# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 22:07:27 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  27  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  OH1   0  -0.625   1.2127   2.4401  -5.1195
 CMY  C1Y   C  C     0   0.675   1.8019   2.6035  -3.9268
 CMY  N1Y   N  NH1   0  -0.632   2.5903   1.5632  -3.6192
 CMY  C2Y   C  CH2   0  -0.300   3.2745   1.4595  -2.3473
 CMY  C3Y   C  CH2   0  -0.429   2.3753   1.0313  -1.1927
 CMY  C4Y   C  CH2   0  -0.414   1.7534  -0.3463  -1.3795
 CMY  C5Y   C  CH2   0  -0.415   0.8516  -0.7485  -0.2190
 CMY  C6Y   C  CH2   0  -0.425   0.2260  -2.1255  -0.3982
 CMY  C7Y   C  CH2   0  -0.270  -0.6931  -2.5099   0.7506
 CMY  N2Y   N  NH2   0  -0.801  -1.2535  -3.8401   0.5518
 CMY  O1    O  O     0  -0.523   1.6369   3.5895  -3.2329
 CMY  H1Y   H  HOH1  0   0.480   0.6610   3.2112  -5.3029
 CMY  H1    H  HNH1  0   0.403   2.6152   0.7751  -4.2447
 CMY  H2Y1  H  HCH2  0   0.249   3.7469   2.4157  -2.1178
 CMY  H2Y2  H  HCH2  0   0.248   4.0789   0.7351  -2.4791
 CMY  H3Y1  H  HCH2  0   0.222   1.5901   1.7793  -1.0509
 CMY  H3Y2  H  HCH2  0   0.223   2.9774   1.0403  -0.2789
 CMY  H4Y1  H  HCH2  0   0.210   2.5473  -1.0919  -1.4987
 CMY  H4Y2  H  HCH2  0   0.212   1.1709  -0.3655  -2.3063
 CMY  H5Y1  H  HCH2  0   0.209   1.4274  -0.7292   0.7129
 CMY  H5Y2  H  HCH2  0   0.209   0.0609   0.0008  -0.1039
 CMY  H6Y1  H  HCH2  0   0.211   1.0116  -2.8814  -0.4951
 CMY  H6Y2  H  HCH2  0   0.209  -0.3416  -2.1456  -1.3360
 CMY  H7Y1  H  HCH2  0   0.185  -1.4568  -1.7271   0.8698
 CMY  H7Y2  H  HCH2  0   0.209  -0.1175  -2.5178   1.6807
 CMY  H11   H  HNH2  0   0.336  -1.8558  -3.8269  -0.2626
 CMY  H12   H  HNH2  0   0.344  -1.8599  -4.0680   1.3297

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   single  1.340  0.020  1.340
 CMY  O1Y  H1Y   single  0.850  0.020  0.980
 CMY  C1Y  N1Y   single  1.341  0.020  1.341
 CMY  C1Y  O1    double  1.217  0.020  1.217
 CMY  N1Y  C2Y   single  1.448  0.020  1.448
 CMY  N1Y  H1    single  0.860  0.020  1.020
 CMY  C2Y  C3Y   single  1.525  0.020  1.525
 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  H1Y   O1Y  C1Y   108.84  3.000
 CMY  O1    C1Y  N1Y   125.27  3.000
 CMY  O1    C1Y  O1Y   123.13  3.000
 CMY  N1Y   C1Y  O1Y   111.59  3.000
 CMY  H1    N1Y  C2Y   118.56  3.000
 CMY  H1    N1Y  C1Y   118.65  3.000
 CMY  C2Y   N1Y  C1Y   122.33  3.000
 CMY  H2Y2  C2Y  H2Y1  106.75  3.000
 CMY  H2Y2  C2Y  C3Y   109.88  3.000
 CMY  H2Y1  C2Y  C3Y   110.01  3.000
 CMY  H2Y2  C2Y  N1Y   106.86  3.000
 CMY  H2Y1  C2Y  N1Y   109.06  3.000
 CMY  C3Y   C2Y  N1Y   113.99  3.000
 CMY  H3Y2  C3Y  H3Y1  106.33  3.000
 CMY  H3Y2  C3Y  C4Y   109.54  3.000
 CMY  H3Y1  C3Y  C4Y   109.96  3.000
 CMY  H3Y2  C3Y  C2Y   107.79  3.000
 CMY  H3Y1  C3Y  C2Y   109.24  3.000
 CMY  C4Y   C3Y  C2Y   113.70  3.000
 CMY  H4Y2  C4Y  H4Y1  106.35  3.000
 CMY  H4Y2  C4Y  C5Y   108.98  3.000
 CMY  H4Y1  C4Y  C5Y   109.40  3.000
 CMY  H4Y2  C4Y  C3Y   109.69  3.000
 CMY  H4Y1  C4Y  C3Y   109.45  3.000
 CMY  C5Y   C4Y  C3Y   112.77  3.000
 CMY  H5Y2  C5Y  H5Y1  106.14  3.000
 CMY  H5Y2  C5Y  C6Y   109.53  3.000
 CMY  H5Y1  C5Y  C6Y   109.38  3.000
 CMY  H5Y2  C5Y  C4Y   109.07  3.000
 CMY  H5Y1  C5Y  C4Y   109.40  3.000
 CMY  C6Y   C5Y  C4Y   113.09  3.000
 CMY  H6Y2  C6Y  H6Y1  106.45  3.000
 CMY  H6Y2  C6Y  C7Y   109.19  3.000
 CMY  H6Y1  C6Y  C7Y   109.03  3.000
 CMY  H6Y2  C6Y  C5Y   109.26  3.000
 CMY  H6Y1  C6Y  C5Y   109.88  3.000
 CMY  C7Y   C6Y  C5Y   112.83  3.000
 CMY  H7Y2  C7Y  H7Y1  106.16  3.000
 CMY  H7Y2  C7Y  N2Y   108.17  3.000
 CMY  H7Y1  C7Y  N2Y   113.41  3.000
 CMY  H7Y2  C7Y  C6Y   109.04  3.000
 CMY  H7Y1  C7Y  C6Y   108.76  3.000
 CMY  N2Y   C7Y  C6Y   111.11  3.000
 CMY  H12   N2Y  H11   105.35  3.000
 CMY  H12   N2Y  C7Y   109.34  3.000
 CMY  H11   N2Y  C7Y   109.05  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  CONST_01  H1Y  O1Y  C1Y  N1Y   180.00   0.0  0
 CMY  Var_01    C2Y  N1Y  C1Y  O1Y  -176.11  30.0  2
 CMY  Var_02    C3Y  C2Y  N1Y  C1Y    77.07  30.0  3
 CMY  Var_03    C4Y  C3Y  C2Y  N1Y    61.49  30.0  3
 CMY  Var_04    C5Y  C4Y  C3Y  C2Y  -179.58  30.0  3
 CMY  Var_05    C6Y  C5Y  C4Y  C3Y  -179.98  30.0  3
 CMY  Var_06    C7Y  C6Y  C5Y  C4Y  -178.92  30.0  3
 CMY  Var_07    N2Y  C7Y  C6Y  C5Y  -179.09  30.0  3
 CMY  Var_08    H11  N2Y  C7Y  C6Y   -65.26  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
 CMY  plan-1  H1Y  0.020

