# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 01:16:58 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-(methylamino)-~{N}-[[3-[[2-(methylamino)ethanoylamino]methyl]phenyl]methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC(=O)NCc1cccc(CNC(=O)CNC)c1
#
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
 M9H  M9H  2-(methylamino)-~{N}-[[3-[[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_M9H
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
 M9H  O1   O  O     0  -0.492  -4.5397   0.7773   1.4423
 M9H  C1   C  C     0   0.529  -4.5655   0.6400   0.2285
 M9H  N1   N  NH1   0  -0.633  -3.5604   1.0080  -0.5858
 M9H  C2   C  CH2   0  -0.335  -2.3512   1.6553  -0.1465
 M9H  C3   C  CR6   0   0.112  -1.1147   0.8020  -0.2996
 M9H  C4   C  CR16  0  -0.369   0.1148   1.4193  -0.5176
 M9H  C5   C  CR6   0   0.139   1.2892   0.6857  -0.6259
 M9H  C6   C  CH2   0  -0.372   2.5985   1.3890  -0.8896
 M9H  N2   N  NH1   0  -0.624   3.6473   0.9994   0.0235
 M9H  C7   C  C     0   0.534   4.6698   0.1891  -0.2963
 M9H  C8   C  CH2   0  -0.385   5.5749  -0.1760   0.8656
 M9H  N3   N  NH1   0  -0.592   6.9147  -0.4568   0.4120
 M9H  C9   C  CH3   0  -0.518   7.7587  -0.9535   1.4779
 M9H  O2   O  O     0  -0.498   4.8530  -0.2612  -1.4182
 M9H  C10  C  CR16  0  -0.312   1.2284  -0.7015  -0.5137
 M9H  C11  C  CR16  0  -0.223   0.0107  -1.3269  -0.2974
 M9H  C12  C  CR16  0  -0.312  -1.1578  -0.5821  -0.1898
 M9H  C13  C  CH2   0  -0.390  -5.7801   0.0818  -0.4898
 M9H  N4   N  NH1   0  -0.591  -6.5649  -0.7565   0.3806
 M9H  C14  C  CH3   0  -0.519  -7.7971  -1.1888  -0.2448
 M9H  H1   H  HNH1  0   0.404  -3.6594   0.8404  -1.5748
 M9H  H2   H  HCH2  0   0.265  -2.2196   2.5876  -0.7005
 M9H  H3   H  HCH2  0   0.270  -2.4793   1.9326   0.9002
 M9H  H4   H  HCR6  0   0.248   0.1575   2.5005  -0.6042
 M9H  H5   H  HCH2  0   0.269   2.9386   1.1800  -1.9040
 M9H  H6   H  HCH2  0   0.269   2.4549   2.4686  -0.8211
 M9H  H7   H  HNH1  0   0.404   3.5661   1.3173   0.9763
 M9H  H8   H  HCH2  0   0.249   5.6039   0.6368   1.5967
 M9H  H9   H  HCH2  0   0.233   5.0985  -1.0281   1.3826
 M9H  H10  H  HNH1  0   0.347   6.8733  -1.1411  -0.3318
 M9H  H12  H  HCH3  0   0.195   7.3680  -1.8495   1.9812
 M9H  H13  H  HCH3  0   0.234   8.7456  -1.1934   1.0834
 M9H  H14  H  HCH3  0   0.223   7.8884  -0.1835   2.2411
 M9H  H15  H  HCR6  0   0.251   2.1270  -1.2995  -0.6048
 M9H  H16  H  HCR6  0   0.255  -0.0323  -2.4054  -0.2154
 M9H  H17  H  HCR6  0   0.249  -2.1005  -1.0889  -0.0245
 M9H  H18  H  HCH2  0   0.236  -6.3396   0.9451  -0.8910
 M9H  H19  H  HCH2  0   0.250  -5.4645  -0.4967  -1.3629
 M9H  H20  H  HNH1  0   0.347  -6.7804  -0.2440   1.2256
 M9H  H22  H  HCH3  0   0.223  -7.5810  -1.8591  -1.0790
 M9H  H23  H  HCH3  0   0.235  -8.3972  -1.7448   0.4749
 M9H  H24  H  HCH3  0   0.195  -8.4141  -0.3675  -0.6368

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
 M9H  O2   C7   double    1.223  0.020  1.223
 M9H  C10  C11  aromatic  1.386  0.020  1.386
 M9H  C10  C5   aromatic  1.393  0.020  1.393
 M9H  N2   C7   single    1.343  0.020  1.343
 M9H  N2   C6   single    1.444  0.020  1.444
 M9H  C11  C12  aromatic  1.390  0.020  1.390
 M9H  C7   C8   single    1.517  0.020  1.517
 M9H  C6   C5   single    1.509  0.020  1.509
 M9H  C5   C4   aromatic  1.389  0.020  1.389
 M9H  C12  C3   aromatic  1.389  0.020  1.389
 M9H  N3   C8   single    1.442  0.020  1.442
 M9H  N3   C9   single    1.448  0.020  1.448
 M9H  C4   C3   aromatic  1.393  0.020  1.393
 M9H  C3   C2   single    1.510  0.020  1.510
 M9H  C2   N1   single    1.440  0.020  1.440
 M9H  C14  N4   single    1.448  0.020  1.448
 M9H  N1   C1   single    1.345  0.020  1.345
 M9H  N4   C13  single    1.441  0.020  1.441
 M9H  C1   C13  single    1.517  0.020  1.517
 M9H  C1   O1   double    1.222  0.020  1.222
 M9H  N1   H1   single    0.860  0.020  1.020
 M9H  C2   H2   single    0.970  0.020  1.090
 M9H  C2   H3   single    0.970  0.020  1.090
 M9H  C4   H4   single    0.930  0.020  1.080
 M9H  C6   H5   single    0.970  0.020  1.090
 M9H  C6   H6   single    0.970  0.020  1.090
 M9H  N2   H7   single    0.860  0.020  1.020
 M9H  C8   H8   single    0.970  0.020  1.090
 M9H  C8   H9   single    0.970  0.020  1.090
 M9H  N3   H10  single    0.890  0.020  1.040
 M9H  C9   H12  single    0.970  0.020  1.090
 M9H  C9   H13  single    0.970  0.020  1.090
 M9H  C9   H14  single    0.970  0.020  1.090
 M9H  C10  H15  single    0.930  0.020  1.080
 M9H  C11  H16  single    0.930  0.020  1.080
 M9H  C12  H17  single    0.930  0.020  1.080
 M9H  C13  H18  single    0.970  0.020  1.090
 M9H  C13  H19  single    0.970  0.020  1.090
 M9H  N4   H20  single    0.890  0.020  1.040
 M9H  C14  H22  single    0.970  0.020  1.090
 M9H  C14  H23  single    0.970  0.020  1.090
 M9H  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
 M9H  C13  C1   N1   114.35  3.000
 M9H  C13  C1   O1   121.90  3.000
 M9H  N1   C1   O1   123.71  3.000
 M9H  H1   N1   C2   117.16  3.000
 M9H  H1   N1   C1   118.37  3.000
 M9H  C2   N1   C1   124.46  3.000
 M9H  H3   C2   H2   106.50  3.000
 M9H  H3   C2   C3   109.70  3.000
 M9H  H2   C2   C3   109.40  3.000
 M9H  H3   C2   N1   107.97  3.000
 M9H  H2   C2   N1   109.27  3.000
 M9H  C3   C2   N1   113.74  3.000
 M9H  C12  C3   C4   118.78  3.000
 M9H  C4   C3   C2   119.22  3.000
 M9H  C12  C3   C2   121.98  3.000
 M9H  H4   C4   C5   119.12  3.000
 M9H  H4   C4   C3   119.25  3.000
 M9H  C5   C4   C3   121.63  3.000
 M9H  C10  C5   C6   121.06  3.000
 M9H  C6   C5   C4   120.06  3.000
 M9H  C10  C5   C4   118.87  3.000
 M9H  H6   C6   H5   106.81  3.000
 M9H  H6   C6   N2   108.83  3.000
 M9H  H5   C6   N2   108.07  3.000
 M9H  H6   C6   C5   109.62  3.000
 M9H  H5   C6   C5   110.11  3.000
 M9H  N2   C6   C5   113.19  3.000
 M9H  H7   N2   C7   118.46  3.000
 M9H  H7   N2   C6   117.02  3.000
 M9H  C7   N2   C6   124.41  3.000
 M9H  O2   C7   C8   121.64  3.000
 M9H  C8   C7   N2   114.64  3.000
 M9H  O2   C7   N2   123.68  3.000
 M9H  H9   C8   H8   105.77  3.000
 M9H  H9   C8   N3   113.43  3.000
 M9H  H8   C8   N3   109.29  3.000
 M9H  H9   C8   C7   106.67  3.000
 M9H  H8   C8   C7   110.42  3.000
 M9H  N3   C8   C7   111.11  3.000
 M9H  H10  N3   C9   109.47  3.000
 M9H  H10  N3   C8   108.97  3.000
 M9H  C9   N3   C8   112.14  3.000
 M9H  H14  C9   H13  107.50  3.000
 M9H  H14  C9   H12  107.27  3.000
 M9H  H13  C9   H12  107.95  3.000
 M9H  H14  C9   N3   110.00  3.000
 M9H  H13  C9   N3   109.70  3.000
 M9H  H12  C9   N3   114.17  3.000
 M9H  H15  C10  C11  119.53  3.000
 M9H  H15  C10  C5   120.44  3.000
 M9H  C11  C10  C5   120.02  3.000
 M9H  H16  C11  C12  119.65  3.000
 M9H  H16  C11  C10  119.75  3.000
 M9H  C12  C11  C10  120.59  3.000
 M9H  H17  C12  C11  119.53  3.000
 M9H  H17  C12  C3   120.35  3.000
 M9H  C11  C12  C3   120.11  3.000
 M9H  H19  C13  H18  105.64  3.000
 M9H  H19  C13  N4   109.37  3.000
 M9H  H18  C13  N4   113.48  3.000
 M9H  H19  C13  C1   109.97  3.000
 M9H  H18  C13  C1   106.85  3.000
 M9H  N4   C13  C1   111.35  3.000
 M9H  H20  N4   C14  109.32  3.000
 M9H  H20  N4   C13  109.02  3.000
 M9H  C14  N4   C13  112.11  3.000
 M9H  H24  C14  H23  107.92  3.000
 M9H  H24  C14  H22  107.29  3.000
 M9H  H23  C14  H22  107.48  3.000
 M9H  H24  C14  N4   114.11  3.000
 M9H  H23  C14  N4   109.62  3.000
 M9H  H22  C14  N4   110.17  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
 M9H  CONST_01  C10  C11  C12  C3      0.00   0.0  0
 M9H  CONST_02  C10  C5   C4   C3      0.00   0.0  0
 M9H  CONST_03  C11  C10  C5   C4      0.00   0.0  0
 M9H  CONST_04  C11  C12  C3   C4      0.00   0.0  0
 M9H  CONST_05  C12  C11  C10  C5      0.00   0.0  0
 M9H  CONST_06  C12  C3   C4   C5      0.00   0.0  0
 M9H  CONST_07  C11  C12  C3   C2    180.00   0.0  0
 M9H  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 M9H  CONST_09  C6   C5   C4   C3    180.00   0.0  0
 M9H  CONST_10  C11  C10  C5   C6    180.00   0.0  0
 M9H  CONST_11  H16  C11  C12  C3    180.00   0.0  0
 M9H  CONST_12  H15  C10  C5   C4    180.00   0.0  0
 M9H  CONST_13  H17  C12  C3   C4    180.00   0.0  0
 M9H  CONST_14  H4   C4   C5   C10   180.00   0.0  0
 M9H  CONST_15  C2   N1   C1   O1      0.00   0.0  0
 M9H  CONST_16  C13  C1   N1   C2    180.00   0.0  0
 M9H  CONST_17  O2   C7   N2   C6      0.00   0.0  0
 M9H  CONST_18  C8   C7   N2   C6    180.00   0.0  0
 M9H  CONST_19  H1   N1   C1   O1    180.00   0.0  0
 M9H  CONST_20  H7   N2   C7   C8      0.00   0.0  0
 M9H  Var_01    C12  C3   C2   N1    -31.37  30.0  3
 M9H  Var_02    N2   C6   C5   C4    129.87  30.0  1
 M9H  Var_03    C3   C2   N1   C1    112.67  30.0  1
 M9H  Var_04    C7   N2   C6   C5    105.16  30.0  2
 M9H  Var_05    N4   C13  C1   O1    -25.17  30.0  3
 M9H  Var_06    C14  N4   C13  C1    174.18  30.0  1
 M9H  Var_07    N3   C8   C7   N2   -152.10  30.0  3
 M9H  Var_08    C9   N3   C8   C7   -173.47  30.0  1
 M9H  Var_09    H12  C9   N3   C8     56.22  30.0  3
 M9H  Var_10    H22  C14  N4   C13    66.84  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
 M9H  plan-1  C2   0.020
 M9H  plan-1  C3   0.020
 M9H  plan-1  C4   0.020
 M9H  plan-1  C5   0.020
 M9H  plan-1  C6   0.020
 M9H  plan-1  C10  0.020
 M9H  plan-1  C11  0.020
 M9H  plan-1  C12  0.020
 M9H  plan-1  H4   0.020
 M9H  plan-1  H15  0.020
 M9H  plan-1  H16  0.020
 M9H  plan-1  H17  0.020
 M9H  plan-2  O1   0.020
 M9H  plan-2  C1   0.020
 M9H  plan-2  N1   0.020
 M9H  plan-2  C2   0.020
 M9H  plan-2  C13  0.020
 M9H  plan-2  H1   0.020
 M9H  plan-3  C6   0.020
 M9H  plan-3  N2   0.020
 M9H  plan-3  C7   0.020
 M9H  plan-3  C8   0.020
 M9H  plan-3  O2   0.020
 M9H  plan-3  H7   0.020

