# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 13:14:54 2020
#   Inital geometry file: a 105 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1C=CC(=O)c2c(N)nc(cc12)c3ccccc3
#
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
 PD6  PD6  'None                     '  ligand  41  22  .  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_PD6
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
 PD6  N3    N  NR6   0  -0.548  20.1625  -6.7011  11.9384
 PD6  C4    C  CR16  0  -0.463  18.2368  -5.2402  11.8374
 PD6  C5    C  CR6   0   0.451  18.1435  -5.0978  14.5722
 PD6  C6    C  CR6   0   0.465  20.1773  -6.5817  14.7791
 PD6  C7    C  CR16  0   0.036  21.0924  -7.3592  12.6725
 PD6  C8    C  CH2   0  -0.370  20.2853  -6.8006  10.4795
 PD6  C15   C  CR6   0   0.072  16.2731  -3.7212  11.7939
 PD6  C17   C  CR16  0  -0.286  15.0314  -3.4790  12.3829
 PD6  C20   C  CR16  0  -0.240  14.0543  -2.7685  11.7026
 PD6  C21   C  CR16  0  -0.241  15.5448  -2.4969   9.8399
 PD6  C22   C  CR16  0  -0.261  14.3072  -2.2743  10.4291
 PD6  C1    C  CR66  0   0.520  19.2040  -5.9470  12.5677
 PD6  C2    C  CR66  0  -0.314  19.1847  -5.8830  13.9754
 PD6  C9    C  CR6   0   0.241  17.3020  -4.4944  12.5255
 PD6  N10   N  N     0  -0.498  17.2477  -4.4293  13.8553
 PD6  N11   N  NH2   0  -0.839  18.0283  -5.0080  15.9021
 PD6  C12   C  CR16  0  -0.489  21.1401  -7.3327  14.0202
 PD6  O13   O  O     0  -0.510  20.2101  -6.5467  16.0186
 PD6  C14   C  CH2   0  -0.416  21.3394  -5.8663   9.9007
 PD6  C16   C  CH2   0  -0.434  21.0902  -4.3799  10.1246
 PD6  C18   C  CR16  0  -0.315  16.5187  -3.2161  10.5165
 PD6  C19   C  CH3   0  -0.658  22.1800  -3.5223   9.4962
 PD6  H4    H  HCR6  0   0.273  18.1969  -5.2824  10.7623
 PD6  H7    H  HCR6  0   0.311  21.8142  -7.9256  12.0997
 PD6  H8    H  HCH2  0   0.287  20.5472  -7.8339  10.2533
 PD6  H8A   H  HCH2  0   0.281  19.3155  -6.6320  10.0212
 PD6  H17   H  HCR6  0   0.253  14.8295  -3.8588  13.3753
 PD6  H20   H  HCR6  0   0.258  13.0916  -2.5999  12.1678
 PD6  H21   H  HCR6  0   0.260  15.7572  -2.1041   8.8543
 PD6  H22   H  HCR6  0   0.260  13.5461  -1.7142   9.9016
 PD6  HN11  H  HNH2  0   0.413  18.7265  -5.4334  16.4921
 PD6  HN1A  H  HNH2  0   0.389  17.3262  -4.4003  16.2869
 PD6  H12   H  HCR6  0   0.272  21.9110  -7.8876  14.5364
 PD6  H14   H  HCH2  0   0.230  22.3203  -6.1371  10.3049
 PD6  H14A  H  HCH2  0   0.241  21.3889  -6.0716   8.8274
 PD6  H16   H  HCH2  0   0.222  20.1197  -4.1003   9.7040
 PD6  H16A  H  HCH2  0   0.224  21.0333  -4.1655  11.1952
 PD6  H18   H  HCR6  0   0.254  17.4859  -3.3598  10.0511
 PD6  H19   H  HCH3  0   0.220  22.2250  -3.6713   8.4160
 PD6  H19A  H  HCH3  0   0.231  22.0058  -2.4617   9.6785
 PD6  H19B  H  HCH3  0   0.220  23.1614  -3.7707   9.9045

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
 PD6  N3   C7    single    1.355  0.020  1.355
 PD6  N3   C8    single    1.467  0.020  1.467
 PD6  N3   C1    single    1.372  0.020  1.372
 PD6  C4   C1    aromatic  1.403  0.020  1.403
 PD6  C4   C9    aromatic  1.380  0.020  1.380
 PD6  C4   H4    single    0.930  0.020  1.080
 PD6  C5   C2    aromatic  1.434  0.020  1.434
 PD6  C5   N10   aromatic  1.328  0.020  1.328
 PD6  C5   N11   single    1.338  0.020  1.338
 PD6  C6   C2    single    1.456  0.020  1.456
 PD6  C6   C12   single    1.438  0.020  1.438
 PD6  C6   O13   double    1.240  0.020  1.240
 PD6  C7   C12   double    1.349  0.020  1.349
 PD6  C7   H7    single    0.930  0.020  1.080
 PD6  C8   C14   single    1.523  0.020  1.523
 PD6  C8   H8    single    0.970  0.020  1.090
 PD6  C8   H8A   single    0.970  0.020  1.090
 PD6  C15  C17   aromatic  1.396  0.020  1.396
 PD6  C15  C9    single    1.480  0.020  1.480
 PD6  C15  C18   aromatic  1.395  0.020  1.395
 PD6  C17  C20   aromatic  1.386  0.020  1.386
 PD6  C17  H17   single    0.930  0.020  1.080
 PD6  C20  C22   aromatic  1.389  0.020  1.389
 PD6  C20  H20   single    0.930  0.020  1.080
 PD6  C21  C22   aromatic  1.389  0.020  1.389
 PD6  C21  C18   aromatic  1.387  0.020  1.387
 PD6  C21  H21   single    0.930  0.020  1.080
 PD6  C22  H22   single    0.930  0.020  1.080
 PD6  C1   C2    aromatic  1.409  0.020  1.409
 PD6  C9   N10   aromatic  1.332  0.020  1.332
 PD6  N11  HN11  single    0.860  0.020  1.020
 PD6  N11  HN1A  single    0.860  0.020  1.020
 PD6  C12  H12   single    0.930  0.020  1.080
 PD6  C14  C16   single    1.524  0.020  1.524
 PD6  C14  H14   single    0.970  0.020  1.090
 PD6  C14  H14A  single    0.970  0.020  1.090
 PD6  C16  C19   single    1.522  0.020  1.522
 PD6  C16  H16   single    0.970  0.020  1.090
 PD6  C16  H16A  single    0.970  0.020  1.090
 PD6  C18  H18   single    0.930  0.020  1.080
 PD6  C19  H19   single    0.970  0.020  1.090
 PD6  C19  H19A  single    0.970  0.020  1.090
 PD6  C19  H19B  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
 PD6  C1    N3   C8    123.48  3.000
 PD6  C1    N3   C7    119.85  3.000
 PD6  C8    N3   C7    116.63  3.000
 PD6  H4    C4   C9    119.61  3.000
 PD6  H4    C4   C1    121.70  3.000
 PD6  C9    C4   C1    118.67  3.000
 PD6  N11   C5   N10   116.41  3.000
 PD6  N11   C5   C2    120.86  3.000
 PD6  N10   C5   C2    122.73  3.000
 PD6  O13   C6   C12   121.63  3.000
 PD6  O13   C6   C2    123.79  3.000
 PD6  C12   C6   C2    114.57  3.000
 PD6  H7    C7   C12   121.05  3.000
 PD6  H7    C7   N3    115.17  3.000
 PD6  C12   C7   N3    123.78  3.000
 PD6  H8A   C8   H8    105.92  3.000
 PD6  H8A   C8   C14   111.26  3.000
 PD6  H8    C8   C14   109.67  3.000
 PD6  H8A   C8   N3    109.53  3.000
 PD6  H8    C8   N3    106.90  3.000
 PD6  C14   C8   N3    113.22  3.000
 PD6  C18   C15  C9    121.28  3.000
 PD6  C18   C15  C17   118.69  3.000
 PD6  C9    C15  C17   120.03  3.000
 PD6  H17   C17  C20   119.91  3.000
 PD6  H17   C17  C15   119.50  3.000
 PD6  C20   C17  C15   120.59  3.000
 PD6  H20   C20  C22   120.03  3.000
 PD6  H20   C20  C17   119.72  3.000
 PD6  C22   C20  C17   120.25  3.000
 PD6  H21   C21  C18   119.65  3.000
 PD6  H21   C21  C22   120.22  3.000
 PD6  C18   C21  C22   120.13  3.000
 PD6  H22   C22  C21   120.20  3.000
 PD6  H22   C22  C20   120.19  3.000
 PD6  C21   C22  C20   119.61  3.000
 PD6  C2    C1   C4    119.19  3.000
 PD6  C2    C1   N3    119.51  3.000
 PD6  C4    C1   N3    121.31  3.000
 PD6  C1    C2   C6    121.36  3.000
 PD6  C1    C2   C5    116.77  3.000
 PD6  C6    C2   C5    121.87  3.000
 PD6  N10   C9   C15   116.07  3.000
 PD6  N10   C9   C4    123.49  3.000
 PD6  C15   C9   C4    120.44  3.000
 PD6  C9    N10  C5    119.13  3.000
 PD6  HN1A  N11  HN11  120.99  3.000
 PD6  HN1A  N11  C5    118.77  3.000
 PD6  HN11  N11  C5    119.59  3.000
 PD6  H12   C12  C7    119.49  3.000
 PD6  H12   C12  C6    119.58  3.000
 PD6  C7    C12  C6    120.93  3.000
 PD6  H14A  C14  H14   105.98  3.000
 PD6  H14A  C14  C16   109.55  3.000
 PD6  H14   C14  C16   109.48  3.000
 PD6  H14A  C14  C8    106.81  3.000
 PD6  H14   C14  C8    109.15  3.000
 PD6  C16   C14  C8    115.43  3.000
 PD6  H16A  C16  H16   106.27  3.000
 PD6  H16A  C16  C19   109.33  3.000
 PD6  H16   C16  C19   109.42  3.000
 PD6  H16A  C16  C14   110.10  3.000
 PD6  H16   C16  C14   109.75  3.000
 PD6  C19   C16  C14   111.83  3.000
 PD6  H18   C18  C21   119.10  3.000
 PD6  H18   C18  C15   120.17  3.000
 PD6  C21   C18  C15   120.71  3.000
 PD6  H19B  C19  H19A  107.61  3.000
 PD6  H19B  C19  H19   107.59  3.000
 PD6  H19A  C19  H19   107.75  3.000
 PD6  H19B  C19  C16   111.16  3.000
 PD6  H19A  C19  C16   111.38  3.000
 PD6  H19   C19  C16   111.17  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
 PD6  CONST_01  C5    C2   C1   C4      0.00   0.0  0
 PD6  CONST_04  C5    N10  C9   C4      0.00   0.0  0
 PD6  CONST_05  C15   C9   N10  C5    180.00   0.0  0
 PD6  CONST_06  C22   C20  C17  C15     0.00   0.0  0
 PD6  CONST_07  C1    C4   C9   C15   180.00   0.0  0
 PD6  CONST_08  C22   C21  C18  C15     0.00   0.0  0
 PD6  CONST_10  C21   C18  C15  C17     0.00   0.0  0
 PD6  CONST_11  C21   C22  C20  C17     0.00   0.0  0
 PD6  CONST_12  C9    C15  C17  C20   180.00   0.0  0
 PD6  CONST_13  C18   C15  C17  C20     0.00   0.0  0
 PD6  CONST_14  C18   C21  C22  C20     0.00   0.0  0
 PD6  CONST_15  C9    C15  C18  C21   180.00   0.0  0
 PD6  CONST_16  N10   C9   C4   C1      0.00   0.0  0
 PD6  CONST_17  N10   C5   C2   C1      0.00   0.0  0
 PD6  CONST_18  C9    N10  C5   C2      0.00   0.0  0
 PD6  CONST_19  C9    C4   C1   C2      0.00   0.0  0
 PD6  CONST_21  N11   C5   C2   C6      0.00   0.0  0
 PD6  CONST_22  N11   C5   C2   C1    180.00   0.0  0
 PD6  CONST_23  N11   C5   N10  C9    180.00   0.0  0
 PD6  CONST_24  H4    C4   C1   N3      0.00   0.0  0
 PD6  CONST_25  H20   C20  C17  C15   180.00   0.0  0
 PD6  CONST_26  H21   C21  C18  C15   180.00   0.0  0
 PD6  CONST_27  H18   C18  C15  C17   180.00   0.0  0
 PD6  CONST_28  H22   C22  C20  C17   180.00   0.0  0
 PD6  CONST_29  H17   C17  C20  C22   180.00   0.0  0
 PD6  CONST_30  HN11  N11  C5   C2      0.00   0.0  0
 PD6  CONST_31  HN1A  N11  C5   C2    180.00   0.0  0
 PD6  Var_01    C14   C8   N3   C7    -79.64  30.0  3
 PD6  Var_02    C16   C14  C8   N3    -61.56  30.0  3
 PD6  Var_03    C19   C16  C14  C8   -179.15  30.0  3
 PD6  Var_04    H19   C19  C16  C14    61.00  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
 PD6  plan-1  C15   0.020
 PD6  plan-1  C17   0.020
 PD6  plan-1  C20   0.020
 PD6  plan-1  C21   0.020
 PD6  plan-1  C22   0.020
 PD6  plan-1  C9    0.020
 PD6  plan-1  C18   0.020
 PD6  plan-1  H17   0.020
 PD6  plan-1  H20   0.020
 PD6  plan-1  H21   0.020
 PD6  plan-1  H22   0.020
 PD6  plan-1  H18   0.020
 PD6  plan-2  N3    0.020
 PD6  plan-2  C4    0.020
 PD6  plan-2  C5    0.020
 PD6  plan-2  C6    0.020
 PD6  plan-2  C7    0.020
 PD6  plan-2  C8    0.020
 PD6  plan-2  C15   0.020
 PD6  plan-2  C1    0.020
 PD6  plan-2  C2    0.020
 PD6  plan-2  C9    0.020
 PD6  plan-2  N10   0.020
 PD6  plan-2  N11   0.020
 PD6  plan-2  C12   0.020
 PD6  plan-2  O13   0.020
 PD6  plan-2  H4    0.020
 PD6  plan-2  H7    0.020
 PD6  plan-2  H12   0.020
 PD6  plan-3  C5    0.020
 PD6  plan-3  N11   0.020
 PD6  plan-3  HN11  0.020
 PD6  plan-3  HN1A  0.020

