# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Sep 21 01:05:03 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  44  18  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.529  14.7029  20.5560  34.4494
 9RI  O    O  O     0  -0.432  14.6624  19.3687  34.2513
 9RI  CA   C  CH1   0  -0.171  13.4934  21.4250  34.7422
 9RI  CB   C  CH2   0  -0.438  13.0947  21.2548  36.2135
 9RI  N    N  NH2   0  -0.797  12.3914  20.9988  33.8979
 9RI  CG   C  CH2   0  -0.423  14.1492  21.6851  37.2242
 9RI  CD   C  CH2   0  -0.414  13.6200  21.6458  38.6520
 9RI  CE   C  CH2   0  -0.308  14.6809  22.0068  39.6873
 9RI  NZ   N  NT    0  -0.422  15.2303  23.3501  39.5142
 9RI  CM   C  CH3   0  -0.534  16.6794  23.3291  39.5070
 9RI  C4   C  CH1   0  -0.023  14.7336  24.3326  40.4715
 9RI  C5   C  CH2   0  -0.449  15.0985  25.7808  40.0302
 9RI  C6   C  CH1   0  -0.253  13.7464  26.4961  39.9249
 9RI  C1   C  CH2   0  -0.434  13.2038  26.7134  41.3413
 9RI  C7   C  CH2   0  -0.428  12.8498  25.3653  39.4124
 9RI  C3   C  CH1   0  -0.287  13.1984  24.4166  40.5625
 9RI  C2   C  CH2   0  -0.436  12.8523  25.2732  41.7910
 9RI  H2   H  HCH1  0   0.234  13.7817  22.4739  34.5891
 9RI  H3   H  HCH2  0   0.236  12.1903  21.8522  36.3682
 9RI  H4   H  HCH2  0   0.228  12.8097  20.2121  36.3807
 9RI  H5   H  HNH2  0   0.352  11.5721  21.5437  34.1371
 9RI  H6   H  HNH2  0   0.351  12.5895  21.2157  32.9286
 9RI  H8   H  HCH2  0   0.214  15.0305  21.0388  37.1575
 9RI  H9   H  HCH2  0   0.218  14.4907  22.6983  36.9967
 9RI  H10  H  HCH2  0   0.220  12.7579  22.3132  38.7361
 9RI  H11  H  HCH2  0   0.212  13.2511  20.6397  38.8781
 9RI  H12  H  HCH2  0   0.221  14.2819  21.8635  40.7000
 9RI  H13  H  HCH2  0   0.227  15.4928  21.2793  39.5955
 9RI  H15  H  HCH3  0   0.234  17.0842  24.3145  39.2752
 9RI  H16  H  HCH3  0   0.189  17.1160  23.0147  40.4684
 9RI  H17  H  HCH3  0   0.231  17.0401  22.6458  38.7377
 9RI  H18  H  HCH1  0   0.194  15.1443  24.1147  41.4741
 9RI  H19  H  HCH2  0   0.227  15.7814  26.2778  40.7222
 9RI  H20  H  HCH2  0   0.233  15.5826  25.7587  39.0520
 9RI  H21  H  HCH1  0   0.218  13.7783  27.4027  39.3191
 9RI  H22  H  HCH2  0   0.223  13.9361  27.1963  41.9914
 9RI  H23  H  HCH2  0   0.228  12.3167  27.3500  41.3282
 9RI  H24  H  HCH2  0   0.229  13.1503  24.9833  38.4340
 9RI  H25  H  HCH2  0   0.226  11.7906  25.6314  39.3751
 9RI  H26  H  HCH1  0   0.233  12.6880  23.4547  40.5749
 9RI  H27  H  HCH2  0   0.232  11.7905  25.1835  42.0266
 9RI  H28  H  HCH2  0   0.225  13.4024  24.9571  42.6798
 9RI  OXT  O  OH1   0  -0.591  15.8349  21.2540  34.4609
 9RI  HXT  H  HOH1  0   0.475  16.5893  20.6613  34.3209

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  1.452  0.020  1.452
 9RI  CA   C    single  1.518  0.020  1.518
 9RI  CA   CB   single  1.534  0.020  1.534
 9RI  O    C    double  1.204  0.020  1.204
 9RI  CB   CG   single  1.523  0.020  1.523
 9RI  CG   CD   single  1.523  0.020  1.523
 9RI  CD   CE   single  1.526  0.020  1.526
 9RI  CM   NZ   single  1.449  0.020  1.449
 9RI  CE   NZ   single  1.462  0.020  1.462
 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  1.557  0.020  1.557
 9RI  C4   C3   single  1.540  0.020  1.540
 9RI  C5   C6   single  1.533  0.020  1.533
 9RI  C3   C2   single  1.537  0.020  1.537
 9RI  C6   C1   single  1.532  0.020  1.532
 9RI  C2   C1   single  1.549  0.020  1.549
 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  single  1.330  0.020  1.330
 9RI  OXT  HXT  single  0.850  0.020  0.980

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   112.09  3.000
 9RI  OXT  C    O    123.19  3.000
 9RI  CA   C    O    124.70  3.000
 9RI  H2   CA   N    113.48  3.000
 9RI  H2   CA   CB   107.93  3.000
 9RI  N    CA   CB   109.14  3.000
 9RI  H2   CA   C    108.10  3.000
 9RI  CB   CA   C    109.19  3.000
 9RI  N    CA   C    108.94  3.000
 9RI  H4   CB   H3   106.46  3.000
 9RI  H4   CB   CG   110.39  3.000
 9RI  H3   CB   CG   108.91  3.000
 9RI  H4   CB   CA   108.67  3.000
 9RI  H3   CB   CA   106.84  3.000
 9RI  CG   CB   CA   115.17  3.000
 9RI  H6   N    H5   105.61  3.000
 9RI  H6   N    CA   110.19  3.000
 9RI  H5   N    CA   108.59  3.000
 9RI  H9   CG   H8   106.43  3.000
 9RI  H9   CG   CD   109.12  3.000
 9RI  H8   CG   CD   108.75  3.000
 9RI  H9   CG   CB   109.89  3.000
 9RI  H8   CG   CB   110.50  3.000
 9RI  CD   CG   CB   111.98  3.000
 9RI  H11  CD   H10  106.21  3.000
 9RI  H11  CD   CE   108.15  3.000
 9RI  H10  CD   CE   110.58  3.000
 9RI  H11  CD   CG   109.53  3.000
 9RI  H10  CD   CG   109.28  3.000
 9RI  CE   CD   CG   112.86  3.000
 9RI  H13  CE   H12  105.08  3.000
 9RI  H13  CE   NZ   108.80  3.000
 9RI  H12  CE   NZ   111.46  3.000
 9RI  H13  CE   CD   107.56  3.000
 9RI  H12  CE   CD   110.02  3.000
 9RI  NZ   CE   CD   113.48  3.000
 9RI  C4   NZ   CM   110.70  3.000
 9RI  C4   NZ   CE   114.40  3.000
 9RI  CM   NZ   CE   111.29  3.000
 9RI  H17  CM   H16  107.80  3.000
 9RI  H17  CM   H15  107.07  3.000
 9RI  H16  CM   H15  107.24  3.000
 9RI  H17  CM   NZ   110.08  3.000
 9RI  H16  CM   NZ   113.33  3.000
 9RI  H15  CM   NZ   111.06  3.000
 9RI  H18  C4   C3   109.13  3.000
 9RI  H18  C4   C5   110.69  3.000
 9RI  C3   C4   C5   101.51  3.000
 9RI  H18  C4   NZ   109.63  3.000
 9RI  C3   C4   NZ   114.51  3.000
 9RI  C5   C4   NZ   111.13  3.000
 9RI  H20  C5   H19  107.45  3.000
 9RI  H20  C5   C6   109.81  3.000
 9RI  H19  C5   C6   112.50  3.000
 9RI  H20  C5   C4   109.82  3.000
 9RI  H19  C5   C4   112.97  3.000
 9RI  C6   C5   C4   104.28  3.000
 9RI  H21  C6   C7   116.43  3.000
 9RI  H21  C6   C1   113.94  3.000
 9RI  C7   C6   C1   101.93  3.000
 9RI  H21  C6   C5   113.58  3.000
 9RI  C1   C6   C5   108.36  3.000
 9RI  C7   C6   C5   101.23  3.000
 9RI  H23  C1   H22  107.11  3.000
 9RI  H23  C1   C2   111.17  3.000
 9RI  H22  C1   C2   112.99  3.000
 9RI  H23  C1   C6   111.06  3.000
 9RI  H22  C1   C6   112.06  3.000
 9RI  C2   C1   C6   102.52  3.000
 9RI  H25  C7   H24  108.73  3.000
 9RI  H25  C7   C3   113.41  3.000
 9RI  H24  C7   C3   113.17  3.000
 9RI  H25  C7   C6   113.52  3.000
 9RI  H24  C7   C6   113.38  3.000
 9RI  C3   C7   C6    94.18  3.000
 9RI  H26  C3   C2   112.18  3.000
 9RI  H26  C3   C7   116.69  3.000
 9RI  C2   C3   C7   101.76  3.000
 9RI  H26  C3   C4   114.82  3.000
 9RI  C2   C3   C4   107.58  3.000
 9RI  C7   C3   C4   102.50  3.000
 9RI  H28  C2   H27  106.89  3.000
 9RI  H28  C2   C3   112.07  3.000
 9RI  H27  C2   C3   110.23  3.000
 9RI  H28  C2   C1   113.02  3.000
 9RI  H27  C2   C1   111.09  3.000
 9RI  C3   C2   C1   103.59  3.000
 9RI  HXT  OXT  C    109.89  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  CONST_01  HXT  OXT  C   O      0.00   0.0  0
 9RI  CONST_02  HXT  OXT  C   CA   180.00   0.0  0
 9RI  Var_01    C3   C2   C1  C6    -1.60  30.0  1
 9RI  Var_02    H27  C2   C1  C6  -119.93  30.0  1
 9RI  Var_03    H28  C2   C1  C6   119.92  30.0  1
 9RI  Var_04    H22  C1   C2  C3  -122.41  30.0  1
 9RI  Var_05    H23  C1   C2  C3   117.13  30.0  1
 9RI  Var_06    C4   NZ   CE  CD   104.09  30.0  3
 9RI  Var_07    H15  CM   NZ  C4   -57.46  30.0  3
 9RI  Var_08    H16  CM   NZ  C4    63.34  30.0  3
 9RI  Var_09    H17  CM   NZ  C4  -175.86  30.0  3
 9RI  Var_10    H12  CE   NZ  C4   -20.80  30.0  2
 9RI  Var_11    H13  CE   NZ  C4  -136.22  30.0  2
 9RI  Var_12    CD   CG   CB  CA   173.07  30.0  3
 9RI  Var_13    CE   CD   CG  CB   177.16  30.0  3
 9RI  Var_14    NZ   CE   CD  CG    60.19  30.0  3
 9RI  Var_15    CM   NZ   CE  CD  -129.52  30.0  3
 9RI  Var_16    H8   CG   CB  CA   -65.53  30.0  3
 9RI  Var_17    H9   CG   CB  CA    51.63  30.0  3
 9RI  Var_18    H10  CD   CG  CB   -59.36  30.0  3
 9RI  Var_19    H11  CD   CG  CB    56.61  30.0  3
 9RI  Var_20    H12  CE   CD  CG  -174.15  30.0  3
 9RI  Var_21    H13  CE   CD  CG   -60.21  30.0  3
 9RI  Var_22    H3   CB   CG  CD    53.11  30.0  1
 9RI  Var_23    H4   CB   CG  CD   -63.43  30.0  1
 9RI  Var_24    H8   CG   CD  CE    54.75  30.0  1
 9RI  Var_25    H9   CG   CD  CE   -60.96  30.0  1
 9RI  Var_26    H15  CM   NZ  CE   174.13  30.0  3
 9RI  Var_27    H16  CM   NZ  CE   -65.08  30.0  3
 9RI  Var_28    H17  CM   NZ  CE    55.73  30.0  3
 9RI  Var_29    H10  CD   CE  NZ   -62.57  30.0  1
 9RI  Var_30    H11  CD   CE  NZ  -178.48  30.0  1
 9RI  Var_31    H12  CE   NZ  CM   105.60  30.0  2
 9RI  Var_32    H13  CE   NZ  CM    -9.82  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
 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
 9RI  plan-1  HXT  0.020

