# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:19:33 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(Cn2ccc3ccc(cc23)C(=O)NO)cc1
#
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
 R5G  R5G  N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide  ligand  39  24  .  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_R5G
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
 R5G  C10  C  CR15  0  -0.010  27.6245  42.8717  35.0699
 R5G  C13  C  CR56  0   0.400  28.4300  41.0938  36.1321
 R5G  C15  C  CR6   0  -0.078  29.4798  39.6809  37.7326
 R5G  C20  C  CR16  0  -0.288  29.7576  40.8080  38.5306
 R5G  C21  C  CR16  0  -0.334  29.3943  42.0737  38.1283
 R5G  C22  C  CR16  0  -0.301  24.8515  41.0374  33.1499
 R5G  C04  C  CR6   0  -0.062  22.9310  40.3052  34.4049
 R5G  C05  C  CR16  0  -0.266  23.7849  39.7981  35.3836
 R5G  C06  C  CR16  0  -0.271  25.1577  39.9102  35.2414
 R5G  C07  C  CR6   0   0.139  25.7058  40.5297  34.1217
 R5G  C11  C  CR15  0  -0.417  28.1933  43.3591  36.2101
 R5G  C12  C  CR56  0   0.056  28.7182  42.2361  36.9133
 R5G  C14  C  CR16  0  -0.345  28.8037  39.8137  36.5287
 R5G  C16  C  C     0   0.488  29.9010  38.3475  38.2471
 R5G  C23  C  CR16  0  -0.251  23.4763  40.9357  33.2918
 R5G  N02  N  NH1   0  -0.376  20.9783  39.1528  35.1471
 R5G  N09  N  NR5   0  -0.522  27.7678  41.5129  35.0096
 R5G  N17  N  NH1   0  -0.376  30.2695  37.4776  37.2888
 R5G  O01  O  OH1   0  -0.538  19.6608  39.0544  35.4660
 R5G  O18  O  OH1   0  -0.540  30.5623  36.1881  37.6016
 R5G  O19  O  O     0  -0.474  29.9296  38.0802  39.4376
 R5G  O24  O  O     0  -0.468  20.7215  41.1168  34.0636
 R5G  H1   H  HCR5  0   0.290  27.1218  43.3995  34.2741
 R5G  H2   H  HCR6  0   0.254  30.2763  40.6729  39.4704
 R5G  H3   H  HCR6  0   0.253  29.6262  42.9313  38.7472
 R5G  H4   H  HCR6  0   0.265  25.2620  41.5217  32.2724
 R5G  H5   H  HCR6  0   0.267  23.3924  39.3320  36.2784
 R5G  H6   H  HCR6  0   0.263  25.7997  39.5130  36.0187
 R5G  H7   H  HCH2  0   0.293  27.6847  39.6997  34.0208
 R5G  H8   H  HCH2  0   0.296  27.4456  41.0986  33.0029
 R5G  H9   H  HCR5  0   0.254  28.2353  44.3943  36.5083
 R5G  H10  H  HCR6  0   0.275  28.5507  38.9482  35.9286
 R5G  H11  H  HCR6  0   0.266  22.8285  41.3449  32.5280
 R5G  H12  H  HNH1  0   0.424  21.5655  38.4169  35.5110
 R5G  H13  H  HNH1  0   0.421  30.3571  37.7210  36.3132
 R5G  H14  H  HOH1  0   0.479  19.2306  38.6149  34.7201
 R5G  H15  H  HOH1  0   0.477  31.5063  36.1615  37.8090
 R5G  C08  C  CH2   0  -0.434  27.1988  40.6742  33.9765
 R5G  C03  C  C     0   0.493  21.4438  40.2489  34.5242

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
 R5G  O24  C03  double    1.220  0.020  1.220
 R5G  C23  C22  aromatic  1.386  0.020  1.386
 R5G  C23  C04  aromatic  1.391  0.020  1.391
 R5G  C22  C07  aromatic  1.390  0.020  1.390
 R5G  C03  C04  single    1.493  0.020  1.493
 R5G  C03  N02  single    1.344  0.020  1.344
 R5G  C04  C05  aromatic  1.394  0.020  1.394
 R5G  O01  N02  single    1.359  0.020  1.359
 R5G  C07  C08  single    1.507  0.020  1.507
 R5G  C07  C06  aromatic  1.392  0.020  1.392
 R5G  C08  N09  single    1.447  0.020  1.447
 R5G  C05  C06  aromatic  1.385  0.020  1.385
 R5G  N09  C10  aromatic  1.368  0.020  1.368
 R5G  N09  C13  aromatic  1.369  0.020  1.369
 R5G  C10  C11  aromatic  1.364  0.020  1.364
 R5G  C13  C14  aromatic  1.391  0.020  1.391
 R5G  C13  C12  aromatic  1.414  0.020  1.414
 R5G  C11  C12  aromatic  1.425  0.020  1.425
 R5G  C14  C15  aromatic  1.387  0.020  1.387
 R5G  N17  O18  single    1.359  0.020  1.359
 R5G  N17  C16  single    1.346  0.020  1.346
 R5G  C12  C21  aromatic  1.400  0.020  1.400
 R5G  C15  C16  single    1.490  0.020  1.490
 R5G  C15  C20  aromatic  1.409  0.020  1.409
 R5G  C21  C20  aromatic  1.377  0.020  1.377
 R5G  C16  O19  double    1.220  0.020  1.220
 R5G  C10  H1   single    0.930  0.020  1.080
 R5G  C20  H2   single    0.930  0.020  1.080
 R5G  C21  H3   single    0.930  0.020  1.080
 R5G  C22  H4   single    0.930  0.020  1.080
 R5G  C05  H5   single    0.930  0.020  1.080
 R5G  C06  H6   single    0.930  0.020  1.080
 R5G  C08  H7   single    0.970  0.020  1.090
 R5G  C08  H8   single    0.970  0.020  1.090
 R5G  C11  H9   single    0.930  0.020  1.080
 R5G  C14  H10  single    0.930  0.020  1.080
 R5G  C23  H11  single    0.930  0.020  1.080
 R5G  N02  H12  single    0.860  0.020  1.020
 R5G  N17  H13  single    0.860  0.020  1.020
 R5G  O01  H14  single    0.850  0.020  0.980
 R5G  O18  H15  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
 R5G  H1   C10  N09  120.15  3.000
 R5G  H1   C10  C11  129.48  3.000
 R5G  N09  C10  C11  110.37  3.000
 R5G  N09  C13  C14  130.19  3.000
 R5G  C14  C13  C12  122.09  3.000
 R5G  N09  C13  C12  107.72  3.000
 R5G  C16  C15  C14  121.54  3.000
 R5G  C16  C15  C20  117.69  3.000
 R5G  C14  C15  C20  120.74  3.000
 R5G  H2   C20  C21  119.67  3.000
 R5G  H2   C20  C15  119.13  3.000
 R5G  C21  C20  C15  121.20  3.000
 R5G  H3   C21  C12  120.50  3.000
 R5G  H3   C21  C20  120.31  3.000
 R5G  C12  C21  C20  119.19  3.000
 R5G  H4   C22  C23  119.46  3.000
 R5G  H4   C22  C07  119.79  3.000
 R5G  C23  C22  C07  120.76  3.000
 R5G  C23  C04  C05  119.11  3.000
 R5G  C05  C04  C03  122.70  3.000
 R5G  C23  C04  C03  118.14  3.000
 R5G  H5   C05  C06  118.63  3.000
 R5G  H5   C05  C04  120.98  3.000
 R5G  C06  C05  C04  120.38  3.000
 R5G  H6   C06  C07  120.45  3.000
 R5G  H6   C06  C05  118.95  3.000
 R5G  C07  C06  C05  120.59  3.000
 R5G  C08  C07  C06  120.68  3.000
 R5G  C06  C07  C22  118.87  3.000
 R5G  C08  C07  C22  120.44  3.000
 R5G  H9   C11  C12  127.28  3.000
 R5G  H9   C11  C10  126.19  3.000
 R5G  C12  C11  C10  106.52  3.000
 R5G  C11  C12  C21  134.23  3.000
 R5G  C21  C12  C13  118.97  3.000
 R5G  C11  C12  C13  106.80  3.000
 R5G  H10  C14  C15  121.21  3.000
 R5G  H10  C14  C13  120.97  3.000
 R5G  C15  C14  C13  117.80  3.000
 R5G  O19  C16  N17  123.14  3.000
 R5G  O19  C16  C15  122.65  3.000
 R5G  N17  C16  C15  114.20  3.000
 R5G  H11  C23  C04  120.12  3.000
 R5G  H11  C23  C22  119.60  3.000
 R5G  C04  C23  C22  120.28  3.000
 R5G  H12  N02  O01  115.25  3.000
 R5G  H12  N02  C03  124.07  3.000
 R5G  O01  N02  C03  120.24  3.000
 R5G  C08  N09  C13  126.73  3.000
 R5G  C13  N09  C10  108.59  3.000
 R5G  C08  N09  C10  124.47  3.000
 R5G  H13  N17  O18  115.64  3.000
 R5G  H13  N17  C16  123.79  3.000
 R5G  O18  N17  C16  120.57  3.000
 R5G  H14  O01  N02  106.46  3.000
 R5G  H15  O18  N17  106.61  3.000
 R5G  H8   C08  H7   106.47  3.000
 R5G  H8   C08  N09  108.84  3.000
 R5G  H7   C08  N09  108.29  3.000
 R5G  H8   C08  C07  110.34  3.000
 R5G  H7   C08  C07  110.61  3.000
 R5G  N09  C08  C07  112.10  3.000
 R5G  O24  C03  N02  123.39  3.000
 R5G  N02  C03  C04  114.38  3.000
 R5G  O24  C03  C04  122.21  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
 R5G  CONST_01  C14  C13  N09  C10   180.00   0.0  0
 R5G  CONST_02  C12  C13  N09  C10     0.00   0.0  0
 R5G  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 R5G  CONST_04  C21  C12  C11  C10   180.00   0.0  0
 R5G  CONST_05  C11  C10  N09  C13     0.00   0.0  0
 R5G  CONST_06  C20  C15  C14  C13     0.00   0.0  0
 R5G  CONST_07  C20  C21  C12  C13     0.00   0.0  0
 R5G  CONST_08  N09  C13  C14  C15   180.00   0.0  0
 R5G  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 R5G  CONST_10  C12  C21  C20  C15     0.00   0.0  0
 R5G  CONST_11  C11  C12  C21  C20   180.00   0.0  0
 R5G  CONST_12  N09  C13  C12  C21   180.00   0.0  0
 R5G  CONST_13  C14  C13  C12  C21     0.00   0.0  0
 R5G  CONST_14  C14  C15  C20  C21     0.00   0.0  0
 R5G  CONST_15  C05  C04  C23  C22     0.00   0.0  0
 R5G  CONST_16  C05  C06  C07  C22     0.00   0.0  0
 R5G  CONST_17  C07  C22  C23  C04     0.00   0.0  0
 R5G  CONST_18  C07  C06  C05  C04     0.00   0.0  0
 R5G  CONST_19  C23  C22  C07  C06     0.00   0.0  0
 R5G  CONST_20  C23  C04  C05  C06     0.00   0.0  0
 R5G  CONST_21  N09  C13  C12  C11     0.00   0.0  0
 R5G  CONST_22  C14  C13  C12  C11   180.00   0.0  0
 R5G  CONST_23  N09  C10  C11  C12     0.00   0.0  0
 R5G  CONST_24  C16  C15  C14  C13   180.00   0.0  0
 R5G  CONST_25  C16  C15  C20  C21   180.00   0.0  0
 R5G  CONST_26  C03  C04  C23  C22   180.00   0.0  0
 R5G  CONST_27  C06  C05  C04  C03   180.00   0.0  0
 R5G  CONST_28  C08  C07  C06  C05   180.00   0.0  0
 R5G  CONST_29  C23  C22  C07  C08   180.00   0.0  0
 R5G  CONST_30  C11  C10  N09  C08   180.00   0.0  0
 R5G  CONST_31  C14  C13  N09  C08     0.00   0.0  0
 R5G  CONST_32  C12  C13  N09  C08   180.00   0.0  0
 R5G  CONST_33  H1   C10  N09  C13   180.00   0.0  0
 R5G  CONST_34  H9   C11  C12  C13   180.00   0.0  0
 R5G  CONST_35  H3   C21  C12  C13   180.00   0.0  0
 R5G  CONST_36  H10  C14  C15  C20   180.00   0.0  0
 R5G  CONST_37  H6   C06  C07  C22   180.00   0.0  0
 R5G  CONST_38  H4   C22  C23  C04   180.00   0.0  0
 R5G  CONST_39  H11  C23  C04  C05   180.00   0.0  0
 R5G  CONST_40  H5   C05  C06  C07   180.00   0.0  0
 R5G  CONST_41  H2   C20  C21  C12   180.00   0.0  0
 R5G  CONST_42  O18  N17  C16  C15   180.00   0.0  0
 R5G  CONST_43  O01  N02  C03  C04   180.00   0.0  0
 R5G  CONST_44  H13  N17  C16  C15     0.00   0.0  0
 R5G  CONST_45  H12  N02  C03  C04     0.00   0.0  0
 R5G  CONST_46  O24  C03  N02  O01     0.00   0.0  0
 R5G  CONST_47  O19  C16  N17  O18     0.00   0.0  0
 R5G  Var_01    C07  C08  N09  C10   -72.81  30.0  2
 R5G  Var_02    N09  C08  C07  C22   115.07  30.0  2
 R5G  Var_03    N17  C16  C15  C20  -146.84  30.0  2
 R5G  Var_04    O24  C03  C04  C05   147.23  30.0  2

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
 R5G  plan-1  C22  0.020
 R5G  plan-1  C04  0.020
 R5G  plan-1  C05  0.020
 R5G  plan-1  C06  0.020
 R5G  plan-1  C07  0.020
 R5G  plan-1  C23  0.020
 R5G  plan-1  H4   0.020
 R5G  plan-1  H5   0.020
 R5G  plan-1  H6   0.020
 R5G  plan-1  H11  0.020
 R5G  plan-1  C08  0.020
 R5G  plan-1  C03  0.020
 R5G  plan-2  C10  0.020
 R5G  plan-2  C13  0.020
 R5G  plan-2  C15  0.020
 R5G  plan-2  C20  0.020
 R5G  plan-2  C21  0.020
 R5G  plan-2  C11  0.020
 R5G  plan-2  C12  0.020
 R5G  plan-2  C14  0.020
 R5G  plan-2  C16  0.020
 R5G  plan-2  N09  0.020
 R5G  plan-2  H1   0.020
 R5G  plan-2  H2   0.020
 R5G  plan-2  H3   0.020
 R5G  plan-2  H9   0.020
 R5G  plan-2  H10  0.020
 R5G  plan-2  C08  0.020
 R5G  plan-3  C15  0.020
 R5G  plan-3  C16  0.020
 R5G  plan-3  N17  0.020
 R5G  plan-3  O18  0.020
 R5G  plan-3  O19  0.020
 R5G  plan-3  H13  0.020
 R5G  plan-4  C04  0.020
 R5G  plan-4  N02  0.020
 R5G  plan-4  O01  0.020
 R5G  plan-4  O24  0.020
 R5G  plan-4  H12  0.020
 R5G  plan-4  C03  0.020

