# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:25:06 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 6,7-dichloro-N-cyclopentyl-4-(pyridin-4-yl)phthalazin-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc2c(NC3CCCC3)nnc(c4ccncc4)c2cc1Cl
#
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
 539  539  6,7-dichloro-N-cyclopentyl-4-(pyridin-4-yl)phthalazin-1-amine  ligand  40  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_539
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
 539  C5   C   CR16  0  -0.268   0.5921   1.9598  -0.0793
 539  C6   C   CR66  0   0.071   0.4753   0.5632  -0.0788
 539  C7   C   CR66  0   0.096  -0.7929  -0.0290   0.0247
 539  C8   C   CR6   0   0.135  -0.8493  -1.4597  -0.0122
 539  C10  C   CR16  0  -0.379  -3.1670  -1.8889  -0.8736
 539  N12  N   N     0  -0.405  -4.4795  -3.7170  -0.0627
 539  C13  C   CR16  0  -0.060  -3.4744  -4.0318   0.7475
 539  C17  C   CR6   0   0.471   1.6038  -0.3342  -0.1506
 539  C20  C   CH2   0  -0.455   5.2289   0.0066  -0.9229
 539  C21  C   CH2   0  -0.451   6.4243  -0.8473  -0.4858
 539  C22  C   CH2   0  -0.454   5.9942  -1.5427   0.8315
 539  C24  C   CR16  0  -0.307  -1.9195   0.7918   0.1940
 539  C14  C   CR16  0  -0.351  -2.2854  -3.3237   0.8069
 539  C11  C   CR16  0  -0.058  -4.3150  -2.6661  -0.8562
 539  C9   C   CR6   0   0.140  -2.1189  -2.2135  -0.0162
 539  C2   C   CR6   0   0.008  -1.7885   2.1559   0.2085
 539  C3   C   CR6   0   0.010  -0.5223   2.7481   0.0531
 539  C23  C   CH2   0  -0.441   4.5588  -1.0774   1.1017
 539  C19  C   CH1   0  -0.068   4.0334  -0.6917  -0.2835
 539  N15  N   N     0  -0.259   0.2329  -2.1804  -0.0497
 539  N16  N   N     0  -0.349   1.4461  -1.6427  -0.0924
 539  N18  N   NH1   0  -0.684   2.8518   0.1402  -0.2815
 539  CL1  CL  CL    0  -0.072  -3.1785   3.1397   0.4256
 539  CL4  CL  CL    0  -0.070  -0.3631   4.4571   0.0420
 539  H1   H   HCR6  0   0.282   1.5509   2.4486  -0.1817
 539  H2   H   HCR6  0   0.286  -3.0953  -1.0600  -1.5652
 539  H3   H   HCR6  0   0.267  -3.6193  -4.8941   1.3888
 539  H4   H   HCH2  0   0.227   5.3155   1.0214  -0.5210
 539  H5   H   HCH2  0   0.246   5.1368   0.0920  -2.0062
 539  H6   H   HCH2  0   0.232   6.6531  -1.5920  -1.2493
 539  H7   H   HCH2  0   0.235   7.3218  -0.2424  -0.3587
 539  H8   H   HCH2  0   0.231   6.0308  -2.6268   0.7159
 539  H9   H   HCH2  0   0.234   6.6577  -1.2963   1.6604
 539  H10  H   HCR6  0   0.304  -2.8992   0.3573   0.3313
 539  H11  H   HCR6  0   0.270  -1.5060  -3.6291   1.4915
 539  H12  H   HCR6  0   0.268  -5.1363  -2.4254  -1.5218
 539  H13  H   HCH2  0   0.241   3.9414  -1.8337   1.5868
 539  H14  H   HCH2  0   0.222   4.5528  -0.1884   1.7387
 539  H15  H   HCH1  0   0.249   3.8008  -1.5997  -0.8443
 539  H16  H   HNH1  0   0.405   3.0056   1.1286  -0.1715

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
 539  CL1  C2   single    1.717  0.020  1.717
 539  CL4  C3   single    1.716  0.020  1.716
 539  C2   C3   aromatic  1.406  0.020  1.406
 539  C2   C24  aromatic  1.370  0.020  1.370
 539  C3   C5   aromatic  1.372  0.020  1.372
 539  C24  C7   aromatic  1.404  0.020  1.404
 539  C11  C10  aromatic  1.386  0.020  1.386
 539  C11  N12  aromatic  1.327  0.020  1.327
 539  C10  C9   aromatic  1.392  0.020  1.392
 539  C5   C6   aromatic  1.401  0.020  1.401
 539  C7   C6   aromatic  1.403  0.020  1.403
 539  C7   C8   aromatic  1.432  0.020  1.432
 539  N12  C13  aromatic  1.329  0.020  1.329
 539  C6   C17  aromatic  1.444  0.020  1.444
 539  C9   C8   single    1.477  0.020  1.477
 539  C9   C14  aromatic  1.392  0.020  1.392
 539  C8   N15  aromatic  1.301  0.020  1.301
 539  C13  C14  aromatic  1.385  0.020  1.385
 539  C17  N18  single    1.341  0.020  1.341
 539  C17  N16  aromatic  1.319  0.020  1.319
 539  N15  N16  aromatic  1.328  0.020  1.328
 539  N18  C19  single    1.445  0.020  1.445
 539  C19  C20  single    1.525  0.020  1.525
 539  C19  C23  single    1.531  0.020  1.531
 539  C20  C21  single    1.533  0.020  1.533
 539  C23  C22  single    1.533  0.020  1.533
 539  C21  C22  single    1.550  0.020  1.550
 539  C5   H1   single    0.930  0.020  1.080
 539  C10  H2   single    0.930  0.020  1.080
 539  C13  H3   single    0.930  0.020  1.080
 539  C20  H4   single    0.970  0.020  1.090
 539  C20  H5   single    0.970  0.020  1.090
 539  C21  H6   single    0.970  0.020  1.090
 539  C21  H7   single    0.970  0.020  1.090
 539  C22  H8   single    0.970  0.020  1.090
 539  C22  H9   single    0.970  0.020  1.090
 539  C24  H10  single    0.930  0.020  1.080
 539  C14  H11  single    0.930  0.020  1.080
 539  C11  H12  single    0.930  0.020  1.080
 539  C23  H13  single    0.970  0.020  1.090
 539  C23  H14  single    0.970  0.020  1.090
 539  C19  H15  single    0.970  0.020  1.090
 539  N18  H16  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
 539  H1   C5   C3   118.03  3.000
 539  H1   C5   C6   121.64  3.000
 539  C3   C5   C6   120.34  3.000
 539  C17  C6   C7   116.60  3.000
 539  C17  C6   C5   123.66  3.000
 539  C7   C6   C5   119.72  3.000
 539  C24  C7   C8   123.74  3.000
 539  C8   C7   C6   117.07  3.000
 539  C24  C7   C6   119.16  3.000
 539  N15  C8   C9   115.63  3.000
 539  N15  C8   C7   121.43  3.000
 539  C9   C8   C7   122.95  3.000
 539  H2   C10  C9   121.49  3.000
 539  H2   C10  C11  119.50  3.000
 539  C9   C10  C11  119.00  3.000
 539  C11  N12  C13  117.28  3.000
 539  H3   C13  C14  119.72  3.000
 539  H3   C13  N12  116.61  3.000
 539  C14  C13  N12  123.67  3.000
 539  N18  C17  N16  117.79  3.000
 539  N16  C17  C6   121.40  3.000
 539  N18  C17  C6   120.82  3.000
 539  H5   C20  H4   107.37  3.000
 539  H5   C20  C19  112.71  3.000
 539  H4   C20  C19  109.42  3.000
 539  H5   C20  C21  113.13  3.000
 539  H4   C20  C21  110.49  3.000
 539  C19  C20  C21  103.70  3.000
 539  H7   C21  H6   106.73  3.000
 539  H7   C21  C22  112.23  3.000
 539  H6   C21  C22  110.28  3.000
 539  H7   C21  C20  111.49  3.000
 539  H6   C21  C20  110.14  3.000
 539  C22  C21  C20  106.01  3.000
 539  H9   C22  H8   106.55  3.000
 539  H9   C22  C23  111.55  3.000
 539  H8   C22  C23  110.59  3.000
 539  H9   C22  C21  112.08  3.000
 539  H8   C22  C21  110.27  3.000
 539  C23  C22  C21  105.87  3.000
 539  H10  C24  C2   119.06  3.000
 539  H10  C24  C7   120.51  3.000
 539  C2   C24  C7   120.42  3.000
 539  H11  C14  C9   120.89  3.000
 539  H11  C14  C13  120.09  3.000
 539  C9   C14  C13  119.01  3.000
 539  H12  C11  N12  116.68  3.000
 539  H12  C11  C10  119.67  3.000
 539  N12  C11  C10  123.65  3.000
 539  C14  C9   C10  117.39  3.000
 539  C14  C9   C8   120.56  3.000
 539  C10  C9   C8   121.99  3.000
 539  CL1  C2   C3   120.11  3.000
 539  C3   C2   C24  120.27  3.000
 539  CL1  C2   C24  119.62  3.000
 539  CL4  C3   C2   120.23  3.000
 539  C2   C3   C5   120.01  3.000
 539  CL4  C3   C5   119.76  3.000
 539  H14  C23  H13  107.56  3.000
 539  H14  C23  C19  108.68  3.000
 539  H13  C23  C19  112.52  3.000
 539  H14  C23  C22  110.76  3.000
 539  H13  C23  C22  113.46  3.000
 539  C19  C23  C22  103.79  3.000
 539  H15  C19  N18  107.77  3.000
 539  H15  C19  C23  109.16  3.000
 539  N18  C19  C23  115.11  3.000
 539  H15  C19  C20  109.41  3.000
 539  C23  C19  C20  103.05  3.000
 539  N18  C19  C20  112.21  3.000
 539  N16  N15  C8   122.47  3.000
 539  N15  N16  C17  120.82  3.000
 539  H16  N18  C19  116.14  3.000
 539  H16  N18  C17  118.61  3.000
 539  C19  N18  C17  123.87  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
 539  CONST_01  C24  C2   C3   C5     0.00   0.0  0
 539  CONST_02  C24  C7   C6   C5     0.00   0.0  0
 539  CONST_03  C8   C7   C6   C5   180.00   0.0  0
 539  CONST_04  N16  C17  C6   C5   180.00   0.0  0
 539  CONST_05  C2   C3   C5   C6     0.00   0.0  0
 539  CONST_06  C2   C24  C7   C6     0.00   0.0  0
 539  CONST_07  C9   C8   C7   C6   180.00   0.0  0
 539  CONST_08  N15  C8   C7   C6     0.00   0.0  0
 539  CONST_09  N15  N16  C17  C6     0.00   0.0  0
 539  CONST_10  C3   C2   C24  C7     0.00   0.0  0
 539  CONST_11  C3   C5   C6   C7     0.00   0.0  0
 539  CONST_12  N16  C17  C6   C7     0.00   0.0  0
 539  CONST_15  N16  N15  C8   C7     0.00   0.0  0
 539  CONST_16  C2   C24  C7   C8   180.00   0.0  0
 539  CONST_17  C17  C6   C7   C8     0.00   0.0  0
 539  CONST_18  C11  C10  C9   C8   180.00   0.0  0
 539  CONST_19  C13  C14  C9   C8   180.00   0.0  0
 539  CONST_20  C17  N16  N15  C8     0.00   0.0  0
 539  CONST_21  C13  N12  C11  C10    0.00   0.0  0
 539  CONST_23  C13  C14  C9   C10    0.00   0.0  0
 539  CONST_24  C9   C10  C11  N12    0.00   0.0  0
 539  CONST_25  C9   C14  C13  N12    0.00   0.0  0
 539  CONST_26  C3   C5   C6   C17  180.00   0.0  0
 539  CONST_27  C24  C7   C6   C17  180.00   0.0  0
 539  CONST_28  C9   C8   C7   C24    0.00   0.0  0
 539  CONST_29  N15  C8   C7   C24  180.00   0.0  0
 539  CONST_30  C11  C10  C9   C14    0.00   0.0  0
 539  CONST_32  C11  N12  C13  C14    0.00   0.0  0
 539  CONST_33  N16  N15  C8   C9   180.00   0.0  0
 539  CONST_34  CL1  C2   C3   C5   180.00   0.0  0
 539  CONST_35  N18  C17  C6   C5     0.00   0.0  0
 539  CONST_36  CL4  C3   C5   C6   180.00   0.0  0
 539  CONST_37  CL1  C2   C24  C7   180.00   0.0  0
 539  CONST_38  N18  C17  C6   C7   180.00   0.0  0
 539  CONST_39  CL4  C3   C2   C24  180.00   0.0  0
 539  CONST_40  N18  C17  N16  N15  180.00   0.0  0
 539  CONST_41  C19  N18  C17  C6   180.00   0.0  0
 539  CONST_42  N16  C17  N18  C19    0.00   0.0  0
 539  CONST_43  H10  C24  C7   C6   180.00   0.0  0
 539  CONST_44  H1   C5   C6   C7   180.00   0.0  0
 539  CONST_45  H2   C10  C9   C8     0.00   0.0  0
 539  CONST_46  H11  C14  C9   C8     0.00   0.0  0
 539  CONST_47  H12  C11  N12  C13  180.00   0.0  0
 539  CONST_48  H3   C13  N12  C11  180.00   0.0  0
 539  CONST_49  H16  N18  C17  C6     0.00   0.0  0
 539  Var_01    C23  C22  C21  C20    0.58  30.0  1
 539  Var_02    C19  C23  C22  C21   24.25  30.0  1
 539  Var_03    C19  C20  C21  C22  -25.29  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 539  chir_01  C19  N18  C20  C23  negativ

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
 539  plan-1  C8   0.020
 539  plan-1  C10  0.020
 539  plan-1  N12  0.020
 539  plan-1  C13  0.020
 539  plan-1  C14  0.020
 539  plan-1  C11  0.020
 539  plan-1  C9   0.020
 539  plan-1  H2   0.020
 539  plan-1  H3   0.020
 539  plan-1  H11  0.020
 539  plan-1  H12  0.020
 539  plan-2  C5   0.020
 539  plan-2  C6   0.020
 539  plan-2  C7   0.020
 539  plan-2  C8   0.020
 539  plan-2  C17  0.020
 539  plan-2  C24  0.020
 539  plan-2  C9   0.020
 539  plan-2  C2   0.020
 539  plan-2  C3   0.020
 539  plan-2  N15  0.020
 539  plan-2  N16  0.020
 539  plan-2  N18  0.020
 539  plan-2  CL1  0.020
 539  plan-2  CL4  0.020
 539  plan-2  H1   0.020
 539  plan-2  H10  0.020
 539  plan-3  C17  0.020
 539  plan-3  C19  0.020
 539  plan-3  N18  0.020
 539  plan-3  H16  0.020

