# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 08:07:31 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-(2-chlorophenyl)-7-methyl-1~{H}-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2c1[nH]c(C(O)=O)c2c3ccccc3Cl
#
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
 R9K  R9K  "3-(2-chlorophenyl)-7-methyl-1~{H}-indole-2-carboxylic acid"  ligand  31  20  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R9K
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
 R9K  C10   C   CR5    0  -0.018  -24.1383   0.8421  61.6866
 R9K  C15   C   CR16   0  -0.280  -24.7543   4.9997  60.8789
 R9K  C17   C   CR16   0  -0.320  -24.4764   2.7412  60.1138
 R9K  C01   C   CH3    0  -0.733  -24.6931  -3.7738  62.8381
 R9K  C02   C   CR6    0   0.054  -25.2894  -2.3996  62.8483
 R9K  C03   C   CR16   0  -0.346  -26.5428  -2.1289  63.3667
 R9K  C04   C   CR16   0  -0.256  -27.0916  -0.8335  63.3622
 R9K  C05   C   CR16   0  -0.394  -26.3960   0.2360  62.8397
 R9K  C06   C   CR56   0   0.082  -25.1214   0.0054  62.3064
 R9K  C07   C   CR56   0   0.318  -24.5974  -1.3034  62.3184
 R9K  C09   C   CR5    0   0.109  -23.0811   0.0291  61.3485
 R9K  C11   C   CR6    0   0.148  -24.3102   2.2752  61.4193
 R9K  C12   C   CR6    0  -0.142  -24.3745   3.2229  62.4393
 R9K  C14   C   CR16   0  -0.196  -24.5946   4.5702  62.1863
 R9K  C16   C   CR16   0  -0.234  -24.6936   4.0808  59.8390
 R9K  C18   C   C      0   0.360  -21.7519   0.3189  60.6941
 R9K  N08   N   NR15   0  -0.722  -23.3684  -1.2493  61.7367
 R9K  O19   O   OC    -1  -0.569  -21.4903   1.5100  60.4615
 R9K  O20   O   O      0  -0.595  -21.0521  -0.6870  60.4620
 R9K  CL1   CL  CL     0  -0.139  -24.1490   2.7287  64.0886
 R9K  H011  H   HCH3   0   0.242  -23.7482  -3.8051  63.3849
 R9K  H012  H   HCH3   0   0.249  -25.3659  -4.4982  63.2942
 R9K  H013  H   HCH3   0   0.243  -24.4827  -4.1110  61.8207
 R9K  H031  H   HCR6   0   0.237  -27.1212  -2.9428  63.7881
 R9K  H041  H   HCR6   0   0.239  -28.0786  -0.6808  63.7802
 R9K  H051  H   HCR6   0   0.234  -26.8266   1.2297  62.8361
 R9K  H141  H   HCR6   0   0.273  -24.6354   5.2762  63.0048
 R9K  H161  H   HCR6   0   0.256  -24.8185   4.4085  58.8152
 R9K  H081  H   HNR5   0   0.395  -22.7313  -2.0148  61.5861
 R9K  H151  H   HCR6   0   0.261  -24.9261   6.0488  60.6779
 R9K  H171  H   HCR6   0   0.245  -24.4402   2.0237  59.3046

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
 R9K  C16  C17   aromatic  1.385  0.020  1.385
 R9K  C16  C15   aromatic  1.389  0.020  1.389
 R9K  O20  C18   deloc     1.247  0.020  1.247
 R9K  C17  C11   aromatic  1.396  0.020  1.396
 R9K  C18  O19   deloc     1.241  0.020  1.241
 R9K  C18  C09   single    1.510  0.020  1.510
 R9K  C15  C14   aromatic  1.385  0.020  1.385
 R9K  C09  N08   aromatic  1.367  0.020  1.367
 R9K  C09  C10   aromatic  1.376  0.020  1.376
 R9K  C11  C10   single    1.468  0.020  1.468
 R9K  C11  C12   aromatic  1.394  0.020  1.394
 R9K  N08  C07   aromatic  1.361  0.020  1.361
 R9K  C10  C06   aromatic  1.432  0.020  1.432
 R9K  C14  C12   aromatic  1.388  0.020  1.388
 R9K  C07  C06   aromatic  1.410  0.020  1.410
 R9K  C07  C02   aromatic  1.400  0.020  1.400
 R9K  C06  C05   aromatic  1.401  0.020  1.401
 R9K  C12  CL1   single    1.736  0.020  1.736
 R9K  C01  C02   single    1.498  0.020  1.498
 R9K  C02  C03   aromatic  1.383  0.020  1.383
 R9K  C05  C04   aromatic  1.379  0.020  1.379
 R9K  C03  C04   aromatic  1.407  0.020  1.407
 R9K  C15  H151  single    0.930  0.020  1.080
 R9K  C17  H171  single    0.930  0.020  1.080
 R9K  C01  H011  single    0.970  0.020  1.090
 R9K  C01  H012  single    0.970  0.020  1.090
 R9K  C01  H013  single    0.970  0.020  1.090
 R9K  C03  H031  single    0.930  0.020  1.080
 R9K  C04  H041  single    0.930  0.020  1.080
 R9K  C05  H051  single    0.930  0.020  1.080
 R9K  C14  H141  single    0.930  0.020  1.080
 R9K  C16  H161  single    0.930  0.020  1.080
 R9K  N08  H081  single    0.860  0.020  1.020

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
 R9K  C11   C10  C09   128.47  3.000
 R9K  C11   C10  C06   124.67  3.000
 R9K  C09   C10  C06   106.78  3.000
 R9K  H151  C15  C16   120.62  3.000
 R9K  H151  C15  C14   119.62  3.000
 R9K  C16   C15  C14   119.76  3.000
 R9K  H171  C17  C16   119.89  3.000
 R9K  H171  C17  C11   118.30  3.000
 R9K  C16   C17  C11   121.81  3.000
 R9K  H013  C01  H012  107.69  3.000
 R9K  H013  C01  H011  106.91  3.000
 R9K  H012  C01  H011  107.80  3.000
 R9K  H013  C01  C02   111.48  3.000
 R9K  H012  C01  C02   111.19  3.000
 R9K  H011  C01  C02   111.55  3.000
 R9K  C07   C02  C03   115.88  3.000
 R9K  C03   C02  C01   122.87  3.000
 R9K  C07   C02  C01   121.25  3.000
 R9K  H031  C03  C04   118.98  3.000
 R9K  H031  C03  C02   118.84  3.000
 R9K  C04   C03  C02   122.17  3.000
 R9K  H041  C04  C05   119.80  3.000
 R9K  H041  C04  C03   118.96  3.000
 R9K  C05   C04  C03   121.24  3.000
 R9K  H051  C05  C06   120.76  3.000
 R9K  H051  C05  C04   120.83  3.000
 R9K  C06   C05  C04   118.41  3.000
 R9K  C07   C06  C05   119.19  3.000
 R9K  C05   C06  C10   133.89  3.000
 R9K  C07   C06  C10   106.92  3.000
 R9K  N08   C07  C06   107.16  3.000
 R9K  C06   C07  C02   123.11  3.000
 R9K  N08   C07  C02   129.73  3.000
 R9K  N08   C09  C18   119.20  3.000
 R9K  N08   C09  C10   108.74  3.000
 R9K  C18   C09  C10   132.04  3.000
 R9K  C12   C11  C17   116.87  3.000
 R9K  C12   C11  C10   122.40  3.000
 R9K  C17   C11  C10   120.67  3.000
 R9K  CL1   C12  C14   118.03  3.000
 R9K  CL1   C12  C11   119.71  3.000
 R9K  C14   C12  C11   122.25  3.000
 R9K  H141  C14  C12   120.09  3.000
 R9K  H141  C14  C15   120.49  3.000
 R9K  C12   C14  C15   119.42  3.000
 R9K  H161  C16  C17   119.93  3.000
 R9K  H161  C16  C15   120.19  3.000
 R9K  C17   C16  C15   119.89  3.000
 R9K  O20   C18  O19   128.37  3.000
 R9K  O19   C18  C09   116.81  3.000
 R9K  O20   C18  C09   114.83  3.000
 R9K  H081  N08  C09   122.37  3.000
 R9K  H081  N08  C07   127.23  3.000
 R9K  C09   N08  C07   110.40  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
 R9K  CONST_01  C07   N08  C09  C10     0.00   0.0  0
 R9K  CONST_02  C16   C17  C11  C10   180.00   0.0  0
 R9K  CONST_03  C14   C12  C11  C10   180.00   0.0  0
 R9K  CONST_04  N08   C07  C06  C10     0.00   0.0  0
 R9K  CONST_05  C02   C07  C06  C10   180.00   0.0  0
 R9K  CONST_06  C04   C05  C06  C10   180.00   0.0  0
 R9K  CONST_07  C11   C17  C16  C15     0.00   0.0  0
 R9K  CONST_08  C11   C12  C14  C15     0.00   0.0  0
 R9K  CONST_09  C14   C15  C16  C17     0.00   0.0  0
 R9K  CONST_12  C14   C12  C11  C17     0.00   0.0  0
 R9K  CONST_13  C09   N08  C07  C02   180.00   0.0  0
 R9K  CONST_14  C05   C06  C07  C02     0.00   0.0  0
 R9K  CONST_15  C05   C04  C03  C02     0.00   0.0  0
 R9K  CONST_16  N08   C07  C02  C03   180.00   0.0  0
 R9K  CONST_17  C06   C07  C02  C03     0.00   0.0  0
 R9K  CONST_18  C06   C05  C04  C03     0.00   0.0  0
 R9K  CONST_19  C07   C06  C05  C04     0.00   0.0  0
 R9K  CONST_20  C07   C02  C03  C04     0.00   0.0  0
 R9K  CONST_21  C09   C10  C06  C05   180.00   0.0  0
 R9K  CONST_22  C11   C10  C06  C05     0.00   0.0  0
 R9K  CONST_23  N08   C07  C06  C05   180.00   0.0  0
 R9K  CONST_24  N08   C09  C10  C06     0.00   0.0  0
 R9K  CONST_26  C09   N08  C07  C06     0.00   0.0  0
 R9K  CONST_27  C09   C10  C06  C07     0.00   0.0  0
 R9K  CONST_28  C11   C10  C06  C07   180.00   0.0  0
 R9K  CONST_30  N08   C09  C10  C11   180.00   0.0  0
 R9K  CONST_31  C16   C17  C11  C12     0.00   0.0  0
 R9K  CONST_32  C16   C15  C14  C12     0.00   0.0  0
 R9K  CONST_33  CL1   C12  C11  C10     0.00   0.0  0
 R9K  CONST_34  CL1   C12  C14  C15   180.00   0.0  0
 R9K  CONST_35  CL1   C12  C11  C17   180.00   0.0  0
 R9K  CONST_36  N08   C07  C02  C01     0.00   0.0  0
 R9K  CONST_37  C06   C07  C02  C01   180.00   0.0  0
 R9K  CONST_38  C04   C03  C02  C01   180.00   0.0  0
 R9K  CONST_39  C18   C09  C10  C06   180.00   0.0  0
 R9K  CONST_40  C18   C09  N08  C07   180.00   0.0  0
 R9K  CONST_41  C18   C09  C10  C11     0.00   0.0  0
 R9K  CONST_42  H081  N08  C09  C10   180.00   0.0  0
 R9K  CONST_43  H171  C17  C11  C10     0.00   0.0  0
 R9K  CONST_44  H051  C05  C06  C10     0.00   0.0  0
 R9K  CONST_45  H171  C17  C16  C15   180.00   0.0  0
 R9K  CONST_46  H151  C15  C16  C17   180.00   0.0  0
 R9K  CONST_47  H081  N08  C07  C02     0.00   0.0  0
 R9K  CONST_48  H041  C04  C03  C02   180.00   0.0  0
 R9K  CONST_49  H051  C05  C04  C03   180.00   0.0  0
 R9K  CONST_50  H031  C03  C04  C05   180.00   0.0  0
 R9K  CONST_51  H081  N08  C07  C06   180.00   0.0  0
 R9K  CONST_52  H041  C04  C05  C06   180.00   0.0  0
 R9K  CONST_53  H051  C05  C06  C07   180.00   0.0  0
 R9K  CONST_54  H031  C03  C02  C07   180.00   0.0  0
 R9K  CONST_55  H161  C16  C17  C11   180.00   0.0  0
 R9K  CONST_56  H141  C14  C12  C11   180.00   0.0  0
 R9K  CONST_57  H171  C17  C11  C12   180.00   0.0  0
 R9K  CONST_58  H151  C15  C14  C12   180.00   0.0  0
 R9K  CONST_59  H161  C16  C15  C14   180.00   0.0  0
 R9K  CONST_60  H141  C14  C15  C16   180.00   0.0  0
 R9K  Var_01    O20   C18  C09  C10  -175.90  30.0  2
 R9K  Var_02    O19   C18  C09  C10     4.39  30.0  2
 R9K  Var_03    O20   C18  C09  N08     5.59  30.0  2
 R9K  Var_04    O19   C18  C09  N08  -174.13  30.0  2
 R9K  Var_05    H011  C01  C02  C03  -121.03  30.0  2
 R9K  Var_06    H012  C01  C02  C03    -0.65  30.0  2
 R9K  Var_07    H013  C01  C02  C03   119.54  30.0  2
 R9K  Var_08    H011  C01  C02  C07    59.28  30.0  2
 R9K  Var_09    H012  C01  C02  C07   179.66  30.0  2
 R9K  Var_10    H013  C01  C02  C07   -60.15  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
 R9K  plan-1  C10   0.020
 R9K  plan-1  C15   0.020
 R9K  plan-1  C17   0.020
 R9K  plan-1  C11   0.020
 R9K  plan-1  C12   0.020
 R9K  plan-1  C14   0.020
 R9K  plan-1  C16   0.020
 R9K  plan-1  CL1   0.020
 R9K  plan-1  H141  0.020
 R9K  plan-1  H161  0.020
 R9K  plan-1  H151  0.020
 R9K  plan-1  H171  0.020
 R9K  plan-2  C10   0.020
 R9K  plan-2  C01   0.020
 R9K  plan-2  C02   0.020
 R9K  plan-2  C03   0.020
 R9K  plan-2  C04   0.020
 R9K  plan-2  C05   0.020
 R9K  plan-2  C06   0.020
 R9K  plan-2  C07   0.020
 R9K  plan-2  C09   0.020
 R9K  plan-2  C11   0.020
 R9K  plan-2  C18   0.020
 R9K  plan-2  N08   0.020
 R9K  plan-2  H031  0.020
 R9K  plan-2  H041  0.020
 R9K  plan-2  H051  0.020
 R9K  plan-2  H081  0.020
 R9K  plan-3  C09   0.020
 R9K  plan-3  C18   0.020
 R9K  plan-3  O19   0.020
 R9K  plan-3  O20   0.020

