# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 01:31:36 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 3-[3-(1H-pyrrolo[2,3-b]pyridin-5-yl)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1cccc(c1)c2cnc3[nH]ccc3c2
#
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
 0RA  0RA  '3-[3-(1H-pyrrolo[2,3-b]pyridin-5-yl)phenyl]propanoic acid'  ligand  33  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0RA
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
 0RA  C1   C  C1     0  -0.224  -1.0422   3.0862   0.2622
 0RA  C2   C  C1     0  -0.329  -2.2110   2.3487   0.3958
 0RA  C3   C  C      0   0.159  -2.1632   0.9604   0.4979
 0RA  C4   C  C1     0  -0.383  -0.9190   0.3370   0.4567
 0RA  C5   C  C      0   0.114   0.2667   1.0609   0.3276
 0RA  C6   C  C1     0  -0.338   0.1899   2.4514   0.2305
 0RA  C7   C  CR6    0  -0.022   1.5723   0.3740   0.2940
 0RA  C8   C  CR16   0  -0.279   2.6035   0.8189  -0.5258
 0RA  C9   C  CR56   0   0.031   3.8090   0.1260  -0.5090
 0RA  C10  C  CR15   0  -0.450   5.0691   0.2313  -1.1725
 0RA  C11  C  CR15   0   0.001   5.8379  -0.7938  -0.7022
 0RA  N1   N  NR15   0  -0.662   5.1340  -1.5297   0.2111
 0RA  C12  C  CR56   0   0.459   3.8923  -0.9940   0.3507
 0RA  N2   N  N      0  -0.420   2.9329  -1.4375   1.1464
 0RA  C13  C  CR16   0  -0.127   1.8022  -0.7535   1.1062
 0RA  C14  C  CH2    0  -0.501  -3.4189   0.1403   0.5970
 0RA  C15  C  CH2    0  -0.577  -3.9215  -0.2974  -0.7755
 0RA  C16  C  C      0   0.414  -5.1757  -1.1912  -0.7644
 0RA  O1   O  O      0  -0.606  -5.6269  -1.5477   0.3414
 0RA  O2   O  OC    -1  -0.630  -5.6353  -1.4934  -1.8856
 0RA  H1   H  H      0   0.252  -1.0910   4.1657   0.1961
 0RA  H2   H  H      0   0.244  -3.1669   2.8583   0.4282
 0RA  H3   H  H      0   0.240  -0.8775  -0.7455   0.5131
 0RA  H4   H  H      0   0.249   1.0943   3.0421   0.1520
 0RA  H5   H  HCR6   0   0.259   2.4639   1.6744  -1.1760
 0RA  H6   H  HCR5   0   0.253   5.3695   0.9691  -1.8989
 0RA  H7   H  HCR5   0   0.290   6.8527  -1.0597  -0.9492
 0RA  H8   H  HNR5   0   0.412   5.4803  -2.3393   0.6994
 0RA  H9   H  HCR6   0   0.254   1.0160  -1.0985   1.7692
 0RA  H10  H  HCH2   0   0.229  -3.2305  -0.7410   1.2136
 0RA  H11  H  HCH2   0   0.229  -4.1945   0.7156   1.1074
 0RA  H12  H  HCH2   0   0.227  -4.1273   0.5833  -1.3935
 0RA  H13  H  HCH2   0   0.230  -3.1241  -0.8347  -1.3018

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
 0RA  C11  N1   aromatic  1.368  0.020  1.368
 0RA  C11  C10  aromatic  1.365  0.020  1.365
 0RA  N1   C12  aromatic  1.359  0.020  1.359
 0RA  C10  C9   aromatic  1.428  0.020  1.428
 0RA  C12  C9   aromatic  1.414  0.020  1.414
 0RA  C12  N2   aromatic  1.323  0.020  1.323
 0RA  C9   C8   aromatic  1.391  0.020  1.391
 0RA  N2   C13  aromatic  1.322  0.020  1.322
 0RA  C8   C7   aromatic  1.390  0.020  1.390
 0RA  C13  C7   aromatic  1.408  0.020  1.408
 0RA  C7   C5   single    1.476  0.020  1.476
 0RA  C6   C5   aromatic  1.396  0.020  1.396
 0RA  C6   C1   aromatic  1.386  0.020  1.386
 0RA  C5   C4   aromatic  1.395  0.020  1.395
 0RA  C1   C2   aromatic  1.388  0.020  1.388
 0RA  C4   C3   aromatic  1.392  0.020  1.392
 0RA  C2   C3   aromatic  1.393  0.020  1.393
 0RA  C3   C14  single    1.503  0.020  1.503
 0RA  C14  C15  single    1.526  0.020  1.526
 0RA  C15  C16  single    1.540  0.020  1.540
 0RA  C16  O1   deloc     1.246  0.020  1.246
 0RA  C16  O2   deloc     1.249  0.020  1.249
 0RA  C1   H1   single    0.930  0.020  1.080
 0RA  C2   H2   single    0.930  0.020  1.080
 0RA  C4   H3   single    0.930  0.020  1.080
 0RA  C6   H4   single    0.930  0.020  1.080
 0RA  C8   H5   single    0.930  0.020  1.080
 0RA  C10  H6   single    0.930  0.020  1.080
 0RA  C11  H7   single    0.930  0.020  1.080
 0RA  N1   H8   single    0.860  0.020  1.020
 0RA  C13  H9   single    0.930  0.020  1.080
 0RA  C14  H10  single    0.970  0.020  1.090
 0RA  C14  H11  single    0.970  0.020  1.090
 0RA  C15  H12  single    0.970  0.020  1.090
 0RA  C15  H13  single    0.970  0.020  1.090

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
 0RA  H1   C1   C6   119.68  3.000
 0RA  H1   C1   C2   119.84  3.000
 0RA  C6   C1   C2   120.47  3.000
 0RA  H2   C2   C3   119.78  3.000
 0RA  H2   C2   C1   119.71  3.000
 0RA  C3   C2   C1   120.50  3.000
 0RA  C14  C3   C4   120.28  3.000
 0RA  C14  C3   C2   121.33  3.000
 0RA  C4   C3   C2   118.35  3.000
 0RA  H3   C4   C5   119.35  3.000
 0RA  H3   C4   C3   118.65  3.000
 0RA  C5   C4   C3   122.00  3.000
 0RA  C7   C5   C6   120.71  3.000
 0RA  C6   C5   C4   118.46  3.000
 0RA  C7   C5   C4   120.83  3.000
 0RA  H4   C6   C5   120.15  3.000
 0RA  H4   C6   C1   119.61  3.000
 0RA  C5   C6   C1   120.22  3.000
 0RA  C13  C7   C8   118.37  3.000
 0RA  C13  C7   C5   120.26  3.000
 0RA  C8   C7   C5   121.37  3.000
 0RA  H5   C8   C9   120.82  3.000
 0RA  H5   C8   C7   120.72  3.000
 0RA  C9   C8   C7   118.45  3.000
 0RA  C12  C9   C10  106.79  3.000
 0RA  C12  C9   C8   116.94  3.000
 0RA  C10  C9   C8   136.27  3.000
 0RA  H6   C10  C11  126.10  3.000
 0RA  H6   C10  C9   127.55  3.000
 0RA  C11  C10  C9   106.35  3.000
 0RA  H7   C11  N1   120.32  3.000
 0RA  H7   C11  C10  129.55  3.000
 0RA  N1   C11  C10  110.14  3.000
 0RA  H8   N1   C12  125.53  3.000
 0RA  H8   N1   C11  125.41  3.000
 0RA  C12  N1   C11  109.06  3.000
 0RA  N2   C12  N1   126.30  3.000
 0RA  N2   C12  C9   126.04  3.000
 0RA  N1   C12  C9   107.66  3.000
 0RA  C13  N2   C12  115.37  3.000
 0RA  H9   C13  N2   115.89  3.000
 0RA  H9   C13  C7   119.26  3.000
 0RA  N2   C13  C7   124.84  3.000
 0RA  H11  C14  H10  106.48  3.000
 0RA  H11  C14  C15  109.72  3.000
 0RA  H10  C14  C15  109.47  3.000
 0RA  H11  C14  C3   109.67  3.000
 0RA  H10  C14  C3   109.48  3.000
 0RA  C15  C14  C3   111.86  3.000
 0RA  H13  C15  H12  105.06  3.000
 0RA  H13  C15  C16  108.14  3.000
 0RA  H12  C15  C16  108.52  3.000
 0RA  H13  C15  C14  109.45  3.000
 0RA  H12  C15  C14  109.80  3.000
 0RA  C16  C15  C14  115.36  3.000
 0RA  O2   C16  O1   126.44  3.000
 0RA  O2   C16  C15  115.70  3.000
 0RA  O1   C16  C15  117.85  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
 0RA  CONST_01  C7   C5   C6   C1   180.00   0.0  0
 0RA  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 0RA  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 0RA  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 0RA  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 0RA  CONST_06  C7   C5   C4   C3   180.00   0.0  0
 0RA  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 0RA  CONST_08  C6   C1   C2   C3     0.00   0.0  0
 0RA  CONST_11  C9   C8   C7   C5   180.00   0.0  0
 0RA  CONST_12  N2   C13  C7   C5   180.00   0.0  0
 0RA  CONST_15  C10  C9   C8   C7   180.00   0.0  0
 0RA  CONST_16  C12  C9   C8   C7     0.00   0.0  0
 0RA  CONST_17  C12  N2   C13  C7     0.00   0.0  0
 0RA  CONST_18  C11  C10  C9   C8   180.00   0.0  0
 0RA  CONST_19  N1   C12  C9   C8   180.00   0.0  0
 0RA  CONST_20  N2   C12  C9   C8     0.00   0.0  0
 0RA  CONST_21  N2   C13  C7   C8     0.00   0.0  0
 0RA  CONST_22  N1   C11  C10  C9     0.00   0.0  0
 0RA  CONST_23  C11  N1   C12  C9     0.00   0.0  0
 0RA  CONST_24  C13  N2   C12  C9     0.00   0.0  0
 0RA  CONST_25  C13  C7   C8   C9     0.00   0.0  0
 0RA  CONST_26  C12  N1   C11  C10    0.00   0.0  0
 0RA  CONST_27  N1   C12  C9   C10    0.00   0.0  0
 0RA  CONST_28  N2   C12  C9   C10  180.00   0.0  0
 0RA  CONST_29  N2   C12  N1   C11  180.00   0.0  0
 0RA  CONST_30  C12  C9   C10  C11    0.00   0.0  0
 0RA  CONST_31  C13  N2   C12  N1   180.00   0.0  0
 0RA  CONST_32  C14  C3   C2   C1   180.00   0.0  0
 0RA  CONST_33  C14  C3   C4   C5   180.00   0.0  0
 0RA  CONST_34  H4   C6   C1   C2   180.00   0.0  0
 0RA  CONST_35  H3   C4   C3   C2   180.00   0.0  0
 0RA  CONST_36  H1   C1   C2   C3   180.00   0.0  0
 0RA  CONST_37  H2   C2   C3   C4   180.00   0.0  0
 0RA  CONST_38  H5   C8   C7   C5     0.00   0.0  0
 0RA  CONST_39  H9   C13  C7   C5     0.00   0.0  0
 0RA  CONST_40  H6   C10  C9   C8     0.00   0.0  0
 0RA  CONST_41  H7   C11  C10  C9   180.00   0.0  0
 0RA  CONST_42  H8   N1   C12  C9   180.00   0.0  0
 0RA  Var_01    C15  C14  C3   C2    91.09  30.0  2
 0RA  Var_02    C16  C15  C14  C3   177.68  30.0  3
 0RA  Var_03    O1   C16  C15  C14   -4.18  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
 0RA  plan-1  C1   0.020
 0RA  plan-1  C2   0.020
 0RA  plan-1  C3   0.020
 0RA  plan-1  C4   0.020
 0RA  plan-1  C5   0.020
 0RA  plan-1  C6   0.020
 0RA  plan-1  C7   0.020
 0RA  plan-1  C14  0.020
 0RA  plan-1  H1   0.020
 0RA  plan-1  H2   0.020
 0RA  plan-1  H3   0.020
 0RA  plan-1  H4   0.020
 0RA  plan-2  C5   0.020
 0RA  plan-2  C7   0.020
 0RA  plan-2  C8   0.020
 0RA  plan-2  C9   0.020
 0RA  plan-2  C10  0.020
 0RA  plan-2  C11  0.020
 0RA  plan-2  N1   0.020
 0RA  plan-2  C12  0.020
 0RA  plan-2  N2   0.020
 0RA  plan-2  C13  0.020
 0RA  plan-2  H5   0.020
 0RA  plan-2  H6   0.020
 0RA  plan-2  H7   0.020
 0RA  plan-2  H8   0.020
 0RA  plan-2  H9   0.020
 0RA  plan-3  C15  0.020
 0RA  plan-3  C16  0.020
 0RA  plan-3  O1   0.020
 0RA  plan-3  O2   0.020

