# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 19 12:46:26 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 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)
#   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  54  33  .  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_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  -0.600   7.3964   0.9319   0.6770
 0YQ  C31  C  C      0   0.390   6.9746   1.5500  -0.3199
 0YQ  O32  O  OC    -1  -0.634   7.2062   2.7465  -0.5986
 0YQ  C30  C  CH2    0  -0.461   6.0750   0.8191  -1.3412
 0YQ  N25  N  NT     0  -0.398   5.7225  -0.5677  -1.1273
 0YQ  C26  C  CH2    0  -0.401   6.8280  -1.4902  -1.2576
 0YQ  C27  C  C      0   0.382   7.4227  -1.6170  -2.6754
 0YQ  O29  O  O      0  -0.605   6.7389  -1.2487  -3.6478
 0YQ  O28  O  OC    -1  -0.631   8.5571  -2.1401  -2.7199
 0YQ  C23  C  CH2    0  -0.382   4.9181  -0.7953   0.0409
 0YQ  C22  C  C      0   0.515   3.5379  -0.1603  -0.0717
 0YQ  O24  O  O      0  -0.493   2.9262  -0.0680  -1.1250
 0YQ  N21  N  NH1    0  -0.633   3.0312   0.2626   1.1015
 0YQ  C20  C  CH2    0  -0.289   1.7019   0.8043   1.2443
 0YQ  C19  C  CH2    0  -0.293   0.6330  -0.2850   1.3371
 0YQ  N17  N  NH1    0  -0.637  -0.6820   0.2689   1.5620
 0YQ  C16  C  C      0   0.507  -1.5217   0.6166   0.5726
 0YQ  O18  O  O      0  -0.474  -1.2757   0.4819  -0.6114
 0YQ  C12  C  CH1    0  -0.051  -2.8332   1.2081   1.0751
 0YQ  C11  C  CH1    0  -0.045  -3.6180   0.2573   1.9898
 0YQ  O15  O  OH1    0  -0.660  -3.2616   0.4950   3.3278
 0YQ  C10  C  CH1    0  -0.040  -5.0800   0.6326   1.6838
 0YQ  O14  O  OH1    0  -0.671  -5.5310   1.6273   2.5641
 0YQ  O13  O  O2     0  -0.479  -3.6610   1.4940  -0.0203
 0YQ  C9   C  CH1    0   0.196  -5.0066   1.2617   0.2815
 0YQ  N5   N  NR6    0  -0.568  -5.6229   0.5057  -0.8010
 0YQ  C6   C  CR16   0   0.104  -6.5751   1.1036  -1.5789
 0YQ  C1   C  CR16   0  -0.513  -7.1669   0.4994  -2.6207
 0YQ  C4   C  CR6    0   0.751  -5.1934  -0.7777  -1.0737
 0YQ  O8   O  O      0  -0.466  -4.3472  -1.3420  -0.4156
 0YQ  N3   N  NR16   0  -0.734  -5.8034  -1.3725  -2.1454
 0YQ  C2   C  CR6    0   0.569  -6.7861  -0.8466  -2.9715
 0YQ  O7   O  O      0  -0.461  -7.2413  -1.5044  -3.8878
 0YQ  H2   H  HCH2   0   0.227   5.1539   1.4041  -1.4399
 0YQ  H3   H  HCH2   0   0.237   6.5494   0.8953  -2.3228
 0YQ  H5   H  HCH2   0   0.192   7.6416  -1.2869  -0.5502
 0YQ  H6   H  HCH2   0   0.220   6.4610  -2.4924  -1.0008
 0YQ  H8   H  HCH2   0   0.256   4.7383  -1.8725   0.1389
 0YQ  H9   H  HCH2   0   0.217   5.3939  -0.4817   0.9798
 0YQ  H10  H  HNH1   0   0.399   3.5848   0.1471   1.9344
 0YQ  H11  H  HCH2   0   0.253   1.6849   1.4143   2.1476
 0YQ  H12  H  HCH2   0   0.245   1.4853   1.4627   0.4024
 0YQ  H13  H  HCH2   0   0.252   0.6232  -0.8764   0.4227
 0YQ  H14  H  HCH2   0   0.254   0.8606  -0.9596   2.1628
 0YQ  H15  H  HNH1   0   0.400  -0.9576   0.4435   2.5162
 0YQ  H16  H  HCH1   0   0.271  -2.6056   2.1282   1.6342
 0YQ  H17  H  HCH1   0   0.278  -3.4387  -0.7814   1.7149
 0YQ  H18  H  HOH1   0   0.475  -3.3810  -0.3164   3.8319
 0YQ  H19  H  HCH1   0   0.257  -5.7405  -0.2407   1.7063
 0YQ  H20  H  HOH1   0   0.451  -5.0273   1.5342   3.3843
 0YQ  H21  H  HCH1   0   0.268  -5.5571   2.2056   0.3083
 0YQ  H22  H  HCR6   0   0.330  -6.8332   2.1150  -1.2996
 0YQ  H23  H  HCR6   0   0.295  -7.9162   1.0146  -3.2009
 0YQ  H24  H  HNR6   0   0.428  -5.4938  -2.3158  -2.3462

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  1.216  0.020  1.216
 0YQ  C2   N3   single  1.387  0.020  1.387
 0YQ  C2   C1   single  1.442  0.020  1.442
 0YQ  N3   C4   single  1.369  0.020  1.369
 0YQ  C1   C6   double  1.342  0.020  1.342
 0YQ  C20  C19  single  1.529  0.020  1.529
 0YQ  C20  N21  single  1.442  0.020  1.442
 0YQ  C4   O8   double  1.211  0.020  1.211
 0YQ  C4   N5   single  1.381  0.020  1.381
 0YQ  C19  N17  single  1.445  0.020  1.445
 0YQ  C6   N5   single  1.367  0.020  1.367
 0YQ  N5   C9   single  1.457  0.020  1.457
 0YQ  N21  C22  single  1.346  0.020  1.346
 0YQ  N17  C16  single  1.343  0.020  1.343
 0YQ  O33  C31  deloc   1.247  0.020  1.247
 0YQ  O24  C22  double  1.222  0.020  1.222
 0YQ  C22  C23  single  1.524  0.020  1.524
 0YQ  O13  C9   single  1.399  0.020  1.399
 0YQ  O13  C12  single  1.402  0.020  1.402
 0YQ  C9   C10  single  1.539  0.020  1.539
 0YQ  C31  O32  deloc   1.250  0.020  1.250
 0YQ  C31  C30  single  1.545  0.020  1.545
 0YQ  C23  N25  single  1.437  0.020  1.437
 0YQ  C16  C12  single  1.524  0.020  1.524
 0YQ  C16  O18  double  1.217  0.020  1.217
 0YQ  C12  C11  single  1.535  0.020  1.535
 0YQ  N25  C30  single  1.447  0.020  1.447
 0YQ  N25  C26  single  1.446  0.020  1.446
 0YQ  C10  C11  single  1.540  0.020  1.540
 0YQ  C10  O14  single  1.403  0.020  1.403
 0YQ  O29  C27  deloc   1.245  0.020  1.245
 0YQ  C11  O15  single  1.405  0.020  1.405
 0YQ  C26  C27  single  1.543  0.020  1.543
 0YQ  C27  O28  deloc   1.250  0.020  1.250
 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  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  114.42  3.000
 0YQ  C30  C31  O33  119.41  3.000
 0YQ  O32  C31  O33  126.17  3.000
 0YQ  H3   C30  H2   104.29  3.000
 0YQ  H3   C30  N25  107.78  3.000
 0YQ  H2   C30  N25  108.68  3.000
 0YQ  H3   C30  C31  107.94  3.000
 0YQ  H2   C30  C31  107.25  3.000
 0YQ  N25  C30  C31  119.85  3.000
 0YQ  C23  N25  C26  113.60  3.000
 0YQ  C26  N25  C30  114.33  3.000
 0YQ  C23  N25  C30  114.11  3.000
 0YQ  H6   C26  H5   105.44  3.000
 0YQ  H6   C26  C27  105.60  3.000
 0YQ  H5   C26  C27  108.78  3.000
 0YQ  H6   C26  N25  107.81  3.000
 0YQ  H5   C26  N25  113.00  3.000
 0YQ  C27  C26  N25  115.47  3.000
 0YQ  O28  C27  O29  126.49  3.000
 0YQ  O28  C27  C26  114.65  3.000
 0YQ  O29  C27  C26  118.81  3.000
 0YQ  H9   C23  H8   105.98  3.000
 0YQ  H9   C23  C22  109.67  3.000
 0YQ  H8   C23  C22  105.52  3.000
 0YQ  H9   C23  N25  114.04  3.000
 0YQ  H8   C23  N25  108.67  3.000
 0YQ  C22  C23  N25  112.40  3.000
 0YQ  N21  C22  O24  122.64  3.000
 0YQ  O24  C22  C23  123.29  3.000
 0YQ  N21  C22  C23  114.05  3.000
 0YQ  H10  N21  C20  117.90  3.000
 0YQ  H10  N21  C22  118.55  3.000
 0YQ  C20  N21  C22  123.44  3.000
 0YQ  H12  C20  H11  107.38  3.000
 0YQ  H12  C20  C19  109.76  3.000
 0YQ  H11  C20  C19  109.72  3.000
 0YQ  H12  C20  N21  109.48  3.000
 0YQ  H11  C20  N21  107.85  3.000
 0YQ  C19  C20  N21  112.50  3.000
 0YQ  H14  C19  H13  107.57  3.000
 0YQ  H14  C19  N17  108.02  3.000
 0YQ  H13  C19  N17  109.31  3.000
 0YQ  H14  C19  C20  109.93  3.000
 0YQ  H13  C19  C20  110.01  3.000
 0YQ  N17  C19  C20  111.88  3.000
 0YQ  H15  N17  C16  118.77  3.000
 0YQ  H15  N17  C19  117.55  3.000
 0YQ  C16  N17  C19  123.61  3.000
 0YQ  C12  C16  O18  122.53  3.000
 0YQ  O18  C16  N17  124.17  3.000
 0YQ  C12  C16  N17  113.30  3.000
 0YQ  H16  C12  O13  110.40  3.000
 0YQ  H16  C12  C11  108.72  3.000
 0YQ  O13  C12  C11  106.85  3.000
 0YQ  H16  C12  C16  108.30  3.000
 0YQ  C11  C12  C16  113.33  3.000
 0YQ  O13  C12  C16  109.24  3.000
 0YQ  H17  C11  C10  109.79  3.000
 0YQ  H17  C11  O15  111.09  3.000
 0YQ  C10  C11  O15  112.88  3.000
 0YQ  H17  C11  C12  110.86  3.000
 0YQ  O15  C11  C12  109.45  3.000
 0YQ  C10  C11  C12  102.47  3.000
 0YQ  H18  O15  C11  108.95  3.000
 0YQ  H19  C10  C9   111.93  3.000
 0YQ  H19  C10  O14  111.01  3.000
 0YQ  C9   C10  O14  107.30  3.000
 0YQ  H19  C10  C11  111.97  3.000
 0YQ  O14  C10  C11  110.69  3.000
 0YQ  C9   C10  C11  103.62  3.000
 0YQ  H20  O14  C10  107.25  3.000
 0YQ  C9   O13  C12  111.44  3.000
 0YQ  H21  C9   N5   104.67  3.000
 0YQ  H21  C9   O13  110.27  3.000
 0YQ  N5   C9   O13  109.44  3.000
 0YQ  H21  C9   C10  107.86  3.000
 0YQ  O13  C9   C10  108.09  3.000
 0YQ  N5   C9   C10  116.41  3.000
 0YQ  C4   N5   C6   120.72  3.000
 0YQ  C6   N5   C9   119.37  3.000
 0YQ  C4   N5   C9   119.83  3.000
 0YQ  H22  C6   C1   121.12  3.000
 0YQ  H22  C6   N5   115.38  3.000
 0YQ  C1   C6   N5   123.50  3.000
 0YQ  H23  C1   C2   119.89  3.000
 0YQ  H23  C1   C6   120.59  3.000
 0YQ  C2   C1   C6   119.52  3.000
 0YQ  N3   C4   O8   122.28  3.000
 0YQ  O8   C4   N5   122.89  3.000
 0YQ  N3   C4   N5   114.83  3.000
 0YQ  H24  N3   C2   116.84  3.000
 0YQ  H24  N3   C4   115.06  3.000
 0YQ  C2   N3   C4   128.10  3.000
 0YQ  O7   C2   N3   120.57  3.000
 0YQ  N3   C2   C1   113.33  3.000
 0YQ  O7   C2   C1   126.10  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  Var_01    N25  C30  C31  O33     0.48  30.0  3
 0YQ  Var_02    C23  N25  C30  C31    64.58  30.0  2
 0YQ  Var_03    C22  C23  N25  C30    65.83  30.0  1
 0YQ  Var_04    C27  C26  N25  C30   -66.49  30.0  3
 0YQ  Var_05    N21  C22  C23  N25  -147.81  30.0  1
 0YQ  Var_06    O29  C27  C26  N25   -19.47  30.0  3
 0YQ  Var_07    C19  C20  N21  C22    81.14  30.0  1
 0YQ  Var_08    N17  C19  C20  N21   176.45  30.0  3
 0YQ  Var_09    C16  N17  C19  C20    90.12  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-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

