# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 12:08:43 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 7-({[3-(5-fluoropyridin-3-yl)propyl]amino}methyl)quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2ccc(CNCCCc3cncc(F)c3)cc2n1
#
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
 9P4  9P4  7-({[3-(5-fluoropyridin-3-yl)propyl]amino}methyl)quinolin-2-amine  ligand  42  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9P4
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
 9P4  F23  F  F     0  -0.304  -7.0363   2.2686  -0.5307
 9P4  C23  C  CR6   0   0.440  -6.5500   1.0208  -0.5268
 9P4  C22  C  CR16  0  -0.210  -7.1261   0.0687  -1.3483
 9P4  N21  N  N     0  -0.384  -6.6760  -1.1773  -1.3723
 9P4  C26  C  CR16  0  -0.113  -5.6550  -1.5008  -0.5898
 9P4  C24  C  CR16  0  -0.342  -5.4888   0.7007   0.2917
 9P4  C25  C  CR6   0   0.053  -5.0171  -0.6073   0.2669
 9P4  C15  C  CH2   0  -0.510  -3.8422  -1.0314   1.0965
 9P4  C14  C  CH2   0  -0.439  -2.5149  -0.6049   0.4695
 9P4  C13  C  CH2   0  -0.252  -1.3194  -1.0660   1.2886
 9P4  N12  N  NH1   0  -0.593  -0.0768  -0.7104   0.6319
 9P4  C11  C  CH2   0  -0.329   1.1018  -1.1416   1.3578
 9P4  C08  C  CR6   0   0.098   2.3476  -0.8677   0.5605
 9P4  C07  C  CR16  0  -0.295   2.4719  -1.4124  -0.7376
 9P4  C06  C  CR16  0  -0.306   3.5972  -1.1791  -1.4812
 9P4  C09  C  CR16  0  -0.381   3.3595  -0.0911   1.0693
 9P4  C10  C  CR66  0   0.235   4.5320   0.1713   0.3244
 9P4  N01  N  N     0  -0.507   5.4950   0.9491   0.8727
 9P4  C05  C  CR66  0   0.042   4.6439  -0.3853  -0.9703
 9P4  C04  C  CR16  0  -0.180   5.8277  -0.0975  -1.6948
 9P4  C03  C  CR16  0  -0.378   6.7912   0.6796  -1.1383
 9P4  C02  C  CR6   0   0.434   6.5825   1.1951   0.1791
 9P4  N02  N  NH2   0  -0.836   7.5610   1.9364   0.7586
 9P4  H1   H  HCR6  0   0.281  -7.9633   0.3218  -1.9900
 9P4  H2   H  HCR6  0   0.260  -5.3183  -2.5314  -0.6364
 9P4  H3   H  HCR6  0   0.290  -5.0413   1.4483   0.9361
 9P4  H4   H  HCH2  0   0.251  -3.9297  -0.6086   2.1006
 9P4  H5   H  HCH2  0   0.248  -3.8565  -2.1179   1.2126
 9P4  H6   H  HCH2  0   0.232  -2.4357  -1.0138  -0.5413
 9P4  H7   H  HCH2  0   0.230  -2.4920   0.4852   0.3694
 9P4  H8   H  HCH2  0   0.191  -1.3978  -0.6614   2.3106
 9P4  H9   H  HCH2  0   0.219  -1.3503  -2.1556   1.3890
 9P4  H10  H  HNH1  0   0.341  -0.0377   0.2957   0.5159
 9P4  H12  H  HCH2  0   0.216   1.1943  -0.6841   2.3539
 9P4  H13  H  HCH2  0   0.237   1.0145  -2.2204   1.5245
 9P4  H14  H  HCR6  0   0.245   1.6677  -2.0148  -1.1396
 9P4  H15  H  HCR6  0   0.253   3.6964  -1.6022  -2.4742
 9P4  H16  H  HCR6  0   0.244   3.2723   0.3405   2.0602
 9P4  H17  H  HCR6  0   0.267   5.9577  -0.5000  -2.6920
 9P4  H18  H  HCR6  0   0.272   7.7035   0.9125  -1.6717
 9P4  H19  H  HNH2  0   0.395   8.2554   2.3649   0.1710
 9P4  H20  H  HNH2  0   0.385   7.3185   2.4565   1.5852

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
 9P4  C04  C03  aromatic  1.357  0.020  1.357
 9P4  C04  C05  aromatic  1.417  0.020  1.417
 9P4  C03  C02  aromatic  1.430  0.020  1.430
 9P4  C06  C05  aromatic  1.410  0.020  1.410
 9P4  C06  C07  aromatic  1.369  0.020  1.369
 9P4  C05  C10  aromatic  1.414  0.020  1.414
 9P4  C02  N02  single    1.358  0.020  1.358
 9P4  C02  N01  aromatic  1.313  0.020  1.313
 9P4  C07  C08  aromatic  1.413  0.020  1.413
 9P4  C10  N01  aromatic  1.354  0.020  1.354
 9P4  C10  C09  aromatic  1.414  0.020  1.414
 9P4  C08  C09  aromatic  1.373  0.020  1.373
 9P4  C08  C11  single    1.504  0.020  1.504
 9P4  C11  N12  single    1.450  0.020  1.450
 9P4  N12  C13  single    1.450  0.020  1.450
 9P4  C13  C14  single    1.521  0.020  1.521
 9P4  C14  C15  single    1.529  0.020  1.529
 9P4  C15  C25  single    1.500  0.020  1.500
 9P4  C25  C26  aromatic  1.392  0.020  1.392
 9P4  C25  C24  aromatic  1.391  0.020  1.391
 9P4  C26  N21  aromatic  1.326  0.020  1.326
 9P4  C24  C23  aromatic  1.378  0.020  1.378
 9P4  N21  C22  aromatic  1.325  0.020  1.325
 9P4  C23  C22  aromatic  1.383  0.020  1.383
 9P4  C23  F23  single    1.339  0.020  1.339
 9P4  C22  H1   single    0.930  0.020  1.080
 9P4  C26  H2   single    0.930  0.020  1.080
 9P4  C24  H3   single    0.930  0.020  1.080
 9P4  C15  H4   single    0.970  0.020  1.090
 9P4  C15  H5   single    0.970  0.020  1.090
 9P4  C14  H6   single    0.970  0.020  1.090
 9P4  C14  H7   single    0.970  0.020  1.090
 9P4  C13  H8   single    0.970  0.020  1.090
 9P4  C13  H9   single    0.970  0.020  1.090
 9P4  N12  H10  single    0.890  0.020  1.040
 9P4  C11  H12  single    0.970  0.020  1.090
 9P4  C11  H13  single    0.970  0.020  1.090
 9P4  C07  H14  single    0.930  0.020  1.080
 9P4  C06  H15  single    0.930  0.020  1.080
 9P4  C09  H16  single    0.930  0.020  1.080
 9P4  C04  H17  single    0.930  0.020  1.080
 9P4  C03  H18  single    0.930  0.020  1.080
 9P4  N02  H19  single    0.890  0.020  1.040
 9P4  N02  H20  single    0.890  0.020  1.040

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
 9P4  C24  C23  C22  120.91  3.000
 9P4  C22  C23  F23  119.24  3.000
 9P4  C24  C23  F23  119.86  3.000
 9P4  H1   C22  N21  118.09  3.000
 9P4  H1   C22  C23  120.80  3.000
 9P4  N21  C22  C23  121.10  3.000
 9P4  C26  N21  C22  118.69  3.000
 9P4  H2   C26  C25  119.58  3.000
 9P4  H2   C26  N21  116.42  3.000
 9P4  C25  C26  N21  123.99  3.000
 9P4  H3   C24  C25  121.29  3.000
 9P4  H3   C24  C23  120.73  3.000
 9P4  C25  C24  C23  117.98  3.000
 9P4  C15  C25  C24  121.46  3.000
 9P4  C24  C25  C26  117.33  3.000
 9P4  C15  C25  C26  121.19  3.000
 9P4  H5   C15  H4   106.61  3.000
 9P4  H5   C15  C14  109.41  3.000
 9P4  H4   C15  C14  109.78  3.000
 9P4  H5   C15  C25  109.24  3.000
 9P4  H4   C15  C25  109.64  3.000
 9P4  C14  C15  C25  112.00  3.000
 9P4  H7   C14  H6   106.63  3.000
 9P4  H7   C14  C13  109.55  3.000
 9P4  H6   C14  C13  109.13  3.000
 9P4  H7   C14  C15  109.48  3.000
 9P4  H6   C14  C15  109.74  3.000
 9P4  C13  C14  C15  112.16  3.000
 9P4  H9   C13  H8   106.16  3.000
 9P4  H9   C13  N12  108.05  3.000
 9P4  H8   C13  N12  113.02  3.000
 9P4  H9   C13  C14  109.21  3.000
 9P4  H8   C13  C14  109.41  3.000
 9P4  N12  C13  C14  110.82  3.000
 9P4  H10  N12  C11  108.73  3.000
 9P4  H10  N12  C13  109.17  3.000
 9P4  C11  N12  C13  113.39  3.000
 9P4  H13  C11  H12  106.17  3.000
 9P4  H13  C11  C08  109.03  3.000
 9P4  H12  C11  C08  109.55  3.000
 9P4  H13  C11  N12  107.72  3.000
 9P4  H12  C11  N12  113.46  3.000
 9P4  C08  C11  N12  110.71  3.000
 9P4  C09  C08  C07  119.57  3.000
 9P4  C09  C08  C11  121.12  3.000
 9P4  C07  C08  C11  119.31  3.000
 9P4  H14  C07  C06  120.26  3.000
 9P4  H14  C07  C08  119.37  3.000
 9P4  C06  C07  C08  120.37  3.000
 9P4  H15  C06  C05  118.94  3.000
 9P4  H15  C06  C07  120.43  3.000
 9P4  C05  C06  C07  120.64  3.000
 9P4  H16  C09  C10  118.31  3.000
 9P4  H16  C09  C08  120.30  3.000
 9P4  C10  C09  C08  121.39  3.000
 9P4  C05  C10  N01  122.74  3.000
 9P4  N01  C10  C09  118.89  3.000
 9P4  C05  C10  C09  118.37  3.000
 9P4  C02  N01  C10  118.86  3.000
 9P4  C04  C05  C10  117.01  3.000
 9P4  C10  C05  C06  119.66  3.000
 9P4  C04  C05  C06  123.32  3.000
 9P4  H17  C04  C03  120.33  3.000
 9P4  H17  C04  C05  119.69  3.000
 9P4  C03  C04  C05  119.98  3.000
 9P4  H18  C03  C02  119.98  3.000
 9P4  H18  C03  C04  121.31  3.000
 9P4  C02  C03  C04  118.72  3.000
 9P4  N02  C02  C03  119.00  3.000
 9P4  N02  C02  N01  118.28  3.000
 9P4  C03  C02  N01  122.69  3.000
 9P4  H20  N02  H19  115.23  3.000
 9P4  H20  N02  C02  117.33  3.000
 9P4  H19  N02  C02  118.76  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
 9P4  CONST_01  C26  C25  C24  C23     0.00   0.0  0
 9P4  CONST_02  C26  N21  C22  C23     0.00   0.0  0
 9P4  CONST_03  C25  C26  N21  C22     0.00   0.0  0
 9P4  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 9P4  CONST_05  C24  C25  C26  N21     0.00   0.0  0
 9P4  CONST_06  C24  C23  C22  N21     0.00   0.0  0
 9P4  CONST_07  C05  C06  C07  C08     0.00   0.0  0
 9P4  CONST_08  C05  C10  C09  C08     0.00   0.0  0
 9P4  CONST_09  N01  C10  C09  C08   180.00   0.0  0
 9P4  CONST_10  C04  C05  C06  C07   180.00   0.0  0
 9P4  CONST_11  C10  C05  C06  C07     0.00   0.0  0
 9P4  CONST_12  C10  C09  C08  C07     0.00   0.0  0
 9P4  CONST_13  C03  C04  C05  C06   180.00   0.0  0
 9P4  CONST_14  N01  C10  C05  C06   180.00   0.0  0
 9P4  CONST_15  C09  C10  C05  C06     0.00   0.0  0
 9P4  CONST_16  C09  C08  C07  C06     0.00   0.0  0
 9P4  CONST_17  C04  C05  C10  C09   180.00   0.0  0
 9P4  CONST_18  C02  N01  C10  C09   180.00   0.0  0
 9P4  CONST_19  C03  C04  C05  C10     0.00   0.0  0
 9P4  CONST_20  C03  C02  N01  C10     0.00   0.0  0
 9P4  CONST_21  C04  C03  C02  N01     0.00   0.0  0
 9P4  CONST_22  C04  C05  C10  N01     0.00   0.0  0
 9P4  CONST_23  C02  C03  C04  C05     0.00   0.0  0
 9P4  CONST_24  C02  N01  C10  C05     0.00   0.0  0
 9P4  CONST_25  C25  C24  C23  F23   180.00   0.0  0
 9P4  CONST_26  N21  C22  C23  F23   180.00   0.0  0
 9P4  CONST_27  C15  C25  C24  C23   180.00   0.0  0
 9P4  CONST_28  C15  C25  C26  N21   180.00   0.0  0
 9P4  CONST_29  C06  C07  C08  C11   180.00   0.0  0
 9P4  CONST_30  C10  C09  C08  C11   180.00   0.0  0
 9P4  CONST_31  N02  C02  N01  C10   180.00   0.0  0
 9P4  CONST_32  N02  C02  C03  C04   180.00   0.0  0
 9P4  CONST_33  H2   C26  N21  C22   180.00   0.0  0
 9P4  CONST_34  H3   C24  C23  C22   180.00   0.0  0
 9P4  CONST_35  H1   C22  N21  C26   180.00   0.0  0
 9P4  CONST_36  H15  C06  C07  C08   180.00   0.0  0
 9P4  CONST_37  H16  C09  C08  C07   180.00   0.0  0
 9P4  CONST_38  H17  C04  C05  C06     0.00   0.0  0
 9P4  CONST_39  H14  C07  C08  C09   180.00   0.0  0
 9P4  CONST_40  H18  C03  C02  N01   180.00   0.0  0
 9P4  Var_01    C14  C15  C25  C26    99.47  30.0  2
 9P4  Var_02    C07  C08  C11  N12   -56.77  30.0  2
 9P4  Var_03    C13  C14  C15  C25  -178.45  30.0  1
 9P4  Var_04    C08  C11  N12  C13   174.27  30.0  1
 9P4  Var_05    N12  C13  C14  C15   176.89  30.0  1
 9P4  Var_06    C11  N12  C13  C14  -179.18  30.0  1

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
 9P4  plan-1  F23  0.020
 9P4  plan-1  C23  0.020
 9P4  plan-1  C22  0.020
 9P4  plan-1  N21  0.020
 9P4  plan-1  C26  0.020
 9P4  plan-1  C24  0.020
 9P4  plan-1  C25  0.020
 9P4  plan-1  C15  0.020
 9P4  plan-1  H1   0.020
 9P4  plan-1  H2   0.020
 9P4  plan-1  H3   0.020
 9P4  plan-2  C11  0.020
 9P4  plan-2  C08  0.020
 9P4  plan-2  C07  0.020
 9P4  plan-2  C06  0.020
 9P4  plan-2  C09  0.020
 9P4  plan-2  C10  0.020
 9P4  plan-2  N01  0.020
 9P4  plan-2  C05  0.020
 9P4  plan-2  C04  0.020
 9P4  plan-2  C03  0.020
 9P4  plan-2  C02  0.020
 9P4  plan-2  N02  0.020
 9P4  plan-2  H14  0.020
 9P4  plan-2  H15  0.020
 9P4  plan-2  H16  0.020
 9P4  plan-2  H17  0.020
 9P4  plan-2  H18  0.020
 9P4  plan-3  C02  0.020
 9P4  plan-3  N02  0.020
 9P4  plan-3  H19  0.020
 9P4  plan-3  H20  0.020

