# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 03:08:16 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2R)-N~4~-hydroxy-2-(3-hydroxybenzyl)-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)C[C@@H](Cc1cccc(O)c1)C(=O)N[C@@H]2[C@H](O)Cc3ccccc23
#
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
 099  099  (2R)-N~4~-hydroxy-2-(3-hydroxybenzyl)-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide  ligand  49  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_099
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
 099  C4    C  CR16  0  -0.325  -5.2439  -0.3559   0.9997
 099  C5    C  CR16  0  -0.289  -3.6260  -0.7550  -1.2569
 099  C6    C  CR16  0  -0.358   4.0105  -1.3179  -0.4472
 099  C7    C  CR16  0  -0.354   5.8893  -0.4459   0.7923
 099  C8    C  CR16  0  -0.439   4.1343   1.0279   0.0431
 099  C10   C  CH2   0  -0.507   2.1423   0.1793  -1.2287
 099  C13   C  CR6   0   0.374   5.3434   0.8342   0.7031
 099  C15   C  CR56  0   0.143  -3.5363   0.4119  -0.5163
 099  C20   C  CH1   0  -0.405   1.0195   0.5473  -0.2532
 099  C1    C  CR16  0  -0.256  -5.3446  -1.5253   0.2533
 099  C2    C  CR16  0  -0.266  -4.5414  -1.7253  -0.8661
 099  C3    C  CR16  0  -0.225   5.2185  -1.5096   0.2138
 099  C9    C  CH2   0  -0.541  -4.0086   1.9320   1.2471
 099  C11   C  CH2   0  -0.593   0.8577  -0.4858   0.8687
 099  C12   C  CR6   0   0.142   3.4581  -0.0445  -0.5346
 099  C14   C  CR56  0   0.079  -4.3295   0.6112   0.6098
 099  C16   C  C     0   0.534   0.4820  -1.8536   0.3479
 099  C18   C  CR15  0   0.049  -3.3091   2.6821   0.0999
 099  C19   C  CR15  0  -0.230  -2.6071   1.5825  -0.7239
 099  N21   N  NH1   0  -0.376   1.1865  -2.8549   0.9129
 099  N22   N  NH1   0  -0.623  -1.2767   1.3045  -0.2264
 099  O24   O  OH1   0  -0.663  -2.3997   3.6718   0.4892
 099  O25   O  OH1   0  -0.544   1.0516  -4.1268   0.4437
 099  O26   O  O     0  -0.450  -0.4055  -2.0271  -0.4656
 099  H4    H  HCR6  0   0.248  -5.8715  -0.2106   1.8705
 099  H5    H  HCR6  0   0.243  -2.9942  -0.9057  -2.1223
 099  H6    H  HCR6  0   0.248   3.5052  -2.1578  -0.9073
 099  H7    H  HCR6  0   0.261   6.8304  -0.5977   1.3057
 099  H8    H  HCR6  0   0.263   3.7173   2.0282  -0.0302
 099  H10   H  HCH2  0   0.253   1.8717  -0.7155  -1.7918
 099  H10A  H  HCH2  0   0.264   2.2494   0.9829  -1.9601
 099  H20   H  HCH1  0   0.293   1.2921   1.4852   0.2428
 099  H1    H  HCR6  0   0.253  -6.0551  -2.2882   0.5454
 099  H2    H  HCR6  0   0.252  -4.6310  -2.6423  -1.4344
 099  H3    H  HCR6  0   0.256   5.6444  -2.5027   0.2788
 099  H9    H  HCH2  0   0.261  -4.8860   2.4625   1.6212
 099  H9A   H  HCH2  0   0.253  -3.3259   1.7976   2.0937
 099  H11   H  HCH2  0   0.273   1.7758  -0.5157   1.4583
 099  H11A  H  HCH2  0   0.287   0.0774  -0.1801   1.5707
 099  H18   H  HCR5  0   0.237  -4.0938   3.0949  -0.5485
 099  H19   H  HCR5  0   0.273  -2.5201   1.8670  -1.7723
 099  HN21  H  HNH1  0   0.410   2.0436  -2.6827   1.4188
 099  HN22  H  HNH1  0   0.392  -1.1193   1.3878   0.7649
 099  HO23  H  HOH1  0   0.473   5.5584   2.6807   1.1452
 099  HO24  H  HOH1  0   0.457  -2.8819   4.3555   0.9645
 099  HO25  H  HOH1  0   0.478   0.4481  -4.5743   1.0505
 099  C17   C  C     0   0.624  -0.2854   0.8241  -0.9984
 099  O23   O  OH1   0  -0.634   6.0279   1.8486   1.2702
 099  O27   O  O     0  -0.498  -0.3966   0.6855  -2.2065

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
 099  C4   C1    aromatic  1.391  0.020  1.391
 099  C4   C14   aromatic  1.387  0.020  1.387
 099  C5   C15   aromatic  1.385  0.020  1.385
 099  C5   C2    aromatic  1.390  0.020  1.390
 099  C6   C3    aromatic  1.390  0.020  1.390
 099  C6   C12   aromatic  1.391  0.020  1.391
 099  C7   C13   aromatic  1.395  0.020  1.395
 099  C7   C3    aromatic  1.384  0.020  1.384
 099  C8   C13   aromatic  1.391  0.020  1.391
 099  C8   C12   aromatic  1.393  0.020  1.393
 099  C10  C20   single    1.532  0.020  1.532
 099  C10  C12   single    1.504  0.020  1.504
 099  C13  O23   single    1.349  0.020  1.349
 099  C15  C14   aromatic  1.392  0.020  1.392
 099  C15  C19   single    1.509  0.020  1.509
 099  C17  C20   single    1.528  0.020  1.528
 099  C17  N22   single    1.345  0.020  1.345
 099  C17  O27   double    1.221  0.020  1.221
 099  C20  C11   single    1.534  0.020  1.534
 099  C1   C2    aromatic  1.392  0.020  1.392
 099  C9   C14   single    1.501  0.020  1.501
 099  C9   C18   single    1.539  0.020  1.539
 099  C11  C16   single    1.511  0.020  1.511
 099  C16  N21   single    1.348  0.020  1.348
 099  C16  O26   double    1.216  0.020  1.216
 099  C18  C19   single    1.543  0.020  1.543
 099  C18  O24   single    1.399  0.020  1.399
 099  C19  N22   single    1.447  0.020  1.447
 099  N21  O25   single    1.362  0.020  1.362
 099  C4   H4    single    0.930  0.020  1.080
 099  C5   H5    single    0.930  0.020  1.080
 099  C6   H6    single    0.930  0.020  1.080
 099  C7   H7    single    0.930  0.020  1.080
 099  C8   H8    single    0.930  0.020  1.080
 099  C10  H10   single    0.970  0.020  1.090
 099  C10  H10A  single    0.970  0.020  1.090
 099  C20  H20   single    0.970  0.020  1.090
 099  C1   H1    single    0.930  0.020  1.080
 099  C2   H2    single    0.930  0.020  1.080
 099  C3   H3    single    0.930  0.020  1.080
 099  C9   H9    single    0.970  0.020  1.090
 099  C9   H9A   single    0.970  0.020  1.090
 099  C11  H11   single    0.970  0.020  1.090
 099  C11  H11A  single    0.970  0.020  1.090
 099  C18  H18   single    0.970  0.020  1.090
 099  C19  H19   single    0.970  0.020  1.090
 099  N21  HN21  single    0.890  0.020  1.040
 099  N22  HN22  single    0.860  0.020  1.020
 099  O23  HO23  single    0.850  0.020  0.980
 099  O24  HO24  single    0.850  0.020  0.980
 099  O25  HO25  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
 099  H4    C4   C14  120.97  3.000
 099  H4    C4   C1   120.14  3.000
 099  C14   C4   C1   118.89  3.000
 099  H5    C5   C2   120.80  3.000
 099  H5    C5   C15  120.48  3.000
 099  C2    C5   C15  118.72  3.000
 099  H6    C6   C12  119.88  3.000
 099  H6    C6   C3   120.04  3.000
 099  C12   C6   C3   120.08  3.000
 099  H7    C7   C3   120.77  3.000
 099  H7    C7   C13  119.95  3.000
 099  C3    C7   C13  119.27  3.000
 099  H8    C8   C12  119.64  3.000
 099  H8    C8   C13  119.60  3.000
 099  C12   C8   C13  120.76  3.000
 099  H10A  C10  H10  106.39  3.000
 099  H10A  C10  C12  109.43  3.000
 099  H10   C10  C12  109.45  3.000
 099  H10A  C10  C20  108.76  3.000
 099  H10   C10  C20  110.11  3.000
 099  C12   C10  C20  112.52  3.000
 099  O23   C13  C8   122.41  3.000
 099  O23   C13  C7   117.70  3.000
 099  C8    C13  C7   119.89  3.000
 099  C19   C15  C14  110.56  3.000
 099  C19   C15  C5   128.32  3.000
 099  C14   C15  C5   121.09  3.000
 099  H20   C20  C11  105.77  3.000
 099  H20   C20  C17  106.16  3.000
 099  C11   C20  C17  112.87  3.000
 099  H20   C20  C10  108.16  3.000
 099  C11   C20  C10  112.41  3.000
 099  C17   C20  C10  111.03  3.000
 099  H1    C1   C2   119.63  3.000
 099  H1    C1   C4   119.68  3.000
 099  C2    C1   C4   120.69  3.000
 099  H2    C2   C1   119.74  3.000
 099  H2    C2   C5   119.88  3.000
 099  C1    C2   C5   120.38  3.000
 099  H3    C3   C7   119.29  3.000
 099  H3    C3   C6   119.79  3.000
 099  C7    C3   C6   120.92  3.000
 099  H9A   C9   H9   107.20  3.000
 099  H9A   C9   C18  110.64  3.000
 099  H9    C9   C18  112.58  3.000
 099  H9A   C9   C14  110.69  3.000
 099  H9    C9   C14  113.66  3.000
 099  C18   C9   C14  102.10  3.000
 099  H11A  C11  H11  105.14  3.000
 099  H11A  C11  C16  107.28  3.000
 099  H11   C11  C16  111.75  3.000
 099  H11A  C11  C20  110.90  3.000
 099  H11   C11  C20  108.95  3.000
 099  C16   C11  C20  112.57  3.000
 099  C10   C12  C8   120.09  3.000
 099  C10   C12  C6   120.83  3.000
 099  C8    C12  C6   119.08  3.000
 099  C9    C14  C15  110.34  3.000
 099  C9    C14  C4   129.43  3.000
 099  C15   C14  C4   120.22  3.000
 099  O26   C16  N21  123.75  3.000
 099  O26   C16  C11  122.75  3.000
 099  N21   C16  C11  113.45  3.000
 099  H18   C18  O24  111.27  3.000
 099  H18   C18  C19  106.12  3.000
 099  O24   C18  C19  110.91  3.000
 099  H18   C18  C9   107.37  3.000
 099  O24   C18  C9   115.64  3.000
 099  C19   C18  C9   104.92  3.000
 099  H19   C19  N22  107.91  3.000
 099  H19   C19  C18  111.34  3.000
 099  N22   C19  C18  111.82  3.000
 099  H19   C19  C15  112.58  3.000
 099  N22   C19  C15  111.70  3.000
 099  C18   C19  C15  101.50  3.000
 099  HN21  N21  O25  114.56  3.000
 099  HN21  N21  C16  121.77  3.000
 099  O25   N21  C16  119.82  3.000
 099  HN22  N22  C19  117.78  3.000
 099  HN22  N22  C17  118.64  3.000
 099  C19   N22  C17  123.28  3.000
 099  HO24  O24  C18  108.32  3.000
 099  HO25  O25  N21  106.15  3.000
 099  O27   C17  N22  122.77  3.000
 099  O27   C17  C20  122.67  3.000
 099  N22   C17  C20  114.47  3.000
 099  HO23  O23  C13  110.34  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
 099  CONST_01  C5    C2   C1   C4      0.00   0.0  0
 099  CONST_02  C5    C15  C14  C4      0.00   0.0  0
 099  CONST_03  C13   C7   C3   C6      0.00   0.0  0
 099  CONST_04  C13   C8   C12  C6      0.00   0.0  0
 099  CONST_05  C12   C8   C13  C7      0.00   0.0  0
 099  CONST_06  C12   C6   C3   C7      0.00   0.0  0
 099  CONST_07  C3    C7   C13  C8      0.00   0.0  0
 099  CONST_08  C3    C6   C12  C8      0.00   0.0  0
 099  CONST_09  C1    C2   C5   C15     0.00   0.0  0
 099  CONST_10  C1    C4   C14  C15     0.00   0.0  0
 099  CONST_11  C14   C15  C5   C2      0.00   0.0  0
 099  CONST_12  C14   C4   C1   C2      0.00   0.0  0
 099  CONST_13  C3    C6   C12  C10   180.00   0.0  0
 099  CONST_14  C13   C8   C12  C10   180.00   0.0  0
 099  CONST_15  O23   C13  C7   C3    180.00   0.0  0
 099  CONST_16  O23   C13  C8   C12   180.00   0.0  0
 099  CONST_17  H2    C2   C1   C4    180.00   0.0  0
 099  CONST_18  H1    C1   C2   C5    180.00   0.0  0
 099  CONST_19  H7    C7   C3   C6    180.00   0.0  0
 099  CONST_20  H8    C8   C12  C6    180.00   0.0  0
 099  CONST_21  H6    C6   C3   C7    180.00   0.0  0
 099  CONST_22  H3    C3   C7   C13   180.00   0.0  0
 099  CONST_23  H4    C4   C14  C15   180.00   0.0  0
 099  CONST_24  H5    C5   C2   C1    180.00   0.0  0
 099  CONST_25  C19   N22  C17  C20   180.00   0.0  0
 099  CONST_26  O27   C17  N22  C19     0.00   0.0  0
 099  CONST_27  O25   N21  C16  C11   180.00   0.0  0
 099  CONST_28  O26   C16  N21  O25     0.00   0.0  0
 099  CONST_29  HN22  N22  C17  C20     0.00   0.0  0
 099  Var_01    C18   C9   C14  C4   -161.47  30.0  1
 099  Var_02    C20   C10  C12  C6    110.26  30.0  1
 099  Var_03    N21   C16  C11  C20   134.98  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
 099  chir_01  C20  C10  C17  C11  negativ
 099  chir_02  C18  O24  C9   C19  positiv
 099  chir_03  C19  N22  C18  C15  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
 099  plan-1  C6    0.020
 099  plan-1  C7    0.020
 099  plan-1  C8    0.020
 099  plan-1  C10   0.020
 099  plan-1  C13   0.020
 099  plan-1  C3    0.020
 099  plan-1  C12   0.020
 099  plan-1  H6    0.020
 099  plan-1  H7    0.020
 099  plan-1  H8    0.020
 099  plan-1  H3    0.020
 099  plan-1  O23   0.020
 099  plan-2  C4    0.020
 099  plan-2  C5    0.020
 099  plan-2  C15   0.020
 099  plan-2  C1    0.020
 099  plan-2  C2    0.020
 099  plan-2  C9    0.020
 099  plan-2  C14   0.020
 099  plan-2  C19   0.020
 099  plan-2  H4    0.020
 099  plan-2  H5    0.020
 099  plan-2  H1    0.020
 099  plan-2  H2    0.020
 099  plan-3  C11   0.020
 099  plan-3  C16   0.020
 099  plan-3  N21   0.020
 099  plan-3  O25   0.020
 099  plan-3  O26   0.020
 099  plan-3  HN21  0.020
 099  plan-4  C20   0.020
 099  plan-4  C19   0.020
 099  plan-4  N22   0.020
 099  plan-4  HN22  0.020
 099  plan-4  C17   0.020
 099  plan-4  O27   0.020

