# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 01:14:49 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(C[C@H](N)C(O)=O)C(=O)N(Cc2ccsc2C(O)=O)C1=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
 UBA  UBA  '3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)thiophene-2-carboxylic acid'  ligand  39  24  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UBA
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
 UBA  O     O  O     0  -0.430   5.6450  -2.0205   0.4181
 UBA  C     C  C     0   0.527   4.5629  -1.9982  -0.1093
 UBA  OXT   O  OH1   0  -0.589   4.1961  -2.8286  -1.0759
 UBA  CA    C  CH1   0  -0.222   3.4516  -1.0155   0.2447
 UBA  N     N  NH2   0  -0.774   3.7022  -0.2394   1.4282
 UBA  CB    C  CH2   0  -0.328   3.2055  -0.0836  -0.9519
 UBA  N4    N  NR6   0  -0.524   2.0695   0.7912  -0.7160
 UBA  C5    C  CR6   0   0.768   0.8120   0.3013  -0.9550
 UBA  O8    O  OC    0  -0.481   0.6238  -0.8192  -1.3859
 UBA  N6    N  NR6   0  -0.611  -0.2299   1.1630  -0.6718
 UBA  C1    C  CR6   0   0.587  -0.0941   2.4262  -0.0905
 UBA  O7    O  OC    0  -0.455  -1.0802   3.0882   0.1784
 UBA  C2    C  CR6   0  -0.181   1.2624   2.8598   0.1554
 UBA  C6    C  CH3   0  -0.706   1.4868   4.2083   0.7575
 UBA  C3    C  CR16  0   0.066   2.2646   2.0217  -0.1585
 UBA  C17   C  CH2   0  -0.371  -1.5723   0.6843  -0.9620
 UBA  C18   C  CR5   0   0.214  -2.1638  -0.0942   0.1786
 UBA  C23   C  CR15  0  -0.208  -1.5207  -0.2992   1.4248
 UBA  C22   C  CR15  0  -0.443  -2.2670  -1.0408   2.2935
 UBA  S20   S  S2    0   0.284  -3.7580  -1.5075   1.6272
 UBA  C19   C  CR5   0  -0.387  -3.3996  -0.6997   0.1480
 UBA  C10   C  C     0   0.523  -4.3516  -0.7074  -0.9569
 UBA  O2    O  OH1   0  -0.602  -5.4420  -1.4076  -0.6671
 UBA  O1    O  O     0  -0.437  -4.1738  -0.1448  -2.0126
 UBA  HO    H  HOH1  0   0.485   4.9215  -3.4335  -1.2936
 UBA  HA    H  HCH1  0   0.294   2.5452  -1.6074   0.4026
 UBA  HN1   H  HNH2  0   0.366   3.6438  -0.8205   2.2536
 UBA  HN2   H  HNH2  0   0.351   4.6368   0.1502   1.4120
 UBA  HB1   H  HCH2  0   0.294   3.0370  -0.6451  -1.8670
 UBA  HB2   H  HCH2  0   0.286   4.0771   0.5521  -1.1131
 UBA  H61   H  HCH3  0   0.245   1.0504   4.9972   0.1437
 UBA  H62   H  HCH3  0   0.246   1.0378   4.2846   1.7488
 UBA  H63   H  HCH3  0   0.246   2.5515   4.4127   0.8575
 UBA  H3    H  HCR6  0   0.309   3.2978   2.2929   0.0041
 UBA  H171  H  HCH2  0   0.294  -2.1941   1.5452  -1.1961
 UBA  H172  H  HCH2  0   0.292  -1.5381   0.0745  -1.8612
 UBA  H23   H  HCR5  0   0.265  -0.5442   0.0833   1.6827
 UBA  H22   H  HCR5  0   0.312  -2.0017  -1.3324   3.2980
 UBA  HO2   H  HOH1  0   0.492  -6.0573  -1.3977  -1.4155

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
 UBA  O    C     double    1.204  0.020  1.204
 UBA  C    OXT   single    1.326  0.020  1.326
 UBA  C    CA    single    1.525  0.020  1.525
 UBA  OXT  HO    single    0.850  0.020  0.980
 UBA  CA   N     single    1.437  0.020  1.437
 UBA  CA   CB    single    1.537  0.020  1.537
 UBA  CA   HA    single    0.970  0.020  1.090
 UBA  N    HN1   single    0.890  0.020  1.040
 UBA  N    HN2   single    0.890  0.020  1.040
 UBA  CB   N4    single    1.453  0.020  1.453
 UBA  CB   HB1   single    0.970  0.020  1.090
 UBA  CB   HB2   single    0.970  0.020  1.090
 UBA  N4   C5    aromatic  1.371  0.020  1.371
 UBA  N4   C3    aromatic  1.365  0.020  1.365
 UBA  C5   O8    double    1.215  0.020  1.215
 UBA  C5   N6    aromatic  1.381  0.020  1.381
 UBA  N6   C1    aromatic  1.397  0.020  1.397
 UBA  N6   C17   single    1.455  0.020  1.455
 UBA  C1   O7    double    1.218  0.020  1.218
 UBA  C1   C2    aromatic  1.445  0.020  1.445
 UBA  C2   C6    single    1.494  0.020  1.494
 UBA  C2   C3    aromatic  1.344  0.020  1.344
 UBA  C6   H61   single    0.970  0.020  1.090
 UBA  C6   H62   single    0.970  0.020  1.090
 UBA  C6   H63   single    0.970  0.020  1.090
 UBA  C3   H3    single    0.930  0.020  1.080
 UBA  C17  C18   single    1.502  0.020  1.502
 UBA  C17  H171  single    0.970  0.020  1.090
 UBA  C17  H172  single    0.970  0.020  1.090
 UBA  C18  C23   aromatic  1.417  0.020  1.417
 UBA  C18  C19   aromatic  1.377  0.020  1.377
 UBA  C23  C22   aromatic  1.364  0.020  1.364
 UBA  C23  H23   single    0.930  0.020  1.080
 UBA  C22  S20   aromatic  1.698  0.020  1.698
 UBA  C22  H22   single    0.930  0.020  1.080
 UBA  S20  C19   aromatic  1.723  0.020  1.723
 UBA  C19  C10   single    1.459  0.020  1.459
 UBA  C10  O2    single    1.328  0.020  1.328
 UBA  C10  O1    double    1.209  0.020  1.209
 UBA  O2   HO2   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
 UBA  CA    C    OXT   111.79  3.000
 UBA  CA    C    O     124.41  3.000
 UBA  OXT   C    O     123.80  3.000
 UBA  HO    OXT  C     110.33  3.000
 UBA  HA    CA   CB    107.93  3.000
 UBA  HA    CA   N     108.53  3.000
 UBA  CB    CA   N     109.98  3.000
 UBA  HA    CA   C     106.77  3.000
 UBA  CB    CA   C     109.07  3.000
 UBA  N     CA   C     114.33  3.000
 UBA  HN2   N    HN1   106.71  3.000
 UBA  HN2   N    CA    110.82  3.000
 UBA  HN1   N    CA    110.60  3.000
 UBA  HB2   CB   HB1   107.49  3.000
 UBA  HB2   CB   N4    107.33  3.000
 UBA  HB1   CB   N4    109.06  3.000
 UBA  HB2   CB   CA    109.91  3.000
 UBA  HB1   CB   CA    111.54  3.000
 UBA  N4    CB   CA    111.34  3.000
 UBA  C3    N4   C5    121.64  3.000
 UBA  C3    N4   CB    119.82  3.000
 UBA  C5    N4   CB    118.28  3.000
 UBA  N6    C5   O8    122.08  3.000
 UBA  N6    C5   N4    115.68  3.000
 UBA  O8    C5   N4    122.25  3.000
 UBA  C17   N6   C1    118.05  3.000
 UBA  C17   N6   C5    116.74  3.000
 UBA  C1    N6   C5    125.17  3.000
 UBA  C2    C1   O7    124.02  3.000
 UBA  C2    C1   N6    115.68  3.000
 UBA  O7    C1   N6    120.31  3.000
 UBA  C3    C2   C6    123.04  3.000
 UBA  C3    C2   C1    118.25  3.000
 UBA  C6    C2   C1    118.71  3.000
 UBA  H63   C6   H62   107.81  3.000
 UBA  H63   C6   H61   107.89  3.000
 UBA  H62   C6   H61   107.22  3.000
 UBA  H63   C6   C2    110.70  3.000
 UBA  H62   C6   C2    111.57  3.000
 UBA  H61   C6   C2    111.47  3.000
 UBA  H3    C3   C2    121.44  3.000
 UBA  H3    C3   N4    115.11  3.000
 UBA  C2    C3   N4    123.44  3.000
 UBA  H172  C17  H171  106.50  3.000
 UBA  H172  C17  C18   110.48  3.000
 UBA  H171  C17  C18   110.40  3.000
 UBA  H172  C17  N6    108.70  3.000
 UBA  H171  C17  N6    108.06  3.000
 UBA  C18   C17  N6    112.49  3.000
 UBA  C19   C18  C23   111.30  3.000
 UBA  C19   C18  C17   124.37  3.000
 UBA  C23   C18  C17   124.32  3.000
 UBA  H23   C23  C22   122.35  3.000
 UBA  H23   C23  C18   124.68  3.000
 UBA  C22   C23  C18   112.97  3.000
 UBA  H22   C22  S20   120.45  3.000
 UBA  H22   C22  C23   127.23  3.000
 UBA  S20   C22  C23   112.32  3.000
 UBA  C19   S20  C22    91.45  3.000
 UBA  C10   C19  S20   120.81  3.000
 UBA  C10   C19  C18   127.24  3.000
 UBA  S20   C19  C18   111.95  3.000
 UBA  O1    C10  O2    123.82  3.000
 UBA  O1    C10  C19   124.26  3.000
 UBA  O2    C10  C19   111.92  3.000
 UBA  HO2   O2   C10   110.33  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
 UBA  CONST_01  C1   N6   C5   N4     0.00   0.0  0
 UBA  CONST_02  C1   C2   C3   N4     0.00   0.0  0
 UBA  CONST_03  C2   C3   N4   C5     0.00   0.0  0
 UBA  CONST_04  C2   C1   N6   C5     0.00   0.0  0
 UBA  CONST_05  C3   N4   C5   N6     0.00   0.0  0
 UBA  CONST_06  C3   C2   C1   N6     0.00   0.0  0
 UBA  CONST_07  S20  C22  C23  C18    0.00   0.0  0
 UBA  CONST_08  C22  S20  C19  C18    0.00   0.0  0
 UBA  CONST_09  S20  C19  C18  C23    0.00   0.0  0
 UBA  CONST_10  C19  S20  C22  C23    0.00   0.0  0
 UBA  CONST_11  C19  C18  C23  C22    0.00   0.0  0
 UBA  CONST_12  N6   C5   N4   CB   180.00   0.0  0
 UBA  CONST_13  C2   C3   N4   CB   180.00   0.0  0
 UBA  CONST_14  C17  N6   C5   N4   180.00   0.0  0
 UBA  CONST_15  C6   C2   C3   N4   180.00   0.0  0
 UBA  CONST_16  O7   C1   N6   C5   180.00   0.0  0
 UBA  CONST_17  C3   N4   C5   O8   180.00   0.0  0
 UBA  CONST_18  C1   N6   C5   O8   180.00   0.0  0
 UBA  CONST_19  C6   C2   C1   N6   180.00   0.0  0
 UBA  CONST_20  C3   C2   C1   O7   180.00   0.0  0
 UBA  CONST_21  C17  N6   C1   C2   180.00   0.0  0
 UBA  CONST_22  C22  C23  C18  C17  180.00   0.0  0
 UBA  CONST_23  S20  C19  C18  C17  180.00   0.0  0
 UBA  CONST_24  C10  C19  C18  C23  180.00   0.0  0
 UBA  CONST_25  C10  C19  S20  C22  180.00   0.0  0
 UBA  CONST_26  H3   C3   N4   C5   180.00   0.0  0
 UBA  CONST_27  H22  C22  C23  C18  180.00   0.0  0
 UBA  CONST_28  H23  C23  C22  S20  180.00   0.0  0
 UBA  CONST_29  O8   C5   N4   CB     0.00   0.0  0
 UBA  CONST_30  C17  N6   C5   O8     0.00   0.0  0
 UBA  CONST_31  C17  N6   C1   O7     0.00   0.0  0
 UBA  CONST_32  HO2  O2   C10  C19  180.00   0.0  0
 UBA  CONST_33  HO   OXT  C    O      0.00   0.0  0
 UBA  Var_01    C18  C17  N6   C5    87.03  30.0  2
 UBA  Var_02    C23  C18  C17  N6     2.52  30.0  2
 UBA  Var_03    C5   N4   CB   CA   -82.54  30.0  2
 UBA  Var_04    O2   C10  C19  C18  178.78  30.0  2
 UBA  Var_05    H61  C6   C2   C1   -58.19  30.0  2

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
 UBA  chir_01  CA  C  N  CB  negativ

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
 UBA  plan-1  C17  0.020
 UBA  plan-1  C18  0.020
 UBA  plan-1  C23  0.020
 UBA  plan-1  C22  0.020
 UBA  plan-1  S20  0.020
 UBA  plan-1  C19  0.020
 UBA  plan-1  C10  0.020
 UBA  plan-1  H23  0.020
 UBA  plan-1  H22  0.020
 UBA  plan-2  C19  0.020
 UBA  plan-2  C10  0.020
 UBA  plan-2  O2   0.020
 UBA  plan-2  O1   0.020
 UBA  plan-2  HO2  0.020
 UBA  plan-3  CB   0.020
 UBA  plan-3  N4   0.020
 UBA  plan-3  C5   0.020
 UBA  plan-3  O8   0.020
 UBA  plan-3  N6   0.020
 UBA  plan-3  C1   0.020
 UBA  plan-3  O7   0.020
 UBA  plan-3  C2   0.020
 UBA  plan-3  C6   0.020
 UBA  plan-3  C3   0.020
 UBA  plan-3  C17  0.020
 UBA  plan-3  H3   0.020
 UBA  plan-4  O    0.020
 UBA  plan-4  C    0.020
 UBA  plan-4  OXT  0.020
 UBA  plan-4  CA   0.020
 UBA  plan-4  HO   0.020

