# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:50:30 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 7-{[3-({[(pyridin-2-yl)methyl]amino}methyl)phenoxy]methyl}quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2ccc(COc3cccc(CNCc4ccccn4)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
 V4V  V4V  7-{[3-({[(pyridin-2-yl)methyl]amino}methyl)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 PERFECT
;

data_comp_V4V
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
 V4V  C02  C  CR6   0   0.438  83.8249  113.6643  88.2196
 V4V  C03  C  CR16  0  -0.376  83.3458  114.6927  87.3483
 V4V  C04  C  CR16  0  -0.177  83.7856  114.7178  86.0655
 V4V  C05  C  CR66  0   0.044  84.6978  113.7326  85.6107
 V4V  C06  C  CR16  0  -0.302  85.1986  113.6885  84.2958
 V4V  C07  C  CR16  0  -0.296  86.0707  112.7044  83.9158
 V4V  C08  C  CR6   0   0.037  86.4809  111.7170  84.8387
 V4V  C09  C  CH2   0  -0.198  87.4497  110.6783  84.3509
 V4V  C11  C  CR6   0   0.419  88.2851  108.5471  84.9808
 V4V  C12  C  CR16  0  -0.393  89.1003  108.4491  83.8586
 V4V  C13  C  CR16  0  -0.227  89.8433  107.2882  83.6643
 V4V  C14  C  CR16  0  -0.303  89.7848  106.2375  84.5615
 V4V  C15  C  CR6   0   0.105  88.9675  106.3351  85.6887
 V4V  C16  C  CH2   0  -0.338  88.9108  105.2142  86.6983
 V4V  C18  C  CH2   0  -0.305  87.6389  103.5982  85.4281
 V4V  C19  C  CR6   0   0.211  87.7083  102.3679  84.5614
 V4V  C20  C  CR16  0  -0.331  88.9149  101.8734  84.0749
 V4V  C21  C  CR16  0  -0.149  88.8986  100.7602  83.2495
 V4V  C22  C  CR16  0  -0.327  87.6818  100.1774  82.9298
 V4V  C23  C  CR16  0  -0.080  86.5337  100.7424  83.4636
 V4V  C25  C  CR16  0  -0.414  88.2226  107.4861  85.8867
 V4V  C26  C  CR16  0  -0.372  86.0078  111.7484  86.1269
 V4V  C27  C  CR66  0   0.241  85.1067  112.7538  86.5452
 V4V  N01  N  NH2   0  -0.834  83.3617  113.6136  89.4928
 V4V  N17  N  NH1   0  -0.604  88.8976  103.9118  86.0645
 V4V  N24  N  N     0  -0.427  86.5405  101.8032  84.2603
 V4V  N28  N  N     0  -0.506  84.6709  112.7400  87.8266
 V4V  O10  O  O2    0  -0.481  87.5150  109.6172  85.2728
 V4V  H1   H  HCR6  0   0.271  82.6469  115.4315  87.7187
 V4V  H2   H  HCR6  0   0.266  83.4436  115.4863  85.3824
 V4V  H3   H  HCR6  0   0.255  84.8805  114.4417  83.5846
 V4V  H4   H  HCR6  0   0.250  86.4450  112.6742  82.8995
 V4V  H5   H  HCH2  0   0.242  87.1302  110.3179  83.3651
 V4V  H6   H  HCH2  0   0.247  88.4378  111.1370  84.2149
 V4V  H7   H  HCR6  0   0.277  89.1715  109.2475  83.1326
 V4V  H8   H  HCR6  0   0.253  90.4765  107.2145  82.7891
 V4V  H9   H  HCR6  0   0.243  90.3618  105.3387  84.3893
 V4V  H10  H  HCH2  0   0.216  88.0524  105.3779  87.3670
 V4V  H11  H  HCH2  0   0.257  89.8023  105.2638  87.3293
 V4V  H12  H  HCH2  0   0.254  87.3624  104.4407  84.7851
 V4V  H13  H  HCH2  0   0.225  86.8067  103.4800  86.1369
 V4V  H14  H  HCR6  0   0.261  89.8442  102.3560  84.3420
 V4V  H15  H  HCR6  0   0.268  89.8237  100.3552  82.8596
 V4V  H16  H  HCR6  0   0.265  87.6192   99.3086  82.2890
 V4V  H17  H  HCR6  0   0.257  85.5618  100.3148  83.2406
 V4V  H18  H  HCR6  0   0.253  87.5728  107.5702  86.7510
 V4V  H19  H  HCR6  0   0.244  86.3052  111.0064  86.8558
 V4V  H20  H  HNH2  0   0.385  83.8483  113.0209  90.1445
 V4V  H21  H  HNH2  0   0.396  82.9308  114.4316  89.8883
 V4V  H22  H  HNH1  0   0.358  89.1204  103.2022  86.7506

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
 V4V  C22  C23  aromatic  1.386  0.020  1.386
 V4V  C22  C21  aromatic  1.387  0.020  1.387
 V4V  C23  N24  aromatic  1.327  0.020  1.327
 V4V  C21  C20  aromatic  1.386  0.020  1.386
 V4V  C13  C12  aromatic  1.392  0.020  1.392
 V4V  C13  C14  aromatic  1.383  0.020  1.383
 V4V  C07  C06  aromatic  1.369  0.020  1.369
 V4V  C07  C08  aromatic  1.412  0.020  1.412
 V4V  C12  C11  aromatic  1.390  0.020  1.390
 V4V  N24  C19  aromatic  1.332  0.020  1.332
 V4V  C20  C19  aromatic  1.392  0.020  1.392
 V4V  C09  C08  single    1.502  0.020  1.502
 V4V  C09  O10  single    1.407  0.020  1.407
 V4V  C06  C05  aromatic  1.408  0.020  1.408
 V4V  C19  C18  single    1.507  0.020  1.507
 V4V  C14  C15  aromatic  1.396  0.020  1.396
 V4V  C08  C26  aromatic  1.373  0.020  1.373
 V4V  C11  O10  single    1.350  0.020  1.350
 V4V  C11  C25  aromatic  1.397  0.020  1.397
 V4V  C18  N17  single    1.445  0.020  1.445
 V4V  N17  C16  single    1.449  0.020  1.449
 V4V  C15  C25  aromatic  1.385  0.020  1.385
 V4V  C15  C16  single    1.510  0.020  1.510
 V4V  C05  C04  aromatic  1.418  0.020  1.418
 V4V  C05  C27  aromatic  1.414  0.020  1.414
 V4V  C04  C03  aromatic  1.356  0.020  1.356
 V4V  C26  C27  aromatic  1.413  0.020  1.413
 V4V  C27  N28  aromatic  1.354  0.020  1.354
 V4V  C03  C02  aromatic  1.430  0.020  1.430
 V4V  N28  C02  aromatic  1.313  0.020  1.313
 V4V  C02  N01  single    1.356  0.020  1.356
 V4V  C03  H1   single    0.930  0.020  1.080
 V4V  C04  H2   single    0.930  0.020  1.080
 V4V  C06  H3   single    0.930  0.020  1.080
 V4V  C07  H4   single    0.930  0.020  1.080
 V4V  C09  H5   single    0.970  0.020  1.090
 V4V  C09  H6   single    0.970  0.020  1.090
 V4V  C12  H7   single    0.930  0.020  1.080
 V4V  C13  H8   single    0.930  0.020  1.080
 V4V  C14  H9   single    0.930  0.020  1.080
 V4V  C16  H10  single    0.970  0.020  1.090
 V4V  C16  H11  single    0.970  0.020  1.090
 V4V  C18  H12  single    0.970  0.020  1.090
 V4V  C18  H13  single    0.970  0.020  1.090
 V4V  C20  H14  single    0.930  0.020  1.080
 V4V  C21  H15  single    0.930  0.020  1.080
 V4V  C22  H16  single    0.930  0.020  1.080
 V4V  C23  H17  single    0.930  0.020  1.080
 V4V  C25  H18  single    0.930  0.020  1.080
 V4V  C26  H19  single    0.930  0.020  1.080
 V4V  N01  H20  single    0.890  0.020  1.040
 V4V  N01  H21  single    0.890  0.020  1.040
 V4V  N17  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
 V4V  N28  C02  N01  118.35  3.000
 V4V  N01  C02  C03  118.98  3.000
 V4V  N28  C02  C03  122.65  3.000
 V4V  H1   C03  C04  121.36  3.000
 V4V  H1   C03  C02  119.90  3.000
 V4V  C04  C03  C02  118.74  3.000
 V4V  H2   C04  C05  119.59  3.000
 V4V  H2   C04  C03  120.47  3.000
 V4V  C05  C04  C03  119.94  3.000
 V4V  C27  C05  C06  119.53  3.000
 V4V  C27  C05  C04  117.08  3.000
 V4V  C06  C05  C04  123.39  3.000
 V4V  H3   C06  C07  120.30  3.000
 V4V  H3   C06  C05  119.13  3.000
 V4V  C07  C06  C05  120.56  3.000
 V4V  H4   C07  C08  119.55  3.000
 V4V  H4   C07  C06  120.04  3.000
 V4V  C08  C07  C06  120.42  3.000
 V4V  C26  C08  C09  122.88  3.000
 V4V  C26  C08  C07  119.81  3.000
 V4V  C09  C08  C07  117.30  3.000
 V4V  H6   C09  H5   106.75  3.000
 V4V  H6   C09  O10  110.76  3.000
 V4V  H5   C09  O10  110.76  3.000
 V4V  H6   C09  C08  109.38  3.000
 V4V  H5   C09  C08  109.34  3.000
 V4V  O10  C09  C08  109.79  3.000
 V4V  O10  C11  C25  115.86  3.000
 V4V  C25  C11  C12  119.75  3.000
 V4V  O10  C11  C12  124.39  3.000
 V4V  H7   C12  C13  119.13  3.000
 V4V  H7   C12  C11  121.89  3.000
 V4V  C13  C12  C11  118.98  3.000
 V4V  H8   C13  C14  119.83  3.000
 V4V  H8   C13  C12  118.81  3.000
 V4V  C14  C13  C12  121.36  3.000
 V4V  H9   C14  C15  119.93  3.000
 V4V  H9   C14  C13  120.36  3.000
 V4V  C15  C14  C13  119.71  3.000
 V4V  C25  C15  C16  120.08  3.000
 V4V  C16  C15  C14  120.68  3.000
 V4V  C25  C15  C14  119.24  3.000
 V4V  H11  C16  H10  106.18  3.000
 V4V  H11  C16  N17  107.51  3.000
 V4V  H10  C16  N17  113.11  3.000
 V4V  H11  C16  C15  108.76  3.000
 V4V  H10  C16  C15  108.98  3.000
 V4V  N17  C16  C15  112.04  3.000
 V4V  H13  C18  H12  105.67  3.000
 V4V  H13  C18  N17  113.50  3.000
 V4V  H12  C18  N17  108.16  3.000
 V4V  H13  C18  C19  108.54  3.000
 V4V  H12  C18  C19  107.57  3.000
 V4V  N17  C18  C19  112.98  3.000
 V4V  N24  C19  C20  122.04  3.000
 V4V  C20  C19  C18  122.09  3.000
 V4V  N24  C19  C18  115.85  3.000
 V4V  H14  C20  C21  121.07  3.000
 V4V  H14  C20  C19  120.03  3.000
 V4V  C21  C20  C19  118.91  3.000
 V4V  H15  C21  C22  120.64  3.000
 V4V  H15  C21  C20  120.33  3.000
 V4V  C22  C21  C20  119.03  3.000
 V4V  H16  C22  C23  120.50  3.000
 V4V  H16  C22  C21  121.68  3.000
 V4V  C23  C22  C21  117.82  3.000
 V4V  H17  C23  N24  116.30  3.000
 V4V  H17  C23  C22  120.14  3.000
 V4V  N24  C23  C22  123.56  3.000
 V4V  H18  C25  C15  120.03  3.000
 V4V  H18  C25  C11  119.00  3.000
 V4V  C15  C25  C11  120.96  3.000
 V4V  H19  C26  C27  117.63  3.000
 V4V  H19  C26  C08  121.46  3.000
 V4V  C27  C26  C08  120.91  3.000
 V4V  N28  C27  C26  118.57  3.000
 V4V  N28  C27  C05  122.66  3.000
 V4V  C26  C27  C05  118.77  3.000
 V4V  H21  N01  H20  115.57  3.000
 V4V  H21  N01  C02  119.03  3.000
 V4V  H20  N01  C02  117.71  3.000
 V4V  H22  N17  C18  109.77  3.000
 V4V  H22  N17  C16  109.38  3.000
 V4V  C18  N17  C16  113.32  3.000
 V4V  C23  N24  C19  118.64  3.000
 V4V  C27  N28  C02  118.92  3.000
 V4V  C11  O10  C09  118.84  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
 V4V  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 V4V  CONST_02  C05  C27  N28  C02     0.00   0.0  0
 V4V  CONST_03  C26  C27  N28  C02   180.00   0.0  0
 V4V  CONST_04  C06  C05  C04  C03   180.00   0.0  0
 V4V  CONST_05  C27  C05  C04  C03     0.00   0.0  0
 V4V  CONST_06  C27  N28  C02  C03     0.00   0.0  0
 V4V  CONST_07  C07  C06  C05  C04   180.00   0.0  0
 V4V  CONST_08  C26  C27  C05  C04   180.00   0.0  0
 V4V  CONST_09  N28  C27  C05  C04     0.00   0.0  0
 V4V  CONST_10  N28  C02  C03  C04     0.00   0.0  0
 V4V  CONST_11  C08  C07  C06  C05     0.00   0.0  0
 V4V  CONST_12  C08  C26  C27  C05     0.00   0.0  0
 V4V  CONST_13  C26  C08  C07  C06     0.00   0.0  0
 V4V  CONST_14  C26  C27  C05  C06     0.00   0.0  0
 V4V  CONST_15  N28  C27  C05  C06   180.00   0.0  0
 V4V  CONST_16  C27  C05  C06  C07     0.00   0.0  0
 V4V  CONST_17  C27  C26  C08  C07     0.00   0.0  0
 V4V  CONST_18  N28  C27  C26  C08   180.00   0.0  0
 V4V  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 V4V  CONST_20  C14  C15  C25  C11     0.00   0.0  0
 V4V  CONST_21  C15  C14  C13  C12     0.00   0.0  0
 V4V  CONST_22  C15  C25  C11  C12     0.00   0.0  0
 V4V  CONST_23  C25  C11  C12  C13     0.00   0.0  0
 V4V  CONST_24  C25  C15  C14  C13     0.00   0.0  0
 V4V  CONST_25  C22  C23  N24  C19     0.00   0.0  0
 V4V  CONST_26  C22  C21  C20  C19     0.00   0.0  0
 V4V  CONST_27  C23  C22  C21  C20     0.00   0.0  0
 V4V  CONST_28  C23  N24  C19  C20     0.00   0.0  0
 V4V  CONST_29  N24  C23  C22  C21     0.00   0.0  0
 V4V  CONST_30  N24  C19  C20  C21     0.00   0.0  0
 V4V  CONST_31  N01  C02  C03  C04   180.00   0.0  0
 V4V  CONST_32  C09  C08  C07  C06   180.00   0.0  0
 V4V  CONST_33  C27  C26  C08  C09   180.00   0.0  0
 V4V  CONST_34  C16  C15  C25  C11   180.00   0.0  0
 V4V  CONST_35  O10  C11  C12  C13   180.00   0.0  0
 V4V  CONST_36  C16  C15  C14  C13   180.00   0.0  0
 V4V  CONST_37  O10  C11  C25  C15   180.00   0.0  0
 V4V  CONST_38  C23  N24  C19  C18   180.00   0.0  0
 V4V  CONST_39  C21  C20  C19  C18   180.00   0.0  0
 V4V  CONST_40  N01  C02  N28  C27   180.00   0.0  0
 V4V  CONST_41  H2   C04  C03  C02   180.00   0.0  0
 V4V  CONST_42  H3   C06  C05  C04     0.00   0.0  0
 V4V  CONST_43  H4   C07  C06  C05   180.00   0.0  0
 V4V  CONST_44  H1   C03  C04  C05   180.00   0.0  0
 V4V  CONST_45  H19  C26  C27  C05   180.00   0.0  0
 V4V  CONST_46  H8   C13  C12  C11   180.00   0.0  0
 V4V  CONST_47  H9   C14  C13  C12   180.00   0.0  0
 V4V  CONST_48  H18  C25  C11  C12   180.00   0.0  0
 V4V  CONST_49  H7   C12  C13  C14   180.00   0.0  0
 V4V  CONST_50  H17  C23  N24  C19   180.00   0.0  0
 V4V  CONST_51  H15  C21  C20  C19   180.00   0.0  0
 V4V  CONST_52  H16  C22  C21  C20   180.00   0.0  0
 V4V  CONST_53  H14  C20  C21  C22   180.00   0.0  0
 V4V  CONST_54  H20  N01  C02  C03   180.00   0.0  0
 V4V  Var_01    O10  C09  C08  C07  -166.61  30.0  2
 V4V  Var_02    C12  C11  O10  C09     4.41  30.0  2
 V4V  Var_03    N17  C16  C15  C14   -40.92  30.0  2
 V4V  Var_04    N17  C18  C19  C20   -20.29  30.0  2
 V4V  Var_05    C18  N17  C16  C15   -72.97  30.0  1
 V4V  Var_06    C19  C18  N17  C16   169.41  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
 V4V  plan-1  C11  0.020
 V4V  plan-1  C12  0.020
 V4V  plan-1  C13  0.020
 V4V  plan-1  C14  0.020
 V4V  plan-1  C15  0.020
 V4V  plan-1  C16  0.020
 V4V  plan-1  C25  0.020
 V4V  plan-1  O10  0.020
 V4V  plan-1  H7   0.020
 V4V  plan-1  H8   0.020
 V4V  plan-1  H9   0.020
 V4V  plan-1  H18  0.020
 V4V  plan-2  C18  0.020
 V4V  plan-2  C19  0.020
 V4V  plan-2  C20  0.020
 V4V  plan-2  C21  0.020
 V4V  plan-2  C22  0.020
 V4V  plan-2  C23  0.020
 V4V  plan-2  N24  0.020
 V4V  plan-2  H14  0.020
 V4V  plan-2  H15  0.020
 V4V  plan-2  H16  0.020
 V4V  plan-2  H17  0.020
 V4V  plan-3  C02  0.020
 V4V  plan-3  C03  0.020
 V4V  plan-3  C04  0.020
 V4V  plan-3  C05  0.020
 V4V  plan-3  C06  0.020
 V4V  plan-3  C07  0.020
 V4V  plan-3  C08  0.020
 V4V  plan-3  C09  0.020
 V4V  plan-3  C26  0.020
 V4V  plan-3  C27  0.020
 V4V  plan-3  N01  0.020
 V4V  plan-3  N28  0.020
 V4V  plan-3  H1   0.020
 V4V  plan-3  H2   0.020
 V4V  plan-3  H3   0.020
 V4V  plan-3  H4   0.020
 V4V  plan-3  H19  0.020
 V4V  plan-4  C02  0.020
 V4V  plan-4  N01  0.020
 V4V  plan-4  H20  0.020
 V4V  plan-4  H21  0.020

