# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:51:54 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-{[(2S)-3,3-dimethyl-2-(pyridin-3-yl)-2,3-dihydro-1H-indol-1-yl]methyl}-N-hydroxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)[C@H](N(Cc2ccc(cc2)C(=O)NO)c3ccccc13)c4cccnc4
#
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
 QQD  QQD  4-{[(2S)-3,3-dimethyl-2-(pyridin-3-yl)-2,3-dihydro-1H-indol-1-yl]methyl}-N-hydroxybenzamide  ligand  51  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QQD
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
 QQD  C13  C  CR16  0  -0.104  52.6001   2.9001  30.6692
 QQD  C15  C  CR16  0  -0.073  52.6618   0.6733  31.1143
 QQD  C17  C  CR16  0  -0.189  50.8634   1.5333  29.8044
 QQD  C20  C  CH3   0  -0.643  49.5369   6.1224  30.0112
 QQD  C21  C  CR56  0   0.092  48.4216   3.9963  29.3893
 QQD  C22  C  CR16  0  -0.355  47.0923   3.8678  29.7219
 QQD  C24  C  CR16  0  -0.264  46.6637   2.9361  27.5404
 QQD  C26  C  CR56  0   0.391  48.8795   3.5944  28.1307
 QQD  C28  C  CR16  0  -0.254  50.9320   4.0040  23.2323
 QQD  C05  C  CR6   0  -0.065  50.5378   5.3397  23.1929
 QQD  C06  C  CR16  0  -0.270  50.2614   5.9950  24.3907
 QQD  C07  C  CR16  0  -0.277  50.3994   5.3352  25.6023
 QQD  C08  C  CR6   0   0.089  50.8156   4.0100  25.6443
 QQD  C09  C  CH2   0  -0.350  51.0243   3.2843  26.9523
 QQD  C11  C  CR15  0  -0.187  50.7965   4.0425  29.3520
 QQD  C12  C  CR6   0   0.071  51.4194   2.8013  29.9418
 QQD  C16  C  CR16  0  -0.318  51.4921   0.4529  30.4006
 QQD  C18  C  CR5   0  -0.132  49.5753   4.5960  30.1598
 QQD  C19  C  CH3   0  -0.652  49.5882   4.2269  31.6370
 QQD  C23  C  CR16  0  -0.280  46.2013   3.3276  28.7880
 QQD  C25  C  CR16  0  -0.339  48.0085   3.0623  27.1891
 QQD  C27  C  CR16  0  -0.291  51.0730   3.3517  24.4445
 QQD  N03  N  NH1   0  -0.379  50.6369   7.3083  21.8487
 QQD  N10  N  NR5   0  -0.521  50.2353   3.8088  28.0291
 QQD  N14  N  N     0  -0.401  53.2121   1.8734  31.2465
 QQD  O01  O  O     0  -0.471  50.0877   5.3566  20.8566
 QQD  O04  O  OH1   0  -0.539  50.3762   8.0473  20.7379
 QQD  H1   H  HCR6  0   0.258  53.0754   3.8704  30.7851
 QQD  H2   H  HCR6  0   0.264  53.1762  -0.1538  31.5910
 QQD  H3   H  HCR6  0   0.269  49.9506   1.3819  29.2413
 QQD  H4   H  HCH3  0   0.236  48.6184   6.5257  30.4403
 QQD  H5   H  HCH3  0   0.233  50.3820   6.5820  30.5282
 QQD  H6   H  HCH3  0   0.240  49.5772   6.4256  28.9635
 QQD  H7   H  HCR6  0   0.243  46.7350   4.1815  30.6962
 QQD  H8   H  HCR6  0   0.249  45.9717   2.5178  26.8199
 QQD  H9   H  HCR6  0   0.262  51.1319   3.4730  22.3111
 QQD  H10  H  HCR6  0   0.261  49.9085   7.0187  24.3984
 QQD  H11  H  HCR6  0   0.268  50.1712   5.8560  26.5234
 QQD  H12  H  HCH2  0   0.248  50.8496   2.2109  26.7994
 QQD  H13  H  HCH2  0   0.285  52.0772   3.3766  27.2311
 QQD  H14  H  HCR5  0   0.265  51.5715   4.8139  29.2947
 QQD  H15  H  HCR6  0   0.272  51.0869  -0.5458  30.3140
 QQD  H16  H  HCH3  0   0.238  48.7373   4.6838  32.1448
 QQD  H17  H  HCH3  0   0.237  49.5299   3.1505  31.7931
 QQD  H18  H  HCH3  0   0.236  50.4947   4.5899  32.1257
 QQD  H19  H  HCR6  0   0.243  45.1546   3.2164  29.0383
 QQD  H20  H  HCR6  0   0.253  48.3481   2.7443  26.2120
 QQD  H21  H  HCR6  0   0.256  51.3820   2.3129  24.4576
 QQD  H22  H  HNH1  0   0.423  50.9018   7.8377  22.6659
 QQD  H23  H  HOH1  0   0.479  51.1983   8.0792  20.2304
 QQD  C02  C  C     0   0.493  50.3841   5.9877  21.8576

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
 QQD  O04  N03  single    1.359  0.020  1.359
 QQD  O01  C02  double    1.220  0.020  1.220
 QQD  C02  N03  single    1.345  0.020  1.345
 QQD  C02  C05  single    1.492  0.020  1.492
 QQD  C05  C28  aromatic  1.393  0.020  1.393
 QQD  C05  C06  aromatic  1.393  0.020  1.393
 QQD  C28  C27  aromatic  1.384  0.020  1.384
 QQD  C06  C07  aromatic  1.387  0.020  1.387
 QQD  C27  C08  aromatic  1.393  0.020  1.393
 QQD  C07  C08  aromatic  1.390  0.020  1.390
 QQD  C08  C09  single    1.510  0.020  1.510
 QQD  C09  N10  single    1.434  0.020  1.434
 QQD  C25  C24  aromatic  1.396  0.020  1.396
 QQD  C25  C26  aromatic  1.389  0.020  1.389
 QQD  C24  C23  aromatic  1.387  0.020  1.387
 QQD  N10  C26  single    1.376  0.020  1.376
 QQD  N10  C11  single    1.456  0.020  1.456
 QQD  C26  C21  aromatic  1.398  0.020  1.398
 QQD  C23  C22  aromatic  1.399  0.020  1.399
 QQD  C11  C12  single    1.509  0.020  1.509
 QQD  C11  C18  single    1.565  0.020  1.565
 QQD  C21  C22  aromatic  1.376  0.020  1.376
 QQD  C21  C18  single    1.511  0.020  1.511
 QQD  C17  C12  aromatic  1.391  0.020  1.391
 QQD  C17  C16  aromatic  1.385  0.020  1.385
 QQD  C12  C13  aromatic  1.390  0.020  1.390
 QQD  C18  C20  single    1.534  0.020  1.534
 QQD  C18  C19  single    1.523  0.020  1.523
 QQD  C16  C15  aromatic  1.388  0.020  1.388
 QQD  C13  N14  aromatic  1.327  0.020  1.327
 QQD  C15  N14  aromatic  1.327  0.020  1.327
 QQD  C13  H1   single    0.930  0.020  1.080
 QQD  C15  H2   single    0.930  0.020  1.080
 QQD  C17  H3   single    0.930  0.020  1.080
 QQD  C20  H4   single    0.970  0.020  1.090
 QQD  C20  H5   single    0.970  0.020  1.090
 QQD  C20  H6   single    0.970  0.020  1.090
 QQD  C22  H7   single    0.930  0.020  1.080
 QQD  C24  H8   single    0.930  0.020  1.080
 QQD  C28  H9   single    0.930  0.020  1.080
 QQD  C06  H10  single    0.930  0.020  1.080
 QQD  C07  H11  single    0.930  0.020  1.080
 QQD  C09  H12  single    0.970  0.020  1.090
 QQD  C09  H13  single    0.970  0.020  1.090
 QQD  C11  H14  single    0.970  0.020  1.090
 QQD  C16  H15  single    0.930  0.020  1.080
 QQD  C19  H16  single    0.970  0.020  1.090
 QQD  C19  H17  single    0.970  0.020  1.090
 QQD  C19  H18  single    0.970  0.020  1.090
 QQD  C23  H19  single    0.930  0.020  1.080
 QQD  C25  H20  single    0.930  0.020  1.080
 QQD  C27  H21  single    0.930  0.020  1.080
 QQD  N03  H22  single    0.860  0.020  1.020
 QQD  O04  H23  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
 QQD  H1   C13  N14  116.27  3.000
 QQD  H1   C13  C12  119.39  3.000
 QQD  N14  C13  C12  124.35  3.000
 QQD  H2   C15  N14  116.70  3.000
 QQD  H2   C15  C16  120.31  3.000
 QQD  N14  C15  C16  122.98  3.000
 QQD  H3   C17  C16  119.82  3.000
 QQD  H3   C17  C12  121.03  3.000
 QQD  C16  C17  C12  119.14  3.000
 QQD  H6   C20  H5   108.00  3.000
 QQD  H6   C20  H4   107.82  3.000
 QQD  H5   C20  H4   108.04  3.000
 QQD  H6   C20  C18  111.62  3.000
 QQD  H5   C20  C18  110.70  3.000
 QQD  H4   C20  C18  110.53  3.000
 QQD  C18  C21  C26  108.84  3.000
 QQD  C18  C21  C22  130.63  3.000
 QQD  C26  C21  C22  120.46  3.000
 QQD  H7   C22  C23  120.11  3.000
 QQD  H7   C22  C21  120.56  3.000
 QQD  C23  C22  C21  119.33  3.000
 QQD  H8   C24  C25  118.89  3.000
 QQD  H8   C24  C23  119.64  3.000
 QQD  C25  C24  C23  121.47  3.000
 QQD  N10  C26  C25  128.87  3.000
 QQD  N10  C26  C21  110.13  3.000
 QQD  C25  C26  C21  121.00  3.000
 QQD  H9   C28  C27  119.71  3.000
 QQD  H9   C28  C05  119.92  3.000
 QQD  C27  C28  C05  120.37  3.000
 QQD  C06  C05  C02  123.01  3.000
 QQD  C06  C05  C28  118.87  3.000
 QQD  C02  C05  C28  118.08  3.000
 QQD  H10  C06  C07  118.43  3.000
 QQD  H10  C06  C05  121.03  3.000
 QQD  C07  C06  C05  120.52  3.000
 QQD  H11  C07  C08  119.75  3.000
 QQD  H11  C07  C06  119.58  3.000
 QQD  C08  C07  C06  120.66  3.000
 QQD  C27  C08  C09  119.57  3.000
 QQD  C09  C08  C07  121.72  3.000
 QQD  C27  C08  C07  118.69  3.000
 QQD  H13  C09  H12  105.74  3.000
 QQD  H13  C09  N10  107.91  3.000
 QQD  H12  C09  N10  111.99  3.000
 QQD  H13  C09  C08  108.26  3.000
 QQD  H12  C09  C08  109.09  3.000
 QQD  N10  C09  C08  113.48  3.000
 QQD  H14  C11  N10  109.78  3.000
 QQD  H14  C11  C18  109.27  3.000
 QQD  N10  C11  C18  103.00  3.000
 QQD  H14  C11  C12  107.93  3.000
 QQD  C18  C11  C12  114.28  3.000
 QQD  N10  C11  C12  112.48  3.000
 QQD  C11  C12  C17  123.10  3.000
 QQD  C17  C12  C13  117.12  3.000
 QQD  C11  C12  C13  119.78  3.000
 QQD  H15  C16  C17  121.06  3.000
 QQD  H15  C16  C15  120.24  3.000
 QQD  C17  C16  C15  118.69  3.000
 QQD  C19  C18  C11  114.10  3.000
 QQD  C19  C18  C21  113.88  3.000
 QQD  C11  C18  C21  101.08  3.000
 QQD  C19  C18  C20  109.59  3.000
 QQD  C21  C18  C20  109.05  3.000
 QQD  C11  C18  C20  108.75  3.000
 QQD  H18  C19  H17  107.99  3.000
 QQD  H18  C19  H16  107.45  3.000
 QQD  H17  C19  H16  107.78  3.000
 QQD  H18  C19  C18  111.14  3.000
 QQD  H17  C19  C18  112.22  3.000
 QQD  H16  C19  C18  110.08  3.000
 QQD  H19  C23  C24  120.10  3.000
 QQD  H19  C23  C22  120.09  3.000
 QQD  C24  C23  C22  119.81  3.000
 QQD  H20  C25  C26  121.86  3.000
 QQD  H20  C25  C24  120.20  3.000
 QQD  C26  C25  C24  117.93  3.000
 QQD  H21  C27  C08  119.70  3.000
 QQD  H21  C27  C28  119.44  3.000
 QQD  C08  C27  C28  120.87  3.000
 QQD  H22  N03  O04  115.27  3.000
 QQD  H22  N03  C02  124.00  3.000
 QQD  O04  N03  C02  120.22  3.000
 QQD  C11  N10  C09  121.93  3.000
 QQD  C11  N10  C26  109.74  3.000
 QQD  C09  N10  C26  122.70  3.000
 QQD  C15  N14  C13  117.71  3.000
 QQD  H23  O04  N03  106.49  3.000
 QQD  O01  C02  N03  123.25  3.000
 QQD  N03  C02  C05  114.40  3.000
 QQD  O01  C02  C05  122.32  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
 QQD  CONST_01  C16  C17  C12  C13    0.00   0.0  0
 QQD  CONST_02  C16  C15  N14  C13    0.00   0.0  0
 QQD  CONST_03  C12  C17  C16  C15    0.00   0.0  0
 QQD  CONST_04  C12  C13  N14  C15    0.00   0.0  0
 QQD  CONST_05  N14  C13  C12  C17    0.00   0.0  0
 QQD  CONST_06  N14  C15  C16  C17    0.00   0.0  0
 QQD  CONST_07  C24  C25  C26  C21    0.00   0.0  0
 QQD  CONST_08  C24  C23  C22  C21    0.00   0.0  0
 QQD  CONST_09  C25  C24  C23  C22    0.00   0.0  0
 QQD  CONST_10  C25  C26  C21  C22    0.00   0.0  0
 QQD  CONST_11  C23  C24  C25  C26    0.00   0.0  0
 QQD  CONST_12  C23  C22  C21  C26    0.00   0.0  0
 QQD  CONST_13  C07  C06  C05  C28    0.00   0.0  0
 QQD  CONST_14  C07  C08  C27  C28    0.00   0.0  0
 QQD  CONST_15  C08  C27  C28  C05    0.00   0.0  0
 QQD  CONST_16  C08  C07  C06  C05    0.00   0.0  0
 QQD  CONST_17  C27  C28  C05  C06    0.00   0.0  0
 QQD  CONST_18  C27  C08  C07  C06    0.00   0.0  0
 QQD  CONST_19  C16  C17  C12  C11  180.00   0.0  0
 QQD  CONST_20  N14  C13  C12  C11  180.00   0.0  0
 QQD  CONST_21  C09  C08  C27  C28  180.00   0.0  0
 QQD  CONST_22  C27  C28  C05  C02  180.00   0.0  0
 QQD  CONST_23  C07  C06  C05  C02  180.00   0.0  0
 QQD  CONST_24  C09  C08  C07  C06  180.00   0.0  0
 QQD  CONST_25  H3   C17  C12  C13  180.00   0.0  0
 QQD  CONST_26  H2   C15  N14  C13  180.00   0.0  0
 QQD  CONST_27  H1   C13  N14  C15  180.00   0.0  0
 QQD  CONST_28  H20  C25  C26  C21  180.00   0.0  0
 QQD  CONST_29  H19  C23  C22  C21  180.00   0.0  0
 QQD  CONST_30  H8   C24  C23  C22  180.00   0.0  0
 QQD  CONST_31  H7   C22  C23  C24  180.00   0.0  0
 QQD  CONST_32  H10  C06  C05  C28  180.00   0.0  0
 QQD  CONST_33  H21  C27  C28  C05  180.00   0.0  0
 QQD  CONST_34  H11  C07  C06  C05  180.00   0.0  0
 QQD  CONST_35  H9   C28  C05  C06  180.00   0.0  0
 QQD  CONST_36  H15  C16  C17  C12  180.00   0.0  0
 QQD  CONST_37  O04  N03  C02  C05  180.00   0.0  0
 QQD  CONST_38  H22  N03  C02  C05    0.00   0.0  0
 QQD  CONST_39  O04  N03  C02  O01    0.00   0.0  0
 QQD  Var_01    C11  N10  C26  C21   14.91  30.0  1
 QQD  Var_02    C11  C18  C21  C22  165.20  30.0  1
 QQD  Var_03    C08  C09  N10  C26   74.01  30.0  2
 QQD  Var_04    N10  C09  C08  C07   26.15  30.0  2
 QQD  Var_05    O01  C02  C05  C28   28.42  30.0  2
 QQD  Var_06    H4   C20  C18  C21   62.42  30.0  3
 QQD  Var_07    H16  C19  C18  C21  -67.34  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
 QQD  chir_01  C11  N10  C12  C18  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
 QQD  plan-1  C13  0.020
 QQD  plan-1  C15  0.020
 QQD  plan-1  C17  0.020
 QQD  plan-1  C11  0.020
 QQD  plan-1  C12  0.020
 QQD  plan-1  C16  0.020
 QQD  plan-1  N14  0.020
 QQD  plan-1  H1   0.020
 QQD  plan-1  H2   0.020
 QQD  plan-1  H3   0.020
 QQD  plan-1  H15  0.020
 QQD  plan-2  C28  0.020
 QQD  plan-2  C05  0.020
 QQD  plan-2  C06  0.020
 QQD  plan-2  C07  0.020
 QQD  plan-2  C08  0.020
 QQD  plan-2  C09  0.020
 QQD  plan-2  C27  0.020
 QQD  plan-2  H9   0.020
 QQD  plan-2  H10  0.020
 QQD  plan-2  H11  0.020
 QQD  plan-2  H21  0.020
 QQD  plan-2  C02  0.020
 QQD  plan-3  C21  0.020
 QQD  plan-3  C22  0.020
 QQD  plan-3  C24  0.020
 QQD  plan-3  C26  0.020
 QQD  plan-3  C18  0.020
 QQD  plan-3  C23  0.020
 QQD  plan-3  C25  0.020
 QQD  plan-3  N10  0.020
 QQD  plan-3  H7   0.020
 QQD  plan-3  H8   0.020
 QQD  plan-3  H19  0.020
 QQD  plan-3  H20  0.020
 QQD  plan-4  C05  0.020
 QQD  plan-4  N03  0.020
 QQD  plan-4  O01  0.020
 QQD  plan-4  O04  0.020
 QQD  plan-4  H22  0.020
 QQD  plan-4  C02  0.020

