# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:20:25 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CN1C=CC(=O)N(Cc2ccc(cc2)C(O)=O)C1=O)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
 VBP  VBP  '4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid'  ligand  37  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VBP
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
 VBP  C10   C  CH2    0  -0.408  -0.8222   1.1994  -1.6235
 VBP  C11   C  CR6    0   0.122  -2.0054   0.4730  -1.0402
 VBP  C12   C  CR16   0  -0.287  -2.7621   1.0469  -0.0209
 VBP  C13   C  CR16   0  -0.274  -3.8641   0.3859   0.4987
 VBP  C14   C  CR6    0  -0.110  -4.2524  -0.8603   0.0101
 VBP  C15   C  CR16   0  -0.280  -3.4962  -1.4277  -1.0111
 VBP  C16   C  CR16   0  -0.290  -2.3845  -0.7738  -1.5246
 VBP  C17   C  C      0   0.394  -5.4722  -1.5769   0.5754
 VBP  C20   C  CR6    0   0.780   1.0176   0.3555  -0.3122
 VBP  C22   C  C      0   0.394   4.9911  -1.7753   0.3747
 VBP  N01   N  NH2    0  -0.785   4.7695   0.7281  -0.0307
 VBP  C02   C  CH1    0  -0.226   4.1055  -0.5608  -0.0155
 VBP  N04   N  NR6    0  -0.520   1.9944   0.5698   0.6325
 VBP  C05   C  CR16   0   0.117   2.2006   1.8008   1.1622
 VBP  C06   C  CR16   0  -0.525   1.4434   2.8656   0.8460
 VBP  C07   C  CR6    0   0.604   0.3754   2.7284  -0.1035
 VBP  O08   O  O      0  -0.488  -0.3735   3.6330  -0.4367
 VBP  N09   N  NR6    0  -0.593   0.2340   1.4451  -0.6408
 VBP  O18   O  OC    -1  -0.594  -5.7695  -2.6696   0.0552
 VBP  O19   O  O      0  -0.594  -6.0696  -1.0092   1.5102
 VBP  H10   H  HCH2   0   0.281  -0.4036   0.6389  -2.4571
 VBP  H10A  H  HCH2   0   0.285  -1.1293   2.1688  -2.0081
 VBP  H12   H  HCR6   0   0.245  -2.4979   2.0240   0.3656
 VBP  H13   H  HCR6   0   0.240  -4.4401   0.8486   1.2892
 VBP  H15   H  HCR6   0   0.241  -3.7745  -2.3962  -1.4060
 VBP  H16   H  HCR6   0   0.242  -1.8048  -1.2391  -2.3127
 VBP  HN01  H  HNH2   0   0.331   5.4617   0.7356   0.7099
 VBP  HN0A  H  HNH2   0   0.346   5.3025   0.8181  -0.8861
 VBP  H02   H  HCH1   0   0.238   3.7066  -0.7511  -1.0166
 VBP  H05   H  HCR6   0   0.309   2.9995   1.8701   1.8846
 VBP  H06   H  HCR6   0   0.282   1.6185   3.8260   1.3053
 VBP  C03   C  CH2    0  -0.317   2.9174  -0.5143   0.9485
 VBP  O23   O  OC    -1  -0.613   4.4472  -2.8927   0.2720
 VBP  H03   H  HCH2   0   0.272   2.3757  -1.4550   0.9402
 VBP  H03A  H  HCH2   0   0.259   3.2668  -0.3473   1.9691
 VBP  O21   O  O      0  -0.480   0.8500  -0.7300  -0.8308
 VBP  O24   O  O      0  -0.596   6.1466  -1.5368   0.7716

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
 VBP  C11  C10   single    1.506  0.020  1.506
 VBP  C11  C12   aromatic  1.393  0.020  1.393
 VBP  C13  C12   aromatic  1.386  0.020  1.386
 VBP  C14  C13   aromatic  1.394  0.020  1.394
 VBP  C15  C14   aromatic  1.392  0.020  1.392
 VBP  C15  C16   aromatic  1.388  0.020  1.388
 VBP  C16  C11   aromatic  1.390  0.020  1.390
 VBP  C17  C14   single    1.523  0.020  1.523
 VBP  C17  O19   deloc     1.246  0.020  1.246
 VBP  C20  N09   single    1.382  0.020  1.382
 VBP  C22  C02   single    1.553  0.020  1.553
 VBP  C02  N01   single    1.450  0.020  1.450
 VBP  C02  C03   single    1.531  0.020  1.531
 VBP  C03  N04   single    1.459  0.020  1.459
 VBP  N04  C20   single    1.376  0.020  1.376
 VBP  N04  C05   single    1.356  0.020  1.356
 VBP  C05  C06   double    1.344  0.020  1.344
 VBP  C06  C07   single    1.436  0.020  1.436
 VBP  C07  O08   double    1.221  0.020  1.221
 VBP  N09  C10   single    1.463  0.020  1.463
 VBP  N09  C07   single    1.398  0.020  1.398
 VBP  O18  C17   deloc     1.246  0.020  1.246
 VBP  O21  C20   double    1.215  0.020  1.215
 VBP  O23  C22   deloc     1.247  0.020  1.247
 VBP  O24  C22   deloc     1.245  0.020  1.245
 VBP  C10  H10   single    0.970  0.020  1.090
 VBP  C10  H10A  single    0.970  0.020  1.090
 VBP  C12  H12   single    0.930  0.020  1.080
 VBP  C13  H13   single    0.930  0.020  1.080
 VBP  C15  H15   single    0.930  0.020  1.080
 VBP  C16  H16   single    0.930  0.020  1.080
 VBP  N01  HN01  single    0.890  0.020  1.040
 VBP  N01  HN0A  single    0.890  0.020  1.040
 VBP  C02  H02   single    0.970  0.020  1.090
 VBP  C03  H03   single    0.970  0.020  1.090
 VBP  C03  H03A  single    0.970  0.020  1.090
 VBP  C05  H05   single    0.930  0.020  1.080
 VBP  C06  H06   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
 VBP  H10A  C10  H10   107.27  3.000
 VBP  H10A  C10  N09   106.96  3.000
 VBP  H10   C10  N09   108.86  3.000
 VBP  H10A  C10  C11   110.20  3.000
 VBP  H10   C10  C11   110.51  3.000
 VBP  N09   C10  C11   112.83  3.000
 VBP  C16   C11  C12   118.44  3.000
 VBP  C16   C11  C10   120.79  3.000
 VBP  C12   C11  C10   120.76  3.000
 VBP  H12   C12  C13   119.36  3.000
 VBP  H12   C12  C11   120.00  3.000
 VBP  C13   C12  C11   120.64  3.000
 VBP  H13   C13  C14   119.35  3.000
 VBP  H13   C13  C12   119.54  3.000
 VBP  C14   C13  C12   121.10  3.000
 VBP  C17   C14  C15   121.04  3.000
 VBP  C17   C14  C13   120.90  3.000
 VBP  C15   C14  C13   118.06  3.000
 VBP  H15   C15  C16   119.50  3.000
 VBP  H15   C15  C14   119.53  3.000
 VBP  C16   C15  C14   120.97  3.000
 VBP  H16   C16  C15   119.69  3.000
 VBP  H16   C16  C11   119.52  3.000
 VBP  C15   C16  C11   120.79  3.000
 VBP  O19   C17  O18   126.75  3.000
 VBP  O18   C17  C14   116.65  3.000
 VBP  O19   C17  C14   116.61  3.000
 VBP  O21   C20  N09   121.67  3.000
 VBP  O21   C20  N04   122.03  3.000
 VBP  N09   C20  N04   116.30  3.000
 VBP  O24   C22  O23   127.08  3.000
 VBP  O24   C22  C02   117.36  3.000
 VBP  O23   C22  C02   115.55  3.000
 VBP  HN0A  N01  HN01  104.91  3.000
 VBP  HN0A  N01  C02   109.22  3.000
 VBP  HN01  N01  C02   108.16  3.000
 VBP  H02   C02  C03   107.37  3.000
 VBP  H02   C02  N01   108.18  3.000
 VBP  C03   C02  N01   109.58  3.000
 VBP  H02   C02  C22   107.56  3.000
 VBP  C03   C02  C22   107.95  3.000
 VBP  N01   C02  C22   115.89  3.000
 VBP  C05   N04  C03   119.60  3.000
 VBP  C05   N04  C20   121.18  3.000
 VBP  C03   N04  C20   118.84  3.000
 VBP  H05   C05  C06   121.57  3.000
 VBP  H05   C05  N04   115.61  3.000
 VBP  C06   C05  N04   122.79  3.000
 VBP  H06   C06  C07   119.17  3.000
 VBP  H06   C06  C05   120.90  3.000
 VBP  C07   C06  C05   119.93  3.000
 VBP  N09   C07  O08   120.87  3.000
 VBP  N09   C07  C06   114.65  3.000
 VBP  O08   C07  C06   124.48  3.000
 VBP  C07   N09  C20   125.09  3.000
 VBP  C07   N09  C10   119.02  3.000
 VBP  C20   N09  C10   115.89  3.000
 VBP  H03A  C03  H03   107.42  3.000
 VBP  H03A  C03  N04   106.94  3.000
 VBP  H03   C03  N04   109.06  3.000
 VBP  H03A  C03  C02   110.19  3.000
 VBP  H03   C03  C02   110.87  3.000
 VBP  N04   C03  C02   112.17  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
 VBP  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 VBP  CONST_02  C14  C15  C16  C11    0.00   0.0  0
 VBP  CONST_03  C15  C16  C11  C12    0.00   0.0  0
 VBP  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 VBP  CONST_05  C16  C11  C12  C13    0.00   0.0  0
 VBP  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 VBP  CONST_07  C06  C07  N09  C20    0.00   0.0  0
 VBP  CONST_08  C07  N09  C20  N04    0.00   0.0  0
 VBP  CONST_09  N09  C20  N04  C05    0.00   0.0  0
 VBP  CONST_10  C13  C12  C11  C10  180.00   0.0  0
 VBP  CONST_11  C15  C16  C11  C10  180.00   0.0  0
 VBP  CONST_12  C17  C14  C13  C12  180.00   0.0  0
 VBP  CONST_13  C17  C14  C15  C16  180.00   0.0  0
 VBP  CONST_14  N04  C20  N09  C10  180.00   0.0  0
 VBP  CONST_15  C06  C07  N09  C10  180.00   0.0  0
 VBP  CONST_16  O08  C07  N09  C20  180.00   0.0  0
 VBP  CONST_17  N09  C20  N04  C03  180.00   0.0  0
 VBP  CONST_18  O21  C20  N04  C05  180.00   0.0  0
 VBP  CONST_19  O21  C20  N09  C07  180.00   0.0  0
 VBP  CONST_20  H13  C13  C12  C11  180.00   0.0  0
 VBP  CONST_21  H15  C15  C16  C11  180.00   0.0  0
 VBP  CONST_22  H16  C16  C11  C12  180.00   0.0  0
 VBP  CONST_23  H12  C12  C13  C14  180.00   0.0  0
 VBP  CONST_24  O21  C20  N09  C10    0.00   0.0  0
 VBP  CONST_25  O08  C07  N09  C10    0.00   0.0  0
 VBP  CONST_26  O21  C20  N04  C03    0.00   0.0  0
 VBP  Var_01    C20  N09  C10  C11   76.31  30.0  1
 VBP  Var_02    N09  C10  C11  C12   62.40  30.0  2
 VBP  Var_03    O19  C17  C14  C13   -1.92  30.0  2
 VBP  Var_04    C02  C03  N04  C20   85.18  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VBP  chir_01  C02  C22  N01  C03  positiv

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
 VBP  plan-1  C10  0.020
 VBP  plan-1  C11  0.020
 VBP  plan-1  C12  0.020
 VBP  plan-1  C13  0.020
 VBP  plan-1  C14  0.020
 VBP  plan-1  C15  0.020
 VBP  plan-1  C16  0.020
 VBP  plan-1  C17  0.020
 VBP  plan-1  H12  0.020
 VBP  plan-1  H13  0.020
 VBP  plan-1  H15  0.020
 VBP  plan-1  H16  0.020
 VBP  plan-2  C10  0.020
 VBP  plan-2  C20  0.020
 VBP  plan-2  N04  0.020
 VBP  plan-2  C05  0.020
 VBP  plan-2  C06  0.020
 VBP  plan-2  C07  0.020
 VBP  plan-2  O08  0.020
 VBP  plan-2  N09  0.020
 VBP  plan-2  H05  0.020
 VBP  plan-2  H06  0.020
 VBP  plan-2  C03  0.020
 VBP  plan-2  O21  0.020
 VBP  plan-3  C14  0.020
 VBP  plan-3  C17  0.020
 VBP  plan-3  O18  0.020
 VBP  plan-3  O19  0.020
 VBP  plan-4  C22  0.020
 VBP  plan-4  C02  0.020
 VBP  plan-4  O23  0.020
 VBP  plan-4  O24  0.020

