# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 03:27:36 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-({3-[(2S)-2-amino-2-carboxyethyl]-5-bromo-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: N[C@@H](CN1C=C(Br)C(=O)N(Cc2ccsc2C(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
 UBF  UBF  '3-({3-[(2S)-2-amino-2-carboxyethyl]-5-bromo-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)thiophene-2-carboxylic acid'  ligand  36  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UBF
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
 UBF  O23   O   OH1   0  -0.601   6.0144   0.9546  -0.5405
 UBF  C22   C   C     0   0.525   4.8093   0.5523  -0.9245
 UBF  O24   O   O     0  -0.437   4.5426   0.1981  -2.0496
 UBF  C21   C   CR5   0  -0.385   3.8492   0.5859   0.1734
 UBF  S20   S   S2    0   0.288   4.3282   1.0807   1.7521
 UBF  C19   C   CR15  0  -0.442   2.7599   0.8311   2.3539
 UBF  C18   C   CR15  0  -0.206   1.9002   0.3878   1.3914
 UBF  C17   C   CR5   0   0.214   2.5171   0.2436   0.1241
 UBF  C16   C   CH2   0  -0.374   1.8137  -0.2326  -1.1151
 UBF  N3    N   NR6   0  -0.613   0.3882  -0.4462  -0.8977
 UBF  C4    C   CR6   0   0.782  -0.4256   0.6637  -1.0232
 UBF  O15   O   O     0  -0.459   0.0185   1.7668  -1.2514
 UBF  C2    C   CR6   0   0.632  -0.0325  -1.7298  -0.5475
 UBF  O14   O   O     0  -0.428   0.7610  -2.6322  -0.3937
 UBF  C1    C   CR6   0  -0.369  -1.4659  -1.8555  -0.3943
 UBF  BR13  BR  BR    0   0.012  -2.1458  -3.5377   0.0381
 UBF  C6    C   CR16  0   0.100  -2.2666  -0.7888  -0.5558
 UBF  N5    N   NR6   0  -0.534  -1.7771   0.4405  -0.8667
 UBF  C7    C   CH2   0  -0.340  -2.6807   1.5809  -0.9694
 UBF  C8    C   CH1   0  -0.233  -2.7619   2.3534   0.3653
 UBF  N9    N   NH2   0  -0.778  -3.1753   1.5754   1.5020
 UBF  C10   C   C     0   0.555  -3.6997   3.5349   0.1845
 UBF  O11   O   OH1   0  -0.591  -3.2479   4.3744  -0.7372
 UBF  O12   O   O     0  -0.424  -4.7289   3.6895   0.7863
 UBF  HO23  H   HOH1  0   0.493   6.6365   0.9146  -1.2824
 UBF  H19   H   HCR5  0   0.313   2.5357   1.0195   3.3926
 UBF  H18   H   HCR5  0   0.261   0.8631   0.1704   1.6005
 UBF  H161  H   HCH2  0   0.298   1.9351   0.4818  -1.9252
 UBF  H162  H   HCH2  0   0.301   2.2440  -1.1710  -1.4564
 UBF  H6    H   HCR6  0   0.341  -3.3405  -0.8551  -0.4521
 UBF  H71   H   HCH2  0   0.297  -2.3462   2.2154  -1.7859
 UBF  H72   H   HCH2  0   0.295  -3.6638   1.1931  -1.2379
 UBF  H8    H   HCH1  0   0.300  -1.7705   2.7661   0.5776
 UBF  HN91  H   HNH2  0   0.355  -4.0461   1.0885   1.3327
 UBF  HN92  H   HNH2  0   0.362  -2.4779   0.8885   1.7521
 UBF  HO11  H   HOH1  0   0.487  -3.8709   5.1069  -0.8587

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
 UBF  C19   S20   aromatic  1.698  0.020  1.698
 UBF  C19   C18   aromatic  1.365  0.020  1.365
 UBF  S20   C21   aromatic  1.722  0.020  1.722
 UBF  C18   C17   aromatic  1.417  0.020  1.417
 UBF  C17   C21   aromatic  1.376  0.020  1.376
 UBF  C17   C16   single    1.502  0.020  1.502
 UBF  C21   C22   single    1.459  0.020  1.459
 UBF  C7    N5    single    1.459  0.020  1.459
 UBF  C7    C8    single    1.544  0.020  1.544
 UBF  C6    N5    single    1.359  0.020  1.359
 UBF  C6    C1    double    1.344  0.020  1.344
 UBF  N5    C4    single    1.379  0.020  1.379
 UBF  BR13  C1    single    1.865  0.020  1.865
 UBF  C1    C2    single    1.447  0.020  1.447
 UBF  C4    O15   double    1.211  0.020  1.211
 UBF  C4    N3    single    1.382  0.020  1.382
 UBF  C2    N3    single    1.395  0.020  1.395
 UBF  C2    O14   double    1.211  0.020  1.211
 UBF  N3    C16   single    1.458  0.020  1.458
 UBF  O12   C10   double    1.202  0.020  1.202
 UBF  O24   C22   double    1.209  0.020  1.209
 UBF  C22   O23   single    1.327  0.020  1.327
 UBF  C10   C8    single    1.519  0.020  1.519
 UBF  C10   O11   single    1.326  0.020  1.326
 UBF  C8    N9    single    1.438  0.020  1.438
 UBF  O23   HO23  single    0.850  0.020  0.980
 UBF  C19   H19   single    0.930  0.020  1.080
 UBF  C18   H18   single    0.930  0.020  1.080
 UBF  C16   H161  single    0.970  0.020  1.090
 UBF  C16   H162  single    0.970  0.020  1.090
 UBF  C6    H6    single    0.930  0.020  1.080
 UBF  C7    H71   single    0.970  0.020  1.090
 UBF  C7    H72   single    0.970  0.020  1.090
 UBF  C8    H8    single    0.970  0.020  1.090
 UBF  N9    HN91  single    0.890  0.020  1.040
 UBF  N9    HN92  single    0.890  0.020  1.040
 UBF  O11   HO11  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
 UBF  HO23  O23  C22   110.42  3.000
 UBF  C21   C22  O24   124.18  3.000
 UBF  O24   C22  O23   123.93  3.000
 UBF  C21   C22  O23   111.89  3.000
 UBF  C17   C21  S20   111.93  3.000
 UBF  C17   C21  C22   127.18  3.000
 UBF  S20   C21  C22   120.89  3.000
 UBF  C19   S20  C21    91.48  3.000
 UBF  H19   C19  C18   127.21  3.000
 UBF  H19   C19  S20   120.49  3.000
 UBF  C18   C19  S20   112.31  3.000
 UBF  H18   C18  C17   124.81  3.000
 UBF  H18   C18  C19   122.26  3.000
 UBF  C17   C18  C19   112.93  3.000
 UBF  C16   C17  C18   124.48  3.000
 UBF  C16   C17  C21   124.17  3.000
 UBF  C18   C17  C21   111.35  3.000
 UBF  H162  C16  H161  106.80  3.000
 UBF  H162  C16  N3    107.91  3.000
 UBF  H161  C16  N3    108.46  3.000
 UBF  H162  C16  C17   110.31  3.000
 UBF  H161  C16  C17   110.74  3.000
 UBF  N3    C16  C17   112.41  3.000
 UBF  C2    N3   C4    125.74  3.000
 UBF  C2    N3   C16   117.84  3.000
 UBF  C4    N3   C16   116.40  3.000
 UBF  N5    C4   O15   121.89  3.000
 UBF  O15   C4   N3    122.20  3.000
 UBF  N5    C4   N3    115.91  3.000
 UBF  C1    C2   O14   124.79  3.000
 UBF  O14   C2   N3    121.31  3.000
 UBF  C1    C2   N3    113.90  3.000
 UBF  C6    C1   BR13  121.79  3.000
 UBF  BR13  C1   C2    117.64  3.000
 UBF  C6    C1   C2    120.57  3.000
 UBF  H6    C6   N5    115.80  3.000
 UBF  H6    C6   C1    122.13  3.000
 UBF  N5    C6   C1    122.07  3.000
 UBF  C7    N5   C6    120.01  3.000
 UBF  C6    N5   C4    121.69  3.000
 UBF  C7    N5   C4    118.21  3.000
 UBF  H72   C7   H71   107.47  3.000
 UBF  H72   C7   C8    110.08  3.000
 UBF  H71   C7   C8    111.92  3.000
 UBF  H72   C7   N5    107.33  3.000
 UBF  H71   C7   N5    108.59  3.000
 UBF  C8    C7   N5    111.27  3.000
 UBF  H8    C8   C10   106.80  3.000
 UBF  H8    C8   N9    108.12  3.000
 UBF  C10   C8   N9    109.71  3.000
 UBF  H8    C8   C7    107.98  3.000
 UBF  N9    C8   C7    115.32  3.000
 UBF  C10   C8   C7    108.58  3.000
 UBF  HN92  N9   HN91  107.96  3.000
 UBF  HN92  N9   C8    111.41  3.000
 UBF  HN91  N9   C8    112.05  3.000
 UBF  O12   C10  O11   123.93  3.000
 UBF  O11   C10  C8    111.39  3.000
 UBF  O12   C10  C8    124.67  3.000
 UBF  HO11  O11  C10   110.28  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
 UBF  CONST_01  C18   C19  S20  C21     0.00   0.0  0
 UBF  CONST_02  C19   C18  C17  C21     0.00   0.0  0
 UBF  CONST_03  C17   C18  C19  S20     0.00   0.0  0
 UBF  CONST_04  C18   C17  C21  S20     0.00   0.0  0
 UBF  CONST_05  C17   C21  S20  C19     0.00   0.0  0
 UBF  CONST_06  C6    N5   C4   N3      0.00   0.0  0
 UBF  CONST_07  N5    C4   N3   C2      0.00   0.0  0
 UBF  CONST_08  C19   S20  C21  C22   180.00   0.0  0
 UBF  CONST_09  C18   C17  C21  C22   180.00   0.0  0
 UBF  CONST_10  C16   C17  C21  S20   180.00   0.0  0
 UBF  CONST_11  C16   C17  C18  C19   180.00   0.0  0
 UBF  CONST_12  N5    C4   N3   C16   180.00   0.0  0
 UBF  CONST_13  C7    N5   C4   N3    180.00   0.0  0
 UBF  CONST_14  C6    N5   C4   O15   180.00   0.0  0
 UBF  CONST_15  C2    N3   C4   O15   180.00   0.0  0
 UBF  CONST_16  H19   C19  S20  C21   180.00   0.0  0
 UBF  CONST_17  H18   C18  C17  C21   180.00   0.0  0
 UBF  CONST_18  O15   C4   N3   C16     0.00   0.0  0
 UBF  CONST_19  C7    N5   C4   O15     0.00   0.0  0
 UBF  CONST_20  HO23  O23  C22  C21   180.00   0.0  0
 UBF  CONST_21  HO11  O11  C10  C8    180.00   0.0  0
 UBF  Var_01    N3    C16  C17  C21  -176.51  30.0  2
 UBF  Var_02    C4    N3   C16  C17    84.91  30.0  2
 UBF  Var_03    S20   C21  C22  O23    -0.90  30.0  2
 UBF  Var_04    C8    C7   N5   C4    -82.80  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
 UBF  chir_01  C8  C7  C10  N9  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
 UBF  plan-1  C22   0.020
 UBF  plan-1  C21   0.020
 UBF  plan-1  S20   0.020
 UBF  plan-1  C19   0.020
 UBF  plan-1  C18   0.020
 UBF  plan-1  C17   0.020
 UBF  plan-1  C16   0.020
 UBF  plan-1  H19   0.020
 UBF  plan-1  H18   0.020
 UBF  plan-2  C16   0.020
 UBF  plan-2  N3    0.020
 UBF  plan-2  C4    0.020
 UBF  plan-2  O15   0.020
 UBF  plan-2  C2    0.020
 UBF  plan-2  O14   0.020
 UBF  plan-2  C1    0.020
 UBF  plan-2  BR13  0.020
 UBF  plan-2  C6    0.020
 UBF  plan-2  N5    0.020
 UBF  plan-2  C7    0.020
 UBF  plan-2  H6    0.020
 UBF  plan-3  O23   0.020
 UBF  plan-3  C22   0.020
 UBF  plan-3  O24   0.020
 UBF  plan-3  C21   0.020
 UBF  plan-3  HO23  0.020
 UBF  plan-4  C8    0.020
 UBF  plan-4  C10   0.020
 UBF  plan-4  O11   0.020
 UBF  plan-4  O12   0.020
 UBF  plan-4  HO11  0.020

