# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Nov 19 08:13:29 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)N1CCc2ccccc12
#
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
 SRK  SRK  "4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid"  ligand  29  16  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SRK
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
 SRK  C02  C  C     0   0.541  23.2171  67.8503  72.9745
 SRK  C04  C  CH2   0  -0.557  23.4457  67.3717  71.5663
 SRK  C05  C  CH2   0  -0.608  24.5068  66.2957  71.4152
 SRK  C06  C  C     0   0.565  25.8457  66.7477  71.9571
 SRK  C09  C  CH2   0  -0.292  26.6514  64.4462  71.4494
 SRK  C10  C  CH2   0  -0.497  28.0588  63.8374  71.4216
 SRK  C11  C  CR56  0  -0.024  28.8932  64.8497  72.1457
 SRK  C12  C  CR16  0  -0.316  30.2175  64.7692  72.5271
 SRK  C13  C  CR16  0  -0.261  30.8087  65.8536  73.1695
 SRK  C14  C  CR16  0  -0.261  30.0644  66.9985  73.4149
 SRK  C15  C  CR16  0  -0.297  28.7279  67.0939  73.0350
 SRK  C16  C  CR56  0   0.405  28.1500  66.0018  72.3980
 SRK  N08  N  NR5   0  -0.604  26.8393  65.8266  71.9260
 SRK  O01  O  OH1   0  -0.594  23.3974  66.8878  73.8746
 SRK  O03  O  O     0  -0.446  22.8540  68.9619  73.2668
 SRK  O07  O  O     0  -0.472  26.0042  67.8788  72.3904
 SRK  H1   H  HCH2  0   0.274  23.6709  68.2384  70.9470
 SRK  H2   H  HCH2  0   0.292  22.4935  66.9721  71.2036
 SRK  H3   H  HCH2  0   0.283  24.1964  65.3683  71.9014
 SRK  H4   H  HCH2  0   0.296  24.6103  66.0508  70.3542
 SRK  H6   H  HCH2  0   0.265  25.9975  63.9046  72.1355
 SRK  H7   H  HCH2  0   0.270  28.0802  62.8586  71.9003
 SRK  H8   H  HCH2  0   0.268  28.4131  63.7017  70.3977
 SRK  H9   H  HCR6  0   0.251  30.7884  63.8704  72.3283
 SRK  H10  H  HCR6  0   0.251  31.8458  65.8038  73.4745
 SRK  H11  H  HCR6  0   0.253  30.5249  67.8417  73.9134
 SRK  H12  H  HCR6  0   0.272  28.1733  67.9945  73.2387
 SRK  H13  H  HOH1  0   0.476  23.2155  67.2301  74.7628
 SRK  H5   H  HCH2  0   0.267  26.1867  64.4394  70.4653

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
 SRK  C10  C09  single    1.534  0.020  1.534
 SRK  C10  C11  single    1.498  0.020  1.498
 SRK  C09  N08  single    1.472  0.020  1.472
 SRK  C05  C04  single    1.519  0.020  1.519
 SRK  C05  C06  single    1.513  0.020  1.513
 SRK  C04  C02  single    1.505  0.020  1.505
 SRK  N08  C06  single    1.355  0.020  1.355
 SRK  N08  C16  single    1.404  0.020  1.404
 SRK  C06  O07  double    1.222  0.020  1.222
 SRK  C11  C16  aromatic  1.394  0.020  1.394
 SRK  C11  C12  aromatic  1.380  0.020  1.380
 SRK  C16  C15  aromatic  1.390  0.020  1.390
 SRK  C12  C13  aromatic  1.392  0.020  1.392
 SRK  C02  O03  double    1.205  0.020  1.205
 SRK  C02  O01  single    1.330  0.020  1.330
 SRK  C13  C14  aromatic  1.387  0.020  1.387
 SRK  C15  C14  aromatic  1.393  0.020  1.393
 SRK  C04  H1   single    0.970  0.020  1.090
 SRK  C04  H2   single    0.970  0.020  1.090
 SRK  C05  H3   single    0.970  0.020  1.090
 SRK  C05  H4   single    0.970  0.020  1.090
 SRK  C09  H5   single    0.970  0.020  1.090
 SRK  C09  H6   single    0.970  0.020  1.090
 SRK  C10  H7   single    0.970  0.020  1.090
 SRK  C10  H8   single    0.970  0.020  1.090
 SRK  C12  H9   single    0.930  0.020  1.080
 SRK  C13  H10  single    0.930  0.020  1.080
 SRK  C14  H11  single    0.930  0.020  1.080
 SRK  C15  H12  single    0.930  0.020  1.080
 SRK  O01  H13  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
 SRK  O03  C02  O01  122.96  3.000
 SRK  O01  C02  C04  112.49  3.000
 SRK  O03  C02  C04  124.48  3.000
 SRK  H2   C04  H1   106.38  3.000
 SRK  H2   C04  C05  108.44  3.000
 SRK  H1   C04  C05  111.28  3.000
 SRK  H2   C04  C02  107.10  3.000
 SRK  H1   C04  C02  108.09  3.000
 SRK  C05  C04  C02  115.13  3.000
 SRK  H4   C05  H3   105.58  3.000
 SRK  H4   C05  C06  109.30  3.000
 SRK  H3   C05  C06  110.22  3.000
 SRK  H4   C05  C04  108.74  3.000
 SRK  H3   C05  C04  111.02  3.000
 SRK  C06  C05  C04  111.77  3.000
 SRK  O07  C06  N08  122.84  3.000
 SRK  O07  C06  C05  121.22  3.000
 SRK  N08  C06  C05  115.94  3.000
 SRK  H6   C09  H5   108.03  3.000
 SRK  H6   C09  N08  109.76  3.000
 SRK  H5   C09  N08  110.68  3.000
 SRK  H6   C09  C10  111.35  3.000
 SRK  H5   C09  C10  111.90  3.000
 SRK  N08  C09  C10  105.12  3.000
 SRK  H8   C10  H7   107.09  3.000
 SRK  H8   C10  C11  110.88  3.000
 SRK  H7   C10  C11  112.55  3.000
 SRK  H8   C10  C09  111.35  3.000
 SRK  H7   C10  C09  111.51  3.000
 SRK  C11  C10  C09  103.54  3.000
 SRK  C16  C11  C12  120.64  3.000
 SRK  C12  C11  C10  128.93  3.000
 SRK  C16  C11  C10  110.42  3.000
 SRK  H9   C12  C13  120.48  3.000
 SRK  H9   C12  C11  120.22  3.000
 SRK  C13  C12  C11  119.30  3.000
 SRK  H10  C13  C14  120.15  3.000
 SRK  H10  C13  C12  120.08  3.000
 SRK  C14  C13  C12  119.77  3.000
 SRK  H11  C14  C15  118.72  3.000
 SRK  H11  C14  C13  119.74  3.000
 SRK  C15  C14  C13  121.54  3.000
 SRK  H12  C15  C16  121.97  3.000
 SRK  H12  C15  C14  119.99  3.000
 SRK  C16  C15  C14  118.04  3.000
 SRK  N08  C16  C15  129.80  3.000
 SRK  C15  C16  C11  120.70  3.000
 SRK  N08  C16  C11  109.50  3.000
 SRK  C16  N08  C09  110.18  3.000
 SRK  C16  N08  C06  126.29  3.000
 SRK  C09  N08  C06  123.44  3.000
 SRK  H13  O01  C02  109.83  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
 SRK  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 SRK  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 SRK  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 SRK  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 SRK  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 SRK  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 SRK  CONST_07  H9   C12  C11  C10     0.00   0.0  0
 SRK  CONST_08  H12  C15  C16  C11   180.00   0.0  0
 SRK  CONST_09  H10  C13  C12  C11   180.00   0.0  0
 SRK  CONST_10  H11  C14  C13  C12   180.00   0.0  0
 SRK  CONST_11  H12  C15  C14  C13   180.00   0.0  0
 SRK  CONST_12  H9   C12  C13  C14   180.00   0.0  0
 SRK  CONST_13  H10  C13  C14  C15   180.00   0.0  0
 SRK  CONST_14  H9   C12  C11  C16   180.00   0.0  0
 SRK  CONST_15  H11  C14  C15  C16   180.00   0.0  0
 SRK  CONST_16  H12  C15  C16  N08     0.00   0.0  0
 SRK  CONST_17  C09  N08  C06  C05     0.00   0.0  0
 SRK  CONST_18  C16  N08  C06  C05   180.00   0.0  0
 SRK  CONST_19  O07  C06  N08  C09   180.00   0.0  0
 SRK  CONST_20  O07  C06  N08  C16     0.00   0.0  0
 SRK  CONST_21  H13  O01  C02  C04   180.00   0.0  0
 SRK  CONST_22  H13  O01  C02  O03     0.00   0.0  0
 SRK  Var_01    C16  C11  C10  C09    -8.01  30.0  1
 SRK  Var_02    C12  C11  C10  C09   173.43  30.0  1
 SRK  Var_03    C11  C16  N08  C09     5.69  30.0  1
 SRK  Var_04    C15  C16  N08  C09  -173.96  30.0  1
 SRK  Var_05    C16  N08  C09  C10   -10.48  30.0  1
 SRK  Var_06    N08  C09  C10  C11    10.80  30.0  1
 SRK  Var_07    C10  C09  N08  C06   172.81  30.0  1
 SRK  Var_08    C11  C16  N08  C06  -177.72  30.0  1
 SRK  Var_09    C15  C16  N08  C06     2.63  30.0  1
 SRK  Var_10    H5   C09  C10  C11   130.99  30.0  1
 SRK  Var_11    H6   C09  C10  C11  -108.00  30.0  1
 SRK  Var_12    H7   C10  C11  C12    52.88  30.0  1
 SRK  Var_13    H8   C10  C11  C12   -67.05  30.0  1
 SRK  Var_14    H5   C09  N08  C16  -131.47  30.0  1
 SRK  Var_15    H6   C09  N08  C16   109.38  30.0  1
 SRK  Var_16    H7   C10  C11  C16  -128.56  30.0  1
 SRK  Var_17    H8   C10  C11  C16   111.51  30.0  1
 SRK  Var_18    H7   C10  C09  N08   132.06  30.0  1
 SRK  Var_19    H8   C10  C09  N08  -108.39  30.0  1
 SRK  Var_20    H5   C09  N08  C06    51.82  30.0  1
 SRK  Var_21    H6   C09  N08  C06   -67.33  30.0  1
 SRK  Var_22    N08  C06  C05  C04   176.81  30.0  3
 SRK  Var_23    H3   C05  C06  N08    52.84  30.0  1
 SRK  Var_24    H4   C05  C06  N08   -62.77  30.0  1
 SRK  Var_25    C06  C05  C04  C02   -57.39  30.0  1
 SRK  Var_26    O07  C06  C05  C04    -3.32  30.0  3
 SRK  Var_27    O03  C02  C04  C05   150.19  30.0  3
 SRK  Var_28    O01  C02  C04  C05   -32.89  30.0  3
 SRK  Var_29    H3   C05  C04  C02    66.13  30.0  1
 SRK  Var_30    H4   C05  C04  C02  -178.13  30.0  1
 SRK  Var_31    H1   C04  C05  C06    66.03  30.0  3
 SRK  Var_32    H2   C04  C05  C06  -177.30  30.0  3
 SRK  Var_33    H1   C04  C02  O01  -157.98  30.0  2
 SRK  Var_34    H2   C04  C02  O01    87.76  30.0  2
 SRK  Var_35    H1   C04  C02  O03    25.10  30.0  2
 SRK  Var_36    H2   C04  C02  O03   -89.16  30.0  2
 SRK  Var_37    H3   C05  C06  O07  -127.28  30.0  1
 SRK  Var_38    H4   C05  C06  O07   117.10  30.0  1

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
 SRK  plan-1  C05  0.020
 SRK  plan-1  C06  0.020
 SRK  plan-1  C09  0.020
 SRK  plan-1  C16  0.020
 SRK  plan-1  N08  0.020
 SRK  plan-1  O07  0.020
 SRK  plan-2  C10  0.020
 SRK  plan-2  C11  0.020
 SRK  plan-2  C12  0.020
 SRK  plan-2  C13  0.020
 SRK  plan-2  C14  0.020
 SRK  plan-2  C15  0.020
 SRK  plan-2  C16  0.020
 SRK  plan-2  N08  0.020
 SRK  plan-2  H9   0.020
 SRK  plan-2  H10  0.020
 SRK  plan-2  H11  0.020
 SRK  plan-2  H12  0.020
 SRK  plan-3  C02  0.020
 SRK  plan-3  C04  0.020
 SRK  plan-3  O01  0.020
 SRK  plan-3  O03  0.020
 SRK  plan-3  H13  0.020

