# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:25:05 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  34  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_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   OC    -1  -0.597   6.0466   0.8675  -0.5225
 UBF  C22   C   C      0   0.403   4.9101   0.5090  -0.8859
 UBF  O24   O   O      0  -0.579   4.5513   0.1380  -2.0197
 UBF  C21   C   CR5    0  -0.396   3.8570   0.5300   0.1833
 UBF  S20   S   S2     0   0.212   4.3295   1.0249   1.7620
 UBF  C19   C   CR15   0  -0.469   2.7496   0.8072   2.3708
 UBF  C18   C   CR15   0  -0.213   1.8937   0.3729   1.4028
 UBF  C17   C   CR5    0   0.168   2.5248   0.2116   0.1361
 UBF  C16   C   CH2    0  -0.358   1.8247  -0.2595  -1.1091
 UBF  N3    N   NR6    0  -0.609   0.3929  -0.4611  -0.8981
 UBF  C4    C   CR6    0   0.774  -0.4168   0.6490  -1.0515
 UBF  O15   O   O      0  -0.465   0.0323   1.7414  -1.3220
 UBF  C2    C   CR6    0   0.626  -0.0336  -1.7314  -0.5173
 UBF  O14   O   O      0  -0.438   0.7540  -2.6386  -0.3463
 UBF  C1    C   CR6    0  -0.373  -1.4655  -1.8450  -0.3539
 UBF  BR13  BR  BR     0  -0.000  -2.1559  -3.5128   0.1221
 UBF  C6    C   CR16   0   0.092  -2.2609  -0.7755  -0.5346
 UBF  N5    N   NR6    0  -0.529  -1.7685   0.4406  -0.8777
 UBF  C7    C   CH2    0  -0.327  -2.6732   1.5880  -0.9782
 UBF  C8    C   CH1    0  -0.229  -2.7764   2.3820   0.3344
 UBF  N9    N   NH2    0  -0.785  -3.1655   1.6034   1.4882
 UBF  C10   C   C      0   0.411  -3.7550   3.5552   0.0704
 UBF  O11   O   OC    -1  -0.613  -3.3791   4.3749  -0.7908
 UBF  O12   O   O      0  -0.592  -4.8250   3.5649   0.7018
 UBF  H19   H   HCR5   0   0.290   2.5178   1.0046   3.4062
 UBF  H18   H   HCR5   0   0.244   0.8491   0.1756   1.6007
 UBF  H161  H   HCH2   0   0.280   1.9549   0.4536  -1.9172
 UBF  H162  H   HCH2   0   0.281   2.2463  -1.1995  -1.4538
 UBF  H6    H   HCR6   0   0.337  -3.3347  -0.8314  -0.4210
 UBF  H71   H   HCH2   0   0.274  -2.3332   2.2262  -1.7883
 UBF  H72   H   HCH2   0   0.268  -3.6507   1.1918  -1.2582
 UBF  H8    H   HCH1   0   0.239  -1.7906   2.8132   0.5371
 UBF  HN91  H   HNH2   0   0.336  -4.1016   1.2363   1.3768
 UBF  HN92  H   HNH2   0   0.338  -2.5427   0.8222   1.6461

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  1.707  0.020  1.707
 UBF  C19   C18   aromatic  1.363  0.020  1.363
 UBF  S20   C21   aromatic  1.721  0.020  1.721
 UBF  C18   C17   aromatic  1.424  0.020  1.424
 UBF  C17   C21   aromatic  1.371  0.020  1.371
 UBF  C17   C16   single    1.504  0.020  1.504
 UBF  C21   C22   single    1.501  0.020  1.501
 UBF  C7    N5    single    1.465  0.020  1.465
 UBF  C7    C8    single    1.538  0.020  1.538
 UBF  C6    N5    single    1.356  0.020  1.356
 UBF  C6    C1    double    1.345  0.020  1.345
 UBF  N5    C4    single    1.379  0.020  1.379
 UBF  BR13  C1    single    1.867  0.020  1.867
 UBF  C1    C2    single    1.446  0.020  1.446
 UBF  C4    O15   double    1.212  0.020  1.212
 UBF  C4    N3    single    1.383  0.020  1.383
 UBF  C2    N3    single    1.393  0.020  1.393
 UBF  C2    O14   double    1.214  0.020  1.214
 UBF  N3    C16   single    1.461  0.020  1.461
 UBF  O12   C10   deloc     1.242  0.020  1.242
 UBF  O24   C22   deloc     1.246  0.020  1.246
 UBF  C22   O23   deloc     1.246  0.020  1.246
 UBF  C10   C8    single    1.550  0.020  1.550
 UBF  C10   O11   deloc     1.247  0.020  1.247
 UBF  C8    N9    single    1.445  0.020  1.445
 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

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  C21   C22  O24   116.77  3.000
 UBF  O24   C22  O23   127.87  3.000
 UBF  C21   C22  O23   115.36  3.000
 UBF  C17   C21  S20   111.43  3.000
 UBF  C17   C21  C22   130.86  3.000
 UBF  S20   C21  C22   117.71  3.000
 UBF  C19   S20  C21    92.08  3.000
 UBF  H19   C19  C18   127.21  3.000
 UBF  H19   C19  S20   121.17  3.000
 UBF  C18   C19  S20   111.62  3.000
 UBF  H18   C18  C17   124.76  3.000
 UBF  H18   C18  C19   122.32  3.000
 UBF  C17   C18  C19   112.92  3.000
 UBF  C16   C17  C18   124.43  3.000
 UBF  C16   C17  C21   123.62  3.000
 UBF  C18   C17  C21   111.95  3.000
 UBF  H162  C16  H161  106.59  3.000
 UBF  H162  C16  N3    107.86  3.000
 UBF  H161  C16  N3    108.40  3.000
 UBF  H162  C16  C17   110.67  3.000
 UBF  H161  C16  C17   110.78  3.000
 UBF  N3    C16  C17   112.32  3.000
 UBF  C2    N3   C4    125.67  3.000
 UBF  C2    N3   C16   117.73  3.000
 UBF  C4    N3   C16   116.55  3.000
 UBF  N5    C4   O15   121.86  3.000
 UBF  O15   C4   N3    122.11  3.000
 UBF  N5    C4   N3    116.03  3.000
 UBF  C1    C2   O14   124.62  3.000
 UBF  O14   C2   N3    121.43  3.000
 UBF  C1    C2   N3    113.94  3.000
 UBF  C6    C1   BR13  121.73  3.000
 UBF  BR13  C1   C2    117.73  3.000
 UBF  C6    C1   C2    120.54  3.000
 UBF  H6    C6   N5    115.69  3.000
 UBF  H6    C6   C1    122.15  3.000
 UBF  N5    C6   C1    122.16  3.000
 UBF  C7    N5   C6    119.71  3.000
 UBF  C6    N5   C4    121.57  3.000
 UBF  C7    N5   C4    118.59  3.000
 UBF  H72   C7   H71   107.60  3.000
 UBF  H72   C7   C8    110.27  3.000
 UBF  H71   C7   C8    110.76  3.000
 UBF  H72   C7   N5    106.65  3.000
 UBF  H71   C7   N5    108.55  3.000
 UBF  C8    C7   N5    112.80  3.000
 UBF  H8    C8   C10   107.57  3.000
 UBF  H8    C8   N9    107.86  3.000
 UBF  C10   C8   N9    111.94  3.000
 UBF  H8    C8   C7    107.51  3.000
 UBF  N9    C8   C7    114.92  3.000
 UBF  C10   C8   C7    106.73  3.000
 UBF  HN92  N9   HN91  107.86  3.000
 UBF  HN92  N9   C8    112.02  3.000
 UBF  HN91  N9   C8    110.89  3.000
 UBF  O12   C10  O11   127.26  3.000
 UBF  O11   C10  C8    115.13  3.000
 UBF  O12   C10  C8    117.58  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  Var_01    N3   C16  C17  C21  -176.97  30.0  2
 UBF  Var_02    C4   N3   C16  C17    86.06  30.0  1
 UBF  Var_03    S20  C21  C22  O23    -0.46  30.0  3
 UBF  Var_04    C8   C7   N5   C4    -83.62  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-4  C8    0.020
 UBF  plan-4  C10   0.020
 UBF  plan-4  O11   0.020
 UBF  plan-4  O12   0.020

