# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 20:59:15 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)-5-phenylthiophene-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(Cc2cc(sc2C(O)=O)c3ccccc3)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
 UBE  UBE  '3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)-5-phenylthiophene-2-carboxylic acid'  ligand  47  30  .  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_UBE
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
 UBE  O24   O  O      0  -0.577  -3.2346  -3.4448  -1.2708
 UBE  C22   C  C      0   0.403  -3.7501  -2.3117  -1.2903
 UBE  O23   O  OC    -1  -0.597  -4.8664  -1.9840  -1.7369
 UBE  C21   C  CR5    0  -0.420  -2.9448  -1.1897  -0.7043
 UBE  S20   S  S2     0   0.224  -3.6542   0.3756  -0.7154
 UBE  C19   C  CR5    0  -0.204  -2.2863   1.0812   0.0536
 UBE  C25   C  CR6    0   0.145  -2.2261   2.5077   0.3679
 UBE  C30   C  CR16   0  -0.321  -2.9545   3.4450  -0.3696
 UBE  C29   C  CR16   0  -0.236  -2.8896   4.7954  -0.0619
 UBE  C28   C  CR16   0  -0.268  -2.0897   5.2388   0.9828
 UBE  C27   C  CR16   0  -0.234  -1.3580   4.3166   1.7206
 UBE  C26   C  CR16   0  -0.326  -1.4284   2.9654   1.4207
 UBE  C18   C  CR15   0  -0.270  -1.3357   0.1269   0.3055
 UBE  C17   C  CR5    0   0.214  -1.7014  -1.1743  -0.1278
 UBE  C16   C  CH2    0  -0.357  -0.8322  -2.3923   0.0306
 UBE  N3    N  NR6    0  -0.606   0.4823  -2.0640   0.5698
 UBE  C4    C  CR6    0   0.741   1.4354  -1.6450  -0.3426
 UBE  O15   O  O      0  -0.478   1.1878  -1.5626  -1.5293
 UBE  C2    C  CR6    0   0.582   0.6630  -2.1348   1.9503
 UBE  O14   O  O      0  -0.458  -0.2586  -2.4507   2.6824
 UBE  C1    C  CR6    0  -0.172   1.9887  -1.8064   2.4272
 UBE  C13   C  CH3    0  -0.708   2.2704  -1.8944   3.8917
 UBE  C6    C  CR16   0   0.048   2.9049  -1.4193   1.5248
 UBE  N5    N  NR6    0  -0.533   2.6619  -1.3318   0.1847
 UBE  C7    C  CH2    0  -0.339   3.7222  -0.8167  -0.6815
 UBE  C8    C  CH1    0  -0.226   3.8649   0.7134  -0.5942
 UBE  N9    N  NH2    0  -0.779   2.6584   1.4630  -0.8658
 UBE  C10   C  C      0   0.412   5.0181   1.1057  -1.5499
 UBE  O11   O  O      0  -0.593   4.7244   1.7487  -2.5722
 UBE  O12   O  OC    -1  -0.616   6.1481   0.6972  -1.2147
 UBE  H30   H  HCR6   0   0.253  -3.5673   3.1240  -1.2036
 UBE  H29   H  HCR6   0   0.260  -3.4633   5.5028  -0.6463
 UBE  H28   H  HCR6   0   0.259  -2.0377   6.2929   1.2218
 UBE  H27   H  HCR6   0   0.260  -0.7373   4.6491   2.5427
 UBE  H26   H  HCR6   0   0.252  -0.8691   2.2606   2.0231
 UBE  H18   H  HCR5   0   0.231  -0.3901   0.3666   0.7720
 UBE  H161  H  HCH2   0   0.279  -1.3002  -3.1051   0.7041
 UBE  H162  H  HCH2   0   0.278  -0.7061  -2.8986  -0.9213
 UBE  H131  H  HCH3   0   0.246   1.6177  -1.2331   4.4629
 UBE  H132  H  HCH3   0   0.246   2.1149  -2.9064   4.2673
 UBE  H133  H  HCH3   0   0.246   3.2999  -1.6113   4.1048
 UBE  H6    H  HCR6   0   0.311   3.9095  -1.1494   1.8236
 UBE  H71   H  HCH2   0   0.266   4.6531  -1.2977  -0.3835
 UBE  H72   H  HCH2   0   0.272   3.5030  -1.1241  -1.7016
 UBE  H8    H  HCH1   0   0.231   4.1832   0.9559   0.4268
 UBE  HN91  H  HNH2   0   0.335   2.3591   1.3119  -1.8201
 UBE  HN92  H  HNH2   0   0.326   1.9015   1.1647  -0.2637

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
 UBE  N9   C8    single    1.446  0.020  1.446
 UBE  O11  C10   deloc     1.243  0.020  1.243
 UBE  O24  C22   deloc     1.245  0.020  1.245
 UBE  C10  C8    single    1.548  0.020  1.548
 UBE  C10  O12   deloc     1.247  0.020  1.247
 UBE  C8   C7    single    1.539  0.020  1.539
 UBE  C22  O23   deloc     1.246  0.020  1.246
 UBE  C22  C21   single    1.500  0.020  1.500
 UBE  C16  N3    single    1.458  0.020  1.458
 UBE  C16  C17   single    1.505  0.020  1.505
 UBE  O14  C2    double    1.219  0.020  1.219
 UBE  N3   C2    single    1.394  0.020  1.394
 UBE  N3   C4    single    1.384  0.020  1.384
 UBE  C2   C1    single    1.447  0.020  1.447
 UBE  O15  C4    double    1.215  0.020  1.215
 UBE  C4   N5    single    1.371  0.020  1.371
 UBE  C1   C13   single    1.494  0.020  1.494
 UBE  C1   C6    double    1.343  0.020  1.343
 UBE  N5   C6    single    1.365  0.020  1.365
 UBE  N5   C7    single    1.463  0.020  1.463
 UBE  C21  C17   aromatic  1.371  0.020  1.371
 UBE  C21  S20   aromatic  1.719  0.020  1.719
 UBE  C17  C18   aromatic  1.419  0.020  1.419
 UBE  C18  C19   aromatic  1.370  0.020  1.370
 UBE  S20  C19   aromatic  1.721  0.020  1.721
 UBE  C19  C25   single    1.462  0.020  1.462
 UBE  C25  C30   aromatic  1.397  0.020  1.397
 UBE  C25  C26   aromatic  1.398  0.020  1.398
 UBE  C30  C29   aromatic  1.387  0.020  1.387
 UBE  C26  C27   aromatic  1.386  0.020  1.386
 UBE  C29  C28   aromatic  1.389  0.020  1.389
 UBE  C27  C28   aromatic  1.389  0.020  1.389
 UBE  C30  H30   single    0.930  0.020  1.080
 UBE  C29  H29   single    0.930  0.020  1.080
 UBE  C28  H28   single    0.930  0.020  1.080
 UBE  C27  H27   single    0.930  0.020  1.080
 UBE  C26  H26   single    0.930  0.020  1.080
 UBE  C18  H18   single    0.930  0.020  1.080
 UBE  C16  H161  single    0.970  0.020  1.090
 UBE  C16  H162  single    0.970  0.020  1.090
 UBE  C13  H131  single    0.970  0.020  1.090
 UBE  C13  H132  single    0.970  0.020  1.090
 UBE  C13  H133  single    0.970  0.020  1.090
 UBE  C6   H6    single    0.930  0.020  1.080
 UBE  C7   H71   single    0.970  0.020  1.090
 UBE  C7   H72   single    0.970  0.020  1.090
 UBE  C8   H8    single    0.970  0.020  1.090
 UBE  N9   HN91  single    0.890  0.020  1.040
 UBE  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
 UBE  C21   C22  O23   115.10  3.000
 UBE  C21   C22  O24   116.89  3.000
 UBE  O23   C22  O24   128.01  3.000
 UBE  C17   C21  S20   111.53  3.000
 UBE  S20   C21  C22   117.20  3.000
 UBE  C17   C21  C22   131.27  3.000
 UBE  C19   S20  C21    92.44  3.000
 UBE  C18   C19  C25   127.69  3.000
 UBE  C25   C19  S20   121.94  3.000
 UBE  C18   C19  S20   110.37  3.000
 UBE  C26   C25  C30   118.38  3.000
 UBE  C26   C25  C19   120.32  3.000
 UBE  C30   C25  C19   121.30  3.000
 UBE  H30   C30  C29   119.06  3.000
 UBE  H30   C30  C25   120.15  3.000
 UBE  C29   C30  C25   120.78  3.000
 UBE  H29   C29  C28   120.20  3.000
 UBE  H29   C29  C30   119.48  3.000
 UBE  C28   C29  C30   120.32  3.000
 UBE  H28   C28  C27   120.27  3.000
 UBE  H28   C28  C29   120.32  3.000
 UBE  C27   C28  C29   119.41  3.000
 UBE  H27   C27  C26   119.54  3.000
 UBE  H27   C27  C28   120.09  3.000
 UBE  C26   C27  C28   120.36  3.000
 UBE  H26   C26  C27   119.20  3.000
 UBE  H26   C26  C25   120.04  3.000
 UBE  C27   C26  C25   120.74  3.000
 UBE  H18   C18  C17   124.07  3.000
 UBE  H18   C18  C19   122.12  3.000
 UBE  C17   C18  C19   113.80  3.000
 UBE  C16   C17  C18   124.13  3.000
 UBE  C18   C17  C21   111.87  3.000
 UBE  C16   C17  C21   124.01  3.000
 UBE  H162  C16  H161  106.71  3.000
 UBE  H162  C16  N3    108.94  3.000
 UBE  H161  C16  N3    107.87  3.000
 UBE  H162  C16  C17   110.63  3.000
 UBE  H161  C16  C17   110.33  3.000
 UBE  N3    C16  C17   112.18  3.000
 UBE  C2    N3   C4    125.37  3.000
 UBE  C4    N3   C16   116.43  3.000
 UBE  C2    N3   C16   118.13  3.000
 UBE  N5    C4   O15   122.84  3.000
 UBE  N5    C4   N3    115.56  3.000
 UBE  O15   C4   N3    121.59  3.000
 UBE  C1    C2   O14   123.63  3.000
 UBE  C1    C2   N3    115.70  3.000
 UBE  O14   C2   N3    120.67  3.000
 UBE  C6    C1   C13   123.16  3.000
 UBE  C6    C1   C2    117.98  3.000
 UBE  C13   C1   C2    118.85  3.000
 UBE  H133  C13  H132  107.98  3.000
 UBE  H133  C13  H131  107.80  3.000
 UBE  H132  C13  H131  107.28  3.000
 UBE  H133  C13  C1    110.78  3.000
 UBE  H132  C13  C1    111.43  3.000
 UBE  H131  C13  C1    111.40  3.000
 UBE  H6    C6   N5    114.86  3.000
 UBE  H6    C6   C1    121.31  3.000
 UBE  N5    C6   C1    123.83  3.000
 UBE  C7    N5   C6    118.36  3.000
 UBE  C7    N5   C4    120.07  3.000
 UBE  C6    N5   C4    121.48  3.000
 UBE  H72   C7   H71   107.69  3.000
 UBE  H72   C7   C8    110.66  3.000
 UBE  H71   C7   C8    110.13  3.000
 UBE  H72   C7   N5    108.05  3.000
 UBE  H71   C7   N5    107.58  3.000
 UBE  C8    C7   N5    112.56  3.000
 UBE  H8    C8   C10   107.61  3.000
 UBE  H8    C8   N9    107.60  3.000
 UBE  C10   C8   N9    111.97  3.000
 UBE  H8    C8   C7    107.43  3.000
 UBE  C10   C8   C7    106.62  3.000
 UBE  N9    C8   C7    115.29  3.000
 UBE  HN92  N9   HN91  107.21  3.000
 UBE  HN92  N9   C8    111.06  3.000
 UBE  HN91  N9   C8    110.28  3.000
 UBE  O12   C10  O11   127.19  3.000
 UBE  O12   C10  C8    115.20  3.000
 UBE  O11   C10  C8    117.57  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
 UBE  CONST_01  C19   C18  C17  C21    0.00   0.0  0
 UBE  CONST_02  C18   C19  S20  C21    0.00   0.0  0
 UBE  CONST_03  C25   C19  S20  C21  180.00   0.0  0
 UBE  CONST_04  C18   C17  C21  S20    0.00   0.0  0
 UBE  CONST_05  C17   C18  C19  S20    0.00   0.0  0
 UBE  CONST_08  C17   C21  S20  C19    0.00   0.0  0
 UBE  CONST_09  C29   C30  C25  C19  180.00   0.0  0
 UBE  CONST_10  C27   C26  C25  C19  180.00   0.0  0
 UBE  CONST_11  C17   C18  C19  C25  180.00   0.0  0
 UBE  CONST_12  C28   C29  C30  C25    0.00   0.0  0
 UBE  CONST_13  C28   C27  C26  C25    0.00   0.0  0
 UBE  CONST_15  C27   C26  C25  C30    0.00   0.0  0
 UBE  CONST_16  C27   C28  C29  C30    0.00   0.0  0
 UBE  CONST_17  C26   C25  C30  C29    0.00   0.0  0
 UBE  CONST_18  C26   C27  C28  C29    0.00   0.0  0
 UBE  CONST_20  C6    N5   C4   N3     0.00   0.0  0
 UBE  CONST_21  N5    C4   N3   C2     0.00   0.0  0
 UBE  CONST_22  C18   C17  C21  C22  180.00   0.0  0
 UBE  CONST_23  C19   S20  C21  C22  180.00   0.0  0
 UBE  CONST_24  C16   C17  C21  S20  180.00   0.0  0
 UBE  CONST_25  C16   C17  C18  C19  180.00   0.0  0
 UBE  CONST_26  N5    C4   N3   C16  180.00   0.0  0
 UBE  CONST_27  C7    N5   C4   N3   180.00   0.0  0
 UBE  CONST_28  C2    N3   C4   O15  180.00   0.0  0
 UBE  CONST_29  C6    N5   C4   O15  180.00   0.0  0
 UBE  CONST_30  H18   C18  C17  C21  180.00   0.0  0
 UBE  CONST_31  H30   C30  C25  C19    0.00   0.0  0
 UBE  CONST_32  H26   C26  C25  C19    0.00   0.0  0
 UBE  CONST_33  H29   C29  C30  C25  180.00   0.0  0
 UBE  CONST_34  H27   C27  C26  C25  180.00   0.0  0
 UBE  CONST_35  H28   C28  C29  C30  180.00   0.0  0
 UBE  CONST_36  O15   C4   N3   C16    0.00   0.0  0
 UBE  CONST_37  C7    N5   C4   O15    0.00   0.0  0
 UBE  Var_01    N3    C16  C17  C21  174.97  30.0  3
 UBE  Var_02    C2    N3   C16  C17   92.96  30.0  3
 UBE  Var_03    C17   C21  C22  O24   -0.07  30.0  2
 UBE  Var_04    C8    C7   N5   C4   100.06  30.0  3
 UBE  Var_05    H131  C13  C1   C2   -59.47  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
 UBE  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
 UBE  plan-1  C22  0.020
 UBE  plan-1  C21  0.020
 UBE  plan-1  S20  0.020
 UBE  plan-1  C19  0.020
 UBE  plan-1  C25  0.020
 UBE  plan-1  C18  0.020
 UBE  plan-1  C17  0.020
 UBE  plan-1  C16  0.020
 UBE  plan-1  H18  0.020
 UBE  plan-2  C19  0.020
 UBE  plan-2  C25  0.020
 UBE  plan-2  C30  0.020
 UBE  plan-2  C29  0.020
 UBE  plan-2  C28  0.020
 UBE  plan-2  C27  0.020
 UBE  plan-2  C26  0.020
 UBE  plan-2  H30  0.020
 UBE  plan-2  H29  0.020
 UBE  plan-2  H28  0.020
 UBE  plan-2  H27  0.020
 UBE  plan-2  H26  0.020
 UBE  plan-3  C16  0.020
 UBE  plan-3  N3   0.020
 UBE  plan-3  C4   0.020
 UBE  plan-3  O15  0.020
 UBE  plan-3  C2   0.020
 UBE  plan-3  O14  0.020
 UBE  plan-3  C1   0.020
 UBE  plan-3  C13  0.020
 UBE  plan-3  C6   0.020
 UBE  plan-3  N5   0.020
 UBE  plan-3  C7   0.020
 UBE  plan-3  H6   0.020
 UBE  plan-4  O24  0.020
 UBE  plan-4  C22  0.020
 UBE  plan-4  O23  0.020
 UBE  plan-4  C21  0.020
 UBE  plan-5  C8   0.020
 UBE  plan-5  C10  0.020
 UBE  plan-5  O11  0.020
 UBE  plan-5  O12  0.020

