# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:40:21 2021
#   Inital geometry file: a 82 line input string
#   Ligand name: [(2S)-1,9-dimethyl-1,2,3,4,5,6-hexahydropyrido[2,3-b][1,5]diazocin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H](CO)CCNCc2ccc(C)nc12
#
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
 D8P  D8P  '[(2S)-1,9-dimethyl-1,2,3,4,5,6-hexahydropyrido[2,3-b][1,5]diazocin-2-yl]methanol'  ligand  35  16  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D8P
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
 D8P  C4   C  CR6   0   0.002  -4.2215   1.3808  11.1424
 D8P  C5   C  CR6   0   0.377  -3.7317   0.4338  10.2273
 D8P  C6   C  CH1   0  -0.103  -5.3422   0.1102   8.3973
 D8P  N1   N  NT    0  -0.473  -4.5784  -0.4304   9.5223
 D8P  C7   C  CH2   0  -0.477  -6.1001   1.3894   8.7254
 D8P  C8   C  CH2   0  -0.290  -7.1741   1.2525   9.7899
 D8P  N2   N  NH1   0  -0.578  -6.6671   0.7384  11.0453
 D8P  C9   C  CH2   0  -0.351  -5.6458   1.5674  11.6333
 D8P  C10  C  CH2   0  -0.148  -4.4491   0.3273   7.1698
 D8P  C11  C  CH3   0  -0.533  -4.0673  -1.7683   9.3081
 D8P  O    O  OH1   0  -0.674  -5.2671   0.6099   6.0546
 D8P  N    N  N     0  -0.447  -2.4244   0.2798  10.0114
 D8P  C1   C  CR6   0   0.225  -1.5290   1.0461  10.6182
 D8P  C    C  CH3   0  -0.721  -0.0805   0.7633  10.3547
 D8P  C3   C  CR16  0  -0.180  -3.2737   2.2142  11.7281
 D8P  C2   C  CR16  0  -0.350  -1.9237   2.0671  11.4742
 D8P  H1   H  HCH1  0   0.225  -6.0806  -0.6598   8.1415
 D8P  H2   H  HCH2  0   0.229  -5.3954   2.1872   8.9822
 D8P  H3   H  HCH2  0   0.256  -6.5893   1.7291   7.8111
 D8P  H4   H  HCH2  0   0.198  -7.6518   2.2395   9.9073
 D8P  H5   H  HCH2  0   0.223  -7.9515   0.5714   9.4320
 D8P  H6   H  HNH1  0   0.354  -7.4337   0.6701  11.7006
 D8P  H8   H  HCH2  0   0.209  -5.8842   2.6430  11.5575
 D8P  H9   H  HCH2  0   0.257  -5.6321   1.3516  12.7050
 D8P  H10  H  HCH2  0   0.209  -3.8433  -0.5676   6.9867
 D8P  H11  H  HCH2  0   0.188  -3.7491   1.1494   7.3758
 D8P  H12  H  HCH3  0   0.236  -3.7379  -2.1945  10.2559
 D8P  H13  H  HCH3  0   0.228  -4.8803  -2.3926   8.9329
 D8P  H14  H  HCH3  0   0.208  -3.2325  -1.8483   8.6056
 D8P  H15  H  HOH1  0   0.455  -4.6969   0.7533   5.2945
 D8P  H16  H  HCH3  0   0.244   0.0611   0.3354   9.3636
 D8P  H17  H  HCH3  0   0.242   0.5245   1.6656  10.4353
 D8P  H18  H  HCH3  0   0.249   0.3103   0.0458  11.0799
 D8P  H19  H  HCR6  0   0.255  -3.6046   2.9796  12.4226
 D8P  H20  H  HCR6  0   0.254  -1.1947   2.7161  11.9414

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
 D8P  O    C10  single    1.412  0.020  1.412
 D8P  C10  C6   single    1.533  0.020  1.533
 D8P  C6   C7   single    1.523  0.020  1.523
 D8P  C6   N1   single    1.463  0.020  1.463
 D8P  C7   C8   single    1.518  0.020  1.518
 D8P  N1   C11  single    1.448  0.020  1.448
 D8P  N1   C5   single    1.400  0.020  1.400
 D8P  C8   N2   single    1.448  0.020  1.448
 D8P  N    C5   aromatic  1.334  0.020  1.334
 D8P  N    C1   aromatic  1.326  0.020  1.326
 D8P  C    C1   single    1.499  0.020  1.499
 D8P  C5   C4   aromatic  1.405  0.020  1.405
 D8P  C1   C2   aromatic  1.390  0.020  1.390
 D8P  N2   C9   single    1.441  0.020  1.441
 D8P  C4   C9   single    1.518  0.020  1.518
 D8P  C4   C3   aromatic  1.391  0.020  1.391
 D8P  C2   C3   aromatic  1.381  0.020  1.381
 D8P  C6   H1   single    0.970  0.020  1.090
 D8P  C7   H2   single    0.970  0.020  1.090
 D8P  C7   H3   single    0.970  0.020  1.090
 D8P  C8   H4   single    0.970  0.020  1.090
 D8P  C8   H5   single    0.970  0.020  1.090
 D8P  N2   H6   single    0.890  0.020  1.040
 D8P  C9   H8   single    0.970  0.020  1.090
 D8P  C9   H9   single    0.970  0.020  1.090
 D8P  C10  H10  single    0.970  0.020  1.090
 D8P  C10  H11  single    0.970  0.020  1.090
 D8P  C11  H12  single    0.970  0.020  1.090
 D8P  C11  H13  single    0.970  0.020  1.090
 D8P  C11  H14  single    0.970  0.020  1.090
 D8P  O    H15  single    0.850  0.020  0.980
 D8P  C    H16  single    0.970  0.020  1.090
 D8P  C    H17  single    0.970  0.020  1.090
 D8P  C    H18  single    0.970  0.020  1.090
 D8P  C3   H19  single    0.930  0.020  1.080
 D8P  C2   H20  single    0.930  0.020  1.080

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
 D8P  C3   C4   C9   115.43  3.000
 D8P  C3   C4   C5   116.13  3.000
 D8P  C9   C4   C5   128.35  3.000
 D8P  N    C5   N1   116.10  3.000
 D8P  N    C5   C4   121.66  3.000
 D8P  N1   C5   C4   122.21  3.000
 D8P  H1   C6   C10  107.74  3.000
 D8P  H1   C6   C7   107.75  3.000
 D8P  C10  C6   C7   110.09  3.000
 D8P  H1   C6   N1   105.74  3.000
 D8P  C7   C6   N1   113.86  3.000
 D8P  C10  C6   N1   111.33  3.000
 D8P  C11  N1   C6   114.32  3.000
 D8P  C11  N1   C5   115.54  3.000
 D8P  C6   N1   C5   118.34  3.000
 D8P  H3   C7   H2   104.97  3.000
 D8P  H3   C7   C8   107.36  3.000
 D8P  H2   C7   C8   110.89  3.000
 D8P  H3   C7   C6   107.71  3.000
 D8P  H2   C7   C6   110.01  3.000
 D8P  C8   C7   C6   115.30  3.000
 D8P  H5   C8   H4   106.52  3.000
 D8P  H5   C8   N2   108.14  3.000
 D8P  H4   C8   N2   112.16  3.000
 D8P  H5   C8   C7   109.24  3.000
 D8P  H4   C8   C7   107.47  3.000
 D8P  N2   C8   C7   113.09  3.000
 D8P  H6   N2   C9   108.18  3.000
 D8P  H6   N2   C8   108.69  3.000
 D8P  C9   N2   C8   113.43  3.000
 D8P  H9   C9   H8   105.20  3.000
 D8P  H9   C9   N2   107.18  3.000
 D8P  H8   C9   N2   112.29  3.000
 D8P  H9   C9   C4   106.32  3.000
 D8P  H8   C9   C4   107.46  3.000
 D8P  N2   C9   C4   117.54  3.000
 D8P  H11  C10  H10  106.85  3.000
 D8P  H11  C10  O    111.55  3.000
 D8P  H10  C10  O    110.59  3.000
 D8P  H11  C10  C6   109.07  3.000
 D8P  H10  C10  C6   109.88  3.000
 D8P  O    C10  C6   108.86  3.000
 D8P  H14  C11  H13  107.81  3.000
 D8P  H14  C11  H12  107.41  3.000
 D8P  H13  C11  H12  107.47  3.000
 D8P  H14  C11  N1   115.59  3.000
 D8P  H13  C11  N1   108.44  3.000
 D8P  H12  C11  N1   109.83  3.000
 D8P  H15  O    C10  108.12  3.000
 D8P  C1   N    C5   121.41  3.000
 D8P  C2   C1   C    121.42  3.000
 D8P  C2   C1   N    120.99  3.000
 D8P  C    C1   N    117.59  3.000
 D8P  H18  C    H17  107.23  3.000
 D8P  H18  C    H16  107.45  3.000
 D8P  H17  C    H16  108.70  3.000
 D8P  H18  C    C1   110.66  3.000
 D8P  H17  C    C1   111.55  3.000
 D8P  H16  C    C1   111.08  3.000
 D8P  H19  C3   C2   119.39  3.000
 D8P  H19  C3   C4   118.95  3.000
 D8P  C2   C3   C4   121.63  3.000
 D8P  H20  C2   C3   121.01  3.000
 D8P  H20  C2   C1   121.01  3.000
 D8P  C3   C2   C1   117.97  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
 D8P  CONST_01  C1   C2  C3  C4    0.00   0.0  0
 D8P  CONST_02  C2   C1  N   C5    0.00   0.0  0
 D8P  CONST_03  C3   C2  C1  N     0.00   0.0  0
 D8P  CONST_04  C    C1  N   C5  180.00   0.0  0
 D8P  CONST_05  C3   C2  C1  C   180.00   0.0  0
 D8P  CONST_06  H20  C2  C3  C4  180.00   0.0  0
 D8P  CONST_07  H19  C3  C2  C1  180.00   0.0  0
 D8P  Var_01    H16  C   C1  N    29.09  30.0  2

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
 D8P  chir_01  C6  C10  C7  N1  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
 D8P  plan-1  C4   0.020
 D8P  plan-1  C5   0.020
 D8P  plan-1  N1   0.020
 D8P  plan-1  C9   0.020
 D8P  plan-1  N    0.020
 D8P  plan-1  C1   0.020
 D8P  plan-1  C    0.020
 D8P  plan-1  C3   0.020
 D8P  plan-1  C2   0.020
 D8P  plan-1  H19  0.020
 D8P  plan-1  H20  0.020

