# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 13:06:24 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (3S)-3,7-diaminoheptan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@@H](N)CCCCN
#
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
 CKC  CKC  (3S)-3,7-diaminoheptan-2-one  ligand  26  10  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CKC
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
 CKC  CAK  C  CH3   0  -0.788  -2.8439   1.7396   0.3315
 CKC  CAO  C  C     0   0.384  -2.7249   0.2745   0.0022
 CKC  OAF  O  O     0  -0.401  -3.5852  -0.3051  -0.6226
 CKC  CAR  C  CH1   0  -0.209  -1.4667  -0.4405   0.4808
 CKC  NAC  N  NH2   0  -0.777  -1.4723  -1.8701   0.2756
 CKC  CAL  C  CH2   0  -0.439  -0.2354   0.1987  -0.1748
 CKC  CAH  C  CH2   0  -0.409   1.0833  -0.3404   0.3626
 CKC  CAG  C  CH2   0  -0.429   2.2882   0.3341  -0.2797
 CKC  CAI  C  CH2   0  -0.271   3.6106  -0.1822   0.2654
 CKC  NAM  N  NH2   0  -0.801   4.7365   0.4770  -0.3815
 CKC  H1   H  HCH3  0   0.254  -2.2548   2.0213   1.2035
 CKC  H2   H  HCH3  0   0.273  -2.4782   2.3290  -0.5130
 CKC  H3   H  HCH1  0   0.254  -1.3994  -0.2475   1.5600
 CKC  H4   H  HNH2  0   0.349  -2.2812  -2.2825   0.7231
 CKC  H5   H  HNH2  0   0.339  -1.5707  -2.0731  -0.7124
 CKC  H7   H  HCH2  0   0.228  -0.2862   0.0429  -1.2585
 CKC  H8   H  HCH2  0   0.242  -0.2625   1.2808  -0.0233
 CKC  H9   H  HCH2  0   0.211   1.1153  -0.1927   1.4478
 CKC  H10  H  HCH2  0   0.222   1.1336  -1.4194   0.1999
 CKC  H11  H  HCH2  0   0.213   2.2640   0.1843  -1.3637
 CKC  H12  H  HCH2  0   0.210   2.2291   1.4167  -0.1175
 CKC  H13  H  HCH2  0   0.186   3.6087  -0.0732   1.3603
 CKC  H14  H  HCH2  0   0.210   3.6837  -1.2554   0.0679
 CKC  H15  H  HNH2  0   0.336   4.7365   1.4582  -0.1302
 CKC  H16  H  HNH2  0   0.345   5.6029   0.1037  -0.0156
 CKC  H18  H  HCH3  0   0.269  -3.8855   2.0125   0.4952

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
 CKC  OAF  CAO  double  1.211  0.020  1.211
 CKC  CAK  CAO  single  1.506  0.020  1.506
 CKC  CAO  CAR  single  1.524  0.020  1.524
 CKC  CAI  NAM  single  1.456  0.020  1.456
 CKC  CAI  CAG  single  1.521  0.020  1.521
 CKC  CAH  CAG  single  1.523  0.020  1.523
 CKC  CAH  CAL  single  1.523  0.020  1.523
 CKC  CAR  CAL  single  1.534  0.020  1.534
 CKC  CAR  NAC  single  1.444  0.020  1.444
 CKC  CAK  H1   single  0.970  0.020  1.090
 CKC  CAK  H2   single  0.970  0.020  1.090
 CKC  CAR  H3   single  0.970  0.020  1.090
 CKC  NAC  H4   single  0.890  0.020  1.040
 CKC  NAC  H5   single  0.890  0.020  1.040
 CKC  CAL  H7   single  0.970  0.020  1.090
 CKC  CAL  H8   single  0.970  0.020  1.090
 CKC  CAH  H9   single  0.970  0.020  1.090
 CKC  CAH  H10  single  0.970  0.020  1.090
 CKC  CAG  H11  single  0.970  0.020  1.090
 CKC  CAG  H12  single  0.970  0.020  1.090
 CKC  CAI  H13  single  0.970  0.020  1.090
 CKC  CAI  H14  single  0.970  0.020  1.090
 CKC  NAM  H15  single  0.890  0.020  1.040
 CKC  NAM  H16  single  0.890  0.020  1.040
 CKC  CAK  H18  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
 CKC  H18  CAK  H2   107.52  3.000
 CKC  H18  CAK  H1   109.39  3.000
 CKC  H2   CAK  H1   107.34  3.000
 CKC  H18  CAK  CAO  110.62  3.000
 CKC  H2   CAK  CAO  109.22  3.000
 CKC  H1   CAK  CAO  112.57  3.000
 CKC  CAR  CAO  OAF  121.59  3.000
 CKC  CAR  CAO  CAK  116.93  3.000
 CKC  OAF  CAO  CAK  121.48  3.000
 CKC  H3   CAR  CAL  107.30  3.000
 CKC  H3   CAR  NAC  108.28  3.000
 CKC  CAL  CAR  NAC  110.78  3.000
 CKC  H3   CAR  CAO  106.06  3.000
 CKC  NAC  CAR  CAO  114.62  3.000
 CKC  CAL  CAR  CAO  109.44  3.000
 CKC  H5   NAC  H4   105.77  3.000
 CKC  H5   NAC  CAR  109.71  3.000
 CKC  H4   NAC  CAR  110.09  3.000
 CKC  H8   CAL  H7   106.06  3.000
 CKC  H8   CAL  CAH  108.85  3.000
 CKC  H7   CAL  CAH  109.81  3.000
 CKC  H8   CAL  CAR  109.47  3.000
 CKC  H7   CAL  CAR  109.03  3.000
 CKC  CAH  CAL  CAR  113.37  3.000
 CKC  H10  CAH  H9   106.22  3.000
 CKC  H10  CAH  CAG  109.76  3.000
 CKC  H9   CAH  CAG  109.56  3.000
 CKC  H10  CAH  CAL  109.70  3.000
 CKC  H9   CAH  CAL  109.10  3.000
 CKC  CAG  CAH  CAL  112.31  3.000
 CKC  H12  CAG  H11  106.29  3.000
 CKC  H12  CAG  CAI  109.21  3.000
 CKC  H11  CAG  CAI  109.13  3.000
 CKC  H12  CAG  CAH  109.41  3.000
 CKC  H11  CAG  CAH  109.85  3.000
 CKC  CAI  CAG  CAH  112.74  3.000
 CKC  H14  CAI  H13  106.08  3.000
 CKC  H14  CAI  NAM  108.19  3.000
 CKC  H13  CAI  NAM  113.49  3.000
 CKC  H14  CAI  CAG  109.06  3.000
 CKC  H13  CAI  CAG  108.76  3.000
 CKC  NAM  CAI  CAG  111.07  3.000
 CKC  H16  NAM  H15  105.52  3.000
 CKC  H16  NAM  CAI  109.53  3.000
 CKC  H15  NAM  CAI  109.16  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
 CKC  Var_01  CAG  CAH  CAL  CAR  -178.60  30.0  1
 CKC  Var_02  CAI  CAG  CAH  CAL   179.13  30.0  3
 CKC  Var_03  NAM  CAI  CAG  CAH   179.46  30.0  1
 CKC  Var_04  H1   CAK  CAO  OAF   156.20  30.0  3
 CKC  Var_05  H15  NAM  CAI  CAG    66.04  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CKC  chir_01  CAR  CAO  CAL  NAC  positiv

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
 CKC  plan-1  CAK  0.020
 CKC  plan-1  CAO  0.020
 CKC  plan-1  OAF  0.020
 CKC  plan-1  CAR  0.020

