# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:30:25 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-oxo-5,6,7,12-tetrahydroindolo[3,2-d][1]benzazepine-9-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Cc2c([nH]c3ccc(cc23)C#N)c4ccccc4N1
#
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
 PAK  PAK  6-oxo-5,6,7,12-tetrahydroindolo[3,2-d][1]benzazepine-9-carbonitrile  ligand  32  21  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PAK
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
 PAK  N    N  NH1   0  -0.730  -1.6647  -0.5607  -2.3390
 PAK  C    C  C     0   0.501  -2.3503  -0.1283  -1.2413
 PAK  O    O  O     0  -0.457  -3.4489  -0.5800  -0.9799
 PAK  C1   C  CH2   0  -0.684  -1.6653   0.9169  -0.3939
 PAK  C2   C  CR5   0  -0.036  -0.3772   0.3823   0.1272
 PAK  C3   C  CR56  0   0.075   0.0428   0.1668   1.4731
 PAK  C4   C  CR56  0   0.361   1.3754  -0.3112   1.4114
 PAK  N1   N  NR15  0  -0.753   1.7282  -0.3755   0.1031
 PAK  C5   C  CR5   0   0.378   0.6716   0.0280  -0.6759
 PAK  C6   C  CR6   0   0.044   0.7131   0.0962  -2.1226
 PAK  C7   C  CR6   0   0.291  -0.4428  -0.1434  -2.8848
 PAK  C8   C  CR16  0  -0.309  -0.3637  -0.0754  -4.2772
 PAK  C9   C  CR16  0  -0.256   0.8285   0.2176  -4.9114
 PAK  C10  C  CR16  0  -0.251   1.9744   0.4608  -4.1618
 PAK  C11  C  CR16  0  -0.320   1.9077   0.4014  -2.7839
 PAK  C12  C  CR16  0  -0.298   2.1037  -0.6370   2.5551
 PAK  C13  C  CR16  0  -0.271   1.4881  -0.4681   3.7737
 PAK  C14  C  CR6   0  -0.006   0.1645   0.0172   3.8515
 PAK  C15  C  CSP   0   0.042  -0.4372   0.1795   5.1328
 PAK  N2   N  NS    0  -0.264  -0.9222   0.3093   6.1712
 PAK  C16  C  CR16  0  -0.367  -0.5641   0.3380   2.7133
 PAK  H1   H  HNH1  0   0.408  -2.2021  -1.1769  -2.9343
 PAK  H6   H  HCH2  0   0.287  -2.3373   1.1971   0.4153
 PAK  H7   H  HCH2  0   0.296  -1.4942   1.8148  -0.9985
 PAK  H2   H  HNR5  0   0.420   2.5979  -0.7479  -0.2437
 PAK  H8   H  HCR6  0   0.277  -1.2531  -0.2669  -4.8648
 PAK  H9   H  HCR6  0   0.267   0.8608   0.2618  -5.9916
 PAK  H10  H  HCR6  0   0.265   2.9092   0.7023  -4.6489
 PAK  H11  H  HCR6  0   0.263   2.7967   0.6048  -2.1997
 PAK  H3   H  HCR6  0   0.277   3.1187  -1.0060   2.4921
 PAK  H4   H  HCR6  0   0.277   2.0195  -0.7077   4.6844
 PAK  H5   H  HCR6  0   0.271  -1.5778   0.7081   2.7972

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
 PAK  N    C    single    1.365  0.020  1.365
 PAK  N    C7   single    1.402  0.020  1.402
 PAK  N    H1   single    0.860  0.020  1.020
 PAK  C    O    double    1.216  0.020  1.216
 PAK  C    C1   single    1.510  0.020  1.510
 PAK  C1   C2   single    1.489  0.020  1.489
 PAK  C1   H6   single    0.970  0.020  1.090
 PAK  C1   H7   single    0.970  0.020  1.090
 PAK  C2   C3   aromatic  1.426  0.020  1.426
 PAK  C2   C5   aromatic  1.368  0.020  1.368
 PAK  C3   C4   aromatic  1.417  0.020  1.417
 PAK  C3   C16  aromatic  1.391  0.020  1.391
 PAK  C4   N1   aromatic  1.357  0.020  1.357
 PAK  C4   C12  aromatic  1.394  0.020  1.394
 PAK  N1   C5   aromatic  1.373  0.020  1.373
 PAK  N1   H2   single    0.860  0.020  1.020
 PAK  C5   C6   aromatic  1.449  0.020  1.449
 PAK  C6   C7   aromatic  1.405  0.020  1.405
 PAK  C6   C11  aromatic  1.399  0.020  1.399
 PAK  C7   C8   aromatic  1.396  0.020  1.396
 PAK  C8   C9   aromatic  1.382  0.020  1.382
 PAK  C8   H8   single    0.930  0.020  1.080
 PAK  C9   C10  aromatic  1.391  0.020  1.391
 PAK  C9   H9   single    0.930  0.020  1.080
 PAK  C10  C11  aromatic  1.381  0.020  1.381
 PAK  C10  H10  single    0.930  0.020  1.080
 PAK  C11  H11  single    0.930  0.020  1.080
 PAK  C12  C13  aromatic  1.376  0.020  1.376
 PAK  C12  H3   single    0.930  0.020  1.080
 PAK  C13  C14  aromatic  1.412  0.020  1.412
 PAK  C13  H4   single    0.930  0.020  1.080
 PAK  C14  C15  single    1.425  0.020  1.425
 PAK  C14  C16  aromatic  1.389  0.020  1.389
 PAK  C15  N2   triple    1.153  0.020  1.153
 PAK  C16  H5   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
 PAK  H1   N    C7   114.54  3.000
 PAK  H1   N    C    113.55  3.000
 PAK  C7   N    C    131.06  3.000
 PAK  C1   C    O    123.11  3.000
 PAK  C1   C    N    116.28  3.000
 PAK  O    C    N    120.60  3.000
 PAK  H7   C1   H6   107.19  3.000
 PAK  H7   C1   C2   110.63  3.000
 PAK  H6   C1   C2   111.49  3.000
 PAK  H7   C1   C    109.17  3.000
 PAK  H6   C1   C    108.38  3.000
 PAK  C2   C1   C    109.90  3.000
 PAK  C5   C2   C3   106.81  3.000
 PAK  C5   C2   C1   123.43  3.000
 PAK  C3   C2   C1   129.74  3.000
 PAK  C16  C3   C4   119.37  3.000
 PAK  C16  C3   C2   133.96  3.000
 PAK  C4   C3   C2   106.67  3.000
 PAK  C12  C4   N1   130.09  3.000
 PAK  C12  C4   C3   122.29  3.000
 PAK  N1   C4   C3   107.61  3.000
 PAK  H2   N1   C5   125.26  3.000
 PAK  H2   N1   C4   125.03  3.000
 PAK  C5   N1   C4   109.46  3.000
 PAK  C6   C5   N1   123.94  3.000
 PAK  C6   C5   C2   126.59  3.000
 PAK  N1   C5   C2   109.45  3.000
 PAK  C11  C6   C7   118.89  3.000
 PAK  C11  C6   C5   120.44  3.000
 PAK  C7   C6   C5   120.67  3.000
 PAK  C8   C7   C6   119.08  3.000
 PAK  C8   C7   N    116.88  3.000
 PAK  C6   C7   N    123.82  3.000
 PAK  H8   C8   C9   119.80  3.000
 PAK  H8   C8   C7   119.07  3.000
 PAK  C9   C8   C7   121.12  3.000
 PAK  H9   C9   C10  120.44  3.000
 PAK  H9   C9   C8   119.53  3.000
 PAK  C10  C9   C8   120.04  3.000
 PAK  H10  C10  C11  120.06  3.000
 PAK  H10  C10  C9   120.56  3.000
 PAK  C11  C10  C9   119.38  3.000
 PAK  H11  C11  C10  119.37  3.000
 PAK  H11  C11  C6   119.14  3.000
 PAK  C10  C11  C6   121.49  3.000
 PAK  H3   C12  C13  120.88  3.000
 PAK  H3   C12  C4   121.47  3.000
 PAK  C13  C12  C4   117.65  3.000
 PAK  H4   C13  C14  119.37  3.000
 PAK  H4   C13  C12  119.93  3.000
 PAK  C14  C13  C12  120.70  3.000
 PAK  C16  C14  C15  119.28  3.000
 PAK  C16  C14  C13  121.73  3.000
 PAK  C15  C14  C13  118.99  3.000
 PAK  N2   C15  C14  180.00  3.000
 PAK  H5   C16  C14  120.44  3.000
 PAK  H5   C16  C3   121.31  3.000
 PAK  C14  C16  C3   118.24  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
 PAK  CONST_01  N1   C4   C3   C2     0.00  0.0  0
 PAK  CONST_02  C12  C4   C3   C2   180.00  0.0  0
 PAK  CONST_03  C14  C16  C3   C2   180.00  0.0  0
 PAK  CONST_04  C5   N1   C4   C3     0.00  0.0  0
 PAK  CONST_05  C13  C12  C4   C3     0.00  0.0  0
 PAK  CONST_06  C13  C14  C16  C3     0.00  0.0  0
 PAK  CONST_07  C14  C16  C3   C4     0.00  0.0  0
 PAK  CONST_08  C14  C13  C12  C4     0.00  0.0  0
 PAK  CONST_09  C16  C3   C4   N1   180.00  0.0  0
 PAK  CONST_10  C13  C12  C4   N1   180.00  0.0  0
 PAK  CONST_11  C12  C4   N1   C5   180.00  0.0  0
 PAK  CONST_12  C9   C10  C11  C6     0.00  0.0  0
 PAK  CONST_13  C10  C9   C8   C7     0.00  0.0  0
 PAK  CONST_14  C11  C10  C9   C8     0.00  0.0  0
 PAK  CONST_15  C16  C3   C4   C12    0.00  0.0  0
 PAK  CONST_16  C16  C14  C13  C12    0.00  0.0  0
 PAK  CONST_17  C15  C14  C16  C3   180.00  0.0  0
 PAK  CONST_18  C15  C14  C13  C12  180.00  0.0  0
 PAK  CONST_19  H5   C16  C3   C2     0.00  0.0  0
 PAK  CONST_20  H2   N1   C4   C3   180.00  0.0  0
 PAK  CONST_21  H3   C12  C4   C3   180.00  0.0  0
 PAK  CONST_22  H4   C13  C12  C4   180.00  0.0  0
 PAK  CONST_23  H10  C10  C11  C6   180.00  0.0  0
 PAK  CONST_24  H9   C9   C8   C7   180.00  0.0  0
 PAK  CONST_25  H11  C11  C10  C9   180.00  0.0  0
 PAK  CONST_26  H8   C8   C9   C10  180.00  0.0  0

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
 PAK  plan-1  N    0.020
 PAK  plan-1  C    0.020
 PAK  plan-1  O    0.020
 PAK  plan-1  C1   0.020
 PAK  plan-1  C7   0.020
 PAK  plan-1  H1   0.020
 PAK  plan-2  C1   0.020
 PAK  plan-2  C2   0.020
 PAK  plan-2  C3   0.020
 PAK  plan-2  C4   0.020
 PAK  plan-2  N1   0.020
 PAK  plan-2  C5   0.020
 PAK  plan-2  C6   0.020
 PAK  plan-2  C12  0.020
 PAK  plan-2  C13  0.020
 PAK  plan-2  C14  0.020
 PAK  plan-2  C15  0.020
 PAK  plan-2  N2   0.020
 PAK  plan-2  C16  0.020
 PAK  plan-2  H2   0.020
 PAK  plan-2  H3   0.020
 PAK  plan-2  H4   0.020
 PAK  plan-2  H5   0.020
 PAK  plan-3  N    0.020
 PAK  plan-3  C5   0.020
 PAK  plan-3  C6   0.020
 PAK  plan-3  C7   0.020
 PAK  plan-3  C8   0.020
 PAK  plan-3  C9   0.020
 PAK  plan-3  C10  0.020
 PAK  plan-3  C11  0.020
 PAK  plan-3  H8   0.020
 PAK  plan-3  H9   0.020
 PAK  plan-3  H10  0.020
 PAK  plan-3  H11  0.020

