# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:32:55 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: (2S,5S)-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1N(C)c2cccc3[nH]cc(C[C@@H](CO)NC1=O)c23
#
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
 ILV  ILV  (2S,5S)-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one  ligand  45  22  .  2022-09-15  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_ILV
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
 ILV  CG2  C  CH3   0  -0.672   3.5924  -1.3077  -0.7415
 ILV  CB   C  CH1   0  -0.217   2.2927  -1.9768  -0.2957
 ILV  CG1  C  CH3   0  -0.672   2.5937  -2.9988   0.7927
 ILV  CA   C  CH1   0  -0.131   1.2663  -0.9080   0.1328
 ILV  C    C  C     0   0.499   0.9188  -0.0802  -1.1082
 ILV  O    O  O     0  -0.488   0.6313  -0.6419  -2.1574
 ILV  NAO  N  NH1   0  -0.608   0.9697   1.2603  -1.0391
 ILV  CAQ  C  CH1   0  -0.118   1.0890   2.1529   0.1018
 ILV  CAS  C  CH2   0  -0.135   2.5171   2.3218   0.6009
 ILV  OAV  O  OH1   0  -0.666   3.3271   2.7576  -0.4614
 ILV  CAJ  C  CH2   0  -0.594   0.1315   1.8252   1.2608
 ILV  CAI  C  CR5   0   0.021  -1.2405   1.4631   0.7960
 ILV  CAE  C  CR56  0   0.036  -1.7427   0.1989   0.3241
 ILV  CAH  C  CR15  0  -0.076  -2.2627   2.3575   0.6410
 ILV  NAG  N  NR15  0  -0.688  -3.3554   1.7427   0.1069
 ILV  CAD  C  CR56  0   0.349  -3.0741   0.4254  -0.1013
 ILV  CAC  C  CR16  0  -0.314  -3.8911  -0.5805  -0.6152
 ILV  CAB  C  CR16  0  -0.292  -3.3514  -1.8463  -0.7070
 ILV  CAA  C  CR16  0  -0.309  -2.0365  -2.1011  -0.2909
 ILV  CAF  C  CR6   0   0.166  -1.2222  -1.1103   0.2242
 ILV  N    N  NT    0  -0.508   0.0558  -1.4876   0.7195
 ILV  CAL  C  CH3   0  -0.555   0.0484  -1.6017   2.1684
 ILV  H1   H  HCH3  0   0.216   4.0725  -0.7937   0.0952
 ILV  H2   H  HCH3  0   0.234   4.2973  -2.0516  -1.1152
 ILV  H3   H  HCH3  0   0.234   3.4462  -0.5718  -1.5331
 ILV  H4   H  HCH1  0   0.223   1.8602  -2.5124  -1.1442
 ILV  H5   H  HCH3  0   0.212   3.0203  -2.5305   1.6829
 ILV  H6   H  HCH3  0   0.237   1.7029  -3.5521   1.0881
 ILV  H7   H  HCH3  0   0.232   3.3223  -3.7241   0.4258
 ILV  H8   H  HCH1  0   0.222   1.7626  -0.2710   0.8715
 ILV  H9   H  HNH1  0   0.389   0.7206   1.7127  -1.9060
 ILV  H10  H  HCH1  0   0.270   0.7734   3.1217  -0.2922
 ILV  H11  H  HCH2  0   0.204   2.4952   3.0486   1.4242
 ILV  H12  H  HCH2  0   0.201   2.8836   1.3803   1.0273
 ILV  H13  H  HOH1  0   0.456   4.2378   2.7765  -0.1550
 ILV  H14  H  HCH2  0   0.248   0.5549   1.0457   1.8950
 ILV  H15  H  HCH2  0   0.268   0.0799   2.7147   1.8929
 ILV  H16  H  HCR5  0   0.280  -2.2837   3.4111   0.8739
 ILV  H17  H  HNR5  0   0.407  -4.2352   2.1907  -0.0862
 ILV  H18  H  HCR6  0   0.256  -4.9070  -0.3728  -0.9266
 ILV  H19  H  HCR6  0   0.245  -3.9500  -2.6576  -1.1015
 ILV  H20  H  HCR6  0   0.237  -1.6351  -3.1043  -0.3621
 ILV  H21  H  HCH3  0   0.213  -0.2553  -0.6815   2.6844
 ILV  H22  H  HCH3  0   0.244  -0.6442  -2.3880   2.4729
 ILV  H23  H  HCH3  0   0.244   1.0332  -1.8743   2.5395

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
 ILV  NAG  CAH  aromatic  1.363  0.020  1.363
 ILV  NAG  CAD  aromatic  1.363  0.020  1.363
 ILV  CAC  CAD  aromatic  1.394  0.020  1.394
 ILV  CAC  CAB  aromatic  1.379  0.020  1.379
 ILV  CG2  CB   single    1.528  0.020  1.528
 ILV  CAH  CAI  single    1.367  0.020  1.367
 ILV  CAD  CAE  single    1.416  0.020  1.416
 ILV  CAB  CAA  aromatic  1.403  0.020  1.403
 ILV  CAI  CAE  aromatic  1.440  0.020  1.440
 ILV  CAI  CAJ  single    1.493  0.020  1.493
 ILV  CAE  CAF  aromatic  1.412  0.020  1.412
 ILV  CG1  CB   single    1.523  0.020  1.523
 ILV  CAA  CAF  single    1.382  0.020  1.382
 ILV  CB   CA   single    1.543  0.020  1.543
 ILV  CAF  N    single    1.422  0.020  1.422
 ILV  CAJ  CAQ  single    1.539  0.020  1.539
 ILV  CA   N    single    1.465  0.020  1.465
 ILV  CA   C    single    1.532  0.020  1.532
 ILV  N    CAL  single    1.453  0.020  1.453
 ILV  CAQ  NAO  single    1.453  0.020  1.453
 ILV  CAQ  CAS  single    1.522  0.020  1.522
 ILV  C    NAO  single    1.343  0.020  1.343
 ILV  C    O    double    1.224  0.020  1.224
 ILV  CAS  OAV  single    1.405  0.020  1.405
 ILV  CG2  H1   single    0.970  0.020  1.090
 ILV  CG2  H2   single    0.970  0.020  1.090
 ILV  CG2  H3   single    0.970  0.020  1.090
 ILV  CB   H4   single    0.970  0.020  1.090
 ILV  CG1  H5   single    0.970  0.020  1.090
 ILV  CG1  H6   single    0.970  0.020  1.090
 ILV  CG1  H7   single    0.970  0.020  1.090
 ILV  CA   H8   single    0.970  0.020  1.090
 ILV  NAO  H9   single    0.860  0.020  1.020
 ILV  CAQ  H10  single    0.970  0.020  1.090
 ILV  CAS  H11  single    0.970  0.020  1.090
 ILV  CAS  H12  single    0.970  0.020  1.090
 ILV  OAV  H13  single    0.850  0.020  0.980
 ILV  CAJ  H14  single    0.970  0.020  1.090
 ILV  CAJ  H15  single    0.970  0.020  1.090
 ILV  CAH  H16  single    0.930  0.020  1.080
 ILV  NAG  H17  single    0.860  0.020  1.020
 ILV  CAC  H18  single    0.930  0.020  1.080
 ILV  CAB  H19  single    0.930  0.020  1.080
 ILV  CAA  H20  single    0.930  0.020  1.080
 ILV  CAL  H21  single    0.970  0.020  1.090
 ILV  CAL  H22  single    0.970  0.020  1.090
 ILV  CAL  H23  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
 ILV  H3   CG2  H2   107.35  3.000
 ILV  H3   CG2  H1   107.29  3.000
 ILV  H2   CG2  H1   107.40  3.000
 ILV  H3   CG2  CB   113.15  3.000
 ILV  H2   CG2  CB   110.54  3.000
 ILV  H1   CG2  CB   110.86  3.000
 ILV  H4   CB   CA   106.97  3.000
 ILV  H4   CB   CG1  107.71  3.000
 ILV  CA   CB   CG1  113.45  3.000
 ILV  H4   CB   CG2  108.95  3.000
 ILV  CA   CB   CG2  110.10  3.000
 ILV  CG1  CB   CG2  109.52  3.000
 ILV  H7   CG1  H6   107.42  3.000
 ILV  H7   CG1  H5   107.34  3.000
 ILV  H6   CG1  H5   108.42  3.000
 ILV  H7   CG1  CB   109.74  3.000
 ILV  H6   CG1  CB   111.90  3.000
 ILV  H5   CG1  CB   111.82  3.000
 ILV  H8   CA   N    109.56  3.000
 ILV  H8   CA   C    109.59  3.000
 ILV  N    CA   C    110.54  3.000
 ILV  H8   CA   CB   106.80  3.000
 ILV  C    CA   CB   107.48  3.000
 ILV  N    CA   CB   112.77  3.000
 ILV  NAO  C    O    120.72  3.000
 ILV  O    C    CA   119.98  3.000
 ILV  NAO  C    CA   119.28  3.000
 ILV  H9   NAO  CAQ  114.79  3.000
 ILV  H9   NAO  C    113.19  3.000
 ILV  CAQ  NAO  C    131.02  3.000
 ILV  H10  CAQ  CAJ  106.31  3.000
 ILV  H10  CAQ  CAS  106.91  3.000
 ILV  CAJ  CAQ  CAS  111.13  3.000
 ILV  H10  CAQ  NAO  103.76  3.000
 ILV  CAS  CAQ  NAO  113.73  3.000
 ILV  CAJ  CAQ  NAO  114.17  3.000
 ILV  H12  CAS  H11  106.45  3.000
 ILV  H12  CAS  OAV  111.56  3.000
 ILV  H11  CAS  OAV  111.90  3.000
 ILV  H12  CAS  CAQ  110.23  3.000
 ILV  H11  CAS  CAQ  107.49  3.000
 ILV  OAV  CAS  CAQ  109.11  3.000
 ILV  H13  OAV  CAS  108.14  3.000
 ILV  H15  CAJ  H14  105.31  3.000
 ILV  H15  CAJ  CAI  109.52  3.000
 ILV  H14  CAJ  CAI  111.37  3.000
 ILV  H15  CAJ  CAQ  106.97  3.000
 ILV  H14  CAJ  CAQ  110.41  3.000
 ILV  CAI  CAJ  CAQ  112.88  3.000
 ILV  CAH  CAI  CAE  106.05  3.000
 ILV  CAE  CAI  CAJ  129.45  3.000
 ILV  CAH  CAI  CAJ  124.31  3.000
 ILV  CAF  CAE  CAD  118.26  3.000
 ILV  CAF  CAE  CAI  135.12  3.000
 ILV  CAD  CAE  CAI  106.62  3.000
 ILV  H16  CAH  NAG  120.62  3.000
 ILV  H16  CAH  CAI  128.96  3.000
 ILV  NAG  CAH  CAI  110.41  3.000
 ILV  H17  NAG  CAD  125.57  3.000
 ILV  H17  NAG  CAH  125.13  3.000
 ILV  CAD  NAG  CAH  109.29  3.000
 ILV  CAC  CAD  NAG  129.25  3.000
 ILV  CAC  CAD  CAE  123.12  3.000
 ILV  NAG  CAD  CAE  107.63  3.000
 ILV  H18  CAC  CAB  121.61  3.000
 ILV  H18  CAC  CAD  121.17  3.000
 ILV  CAB  CAC  CAD  117.22  3.000
 ILV  H19  CAB  CAA  119.36  3.000
 ILV  H19  CAB  CAC  119.71  3.000
 ILV  CAA  CAB  CAC  120.92  3.000
 ILV  H20  CAA  CAF  118.05  3.000
 ILV  H20  CAA  CAB  119.76  3.000
 ILV  CAF  CAA  CAB  122.19  3.000
 ILV  N    CAF  CAA  117.99  3.000
 ILV  N    CAF  CAE  123.55  3.000
 ILV  CAA  CAF  CAE  118.28  3.000
 ILV  CAL  N    CAF  111.32  3.000
 ILV  CAL  N    CA   115.76  3.000
 ILV  CAF  N    CA   119.89  3.000
 ILV  H23  CAL  H22  107.40  3.000
 ILV  H23  CAL  H21  107.48  3.000
 ILV  H22  CAL  H21  107.30  3.000
 ILV  H23  CAL  N    110.82  3.000
 ILV  H22  CAL  N    109.76  3.000
 ILV  H21  CAL  N    113.84  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
 ILV  CONST_01  CAD  NAG  CAH  CAI    0.00   0.0  0
 ILV  CONST_02  NAG  CAD  CAE  CAI    0.00   0.0  0
 ILV  CONST_03  CAC  CAD  CAE  CAI  180.00   0.0  0
 ILV  CONST_04  CAA  CAF  CAE  CAI  180.00   0.0  0
 ILV  CONST_05  CAH  NAG  CAD  CAE    0.00   0.0  0
 ILV  CONST_06  CAB  CAC  CAD  CAE    0.00   0.0  0
 ILV  CONST_07  NAG  CAH  CAI  CAE    0.00   0.0  0
 ILV  CONST_08  CAB  CAA  CAF  CAE    0.00   0.0  0
 ILV  CONST_09  CAC  CAD  NAG  CAH  180.00   0.0  0
 ILV  CONST_10  CAD  CAE  CAI  CAH    0.00   0.0  0
 ILV  CONST_11  CAF  CAE  CAI  CAH  180.00   0.0  0
 ILV  CONST_12  CAB  CAC  CAD  NAG  180.00   0.0  0
 ILV  CONST_13  CAF  CAE  CAD  NAG  180.00   0.0  0
 ILV  CONST_14  CAA  CAB  CAC  CAD    0.00   0.0  0
 ILV  CONST_15  CAA  CAF  CAE  CAD    0.00   0.0  0
 ILV  CONST_16  CAF  CAE  CAD  CAC    0.00   0.0  0
 ILV  CONST_17  CAF  CAA  CAB  CAC    0.00   0.0  0
 ILV  CONST_18  CAQ  NAO  C    CA     0.00   0.0  0
 ILV  CONST_19  CAQ  NAO  C    O    180.00   0.0  0
 ILV  CONST_20  H16  CAH  CAI  CAJ    0.00   0.0  0
 ILV  CONST_21  H17  NAG  CAH  CAI  180.00   0.0  0
 ILV  CONST_22  H18  CAC  CAD  CAE  180.00   0.0  0
 ILV  CONST_23  H20  CAA  CAF  CAE  180.00   0.0  0
 ILV  CONST_24  H19  CAB  CAC  CAD  180.00   0.0  0
 ILV  CONST_25  H9   NAO  C    CA   180.00   0.0  0
 ILV  Var_01    CAE  CAF  N    CA   -64.65  30.0  1
 ILV  Var_02    CAH  CAI  CAJ  CAQ  -91.61  30.0  1
 ILV  Var_03    H21  CAL  N    CA    83.70  30.0  3
 ILV  Var_04    H1   CG2  CB   CA    65.17  30.0  3
 ILV  Var_05    H5   CG1  CB   CA   -61.11  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
 ILV  chir_01  CA   CB   N    C    positiv
 ILV  chir_02  CAQ  NAO  CAS  CAJ  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
 ILV  plan-1  CAJ  0.020
 ILV  plan-1  CAI  0.020
 ILV  plan-1  CAE  0.020
 ILV  plan-1  CAH  0.020
 ILV  plan-1  NAG  0.020
 ILV  plan-1  CAD  0.020
 ILV  plan-1  CAC  0.020
 ILV  plan-1  CAB  0.020
 ILV  plan-1  CAA  0.020
 ILV  plan-1  CAF  0.020
 ILV  plan-1  N    0.020
 ILV  plan-1  H16  0.020
 ILV  plan-1  H17  0.020
 ILV  plan-1  H18  0.020
 ILV  plan-1  H19  0.020
 ILV  plan-1  H20  0.020
 ILV  plan-2  CA   0.020
 ILV  plan-2  C    0.020
 ILV  plan-2  O    0.020
 ILV  plan-2  NAO  0.020
 ILV  plan-2  CAQ  0.020
 ILV  plan-2  H9   0.020

