# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 16:34:00 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (6-aminohexyl)carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCCNC(O)=O
#
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
 CMY  CMY  '(6-aminohexyl)carbamic acid'  ligand  26  11  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CMY
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
 CMY  O1Y   O  OC    -1  -0.665   0.9725   2.4301  -4.9316
 CMY  C1Y   C  C      0   0.502   1.7011   2.5993  -3.9280
 CMY  N1Y   N  NH1    0  -0.655   2.6246   1.5758  -3.6606
 CMY  C2Y   C  CH2    0  -0.280   3.2784   1.4576  -2.3810
 CMY  C3Y   C  CH2    0  -0.423   2.3770   1.0406  -1.2191
 CMY  C4Y   C  CH2    0  -0.413   1.7447  -0.3339  -1.3965
 CMY  C5Y   C  CH2    0  -0.413   0.8544  -0.7358  -0.2269
 CMY  C6Y   C  CH2    0  -0.424   0.2252  -2.1127  -0.3972
 CMY  C7Y   C  CH2    0  -0.270  -0.6710  -2.5007   0.7683
 CMY  N2Y   N  NH2    0  -0.801  -1.2364  -3.8297   0.5765
 CMY  O1    O  O      0  -0.649   1.7160   3.5942  -3.1715
 CMY  H1    H  HNH1   0   0.344   2.4231   0.7049  -4.1250
 CMY  H2Y1  H  HCH2   0   0.216   3.7543   2.4097  -2.1410
 CMY  H2Y2  H  HCH2   0   0.208   4.0873   0.7276  -2.4835
 CMY  H3Y1  H  HCH2   0   0.210   1.5962   1.7953  -1.0899
 CMY  H3Y2  H  HCH2   0   0.203   2.9715   1.0470  -0.2988
 CMY  H4Y1  H  HCH2   0   0.203   2.5330  -1.0847  -1.5250
 CMY  H4Y2  H  HCH2   0   0.205   1.1516  -0.3510  -2.3170
 CMY  H5Y1  H  HCH2   0   0.206   1.4406  -0.7171   0.6987
 CMY  H5Y2  H  HCH2   0   0.207   0.0658   0.0143  -0.1025
 CMY  H6Y1  H  HCH2   0   0.210   1.0092  -2.8680  -0.5112
 CMY  H6Y2  H  HCH2   0   0.208  -0.3599  -2.1306  -1.3242
 CMY  H7Y1  H  HCH2   0   0.185  -1.4314  -1.7176   0.9058
 CMY  H7Y2  H  HCH2   0   0.208  -0.0764  -2.5126   1.6864
 CMY  H11   H  HNH2   0   0.336  -1.8523  -3.8139  -0.2276
 CMY  H12   H  HNH2   0   0.344  -1.8295  -4.0592   1.3640

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
 CMY  O1Y  C1Y   deloc   1.252  0.020  1.252
 CMY  C1Y  N1Y   single  1.404  0.020  1.404
 CMY  C1Y  O1    deloc   1.250  0.020  1.250
 CMY  N1Y  C2Y   single  1.442  0.020  1.442
 CMY  N1Y  H1    single  0.890  0.020  1.040
 CMY  C2Y  C3Y   single  1.529  0.020  1.529
 CMY  C2Y  H2Y1  single  0.970  0.020  1.090
 CMY  C2Y  H2Y2  single  0.970  0.020  1.090
 CMY  C3Y  C4Y   single  1.523  0.020  1.523
 CMY  C3Y  H3Y1  single  0.970  0.020  1.090
 CMY  C3Y  H3Y2  single  0.970  0.020  1.090
 CMY  C4Y  C5Y   single  1.524  0.020  1.524
 CMY  C4Y  H4Y1  single  0.970  0.020  1.090
 CMY  C4Y  H4Y2  single  0.970  0.020  1.090
 CMY  C5Y  C6Y   single  1.523  0.020  1.523
 CMY  C5Y  H5Y1  single  0.970  0.020  1.090
 CMY  C5Y  H5Y2  single  0.970  0.020  1.090
 CMY  C6Y  C7Y   single  1.521  0.020  1.521
 CMY  C6Y  H6Y1  single  0.970  0.020  1.090
 CMY  C6Y  H6Y2  single  0.970  0.020  1.090
 CMY  C7Y  N2Y   single  1.457  0.020  1.457
 CMY  C7Y  H7Y1  single  0.970  0.020  1.090
 CMY  C7Y  H7Y2  single  0.970  0.020  1.090
 CMY  N2Y  H11   single  0.890  0.020  1.040
 CMY  N2Y  H12   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
 CMY  O1    C1Y  N1Y   117.19  3.000
 CMY  O1    C1Y  O1Y   126.86  3.000
 CMY  N1Y   C1Y  O1Y   115.91  3.000
 CMY  H1    N1Y  C2Y   115.40  3.000
 CMY  H1    N1Y  C1Y   114.26  3.000
 CMY  C2Y   N1Y  C1Y   121.80  3.000
 CMY  H2Y2  C2Y  H2Y1  106.28  3.000
 CMY  H2Y2  C2Y  C3Y   108.97  3.000
 CMY  H2Y1  C2Y  C3Y   109.15  3.000
 CMY  H2Y2  C2Y  N1Y   107.86  3.000
 CMY  H2Y1  C2Y  N1Y   108.75  3.000
 CMY  C3Y   C2Y  N1Y   115.44  3.000
 CMY  H3Y2  C3Y  H3Y1  106.51  3.000
 CMY  H3Y2  C3Y  C4Y   109.17  3.000
 CMY  H3Y1  C3Y  C4Y   109.88  3.000
 CMY  H3Y2  C3Y  C2Y   108.47  3.000
 CMY  H3Y1  C3Y  C2Y   108.82  3.000
 CMY  C4Y   C3Y  C2Y   113.73  3.000
 CMY  H4Y2  C4Y  H4Y1  106.27  3.000
 CMY  H4Y2  C4Y  C5Y   108.94  3.000
 CMY  H4Y1  C4Y  C5Y   109.24  3.000
 CMY  H4Y2  C4Y  C3Y   109.68  3.000
 CMY  H4Y1  C4Y  C3Y   109.46  3.000
 CMY  C5Y   C4Y  C3Y   113.02  3.000
 CMY  H5Y2  C5Y  H5Y1  106.11  3.000
 CMY  H5Y2  C5Y  C6Y   109.53  3.000
 CMY  H5Y1  C5Y  C6Y   109.32  3.000
 CMY  H5Y2  C5Y  C4Y   109.10  3.000
 CMY  H5Y1  C5Y  C4Y   109.35  3.000
 CMY  C6Y   C5Y  C4Y   113.20  3.000
 CMY  H6Y2  C6Y  H6Y1  106.44  3.000
 CMY  H6Y2  C6Y  C7Y   109.23  3.000
 CMY  H6Y1  C6Y  C7Y   109.02  3.000
 CMY  H6Y2  C6Y  C5Y   109.25  3.000
 CMY  H6Y1  C6Y  C5Y   109.84  3.000
 CMY  C7Y   C6Y  C5Y   112.85  3.000
 CMY  H7Y2  C7Y  H7Y1  106.17  3.000
 CMY  H7Y2  C7Y  N2Y   108.15  3.000
 CMY  H7Y1  C7Y  N2Y   113.43  3.000
 CMY  H7Y2  C7Y  C6Y   109.01  3.000
 CMY  H7Y1  C7Y  C6Y   108.75  3.000
 CMY  N2Y   C7Y  C6Y   111.13  3.000
 CMY  H12   N2Y  H11   105.36  3.000
 CMY  H12   N2Y  C7Y   109.38  3.000
 CMY  H11   N2Y  C7Y   109.04  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
 CMY  Var_01  C2Y  N1Y  C1Y  O1Y  -163.83  30.0  2
 CMY  Var_02  C3Y  C2Y  N1Y  C1Y    69.35  30.0  3
 CMY  Var_03  C4Y  C3Y  C2Y  N1Y    61.82  30.0  3
 CMY  Var_04  C5Y  C4Y  C3Y  C2Y   179.76  30.0  3
 CMY  Var_05  C6Y  C5Y  C4Y  C3Y  -179.73  30.0  3
 CMY  Var_06  C7Y  C6Y  C5Y  C4Y  -179.50  30.0  3
 CMY  Var_07  N2Y  C7Y  C6Y  C5Y  -179.15  30.0  3
 CMY  Var_08  H11  N2Y  C7Y  C6Y   -65.07  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
 CMY  plan-1  O1Y  0.020
 CMY  plan-1  C1Y  0.020
 CMY  plan-1  N1Y  0.020
 CMY  plan-1  O1   0.020

