# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:30:57 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-(phenylmethyl)-1~{H}-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(c1ccccc1)c2c[nH]c3ncccc23
#
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
 SVK  SVK  3-(phenylmethyl)-1~{H}-pyrrolo[2,3-b]pyridine  ligand  28  16  .  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_SVK
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
 SVK  C1   C  CR16  0  -0.243  192.7967  -31.0890  77.8532
 SVK  C2   C  CR16  0  -0.297  193.8781  -31.2730  78.7052
 SVK  C3   C  CR6   0   0.094  193.7280  -31.1517  80.0840
 SVK  C7   C  CR5   0  -0.057  195.6234  -30.0158  81.2491
 SVK  C8   C  CR15  0  -0.030  195.3809  -28.7990  80.6782
 SVK  C9   C  CR56  0   0.464  197.0933  -28.4524  82.0531
 SVK  C10  C  CR56  0  -0.013  196.7245  -29.8161  82.1416
 SVK  C11  C  CR16  0  -0.240  197.4565  -30.6116  83.0189
 SVK  C12  C  CR16  0  -0.345  198.4816  -30.0076  83.7280
 SVK  C13  C  CR16  0  -0.091  198.7460  -28.6458  83.5459
 SVK  N1   N  N     0  -0.427  198.0689  -27.8582  82.7214
 SVK  N    N  NR15  0  -0.673  196.2600  -27.8620  81.1573
 SVK  C6   C  CH2   0  -0.566  194.9092  -31.3093  81.0018
 SVK  C4   C  CR16  0  -0.297  192.4701  -30.8395  80.5933
 SVK  C5   C  CR16  0  -0.243  191.3854  -30.6565  79.7461
 SVK  C    C  CR16  0  -0.271  191.5460  -30.7798  78.3719
 SVK  H1   H  HCR6  0   0.254  192.9310  -31.1886  76.7836
 SVK  H2   H  HCR6  0   0.248  194.8505  -31.5175  78.2933
 SVK  H3   H  HCR5  0   0.284  194.6330  -28.5221  79.9521
 SVK  H4   H  HCR6  0   0.260  197.2359  -31.6641  83.1487
 SVK  H5   H  HCR6  0   0.262  199.0823  -30.5757  84.4246
 SVK  H6   H  HCR6  0   0.254  199.5499  -28.1779  84.1027
 SVK  H7   H  HNR5  0   0.408  196.2820  -26.8923  80.8885
 SVK  H8   H  HCH2  0   0.255  194.5801  -31.7312  81.9562
 SVK  H9   H  HCH2  0   0.256  195.6086  -32.0359  80.5772
 SVK  H10  H  HCR6  0   0.248  192.3381  -30.7415  81.6648
 SVK  H11  H  HCR6  0   0.253  190.4138  -30.4177  80.1594
 SVK  H12  H  HCR6  0   0.254  190.7019  -30.6383  77.7094

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
 SVK  C    C1   aromatic  1.389  0.020  1.389
 SVK  C    C5   aromatic  1.389  0.020  1.389
 SVK  C1   C2   aromatic  1.389  0.020  1.389
 SVK  C5   C4   aromatic  1.389  0.020  1.389
 SVK  C2   C3   aromatic  1.392  0.020  1.392
 SVK  C4   C3   aromatic  1.393  0.020  1.393
 SVK  C3   C6   single    1.504  0.020  1.504
 SVK  C6   C7   single    1.498  0.020  1.498
 SVK  C8   C7   aromatic  1.366  0.020  1.366
 SVK  C8   N    aromatic  1.371  0.020  1.371
 SVK  C7   C10  aromatic  1.431  0.020  1.431
 SVK  N    C9   aromatic  1.358  0.020  1.358
 SVK  C10  C9   aromatic  1.415  0.020  1.415
 SVK  C10  C11  aromatic  1.392  0.020  1.392
 SVK  C9   N1   aromatic  1.323  0.020  1.323
 SVK  C11  C12  aromatic  1.385  0.020  1.385
 SVK  N1   C13  aromatic  1.326  0.020  1.326
 SVK  C12  C13  aromatic  1.399  0.020  1.399
 SVK  C1   H1   single    0.930  0.020  1.080
 SVK  C2   H2   single    0.930  0.020  1.080
 SVK  C8   H3   single    0.930  0.020  1.080
 SVK  C11  H4   single    0.930  0.020  1.080
 SVK  C12  H5   single    0.930  0.020  1.080
 SVK  C13  H6   single    0.930  0.020  1.080
 SVK  N    H7   single    0.860  0.020  1.020
 SVK  C6   H8   single    0.970  0.020  1.090
 SVK  C6   H9   single    0.970  0.020  1.090
 SVK  C4   H10  single    0.930  0.020  1.080
 SVK  C5   H11  single    0.930  0.020  1.080
 SVK  C    H12  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
 SVK  H1   C1   C    120.07  3.000
 SVK  H1   C1   C2   119.82  3.000
 SVK  C    C1   C2   120.10  3.000
 SVK  H2   C2   C3   119.52  3.000
 SVK  H2   C2   C1   119.69  3.000
 SVK  C3   C2   C1   120.80  3.000
 SVK  C4   C3   C6   120.64  3.000
 SVK  C6   C3   C2   120.70  3.000
 SVK  C4   C3   C2   118.63  3.000
 SVK  C6   C7   C10  126.17  3.000
 SVK  C10  C7   C8   105.84  3.000
 SVK  C6   C7   C8   128.00  3.000
 SVK  H3   C8   N    120.29  3.000
 SVK  H3   C8   C7   129.29  3.000
 SVK  N    C8   C7   110.42  3.000
 SVK  N    C9   N1   126.16  3.000
 SVK  N1   C9   C10  126.37  3.000
 SVK  N    C9   C10  107.47  3.000
 SVK  C11  C10  C9   116.93  3.000
 SVK  C11  C10  C7   135.86  3.000
 SVK  C9   C10  C7   107.21  3.000
 SVK  H4   C11  C12  120.87  3.000
 SVK  H4   C11  C10  121.57  3.000
 SVK  C12  C11  C10  117.55  3.000
 SVK  H5   C12  C13  119.36  3.000
 SVK  H5   C12  C11  120.79  3.000
 SVK  C13  C12  C11  119.85  3.000
 SVK  H6   C13  N1   116.21  3.000
 SVK  H6   C13  C12  119.56  3.000
 SVK  N1   C13  C12  124.23  3.000
 SVK  C13  N1   C9   115.07  3.000
 SVK  H7   N    C9   125.56  3.000
 SVK  H7   N    C8   125.38  3.000
 SVK  C9   N    C8   109.07  3.000
 SVK  H9   C6   H8   105.94  3.000
 SVK  H9   C6   C7   109.43  3.000
 SVK  H8   C6   C7   109.41  3.000
 SVK  H9   C6   C3   109.55  3.000
 SVK  H8   C6   C3   109.66  3.000
 SVK  C7   C6   C3   112.62  3.000
 SVK  H10  C4   C5   119.74  3.000
 SVK  H10  C4   C3   119.46  3.000
 SVK  C5   C4   C3   120.80  3.000
 SVK  H11  C5   C    120.07  3.000
 SVK  H11  C5   C4   119.82  3.000
 SVK  C    C5   C4   120.11  3.000
 SVK  H12  C    C5   120.24  3.000
 SVK  H12  C    C1   120.19  3.000
 SVK  C5   C    C1   119.56  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
 SVK  CONST_01  C4   C5   C    C1     0.00   0.0  0
 SVK  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 SVK  CONST_03  C5   C    C1   C2     0.00   0.0  0
 SVK  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 SVK  CONST_05  C    C1   C2   C3     0.00   0.0  0
 SVK  CONST_06  C    C5   C4   C3     0.00   0.0  0
 SVK  CONST_07  C9   N    C8   C7     0.00   0.0  0
 SVK  CONST_08  N    C9   C10  C7     0.00   0.0  0
 SVK  CONST_09  N1   C9   C10  C7   180.00   0.0  0
 SVK  CONST_10  C12  C11  C10  C7   180.00   0.0  0
 SVK  CONST_11  C9   C10  C7   C8     0.00   0.0  0
 SVK  CONST_12  C11  C10  C7   C8   180.00   0.0  0
 SVK  CONST_13  C10  C9   N    C8     0.00   0.0  0
 SVK  CONST_14  N1   C9   N    C8   180.00   0.0  0
 SVK  CONST_15  C12  C11  C10  C9     0.00   0.0  0
 SVK  CONST_16  C12  C13  N1   C9     0.00   0.0  0
 SVK  CONST_17  N    C8   C7   C10    0.00   0.0  0
 SVK  CONST_18  C13  N1   C9   C10    0.00   0.0  0
 SVK  CONST_19  C13  C12  C11  C10    0.00   0.0  0
 SVK  CONST_20  N    C9   C10  C11  180.00   0.0  0
 SVK  CONST_21  N1   C9   C10  C11    0.00   0.0  0
 SVK  CONST_22  N1   C13  C12  C11    0.00   0.0  0
 SVK  CONST_23  N    C9   N1   C13  180.00   0.0  0
 SVK  CONST_24  C6   C3   C2   C1   180.00   0.0  0
 SVK  CONST_25  C6   C7   C10  C9   180.00   0.0  0
 SVK  CONST_26  C6   C7   C10  C11    0.00   0.0  0
 SVK  CONST_27  C6   C7   C8   N    180.00   0.0  0
 SVK  CONST_28  C5   C4   C3   C6   180.00   0.0  0
 SVK  CONST_29  H11  C5   C    C1   180.00   0.0  0
 SVK  CONST_30  H12  C    C1   C2   180.00   0.0  0
 SVK  CONST_31  H10  C4   C3   C2   180.00   0.0  0
 SVK  CONST_32  H1   C1   C2   C3   180.00   0.0  0
 SVK  CONST_33  H7   N    C8   C7   180.00   0.0  0
 SVK  CONST_34  H4   C11  C10  C7     0.00   0.0  0
 SVK  CONST_35  H3   C8   N    C9   180.00   0.0  0
 SVK  CONST_36  H6   C13  N1   C9   180.00   0.0  0
 SVK  CONST_37  H5   C12  C11  C10  180.00   0.0  0
 SVK  CONST_38  H2   C2   C3   C4   180.00   0.0  0
 SVK  Var_01    C7   C6   C3   C2    89.34  30.0  2
 SVK  Var_02    C8   C7   C6   C3    -5.04  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
 SVK  plan-1  C1   0.020
 SVK  plan-1  C2   0.020
 SVK  plan-1  C3   0.020
 SVK  plan-1  C6   0.020
 SVK  plan-1  C4   0.020
 SVK  plan-1  C5   0.020
 SVK  plan-1  C    0.020
 SVK  plan-1  H1   0.020
 SVK  plan-1  H2   0.020
 SVK  plan-1  H10  0.020
 SVK  plan-1  H11  0.020
 SVK  plan-1  H12  0.020
 SVK  plan-2  C7   0.020
 SVK  plan-2  C8   0.020
 SVK  plan-2  C9   0.020
 SVK  plan-2  C10  0.020
 SVK  plan-2  C11  0.020
 SVK  plan-2  C12  0.020
 SVK  plan-2  C13  0.020
 SVK  plan-2  N1   0.020
 SVK  plan-2  N    0.020
 SVK  plan-2  C6   0.020
 SVK  plan-2  H3   0.020
 SVK  plan-2  H4   0.020
 SVK  plan-2  H5   0.020
 SVK  plan-2  H6   0.020
 SVK  plan-2  H7   0.020

