# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:21:53 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 2-[4-[3-[(4-oxidanylidene-3~{H}-phthalazin-1-yl)methyl]phenyl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NN=C(Cc2cccc(c2)C(=O)N3CCN(CC3)c4ncccc4C#N)c5ccccc15
#
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
 5N2  5N2  2-[4-[3-[(4-oxidanylidene-3~{H}-phthalazin-1-yl)methyl]phenyl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile  ligand  56  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5N2
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
 5N2  C1   C  CR16  0  -0.225   7.3264  -0.6051  -0.9857
 5N2  C2   C  CR16  0  -0.245   7.4638  -1.9080  -0.5011
 5N2  C3   C  CR16  0  -0.273   6.4580  -2.4740   0.2535
 5N2  C7   C  CR6   0   0.194   3.9355   0.2780   0.3634
 5N2  C10  C  CR6   0   0.509   4.2314  -2.3354   1.3278
 5N2  C12  C  CH2   0  -0.616   3.7305   1.6867  -0.1271
 5N2  C13  C  CR6   0   0.176   2.4153   2.2792   0.2864
 5N2  C14  C  CR16  0  -0.302   2.2943   2.9655   1.4901
 5N2  C15  C  CR16  0  -0.231   1.0733   3.4940   1.8833
 5N2  C16  C  CR16  0  -0.273  -0.0476   3.3266   1.0838
 5N2  C22  C  CH2   0  -0.314  -2.3409   1.1642   0.5857
 5N2  C27  C  CR6   0   0.543  -4.8275  -1.2787  -0.6251
 5N2  C30  C  CR16  0  -0.351  -6.4785  -3.4850  -0.7609
 5N2  C31  C  CR16  0  -0.034  -6.0759  -2.7508  -1.8656
 5N2  C4   C  CR66  0  -0.055   5.3031  -1.7415   0.5295
 5N2  C5   C  CR66  0   0.115   5.1569  -0.4342   0.0466
 5N2  C6   C  CR16  0  -0.334   6.1883   0.1264  -0.7170
 5N2  N8   N  N     0  -0.217   3.0034  -0.2580   1.0637
 5N2  N9   N  NR16  0  -0.508   3.1667  -1.5070   1.5128
 5N2  O11  O  O     0  -0.472   4.2532  -3.4635   1.8001
 5N2  C17  C  CR6   0  -0.059   0.0627   2.6467  -0.1255
 5N2  C18  C  CR16  0  -0.326   1.2954   2.1426  -0.5239
 5N2  O20  O  O     0  -0.483  -0.9921   2.9849  -2.2013
 5N2  N21  N  NT    0  -0.455  -2.2476   2.0277  -0.5781
 5N2  C23  C  CH2   0  -0.315  -2.7436  -0.2356   0.1548
 5N2  N24  N  NT    0  -0.508  -3.9891  -0.1968  -0.5997
 5N2  C25  C  CH2   0  -0.299  -3.8680   0.6279  -1.7903
 5N2  C26  C  CH2   0  -0.319  -3.4606   2.0332  -1.3759
 5N2  C28  C  CR6   0  -0.126  -5.2646  -1.9062   0.5678
 5N2  C29  C  CR16  0  -0.125  -6.0738  -3.0348   0.4815
 5N2  N32  N  N     0  -0.452  -5.2725  -1.6993  -1.8036
 5N2  N34  N  NS    0  -0.248  -4.8314  -0.8911   2.8934
 5N2  H1   H  HCR6  0   0.275   8.1184  -0.1648  -1.5764
 5N2  H2   H  HCR6  0   0.273   8.3605  -2.4723  -0.7192
 5N2  H3   H  HCR6  0   0.271   6.5600  -3.4818   0.6323
 5N2  H4   H  HCH2  0   0.283   4.5514   2.3081   0.2435
 5N2  H5   H  HCH2  0   0.283   3.8170   1.6966  -1.2177
 5N2  H6   H  HCR6  0   0.253   3.1640   3.0904   2.1242
 5N2  H7   H  HCR6  0   0.260   0.9936   4.0379   2.8155
 5N2  H8   H  HCR6  0   0.265  -1.0004   3.7362   1.3961
 5N2  H9   H  HCH2  0   0.281  -1.3870   1.1116   1.1031
 5N2  H10  H  HCH2  0   0.255  -3.0803   1.5655   1.2843
 5N2  H11  H  HCR6  0   0.280  -7.1104  -4.3538  -0.8696
 5N2  H12  H  HCR6  0   0.277  -6.4110  -3.0327  -2.8573
 5N2  H13  H  HCR6  0   0.275   6.0998   1.1340  -1.0999
 5N2  H14  H  HNR6  0   0.422   2.3883  -1.8533   2.0563
 5N2  H15  H  HCR6  0   0.254   1.3821   1.6241  -1.4721
 5N2  H16  H  HCH2  0   0.253  -1.9501  -0.6639  -0.4722
 5N2  H17  H  HCH2  0   0.276  -2.8233  -0.8666   1.0354
 5N2  H18  H  HCH2  0   0.237  -3.1362   0.2103  -2.4928
 5N2  H19  H  HCH2  0   0.268  -4.8266   0.6756  -2.3025
 5N2  H20  H  HCH2  0   0.256  -4.2615   2.4761  -0.7768
 5N2  H21  H  HCH2  0   0.274  -3.3206   2.6520  -2.2578
 5N2  H22  H  HCR6  0   0.295  -6.4021  -3.5288   1.3862
 5N2  C19  C  C     0   0.517  -1.1000   2.5517  -1.0622
 5N2  C33  C  CSP   0   0.043  -5.0063  -1.3450   1.8474

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
 5N2  N34  C33  triple    1.154  0.020  1.154
 5N2  C33  C28  single    1.421  0.020  1.421
 5N2  C29  C28  aromatic  1.391  0.020  1.391
 5N2  C29  C30  aromatic  1.382  0.020  1.382
 5N2  C28  C27  aromatic  1.417  0.020  1.417
 5N2  O11  C10  double    1.223  0.020  1.223
 5N2  C25  C26  single    1.521  0.020  1.521
 5N2  C25  N24  single    1.453  0.020  1.453
 5N2  C26  N21  single    1.452  0.020  1.452
 5N2  O20  C19  double    1.223  0.020  1.223
 5N2  C30  C31  aromatic  1.386  0.020  1.386
 5N2  C27  N24  single    1.369  0.020  1.369
 5N2  C27  N32  aromatic  1.328  0.020  1.328
 5N2  C10  N9   single    1.362  0.020  1.362
 5N2  C10  C4   single    1.462  0.020  1.462
 5N2  N24  C23  single    1.457  0.020  1.457
 5N2  N21  C19  single    1.351  0.020  1.351
 5N2  N21  C22  single    1.452  0.020  1.452
 5N2  C3   C4   aromatic  1.395  0.020  1.395
 5N2  C3   C2   aromatic  1.379  0.020  1.379
 5N2  N9   N8   single    1.337  0.020  1.337
 5N2  C19  C17  single    1.496  0.020  1.496
 5N2  C4   C5   aromatic  1.401  0.020  1.401
 5N2  C31  N32  aromatic  1.325  0.020  1.325
 5N2  C2   C1   aromatic  1.397  0.020  1.397
 5N2  C23  C22  single    1.519  0.020  1.519
 5N2  N8   C7   double    1.283  0.020  1.283
 5N2  C17  C18  aromatic  1.390  0.020  1.390
 5N2  C17  C16  aromatic  1.392  0.020  1.392
 5N2  C5   C7   single    1.449  0.020  1.449
 5N2  C5   C6   aromatic  1.400  0.020  1.400
 5N2  C18  C13  aromatic  1.389  0.020  1.389
 5N2  C1   C6   aromatic  1.379  0.020  1.379
 5N2  C7   C12  single    1.506  0.020  1.506
 5N2  C16  C15  aromatic  1.387  0.020  1.387
 5N2  C13  C12  single    1.501  0.020  1.501
 5N2  C13  C14  aromatic  1.391  0.020  1.391
 5N2  C15  C14  aromatic  1.387  0.020  1.387
 5N2  C1   H1   single    0.930  0.020  1.080
 5N2  C2   H2   single    0.930  0.020  1.080
 5N2  C3   H3   single    0.930  0.020  1.080
 5N2  C12  H4   single    0.970  0.020  1.090
 5N2  C12  H5   single    0.970  0.020  1.090
 5N2  C14  H6   single    0.930  0.020  1.080
 5N2  C15  H7   single    0.930  0.020  1.080
 5N2  C16  H8   single    0.930  0.020  1.080
 5N2  C22  H9   single    0.970  0.020  1.090
 5N2  C22  H10  single    0.970  0.020  1.090
 5N2  C30  H11  single    0.930  0.020  1.080
 5N2  C31  H12  single    0.930  0.020  1.080
 5N2  C6   H13  single    0.930  0.020  1.080
 5N2  N9   H14  single    0.860  0.020  1.020
 5N2  C18  H15  single    0.930  0.020  1.080
 5N2  C23  H16  single    0.970  0.020  1.090
 5N2  C23  H17  single    0.970  0.020  1.090
 5N2  C25  H18  single    0.970  0.020  1.090
 5N2  C25  H19  single    0.970  0.020  1.090
 5N2  C26  H20  single    0.970  0.020  1.090
 5N2  C26  H21  single    0.970  0.020  1.090
 5N2  C29  H22  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
 5N2  H1   C1   C6   119.64  3.000
 5N2  H1   C1   C2   119.81  3.000
 5N2  C6   C1   C2   120.55  3.000
 5N2  H2   C2   C3   120.05  3.000
 5N2  H2   C2   C1   119.88  3.000
 5N2  C3   C2   C1   120.06  3.000
 5N2  H3   C3   C4   119.87  3.000
 5N2  H3   C3   C2   120.36  3.000
 5N2  C4   C3   C2   119.77  3.000
 5N2  N8   C7   C5   121.76  3.000
 5N2  C5   C7   C12  120.23  3.000
 5N2  N8   C7   C12  118.01  3.000
 5N2  O11  C10  N9   121.51  3.000
 5N2  N9   C10  C4   113.58  3.000
 5N2  O11  C10  C4   124.91  3.000
 5N2  H5   C12  H4   105.85  3.000
 5N2  H5   C12  C13  109.90  3.000
 5N2  H4   C12  C13  109.87  3.000
 5N2  H5   C12  C7   108.81  3.000
 5N2  H4   C12  C7   108.59  3.000
 5N2  C13  C12  C7   113.52  3.000
 5N2  C18  C13  C14  118.90  3.000
 5N2  C14  C13  C12  120.64  3.000
 5N2  C18  C13  C12  120.47  3.000
 5N2  H6   C14  C15  119.78  3.000
 5N2  H6   C14  C13  119.57  3.000
 5N2  C15  C14  C13  120.65  3.000
 5N2  H7   C15  C16  119.85  3.000
 5N2  H7   C15  C14  120.02  3.000
 5N2  C16  C15  C14  120.12  3.000
 5N2  H8   C16  C17  120.33  3.000
 5N2  H8   C16  C15  119.94  3.000
 5N2  C17  C16  C15  119.73  3.000
 5N2  H10  C22  H9   107.89  3.000
 5N2  H10  C22  C23  109.88  3.000
 5N2  H9   C22  C23  108.86  3.000
 5N2  H10  C22  N21  109.71  3.000
 5N2  H9   C22  N21  110.74  3.000
 5N2  C23  C22  N21  109.73  3.000
 5N2  N32  C27  C28  120.23  3.000
 5N2  N32  C27  N24  118.16  3.000
 5N2  C28  C27  N24  121.55  3.000
 5N2  H11  C30  C29  121.60  3.000
 5N2  H11  C30  C31  121.06  3.000
 5N2  C29  C30  C31  117.31  3.000
 5N2  H12  C31  N32  115.89  3.000
 5N2  H12  C31  C30  120.11  3.000
 5N2  N32  C31  C30  124.01  3.000
 5N2  C5   C4   C10  119.38  3.000
 5N2  C5   C4   C3   120.53  3.000
 5N2  C10  C4   C3   120.09  3.000
 5N2  C6   C5   C4   118.98  3.000
 5N2  C6   C5   C7   122.91  3.000
 5N2  C4   C5   C7   118.11  3.000
 5N2  H13  C6   C5   120.38  3.000
 5N2  H13  C6   C1   119.52  3.000
 5N2  C5   C6   C1   120.10  3.000
 5N2  N9   N8   C7   118.99  3.000
 5N2  H14  N9   N8   113.99  3.000
 5N2  H14  N9   C10  117.83  3.000
 5N2  N8   N9   C10  128.18  3.000
 5N2  C18  C17  C19  119.13  3.000
 5N2  C18  C17  C16  119.76  3.000
 5N2  C19  C17  C16  120.90  3.000
 5N2  H15  C18  C17  119.67  3.000
 5N2  H15  C18  C13  119.52  3.000
 5N2  C17  C18  C13  120.81  3.000
 5N2  C26  N21  C22  112.89  3.000
 5N2  C22  N21  C19  124.91  3.000
 5N2  C26  N21  C19  120.75  3.000
 5N2  H17  C23  H16  106.81  3.000
 5N2  H17  C23  N24  111.88  3.000
 5N2  H16  C23  N24  109.42  3.000
 5N2  H17  C23  C22  108.95  3.000
 5N2  H16  C23  C22  109.25  3.000
 5N2  N24  C23  C22  110.43  3.000
 5N2  C25  N24  C23  111.60  3.000
 5N2  C23  N24  C27  120.81  3.000
 5N2  C25  N24  C27  118.96  3.000
 5N2  H19  C25  H18  107.63  3.000
 5N2  H19  C25  C26  108.89  3.000
 5N2  H18  C25  C26  110.34  3.000
 5N2  H19  C25  N24  109.71  3.000
 5N2  H18  C25  N24  111.36  3.000
 5N2  C26  C25  N24  108.87  3.000
 5N2  H21  C26  H20  107.96  3.000
 5N2  H21  C26  C25  109.86  3.000
 5N2  H20  C26  C25  109.10  3.000
 5N2  H21  C26  N21  109.91  3.000
 5N2  H20  C26  N21  108.20  3.000
 5N2  C25  C26  N21  111.72  3.000
 5N2  C29  C28  C33  118.81  3.000
 5N2  C29  C28  C27  119.10  3.000
 5N2  C33  C28  C27  121.81  3.000
 5N2  H22  C29  C28  119.67  3.000
 5N2  H22  C29  C30  120.94  3.000
 5N2  C28  C29  C30  119.36  3.000
 5N2  C31  N32  C27  119.74  3.000
 5N2  N21  C19  O20  123.08  3.000
 5N2  N21  C19  C17  117.41  3.000
 5N2  O20  C19  C17  119.46  3.000
 5N2  N34  C33  C28  180.00  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
 5N2  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 5N2  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 5N2  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 5N2  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 5N2  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 5N2  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 5N2  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 5N2  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 5N2  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 5N2  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 5N2  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 5N2  CONST_12  C18  C13  C14  C15    0.00   0.0  0
 5N2  CONST_13  C30  C29  C28  C27    0.00   0.0  0
 5N2  CONST_14  C30  C31  N32  C27    0.00   0.0  0
 5N2  CONST_15  C28  C29  C30  C31    0.00   0.0  0
 5N2  CONST_16  C28  C27  N32  C31    0.00   0.0  0
 5N2  CONST_17  N32  C27  C28  C29    0.00   0.0  0
 5N2  CONST_18  N32  C31  C30  C29    0.00   0.0  0
 5N2  CONST_19  N24  C27  N32  C31  180.00   0.0  0
 5N2  CONST_20  C29  C28  C27  N24  180.00   0.0  0
 5N2  CONST_21  N8   N9   C10  C4     0.00   0.0  0
 5N2  CONST_22  C17  C18  C13  C12  180.00   0.0  0
 5N2  CONST_23  C15  C14  C13  C12  180.00   0.0  0
 5N2  CONST_24  C19  C17  C18  C13  180.00   0.0  0
 5N2  CONST_25  C19  C17  C16  C15  180.00   0.0  0
 5N2  CONST_26  C33  C28  C29  C30  180.00   0.0  0
 5N2  CONST_27  N24  C27  C28  C33    0.00   0.0  0
 5N2  CONST_28  N32  C27  C28  C33  180.00   0.0  0
 5N2  CONST_30  C26  N21  C19  C17  180.00   0.0  0
 5N2  CONST_31  O11  C10  N9   N8   180.00   0.0  0
 5N2  CONST_32  H3   C3   C2   C1   180.00   0.0  0
 5N2  CONST_33  H13  C6   C1   C2   180.00   0.0  0
 5N2  CONST_34  H1   C1   C2   C3   180.00   0.0  0
 5N2  CONST_35  H7   C15  C14  C13  180.00   0.0  0
 5N2  CONST_36  H15  C18  C13  C14  180.00   0.0  0
 5N2  CONST_37  H8   C16  C15  C14  180.00   0.0  0
 5N2  CONST_38  H6   C14  C15  C16  180.00   0.0  0
 5N2  CONST_39  H22  C29  C28  C27  180.00   0.0  0
 5N2  CONST_40  H12  C31  N32  C27  180.00   0.0  0
 5N2  CONST_41  H2   C2   C3   C4   180.00   0.0  0
 5N2  CONST_42  H11  C30  C29  C28  180.00   0.0  0
 5N2  CONST_43  H14  N9   C10  C4   180.00   0.0  0
 5N2  CONST_45  C26  N21  C19  O20    0.00   0.0  0
 5N2  Var_01    C25  C26  N21  C22  -54.89  30.0  1
 5N2  Var_02    C25  N24  C23  C22   59.58  30.0  1
 5N2  Var_03    C26  C25  N24  C27  153.79  30.0  1
 5N2  Var_04    N24  C25  C26  N21   55.14  30.0  1
 5N2  Var_05    N24  C23  C22  N21  -55.95  30.0  1
 5N2  Var_06    C28  C27  N24  C23   51.85  30.0  3
 5N2  Var_07    C26  N21  C22  C23   54.36  30.0  1
 5N2  Var_08    C18  C13  C12  C7   -90.39  30.0  2
 5N2  Var_09    N8   C7   C12  C13   -0.18  30.0  2
 5N2  Var_10    N21  C19  C17  C16  -56.04  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
 5N2  plan-1  C12  0.020
 5N2  plan-1  C13  0.020
 5N2  plan-1  C14  0.020
 5N2  plan-1  C15  0.020
 5N2  plan-1  C16  0.020
 5N2  plan-1  C17  0.020
 5N2  plan-1  C18  0.020
 5N2  plan-1  H6   0.020
 5N2  plan-1  H7   0.020
 5N2  plan-1  H8   0.020
 5N2  plan-1  H15  0.020
 5N2  plan-1  C19  0.020
 5N2  plan-2  C27  0.020
 5N2  plan-2  C30  0.020
 5N2  plan-2  C31  0.020
 5N2  plan-2  N24  0.020
 5N2  plan-2  C28  0.020
 5N2  plan-2  C29  0.020
 5N2  plan-2  N32  0.020
 5N2  plan-2  N34  0.020
 5N2  plan-2  H11  0.020
 5N2  plan-2  H12  0.020
 5N2  plan-2  H22  0.020
 5N2  plan-2  C33  0.020
 5N2  plan-3  C1   0.020
 5N2  plan-3  C2   0.020
 5N2  plan-3  C3   0.020
 5N2  plan-3  C7   0.020
 5N2  plan-3  C10  0.020
 5N2  plan-3  C12  0.020
 5N2  plan-3  C4   0.020
 5N2  plan-3  C5   0.020
 5N2  plan-3  C6   0.020
 5N2  plan-3  N8   0.020
 5N2  plan-3  N9   0.020
 5N2  plan-3  O11  0.020
 5N2  plan-3  H1   0.020
 5N2  plan-3  H2   0.020
 5N2  plan-3  H3   0.020
 5N2  plan-3  H13  0.020
 5N2  plan-3  H14  0.020
 5N2  plan-4  C22  0.020
 5N2  plan-4  C17  0.020
 5N2  plan-4  O20  0.020
 5N2  plan-4  N21  0.020
 5N2  plan-4  C26  0.020
 5N2  plan-4  C19  0.020

