# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 02:08:34 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)-4,5-dibromothiophene-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(Cc2c(Br)c(Br)sc2C(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
 UB1  UB1  '3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)-4,5-dibromothiophene-2-carboxylic acid'  ligand  39  26  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UB1
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
 UB1  O23   O   O     0  -0.420  -2.4920  -2.6564   2.3929
 UB1  C22   C   C     0   0.542  -2.7153  -1.4720   2.4008
 UB1  O24   O   OH1   0  -0.601  -3.2204  -0.8208   3.4410
 UB1  C21   C   CR5   0  -0.414  -2.4889  -0.5522   1.2782
 UB1  S20   S   S2    0   0.364  -3.0202   1.0787   1.4423
 UB1  C19   C   CR5   0  -0.355  -2.4131   1.4702  -0.0996
 UB1  BR26  BR  BR    0   0.075  -2.5995   3.1779  -0.7762
 UB1  C18   C   CR5   0  -0.022  -1.8297   0.3966  -0.7102
 UB1  BR25  BR  BR    0   0.028  -1.1064   0.4922  -2.4225
 UB1  C17   C   CR5   0   0.306  -1.8583  -0.7850   0.0831
 UB1  C16   C   CH2   0  -0.416  -1.2850  -2.0979  -0.3655
 UB1  N3    N   NR6   0  -0.605   0.1423  -2.0150  -0.6650
 UB1  C2    C   CR6   0   0.603   0.5932  -2.4142  -1.9276
 UB1  O14   O   O     0  -0.458  -0.1801  -2.8649  -2.7527
 UB1  C1    C   CR6   0  -0.188   2.0085  -2.2418  -2.1659
 UB1  C13   C   CH3   0  -0.707   2.5510  -2.5820  -3.5159
 UB1  C6    C   CR16  0   0.069   2.7765  -1.7926  -1.1591
 UB1  C4    C   CR6   0   0.788   0.9577  -1.6246   0.3786
 UB1  O15   O   O     0  -0.474   0.5127  -1.3835   1.4822
 UB1  N5    N   NR6   0  -0.529   2.2938  -1.5203   0.0870
 UB1  C7    C   CH2   0  -0.330   3.1841  -1.0119   1.1154
 UB1  C8    C   CH1   0  -0.219   3.2136   0.5247   1.1116
 UB1  N9    N   NH2   0  -0.771   3.6478   1.0016  -0.1728
 UB1  C10   C   C     0   0.528   4.0668   1.0080   2.2795
 UB1  O11   O   O     0  -0.430   5.1166   1.5856   2.1601
 UB1  O12   O   OH1   0  -0.590   3.5191   0.7077   3.4493
 UB1  HO24  H   HOH1  0   0.498  -3.3961  -1.4309   4.1734
 UB1  H161  H   HCH2  0   0.309  -1.4588  -2.8654   0.3817
 UB1  H162  H   HCH2  0   0.307  -1.7865  -2.4133  -1.2784
 UB1  H131  H   HCH3  0   0.245   2.4011  -3.6364  -3.7522
 UB1  H132  H   HCH3  0   0.244   2.0636  -2.0024  -4.3008
 UB1  H133  H   HCH3  0   0.246   3.6195  -2.3781  -3.5659
 UB1  H6    H   HCR6  0   0.305   3.8412  -1.6520  -1.2797
 UB1  H71   H   HCH2  0   0.294   2.8708  -1.4030   2.0796
 UB1  H72   H   HCH2  0   0.285   4.1816  -1.4033   0.9124
 UB1  H8    H   HCH1  0   0.292   2.1946   0.8814   1.2909
 UB1  HN91  H   HNH2  0   0.365   3.4580   1.9898  -0.2692
 UB1  HN92  H   HNH2  0   0.351   4.6482   0.8854  -0.2781
 UB1  HO12  H   HOH1  0   0.485   4.0941   0.9962   4.1744

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
 UB1  N9   C8    single    1.437  0.020  1.437
 UB1  O11  C10   double    1.204  0.020  1.204
 UB1  C8   C10   single    1.525  0.020  1.525
 UB1  C8   C7    single    1.537  0.020  1.537
 UB1  C10  O12   single    1.326  0.020  1.326
 UB1  O23  C22   double    1.205  0.020  1.205
 UB1  C13  C1    single    1.494  0.020  1.494
 UB1  O14  C2    double    1.217  0.020  1.217
 UB1  C1   C2    single    1.446  0.020  1.446
 UB1  C1   C6    double    1.344  0.020  1.344
 UB1  C2   N3    single    1.399  0.020  1.399
 UB1  C6   N5    single    1.364  0.020  1.364
 UB1  C16  N3    single    1.461  0.020  1.461
 UB1  C16  C17   single    1.501  0.020  1.501
 UB1  N3   C4    single    1.381  0.020  1.381
 UB1  C22  O24   single    1.327  0.020  1.327
 UB1  C22  C21   single    1.469  0.020  1.469
 UB1  N5   C4    single    1.371  0.020  1.371
 UB1  N5   C7    single    1.452  0.020  1.452
 UB1  C4   O15   double    1.214  0.020  1.214
 UB1  C17  C21   aromatic  1.371  0.020  1.371
 UB1  C17  C18   aromatic  1.423  0.020  1.423
 UB1  C21  S20   aromatic  1.723  0.020  1.723
 UB1  C18  BR25  single    1.861  0.020  1.861
 UB1  C18  C19   aromatic  1.366  0.020  1.366
 UB1  S20  C19   aromatic  1.703  0.020  1.703
 UB1  C19  BR26  single    1.846  0.020  1.846
 UB1  O24  HO24  single    0.850  0.020  0.980
 UB1  C16  H161  single    0.970  0.020  1.090
 UB1  C16  H162  single    0.970  0.020  1.090
 UB1  C13  H131  single    0.970  0.020  1.090
 UB1  C13  H132  single    0.970  0.020  1.090
 UB1  C13  H133  single    0.970  0.020  1.090
 UB1  C6   H6    single    0.930  0.020  1.080
 UB1  C7   H71   single    0.970  0.020  1.090
 UB1  C7   H72   single    0.970  0.020  1.090
 UB1  C8   H8    single    0.970  0.020  1.090
 UB1  N9   HN91  single    0.890  0.020  1.040
 UB1  N9   HN92  single    0.890  0.020  1.040
 UB1  O12  HO12  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
 UB1  C21   C22  O24   110.51  3.000
 UB1  C21   C22  O23   125.57  3.000
 UB1  O24   C22  O23   123.91  3.000
 UB1  HO24  O24  C22   110.64  3.000
 UB1  C17   C21  S20   112.68  3.000
 UB1  S20   C21  C22   118.19  3.000
 UB1  C17   C21  C22   129.10  3.000
 UB1  C19   S20  C21    91.22  3.000
 UB1  C18   C19  BR26  127.33  3.000
 UB1  BR26  C19  S20   120.56  3.000
 UB1  C18   C19  S20   112.11  3.000
 UB1  C17   C18  BR25  124.27  3.000
 UB1  BR25  C18  C19   122.47  3.000
 UB1  C17   C18  C19   113.25  3.000
 UB1  C16   C17  C18   123.49  3.000
 UB1  C18   C17  C21   110.73  3.000
 UB1  C16   C17  C21   125.77  3.000
 UB1  H162  C16  H161  107.39  3.000
 UB1  H162  C16  N3    107.14  3.000
 UB1  H161  C16  N3    109.74  3.000
 UB1  H162  C16  C17   109.15  3.000
 UB1  H161  C16  C17   110.59  3.000
 UB1  N3    C16  C17   112.63  3.000
 UB1  C4    N3   C2    124.92  3.000
 UB1  C4    N3   C16   115.99  3.000
 UB1  C2    N3   C16   118.94  3.000
 UB1  C1    C2   O14   123.66  3.000
 UB1  C1    C2   N3    115.49  3.000
 UB1  O14   C2   N3    120.84  3.000
 UB1  C6    C1   C13   123.07  3.000
 UB1  C6    C1   C2    118.42  3.000
 UB1  C13   C1   C2    118.51  3.000
 UB1  H133  C13  H132  107.82  3.000
 UB1  H133  C13  H131  107.81  3.000
 UB1  H132  C13  H131  107.24  3.000
 UB1  H133  C13  C1    110.80  3.000
 UB1  H132  C13  C1    111.53  3.000
 UB1  H131  C13  C1    111.46  3.000
 UB1  H6    C6   N5    115.13  3.000
 UB1  H6    C6   C1    121.54  3.000
 UB1  N5    C6   C1    123.31  3.000
 UB1  N5    C4   O15   122.36  3.000
 UB1  O15   C4   N3    121.78  3.000
 UB1  N5    C4   N3    115.86  3.000
 UB1  C7    N5   C4    118.25  3.000
 UB1  C7    N5   C6    120.00  3.000
 UB1  C4    N5   C6    121.59  3.000
 UB1  H72   C7   H71   107.44  3.000
 UB1  H72   C7   C8    109.92  3.000
 UB1  H71   C7   C8    111.57  3.000
 UB1  H72   C7   N5    107.65  3.000
 UB1  H71   C7   N5    109.00  3.000
 UB1  C8    C7   N5    111.10  3.000
 UB1  H8    C8   C10   106.99  3.000
 UB1  H8    C8   N9    108.64  3.000
 UB1  C10   C8   N9    114.22  3.000
 UB1  H8    C8   C7    107.91  3.000
 UB1  C10   C8   C7    109.00  3.000
 UB1  N9    C8   C7    109.87  3.000
 UB1  HN92  N9   HN91  106.72  3.000
 UB1  HN92  N9   C8    110.69  3.000
 UB1  HN91  N9   C8    110.66  3.000
 UB1  O12   C10  O11   123.79  3.000
 UB1  O12   C10  C8    111.88  3.000
 UB1  O11   C10  C8    124.33  3.000
 UB1  HO12  O12  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
 UB1  CONST_01  C19   C18  C17  C21      0.00   0.0  0
 UB1  CONST_02  C18   C19  S20  C21      0.00   0.0  0
 UB1  CONST_03  C18   C17  C21  S20      0.00   0.0  0
 UB1  CONST_04  C17   C18  C19  S20      0.00   0.0  0
 UB1  CONST_05  C17   C21  S20  C19      0.00   0.0  0
 UB1  CONST_06  C6    N5   C4   N3       0.00   0.0  0
 UB1  CONST_07  N5    C4   N3   C2       0.00   0.0  0
 UB1  CONST_08  C4    N3   C2   C1       0.00   0.0  0
 UB1  CONST_09  C18   C17  C21  C22    180.00   0.0  0
 UB1  CONST_10  C19   S20  C21  C22    180.00   0.0  0
 UB1  CONST_11  BR25  C18  C17  C21    180.00   0.0  0
 UB1  CONST_12  BR26  C19  S20  C21    180.00   0.0  0
 UB1  CONST_13  C16   C17  C21  S20    180.00   0.0  0
 UB1  CONST_14  BR25  C18  C19  S20    180.00   0.0  0
 UB1  CONST_15  C16   C17  C18  C19    180.00   0.0  0
 UB1  CONST_16  C17   C18  C19  BR26   180.00   0.0  0
 UB1  CONST_17  C1    C2   N3   C16    180.00   0.0  0
 UB1  CONST_18  N5    C4   N3   C16    180.00   0.0  0
 UB1  CONST_19  C7    N5   C4   N3     180.00   0.0  0
 UB1  CONST_20  O15   C4   N3   C2     180.00   0.0  0
 UB1  CONST_21  C4    N3   C2   O14    180.00   0.0  0
 UB1  CONST_22  O15   C4   N5   C6     180.00   0.0  0
 UB1  CONST_23  O14   C2   N3   C16      0.00   0.0  0
 UB1  CONST_24  O15   C4   N3   C16      0.00   0.0  0
 UB1  CONST_25  C7    N5   C4   O15      0.00   0.0  0
 UB1  CONST_26  HO24  O24  C22  C21    180.00   0.0  0
 UB1  CONST_27  HO12  O12  C10  C8     180.00   0.0  0
 UB1  Var_01    N3    C16  C17  C21   -121.70  30.0  2
 UB1  Var_02    C2    N3   C16  C17   -124.38  30.0  3
 UB1  Var_03    C17   C21  C22  O23     -8.23  30.0  2
 UB1  Var_04    C8    C7   N5   C6      90.75  30.0  3
 UB1  Var_05    H131  C13  C1   C2     -61.62  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
 UB1  chir_01  C8  N9  C10  C7  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
 UB1  plan-1  C22   0.020
 UB1  plan-1  C21   0.020
 UB1  plan-1  S20   0.020
 UB1  plan-1  C19   0.020
 UB1  plan-1  BR26  0.020
 UB1  plan-1  C18   0.020
 UB1  plan-1  BR25  0.020
 UB1  plan-1  C17   0.020
 UB1  plan-1  C16   0.020
 UB1  plan-2  C16   0.020
 UB1  plan-2  N3    0.020
 UB1  plan-2  C2    0.020
 UB1  plan-2  O14   0.020
 UB1  plan-2  C1    0.020
 UB1  plan-2  C13   0.020
 UB1  plan-2  C6    0.020
 UB1  plan-2  C4    0.020
 UB1  plan-2  O15   0.020
 UB1  plan-2  N5    0.020
 UB1  plan-2  C7    0.020
 UB1  plan-2  H6    0.020
 UB1  plan-3  O23   0.020
 UB1  plan-3  C22   0.020
 UB1  plan-3  O24   0.020
 UB1  plan-3  C21   0.020
 UB1  plan-3  HO24  0.020
 UB1  plan-4  C8    0.020
 UB1  plan-4  C10   0.020
 UB1  plan-4  O11   0.020
 UB1  plan-4  O12   0.020
 UB1  plan-4  HO12  0.020

