# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:18:34 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-(methylamino)-~{N}-[[4-[[2-(methylamino)ethanoylamino]methyl]phenyl]methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC(=O)NCc1ccc(CNC(=O)CNC)cc1
#
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
 M9E  M9E  2-(methylamino)-~{N}-[[4-[[2-(methylamino)ethanoylamino]methyl]phenyl]methyl]ethanamide  ligand  42  20  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M9E
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
 M9E  O1   O  O     0  -0.501   5.0921  -1.7633  -0.1279
 M9E  C1   C  C     0   0.537   4.7286  -0.5953  -0.1084
 M9E  N1   N  NH1   0  -0.632   3.5957  -0.1884   0.4823
 M9E  C2   C  CH2   0  -0.325   2.6761  -1.0890   1.1471
 M9E  C3   C  CR6   0   0.059   1.2844  -0.5184   1.1560
 M9E  C4   C  CR16  0  -0.268   0.6179  -0.2569  -0.0418
 M9E  C5   C  CR16  0  -0.268  -0.6640   0.2640  -0.0375
 M9E  C6   C  CR6   0   0.061  -1.3173   0.5384   1.1647
 M9E  C7   C  CH2   0  -0.326  -2.7101   1.1071   1.1659
 M9E  N2   N  NH1   0  -0.632  -3.6329   0.2079   0.5045
 M9E  C8   C  C     0   0.537  -4.7568   0.6157  -0.1033
 M9E  C9   C  CH2   0  -0.382  -5.5500  -0.4785  -0.7923
 M9E  N3   N  NH1   0  -0.593  -6.9670  -0.2269  -0.6808
 M9E  C10  C  CH3   0  -0.517  -7.7518  -1.1618  -1.4593
 M9E  O2   O  O     0  -0.501  -5.1092   1.7864  -0.1471
 M9E  C11  C  CR16  0  -0.291  -0.6549   0.2757   2.3553
 M9E  C12  C  CR16  0  -0.290   0.6357  -0.2422   2.3511
 M9E  C13  C  CH2   0  -0.382   5.5174   0.4930  -0.8115
 M9E  N4   N  NH1   0  -0.593   6.9357   0.2556  -0.6858
 M9E  C14  C  CH3   0  -0.517   7.7179   1.1836  -1.4751
 M9E  H1   H  HNH1  0   0.404   3.4097   0.7996   0.5460
 M9E  H2   H  HCH2  0   0.263   2.6846  -2.0426   0.6169
 M9E  H3   H  HCH2  0   0.256   3.0021  -1.2919   2.1712
 M9E  H4   H  HCR6  0   0.255   1.1059  -0.4632  -0.9870
 M9E  H5   H  HCR6  0   0.254  -1.1626   0.4594  -0.9796
 M9E  H6   H  HCH2  0   0.257  -3.0296   1.3047   2.1930
 M9E  H7   H  HCH2  0   0.263  -2.7245   2.0628   0.6399
 M9E  H8   H  HNH1  0   0.404  -3.4582  -0.7811   0.5854
 M9E  H9   H  HCH2  0   0.233  -5.1944  -0.5221  -1.8371
 M9E  H10  H  HCH2  0   0.245  -5.3197  -1.4546  -0.3566
 M9E  H11  H  HNH1  0   0.347  -7.1571   0.7147  -0.9980
 M9E  H13  H  HCH3  0   0.234  -8.8066  -0.8953  -1.3978
 M9E  H14  H  HCH3  0   0.195  -7.4742  -1.2043  -2.5220
 M9E  H15  H  HCH3  0   0.223  -7.6453  -2.1700  -1.0541
 M9E  H16  H  HCR6  0   0.256  -1.1453   0.4783   3.2998
 M9E  H17  H  HCR6  0   0.256   1.1359  -0.4360   3.2923
 M9E  H18  H  HCH2  0   0.233   5.1689   0.5135  -1.8594
 M9E  H19  H  HCH2  0   0.246   5.2750   1.4752  -0.3967
 M9E  H20  H  HNH1  0   0.347   7.1347  -0.6895  -0.9869
 M9E  H22  H  HCH3  0   0.234   8.7748   0.9295  -1.3991
 M9E  H23  H  HCH3  0   0.195   7.4498   1.2033  -2.5409
 M9E  H24  H  HCH3  0   0.223   7.5974   2.1982  -1.0904

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
 M9E  C10  N3   single    1.448  0.020  1.448
 M9E  C9   N3   single    1.443  0.020  1.443
 M9E  C9   C8   single    1.517  0.020  1.517
 M9E  C8   O2   double    1.223  0.020  1.223
 M9E  C8   N2   single    1.341  0.020  1.341
 M9E  N2   C7   single    1.448  0.020  1.448
 M9E  C11  C12  aromatic  1.391  0.020  1.391
 M9E  C11  C6   aromatic  1.388  0.020  1.388
 M9E  C12  C3   aromatic  1.388  0.020  1.388
 M9E  C7   C6   single    1.504  0.020  1.504
 M9E  C6   C5   aromatic  1.395  0.020  1.395
 M9E  C3   C2   single    1.504  0.020  1.504
 M9E  C3   C4   aromatic  1.396  0.020  1.396
 M9E  C2   N1   single    1.449  0.020  1.449
 M9E  C5   C4   aromatic  1.384  0.020  1.384
 M9E  O1   C1   double    1.223  0.020  1.223
 M9E  N1   C1   single    1.341  0.020  1.341
 M9E  C1   C13  single    1.517  0.020  1.517
 M9E  C14  N4   single    1.448  0.020  1.448
 M9E  C13  N4   single    1.444  0.020  1.444
 M9E  N1   H1   single    0.860  0.020  1.020
 M9E  C2   H2   single    0.970  0.020  1.090
 M9E  C2   H3   single    0.970  0.020  1.090
 M9E  C4   H4   single    0.930  0.020  1.080
 M9E  C5   H5   single    0.930  0.020  1.080
 M9E  C7   H6   single    0.970  0.020  1.090
 M9E  C7   H7   single    0.970  0.020  1.090
 M9E  N2   H8   single    0.860  0.020  1.020
 M9E  C9   H9   single    0.970  0.020  1.090
 M9E  C9   H10  single    0.970  0.020  1.090
 M9E  N3   H11  single    0.890  0.020  1.040
 M9E  C10  H13  single    0.970  0.020  1.090
 M9E  C10  H14  single    0.970  0.020  1.090
 M9E  C10  H15  single    0.970  0.020  1.090
 M9E  C11  H16  single    0.930  0.020  1.080
 M9E  C12  H17  single    0.930  0.020  1.080
 M9E  C13  H18  single    0.970  0.020  1.090
 M9E  C13  H19  single    0.970  0.020  1.090
 M9E  N4   H20  single    0.890  0.020  1.040
 M9E  C14  H22  single    0.970  0.020  1.090
 M9E  C14  H23  single    0.970  0.020  1.090
 M9E  C14  H24  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
 M9E  C13  C1   N1   115.21  3.000
 M9E  C13  C1   O1   121.54  3.000
 M9E  N1   C1   O1   123.21  3.000
 M9E  H1   N1   C2   117.62  3.000
 M9E  H1   N1   C1   118.77  3.000
 M9E  C2   N1   C1   123.36  3.000
 M9E  H3   C2   H2   106.89  3.000
 M9E  H3   C2   C3   109.91  3.000
 M9E  H2   C2   C3   109.98  3.000
 M9E  H3   C2   N1   110.84  3.000
 M9E  H2   C2   N1   108.38  3.000
 M9E  C3   C2   N1   110.74  3.000
 M9E  C12  C3   C4   118.60  3.000
 M9E  C4   C3   C2   120.53  3.000
 M9E  C12  C3   C2   120.88  3.000
 M9E  H4   C4   C5   119.44  3.000
 M9E  H4   C4   C3   119.87  3.000
 M9E  C5   C4   C3   120.69  3.000
 M9E  H5   C5   C6   119.87  3.000
 M9E  H5   C5   C4   119.44  3.000
 M9E  C6   C5   C4   120.69  3.000
 M9E  C11  C6   C7   120.85  3.000
 M9E  C7   C6   C5   120.56  3.000
 M9E  C11  C6   C5   118.59  3.000
 M9E  H7   C7   H6   106.90  3.000
 M9E  H7   C7   N2   108.38  3.000
 M9E  H6   C7   N2   110.79  3.000
 M9E  H7   C7   C6   110.06  3.000
 M9E  H6   C7   C6   109.85  3.000
 M9E  N2   C7   C6   110.78  3.000
 M9E  H8   N2   C8   118.69  3.000
 M9E  H8   N2   C7   117.54  3.000
 M9E  C8   N2   C7   123.51  3.000
 M9E  O2   C8   C9   121.56  3.000
 M9E  O2   C8   N2   123.27  3.000
 M9E  C9   C8   N2   115.13  3.000
 M9E  H10  C9   H9   105.90  3.000
 M9E  H10  C9   N3   109.36  3.000
 M9E  H9   C9   N3   113.33  3.000
 M9E  H10  C9   C8   110.66  3.000
 M9E  H9   C9   C8   106.84  3.000
 M9E  N3   C9   C8   110.64  3.000
 M9E  H11  N3   C10  109.30  3.000
 M9E  H11  N3   C9   108.82  3.000
 M9E  C10  N3   C9   112.22  3.000
 M9E  H15  C10  H14  107.36  3.000
 M9E  H15  C10  H13  107.42  3.000
 M9E  H14  C10  H13  107.97  3.000
 M9E  H15  C10  N3   110.11  3.000
 M9E  H14  C10  N3   114.08  3.000
 M9E  H13  C10  N3   109.67  3.000
 M9E  H16  C11  C12  119.50  3.000
 M9E  H16  C11  C6   119.77  3.000
 M9E  C12  C11  C6   120.73  3.000
 M9E  H17  C12  C11  119.51  3.000
 M9E  H17  C12  C3   119.79  3.000
 M9E  C11  C12  C3   120.70  3.000
 M9E  H19  C13  H18  105.86  3.000
 M9E  H19  C13  N4   109.42  3.000
 M9E  H18  C13  N4   113.30  3.000
 M9E  H19  C13  C1   110.70  3.000
 M9E  H18  C13  C1   106.80  3.000
 M9E  N4   C13  C1   110.65  3.000
 M9E  H20  N4   C14  109.28  3.000
 M9E  H20  N4   C13  108.72  3.000
 M9E  C14  N4   C13  112.21  3.000
 M9E  H24  C14  H23  107.35  3.000
 M9E  H24  C14  H22  107.41  3.000
 M9E  H23  C14  H22  107.96  3.000
 M9E  H24  C14  N4   110.12  3.000
 M9E  H23  C14  N4   114.10  3.000
 M9E  H22  C14  N4   109.66  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
 M9E  CONST_01  C6   C11  C12  C3      0.00   0.0  0
 M9E  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 M9E  CONST_03  C11  C12  C3   C4      0.00   0.0  0
 M9E  CONST_04  C11  C6   C5   C4      0.00   0.0  0
 M9E  CONST_05  C12  C11  C6   C5      0.00   0.0  0
 M9E  CONST_06  C12  C3   C4   C5      0.00   0.0  0
 M9E  CONST_07  C11  C12  C3   C2    180.00   0.0  0
 M9E  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 M9E  CONST_09  C7   C6   C5   C4    180.00   0.0  0
 M9E  CONST_10  C12  C11  C6   C7    180.00   0.0  0
 M9E  CONST_11  H16  C11  C12  C3    180.00   0.0  0
 M9E  CONST_12  H5   C5   C4   C3    180.00   0.0  0
 M9E  CONST_13  H17  C12  C3   C4    180.00   0.0  0
 M9E  CONST_14  H4   C4   C5   C6    180.00   0.0  0
 M9E  CONST_15  C2   N1   C1   O1      0.00   0.0  0
 M9E  CONST_16  C13  C1   N1   C2    180.00   0.0  0
 M9E  CONST_17  C9   C8   N2   C7    180.00   0.0  0
 M9E  CONST_18  O2   C8   N2   C7      0.00   0.0  0
 M9E  CONST_19  H1   N1   C1   O1    180.00   0.0  0
 M9E  CONST_20  H8   N2   C8   C9      0.00   0.0  0
 M9E  Var_01    C12  C3   C2   N1   -118.79  30.0  2
 M9E  Var_02    N2   C7   C6   C5     60.41  30.0  3
 M9E  Var_03    C3   C2   N1   C1   -154.44  30.0  1
 M9E  Var_04    C8   N2   C7   C6   -152.98  30.0  1
 M9E  Var_05    N4   C13  C1   O1    -37.59  30.0  3
 M9E  Var_06    C14  N4   C13  C1    173.20  30.0  3
 M9E  Var_07    N3   C9   C8   N2    144.64  30.0  1
 M9E  Var_08    C10  N3   C9   C8    173.17  30.0  3
 M9E  Var_09    H13  C10  N3   C9   -176.34  30.0  3
 M9E  Var_10    H22  C14  N4   C13  -176.52  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
 M9E  plan-1  C2   0.020
 M9E  plan-1  C3   0.020
 M9E  plan-1  C4   0.020
 M9E  plan-1  C5   0.020
 M9E  plan-1  C6   0.020
 M9E  plan-1  C7   0.020
 M9E  plan-1  C11  0.020
 M9E  plan-1  C12  0.020
 M9E  plan-1  H4   0.020
 M9E  plan-1  H5   0.020
 M9E  plan-1  H16  0.020
 M9E  plan-1  H17  0.020
 M9E  plan-2  O1   0.020
 M9E  plan-2  C1   0.020
 M9E  plan-2  N1   0.020
 M9E  plan-2  C2   0.020
 M9E  plan-2  C13  0.020
 M9E  plan-2  H1   0.020
 M9E  plan-3  C7   0.020
 M9E  plan-3  N2   0.020
 M9E  plan-3  C8   0.020
 M9E  plan-3  C9   0.020
 M9E  plan-3  O2   0.020
 M9E  plan-3  H8   0.020

