plan-2  HN7   0.020
 B54  plan-2  HN7A  0.020
 B54  plan-2  H15   0.020
 B54  plan-3  O22   0.020
 B54  plan-3  C21   0.020
 B54  plan-3  O23   0.020
 B54  plan-3  C18   0.020
 B54  plan-4  C5    0.020
 B54  plan-4  N9    0.020
 B54  plan-4  O24   0.020

