# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 06:19:09 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=CC(=O)NC2=O)C(=O)NCCNC(=O)CN(CC(O)=O)CC(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
 0YQ  0YQ  '2,2'-[(2-{[2-({[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)ethyl]amino}-2-oxoethyl)imino]diacetic acid (non-preferred name)'  ligand  56  33  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0YQ
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
 0YQ  O33  O  O     0  -0.429   5.4095  10.2119  35.7775
 0YQ  C31  C  C     0   0.535   5.1615  10.0491  36.9433
 0YQ  O32  O  OH1   0  -0.595   4.9217   8.8627  37.4897
 0YQ  C30  C  CH2   0  -0.412   5.0891  11.1414  37.9857
 0YQ  N25  N  NT    0  -0.435   5.2618  12.4490  37.4163
 0YQ  C26  C  CH2   0  -0.421   5.8904  13.3948  38.2993
 0YQ  C27  C  C     0   0.545   7.3923  13.2279  38.3329
 0YQ  O29  O  O     0  -0.448   8.0060  12.4770  37.6142
 0YQ  O28  O  OH1   0  -0.618   7.9473  14.0222  39.2284
 0YQ  C23  C  CH2   0  -0.401   4.1154  12.9777  36.7189
 0YQ  C22  C  C     0   0.509   4.4884  13.8145  35.5017
 0YQ  O24  O  O     0  -0.509   3.6877  14.6071  35.0216
 0YQ  N21  N  NH1   0  -0.610   5.7025  13.5640  34.9977
 0YQ  C20  C  CH2   0  -0.303   6.2089  14.1721  33.7932
 0YQ  C19  C  CH2   0  -0.297   7.1985  15.3061  34.0371
 0YQ  N17  N  NH1   0  -0.630   8.4566  14.8457  34.5850
 0YQ  C16  C  C     0   0.533   8.8507  15.0348  35.8500
 0YQ  O18  O  O     0  -0.476   8.2057  15.6359  36.6944
 0YQ  C12  C  CH1   0  -0.092  10.1963  14.4118  36.2120
 0YQ  C11  C  CH1   0  -0.012  10.9385  15.1427  37.3289
 0YQ  O15  O  OH1   0  -0.673  10.5818  14.6350  38.5926
 0YQ  C10  C  CH1   0  -0.039  12.4001  14.8451  36.9735
 0YQ  O14  O  OH1   0  -0.660  12.7548  13.5415  37.3371
 0YQ  O13  O  O2    0  -0.496  11.0838  14.4146  35.0958
 0YQ  C9   C  CH1   0   0.178  12.3494  14.8760  35.4484
 0YQ  N5   N  NR6   0  -0.571  12.5613  16.2406  34.9189
 0YQ  C6   C  CR16  0   0.098  11.5467  17.0203  34.4480
 0YQ  C1   C  CR16  0  -0.505  11.7370  18.2600  33.9664
 0YQ  C4   C  CR6   0   0.742  13.8677  16.6849  34.8914
 0YQ  O8   O  O     0  -0.478  14.7917  16.0033  35.2856
 0YQ  N3   N  NR16  0  -0.731  14.0400  17.9457  34.3909
 0YQ  C2   C  CR6   0   0.568  13.0669  18.8136  33.9167
 0YQ  O7   O  O     0  -0.462  13.3702  19.9182  33.5066
 0YQ  H1   H  HOH1  0   0.483   4.9915   8.1656  36.8205
 0YQ  H2   H  HCH2  0   0.269   4.1543  11.0311  38.5543
 0YQ  H3   H  HCH2  0   0.297   5.8893  10.9435  38.7037
 0YQ  H5   H  HCH2  0   0.295   5.7084  14.4106  37.9361
 0YQ  H6   H  HCH2  0   0.270   5.4937  13.3744  39.3241
 0YQ  H7   H  HOH1  0   0.483   8.9125  14.1064  39.0629
 0YQ  H8   H  HCH2  0   0.254   3.4543  13.5778  37.3566
 0YQ  H9   H  HCH2  0   0.282   3.5037  12.1543  36.3419
 0YQ  H10  H  HNH1  0   0.406   6.2586  12.8775  35.4889
 0YQ  H11  H  HCH2  0   0.255   5.3709  14.5649  33.2181
 0YQ  H12  H  HCH2  0   0.255   6.6800  13.4003  33.1811
 0YQ  H13  H  HCH2  0   0.261   7.3991  15.8013  33.0854
 0YQ  H14  H  HCH2  0   0.258   6.7688  16.0461  34.7093
 0YQ  H15  H  HNH1  0   0.409   9.0589  14.3272  33.9644
 0YQ  H16  H  HCH1  0   0.301  10.0076  13.3742  36.5108
 0YQ  H17  H  HCH1  0   0.268  10.7563  16.2215  37.2778
 0YQ  H18  H  HOH1  0   0.485  10.8518  15.2678  39.2690
 0YQ  H19  H  HCH1  0   0.272  13.0838  15.5921  37.3913
 0YQ  H20  H  HOH1  0   0.456  12.4403  13.3807  38.2347
 0YQ  H21  H  HCH1  0   0.301  13.1086  14.2337  35.0007
 0YQ  H22  H  HCR6  0   0.313  10.5589  16.5870  34.4586
 0YQ  H23  H  HCR6  0   0.294  10.9010  18.8391  33.6063
 0YQ  H24  H  HNR6  0   0.429  14.9978  18.2748  34.3703

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
 0YQ  O7   C2   double  1.217  0.020  1.217
 0YQ  C2   N3   single  1.387  0.020  1.387
 0YQ  C2   C1   single  1.441  0.020  1.441
 0YQ  N3   C4   single  1.367  0.020  1.367
 0YQ  C1   C6   double  1.343  0.020  1.343
 0YQ  C20  C19  single  1.525  0.020  1.525
 0YQ  C20  N21  single  1.441  0.020  1.441
 0YQ  C4   O8   double  1.214  0.020  1.214
 0YQ  C4   N5   single  1.380  0.020  1.380
 0YQ  C19  N17  single  1.447  0.020  1.447
 0YQ  C6   N5   single  1.364  0.020  1.364
 0YQ  N5   C9   single  1.479  0.020  1.479
 0YQ  N21  C22  single  1.338  0.020  1.338
 0YQ  N17  C16  single  1.338  0.020  1.338
 0YQ  O33  C31  double  1.203  0.020  1.203
 0YQ  O24  C22  double  1.225  0.020  1.225
 0YQ  C22  C23  single  1.523  0.020  1.523
 0YQ  O13  C9   single  1.392  0.020  1.392
 0YQ  O13  C12  single  1.426  0.020  1.426
 0YQ  C9   C10  single  1.526  0.020  1.526
 0YQ  C31  O32  single  1.328  0.020  1.328
 0YQ  C31  C30  single  1.512  0.020  1.512
 0YQ  C23  N25  single  1.442  0.020  1.442
 0YQ  C16  C12  single  1.526  0.020  1.526
 0YQ  C16  O18  double  1.221  0.020  1.221
 0YQ  C12  C11  single  1.527  0.020  1.527
 0YQ  N25  C30  single  1.437  0.020  1.437
 0YQ  N25  C26  single  1.439  0.020  1.439
 0YQ  C10  C11  single  1.533  0.020  1.533
 0YQ  C10  O14  single  1.399  0.020  1.399
 0YQ  O29  C27  double  1.207  0.020  1.207
 0YQ  C11  O15  single  1.408  0.020  1.408
 0YQ  C26  C27  single  1.512  0.020  1.512
 0YQ  C27  O28  single  1.319  0.020  1.319
 0YQ  O32  H1   single  0.850  0.020  0.980
 0YQ  C30  H2   single  0.970  0.020  1.090
 0YQ  C30  H3   single  0.970  0.020  1.090
 0YQ  C26  H5   single  0.970  0.020  1.090
 0YQ  C26  H6   single  0.970  0.020  1.090
 0YQ  O28  H7   single  0.850  0.020  0.980
 0YQ  C23  H8   single  0.970  0.020  1.090
 0YQ  C23  H9   single  0.970  0.020  1.090
 0YQ  N21  H10  single  0.860  0.020  1.020
 0YQ  C20  H11  single  0.970  0.020  1.090
 0YQ  C20  H12  single  0.970  0.020  1.090
 0YQ  C19  H13  single  0.970  0.020  1.090
 0YQ  C19  H14  single  0.970  0.020  1.090
 0YQ  N17  H15  single  0.860  0.020  1.020
 0YQ  C12  H16  single  0.970  0.020  1.090
 0YQ  C11  H17  single  0.970  0.020  1.090
 0YQ  O15  H18  single  0.850  0.020  0.980
 0YQ  C10  H19  single  0.970  0.020  1.090
 0YQ  O14  H20  single  0.850  0.020  0.980
 0YQ  C9   H21  single  0.970  0.020  1.090
 0YQ  C6   H22  single  0.930  0.020  1.080
 0YQ  C1   H23  single  0.930  0.020  1.080
 0YQ  N3   H24  single  0.860  0.020  1.020

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
 0YQ  C30  C31  O32  110.68  3.000
 0YQ  C30  C31  O33  125.48  3.000
 0YQ  O32  C31  O33  123.84  3.000
 0YQ  H1   O32  C31  110.21  3.000
 0YQ  H3   C30  H2   105.34  3.000
 0YQ  H3   C30  N25  109.70  3.000
 0YQ  H2   C30  N25  113.47  3.000
 0YQ  H3   C30  C31  106.69  3.000
 0YQ  H2   C30  C31  108.96  3.000
 0YQ  N25  C30  C31  112.25  3.000
 0YQ  C23  N25  C26  113.78  3.000
 0YQ  C26  N25  C30  114.06  3.000
 0YQ  C23  N25  C30  115.45  3.000
 0YQ  H6   C26  H5   105.47  3.000
 0YQ  H6   C26  C27  109.62  3.000
 0YQ  H5   C26  C27  105.98  3.000
 0YQ  H6   C26  N25  113.73  3.000
 0YQ  H5   C26  N25  109.51  3.000
 0YQ  C27  C26  N25  112.04  3.000
 0YQ  O28  C27  O29  124.38  3.000
 0YQ  O28  C27  C26  111.51  3.000
 0YQ  O29  C27  C26  124.10  3.000
 0YQ  H7   O28  C27  110.51  3.000
 0YQ  H9   C23  H8   105.98  3.000
 0YQ  H9   C23  C22  105.98  3.000
 0YQ  H8   C23  C22  108.15  3.000
 0YQ  H9   C23  N25  109.60  3.000
 0YQ  H8   C23  N25  113.47  3.000
 0YQ  C22  C23  N25  113.15  3.000
 0YQ  N21  C22  O24  124.52  3.000
 0YQ  O24  C22  C23  120.58  3.000
 0YQ  N21  C22  C23  114.84  3.000
 0YQ  H10  N21  C20  119.96  3.000
 0YQ  H10  N21  C22  116.31  3.000
 0YQ  C20  N21  C22  123.68  3.000
 0YQ  H12  C20  H11  106.90  3.000
 0YQ  H12  C20  C19  109.59  3.000
 0YQ  H11  C20  C19  108.39  3.000
 0YQ  H12  C20  N21  108.77  3.000
 0YQ  H11  C20  N21  108.85  3.000
 0YQ  C19  C20  N21  114.09  3.000
 0YQ  H14  C19  H13  107.62  3.000
 0YQ  H14  C19  N17  109.01  3.000
 0YQ  H13  C19  N17  108.34  3.000
 0YQ  H14  C19  C20  110.38  3.000
 0YQ  H13  C19  C20  108.50  3.000
 0YQ  N17  C19  C20  112.84  3.000
 0YQ  H15  N17  C16  118.59  3.000
 0YQ  H15  N17  C19  116.73  3.000
 0YQ  C16  N17  C19  124.66  3.000
 0YQ  C12  C16  O18  120.18  3.000
 0YQ  O18  C16  N17  124.59  3.000
 0YQ  C12  C16  N17  115.22  3.000
 0YQ  H16  C12  O13  108.81  3.000
 0YQ  H16  C12  C11  109.72  3.000
 0YQ  O13  C12  C11  105.60  3.000
 0YQ  H16  C12  C16  107.41  3.000
 0YQ  C11  C12  C16  113.99  3.000
 0YQ  O13  C12  C16  111.23  3.000
 0YQ  H17  C11  C10  109.81  3.000
 0YQ  H17  C11  O15  110.78  3.000
 0YQ  C10  C11  O15  112.31  3.000
 0YQ  H17  C11  C12  110.88  3.000
 0YQ  O15  C11  C12  111.14  3.000
 0YQ  C10  C11  C12  101.59  3.000
 0YQ  H18  O15  C11  108.78  3.000
 0YQ  H19  C10  C9   112.83  3.000
 0YQ  H19  C10  O14  112.21  3.000
 0YQ  C9   C10  O14  106.68  3.000
 0YQ  H19  C10  C11  111.97  3.000
 0YQ  O14  C10  C11  111.24  3.000
 0YQ  C9   C10  C11  101.30  3.000
 0YQ  H20  O14  C10  108.33  3.000
 0YQ  C9   O13  C12  111.60  3.000
 0YQ  H21  C9   N5   107.26  3.000
 0YQ  H21  C9   O13  109.49  3.000
 0YQ  N5   C9   O13  110.20  3.000
 0YQ  H21  C9   C10  112.04  3.000
 0YQ  O13  C9   C10  106.05  3.000
 0YQ  N5   C9   C10  111.82  3.000
 0YQ  C4   N5   C6   120.89  3.000
 0YQ  C6   N5   C9   123.00  3.000
 0YQ  C4   N5   C9   116.09  3.000
 0YQ  H22  C6   C1   120.26  3.000
 0YQ  H22  C6   N5   116.64  3.000
 0YQ  C1   C6   N5   123.10  3.000
 0YQ  H23  C1   C2   119.81  3.000
 0YQ  H23  C1   C6   120.35  3.000
 0YQ  C2   C1   C6   119.83  3.000
 0YQ  N3   C4   O8   122.72  3.000
 0YQ  O8   C4   N5   122.23  3.000
 0YQ  N3   C4   N5   115.05  3.000
 0YQ  H24  N3   C2   116.93  3.000
 0YQ  H24  N3   C4   115.22  3.000
 0YQ  C2   N3   C4   127.84  3.000
 0YQ  O7   C2   N3   120.55  3.000
 0YQ  N3   C2   C1   113.27  3.000
 0YQ  O7   C2   C1   126.18  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
 0YQ  CONST_01  N3   C4   N5   C9    180.00   0.0  0
 0YQ  CONST_02  C2   N3   C4   N5      0.00   0.0  0
 0YQ  CONST_03  N3   C4   N5   C6      0.00   0.0  0
 0YQ  CONST_04  C4   N3   C2   C1      0.00   0.0  0
 0YQ  CONST_05  O8   C4   N5   C9      0.00   0.0  0
 0YQ  CONST_06  O8   C4   N5   C6    180.00   0.0  0
 0YQ  CONST_07  O7   C2   N3   C4    180.00   0.0  0
 0YQ  CONST_08  C2   N3   C4   O8    180.00   0.0  0
 0YQ  CONST_09  H24  N3   C4   N5    180.00   0.0  0
 0YQ  CONST_10  C12  C16  N17  C19   180.00   0.0  0
 0YQ  CONST_11  H15  N17  C16  C12     0.00   0.0  0
 0YQ  CONST_12  C20  N21  C22  C23   180.00   0.0  0
 0YQ  CONST_13  C20  N21  C22  O24     0.00   0.0  0
 0YQ  CONST_14  O18  C16  N17  C19     0.00   0.0  0
 0YQ  CONST_15  H10  N21  C22  C23     0.00   0.0  0
 0YQ  CONST_16  H1   O32  C31  O33     0.00   0.0  0
 0YQ  Var_01    N25  C30  C31  O33     4.06  30.0  3
 0YQ  Var_02    C23  N25  C30  C31    76.63  30.0  2
 0YQ  Var_03    C22  C23  N25  C30  -144.64  30.0  2
 0YQ  Var_04    C27  C26  N25  C30    80.28  30.0  3
 0YQ  Var_05    N21  C22  C23  N25    22.15  30.0  1
 0YQ  Var_06    O29  C27  C26  N25     6.45  30.0  3
 0YQ  Var_07    C19  C20  N21  C22   102.39  30.0  2
 0YQ  Var_08    N17  C19  C20  N21    68.84  30.0  3
 0YQ  Var_09    C16  N17  C19  C20  -107.40  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
 0YQ  chir_01  C12  O13  C16  C11  positiv
 0YQ  chir_02  C11  O15  C12  C10  positiv
 0YQ  chir_03  C10  O14  C11  C9   positiv
 0YQ  chir_04  C9   O13  N5   C10  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
 0YQ  plan-1  C26  0.020
 0YQ  plan-1  C27  0.020
 0YQ  plan-1  O29  0.020
 0YQ  plan-1  O28  0.020
 0YQ  plan-1  H7   0.020
 0YQ  plan-2  C9   0.020
 0YQ  plan-2  N5   0.020
 0YQ  plan-2  C6   0.020
 0YQ  plan-2  C1   0.020
 0YQ  plan-2  C4   0.020
 0YQ  plan-2  O8   0.020
 0YQ  plan-2  N3   0.020
 0YQ  plan-2  C2   0.020
 0YQ  plan-2  O7   0.020
 0YQ  plan-2  H22  0.020
 0YQ  plan-2  H23  0.020
 0YQ  plan-2  H24  0.020
 0YQ  plan-3  C19  0.020
 0YQ  plan-3  N17  0.020
 0YQ  plan-3  C16  0.020
 0YQ  plan-3  O18  0.020
 0YQ  plan-3  C12  0.020
 0YQ  plan-3  H15  0.020
 0YQ  plan-4  C23  0.020
 0YQ  plan-4  C22  0.020
 0YQ  plan-4  O24  0.020
 0YQ  plan-4  N21  0.020
 0YQ  plan-4  C20  0.020
 0YQ  plan-4  H10  0.020
 0YQ  plan-5  O33  0.020
 0YQ  plan-5  C31  0.020
 0YQ  plan-5  O32  0.020
 0YQ  plan-5  C30  0.020
 0YQ  plan-5  H1   0.020

