# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:46:05 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-(phenylmethyl)-5~{H}-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Cc2n(Cc3ccccc3)ccc12
#
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
 SV5  SV5  1-(phenylmethyl)-5~{H}-pyrrolo[3,2-c]pyridin-4-one  ligand  29  17  .  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_SV5
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
 SV5  C1   C  CR16  0  -0.240  196.8488  -30.8875  79.0169
 SV5  C2   C  CR16  0  -0.281  197.4661  -31.6176  80.0223
 SV5  C3   C  CR6   0   0.102  196.7204  -32.1285  81.0812
 SV5  C7   C  CR15  0  -0.042  199.8768  -32.9243  82.3397
 SV5  C8   C  CR15  0  -0.396  200.8389  -32.1141  82.8688
 SV5  C9   C  CR56  0  -0.211  200.1533  -31.0342  83.4889
 SV5  C10  C  CR56  0   0.487  198.7872  -31.2427  83.3019
 SV5  C11  C  CR16  0  -0.420  197.8041  -30.3486  83.7965
 SV5  C12  C  CR16  0   0.024  198.2790  -29.2750  84.4688
 SV5  C13  C  CR6   0   0.476  200.6360  -29.8904  84.2047
 SV5  O    O  O     0  -0.504  201.8128  -29.6143  84.4262
 SV5  N1   N  NR16  0  -0.679  199.6162  -29.0718  84.6536
 SV5  N    N  NR5   0  -0.512  198.6357  -32.3970  82.6082
 SV5  C6   C  CH2   0  -0.386  197.3721  -32.9463  82.1692
 SV5  C4   C  CR16  0  -0.307  195.3500  -31.8956  81.1172
 SV5  C5   C  CR16  0  -0.241  194.7292  -31.1687  80.1090
 SV5  C    C  CR16  0  -0.266  195.4779  -30.6623  79.0563
 SV5  H1   H  HCR6  0   0.258  197.4390  -30.4929  78.2000
 SV5  H2   H  HCR6  0   0.254  198.5363  -31.7838  79.9791
 SV5  H3   H  HCR5  0   0.289  199.9674  -33.8458  81.7872
 SV5  H4   H  HCR5  0   0.253  201.9036  -32.2754  82.8218
 SV5  H5   H  HCR6  0   0.280  196.7429  -30.4905  83.6569
 SV5  H7   H  HCR6  0   0.304  197.6334  -28.5216  84.8943
 SV5  H8   H  HCH2  0   0.280  196.6995  -33.0351  83.0246
 SV5  H9   H  HCH2  0   0.293  197.5632  -33.9616  81.8187
 SV5  H10  H  HCR6  0   0.255  194.7620  -32.2823  81.9416
 SV5  H11  H  HCR6  0   0.258  193.6621  -30.9928  80.1521
 SV5  H12  H  HCR6  0   0.258  194.9978  -30.0928  78.2712
 SV5  H6   H  HNR6  0   0.416  199.8980  -28.2457  85.1620

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
 SV5  C    C1   aromatic  1.390  0.020  1.390
 SV5  C    C5   aromatic  1.387  0.020  1.387
 SV5  C1   C2   aromatic  1.387  0.020  1.387
 SV5  C5   C4   aromatic  1.389  0.020  1.389
 SV5  C2   C3   aromatic  1.392  0.020  1.392
 SV5  C4   C3   aromatic  1.390  0.020  1.390
 SV5  C3   C6   single    1.509  0.020  1.509
 SV5  C6   N    single    1.446  0.020  1.446
 SV5  C7   N    aromatic  1.375  0.020  1.375
 SV5  C7   C8   aromatic  1.364  0.020  1.364
 SV5  N    C10  aromatic  1.355  0.020  1.355
 SV5  C8   C9   aromatic  1.421  0.020  1.421
 SV5  C10  C9   aromatic  1.395  0.020  1.395
 SV5  C10  C11  single    1.418  0.020  1.418
 SV5  C9   C13  single    1.433  0.020  1.433
 SV5  C11  C12  double    1.353  0.020  1.353
 SV5  C13  O    double    1.229  0.020  1.229
 SV5  C13  N1   single    1.383  0.020  1.383
 SV5  C12  N1   single    1.365  0.020  1.365
 SV5  C1   H1   single    0.930  0.020  1.080
 SV5  C2   H2   single    0.930  0.020  1.080
 SV5  C7   H3   single    0.930  0.020  1.080
 SV5  C8   H4   single    0.930  0.020  1.080
 SV5  C11  H5   single    0.930  0.020  1.080
 SV5  C12  H7   single    0.930  0.020  1.080
 SV5  C6   H8   single    0.970  0.020  1.090
 SV5  C6   H9   single    0.970  0.020  1.090
 SV5  C4   H10  single    0.930  0.020  1.080
 SV5  C5   H11  single    0.930  0.020  1.080
 SV5  C    H12  single    0.930  0.020  1.080
 SV5  N1   H6   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
 SV5  H1   C1   C    120.01  3.000
 SV5  H1   C1   C2   119.75  3.000
 SV5  C    C1   C2   120.24  3.000
 SV5  H2   C2   C3   120.19  3.000
 SV5  H2   C2   C1   119.42  3.000
 SV5  C3   C2   C1   120.39  3.000
 SV5  C4   C3   C6   119.85  3.000
 SV5  C6   C3   C2   121.06  3.000
 SV5  C4   C3   C2   119.08  3.000
 SV5  H3   C7   N    120.24  3.000
 SV5  H3   C7   C8   130.31  3.000
 SV5  N    C7   C8   109.45  3.000
 SV5  H4   C8   C9   127.52  3.000
 SV5  H4   C8   C7   126.21  3.000
 SV5  C9   C8   C7   106.27  3.000
 SV5  C13  C9   C10  121.08  3.000
 SV5  C13  C9   C8   131.44  3.000
 SV5  C10  C9   C8   107.48  3.000
 SV5  N    C10  C11  129.65  3.000
 SV5  C11  C10  C9   122.56  3.000
 SV5  N    C10  C9   107.79  3.000
 SV5  H5   C11  C12  120.90  3.000
 SV5  H5   C11  C10  123.60  3.000
 SV5  C12  C11  C10  115.50  3.000
 SV5  H7   C12  N1   115.38  3.000
 SV5  H7   C12  C11  122.67  3.000
 SV5  N1   C12  C11  121.95  3.000
 SV5  N1   C13  O    120.98  3.000
 SV5  N1   C13  C9   112.72  3.000
 SV5  O    C13  C9   126.29  3.000
 SV5  H6   N1   C13  116.22  3.000
 SV5  H6   N1   C12  117.59  3.000
 SV5  C13  N1   C12  126.19  3.000
 SV5  C6   N    C10  125.21  3.000
 SV5  C10  N    C7   109.00  3.000
 SV5  C6   N    C7   125.72  3.000
 SV5  H9   C6   H8   106.49  3.000
 SV5  H9   C6   N    107.33  3.000
 SV5  H8   C6   N    109.35  3.000
 SV5  H9   C6   C3   110.39  3.000
 SV5  H8   C6   C3   110.06  3.000
 SV5  N    C6   C3   112.98  3.000
 SV5  H10  C4   C5   119.74  3.000
 SV5  H10  C4   C3   119.64  3.000
 SV5  C5   C4   C3   120.61  3.000
 SV5  H11  C5   C    120.19  3.000
 SV5  H11  C5   C4   119.78  3.000
 SV5  C    C5   C4   120.03  3.000
 SV5  H12  C    C5   120.21  3.000
 SV5  H12  C    C1   120.15  3.000
 SV5  C5   C    C1   119.64  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
 SV5  CONST_01  C4   C5   C    C1      0.00   0.0  0
 SV5  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 SV5  CONST_03  C5   C    C1   C2      0.00   0.0  0
 SV5  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 SV5  CONST_05  C    C1   C2   C3      0.00   0.0  0
 SV5  CONST_06  C    C5   C4   C3      0.00   0.0  0
 SV5  CONST_07  C9   C10  N    C7      0.00   0.0  0
 SV5  CONST_08  C10  C9   C8   C7      0.00   0.0  0
 SV5  CONST_09  C10  N    C7   C8      0.00   0.0  0
 SV5  CONST_10  N    C10  C9   C8      0.00   0.0  0
 SV5  CONST_11  N    C7   C8   C9      0.00   0.0  0
 SV5  CONST_12  C12  N1   C13  C9      0.00   0.0  0
 SV5  CONST_13  C6   C3   C2   C1    180.00   0.0  0
 SV5  CONST_14  C6   N    C7   C8    180.00   0.0  0
 SV5  CONST_15  C6   N    C10  C9    180.00   0.0  0
 SV5  CONST_16  C6   N    C10  C11     0.00   0.0  0
 SV5  CONST_17  C5   C4   C3   C6    180.00   0.0  0
 SV5  CONST_18  O    C13  N1   C12   180.00   0.0  0
 SV5  CONST_19  H11  C5   C    C1    180.00   0.0  0
 SV5  CONST_20  H12  C    C1   C2    180.00   0.0  0
 SV5  CONST_21  H10  C4   C3   C2    180.00   0.0  0
 SV5  CONST_22  H1   C1   C2   C3    180.00   0.0  0
 SV5  CONST_23  H3   C7   C8   C9    180.00   0.0  0
 SV5  CONST_24  H4   C8   C9   C10   180.00   0.0  0
 SV5  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 SV5  CONST_26  H6   N1   C13  C9    180.00   0.0  0
 SV5  Var_01    N    C6   C3   C2     42.87  30.0  2
 SV5  Var_02    C7   N    C6   C3   -107.83  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
 SV5  plan-1  C1   0.020
 SV5  plan-1  C2   0.020
 SV5  plan-1  C3   0.020
 SV5  plan-1  C6   0.020
 SV5  plan-1  C4   0.020
 SV5  plan-1  C5   0.020
 SV5  plan-1  C    0.020
 SV5  plan-1  H1   0.020
 SV5  plan-1  H2   0.020
 SV5  plan-1  H10  0.020
 SV5  plan-1  H11  0.020
 SV5  plan-1  H12  0.020
 SV5  plan-2  C7   0.020
 SV5  plan-2  C8   0.020
 SV5  plan-2  C9   0.020
 SV5  plan-2  C10  0.020
 SV5  plan-2  C11  0.020
 SV5  plan-2  C12  0.020
 SV5  plan-2  C13  0.020
 SV5  plan-2  O    0.020
 SV5  plan-2  N1   0.020
 SV5  plan-2  N    0.020
 SV5  plan-2  C6   0.020
 SV5  plan-2  H3   0.020
 SV5  plan-2  H4   0.020
 SV5  plan-2  H5   0.020
 SV5  plan-2  H7   0.020
 SV5  plan-2  H6   0.020

