# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 03:28:41 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 7-({3-[2-(6-aminopyridin-2-yl)ethyl]phenoxy}methyl)quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(CCc2cccc(OCc3ccc4ccc(N)nc4c3)c2)n1
#
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
 V5G  V5G  7-({3-[2-(6-aminopyridin-2-yl)ethyl]phenoxy}methyl)quinolin-2-amine  ligand  50  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V5G
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
 V5G  C02  C  CR6   0   0.432   7.0266   4.6130  22.1464
 V5G  C03  C  CR16  0  -0.390   5.7176   4.1442  22.3594
 V5G  C04  C  CR16  0  -0.145   4.6798   5.0380  22.2263
 V5G  C05  C  CR16  0  -0.389   4.9446   6.3630  21.8856
 V5G  C06  C  CR6   0   0.264   6.2659   6.7348  21.6935
 V5G  C07  C  CH2   0  -0.485   6.6361   8.1497  21.3511
 V5G  C08  C  CH2   0  -0.507   7.3230   8.8637  22.5239
 V5G  C09  C  CR6   0   0.144   7.7588  10.2510  22.1456
 V5G  C10  C  CR16  0  -0.325   8.9501  10.4449  21.4433
 V5G  C11  C  CR16  0  -0.225   9.3252  11.7180  21.0552
 V5G  C12  C  CR16  0  -0.396   8.5346  12.8238  21.3525
 V5G  C13  C  CR6   0   0.421   7.3480  12.6359  22.0538
 V5G  C15  C  CH2   0  -0.196   6.8399  14.9510  22.0472
 V5G  C16  C  CR6   0   0.035   5.7905  15.9058  22.5385
 V5G  C17  C  CR16  0  -0.294   6.0059  17.2779  22.2785
 V5G  C18  C  CR16  0  -0.303   5.0999  18.2136  22.6971
 V5G  C19  C  CR66  0   0.044   3.9392  17.8245  23.3934
 V5G  C20  C  CR16  0  -0.178   2.9663  18.7434  23.8607
 V5G  C21  C  CR16  0  -0.376   1.8732  18.2916  24.5250
 V5G  C22  C  CR6   0   0.439   1.7318  16.8845  24.7390
 V5G  C25  C  CR66  0   0.242   3.7111  16.4545  23.6560
 V5G  C26  C  CR16  0  -0.376   4.6633  15.5074  23.2119
 V5G  C27  C  CR16  0  -0.417   6.9675  11.3502  22.4436
 V5G  N01  N  NH2   0  -0.835   8.0931   3.7641  22.2169
 V5G  N23  N  NH2   0  -0.835   0.6219  16.4230  25.3658
 V5G  N24  N  N     0  -0.505   2.6190  16.0108  24.3206
 V5G  N28  N  N     0  -0.475   7.2797   5.8777  21.8244
 V5G  O14  O  O2    0  -0.481   6.5044  13.6324  22.4011
 V5G  H1   H  HCR6  0   0.261   5.5402   3.1083  22.6184
 V5G  H2   H  HCR6  0   0.261   3.6607   4.7085  22.3860
 V5G  H3   H  HCR6  0   0.249   4.1466   7.0845  21.7750
 V5G  H4   H  HCH2  0   0.247   7.3105   8.1464  20.4906
 V5G  H5   H  HCH2  0   0.248   5.7458   8.7095  21.0578
 V5G  H6   H  HCH2  0   0.249   6.6377   8.9011  23.3737
 V5G  H7   H  HCH2  0   0.249   8.1891   8.2765  22.8376
 V5G  H8   H  HCR6  0   0.242   9.5805   9.5964  21.2053
 V5G  H9   H  HCR6  0   0.254  10.2501  11.8664  20.5125
 V5G  H10  H  HCR6  0   0.278   8.8607  13.8046  21.0351
 V5G  H11  H  HCH2  0   0.245   6.9364  15.0500  20.9583
 V5G  H12  H  HCH2  0   0.244   7.8092  15.2344  22.4775
 V5G  H13  H  HCR6  0   0.250   6.8969  17.5873  21.7448
 V5G  H14  H  HCR6  0   0.255   5.2682  19.2654  22.4979
 V5G  H15  H  HCR6  0   0.267   3.1030  19.8036  23.6838
 V5G  H16  H  HCR6  0   0.270   1.1152  18.9725  24.8903
 V5G  H17  H  HCR6  0   0.244   4.4719  14.4641  23.4241
 V5G  H18  H  HCR6  0   0.251   6.0399  11.2185  22.9899
 V5G  H19  H  HNH2  0   0.378   8.9971   4.1941  22.3253
 V5G  H20  H  HNH2  0   0.388   7.9770   2.9110  22.7379
 V5G  H21  H  HNH2  0   0.385   0.6270  15.4684  25.6842
 V5G  H22  H  HNH2  0   0.396   0.0653  17.0599  25.9095

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
 V5G  C04  C05  aromatic  1.394  0.020  1.394
 V5G  C04  C03  aromatic  1.376  0.020  1.376
 V5G  C17  C18  aromatic  1.368  0.020  1.368
 V5G  C17  C16  aromatic  1.413  0.020  1.413
 V5G  C05  C06  aromatic  1.386  0.020  1.386
 V5G  C03  C02  aromatic  1.407  0.020  1.407
 V5G  C18  C19  aromatic  1.408  0.020  1.408
 V5G  C06  C07  single    1.502  0.020  1.502
 V5G  C06  N28  aromatic  1.334  0.020  1.334
 V5G  C07  C08  single    1.535  0.020  1.535
 V5G  C02  N28  aromatic  1.329  0.020  1.329
 V5G  C02  N01  single    1.365  0.020  1.365
 V5G  C15  C16  single    1.501  0.020  1.501
 V5G  C15  O14  single    1.406  0.020  1.406
 V5G  C16  C26  aromatic  1.372  0.020  1.372
 V5G  C12  C11  aromatic  1.391  0.020  1.391
 V5G  C12  C13  aromatic  1.391  0.020  1.391
 V5G  C11  C10  aromatic  1.383  0.020  1.383
 V5G  O14  C13  single    1.351  0.020  1.351
 V5G  C13  C27  aromatic  1.396  0.020  1.396
 V5G  C10  C09  aromatic  1.396  0.020  1.396
 V5G  C27  C09  aromatic  1.387  0.020  1.387
 V5G  C09  C08  single    1.503  0.020  1.503
 V5G  C19  C20  aromatic  1.417  0.020  1.417
 V5G  C19  C25  aromatic  1.413  0.020  1.413
 V5G  C20  C21  aromatic  1.357  0.020  1.357
 V5G  C26  C25  aromatic  1.415  0.020  1.415
 V5G  C25  N24  aromatic  1.353  0.020  1.353
 V5G  C21  C22  aromatic  1.430  0.020  1.430
 V5G  N24  C22  aromatic  1.314  0.020  1.314
 V5G  C22  N23  single    1.356  0.020  1.356
 V5G  C03  H1   single    0.930  0.020  1.080
 V5G  C04  H2   single    0.930  0.020  1.080
 V5G  C05  H3   single    0.930  0.020  1.080
 V5G  C07  H4   single    0.970  0.020  1.090
 V5G  C07  H5   single    0.970  0.020  1.090
 V5G  C08  H6   single    0.970  0.020  1.090
 V5G  C08  H7   single    0.970  0.020  1.090
 V5G  C10  H8   single    0.930  0.020  1.080
 V5G  C11  H9   single    0.930  0.020  1.080
 V5G  C12  H10  single    0.930  0.020  1.080
 V5G  C15  H11  single    0.970  0.020  1.090
 V5G  C15  H12  single    0.970  0.020  1.090
 V5G  C17  H13  single    0.930  0.020  1.080
 V5G  C18  H14  single    0.930  0.020  1.080
 V5G  C20  H15  single    0.930  0.020  1.080
 V5G  C21  H16  single    0.930  0.020  1.080
 V5G  C26  H17  single    0.930  0.020  1.080
 V5G  C27  H18  single    0.930  0.020  1.080
 V5G  N01  H19  single    0.890  0.020  1.040
 V5G  N01  H20  single    0.890  0.020  1.040
 V5G  N23  H21  single    0.890  0.020  1.040
 V5G  N23  H22  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
 V5G  N28  C02  N01  117.10  3.000
 V5G  N01  C02  C03  120.79  3.000
 V5G  N28  C02  C03  122.07  3.000
 V5G  H1   C03  C04  121.41  3.000
 V5G  H1   C03  C02  120.51  3.000
 V5G  C04  C03  C02  118.08  3.000
 V5G  H2   C04  C05  120.28  3.000
 V5G  H2   C04  C03  119.86  3.000
 V5G  C05  C04  C03  119.86  3.000
 V5G  H3   C05  C06  120.68  3.000
 V5G  H3   C05  C04  121.28  3.000
 V5G  C06  C05  C04  118.04  3.000
 V5G  N28  C06  C07  116.12  3.000
 V5G  N28  C06  C05  122.59  3.000
 V5G  C07  C06  C05  121.29  3.000
 V5G  H5   C07  H4   107.04  3.000
 V5G  H5   C07  C08  109.37  3.000
 V5G  H4   C07  C08  109.07  3.000
 V5G  H5   C07  C06  110.07  3.000
 V5G  H4   C07  C06  109.19  3.000
 V5G  C08  C07  C06  111.98  3.000
 V5G  H7   C08  H6   107.00  3.000
 V5G  H7   C08  C09  109.80  3.000
 V5G  H6   C08  C09  110.25  3.000
 V5G  H7   C08  C07  108.91  3.000
 V5G  H6   C08  C07  109.24  3.000
 V5G  C09  C08  C07  111.52  3.000
 V5G  C27  C09  C10  119.00  3.000
 V5G  C27  C09  C08  120.81  3.000
 V5G  C10  C09  C08  120.15  3.000
 V5G  H8   C10  C11  120.10  3.000
 V5G  H8   C10  C09  119.87  3.000
 V5G  C11  C10  C09  120.02  3.000
 V5G  H9   C11  C12  118.92  3.000
 V5G  H9   C11  C10  119.91  3.000
 V5G  C12  C11  C10  121.17  3.000
 V5G  H10  C12  C13  121.85  3.000
 V5G  H10  C12  C11  119.13  3.000
 V5G  C13  C12  C11  119.01  3.000
 V5G  O14  C13  C27  115.93  3.000
 V5G  C27  C13  C12  119.83  3.000
 V5G  O14  C13  C12  124.24  3.000
 V5G  H12  C15  H11  106.74  3.000
 V5G  H12  C15  O14  110.75  3.000
 V5G  H11  C15  O14  110.81  3.000
 V5G  H12  C15  C16  108.95  3.000
 V5G  H11  C15  C16  109.19  3.000
 V5G  O14  C15  C16  110.32  3.000
 V5G  C26  C16  C17  119.83  3.000
 V5G  C26  C16  C15  123.37  3.000
 V5G  C17  C16  C15  116.79  3.000
 V5G  H13  C17  C18  120.00  3.000
 V5G  H13  C17  C16  119.55  3.000
 V5G  C18  C17  C16  120.46  3.000
 V5G  H14  C18  C19  119.14  3.000
 V5G  H14  C18  C17  120.32  3.000
 V5G  C19  C18  C17  120.54  3.000
 V5G  C25  C19  C20  117.15  3.000
 V5G  C25  C19  C18  119.52  3.000
 V5G  C20  C19  C18  123.34  3.000
 V5G  H15  C20  C21  120.49  3.000
 V5G  H15  C20  C19  119.60  3.000
 V5G  C21  C20  C19  119.91  3.000
 V5G  H16  C21  C22  119.94  3.000
 V5G  H16  C21  C20  121.34  3.000
 V5G  C22  C21  C20  118.72  3.000
 V5G  N24  C22  N23  118.28  3.000
 V5G  N23  C22  C21  119.01  3.000
 V5G  N24  C22  C21  122.68  3.000
 V5G  N24  C25  C26  118.55  3.000
 V5G  N24  C25  C19  122.64  3.000
 V5G  C26  C25  C19  118.81  3.000
 V5G  H17  C26  C25  117.71  3.000
 V5G  H17  C26  C16  121.45  3.000
 V5G  C25  C26  C16  120.84  3.000
 V5G  H18  C27  C13  119.04  3.000
 V5G  H18  C27  C09  120.00  3.000
 V5G  C13  C27  C09  120.95  3.000
 V5G  H20  N01  H19  114.19  3.000
 V5G  H20  N01  C02  117.64  3.000
 V5G  H19  N01  C02  116.20  3.000
 V5G  H22  N23  H21  115.63  3.000
 V5G  H22  N23  C22  119.18  3.000
 V5G  H21  N23  C22  117.72  3.000
 V5G  C25  N24  C22  118.91  3.000
 V5G  C06  N28  C02  119.36  3.000
 V5G  C15  O14  C13  118.56  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
 V5G  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 V5G  CONST_02  C05  C06  N28  C02     0.00   0.0  0
 V5G  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 V5G  CONST_04  C06  N28  C02  C03     0.00   0.0  0
 V5G  CONST_05  N28  C06  C05  C04     0.00   0.0  0
 V5G  CONST_06  N28  C02  C03  C04     0.00   0.0  0
 V5G  CONST_07  C12  C11  C10  C09     0.00   0.0  0
 V5G  CONST_08  C12  C13  C27  C09     0.00   0.0  0
 V5G  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 V5G  CONST_10  C13  C27  C09  C10     0.00   0.0  0
 V5G  CONST_11  C27  C13  C12  C11     0.00   0.0  0
 V5G  CONST_12  C27  C09  C10  C11     0.00   0.0  0
 V5G  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 V5G  CONST_14  C19  C25  C26  C16     0.00   0.0  0
 V5G  CONST_15  N24  C25  C26  C16   180.00   0.0  0
 V5G  CONST_16  C20  C19  C18  C17   180.00   0.0  0
 V5G  CONST_17  C25  C19  C18  C17     0.00   0.0  0
 V5G  CONST_18  C25  C26  C16  C17     0.00   0.0  0
 V5G  CONST_19  C26  C16  C17  C18     0.00   0.0  0
 V5G  CONST_20  C21  C20  C19  C18   180.00   0.0  0
 V5G  CONST_21  C26  C25  C19  C18     0.00   0.0  0
 V5G  CONST_22  N24  C25  C19  C18   180.00   0.0  0
 V5G  CONST_23  C22  C21  C20  C19     0.00   0.0  0
 V5G  CONST_24  C22  N24  C25  C19     0.00   0.0  0
 V5G  CONST_25  C26  C25  C19  C20   180.00   0.0  0
 V5G  CONST_26  N24  C25  C19  C20     0.00   0.0  0
 V5G  CONST_27  N24  C22  C21  C20     0.00   0.0  0
 V5G  CONST_28  C25  C19  C20  C21     0.00   0.0  0
 V5G  CONST_29  C25  N24  C22  C21     0.00   0.0  0
 V5G  CONST_30  C26  C25  N24  C22   180.00   0.0  0
 V5G  CONST_31  C07  C06  N28  C02   180.00   0.0  0
 V5G  CONST_32  C07  C06  C05  C04   180.00   0.0  0
 V5G  CONST_33  N01  C02  C03  C04   180.00   0.0  0
 V5G  CONST_34  N01  C02  N28  C06   180.00   0.0  0
 V5G  CONST_35  C11  C10  C09  C08   180.00   0.0  0
 V5G  CONST_36  C13  C27  C09  C08   180.00   0.0  0
 V5G  CONST_37  O14  C13  C27  C09   180.00   0.0  0
 V5G  CONST_38  O14  C13  C12  C11   180.00   0.0  0
 V5G  CONST_39  C18  C17  C16  C15   180.00   0.0  0
 V5G  CONST_40  C25  C26  C16  C15   180.00   0.0  0
 V5G  CONST_41  N23  C22  C21  C20   180.00   0.0  0
 V5G  CONST_42  N23  C22  N24  C25   180.00   0.0  0
 V5G  CONST_43  H2   C04  C03  C02   180.00   0.0  0
 V5G  CONST_44  H3   C05  C04  C03   180.00   0.0  0
 V5G  CONST_45  H1   C03  C04  C05   180.00   0.0  0
 V5G  CONST_46  H9   C11  C10  C09   180.00   0.0  0
 V5G  CONST_47  H10  C12  C11  C10   180.00   0.0  0
 V5G  CONST_48  H18  C27  C09  C10   180.00   0.0  0
 V5G  CONST_49  H8   C10  C11  C12   180.00   0.0  0
 V5G  CONST_50  H14  C18  C17  C16   180.00   0.0  0
 V5G  CONST_51  H17  C26  C16  C17   180.00   0.0  0
 V5G  CONST_52  H15  C20  C19  C18     0.00   0.0  0
 V5G  CONST_53  H13  C17  C18  C19   180.00   0.0  0
 V5G  CONST_54  H16  C21  C20  C19   180.00   0.0  0
 V5G  CONST_57  H21  N23  C22  C21   180.00   0.0  0
 V5G  Var_01    C08  C07  C06  C05   108.47  30.0  2
 V5G  Var_02    C09  C08  C07  C06   176.77  30.0  3
 V5G  Var_03    C10  C09  C08  C07   -81.26  30.0  2
 V5G  Var_04    C16  C15  O14  C13  -179.17  30.0  1
 V5G  Var_05    C27  C13  O14  C15   179.41  30.0  2
 V5G  Var_06    O14  C15  C16  C17   178.79  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
 V5G  plan-1  C02  0.020
 V5G  plan-1  C03  0.020
 V5G  plan-1  C04  0.020
 V5G  plan-1  C05  0.020
 V5G  plan-1  C06  0.020
 V5G  plan-1  C07  0.020
 V5G  plan-1  N01  0.020
 V5G  plan-1  N28  0.020
 V5G  plan-1  H1   0.020
 V5G  plan-1  H2   0.020
 V5G  plan-1  H3   0.020
 V5G  plan-2  C08  0.020
 V5G  plan-2  C09  0.020
 V5G  plan-2  C10  0.020
 V5G  plan-2  C11  0.020
 V5G  plan-2  C12  0.020
 V5G  plan-2  C13  0.020
 V5G  plan-2  C27  0.020
 V5G  plan-2  O14  0.020
 V5G  plan-2  H8   0.020
 V5G  plan-2  H9   0.020
 V5G  plan-2  H10  0.020
 V5G  plan-2  H18  0.020
 V5G  plan-3  C15  0.020
 V5G  plan-3  C16  0.020
 V5G  plan-3  C17  0.020
 V5G  plan-3  C18  0.020
 V5G  plan-3  C19  0.020
 V5G  plan-3  C20  0.020
 V5G  plan-3  C21  0.020
 V5G  plan-3  C22  0.020
 V5G  plan-3  C25  0.020
 V5G  plan-3  C26  0.020
 V5G  plan-3  N23  0.020
 V5G  plan-3  N24  0.020
 V5G  plan-3  H13  0.020
 V5G  plan-3  H14  0.020
 V5G  plan-3  H15  0.020
 V5G  plan-3  H16  0.020
 V5G  plan-3  H17  0.020
 V5G  plan-4  C02  0.020
 V5G  plan-4  N01  0.020
 V5G  plan-4  H19  0.020
 V5G  plan-4  H20  0.020
 V5G  plan-5  C22  0.020
 V5G  plan-5  N23  0.020
 V5G  plan-5  H21  0.020
 V5G  plan-5  H22  0.020

