# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 23:41:18 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C2=C(CCC2)C(=N)C3=C1CCC3
#
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
 36X  36X  4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine  ligand  30  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_36X
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
 36X  N1   N  N     0  -0.668  -0.0585   2.8323  -0.0597
 36X  C6   C  CR6   0   0.173  -0.0021   1.5385  -0.0316
 36X  C5   C  CR56  0  -0.042  -1.2015   0.7389   0.0001
 36X  C4   C  CH2   0  -0.482  -2.6094   1.2482   0.0428
 36X  C3   C  CH2   0  -0.459  -3.4498  -0.0103  -0.2440
 36X  C2   C  CH2   0  -0.507  -2.5504  -1.2125   0.0961
 36X  C1   C  CR56  0   0.297  -1.1767  -0.6158   0.0296
 36X  C7   C  CR56  0  -0.088   1.1878   0.7185  -0.0298
 36X  C11  C  CR56  0   0.301   1.1455  -0.6389   0.0028
 36X  N    N  NR6   0  -0.566  -0.0212  -1.3414   0.0419
 36X  C    C  CH3   0  -0.545  -0.0633  -2.7926   0.0007
 36X  C10  C  CH2   0  -0.510   2.5133  -1.2517  -0.0561
 36X  C9   C  CH2   0  -0.456   3.4311  -0.0480   0.2177
 36X  C8   C  CH2   0  -0.496   2.6042   1.2061  -0.1156
 36X  H1   H  H     0   0.305   0.8816   3.2169  -0.0876
 36X  H3   H  HCH2  0   0.232  -2.8372   1.6744   1.0258
 36X  H4   H  HCH2  0   0.238  -4.3855  -0.0284   0.3132
 36X  H5   H  HCH2  0   0.260  -2.7446  -1.6001   1.1018
 36X  H6   H  HCH3  0   0.257  -0.3057  -3.1551  -0.9989
 36X  H7   H  HCH3  0   0.272   0.8980  -3.2028   0.2922
 36X  H9   H  HCH2  0   0.261   2.6626  -2.0502   0.6723
 36X  H10  H  HCH2  0   0.262   2.6891  -1.6873  -1.0449
 36X  H11  H  HCH2  0   0.243   3.6986  -0.0356   1.2752
 36X  H12  H  HCH2  0   0.241   4.3589  -0.1020  -0.3500
 36X  H13  H  HCH2  0   0.240   2.8255   1.5847  -1.1195
 36X  H14  H  HCH2  0   0.237   2.8165   2.0248   0.5768
 36X  H16  H  HCH2  0   0.234  -2.7896   2.0418  -0.6850
 36X  H17  H  HCH2  0   0.241  -3.7041  -0.0440  -1.3045
 36X  H18  H  HCH2  0   0.260  -2.6932  -2.0449  -0.5952
 36X  H2   H  HCH3  0   0.265  -0.8086  -3.1665   0.6991

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
 36X  N1   C6   double  1.295  0.020  1.295
 36X  C6   C5   single  1.442  0.020  1.442
 36X  C6   C7   single  1.445  0.020  1.445
 36X  C4   C5   single  1.498  0.020  1.498
 36X  C4   C3   single  1.540  0.020  1.540
 36X  C8   C7   single  1.500  0.020  1.500
 36X  C8   C9   single  1.539  0.020  1.539
 36X  C5   C1   double  1.355  0.020  1.355
 36X  C7   C11  double  1.358  0.020  1.358
 36X  C3   C2   single  1.539  0.020  1.539
 36X  C9   C10  single  1.538  0.020  1.538
 36X  C1   C2   single  1.499  0.020  1.499
 36X  C1   N    single  1.365  0.020  1.365
 36X  C11  N    single  1.362  0.020  1.362
 36X  C11  C10  single  1.500  0.020  1.500
 36X  N    C    single  1.452  0.020  1.452
 36X  N1   H1   single  0.890  0.020  1.040
 36X  C4   H3   single  0.970  0.020  1.090
 36X  C3   H4   single  0.970  0.020  1.090
 36X  C2   H5   single  0.970  0.020  1.090
 36X  C    H6   single  0.970  0.020  1.090
 36X  C    H7   single  0.970  0.020  1.090
 36X  C10  H9   single  0.970  0.020  1.090
 36X  C10  H10  single  0.970  0.020  1.090
 36X  C9   H11  single  0.970  0.020  1.090
 36X  C9   H12  single  0.970  0.020  1.090
 36X  C8   H13  single  0.970  0.020  1.090
 36X  C8   H14  single  0.970  0.020  1.090
 36X  C4   H16  single  0.970  0.020  1.090
 36X  C3   H17  single  0.970  0.020  1.090
 36X  C2   H18  single  0.970  0.020  1.090
 36X  C    H2   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
 36X  H1   N1   C6   109.78  3.000
 36X  C7   C6   C5   111.73  3.000
 36X  C7   C6   N1   127.06  3.000
 36X  C5   C6   N1   121.21  3.000
 36X  C1   C5   C4   110.88  3.000
 36X  C1   C5   C6   122.66  3.000
 36X  C4   C5   C6   126.44  3.000
 36X  H16  C4   H3   106.33  3.000
 36X  H16  C4   C3   112.32  3.000
 36X  H3   C4   C3   111.81  3.000
 36X  H16  C4   C5   112.54  3.000
 36X  H3   C4   C5   110.69  3.000
 36X  C3   C4   C5   103.28  3.000
 36X  H17  C3   H4   107.25  3.000
 36X  H17  C3   C2   109.08  3.000
 36X  H4   C3   C2   112.08  3.000
 36X  H17  C3   C4   109.48  3.000
 36X  H4   C3   C4   112.77  3.000
 36X  C2   C3   C4   106.15  3.000
 36X  H18  C2   H5   106.77  3.000
 36X  H18  C2   C1   113.29  3.000
 36X  H5   C2   C1   110.13  3.000
 36X  H18  C2   C3   112.28  3.000
 36X  H5   C2   C3   112.07  3.000
 36X  C1   C2   C3   102.40  3.000
 36X  N    C1   C2   124.33  3.000
 36X  N    C1   C5   123.17  3.000
 36X  C2   C1   C5   112.46  3.000
 36X  C8   C7   C11  110.83  3.000
 36X  C11  C7   C6   122.77  3.000
 36X  C8   C7   C6   126.36  3.000
 36X  C10  C11  N    124.84  3.000
 36X  C10  C11  C7   112.26  3.000
 36X  N    C11  C7   122.86  3.000
 36X  C    N    C11  122.63  3.000
 36X  C    N    C1   120.43  3.000
 36X  C11  N    C1   116.79  3.000
 36X  H2   C    H7   107.74  3.000
 36X  H2   C    H6   108.78  3.000
 36X  H7   C    H6   108.51  3.000
 36X  H2   C    N    110.19  3.000
 36X  H7   C    N    110.15  3.000
 36X  H6   C    N    111.37  3.000
 36X  H10  C10  H9   106.84  3.000
 36X  H10  C10  C9   112.11  3.000
 36X  H9   C10  C9   111.85  3.000
 36X  H10  C10  C11  110.15  3.000
 36X  H9   C10  C11  113.42  3.000
 36X  C9   C10  C11  102.56  3.000
 36X  H12  C9   H11  107.28  3.000
 36X  H12  C9   C8   112.66  3.000
 36X  H11  C9   C8   109.42  3.000
 36X  H12  C9   C10  112.13  3.000
 36X  H11  C9   C10  109.13  3.000
 36X  C8   C9   C10  106.18  3.000
 36X  H14  C8   H13  106.41  3.000
 36X  H14  C8   C9   111.65  3.000
 36X  H13  C8   C9   111.82  3.000
 36X  H14  C8   C7   112.99  3.000
 36X  H13  C8   C7   110.81  3.000
 36X  C9   C8   C7   103.30  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
 36X  Var_01  C3   C4   C5   C6  168.21  30.0  1
 36X  Var_02  C9   C8   C7   C6  168.83  30.0  1
 36X  Var_03  C2   C3   C4   C5   21.07  30.0  1
 36X  Var_04  C3   C2   C1   C5   13.36  30.0  1
 36X  Var_05  C1   C2   C3   C4  -20.86  30.0  1
 36X  Var_06  C10  C9   C8   C7   21.19  30.0  1
 36X  Var_07  C9   C10  C11  C7   13.44  30.0  1
 36X  Var_08  H6   C    N    C1   75.26  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
 36X  plan-1  N1   0.020
 36X  plan-1  C6   0.020
 36X  plan-1  C5   0.020
 36X  plan-1  C4   0.020
 36X  plan-1  C2   0.020
 36X  plan-1  C1   0.020
 36X  plan-1  C7   0.020
 36X  plan-1  C11  0.020
 36X  plan-1  N    0.020
 36X  plan-1  C    0.020
 36X  plan-1  C10  0.020
 36X  plan-1  C8   0.020

