# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 10:22:02 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (3R)-N~2~-(cyclopropylmethyl)-N~1~-hydroxy-3-(3-hydroxybenzyl)-N~4~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-L-aspartamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@@H](NCC1CC1)[C@@H](Cc2cccc(O)c2)C(=O)N[C@@H]3[C@H](O)Cc4ccccc34
#
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
 098  098  (3R)-N~2~-(cyclopropylmethyl)-N~1~-hydroxy-3-(3-hydroxybenzyl)-N~4~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-L-aspartamide  ligand  61  32  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_098
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
 098  C5    C  CH1   0  -0.201   2.2481   1.0277   0.1312
 098  C7    C  CH2   0  -0.274   4.3507   1.9527  -0.6732
 098  C8    C  CH1   0  -0.264   5.5661   1.6308  -1.4958
 098  C10   C  CH2   0  -0.494   6.8563   2.3363  -1.2218
 098  C13   C  CR6   0   0.127   0.5782  -2.4589  -0.4405
 098  C15   C  CR16  0  -0.245  -0.7079  -3.5456  -2.1610
 098  C17   C  CR6   0   0.368  -1.2567  -3.9192   0.1487
 098  C20   C  C     0   0.587  -0.0931   0.1748   0.5492
 098  C24   C  CR15  0  -0.007  -3.4359  -0.8235  -0.0060
 098  C26   C  CH2   0  -0.507  -4.8502  -0.2434   0.0836
 098  C28   C  CR16  0  -0.335  -5.5996   2.1061  -0.7862
 098  N2    N  NH1   0  -0.362   2.1425   2.2181   2.2200
 098  C3    C  C     0   0.525   2.5576   1.0875   1.6286
 098  O4    O  O     0  -0.474   3.1924   0.2191   2.2024
 098  N6    N  NH1   0  -0.599   3.4480   0.8117  -0.6472
 098  C9    C  CH2   0  -0.489   6.7059   0.8882  -0.8629
 098  C11   C  CH1   0  -0.383   1.1924  -0.0360  -0.2290
 098  C12   C  CH2   0  -0.517   1.6528  -1.4915  -0.0256
 098  C14   C  CR16  0  -0.333   0.3276  -2.7011  -1.7912
 098  C16   C  CR16  0  -0.418  -1.5096  -4.1532  -1.2009
 098  O18   O  OH1   0  -0.632  -1.9911  -4.4743   1.1323
 098  C19   C  CR16  0  -0.381  -0.2153  -3.0710   0.5208
 098  O21   O  O     0  -0.480  -0.0978   0.1957   1.7721
 098  N22   N  NH1   0  -0.640  -1.2020   0.2968  -0.2008
 098  C23   C  CR15  0  -0.136  -2.5336   0.3936   0.3300
 098  C27   C  CR56  0   0.093  -4.6649   1.1895  -0.3339
 098  C29   C  CR16  0  -0.257  -5.1778   3.3929  -1.1105
 098  C30   C  CR16  0  -0.261  -3.8404   3.7529  -0.9831
 098  C31   C  CR16  0  -0.320  -2.9030   2.8312  -0.5252
 098  C32   C  CR56  0   0.110  -3.3301   1.5551  -0.2037
 098  H5    H  HCH1  0   0.270   1.8313   1.9905  -0.1874
 098  H7    H  HCH2  0   0.201   4.6731   2.2762   0.3290
 098  H7A   H  HCH2  0   0.235   3.8157   2.7993  -1.1137
 098  H8    H  HCH1  0   0.255   5.3572   1.3933  -2.5340
 098  H10   H  HCH2  0   0.251   7.4867   2.5925  -2.0635
 098  H10A  H  HCH2  0   0.245   6.8795   3.0593  -0.4154
 098  H15   H  HCR6  0   0.265  -0.9053  -3.7345  -3.2083
 098  H24   H  HCR5  0   0.236  -3.2787  -1.6376   0.7094
 098  H26   H  HCH2  0   0.261  -5.5635  -0.7958  -0.5300
 098  H26A  H  HCH2  0   0.263  -5.2052  -0.2970   1.1170
 098  H28   H  HCR6  0   0.249  -6.6413   1.8293  -0.8957
 098  HO1   H  HOH1  0   0.473   1.5728   1.9532   3.9929
 098  HN2   H  HNH1  0   0.411   1.5499   2.8926   1.7584
 098  HN6   H  HNH1  0   0.352   3.9497   0.0109  -0.2798
 098  H9    H  HCH2  0   0.243   6.6266   0.6328   0.1878
 098  H9A   H  HCH2  0   0.250   7.2341   0.1551  -1.4586
 098  H11   H  HCH1  0   0.274   1.0047   0.1047  -1.2978
 098  H12   H  HCH2  0   0.267   1.9264  -1.6604   1.0148
 098  H12A  H  HCH2  0   0.262   2.5448  -1.6609  -0.6315
 098  H14   H  HCR6  0   0.251   0.9397  -2.2278  -2.5493
 098  H16   H  HCR6  0   0.276  -2.3201  -4.8072  -1.5028
 098  HO18  H  HOH1  0   0.475  -2.6874  -5.0261   0.7593
 098  H19   H  HCR6  0   0.261  -0.0327  -2.8841   1.5728
 098  HN22  H  HNH1  0   0.399  -1.1051   0.2682  -1.2039
 098  H23   H  HCR5  0   0.283  -2.4501   0.4761   1.4167
 098  H29   H  HCR6  0   0.254  -5.8962   4.1184  -1.4709
 098  H30   H  HCR6  0   0.254  -3.5269   4.7551  -1.2459
 098  H31   H  HCR6  0   0.244  -1.8599   3.1101  -0.4329
 098  O25   O  OH1   0  -0.667  -3.2257  -1.2598  -1.3282
 098  O1    O  OH1   0  -0.545   2.3070   2.4077   3.5566
 098  HO25  H  HOH1  0   0.455  -2.4464  -1.8253  -1.3489

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
 098  C5   C3    single    1.530  0.020  1.530
 098  C5   N6    single    1.447  0.020  1.447
 098  C5   C11   single    1.541  0.020  1.541
 098  C7   C8    single    1.502  0.020  1.502
 098  C7   N6    single    1.455  0.020  1.455
 098  C8   C10   single    1.496  0.020  1.496
 098  C8   C9    single    1.500  0.020  1.500
 098  C10  C9    single    1.499  0.020  1.499
 098  C13  C12   single    1.504  0.020  1.504
 098  C13  C14   aromatic  1.395  0.020  1.395
 098  C13  C19   aromatic  1.389  0.020  1.389
 098  C15  C14   aromatic  1.386  0.020  1.386
 098  C15  C16   aromatic  1.391  0.020  1.391
 098  C17  C16   aromatic  1.393  0.020  1.393
 098  C17  O18   single    1.347  0.020  1.347
 098  C17  C19   aromatic  1.394  0.020  1.394
 098  C20  C11   single    1.517  0.020  1.517
 098  C20  O21   double    1.223  0.020  1.223
 098  C20  N22   single    1.344  0.020  1.344
 098  C24  C26   single    1.531  0.020  1.531
 098  C24  C23   single    1.552  0.020  1.552
 098  C24  O25   single    1.408  0.020  1.408
 098  C26  C27   single    1.504  0.020  1.504
 098  C28  C27   aromatic  1.385  0.020  1.385
 098  C28  C29   aromatic  1.392  0.020  1.392
 098  O1   N2    single    1.360  0.020  1.360
 098  N2   C3    single    1.342  0.020  1.342
 098  C3   O4    double    1.219  0.020  1.219
 098  C11  C12   single    1.540  0.020  1.540
 098  N22  C23   single    1.437  0.020  1.437
 098  C23  C32   single    1.506  0.020  1.506
 098  C27  C32   aromatic  1.390  0.020  1.390
 098  C29  C30   aromatic  1.391  0.020  1.391
 098  C30  C31   aromatic  1.392  0.020  1.392
 098  C31  C32   aromatic  1.384  0.020  1.384
 098  C5   H5    single    0.970  0.020  1.090
 098  C7   H7    single    0.970  0.020  1.090
 098  C7   H7A   single    0.970  0.020  1.090
 098  C8   H8    single    0.970  0.020  1.090
 098  C10  H10   single    0.970  0.020  1.090
 098  C10  H10A  single    0.970  0.020  1.090
 098  C15  H15   single    0.930  0.020  1.080
 098  C24  H24   single    0.970  0.020  1.090
 098  C26  H26   single    0.970  0.020  1.090
 098  C26  H26A  single    0.970  0.020  1.090
 098  C28  H28   single    0.930  0.020  1.080
 098  O1   HO1   single    0.850  0.020  0.980
 098  N2   HN2   single    0.860  0.020  1.020
 098  N6   HN6   single    0.890  0.020  1.040
 098  C9   H9    single    0.970  0.020  1.090
 098  C9   H9A   single    0.970  0.020  1.090
 098  C11  H11   single    0.970  0.020  1.090
 098  C12  H12   single    0.970  0.020  1.090
 098  C12  H12A  single    0.970  0.020  1.090
 098  C14  H14   single    0.930  0.020  1.080
 098  C16  H16   single    0.930  0.020  1.080
 098  O18  HO18  single    0.850  0.020  0.980
 098  C19  H19   single    0.930  0.020  1.080
 098  N22  HN22  single    0.860  0.020  1.020
 098  C23  H23   single    0.970  0.020  1.090
 098  O25  HO25  single    0.850  0.020  0.980
 098  C29  H29   single    0.930  0.020  1.080
 098  C30  H30   single    0.930  0.020  1.080
 098  C31  H31   single    0.930  0.020  1.080

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
 098  H5    C5   C11  106.13  3.000
 098  H5    C5   N6   106.86  3.000
 098  C11   C5   N6   109.84  3.000
 098  H5    C5   C3   109.08  3.000
 098  C11   C5   C3   113.22  3.000
 098  N6    C5   C3   111.38  3.000
 098  H7A   C7   H7   106.39  3.000
 098  H7A   C7   N6   108.09  3.000
 098  H7    C7   N6   113.30  3.000
 098  H7A   C7   C8   109.94  3.000
 098  H7    C7   C8   108.93  3.000
 098  N6    C7   C8   110.09  3.000
 098  H8    C8   C9   116.20  3.000
 098  H8    C8   C10  116.39  3.000
 098  C9    C8   C10   60.06  3.000
 098  H8    C8   C7   114.52  3.000
 098  C9    C8   C7   119.32  3.000
 098  C10   C8   C7   119.76  3.000
 098  H10A  C10  H10  114.11  3.000
 098  H10A  C10  C9   117.93  3.000
 098  H10   C10  C9   118.24  3.000
 098  H10A  C10  C8   118.01  3.000
 098  H10   C10  C8   118.13  3.000
 098  C9    C10  C8    60.12  3.000
 098  C19   C13  C14  119.41  3.000
 098  C19   C13  C12  120.05  3.000
 098  C14   C13  C12  120.47  3.000
 098  H15   C15  C16  119.12  3.000
 098  H15   C15  C14  120.04  3.000
 098  C16   C15  C14  120.84  3.000
 098  C19   C17  O18  117.60  3.000
 098  C19   C17  C16  119.77  3.000
 098  O18   C17  C16  122.63  3.000
 098  N22   C20  O21  123.58  3.000
 098  N22   C20  C11  115.17  3.000
 098  O21   C20  C11  121.23  3.000
 098  H24   C24  O25  111.20  3.000
 098  H24   C24  C23  110.98  3.000
 098  O25   C24  C23  111.07  3.000
 098  H24   C24  C26  112.09  3.000
 098  O25   C24  C26  108.07  3.000
 098  C23   C24  C26  103.14  3.000
 098  H26A  C26  H26  107.11  3.000
 098  H26A  C26  C27  110.42  3.000
 098  H26   C26  C27  114.01  3.000
 098  H26A  C26  C24  109.66  3.000
 098  H26   C26  C24  112.28  3.000
 098  C27   C26  C24  103.35  3.000
 098  H28   C28  C29  120.25  3.000
 098  H28   C28  C27  120.85  3.000
 098  C29   C28  C27  118.89  3.000
 098  HN2   N2   C3   122.89  3.000
 098  HN2   N2   O1   115.29  3.000
 098  C3    N2   O1   120.89  3.000
 098  O4    C3   N2   123.63  3.000
 098  O4    C3   C5   122.55  3.000
 098  N2    C3   C5   113.69  3.000
 098  HN6   N6   C7   108.60  3.000
 098  HN6   N6   C5   109.48  3.000
 098  C7    N6   C5   114.02  3.000
 098  H9A   C9   H9   114.17  3.000
 098  H9A   C9   C10  118.26  3.000
 098  H9    C9   C10  117.83  3.000
 098  H9A   C9   C8   118.28  3.000
 098  H9    C9   C8   118.03  3.000
 098  C10   C9   C8    59.82  3.000
 098  H11   C11  C12  107.56  3.000
 098  H11   C11  C20  109.74  3.000
 098  C12   C11  C20  108.47  3.000
 098  H11   C11  C5   104.90  3.000
 098  C12   C11  C5   114.62  3.000
 098  C20   C11  C5   111.38  3.000
 098  H12A  C12  H12  107.51  3.000
 098  H12A  C12  C11  108.52  3.000
 098  H12   C12  C11  110.36  3.000
 098  H12A  C12  C13  109.32  3.000
 098  H12   C12  C13  110.07  3.000
 098  C11   C12  C13  110.97  3.000
 098  H14   C14  C15  120.10  3.000
 098  H14   C14  C13  120.02  3.000
 098  C15   C14  C13  119.88  3.000
 098  H16   C16  C17  120.45  3.000
 098  H16   C16  C15  120.15  3.000
 098  C17   C16  C15  119.40  3.000
 098  HO18  O18  C17  110.32  3.000
 098  H19   C19  C17  119.33  3.000
 098  H19   C19  C13  119.97  3.000
 098  C17   C19  C13  120.69  3.000
 098  HN22  N22  C23  117.30  3.000
 098  HN22  N22  C20  118.24  3.000
 098  C23   N22  C20  124.37  3.000
 098  H23   C23  C32  109.54  3.000
 098  H23   C23  N22  107.56  3.000
 098  C32   C23  N22  114.28  3.000
 098  H23   C23  C24  108.59  3.000
 098  C32   C23  C24  102.74  3.000
 098  N22   C23  C24  113.96  3.000
 098  C32   C27  C28  120.30  3.000
 098  C32   C27  C26  110.06  3.000
 098  C28   C27  C26  129.64  3.000
 098  H29   C29  C30  119.67  3.000
 098  H29   C29  C28  119.72  3.000
 098  C30   C29  C28  120.61  3.000
 098  H30   C30  C31  119.86  3.000
 098  H30   C30  C29  119.73  3.000
 098  C31   C30  C29  120.41  3.000
 098  H31   C31  C32  120.98  3.000
 098  H31   C31  C30  120.38  3.000
 098  C32   C31  C30  118.64  3.000
 098  C31   C32  C27  121.15  3.000
 098  C31   C32  C23  129.08  3.000
 098  C27   C32  C23  109.77  3.000
 098  HO25  O25  C24  108.84  3.000
 098  HO1   O1   N2   106.61  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
 098  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 098  CONST_02  C16   C17  C19  C13     0.00   0.0  0
 098  CONST_03  C19   C13  C14  C15     0.00   0.0  0
 098  CONST_04  C19   C17  C16  C15     0.00   0.0  0
 098  CONST_05  C14   C15  C16  C17     0.00   0.0  0
 098  CONST_06  C14   C13  C19  C17     0.00   0.0  0
 098  CONST_07  C31   C32  C27  C28     0.00   0.0  0
 098  CONST_08  C31   C30  C29  C28     0.00   0.0  0
 098  CONST_09  C30   C29  C28  C27     0.00   0.0  0
 098  CONST_10  C30   C31  C32  C27     0.00   0.0  0
 098  CONST_11  C32   C27  C28  C29     0.00   0.0  0
 098  CONST_12  C32   C31  C30  C29     0.00   0.0  0
 098  CONST_13  O18   C17  C19  C13   180.00   0.0  0
 098  CONST_14  C12   C13  C14  C15   180.00   0.0  0
 098  CONST_15  O18   C17  C16  C15   180.00   0.0  0
 098  CONST_16  C12   C13  C19  C17   180.00   0.0  0
 098  CONST_17  H15   C15  C14  C13   180.00   0.0  0
 098  CONST_18  H28   C28  C27  C26     0.00   0.0  0
 098  CONST_19  H30   C30  C29  C28   180.00   0.0  0
 098  CONST_20  H19   C19  C13  C14   180.00   0.0  0
 098  CONST_21  H16   C16  C15  C14   180.00   0.0  0
 098  CONST_22  H14   C14  C15  C16   180.00   0.0  0
 098  CONST_23  H31   C31  C32  C23     0.00   0.0  0
 098  CONST_24  H29   C29  C28  C27   180.00   0.0  0
 098  CONST_25  C23   N22  C20  C11   180.00   0.0  0
 098  CONST_26  C23   N22  C20  O21     0.00   0.0  0
 098  CONST_27  O1    N2   C3   C5    180.00   0.0  0
 098  CONST_28  O4    C3   N2   O1      0.00   0.0  0
 098  CONST_29  HN2   N2   C3   C5      0.00   0.0  0
 098  CONST_30  HN22  N22  C20  C11     0.00   0.0  0
 098  Var_01    C28   C27  C26  C24   160.81  30.0  1
 098  Var_02    C9    C10  C8   C7    108.76  30.0  1
 098  Var_03    H9    C9   C10  C8   -107.92  30.0  1
 098  Var_04    N6    C7   C8   C10  -153.74  30.0  1
 098  Var_05    C14   C13  C12  C11    75.69  30.0  2
 098  Var_06    C8    C7   N6   C5    179.67  30.0  1

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
 098  chir_01  C5   C3   N6   C11  negativ
 098  chir_03  C24  C26  C23  O25  positiv
 098  chir_04  C11  C5   C20  C12  positiv
 098  chir_05  C23  N22  C24  C32  positiv
 098  chir_06  C8   C7   C10  C9   both

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
 098  plan-1  C13   0.020
 098  plan-1  C15   0.020
 098  plan-1  C17   0.020
 098  plan-1  C12   0.020
 098  plan-1  C14   0.020
 098  plan-1  C16   0.020
 098  plan-1  O18   0.020
 098  plan-1  C19   0.020
 098  plan-1  H15   0.020
 098  plan-1  H14   0.020
 098  plan-1  H16   0.020
 098  plan-1  H19   0.020
 098  plan-2  C26   0.020
 098  plan-2  C28   0.020
 098  plan-2  C23   0.020
 098  plan-2  C27   0.020
 098  plan-2  C29   0.020
 098  plan-2  C30   0.020
 098  plan-2  C31   0.020
 098  plan-2  C32   0.020
 098  plan-2  H28   0.020
 098  plan-2  H29   0.020
 098  plan-2  H30   0.020
 098  plan-2  H31   0.020
 098  plan-3  C20   0.020
 098  plan-3  C11   0.020
 098  plan-3  O21   0.020
 098  plan-3  N22   0.020
 098  plan-3  C23   0.020
 098  plan-3  HN22  0.020
 098  plan-4  C5    0.020
 098  plan-4  N2    0.020
 098  plan-4  C3    0.020
 098  plan-4  O4    0.020
 098  plan-4  HN2   0.020
 098  plan-4  O1    0.020

