# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 17:45:40 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 5-[4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-methyl-phenyl]-~{N}1,~{N}3-dimethyl-benzene-1,3-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(cc(c1)c2ccc(O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)c(C)c2)C(=O)NC
#
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
 5U7  5U7  5-[4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-methyl-phenyl]-~{N}1,~{N}3-dimethyl-benzene-1,3-dicarboxamide  ligand  61  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5U7
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
 5U7  C1   C  CR6   0   0.016  -4.4632   1.2339   0.0490
 5U7  C2   C  CR16  0  -0.349  -3.0810   1.0968   0.0239
 5U7  C3   C  CR16  0  -0.319  -0.2040   0.7629  -0.7532
 5U7  C4   C  CR16  0  -0.348  -0.3912  -1.4437   0.1355
 5U7  C5   C  CR16  0  -0.371  -5.2675   0.1297  -0.2149
 5U7  C6   C  CR16  0  -0.346   1.1755   0.6254  -0.8082
 5U7  C7   C  CR6   0   0.012   0.9825  -1.6169   0.0863
 5U7  C8   C  CR16  0  -0.348  -3.3055  -1.2222  -0.5181
 5U7  C9   C  CR6   0   0.087  -1.0136  -0.2675  -0.2883
 5U7  C10  C  CR6   0   0.141  -2.4819  -0.1303  -0.2526
 5U7  C12  C  CR6   0   0.354   1.7680  -0.5672  -0.4096
 5U7  C14  C  CH1   0   0.001   5.9678  -0.9829  -0.0503
 5U7  C15  C  CH1   0   0.029   6.1804   0.3091   0.7306
 5U7  C16  C  CH1   0  -0.021   5.2644  -0.6963  -1.3735
 5U7  C17  C  CH1   0  -0.014   4.8388   1.0203   0.9162
 5U7  C18  C  CH1   0   0.203   3.9728   0.0805  -1.0973
 5U7  C19  C  CH3   0  -0.514  -7.6336  -3.4710  -0.5989
 5U7  C20  C  CH2   0  -0.160   5.0114   2.3866   1.5445
 5U7  O21  O  O     0  -0.489  -5.0282  -3.2261  -1.5003
 5U7  O22  O  O2    0  -0.487   4.1999   1.2171  -0.3377
 5U7  O23  O  OH1   0  -0.672   7.2261  -1.5875  -0.2290
 5U7  O24  O  OH1   0  -0.675   6.7023   0.0449   2.0103
 5U7  O25  O  OH1   0  -0.665   6.1202   0.0741  -2.1759
 5U7  O26  O  OH1   0  -0.667   3.7418   2.9428   1.7881
 5U7  O27  O  O2    0  -0.493   3.0960  -0.8200  -0.4652
 5U7  O3   O  O     0  -0.489  -4.3697   3.6047   0.1005
 5U7  C02  C  C     0   0.532  -5.0258   2.5954   0.3240
 5U7  N1   N  NH1   0  -0.639  -6.2675   2.6397   0.8231
 5U7  C21  C  CH3   0  -0.513  -6.9326   3.8877   1.1159
 5U7  C01  C  CR6   0   0.014  -4.6895  -1.1051  -0.4911
 5U7  N    N  NH1   0  -0.639  -6.7509  -2.3557  -0.3481
 5U7  H17  H  HCR6  0   0.262  -2.4637   1.9598   0.2370
 5U7  H12  H  HCR6  0   0.258  -0.6427   1.6895  -1.1011
 5U7  H13  H  HCR6  0   0.250  -0.9923  -2.2545   0.5314
 5U7  H18  H  HCR6  0   0.262  -6.3432   0.2441  -0.2629
 5U7  H11  H  HCR6  0   0.282   1.7616   1.4607  -1.1640
 5U7  H19  H  HCR6  0   0.263  -2.8657  -2.1777  -0.7736
 5U7  H16  H  HCH3  0   0.245   2.3658  -2.7173   1.3229
 5U7  H15  H  HCH3  0   0.243   0.8706  -3.5720   0.9510
 5U7  H14  H  HCH3  0   0.245   2.1290  -3.4075  -0.2708
 5U7  H2   H  HCH1  0   0.233   5.3105  -1.6270   0.5489
 5U7  H1   H  HCH1  0   0.215   6.8532   0.9681   0.1613
 5U7  H3   H  HCH1  0   0.239   5.0006  -1.6437  -1.8631
 5U7  H    H  HCH1  0   0.230   4.2087   0.4038   1.5731
 5U7  H4   H  HCH1  0   0.261   3.5389   0.4287  -2.0428
 5U7  H22  H  HCH3  0   0.243  -7.7442  -3.6529  -1.6671
 5U7  H20  H  HCH3  0   0.239  -7.2762  -4.3889  -0.1294
 5U7  H21  H  HCH3  0   0.252  -8.6107  -3.2328  -0.1892
 5U7  H26  H  HCH2  0   0.213   5.5856   2.2707   2.4698
 5U7  H27  H  HCH2  0   0.195   5.6106   3.0138   0.8695
 5U7  H8   H  HOH1  0   0.458   7.0998  -2.5307  -0.3675
 5U7  H9   H  HOH1  0   0.452   7.5164  -0.4571   1.8969
 5U7  H7   H  HOH1  0   0.458   5.7585   0.1087  -3.0669
 5U7  H10  H  HOH1  0   0.455   3.8691   3.7700   2.2606
 5U7  H6   H  HNH1  0   0.410  -6.7233   1.7901   1.1069
 5U7  H23  H  HCH3  0   0.243  -6.9617   4.5328   0.2388
 5U7  H24  H  HCH3  0   0.253  -7.9534   3.6698   1.4158
 5U7  H25  H  HCH3  0   0.239  -6.4431   4.4312   1.9258
 5U7  H5   H  HNH1  0   0.410  -7.0573  -1.6595   0.3095
 5U7  C11  C  CH3   0  -0.712   1.6201  -2.8939   0.5465
 5U7  C13  C  C     0   0.533  -5.5003  -2.3201  -0.8259

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
 5U7  O24  C15  single    1.407  0.020  1.407
 5U7  O26  C20  single    1.407  0.020  1.407
 5U7  C20  C17  single    1.514  0.020  1.514
 5U7  C15  C17  single    1.530  0.020  1.530
 5U7  C15  C14  single    1.525  0.020  1.525
 5U7  O23  C14  single    1.407  0.020  1.407
 5U7  C17  O22  single    1.421  0.020  1.421
 5U7  C14  C16  single    1.526  0.020  1.526
 5U7  O22  C18  single    1.386  0.020  1.386
 5U7  O25  C16  single    1.403  0.020  1.403
 5U7  C16  C18  single    1.532  0.020  1.532
 5U7  C11  C7   single    1.500  0.020  1.500
 5U7  C18  O27  single    1.407  0.020  1.407
 5U7  O27  C12  single    1.353  0.020  1.353
 5U7  C7   C12  aromatic  1.402  0.020  1.402
 5U7  C7   C4   aromatic  1.385  0.020  1.385
 5U7  C12  C6   aromatic  1.390  0.020  1.390
 5U7  C4   C9   aromatic  1.397  0.020  1.397
 5U7  C6   C3   aromatic  1.387  0.020  1.387
 5U7  C9   C3   aromatic  1.390  0.020  1.390
 5U7  C9   C10  single    1.475  0.020  1.475
 5U7  C21  N1   single    1.444  0.020  1.444
 5U7  C2   C10  aromatic  1.393  0.020  1.393
 5U7  C2   C1   aromatic  1.389  0.020  1.389
 5U7  N1   C02  single    1.339  0.020  1.339
 5U7  C10  C8   aromatic  1.393  0.020  1.393
 5U7  C02  O3   double    1.224  0.020  1.224
 5U7  C02  C1   single    1.499  0.020  1.499
 5U7  C1   C5   aromatic  1.391  0.020  1.391
 5U7  C8   C01  aromatic  1.389  0.020  1.389
 5U7  C5   C01  aromatic  1.391  0.020  1.391
 5U7  C01  C13  single    1.499  0.020  1.499
 5U7  N    C13  single    1.339  0.020  1.339
 5U7  N    C19  single    1.444  0.020  1.444
 5U7  C13  O21  double    1.224  0.020  1.224
 5U7  C2   H17  single    0.930  0.020  1.080
 5U7  C3   H12  single    0.930  0.020  1.080
 5U7  C4   H13  single    0.930  0.020  1.080
 5U7  C5   H18  single    0.930  0.020  1.080
 5U7  C6   H11  single    0.930  0.020  1.080
 5U7  C8   H19  single    0.930  0.020  1.080
 5U7  C11  H16  single    0.970  0.020  1.090
 5U7  C11  H15  single    0.970  0.020  1.090
 5U7  C11  H14  single    0.970  0.020  1.090
 5U7  C14  H2   single    0.970  0.020  1.090
 5U7  C15  H1   single    0.970  0.020  1.090
 5U7  C16  H3   single    0.970  0.020  1.090
 5U7  C17  H    single    0.970  0.020  1.090
 5U7  C18  H4   single    0.970  0.020  1.090
 5U7  C19  H22  single    0.970  0.020  1.090
 5U7  C19  H20  single    0.970  0.020  1.090
 5U7  C19  H21  single    0.970  0.020  1.090
 5U7  C20  H26  single    0.970  0.020  1.090
 5U7  C20  H27  single    0.970  0.020  1.090
 5U7  O23  H8   single    0.850  0.020  0.980
 5U7  O24  H9   single    0.850  0.020  0.980
 5U7  O25  H7   single    0.850  0.020  0.980
 5U7  O26  H10  single    0.850  0.020  0.980
 5U7  N1   H6   single    0.860  0.020  1.020
 5U7  C21  H23  single    0.970  0.020  1.090
 5U7  C21  H24  single    0.970  0.020  1.090
 5U7  C21  H25  single    0.970  0.020  1.090
 5U7  N    H5   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
 5U7  C02  C1   C5   122.60  3.000
 5U7  C5   C1   C2   119.56  3.000
 5U7  C02  C1   C2   117.81  3.000
 5U7  H17  C2   C10  119.74  3.000
 5U7  H17  C2   C1   119.03  3.000
 5U7  C10  C2   C1   121.22  3.000
 5U7  H12  C3   C9   120.38  3.000
 5U7  H12  C3   C6   118.36  3.000
 5U7  C9   C3   C6   121.25  3.000
 5U7  H13  C4   C9   119.57  3.000
 5U7  H13  C4   C7   117.99  3.000
 5U7  C9   C4   C7   122.44  3.000
 5U7  H18  C5   C01  119.86  3.000
 5U7  H18  C5   C1   119.92  3.000
 5U7  C01  C5   C1   120.13  3.000
 5U7  H11  C6   C12  121.76  3.000
 5U7  H11  C6   C3   118.40  3.000
 5U7  C12  C6   C3   119.83  3.000
 5U7  C12  C7   C11  120.53  3.000
 5U7  C12  C7   C4   118.33  3.000
 5U7  C11  C7   C4   121.14  3.000
 5U7  H19  C8   C01  118.93  3.000
 5U7  H19  C8   C10  119.78  3.000
 5U7  C01  C8   C10  121.27  3.000
 5U7  C10  C9   C4   120.97  3.000
 5U7  C10  C9   C3   121.25  3.000
 5U7  C4   C9   C3   117.78  3.000
 5U7  C9   C10  C8   120.72  3.000
 5U7  C8   C10  C2   118.29  3.000
 5U7  C9   C10  C2   120.98  3.000
 5U7  O27  C12  C7   115.13  3.000
 5U7  C7   C12  C6   120.34  3.000
 5U7  O27  C12  C6   124.53  3.000
 5U7  H2   C14  O23  110.63  3.000
 5U7  H2   C14  C16  107.91  3.000
 5U7  O23  C14  C16  112.51  3.000
 5U7  H2   C14  C15  107.52  3.000
 5U7  C16  C14  C15  110.45  3.000
 5U7  O23  C14  C15  107.72  3.000
 5U7  H1   C15  O24  110.87  3.000
 5U7  H1   C15  C17  108.70  3.000
 5U7  O24  C15  C17  107.59  3.000
 5U7  H1   C15  C14  109.13  3.000
 5U7  C17  C15  C14  109.50  3.000
 5U7  O24  C15  C14  111.01  3.000
 5U7  H3   C16  O25  111.41  3.000
 5U7  H3   C16  C18  108.36  3.000
 5U7  O25  C16  C18  109.80  3.000
 5U7  H3   C16  C14  109.59  3.000
 5U7  C18  C16  C14  109.12  3.000
 5U7  O25  C16  C14  108.53  3.000
 5U7  H    C17  O22  110.32  3.000
 5U7  H    C17  C20  108.88  3.000
 5U7  O22  C17  C20  107.01  3.000
 5U7  H    C17  C15  108.33  3.000
 5U7  O22  C17  C15  110.58  3.000
 5U7  C20  C17  C15  111.71  3.000
 5U7  H4   C18  O27  110.12  3.000
 5U7  H4   C18  O22  106.08  3.000
 5U7  O27  C18  O22  112.39  3.000
 5U7  H4   C18  C16  109.81  3.000
 5U7  O27  C18  C16  106.37  3.000
 5U7  O22  C18  C16  112.11  3.000
 5U7  H21  C19  H20  108.47  3.000
 5U7  H21  C19  H22  108.38  3.000
 5U7  H20  C19  H22  108.35  3.000
 5U7  H21  C19  N    108.35  3.000
 5U7  H20  C19  N    112.01  3.000
 5U7  H22  C19  N    111.18  3.000
 5U7  H27  C20  H26  107.07  3.000
 5U7  H27  C20  O26  111.88  3.000
 5U7  H26  C20  O26  111.62  3.000
 5U7  H27  C20  C17  108.81  3.000
 5U7  H26  C20  C17  108.36  3.000
 5U7  O26  C20  C17  109.01  3.000
 5U7  C18  O22  C17  116.34  3.000
 5U7  H8   O23  C14  108.79  3.000
 5U7  H9   O24  C15  107.72  3.000
 5U7  H7   O25  C16  108.66  3.000
 5U7  H10  O26  C20  107.80  3.000
 5U7  C18  O27  C12  120.71  3.000
 5U7  N1   C02  O3   122.52  3.000
 5U7  O3   C02  C1   120.95  3.000
 5U7  N1   C02  C1   116.53  3.000
 5U7  H6   N1   C21  117.67  3.000
 5U7  H6   N1   C02  119.86  3.000
 5U7  C21  N1   C02  122.10  3.000
 5U7  H25  C21  H24  108.46  3.000
 5U7  H25  C21  H23  108.33  3.000
 5U7  H24  C21  H23  108.43  3.000
 5U7  H25  C21  N1   111.98  3.000
 5U7  H24  C21  N1   108.39  3.000
 5U7  H23  C21  N1   111.15  3.000
 5U7  C13  C01  C8   117.80  3.000
 5U7  C13  C01  C5   122.63  3.000
 5U7  C8   C01  C5   119.52  3.000
 5U7  H5   N    C19  117.52  3.000
 5U7  H5   N    C13  119.97  3.000
 5U7  C19  N    C13  121.95  3.000
 5U7  H14  C11  H15  107.84  3.000
 5U7  H14  C11  H16  106.88  3.000
 5U7  H15  C11  H16  107.88  3.000
 5U7  H14  C11  C7   111.67  3.000
 5U7  H15  C11  C7   110.59  3.000
 5U7  H16  C11  C7   111.78  3.000
 5U7  N    C13  C01  116.56  3.000
 5U7  N    C13  O21  122.48  3.000
 5U7  C01  C13  O21  120.96  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
 5U7  CONST_01  C9   C10  C2   C1    180.00   0.0  0
 5U7  CONST_02  C8   C10  C2   C1      0.00   0.0  0
 5U7  CONST_03  C8   C01  C5   C1      0.00   0.0  0
 5U7  CONST_06  C01  C8   C10  C2      0.00   0.0  0
 5U7  CONST_07  C01  C5   C1   C2      0.00   0.0  0
 5U7  CONST_08  C7   C12  C6   C3      0.00   0.0  0
 5U7  CONST_09  C7   C4   C9   C3      0.00   0.0  0
 5U7  CONST_11  C6   C12  C7   C4      0.00   0.0  0
 5U7  CONST_12  C6   C3   C9   C4      0.00   0.0  0
 5U7  CONST_14  C10  C2   C1   C5      0.00   0.0  0
 5U7  CONST_15  C10  C8   C01  C5      0.00   0.0  0
 5U7  CONST_16  C10  C9   C3   C6    180.00   0.0  0
 5U7  CONST_17  C10  C9   C4   C7    180.00   0.0  0
 5U7  CONST_18  C12  C7   C4   C9      0.00   0.0  0
 5U7  CONST_19  C12  C6   C3   C9      0.00   0.0  0
 5U7  CONST_20  C01  C8   C10  C9    180.00   0.0  0
 5U7  CONST_21  C13  C01  C5   C1    180.00   0.0  0
 5U7  CONST_22  O27  C12  C6   C3    180.00   0.0  0
 5U7  CONST_23  O27  C12  C7   C4    180.00   0.0  0
 5U7  CONST_24  C11  C7   C12  C6    180.00   0.0  0
 5U7  CONST_25  C11  C7   C4   C9    180.00   0.0  0
 5U7  CONST_26  C02  C1   C2   C10   180.00   0.0  0
 5U7  CONST_27  C13  C01  C8   C10   180.00   0.0  0
 5U7  CONST_28  C01  C5   C1   C02   180.00   0.0  0
 5U7  CONST_29  H19  C8   C10  C2    180.00   0.0  0
 5U7  CONST_30  H18  C5   C1   C2    180.00   0.0  0
 5U7  CONST_31  H13  C4   C9   C3    180.00   0.0  0
 5U7  CONST_32  H12  C3   C9   C4    180.00   0.0  0
 5U7  CONST_33  H17  C2   C1   C5    180.00   0.0  0
 5U7  CONST_34  H11  C6   C12  C7    180.00   0.0  0
 5U7  CONST_35  C21  N1   C02  C1    180.00   0.0  0
 5U7  CONST_36  C01  C13  N    C19   180.00   0.0  0
 5U7  CONST_37  H6   N1   C02  C1      0.00   0.0  0
 5U7  CONST_38  H5   N    C13  C01     0.00   0.0  0
 5U7  CONST_39  O21  C13  N    C19     0.00   0.0  0
 5U7  CONST_40  C21  N1   C02  O3      0.00   0.0  0
 5U7  Var_01    N1   C02  C1   C2   -156.24  30.0  2
 5U7  Var_02    N    C13  C01  C5    -26.13  30.0  2
 5U7  Var_03    H16  C11  C7   C4   -123.65  30.0  2
 5U7  Var_04    H22  C19  N    C13   -56.05  30.0  3
 5U7  Var_05    H23  C21  N1   C02    55.50  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
 5U7  chir_01  C14  C15  O23  C16  positiv
 5U7  chir_02  C15  O24  C14  C17  negativ
 5U7  chir_03  C16  O25  C18  C14  positiv
 5U7  chir_04  C17  O22  C15  C20  negativ
 5U7  chir_05  C18  O27  O22  C16  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
 5U7  plan-1  C1   0.020
 5U7  plan-1  C2   0.020
 5U7  plan-1  C5   0.020
 5U7  plan-1  C8   0.020
 5U7  plan-1  C9   0.020
 5U7  plan-1  C10  0.020
 5U7  plan-1  C02  0.020
 5U7  plan-1  C01  0.020
 5U7  plan-1  H17  0.020
 5U7  plan-1  H18  0.020
 5U7  plan-1  H19  0.020
 5U7  plan-1  C13  0.020
 5U7  plan-2  C3   0.020
 5U7  plan-2  C4   0.020
 5U7  plan-2  C6   0.020
 5U7  plan-2  C7   0.020
 5U7  plan-2  C9   0.020
 5U7  plan-2  C10  0.020
 5U7  plan-2  C12  0.020
 5U7  plan-2  O27  0.020
 5U7  plan-2  H12  0.020
 5U7  plan-2  H13  0.020
 5U7  plan-2  H11  0.020
 5U7  plan-2  C11  0.020
 5U7  plan-3  C1   0.020
 5U7  plan-3  O3   0.020
 5U7  plan-3  C02  0.020
 5U7  plan-3  N1   0.020
 5U7  plan-3  C21  0.020
 5U7  plan-3  H6   0.020
 5U7  plan-4  C19  0.020
 5U7  plan-4  O21  0.020
 5U7  plan-4  C01  0.020
 5U7  plan-4  N    0.020
 5U7  plan-4  H5   0.020
 5U7  plan-4  C13  0.020

