# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:11:03 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 5-[[3-(aminomethyl)phenyl]methyl]-3-pentyl-quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCc1cc2c(Cc3cccc(CN)c3)cccc2nc1N
#
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
 M8D  M8D  5-[[3-(aminomethyl)phenyl]methyl]-3-pentyl-quinolin-2-amine  ligand  52  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M8D
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
 M8D  N2   N  NH2   0  -0.791  -1.4428  -4.8473   1.2765
 M8D  C21  C  CH2   0  -0.349  -1.8316  -4.3391  -0.0290
 M8D  C18  C  CR6   0   0.119  -2.4116  -2.9507   0.0638
 M8D  C16  C  CR16  0  -0.393  -2.0349  -1.9670  -0.8447
 M8D  C20  C  CR16  0  -0.306  -3.3433  -2.6262   1.0469
 M8D  C19  C  CR16  0  -0.227  -3.8857  -1.3503   1.1012
 M8D  C17  C  CR16  0  -0.307  -3.5019  -0.3801   0.1846
 M8D  C15  C  CR6   0   0.163  -2.5675  -0.6811  -0.8006
 M8D  C14  C  CH2   0  -0.626  -2.1423   0.3543  -1.8172
 M8D  C3   C  CR6   0   0.115  -1.7817   1.6873  -1.2158
 M8D  C5   C  CR16  0  -0.352  -2.5963   2.7786  -1.4044
 M8D  C4   C  CR16  0  -0.250  -2.2778   4.0283  -0.8412
 M8D  C2   C  CR16  0  -0.322  -1.1418   4.1900  -0.0940
 M8D  C1   C  CR66  0   0.058  -0.6027   1.8399  -0.4415
 M8D  C8   C  CR16  0  -0.265   0.3071   0.7841  -0.1856
 M8D  C7   C  CR6   0   0.037   1.4385   0.9714   0.5481
 M8D  C6   C  CR6   0   0.375   1.6709   2.2942   1.0598
 M8D  N1   N  NH2   0  -0.834   2.8079   2.5607   1.7579
 M8D  N    N  N     0  -0.500   0.8440   3.2917   0.8551
 M8D  C    C  CR66  0   0.199  -0.2734   3.0962   0.1191
 M8D  C10  C  CH2   0  -0.535   2.4152  -0.1486   0.7570
 M8D  C9   C  CH2   0  -0.406   3.5681  -0.1235  -0.2487
 M8D  C12  C  CH2   0  -0.411   4.5515  -1.2670  -0.0366
 M8D  C11  C  CH2   0  -0.420   5.6697  -1.2937  -1.0703
 M8D  C13  C  CH3   0  -0.662   6.6414  -2.4467  -0.8605
 M8D  H1   H  HNH2  0   0.352  -1.1445  -5.8099   1.1840
 M8D  H2   H  HNH2  0   0.342  -0.6343  -4.3358   1.6074
 M8D  H4   H  HCH2  0   0.214  -1.0157  -4.3306  -0.7639
 M8D  H5   H  HCH2  0   0.238  -2.5940  -5.0107  -0.4349
 M8D  H6   H  HCR6  0   0.243  -1.2976  -2.2034  -1.6065
 M8D  H7   H  HCR6  0   0.243  -3.6380  -3.3731   1.7728
 M8D  H8   H  HCR6  0   0.250  -4.6121  -1.1084   1.8671
 M8D  H9   H  HCR6  0   0.245  -3.9270   0.6152   0.2431
 M8D  H10  H  HCH2  0   0.262  -1.3049  -0.0424  -2.3973
 M8D  H11  H  HCH2  0   0.279  -2.9540   0.5039  -2.5339
 M8D  H12  H  HCR6  0   0.249  -3.4971   2.6794  -1.9978
 M8D  H13  H  HCR6  0   0.254  -2.9401   4.8685  -1.0066
 M8D  H14  H  HCR6  0   0.249  -0.8878   5.1488   0.3404
 M8D  H15  H  HCR6  0   0.251   0.1039  -0.2058  -0.5750
 M8D  H16  H  HNH2  0   0.395   3.2991   1.8058   2.2046
 M8D  H17  H  HNH2  0   0.386   2.8231   3.4271   2.2710
 M8D  H18  H  HCH2  0   0.238   2.8140  -0.1430   1.7767
 M8D  H19  H  HCH2  0   0.252   1.8819  -1.0976   0.6601
 M8D  H20  H  HCH2  0   0.223   3.1513  -0.1790  -1.2591
 M8D  H21  H  HCH2  0   0.222   4.0991   0.8315  -0.1904
 M8D  H22  H  HCH2  0   0.212   4.9845  -1.1950   0.9672
 M8D  H23  H  HCH2  0   0.211   4.0094  -2.2189  -0.0636
 M8D  H24  H  HCH2  0   0.212   5.2329  -1.3601  -2.0715
 M8D  H25  H  HCH2  0   0.212   6.2152  -0.3453  -1.0406
 M8D  H26  H  HCH3  0   0.226   7.4240  -2.4549  -1.6199
 M8D  H27  H  HCH3  0   0.216   7.1280  -2.3820   0.1146
 M8D  H28  H  HCH3  0   0.216   6.1272  -3.4087  -0.9051

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
 M8D  C13  C11  single    1.522  0.020  1.522
 M8D  C11  C12  single    1.523  0.020  1.523
 M8D  C12  C9   single    1.523  0.020  1.523
 M8D  C14  C3   single    1.506  0.020  1.506
 M8D  C14  C15  single    1.512  0.020  1.512
 M8D  C9   C10  single    1.530  0.020  1.530
 M8D  C3   C5   aromatic  1.375  0.020  1.375
 M8D  C3   C1   aromatic  1.419  0.020  1.419
 M8D  C17  C15  aromatic  1.391  0.020  1.391
 M8D  C17  C19  aromatic  1.389  0.020  1.389
 M8D  C5   C4   aromatic  1.407  0.020  1.407
 M8D  C15  C16  aromatic  1.393  0.020  1.393
 M8D  C8   C1   aromatic  1.417  0.020  1.417
 M8D  C8   C7   aromatic  1.361  0.020  1.361
 M8D  C1   C    aromatic  1.415  0.020  1.415
 M8D  C4   C2   aromatic  1.369  0.020  1.369
 M8D  C10  C7   single    1.501  0.020  1.501
 M8D  C19  C20  aromatic  1.387  0.020  1.387
 M8D  C7   C6   aromatic  1.437  0.020  1.437
 M8D  C    C2   aromatic  1.413  0.020  1.413
 M8D  C    N    aromatic  1.352  0.020  1.352
 M8D  C16  C18  aromatic  1.391  0.020  1.391
 M8D  C6   N    aromatic  1.312  0.020  1.312
 M8D  C6   N1   single    1.361  0.020  1.361
 M8D  C20  C18  aromatic  1.393  0.020  1.393
 M8D  C18  C21  single    1.508  0.020  1.508
 M8D  C21  N2   single    1.454  0.020  1.454
 M8D  N2   H1   single    0.890  0.020  1.040
 M8D  N2   H2   single    0.890  0.020  1.040
 M8D  C21  H4   single    0.970  0.020  1.090
 M8D  C21  H5   single    0.970  0.020  1.090
 M8D  C16  H6   single    0.930  0.020  1.080
 M8D  C20  H7   single    0.930  0.020  1.080
 M8D  C19  H8   single    0.930  0.020  1.080
 M8D  C17  H9   single    0.930  0.020  1.080
 M8D  C14  H10  single    0.970  0.020  1.090
 M8D  C14  H11  single    0.970  0.020  1.090
 M8D  C5   H12  single    0.930  0.020  1.080
 M8D  C4   H13  single    0.930  0.020  1.080
 M8D  C2   H14  single    0.930  0.020  1.080
 M8D  C8   H15  single    0.930  0.020  1.080
 M8D  N1   H16  single    0.890  0.020  1.040
 M8D  N1   H17  single    0.890  0.020  1.040
 M8D  C10  H18  single    0.970  0.020  1.090
 M8D  C10  H19  single    0.970  0.020  1.090
 M8D  C9   H20  single    0.970  0.020  1.090
 M8D  C9   H21  single    0.970  0.020  1.090
 M8D  C12  H22  single    0.970  0.020  1.090
 M8D  C12  H23  single    0.970  0.020  1.090
 M8D  C11  H24  single    0.970  0.020  1.090
 M8D  C11  H25  single    0.970  0.020  1.090
 M8D  C13  H26  single    0.970  0.020  1.090
 M8D  C13  H27  single    0.970  0.020  1.090
 M8D  C13  H28  single    0.970  0.020  1.090

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
 M8D  H2   N2   H1   105.97  3.000
 M8D  H2   N2   C21  109.30  3.000
 M8D  H1   N2   C21  109.23  3.000
 M8D  H5   C21  H4   105.92  3.000
 M8D  H5   C21  C18  108.67  3.000
 M8D  H4   C21  C18  108.66  3.000
 M8D  H5   C21  N2   107.75  3.000
 M8D  H4   C21  N2   113.89  3.000
 M8D  C18  C21  N2   111.69  3.000
 M8D  C20  C18  C16  118.51  3.000
 M8D  C20  C18  C21  121.03  3.000
 M8D  C16  C18  C21  120.46  3.000
 M8D  H6   C16  C15  118.86  3.000
 M8D  H6   C16  C18  119.21  3.000
 M8D  C15  C16  C18  121.92  3.000
 M8D  H7   C20  C19  120.13  3.000
 M8D  H7   C20  C18  119.64  3.000
 M8D  C19  C20  C18  120.23  3.000
 M8D  H8   C19  C17  119.75  3.000
 M8D  H8   C19  C20  119.69  3.000
 M8D  C17  C19  C20  120.56  3.000
 M8D  H9   C17  C15  120.03  3.000
 M8D  H9   C17  C19  119.83  3.000
 M8D  C15  C17  C19  120.14  3.000
 M8D  C14  C15  C17  121.13  3.000
 M8D  C17  C15  C16  118.63  3.000
 M8D  C14  C15  C16  120.23  3.000
 M8D  H11  C14  H10  105.70  3.000
 M8D  H11  C14  C3   108.57  3.000
 M8D  H10  C14  C3   110.46  3.000
 M8D  H11  C14  C15  109.01  3.000
 M8D  H10  C14  C15  108.88  3.000
 M8D  C3   C14  C15  113.88  3.000
 M8D  C1   C3   C5   118.81  3.000
 M8D  C1   C3   C14  120.80  3.000
 M8D  C5   C3   C14  120.39  3.000
 M8D  H12  C5   C4   119.26  3.000
 M8D  H12  C5   C3   119.68  3.000
 M8D  C4   C5   C3   121.06  3.000
 M8D  H13  C4   C2   119.95  3.000
 M8D  H13  C4   C5   119.32  3.000
 M8D  C2   C4   C5   120.73  3.000
 M8D  H14  C2   C    118.74  3.000
 M8D  H14  C2   C4   121.21  3.000
 M8D  C    C2   C4   120.05  3.000
 M8D  C    C1   C8   116.15  3.000
 M8D  C    C1   C3   120.35  3.000
 M8D  C8   C1   C3   123.50  3.000
 M8D  H15  C8   C7   118.39  3.000
 M8D  H15  C8   C1   119.71  3.000
 M8D  C7   C8   C1   121.90  3.000
 M8D  C10  C7   C6   122.15  3.000
 M8D  C6   C7   C8   116.93  3.000
 M8D  C10  C7   C8   120.88  3.000
 M8D  N    C6   N1   117.26  3.000
 M8D  N1   C6   C7   119.87  3.000
 M8D  N    C6   C7   122.85  3.000
 M8D  H17  N1   H16  114.35  3.000
 M8D  H17  N1   C6   116.27  3.000
 M8D  H16  N1   C6   119.29  3.000
 M8D  C    N    C6   119.73  3.000
 M8D  N    C    C1   122.44  3.000
 M8D  N    C    C2   118.56  3.000
 M8D  C1   C    C2   119.00  3.000
 M8D  H19  C10  H18  105.35  3.000
 M8D  H19  C10  C9   108.88  3.000
 M8D  H18  C10  C9   109.73  3.000
 M8D  H19  C10  C7   108.55  3.000
 M8D  H18  C10  C7   111.28  3.000
 M8D  C9   C10  C7   112.75  3.000
 M8D  H21  C9   H20  106.15  3.000
 M8D  H21  C9   C12  109.55  3.000
 M8D  H20  C9   C12  109.65  3.000
 M8D  H21  C9   C10  110.18  3.000
 M8D  H20  C9   C10  108.61  3.000
 M8D  C12  C9   C10  112.50  3.000
 M8D  H23  C12  H22  105.97  3.000
 M8D  H23  C12  C11  109.35  3.000
 M8D  H22  C12  C11  109.44  3.000
 M8D  H23  C12  C9   109.23  3.000
 M8D  H22  C12  C9   109.47  3.000
 M8D  C11  C12  C9   113.12  3.000
 M8D  H25  C11  H24  106.05  3.000
 M8D  H25  C11  C13  109.54  3.000
 M8D  H24  C11  C13  109.56  3.000
 M8D  H25  C11  C12  109.41  3.000
 M8D  H24  C11  C12  109.20  3.000
 M8D  C13  C11  C12  112.85  3.000
 M8D  H28  C13  H27  107.38  3.000
 M8D  H28  C13  H26  107.64  3.000
 M8D  H27  C13  H26  107.62  3.000
 M8D  H28  C13  C11  111.17  3.000
 M8D  H27  C13  C11  111.26  3.000
 M8D  H26  C13  C11  111.57  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
 M8D  CONST_01  C17  C15  C16  C18     0.00   0.0  0
 M8D  CONST_02  C17  C19  C20  C18     0.00   0.0  0
 M8D  CONST_03  C19  C17  C15  C16     0.00   0.0  0
 M8D  CONST_04  C19  C20  C18  C16     0.00   0.0  0
 M8D  CONST_05  C15  C17  C19  C20     0.00   0.0  0
 M8D  CONST_06  C15  C16  C18  C20     0.00   0.0  0
 M8D  CONST_07  C2   C4   C5   C3      0.00   0.0  0
 M8D  CONST_08  C7   C8   C1   C3    180.00   0.0  0
 M8D  CONST_09  C2   C    C1   C3      0.00   0.0  0
 M8D  CONST_10  N    C    C1   C3    180.00   0.0  0
 M8D  CONST_11  C8   C1   C3   C5    180.00   0.0  0
 M8D  CONST_12  C    C1   C3   C5      0.00   0.0  0
 M8D  CONST_13  C    C2   C4   C5      0.00   0.0  0
 M8D  CONST_14  C1   C3   C5   C4      0.00   0.0  0
 M8D  CONST_15  C1   C    C2   C4      0.00   0.0  0
 M8D  CONST_16  N    C    C2   C4    180.00   0.0  0
 M8D  CONST_17  C8   C1   C    C2    180.00   0.0  0
 M8D  CONST_18  C6   N    C    C2    180.00   0.0  0
 M8D  CONST_19  C6   C7   C8   C1      0.00   0.0  0
 M8D  CONST_20  C6   N    C    C1      0.00   0.0  0
 M8D  CONST_21  N    C    C1   C8      0.00   0.0  0
 M8D  CONST_22  N    C6   C7   C8      0.00   0.0  0
 M8D  CONST_23  C    C1   C8   C7      0.00   0.0  0
 M8D  CONST_24  C    N    C6   C7      0.00   0.0  0
 M8D  CONST_25  C15  C16  C18  C21   180.00   0.0  0
 M8D  CONST_26  C19  C20  C18  C21   180.00   0.0  0
 M8D  CONST_27  C14  C15  C16  C18   180.00   0.0  0
 M8D  CONST_28  C14  C15  C17  C19   180.00   0.0  0
 M8D  CONST_29  C4   C5   C3   C14   180.00   0.0  0
 M8D  CONST_30  C8   C1   C3   C14     0.00   0.0  0
 M8D  CONST_31  C    C1   C3   C14   180.00   0.0  0
 M8D  CONST_32  C10  C7   C8   C1    180.00   0.0  0
 M8D  CONST_33  N1   C6   C7   C8    180.00   0.0  0
 M8D  CONST_34  C    N    C6   N1    180.00   0.0  0
 M8D  CONST_35  C10  C7   C6   N     180.00   0.0  0
 M8D  CONST_36  H8   C19  C20  C18   180.00   0.0  0
 M8D  CONST_37  H9   C17  C15  C16   180.00   0.0  0
 M8D  CONST_38  H7   C20  C18  C16   180.00   0.0  0
 M8D  CONST_39  H6   C16  C18  C20   180.00   0.0  0
 M8D  CONST_40  H13  C4   C5   C3    180.00   0.0  0
 M8D  CONST_41  H15  C8   C1   C3      0.00   0.0  0
 M8D  CONST_42  H14  C2   C4   C5    180.00   0.0  0
 M8D  CONST_43  H12  C5   C4   C2    180.00   0.0  0
 M8D  CONST_45  H17  N1   C6   C7    180.00   0.0  0
 M8D  Var_01    C3   C14  C15  C16  -132.57  30.0  2
 M8D  Var_02    C5   C3   C14  C15  -109.58  30.0  2
 M8D  Var_03    C16  C18  C21  N2    135.77  30.0  2
 M8D  Var_04    C9   C10  C7   C8     95.49  30.0  2
 M8D  Var_05    C12  C9   C10  C7   -179.67  30.0  1
 M8D  Var_06    H1   N2   C21  C18   174.51  30.0  3
 M8D  Var_07    C11  C12  C9   C10   177.32  30.0  1
 M8D  Var_08    C13  C11  C12  C9   -179.45  30.0  1
 M8D  Var_09    H26  C13  C11  C12   179.14  30.0  3

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
 M8D  plan-1  C21  0.020
 M8D  plan-1  C18  0.020
 M8D  plan-1  C16  0.020
 M8D  plan-1  C20  0.020
 M8D  plan-1  C19  0.020
 M8D  plan-1  C17  0.020
 M8D  plan-1  C15  0.020
 M8D  plan-1  C14  0.020
 M8D  plan-1  H6   0.020
 M8D  plan-1  H7   0.020
 M8D  plan-1  H8   0.020
 M8D  plan-1  H9   0.020
 M8D  plan-2  C14  0.020
 M8D  plan-2  C3   0.020
 M8D  plan-2  C5   0.020
 M8D  plan-2  C4   0.020
 M8D  plan-2  C2   0.020
 M8D  plan-2  C1   0.020
 M8D  plan-2  C8   0.020
 M8D  plan-2  C7   0.020
 M8D  plan-2  C6   0.020
 M8D  plan-2  N1   0.020
 M8D  plan-2  N    0.020
 M8D  plan-2  C    0.020
 M8D  plan-2  C10  0.020
 M8D  plan-2  H12  0.020
 M8D  plan-2  H13  0.020
 M8D  plan-2  H14  0.020
 M8D  plan-2  H15  0.020
 M8D  plan-3  C6   0.020
 M8D  plan-3  N1   0.020
 M8D  plan-3  H16  0.020
 M8D  plan-3  H17  0.020

