# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 11:04:54 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: N~6~-[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]-N~6~-methyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCCC[C@H](N)C(O)=O)[C@H]1C[C@@H]2CC[C@H]1C2
#
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
 9RI  9RI  "(2S)-2-amino-6-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl](methyl)amino}hexanal"
  ligand  43  18  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9RI
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
 9RI  C    C  C      0   0.385  15.0242  20.5756  34.3184
 9RI  O    O  O      0  -0.607  14.9169  19.3357  34.2436
 9RI  CA   C  CH1    0  -0.155  13.7464  21.3700  34.6803
 9RI  CB   C  CH2    0  -0.421  13.4266  21.2098  36.1664
 9RI  N    N  NH2    0  -0.807  12.6000  20.8944  33.9102
 9RI  CG   C  CH2    0  -0.414  14.4823  21.7678  37.1115
 9RI  CD   C  CH2    0  -0.409  14.0518  21.6891  38.5705
 9RI  CE   C  CH2    0  -0.307  15.0892  22.2465  39.5387
 9RI  NZ   N  NT     0  -0.420  15.3536  23.6727  39.3433
 9RI  CM   C  CH3    0  -0.534  16.7724  23.9255  39.1880
 9RI  C4   C  CH1    0  -0.023  14.7823  24.5210  40.3833
 9RI  C5   C  CH2    0  -0.451  14.8613  26.0283  40.0036
 9RI  C6   C  CH1    0  -0.253  13.4059  26.5082  40.0545
 9RI  C1   C  CH2    0  -0.433  12.9568  26.5538  41.5185
 9RI  C7   C  CH2    0  -0.426  12.6686  25.2699  39.5369
 9RI  C3   C  CH1    0  -0.286  13.2667  24.3346  40.5906
 9RI  C2   C  CH2    0  -0.437  12.8887  25.0520  41.8969
 9RI  H2   H  HCH1   0   0.164  13.9552  22.4358  34.4999
 9RI  H3   H  HCH2   0   0.203  12.4737  21.7128  36.3732
 9RI  H4   H  HCH2   0   0.201  13.2606  20.1484  36.3771
 9RI  H5   H  HNH2   0   0.328  11.8057  21.4921  34.1078
 9RI  H6   H  HNH2   0   0.332  12.7813  21.0102  32.9204
 9RI  H8   H  HCH2   0   0.206  15.4257  21.2268  36.9864
 9RI  H9   H  HCH2   0   0.203  14.6917  22.8109  36.8569
 9RI  H10  H  HCH2   0   0.212  13.1019  22.2173  38.6950
 9RI  H11  H  HCH2   0   0.205  13.8577  20.6447  38.8380
 9RI  H12  H  HCH2   0   0.220  14.7840  22.0416  40.5724
 9RI  H13  H  HCH2   0   0.225  16.0187  21.6859  39.3978
 9RI  H15  H  HCH3   0   0.233  16.9617  24.9680  38.9324
 9RI  H16  H  HCH3   0   0.188  17.3561  23.6978  40.0943
 9RI  H17  H  HCH3   0   0.231  17.1719  23.3196  38.3743
 9RI  H18  H  HCH1   0   0.193  15.3027  24.3344  41.3405
 9RI  H19  H  HCH2   0   0.227  15.5145  26.5989  40.6668
 9RI  H20  H  HCH2   0   0.234  15.2463  26.1425  38.9886
 9RI  H21  H  HCH1   0   0.218  13.2355  27.4374  39.5091
 9RI  H22  H  HCH2   0   0.223  13.6507  27.1191  42.1435
 9RI  H23  H  HCH2   0   0.227  11.9781  27.0285  41.6129
 9RI  H24  H  HCH2   0   0.227  12.9409  24.9986  38.5147
 9RI  H25  H  HCH2   0   0.226  11.5808  25.3523  39.6000
 9RI  H26  H  HCH1   0   0.233  12.9286  23.2995  40.5695
 9RI  H27  H  HCH2   0   0.232  11.8819  24.7701  42.2100
 9RI  H28  H  HCH2   0   0.224  13.5624  24.7917  42.7158
 9RI  OXT  O  OC    -1  -0.615  16.0660  21.2449  34.1536

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
 9RI  N   CA   single  1.461  0.020  1.461
 9RI  CA  C    single  1.548  0.020  1.548
 9RI  CA  CB   single  1.529  0.020  1.529
 9RI  O   C    deloc   1.247  0.020  1.247
 9RI  CB  CG   single  1.523  0.020  1.523
 9RI  CG  CD   single  1.523  0.020  1.523
 9RI  CD  CE   single  1.525  0.020  1.525
 9RI  CM  NZ   single  1.450  0.020  1.450
 9RI  CE  NZ   single  1.464  0.020  1.464
 9RI  NZ  C4   single  1.459  0.020  1.459
 9RI  C7  C3   single  1.531  0.020  1.531
 9RI  C7  C6   single  1.531  0.020  1.531
 9RI  C4  C5   single  1.556  0.020  1.556
 9RI  C4  C3   single  1.541  0.020  1.541
 9RI  C5  C6   single  1.533  0.020  1.533
 9RI  C3  C2   single  1.538  0.020  1.538
 9RI  C6  C1   single  1.532  0.020  1.532
 9RI  C2  C1   single  1.550  0.020  1.550
 9RI  CA  H2   single  0.970  0.020  1.090
 9RI  CB  H3   single  0.970  0.020  1.090
 9RI  CB  H4   single  0.970  0.020  1.090
 9RI  N   H5   single  0.890  0.020  1.040
 9RI  N   H6   single  0.890  0.020  1.040
 9RI  CG  H8   single  0.970  0.020  1.090
 9RI  CG  H9   single  0.970  0.020  1.090
 9RI  CD  H10  single  0.970  0.020  1.090
 9RI  CD  H11  single  0.970  0.020  1.090
 9RI  CE  H12  single  0.970  0.020  1.090
 9RI  CE  H13  single  0.970  0.020  1.090
 9RI  CM  H15  single  0.970  0.020  1.090
 9RI  CM  H16  single  0.970  0.020  1.090
 9RI  CM  H17  single  0.970  0.020  1.090
 9RI  C4  H18  single  0.970  0.020  1.090
 9RI  C5  H19  single  0.970  0.020  1.090
 9RI  C5  H20  single  0.970  0.020  1.090
 9RI  C6  H21  single  0.970  0.020  1.090
 9RI  C1  H22  single  0.970  0.020  1.090
 9RI  C1  H23  single  0.970  0.020  1.090
 9RI  C7  H24  single  0.970  0.020  1.090
 9RI  C7  H25  single  0.970  0.020  1.090
 9RI  C3  H26  single  0.970  0.020  1.090
 9RI  C2  H27  single  0.970  0.020  1.090
 9RI  C2  H28  single  0.970  0.020  1.090
 9RI  C   OXT  deloc   1.249  0.020  1.249

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
 9RI  OXT  C   CA   116.38  3.000
 9RI  OXT  C   O    126.64  3.000
 9RI  CA   C   O    116.97  3.000
 9RI  H2   CA  N    112.19  3.000
 9RI  H2   CA  CB   107.49  3.000
 9RI  N    CA  CB   108.32  3.000
 9RI  H2   CA  C    107.58  3.000
 9RI  CB   CA  C    110.26  3.000
 9RI  N    CA  C    110.95  3.000
 9RI  H4   CB  H3   106.06  3.000
 9RI  H4   CB  CG   109.94  3.000
 9RI  H3   CB  CG   108.49  3.000
 9RI  H4   CB  CA   108.69  3.000
 9RI  H3   CB  CA   108.47  3.000
 9RI  CG   CB  CA   114.83  3.000
 9RI  H6   N   H5   105.27  3.000
 9RI  H6   N   CA   109.72  3.000
 9RI  H5   N   CA   108.68  3.000
 9RI  H9   CG  H8   106.24  3.000
 9RI  H9   CG  CD   109.04  3.000
 9RI  H8   CG  CD   109.12  3.000
 9RI  H9   CG  CB   109.73  3.000
 9RI  H8   CG  CB   110.20  3.000
 9RI  CD   CG  CB   112.31  3.000
 9RI  H11  CD  H10  106.18  3.000
 9RI  H11  CD  CE   108.31  3.000
 9RI  H10  CD  CE   110.00  3.000
 9RI  H11  CD  CG   109.46  3.000
 9RI  H10  CD  CG   109.24  3.000
 9RI  CE   CD  CG   113.39  3.000
 9RI  H13  CE  H12  105.18  3.000
 9RI  H13  CE  NZ   109.18  3.000
 9RI  H12  CE  NZ   110.98  3.000
 9RI  H13  CE  CD   107.99  3.000
 9RI  H12  CE  CD   109.92  3.000
 9RI  NZ   CE  CD   113.23  3.000
 9RI  C4   NZ  CM   111.00  3.000
 9RI  C4   NZ  CE   113.63  3.000
 9RI  CM   NZ  CE   111.17  3.000
 9RI  H17  CM  H16  107.75  3.000
 9RI  H17  CM  H15  107.03  3.000
 9RI  H16  CM  H15  107.38  3.000
 9RI  H17  CM  NZ   109.98  3.000
 9RI  H16  CM  NZ   113.23  3.000
 9RI  H15  CM  NZ   111.21  3.000
 9RI  H18  C4  C3   109.03  3.000
 9RI  H18  C4  C5   110.54  3.000
 9RI  C3   C4  C5   101.53  3.000
 9RI  H18  C4  NZ   109.57  3.000
 9RI  C3   C4  NZ   114.25  3.000
 9RI  C5   C4  NZ   111.68  3.000
 9RI  H20  C5  H19  107.41  3.000
 9RI  H20  C5  C6   109.44  3.000
 9RI  H19  C5  C6   112.59  3.000
 9RI  H20  C5  C4   110.25  3.000
 9RI  H19  C5  C4   112.85  3.000
 9RI  C6   C5  C4   104.29  3.000
 9RI  H21  C6  C7   116.40  3.000
 9RI  H21  C6  C1   114.00  3.000
 9RI  C7   C6  C1   101.89  3.000
 9RI  H21  C6  C5   113.47  3.000
 9RI  C1   C6  C5   108.62  3.000
 9RI  C7   C6  C5   101.11  3.000
 9RI  H23  C1  H22  107.16  3.000
 9RI  H23  C1  C2   111.14  3.000
 9RI  H22  C1  C2   112.94  3.000
 9RI  H23  C1  C6   111.00  3.000
 9RI  H22  C1  C6   112.10  3.000
 9RI  C2   C1  C6   102.55  3.000
 9RI  H25  C7  H24  108.72  3.000
 9RI  H25  C7  C3   113.28  3.000
 9RI  H24  C7  C3   113.27  3.000
 9RI  H25  C7  C6   113.50  3.000
 9RI  H24  C7  C6   113.40  3.000
 9RI  C3   C7  C6    94.21  3.000
 9RI  H26  C3  C2   112.56  3.000
 9RI  H26  C3  C7   116.50  3.000
 9RI  C2   C3  C7   101.75  3.000
 9RI  H26  C3  C4   114.69  3.000
 9RI  C2   C3  C4   107.43  3.000
 9RI  C7   C3  C4   102.58  3.000
 9RI  H28  C2  H27  107.01  3.000
 9RI  H28  C2  C3   111.98  3.000
 9RI  H27  C2  C3   110.49  3.000
 9RI  H28  C2  C1   112.76  3.000
 9RI  H27  C2  C1   111.15  3.000
 9RI  C3   C2  C1   103.52  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
 9RI  Var_01  C3   C2  C1  C6    -1.62  30.0  1
 9RI  Var_02  H27  C2  C1  C6  -120.23  30.0  1
 9RI  Var_03  H28  C2  C1  C6   119.61  30.0  1
 9RI  Var_04  H22  C1  C2  C3  -122.47  30.0  1
 9RI  Var_05  H23  C1  C2  C3   117.05  30.0  1
 9RI  Var_06  C4   NZ  CE  CD   106.62  30.0  3
 9RI  Var_07  H15  CM  NZ  C4   -58.81  30.0  3
 9RI  Var_08  H16  CM  NZ  C4    62.20  30.0  3
 9RI  Var_09  H17  CM  NZ  C4  -177.20  30.0  3
 9RI  Var_10  H12  CE  NZ  C4   -17.55  30.0  1
 9RI  Var_11  H13  CE  NZ  C4  -133.03  30.0  1
 9RI  Var_12  CD   CG  CB  CA   174.96  30.0  3
 9RI  Var_13  CE   CD  CG  CB  -179.78  30.0  3
 9RI  Var_14  NZ   CE  CD  CG    62.78  30.0  3
 9RI  Var_15  CM   NZ  CE  CD  -127.31  30.0  3
 9RI  Var_16  H8   CG  CB  CA   -63.15  30.0  3
 9RI  Var_17  H9   CG  CB  CA    53.50  30.0  3
 9RI  Var_18  H10  CD  CG  CB   -56.71  30.0  3
 9RI  Var_19  H11  CD  CG  CB    59.16  30.0  3
 9RI  Var_20  H12  CE  CD  CG  -172.48  30.0  3
 9RI  Var_21  H13  CE  CD  CG   -58.24  30.0  3
 9RI  Var_22  H3   CB  CG  CD    53.44  30.0  1
 9RI  Var_23  H4   CB  CG  CD   -62.12  30.0  1
 9RI  Var_24  H8   CG  CD  CE    57.71  30.0  1
 9RI  Var_25  H9   CG  CD  CE   -57.94  30.0  1
 9RI  Var_26  H15  CM  NZ  CE   173.68  30.0  3
 9RI  Var_27  H16  CM  NZ  CE   -65.31  30.0  3
 9RI  Var_28  H17  CM  NZ  CE    55.29  30.0  3
 9RI  Var_29  H10  CD  CE  NZ   -59.87  30.0  1
 9RI  Var_30  H11  CD  CE  NZ  -175.52  30.0  1
 9RI  Var_31  H12  CE  NZ  CM   108.52  30.0  1
 9RI  Var_32  H13  CE  NZ  CM    -6.97  30.0  1

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
 9RI  chir_01  CA  N   C   CB  positiv
 9RI  chir_02  C4  NZ  C5  C3  negativ
 9RI  chir_03  C6  C7  C5  C1  positiv
 9RI  chir_04  C3  C7  C4  C2  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
 9RI  plan-1  C    0.020
 9RI  plan-1  O    0.020
 9RI  plan-1  CA   0.020
 9RI  plan-1  OXT  0.020

