# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:23:15 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-({[(1R,3S)-3-(aminomethyl)cyclohexyl]methyl}amino)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CCC[C@@H](CNc2ccc(cn2)C(N)=O)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
 4H1  4H1  6-({[(1R,3S)-3-(aminomethyl)cyclohexyl]methyl}amino)pyridine-3-carboxamide  ligand  41  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4H1
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
 4H1  C12  C  CR16  0  -0.151   3.3995   1.0412  -0.5920
 4H1  C11  C  CR16  0  -0.401   2.0424   0.9138  -0.4342
 4H1  C14  C  CR16  0  -0.074   3.6719  -1.0489   0.4885
 4H1  C13  C  CR6   0  -0.166   4.2685   0.0523  -0.1173
 4H1  C10  C  CR6   0   0.516   1.5462  -0.2463   0.1975
 4H1  C16  C  C     0   0.485   5.7298   0.2143  -0.3119
 4H1  C5   C  CH2   0  -0.434  -3.8090  -1.8683  -0.6783
 4H1  C4   C  CH2   0  -0.404  -4.8973  -0.8040  -0.7471
 4H1  C6   C  CH2   0  -0.410  -2.4184  -1.2575  -0.8100
 4H1  C19  C  CH2   0  -0.404  -3.2878   0.8920   0.1559
 4H1  C3   C  CH1   0  -0.243  -4.6846   0.2896   0.2963
 4H1  C7   C  CH1   0  -0.288  -2.1894  -0.1653   0.2341
 4H1  C2   C  CH2   0  -0.262  -5.7439   1.3834   0.2214
 4H1  C8   C  CH2   0  -0.234  -0.8184   0.4864   0.1008
 4H1  N15  N  N     0  -0.465   2.3703  -1.2042   0.6441
 4H1  N17  N  NH2   0  -0.824   6.5344  -0.6133   0.3790
 4H1  N1   N  NH2   0  -0.797  -7.0805   0.8637   0.4675
 4H1  N9   N  NH1   0  -0.657   0.2314  -0.4665   0.3759
 4H1  O18  O  O     0  -0.492   6.1726   1.0612  -1.0802
 4H1  H1   H  HCR6  0   0.268   3.7981   1.9220  -1.0777
 4H1  H2   H  HCR6  0   0.275   1.3775   1.6886  -0.7877
 4H1  H3   H  HCR6  0   0.253   4.2709  -1.8736   0.8622
 4H1  H4   H  HCH2  0   0.209  -3.8786  -2.4042   0.2750
 4H1  H5   H  HCH2  0   0.226  -3.9621  -2.6151  -1.4613
 4H1  H6   H  HCH2  0   0.199  -4.8907  -0.3432  -1.7433
 4H1  H7   H  HCH2  0   0.227  -5.8835  -1.2534  -0.6203
 4H1  H8   H  HCH2  0   0.230  -1.6583  -2.0379  -0.7232
 4H1  H9   H  HCH2  0   0.208  -2.3022  -0.8229  -1.8103
 4H1  H10  H  HCH2  0   0.208  -3.2186   1.4218  -0.8036
 4H1  H11  H  HCH2  0   0.227  -3.1301   1.6434   0.9361
 4H1  H12  H  HCH1  0   0.207  -4.7460  -0.1716   1.2930
 4H1  H13  H  HCH1  0   0.224  -2.2458  -0.6265   1.2306
 4H1  H14  H  HCH2  0   0.194  -5.4592   2.1916   0.9123
 4H1  H15  H  HCH2  0   0.206  -5.7268   1.8204  -0.7824
 4H1  H16  H  HCH2  0   0.230  -0.7053   0.8780  -0.9154
 4H1  H17  H  HCH2  0   0.235  -0.7526   1.3444   0.7822
 4H1  H18  H  HNH2  0   0.409   6.2037  -1.1986   1.1254
 4H1  H19  H  HNH2  0   0.402   7.5325  -0.5085   0.2983
 4H1  H20  H  HNH2  0   0.335  -7.1523   0.5767   1.4361
 4H1  H21  H  HNH2  0   0.345  -7.7577   1.6070   0.3533
 4H1  H23  H  HNH1  0   0.385  -0.0012  -1.2691   0.9404

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
 4H1  C5   C4   single    1.524  0.020  1.524
 4H1  C5   C6   single    1.525  0.020  1.525
 4H1  C4   C3   single    1.526  0.020  1.526
 4H1  C6   C7   single    1.528  0.020  1.528
 4H1  N1   C2   single    1.455  0.020  1.455
 4H1  C3   C2   single    1.524  0.020  1.524
 4H1  C3   C19  single    1.528  0.020  1.528
 4H1  C7   C19  single    1.527  0.020  1.527
 4H1  C7   C8   single    1.524  0.020  1.524
 4H1  C8   N9   single    1.444  0.020  1.444
 4H1  N9   C10  single    1.345  0.020  1.345
 4H1  C11  C10  aromatic  1.411  0.020  1.411
 4H1  C11  C12  aromatic  1.372  0.020  1.372
 4H1  C10  N15  aromatic  1.340  0.020  1.340
 4H1  C12  C13  aromatic  1.399  0.020  1.399
 4H1  N15  C14  aromatic  1.320  0.020  1.320
 4H1  C13  C14  aromatic  1.391  0.020  1.391
 4H1  C13  C16  single    1.483  0.020  1.483
 4H1  O18  C16  double    1.226  0.020  1.226
 4H1  C16  N17  single    1.345  0.020  1.345
 4H1  C12  H1   single    0.930  0.020  1.080
 4H1  C11  H2   single    0.930  0.020  1.080
 4H1  C14  H3   single    0.930  0.020  1.080
 4H1  C5   H4   single    0.970  0.020  1.090
 4H1  C5   H5   single    0.970  0.020  1.090
 4H1  C4   H6   single    0.970  0.020  1.090
 4H1  C4   H7   single    0.970  0.020  1.090
 4H1  C6   H8   single    0.970  0.020  1.090
 4H1  C6   H9   single    0.970  0.020  1.090
 4H1  C19  H10  single    0.970  0.020  1.090
 4H1  C19  H11  single    0.970  0.020  1.090
 4H1  C3   H12  single    0.970  0.020  1.090
 4H1  C7   H13  single    0.970  0.020  1.090
 4H1  C2   H14  single    0.970  0.020  1.090
 4H1  C2   H15  single    0.970  0.020  1.090
 4H1  C8   H16  single    0.970  0.020  1.090
 4H1  C8   H17  single    0.970  0.020  1.090
 4H1  N17  H18  single    0.860  0.020  1.020
 4H1  N17  H19  single    0.860  0.020  1.020
 4H1  N1   H20  single    0.890  0.020  1.040
 4H1  N1   H21  single    0.890  0.020  1.040
 4H1  N9   H23  single    0.860  0.020  1.020

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
 4H1  H1   C12  C13  119.92  3.000
 4H1  H1   C12  C11  119.44  3.000
 4H1  C13  C12  C11  120.63  3.000
 4H1  H2   C11  C10  121.31  3.000
 4H1  H2   C11  C12  120.29  3.000
 4H1  C10  C11  C12  118.40  3.000
 4H1  H3   C14  N15  114.46  3.000
 4H1  H3   C14  C13  120.97  3.000
 4H1  N15  C14  C13  124.56  3.000
 4H1  C16  C13  C14  124.48  3.000
 4H1  C16  C13  C12  119.35  3.000
 4H1  C14  C13  C12  116.15  3.000
 4H1  N9   C10  N15  116.10  3.000
 4H1  N15  C10  C11  121.37  3.000
 4H1  N9   C10  C11  122.53  3.000
 4H1  O18  C16  N17  122.06  3.000
 4H1  N17  C16  C13  117.05  3.000
 4H1  O18  C16  C13  120.89  3.000
 4H1  H5   C5   H4   106.27  3.000
 4H1  H5   C5   C6   109.86  3.000
 4H1  H4   C5   C6   109.21  3.000
 4H1  H5   C5   C4   110.18  3.000
 4H1  H4   C5   C4   109.60  3.000
 4H1  C6   C5   C4   111.58  3.000
 4H1  H7   C4   H6   106.49  3.000
 4H1  H7   C4   C3   109.97  3.000
 4H1  H6   C4   C3   108.59  3.000
 4H1  H7   C4   C5   110.65  3.000
 4H1  H6   C4   C5   109.26  3.000
 4H1  C3   C4   C5   111.72  3.000
 4H1  H9   C6   H8   106.36  3.000
 4H1  H9   C6   C7   108.90  3.000
 4H1  H8   C6   C7   110.60  3.000
 4H1  H9   C6   C5   109.52  3.000
 4H1  H8   C6   C5   109.97  3.000
 4H1  C7   C6   C5   111.35  3.000
 4H1  H11  C19  H10  106.41  3.000
 4H1  H11  C19  C7   109.59  3.000
 4H1  H10  C19  C7   109.48  3.000
 4H1  H11  C19  C3   109.69  3.000
 4H1  H10  C19  C3   109.16  3.000
 4H1  C7   C19  C3   112.33  3.000
 4H1  H12  C3   C2   107.85  3.000
 4H1  H12  C3   C19  107.44  3.000
 4H1  C2   C3   C19  110.35  3.000
 4H1  H12  C3   C4   108.14  3.000
 4H1  C19  C3   C4   110.31  3.000
 4H1  C2   C3   C4   112.56  3.000
 4H1  H13  C7   C8   107.74  3.000
 4H1  H13  C7   C19  107.46  3.000
 4H1  C8   C7   C19  110.28  3.000
 4H1  H13  C7   C6   108.16  3.000
 4H1  C8   C7   C6   112.38  3.000
 4H1  C19  C7   C6   110.62  3.000
 4H1  H15  C2   H14  106.16  3.000
 4H1  H15  C2   N1   108.17  3.000
 4H1  H14  C2   N1   113.18  3.000
 4H1  H15  C2   C3   108.69  3.000
 4H1  H14  C2   C3   108.44  3.000
 4H1  N1   C2   C3   111.94  3.000
 4H1  H17  C8   H16  106.88  3.000
 4H1  H17  C8   N9   110.73  3.000
 4H1  H16  C8   N9   109.74  3.000
 4H1  H17  C8   C7   109.51  3.000
 4H1  H16  C8   C7   109.09  3.000
 4H1  N9   C8   C7   110.81  3.000
 4H1  C10  N15  C14  118.88  3.000
 4H1  H19  N17  H18  116.52  3.000
 4H1  H19  N17  C16  119.19  3.000
 4H1  H18  N17  C16  122.90  3.000
 4H1  H21  N1   H20  105.58  3.000
 4H1  H21  N1   C2   109.47  3.000
 4H1  H20  N1   C2   109.15  3.000
 4H1  H23  N9   C8   117.65  3.000
 4H1  H23  N9   C10  115.47  3.000
 4H1  C8   N9   C10  125.26  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
 4H1  CONST_01  N15  C10  C11  C12    0.00   0.0  0
 4H1  CONST_02  N15  C14  C13  C12    0.00   0.0  0
 4H1  CONST_03  C14  N15  C10  C11    0.00   0.0  0
 4H1  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 4H1  CONST_05  C10  C11  C12  C13    0.00   0.0  0
 4H1  CONST_06  C10  N15  C14  C13    0.00   0.0  0
 4H1  CONST_07  N9   C10  C11  C12  180.00   0.0  0
 4H1  CONST_08  C16  C13  C12  C11  180.00   0.0  0
 4H1  CONST_09  N9   C10  N15  C14  180.00   0.0  0
 4H1  CONST_10  N15  C14  C13  C16  180.00   0.0  0
 4H1  CONST_11  H3   C14  C13  C12  180.00   0.0  0
 4H1  CONST_12  H1   C12  C13  C14  180.00   0.0  0
 4H1  CONST_13  H2   C11  C12  C13  180.00   0.0  0
 4H1  CONST_14  C8   N9   C10  C11    0.00   0.0  0
 4H1  CONST_15  N15  C10  N9   C8   180.00   0.0  0
 4H1  CONST_16  H23  N9   C10  C11  180.00   0.0  0
 4H1  CONST_17  H18  N17  C16  C13    0.00   0.0  0
 4H1  CONST_18  H19  N17  C16  C13  180.00   0.0  0
 4H1  Var_01    C7   C6   C5   C4    55.13  30.0  1
 4H1  Var_02    C3   C4   C5   C6   -55.35  30.0  1
 4H1  Var_03    O18  C16  C13  C12  -13.26  30.0  2
 4H1  Var_04    C7   C8   N9   C10  172.11  30.0  1
 4H1  Var_05    H20  N1   C2   C3    68.33  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
 4H1  chir_01  C3  C4  C2   C19  positiv
 4H1  chir_02  C7  C8  C19  C6   negativ

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
 4H1  plan-1  C12  0.020
 4H1  plan-1  C11  0.020
 4H1  plan-1  C14  0.020
 4H1  plan-1  C13  0.020
 4H1  plan-1  C10  0.020
 4H1  plan-1  C16  0.020
 4H1  plan-1  N15  0.020
 4H1  plan-1  N9   0.020
 4H1  plan-1  H1   0.020
 4H1  plan-1  H2   0.020
 4H1  plan-1  H3   0.020
 4H1  plan-2  C13  0.020
 4H1  plan-2  C16  0.020
 4H1  plan-2  N17  0.020
 4H1  plan-2  O18  0.020
 4H1  plan-2  H18  0.020
 4H1  plan-2  H19  0.020
 4H1  plan-3  C10  0.020
 4H1  plan-3  C8   0.020
 4H1  plan-3  N9   0.020
 4H1  plan-3  H23  0.020

