# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 18:13:17 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-(4-azanylbutyl)-3-pentyl-quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCc1cc2c(CCCCN)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
 M4D  M4D  5-(4-azanylbutyl)-3-pentyl-quinolin-2-amine  ligand  48  21  .  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_M4D
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
 M4D  N2   N  NH2   0  -0.801  -4.6108   4.6049  -0.6431
 M4D  C17  C  CH2   0  -0.273  -4.2194   3.2406  -0.9684
 M4D  C16  C  CH2   0  -0.428  -3.6215   2.5397   0.2416
 M4D  C15  C  CH2   0  -0.419  -3.1804   1.1152  -0.0675
 M4D  C14  C  CH2   0  -0.540  -2.6100   0.3971   1.1578
 M4D  C3   C  CR6   0   0.113  -2.1566  -1.0010   0.8398
 M4D  C5   C  CR16  0  -0.349  -2.9892  -2.0686   1.0893
 M4D  C4   C  CR16  0  -0.247  -2.6128  -3.3801   0.7519
 M4D  C2   C  CR16  0  -0.327  -1.4012  -3.6312   0.1629
 M4D  C1   C  CR66  0   0.050  -0.8969  -1.2485   0.2349
 M4D  C8   C  CR16  0  -0.282   0.0497  -0.2308  -0.0497
 M4D  C7   C  CR6   0   0.041   1.2506  -0.5059  -0.6275
 M4D  C6   C  CR6   0   0.379   1.5182  -1.8815  -0.9502
 M4D  N1   N  NH2   0  -0.838   2.6685  -2.2135  -1.5928
 M4D  N    N  N     0  -0.502   0.6744  -2.8509  -0.6905
 M4D  C    C  CR66  0   0.200  -0.5140  -2.5675  -0.1088
 M4D  C10  C  CH2   0  -0.542   2.2682   0.5717  -0.8621
 M4D  C9   C  CH2   0  -0.416   3.3475   0.6081   0.2244
 M4D  C12  C  CH2   0  -0.409   4.3800   1.7037  -0.0067
 M4D  C11  C  CH2   0  -0.420   5.4597   1.7370   1.0672
 M4D  C13  C  CH3   0  -0.662   6.4771   2.8489   0.8526
 M4D  H1   H  HNH2  0   0.345  -4.9641   5.0626  -1.4738
 M4D  H2   H  HNH2  0   0.337  -5.3881   4.5841   0.0059
 M4D  H4   H  HCH2  0   0.187  -5.0454   2.6279  -1.3588
 M4D  H5   H  HCH2  0   0.212  -3.4695   3.2827  -1.7633
 M4D  H6   H  HCH2  0   0.215  -2.7691   3.1205   0.6084
 M4D  H7   H  HCH2  0   0.214  -4.3592   2.5234   1.0518
 M4D  H8   H  HCH2  0   0.224  -4.0279   0.5391  -0.4521
 M4D  H9   H  HCH2  0   0.224  -2.4324   1.1316  -0.8668
 M4D  H10  H  HCH2  0   0.238  -1.7918   0.9891   1.5771
 M4D  H11  H  HCH2  0   0.251  -3.3784   0.3531   1.9335
 M4D  H12  H  HCR6  0   0.243  -3.9526  -1.8954   1.5542
 M4D  H13  H  HCR6  0   0.251  -3.2901  -4.1983   0.9624
 M4D  H14  H  HCR6  0   0.247  -1.1022  -4.6382  -0.0989
 M4D  H15  H  HCR6  0   0.249  -0.1782   0.7992   0.1984
 M4D  H16  H  HNH2  0   0.400   3.4517  -1.5850  -1.5898
 M4D  H17  H  HNH2  0   0.387   2.9063  -3.1905  -1.6292
 M4D  H18  H  HCH2  0   0.241   2.7349   0.4596  -1.8464
 M4D  H19  H  HCH2  0   0.256   1.7578   1.5377  -0.8837
 M4D  H20  H  HCH2  0   0.228   2.8643   0.7566   1.1947
 M4D  H21  H  HCH2  0   0.217   3.8555  -0.3598   0.2886
 M4D  H22  H  HCH2  0   0.212   4.8463   1.5651  -0.9882
 M4D  H23  H  HCH2  0   0.212   3.8743   2.6749  -0.0467
 M4D  H24  H  HCH2  0   0.212   4.9896   1.8563   2.0482
 M4D  H25  H  HCH2  0   0.212   5.9727   0.7705   1.0934
 M4D  H26  H  HCH3  0   0.227   7.2343   2.8553   1.6372
 M4D  H27  H  HCH3  0   0.216   6.9923   2.7362  -0.1032
 M4D  H28  H  HCH3  0   0.216   5.9954   3.8286   0.8501

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
 M4D  N2   C17  single    1.456  0.020  1.456
 M4D  C4   C5   aromatic  1.406  0.020  1.406
 M4D  C4   C2   aromatic  1.370  0.020  1.370
 M4D  C5   C3   aromatic  1.377  0.020  1.377
 M4D  C17  C16  single    1.521  0.020  1.521
 M4D  C2   C    aromatic  1.412  0.020  1.412
 M4D  C16  C15  single    1.523  0.020  1.523
 M4D  C3   C14  single    1.504  0.020  1.504
 M4D  C3   C1   aromatic  1.419  0.020  1.419
 M4D  C14  C15  single    1.531  0.020  1.531
 M4D  C    C1   aromatic  1.416  0.020  1.416
 M4D  C    N    aromatic  1.353  0.020  1.353
 M4D  C1   C8   aromatic  1.419  0.020  1.419
 M4D  N    C6   aromatic  1.311  0.020  1.311
 M4D  C8   C7   aromatic  1.361  0.020  1.361
 M4D  C6   C7   aromatic  1.438  0.020  1.438
 M4D  C6   N1   single    1.359  0.020  1.359
 M4D  C7   C10  single    1.501  0.020  1.501
 M4D  C10  C9   single    1.532  0.020  1.532
 M4D  C12  C9   single    1.523  0.020  1.523
 M4D  C12  C11  single    1.523  0.020  1.523
 M4D  C13  C11  single    1.522  0.020  1.522
 M4D  N2   H1   single    0.890  0.020  1.040
 M4D  N2   H2   single    0.890  0.020  1.040
 M4D  C17  H4   single    0.970  0.020  1.090
 M4D  C17  H5   single    0.970  0.020  1.090
 M4D  C16  H6   single    0.970  0.020  1.090
 M4D  C16  H7   single    0.970  0.020  1.090
 M4D  C15  H8   single    0.970  0.020  1.090
 M4D  C15  H9   single    0.970  0.020  1.090
 M4D  C14  H10  single    0.970  0.020  1.090
 M4D  C14  H11  single    0.970  0.020  1.090
 M4D  C5   H12  single    0.930  0.020  1.080
 M4D  C4   H13  single    0.930  0.020  1.080
 M4D  C2   H14  single    0.930  0.020  1.080
 M4D  C8   H15  single    0.930  0.020  1.080
 M4D  N1   H16  single    0.890  0.020  1.040
 M4D  N1   H17  single    0.890  0.020  1.040
 M4D  C10  H18  single    0.970  0.020  1.090
 M4D  C10  H19  single    0.970  0.020  1.090
 M4D  C9   H20  single    0.970  0.020  1.090
 M4D  C9   H21  single    0.970  0.020  1.090
 M4D  C12  H22  single    0.970  0.020  1.090
 M4D  C12  H23  single    0.970  0.020  1.090
 M4D  C11  H24  single    0.970  0.020  1.090
 M4D  C11  H25  single    0.970  0.020  1.090
 M4D  C13  H26  single    0.970  0.020  1.090
 M4D  C13  H27  single    0.970  0.020  1.090
 M4D  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
 M4D  H2   N2   H1   105.51  3.000
 M4D  H2   N2   C17  109.28  3.000
 M4D  H1   N2   C17  109.52  3.000
 M4D  H5   C17  H4   106.16  3.000
 M4D  H5   C17  C16  109.05  3.000
 M4D  H4   C17  C16  108.72  3.000
 M4D  H5   C17  N2   108.09  3.000
 M4D  H4   C17  N2   113.53  3.000
 M4D  C16  C17  N2   111.09  3.000
 M4D  H7   C16  H6   106.52  3.000
 M4D  H7   C16  C15  109.34  3.000
 M4D  H6   C16  C15  109.80  3.000
 M4D  H7   C16  C17  109.29  3.000
 M4D  H6   C16  C17  109.16  3.000
 M4D  C15  C16  C17  112.55  3.000
 M4D  H9   C15  H8   106.28  3.000
 M4D  H9   C15  C14  109.69  3.000
 M4D  H8   C15  C14  108.84  3.000
 M4D  H9   C15  C16  109.39  3.000
 M4D  H8   C15  C16  109.84  3.000
 M4D  C14  C15  C16  112.60  3.000
 M4D  H11  C14  H10  106.01  3.000
 M4D  H11  C14  C3   108.95  3.000
 M4D  H10  C14  C3   111.03  3.000
 M4D  H11  C14  C15  108.97  3.000
 M4D  H10  C14  C15  109.38  3.000
 M4D  C3   C14  C15  112.29  3.000
 M4D  C1   C3   C5   118.61  3.000
 M4D  C1   C3   C14  121.32  3.000
 M4D  C5   C3   C14  120.02  3.000
 M4D  H12  C5   C4   119.35  3.000
 M4D  H12  C5   C3   119.44  3.000
 M4D  C4   C5   C3   121.21  3.000
 M4D  H13  C4   C2   119.88  3.000
 M4D  H13  C4   C5   119.40  3.000
 M4D  C2   C4   C5   120.72  3.000
 M4D  H14  C2   C    118.73  3.000
 M4D  H14  C2   C4   121.24  3.000
 M4D  C    C2   C4   120.03  3.000
 M4D  C    C1   C8   116.05  3.000
 M4D  C8   C1   C3   123.55  3.000
 M4D  C    C1   C3   120.40  3.000
 M4D  H15  C8   C7   118.36  3.000
 M4D  H15  C8   C1   119.71  3.000
 M4D  C7   C8   C1   121.93  3.000
 M4D  C10  C7   C6   121.71  3.000
 M4D  C10  C7   C8   121.31  3.000
 M4D  C6   C7   C8   116.93  3.000
 M4D  N    C6   N1   117.25  3.000
 M4D  N1   C6   C7   119.83  3.000
 M4D  N    C6   C7   122.89  3.000
 M4D  H17  N1   H16  115.06  3.000
 M4D  H17  N1   C6   117.03  3.000
 M4D  H16  N1   C6   120.39  3.000
 M4D  C    N    C6   119.71  3.000
 M4D  N    C    C1   122.48  3.000
 M4D  N    C    C2   118.49  3.000
 M4D  C1   C    C2   119.03  3.000
 M4D  H19  C10  H18  105.77  3.000
 M4D  H19  C10  C9   108.79  3.000
 M4D  H18  C10  C9   109.86  3.000
 M4D  H19  C10  C7   108.74  3.000
 M4D  H18  C10  C7   110.85  3.000
 M4D  C9   C10  C7   112.58  3.000
 M4D  H21  C9   H20  105.83  3.000
 M4D  H21  C9   C12  109.28  3.000
 M4D  H20  C9   C12  109.65  3.000
 M4D  H21  C9   C10  110.33  3.000
 M4D  H20  C9   C10  108.73  3.000
 M4D  C12  C9   C10  112.78  3.000
 M4D  H23  C12  H22  106.02  3.000
 M4D  H23  C12  C11  109.48  3.000
 M4D  H22  C12  C11  109.43  3.000
 M4D  H23  C12  C9   109.29  3.000
 M4D  H22  C12  C9   109.48  3.000
 M4D  C11  C12  C9   112.91  3.000
 M4D  H25  C11  H24  106.03  3.000
 M4D  H25  C11  C13  109.58  3.000
 M4D  H24  C11  C13  109.51  3.000
 M4D  H25  C11  C12  109.26  3.000
 M4D  H24  C11  C12  109.26  3.000
 M4D  C13  C11  C12  112.97  3.000
 M4D  H28  C13  H27  107.39  3.000
 M4D  H28  C13  H26  107.63  3.000
 M4D  H27  C13  H26  107.63  3.000
 M4D  H28  C13  C11  111.16  3.000
 M4D  H27  C13  C11  111.31  3.000
 M4D  H26  C13  C11  111.52  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
 M4D  CONST_01  C2   C4   C5   C3      0.00   0.0  0
 M4D  CONST_02  C2   C    C1   C3      0.00   0.0  0
 M4D  CONST_03  N    C    C1   C3    180.00   0.0  0
 M4D  CONST_04  C7   C8   C1   C3    180.00   0.0  0
 M4D  CONST_05  C    C2   C4   C5      0.00   0.0  0
 M4D  CONST_06  C    C1   C3   C5      0.00   0.0  0
 M4D  CONST_07  C8   C1   C3   C5    180.00   0.0  0
 M4D  CONST_08  C1   C3   C5   C4      0.00   0.0  0
 M4D  CONST_09  C1   C    C2   C4      0.00   0.0  0
 M4D  CONST_10  N    C    C2   C4    180.00   0.0  0
 M4D  CONST_11  C8   C1   C    C2    180.00   0.0  0
 M4D  CONST_12  C6   N    C    C2    180.00   0.0  0
 M4D  CONST_13  C6   N    C    C1      0.00   0.0  0
 M4D  CONST_14  C6   C7   C8   C1      0.00   0.0  0
 M4D  CONST_15  N    C    C1   C8      0.00   0.0  0
 M4D  CONST_16  N    C6   C7   C8      0.00   0.0  0
 M4D  CONST_17  C    C1   C8   C7      0.00   0.0  0
 M4D  CONST_18  C    N    C6   C7      0.00   0.0  0
 M4D  CONST_19  C4   C5   C3   C14   180.00   0.0  0
 M4D  CONST_20  C    C1   C3   C14   180.00   0.0  0
 M4D  CONST_21  C8   C1   C3   C14     0.00   0.0  0
 M4D  CONST_22  C10  C7   C8   C1    180.00   0.0  0
 M4D  CONST_23  N1   C6   C7   C8    180.00   0.0  0
 M4D  CONST_24  C    N    C6   N1    180.00   0.0  0
 M4D  CONST_25  C10  C7   C6   N     180.00   0.0  0
 M4D  CONST_26  H13  C4   C5   C3    180.00   0.0  0
 M4D  CONST_27  H15  C8   C1   C3      0.00   0.0  0
 M4D  CONST_28  H14  C2   C4   C5    180.00   0.0  0
 M4D  CONST_29  H12  C5   C4   C2    180.00   0.0  0
 M4D  CONST_31  H17  N1   C6   C7    180.00   0.0  0
 M4D  Var_01    C5   C3   C14  C15   -96.72  30.0  2
 M4D  Var_02    C9   C10  C7   C8     98.47  30.0  2
 M4D  Var_03    C3   C14  C15  C16  -179.09  30.0  2
 M4D  Var_04    C12  C9   C10  C7   -179.79  30.0  3
 M4D  Var_05    C15  C16  C17  N2   -179.13  30.0  3
 M4D  Var_06    C14  C15  C16  C17  -178.59  30.0  3
 M4D  Var_07    C11  C12  C9   C10  -179.63  30.0  1
 M4D  Var_08    C13  C11  C12  C9   -178.87  30.0  3
 M4D  Var_09    H1   N2   C17  C16   177.33  30.0  3
 M4D  Var_10    H26  C13  C11  C12   179.62  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
 M4D  plan-1  C14  0.020
 M4D  plan-1  C3   0.020
 M4D  plan-1  C5   0.020
 M4D  plan-1  C4   0.020
 M4D  plan-1  C2   0.020
 M4D  plan-1  C1   0.020
 M4D  plan-1  C8   0.020
 M4D  plan-1  C7   0.020
 M4D  plan-1  C6   0.020
 M4D  plan-1  N1   0.020
 M4D  plan-1  N    0.020
 M4D  plan-1  C    0.020
 M4D  plan-1  C10  0.020
 M4D  plan-1  H12  0.020
 M4D  plan-1  H13  0.020
 M4D  plan-1  H14  0.020
 M4D  plan-1  H15  0.020
 M4D  plan-2  C6   0.020
 M4D  plan-2  N1   0.020
 M4D  plan-2  H16  0.020
 M4D  plan-2  H17  0.020

