# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:03:14 2020
#   Inital geometry file: a 102 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CN(CCO1)c2ncnc3[nH]c4cnccc4c23
#
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
 YM6  YM6  'None                     '  ligand  37  21  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YM6
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
 YM6  N1    N  N     0  -0.478  -0.0653   2.3695  -1.0674
 YM6  C2    C  CR16  0   0.056   1.0855   2.9245  -1.4199
 YM6  N3    N  N     0  -0.450   2.3073   2.5123  -1.1352
 YM6  C4    C  CR56  0   0.489   2.3204   1.3543  -0.4837
 YM6  C5    C  CR56  0  -0.095   1.1855   0.6268  -0.0774
 YM6  C6    C  CR6   0   0.485  -0.0528   1.2451  -0.3455
 YM6  NAA   N  NH2   0  -0.802  -4.4469  -1.8460  -1.3258
 YM6  CAB   C  CR16  0  -0.089   2.0013  -2.8262   1.2778
 YM6  CAD   C  CR16  0  -0.451   1.1294  -1.8237   0.8911
 YM6  CAE   C  CR16  0  -0.101   3.8744  -1.6008   0.7996
 YM6  CAG   C  CH2   0  -0.193  -2.5154  -0.7662   1.4848
 YM6  CAH   C  CH2   0  -0.350  -1.4180   0.2766   1.4409
 YM6  CAI   C  CH2   0  -0.326  -2.4825   1.2972  -0.4504
 YM6  NAJ   N  N     0  -0.409   3.3325  -2.7213   1.2472
 YM6  NAM   N  NR15  0  -0.751   3.4410   0.6641  -0.1646
 YM6  OAN   O  OC2   0  -0.489  -3.7170  -0.2668   0.9407
 YM6  CAP   C  CR56  0   0.257   3.0820  -0.5427   0.3800
 YM6  CAQ   C  CR56  0   0.140   1.6750  -0.6219   0.4429
 YM6  CAT   C  CH1   0  -0.002  -3.5793   0.2395  -0.3779
 YM6  NAU   N  N     0  -0.501  -1.2437   0.7454   0.0731
 YM6  H2    H  HCR6  0   0.257   1.0097   3.8389  -1.9987
 YM6  HNAA  H  HNH2  0   0.349  -4.3364  -2.5229  -2.0690
 YM6  HNAB  H  HNH2  0   0.342  -4.3678  -2.3705  -0.4638
 YM6  HAB   H  HCR6  0   0.263   1.6042  -3.7707   1.6305
 YM6  HAD   H  HCR6  0   0.266   0.0654  -2.0069   0.9260
 YM6  HAE   H  HCR6  0   0.274   4.9570  -1.5408   0.7632
 YM6  HAF   H  HCH2  0   0.203  -2.3682  -1.2954  -1.3172
 YM6  HAFA  H  HCH2  0   0.235  -3.4124  -0.3962  -2.3928
 YM6  HAG   H  HCH2  0   0.213  -2.1881  -1.6765   0.9651
 YM6  HAGA  H  HCH2  0   0.252  -2.7223  -1.0379   2.5205
 YM6  HAH   H  HCH2  0   0.258  -1.6950   1.1286   2.0755
 YM6  HAHA  H  HCH2  0   0.273  -0.4951  -0.1276   1.8468
 YM6  HAI   H  HCH2  0   0.268  -2.3452   1.6066  -1.4844
 YM6  HAIA  H  HCH2  0   0.248  -2.7809   2.1858   0.1197
 YM6  HAT   H  HCH1  0   0.247  -4.5321   0.7285  -0.5977
 YM6  HNAM  H  HNR5  0   0.419   4.3804   0.9646  -0.3720
 YM6  CAF   C  CH2   0  -0.307  -3.3762  -0.8672  -1.4072

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
 YM6  C2   N1    aromatic  1.325  0.020  1.325
 YM6  N1   C6    aromatic  1.336  0.020  1.336
 YM6  N3   C2    aromatic  1.321  0.020  1.321
 YM6  C2   H2    aromatic  0.930  0.020  1.080
 YM6  N3   C4    aromatic  1.329  0.020  1.329
 YM6  C4   NAM   aromatic  1.354  0.020  1.354
 YM6  C4   C5    aromatic  1.408  0.020  1.408
 YM6  C5   C6    aromatic  1.410  0.020  1.410
 YM6  C5   CAQ   aromatic  1.439  0.020  1.439
 YM6  C6   NAU   single    1.358  0.020  1.358
 YM6  CAF  NAA   single    1.453  0.020  1.453
 YM6  NAA  HNAA  single    0.890  0.020  1.040
 YM6  NAA  HNAB  single    0.890  0.020  1.040
 YM6  NAJ  CAB   aromatic  1.336  0.020  1.336
 YM6  CAD  CAB   aromatic  1.384  0.020  1.384
 YM6  CAB  HAB   aromatic  0.930  0.020  1.080
 YM6  CAQ  CAD   aromatic  1.394  0.020  1.394
 YM6  CAD  HAD   single    0.930  0.020  1.080
 YM6  CAP  CAE   aromatic  1.387  0.020  1.387
 YM6  CAE  NAJ   aromatic  1.323  0.020  1.323
 YM6  CAE  HAE   single    0.930  0.020  1.080
 YM6  CAT  CAF   single    1.525  0.020  1.525
 YM6  CAF  HAF   single    0.970  0.020  1.090
 YM6  CAF  HAFA  single    0.970  0.020  1.090
 YM6  CAH  CAG   single    1.514  0.020  1.514
 YM6  OAN  CAG   single    1.410  0.020  1.410
 YM6  CAG  HAG   single    0.970  0.020  1.090
 YM6  CAG  HAGA  single    0.970  0.020  1.090
 YM6  NAU  CAH   aromatic  1.456  0.020  1.456
 YM6  CAH  HAH   aromatic  0.970  0.020  1.090
 YM6  CAH  HAHA  single    0.970  0.020  1.090
 YM6  NAU  CAI   aromatic  1.454  0.020  1.454
 YM6  CAI  CAT   aromatic  1.525  0.020  1.525
 YM6  CAI  HAI   aromatic  0.970  0.020  1.090
 YM6  CAI  HAIA  aromatic  0.970  0.020  1.090
 YM6  NAM  CAP   aromatic  1.372  0.020  1.372
 YM6  CAT  OAN   single    1.419  0.020  1.419
 YM6  CAP  CAQ   aromatic  1.411  0.020  1.411
 YM6  CAT  HAT   single    0.970  0.020  1.090
 YM6  NAM  HNAM  single    0.860  0.020  1.020

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
 YM6  C6    N1   C2    119.20  3.000
 YM6  H2    C2   N3    116.28  3.000
 YM6  H2    C2   N1    115.74  3.000
 YM6  N3    C2   N1    127.97  3.000
 YM6  C4    N3   C2    112.76  3.000
 YM6  NAM   C4   C5    109.61  3.000
 YM6  C5    C4   N3    125.72  3.000
 YM6  NAM   C4   N3    124.60  3.000
 YM6  CAQ   C5   C6    138.44  3.000
 YM6  CAQ   C5   C4    106.18  3.000
 YM6  C6    C5   C4    115.24  3.000
 YM6  NAU   C6   C5    123.40  3.000
 YM6  NAU   C6   N1    117.91  3.000
 YM6  C5    C6   N1    118.69  3.000
 YM6  HNAB  NAA  HNAA  105.69  3.000
 YM6  HNAB  NAA  CAF   109.83  3.000
 YM6  HNAA  NAA  CAF   109.22  3.000
 YM6  HAB   CAB  NAJ   116.18  3.000
 YM6  HAB   CAB  CAD   119.44  3.000
 YM6  NAJ   CAB  CAD   124.38  3.000
 YM6  HAD   CAD  CAQ   122.83  3.000
 YM6  HAD   CAD  CAB   119.26  3.000
 YM6  CAQ   CAD  CAB   117.89  3.000
 YM6  HAE   CAE  CAP   121.19  3.000
 YM6  HAE   CAE  NAJ   117.84  3.000
 YM6  CAP   CAE  NAJ   120.97  3.000
 YM6  HAGA  CAG  HAG   107.43  3.000
 YM6  HAGA  CAG  OAN   107.04  3.000
 YM6  HAG   CAG  OAN   111.40  3.000
 YM6  HAGA  CAG  CAH   109.67  3.000
 YM6  HAG   CAG  CAH   109.95  3.000
 YM6  OAN   CAG  CAH   111.24  3.000
 YM6  HAHA  CAH  HAH   106.69  3.000
 YM6  HAHA  CAH  NAU   111.65  3.000
 YM6  HAH   CAH  NAU   108.86  3.000
 YM6  HAHA  CAH  CAG   110.40  3.000
 YM6  HAH   CAH  CAG   109.56  3.000
 YM6  NAU   CAH  CAG   109.61  3.000
 YM6  HAIA  CAI  HAI   107.32  3.000
 YM6  HAIA  CAI  NAU   110.62  3.000
 YM6  HAI   CAI  NAU   110.04  3.000
 YM6  HAIA  CAI  CAT   109.96  3.000
 YM6  HAI   CAI  CAT   109.46  3.000
 YM6  NAU   CAI  CAT   109.42  3.000
 YM6  CAE   NAJ  CAB   118.86  3.000
 YM6  HNAM  NAM  CAP   126.02  3.000
 YM6  HNAM  NAM  C4    124.80  3.000
 YM6  CAP   NAM  C4    108.98  3.000
 YM6  CAT   OAN  CAG   113.71  3.000
 YM6  CAQ   CAP  NAM   109.16  3.000
 YM6  CAQ   CAP  CAE   120.90  3.000
 YM6  NAM   CAP  CAE   129.92  3.000
 YM6  CAP   CAQ  CAD   116.95  3.000
 YM6  CAP   CAQ  C5    105.93  3.000
 YM6  CAD   CAQ  C5    137.01  3.000
 YM6  HAT   CAT  OAN   105.18  3.000
 YM6  HAT   CAT  CAI   107.87  3.000
 YM6  OAN   CAT  CAI   111.18  3.000
 YM6  HAT   CAT  CAF   107.76  3.000
 YM6  OAN   CAT  CAF   112.41  3.000
 YM6  CAI   CAT  CAF   112.05  3.000
 YM6  CAI   NAU  CAH   111.00  3.000
 YM6  CAI   NAU  C6    119.79  3.000
 YM6  CAH   NAU  C6    120.87  3.000
 YM6  HAFA  CAF  HAF   105.79  3.000
 YM6  HAFA  CAF  CAT   106.95  3.000
 YM6  HAF   CAF  CAT   110.47  3.000
 YM6  HAFA  CAF  NAA   108.45  3.000
 YM6  HAF   CAF  NAA   114.14  3.000
 YM6  CAT   CAF  NAA   110.67  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
 YM6  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 YM6  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 YM6  CONST_03  CAQ   C5   C6   N1   180.00   0.0  0
 YM6  CONST_05  CAI   NAU  C6   N1     0.00   0.0  0
 YM6  CONST_06  C5    C6   N1   C2     0.00   0.0  0
 YM6  CONST_07  NAU   C6   N1   C2   180.00   0.0  0
 YM6  CONST_08  NAM   C4   N3   C2   180.00   0.0  0
 YM6  CONST_09  C5    C4   N3   C2     0.00   0.0  0
 YM6  CONST_10  C6    N1   C2   N3     0.00   0.0  0
 YM6  CONST_11  CAP   NAM  C4   N3   180.00   0.0  0
 YM6  CONST_12  C6    C5   C4   N3     0.00   0.0  0
 YM6  CONST_13  CAQ   C5   C4   N3   180.00   0.0  0
 YM6  CONST_14  CAE   CAP  NAM  C4   180.00   0.0  0
 YM6  CONST_15  CAQ   CAP  NAM  C4     0.00   0.0  0
 YM6  CONST_16  NAU   C6   C5   C4   180.00   0.0  0
 YM6  CONST_17  CAD   CAQ  C5   C4   180.00   0.0  0
 YM6  CONST_18  CAP   CAQ  C5   C4     0.00   0.0  0
 YM6  CONST_19  CAP   NAM  C4   C5     0.00   0.0  0
 YM6  CONST_21  CAI   NAU  C6   C5   180.00   0.0  0
 YM6  CONST_22  CAB   CAD  CAQ  C5   180.00   0.0  0
 YM6  CONST_23  CAE   CAP  CAQ  C5   180.00   0.0  0
 YM6  CONST_24  NAM   CAP  CAQ  C5     0.00   0.0  0
 YM6  CONST_25  NAM   C4   C5   C6   180.00   0.0  0
 YM6  CONST_26  CAD   CAQ  C5   C6     0.00   0.0  0
 YM6  CONST_27  CAP   CAQ  C5   C6   180.00   0.0  0
 YM6  CONST_29  CAP   CAE  NAJ  CAB    0.00   0.0  0
 YM6  CONST_30  CAP   CAQ  CAD  CAB    0.00   0.0  0
 YM6  CONST_31  CAE   NAJ  CAB  CAD    0.00   0.0  0
 YM6  CONST_32  CAE   CAP  CAQ  CAD    0.00   0.0  0
 YM6  CONST_33  NAM   CAP  CAQ  CAD  180.00   0.0  0
 YM6  CONST_35  CAQ   CAD  CAB  NAJ    0.00   0.0  0
 YM6  CONST_36  NAM   CAP  CAE  NAJ  180.00   0.0  0
 YM6  CONST_37  CAQ   CAP  CAE  NAJ    0.00   0.0  0
 YM6  CONST_38  CAQ   C5   C4   NAM    0.00   0.0  0
 YM6  CONST_39  NAU   C6   C5   CAQ    0.00   0.0  0
 YM6  CONST_41  H2    C2   N3   C4   180.00   0.0  0
 YM6  CONST_45  HAB   CAB  NAJ  CAE  180.00   0.0  0
 YM6  CONST_46  HNAM  NAM  C4   N3     0.00   0.0  0
 YM6  CONST_47  HAD   CAD  CAQ  C5     0.00   0.0  0
 YM6  CONST_48  HAE   CAE  NAJ  CAB  180.00   0.0  0
 YM6  Var_01    CAI   CAT  OAN  CAG  -54.65  30.0  1
 YM6  Var_02    NAU   CAH  CAG  OAN  -55.61  30.0  1
 YM6  Var_03    NAU   CAI  CAT  OAN   54.76  30.0  1
 YM6  Var_04    HAG   CAG  OAN  CAT  -67.98  30.0  1
 YM6  Var_05    HNAA  NAA  CAF  CAT  175.01  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
 YM6  chir_01  CAT  CAF  CAI  OAN  both

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
 YM6  plan-1  N1    0.020
 YM6  plan-1  C2    0.020
 YM6  plan-1  N3    0.020
 YM6  plan-1  C4    0.020
 YM6  plan-1  C5    0.020
 YM6  plan-1  C6    0.020
 YM6  plan-1  CAB   0.020
 YM6  plan-1  CAD   0.020
 YM6  plan-1  CAE   0.020
 YM6  plan-1  NAJ   0.020
 YM6  plan-1  NAM   0.020
 YM6  plan-1  CAP   0.020
 YM6  plan-1  CAQ   0.020
 YM6  plan-1  NAU   0.020
 YM6  plan-1  H2    0.020
 YM6  plan-1  HAB   0.020
 YM6  plan-1  HAD   0.020
 YM6  plan-1  HAE   0.020
 YM6  plan-1  HNAM  0.020

