# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 07:40:46 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 3-(3-methoxybenzyl)-1H-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cc2c[nH]c3ncccc23)c1
#
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
 C4F  C4F  3-(3-methoxybenzyl)-1H-pyrrolo[2,3-b]pyridine  ligand  32  18  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C4F
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
 C4F  C15   C  CH3   0  -0.436   5.0179   1.9544   0.0402
 C4F  O14   O  O2    0  -0.474   3.9287   1.4898  -0.7308
 C4F  C13   C  CR6   0   0.396   3.1410   0.5254  -0.2149
 C4F  C16   C  CR16  0  -0.401   3.3261  -0.0563   1.0348
 C4F  C17   C  CR16  0  -0.229   2.4411  -1.0448   1.4580
 C4F  C18   C  CR16  0  -0.309   1.3863  -1.4538   0.6630
 C4F  C12   C  CR16  0  -0.426   2.0755   0.1104  -1.0192
 C4F  C11   C  CR6   0   0.160   1.1987  -0.8733  -0.5926
 C4F  C10   C  CH2   0  -0.610   0.0613  -1.3185  -1.4824
 C4F  C9    C  CR5   0  -0.015  -1.2680  -1.2537  -0.8059
 C4F  C1    C  CR56  0  -0.013  -1.9136  -0.0802  -0.3022
 C4F  C8    C  CR15  0  -0.060  -2.1102  -2.2915  -0.5277
 C4F  N7    N  NR15  0  -0.671  -3.2353  -1.8384   0.1102
 C4F  C6    C  CR56  0   0.466  -3.1444  -0.4904   0.2628
 C4F  N5    N  N     0  -0.427  -4.0449   0.2925   0.8355
 C4F  C4    C  CR16  0  -0.091  -3.7308   1.5804   0.8664
 C4F  C3    C  CR16  0  -0.346  -2.5471   2.1148   0.3454
 C4F  C2    C  CR16  0  -0.243  -1.6170   1.2789  -0.2497
 C4F  H15   H  HCH3  0   0.258   5.5153   2.7164  -0.5547
 C4F  H15A  H  HCH3  0   0.227   4.6921   2.4025   0.9830
 C4F  H15B  H  HCH3  0   0.227   5.7337   1.1575   0.2594
 C4F  H16   H  HCR6  0   0.275   4.1360   0.2421   1.6863
 C4F  H17   H  HCR6  0   0.255   2.5880  -1.4943   2.4319
 C4F  H18   H  HCR6  0   0.240   0.7047  -2.2185   1.0152
 C4F  H12   H  HCR6  0   0.253   1.9384   0.5722  -1.9908
 C4F  H10   H  HCH2  0   0.256   0.0544  -0.7013  -2.3851
 C4F  H10A  H  HCH2  0   0.267   0.2444  -2.3440  -1.8153
 C4F  H8    H  HCR5  0   0.289  -1.9889  -3.3418  -0.7423
 C4F  HN7   H  HNR5  0   0.409  -4.0028  -2.4120   0.4187
 C4F  H4    H  HCR6  0   0.254  -4.4555   2.2392   1.3316
 C4F  H3    H  HCR6  0   0.261  -2.3708   3.1794   0.4152
 C4F  H2    H  HCR6  0   0.257  -0.6933   1.6720  -0.6563

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
 C4F  C15  O14   single    1.413  0.020  1.413
 C4F  O14  C13   single    1.348  0.020  1.348
 C4F  C13  C16   aromatic  1.391  0.020  1.391
 C4F  C13  C12   aromatic  1.398  0.020  1.398
 C4F  C16  C17   aromatic  1.393  0.020  1.393
 C4F  C17  C18   aromatic  1.383  0.020  1.383
 C4F  C18  C11   aromatic  1.396  0.020  1.396
 C4F  C12  C11   aromatic  1.385  0.020  1.385
 C4F  C11  C10   single    1.511  0.020  1.511
 C4F  C10  C9    single    1.493  0.020  1.493
 C4F  C9   C1    aromatic  1.431  0.020  1.431
 C4F  C9   C8    aromatic  1.365  0.020  1.365
 C4F  C1   C6    aromatic  1.415  0.020  1.415
 C4F  C1   C2    aromatic  1.392  0.020  1.392
 C4F  C8   N7    aromatic  1.370  0.020  1.370
 C4F  N7   C6    aromatic  1.360  0.020  1.360
 C4F  C6   N5    aromatic  1.324  0.020  1.324
 C4F  N5   C4    aromatic  1.326  0.020  1.326
 C4F  C4   C3    aromatic  1.399  0.020  1.399
 C4F  C3   C2    aromatic  1.385  0.020  1.385
 C4F  C15  H15   single    0.970  0.020  1.090
 C4F  C15  H15A  single    0.970  0.020  1.090
 C4F  C15  H15B  single    0.970  0.020  1.090
 C4F  C16  H16   single    0.930  0.020  1.080
 C4F  C17  H17   single    0.930  0.020  1.080
 C4F  C18  H18   single    0.930  0.020  1.080
 C4F  C12  H12   single    0.930  0.020  1.080
 C4F  C10  H10   single    0.970  0.020  1.090
 C4F  C10  H10A  single    0.970  0.020  1.090
 C4F  C8   H8    single    0.930  0.020  1.080
 C4F  N7   HN7   single    0.860  0.020  1.020
 C4F  C4   H4    single    0.930  0.020  1.080
 C4F  C3   H3    single    0.930  0.020  1.080
 C4F  C2   H2    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
 C4F  H15B  C15  H15A  108.72  3.000
 C4F  H15B  C15  H15   108.72  3.000
 C4F  H15A  C15  H15   108.72  3.000
 C4F  H15B  C15  O14   111.98  3.000
 C4F  H15A  C15  O14   112.06  3.000
 C4F  H15   C15  O14   106.53  3.000
 C4F  C13   O14  C15   118.48  3.000
 C4F  C12   C13  C16   119.61  3.000
 C4F  C12   C13  O14   115.96  3.000
 C4F  C16   C13  O14   124.43  3.000
 C4F  H16   C16  C17   119.26  3.000
 C4F  H16   C16  C13   121.71  3.000
 C4F  C17   C16  C13   119.04  3.000
 C4F  H17   C17  C18   119.86  3.000
 C4F  H17   C17  C16   118.81  3.000
 C4F  C18   C17  C16   121.33  3.000
 C4F  H18   C18  C11   120.10  3.000
 C4F  H18   C18  C17   120.12  3.000
 C4F  C11   C18  C17   119.78  3.000
 C4F  H12   C12  C11   119.89  3.000
 C4F  H12   C12  C13   119.03  3.000
 C4F  C11   C12  C13   121.07  3.000
 C4F  C10   C11  C12   120.29  3.000
 C4F  C10   C11  C18   120.55  3.000
 C4F  C12   C11  C18   119.16  3.000
 C4F  H10A  C10  H10   106.20  3.000
 C4F  H10A  C10  C9    109.13  3.000
 C4F  H10   C10  C9    110.12  3.000
 C4F  H10A  C10  C11   109.24  3.000
 C4F  H10   C10  C11   108.94  3.000
 C4F  C9    C10  C11   112.99  3.000
 C4F  C8    C9   C1    105.86  3.000
 C4F  C8    C9   C10   127.49  3.000
 C4F  C1    C9   C10   126.65  3.000
 C4F  C2    C1   C6    116.96  3.000
 C4F  C2    C1   C9    135.87  3.000
 C4F  C6    C1   C9    107.17  3.000
 C4F  H8    C8   N7    120.45  3.000
 C4F  H8    C8   C9    129.07  3.000
 C4F  N7    C8   C9    110.49  3.000
 C4F  HN7   N7   C6    125.56  3.000
 C4F  HN7   N7   C8    125.47  3.000
 C4F  C6    N7   C8    108.98  3.000
 C4F  N5    C6   N7    126.12  3.000
 C4F  N5    C6   C1    126.37  3.000
 C4F  N7    C6   C1    107.50  3.000
 C4F  C4    N5   C6    115.05  3.000
 C4F  H4    C4   C3    119.54  3.000
 C4F  H4    C4   N5    116.22  3.000
 C4F  C3    C4   N5    124.24  3.000
 C4F  H3    C3   C2    120.83  3.000
 C4F  H3    C3   C4    119.33  3.000
 C4F  C2    C3   C4    119.84  3.000
 C4F  H2    C2   C3    121.00  3.000
 C4F  H2    C2   C1    121.46  3.000
 C4F  C3    C2   C1    117.54  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
 C4F  CONST_01  C18  C17  C16  C13    0.00   0.0  0
 C4F  CONST_02  C18  C11  C12  C13    0.00   0.0  0
 C4F  CONST_03  C11  C12  C13  C16    0.00   0.0  0
 C4F  CONST_04  C11  C18  C17  C16    0.00   0.0  0
 C4F  CONST_05  C12  C13  C16  C17    0.00   0.0  0
 C4F  CONST_06  C12  C11  C18  C17    0.00   0.0  0
 C4F  CONST_07  N7   C6   C1   C9     0.00   0.0  0
 C4F  CONST_08  N5   C6   C1   C9   180.00   0.0  0
 C4F  CONST_09  C3   C2   C1   C9   180.00   0.0  0
 C4F  CONST_10  C6   N7   C8   C9     0.00   0.0  0
 C4F  CONST_11  N7   C8   C9   C1     0.00   0.0  0
 C4F  CONST_12  C8   N7   C6   C1     0.00   0.0  0
 C4F  CONST_13  C4   N5   C6   C1     0.00   0.0  0
 C4F  CONST_14  C4   C3   C2   C1     0.00   0.0  0
 C4F  CONST_15  C6   C1   C9   C8     0.00   0.0  0
 C4F  CONST_16  C2   C1   C9   C8   180.00   0.0  0
 C4F  CONST_17  N5   C6   N7   C8   180.00   0.0  0
 C4F  CONST_18  C2   C1   C6   N7   180.00   0.0  0
 C4F  CONST_19  C4   N5   C6   N7   180.00   0.0  0
 C4F  CONST_20  C3   C2   C1   C6     0.00   0.0  0
 C4F  CONST_21  C3   C4   N5   C6     0.00   0.0  0
 C4F  CONST_22  C2   C1   C6   N5     0.00   0.0  0
 C4F  CONST_23  C2   C3   C4   N5     0.00   0.0  0
 C4F  CONST_24  C17  C16  C13  O14  180.00   0.0  0
 C4F  CONST_25  C11  C12  C13  O14  180.00   0.0  0
 C4F  CONST_26  C10  C11  C12  C13  180.00   0.0  0
 C4F  CONST_27  C10  C11  C18  C17  180.00   0.0  0
 C4F  CONST_28  C6   C1   C9   C10  180.00   0.0  0
 C4F  CONST_29  C2   C1   C9   C10    0.00   0.0  0
 C4F  CONST_30  N7   C8   C9   C10  180.00   0.0  0
 C4F  CONST_31  H17  C17  C16  C13  180.00   0.0  0
 C4F  CONST_32  H12  C12  C13  C16  180.00   0.0  0
 C4F  CONST_33  H18  C18  C17  C16  180.00   0.0  0
 C4F  CONST_34  H16  C16  C17  C18  180.00   0.0  0
 C4F  CONST_35  H2   C2   C1   C9     0.00   0.0  0
 C4F  CONST_36  HN7  N7   C8   C9   180.00   0.0  0
 C4F  CONST_37  H8   C8   C9   C1   180.00   0.0  0
 C4F  CONST_38  H3   C3   C2   C1   180.00   0.0  0
 C4F  CONST_39  H4   C4   N5   C6   180.00   0.0  0
 C4F  Var_01    C9   C10  C11  C18   53.79  30.0  2
 C4F  Var_02    C1   C9   C10  C11   62.38  30.0  2
 C4F  Var_03    C16  C13  O14  C15   -0.21  30.0  2
 C4F  Var_04    H15  C15  O14  C13  179.82  30.0  3

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
 C4F  plan-1  O14  0.020
 C4F  plan-1  C13  0.020
 C4F  plan-1  C16  0.020
 C4F  plan-1  C17  0.020
 C4F  plan-1  C18  0.020
 C4F  plan-1  C12  0.020
 C4F  plan-1  C11  0.020
 C4F  plan-1  C10  0.020
 C4F  plan-1  H16  0.020
 C4F  plan-1  H17  0.020
 C4F  plan-1  H18  0.020
 C4F  plan-1  H12  0.020
 C4F  plan-2  C10  0.020
 C4F  plan-2  C9   0.020
 C4F  plan-2  C1   0.020
 C4F  plan-2  C8   0.020
 C4F  plan-2  N7   0.020
 C4F  plan-2  C6   0.020
 C4F  plan-2  N5   0.020
 C4F  plan-2  C4   0.020
 C4F  plan-2  C3   0.020
 C4F  plan-2  C2   0.020
 C4F  plan-2  H8   0.020
 C4F  plan-2  HN7  0.020
 C4F  plan-2  H4   0.020
 C4F  plan-2  H3   0.020
 C4F  plan-2  H2   0.020

