# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 09:04:13 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [N-]=[N+]=N[C@@H]1CC[C@@H](CC1)C2=CC(=O)c3ccc4ccccc4c3O2
#
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
 AQ0  AQ0  2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one  ligand  41  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AQ0
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
 AQ0  C1   C  CR16   0  -0.310   4.2143   2.3275   0.0207
 AQ0  C2   C  CR66   0   0.107   3.6251   1.0460   0.0007
 AQ0  C3   C  CR66   0   0.015   2.2132   0.9446   0.0281
 AQ0  C9   C  CR66   0   0.345   1.6491  -0.3605   0.0016
 AQ0  C10  C  CR6    0   0.462   1.7843  -2.8143  -0.0923
 AQ0  C13  C  CH1    0  -0.365  -1.8157  -1.4714   0.0382
 AQ0  C14  C  CH2    0  -0.423  -2.2965  -0.9582   1.4030
 AQ0  C15  C  CH2    0  -0.461  -3.8196  -0.9111   1.4457
 AQ0  C16  C  CH1    0  -0.121  -4.4036  -0.0747   0.3172
 AQ0  C4   C  CR16   0  -0.284   1.4296   2.1177   0.0745
 AQ0  C6   C  CR16   0  -0.314   4.4176  -0.1336  -0.0489
 AQ0  C17  C  CH2    0  -0.458  -3.8872  -0.5505  -1.0385
 AQ0  C18  C  CH2    0  -0.419  -2.3644  -0.5939  -1.0938
 AQ0  N2   N  N     -1  -0.231  -4.8738   3.0166  -0.7932
 AQ0  N    N  N      0  -0.372  -4.0228   1.3308   0.5846
 AQ0  C12  C  CR6    0   0.480  -0.3305  -1.6014  -0.0098
 AQ0  O    O  O      0  -0.456   0.3053  -0.4222   0.0297
 AQ0  C5   C  CR16   0  -0.251   2.0342   3.3475   0.0914
 AQ0  C    C  CR16   0  -0.243   3.4366   3.4546   0.0640
 AQ0  C11  C  CR16   0  -0.538   0.3401  -2.7680  -0.0715
 AQ0  O1   O  O      0  -0.450   2.4271  -3.8563  -0.1426
 AQ0  C8   C  CR66   0  -0.152   2.4253  -1.4955  -0.0527
 AQ0  C7   C  CR16   0  -0.308   3.8370  -1.3614  -0.0758
 AQ0  H1   H  HCR6   0   0.264   5.2941   2.4070  -0.0005
 AQ0  H2   H  HCH1   0   0.268  -2.2093  -2.4839  -0.0990
 AQ0  H3   H  HCH2   0   0.253  -1.9286  -1.6114   2.1971
 AQ0  H4   H  HCH2   0   0.237  -1.8895   0.0378   1.5957
 AQ0  H5   H  HCH2   0   0.245  -4.2201  -1.9244   1.3552
 AQ0  H6   H  HCH2   0   0.254  -4.1585  -0.5237   2.4083
 AQ0  H7   H  HCH1   0   0.274  -5.4954  -0.1527   0.3391
 AQ0  H8   H  HCR6   0   0.260   0.3505   2.0533   0.0956
 AQ0  H9   H  HCR6   0   0.263   5.4957  -0.0364  -0.0675
 AQ0  H10  H  HCH2   0   0.245  -4.2936  -1.5503  -1.2179
 AQ0  H11  H  HCH2   0   0.250  -4.2763   0.0793  -1.8429
 AQ0  H12  H  HCH2   0   0.235  -1.9636   0.4193  -1.0132
 AQ0  H13  H  HCH2   0   0.253  -2.0443  -0.9861  -2.0612
 AQ0  H15  H  HCR6   0   0.267   1.4278   4.2427   0.1260
 AQ0  H16  H  HCR6   0   0.267   3.8996   4.4325   0.0769
 AQ0  H17  H  HCR6   0   0.278  -0.2226  -3.6913  -0.1033
 AQ0  H18  H  HCR6   0   0.267   4.4431  -2.2560  -0.1163
 AQ0  N1   N  N      1   0.372  -4.4882   2.1705  -0.1586

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
 AQ0  C    C5   aromatic  1.407  0.020  1.407
 AQ0  C    C1   aromatic  1.370  0.020  1.370
 AQ0  C5   C4   aromatic  1.371  0.020  1.371
 AQ0  C1   C2   aromatic  1.411  0.020  1.411
 AQ0  C4   C3   aromatic  1.411  0.020  1.411
 AQ0  C2   C3   aromatic  1.416  0.020  1.416
 AQ0  C2   C6   aromatic  1.422  0.020  1.422
 AQ0  C3   C9   aromatic  1.422  0.020  1.422
 AQ0  N2   N1   double    1.126  0.020  1.126
 AQ0  C6   C7   aromatic  1.358  0.020  1.358
 AQ0  N1   N    double    1.214  0.020  1.214
 AQ0  C9   O    single    1.346  0.020  1.346
 AQ0  C9   C8   aromatic  1.376  0.020  1.376
 AQ0  O    C12  single    1.340  0.020  1.340
 AQ0  C14  C15  single    1.524  0.020  1.524
 AQ0  C14  C13  single    1.535  0.020  1.535
 AQ0  C15  C16  single    1.521  0.020  1.521
 AQ0  N    C16  single    1.481  0.020  1.481
 AQ0  C7   C8   aromatic  1.418  0.020  1.418
 AQ0  C8   C10  single    1.467  0.020  1.467
 AQ0  C16  C17  single    1.527  0.020  1.527
 AQ0  C12  C13  single    1.492  0.020  1.492
 AQ0  C12  C11  double    1.347  0.020  1.347
 AQ0  C17  C18  single    1.524  0.020  1.524
 AQ0  C13  C18  single    1.534  0.020  1.534
 AQ0  C10  C11  single    1.445  0.020  1.445
 AQ0  C10  O1   double    1.225  0.020  1.225
 AQ0  C1   H1   single    0.930  0.020  1.080
 AQ0  C13  H2   single    0.970  0.020  1.090
 AQ0  C14  H3   single    0.970  0.020  1.090
 AQ0  C14  H4   single    0.970  0.020  1.090
 AQ0  C15  H5   single    0.970  0.020  1.090
 AQ0  C15  H6   single    0.970  0.020  1.090
 AQ0  C16  H7   single    0.970  0.020  1.090
 AQ0  C4   H8   single    0.930  0.020  1.080
 AQ0  C6   H9   single    0.930  0.020  1.080
 AQ0  C17  H10  single    0.970  0.020  1.090
 AQ0  C17  H11  single    0.970  0.020  1.090
 AQ0  C18  H12  single    0.970  0.020  1.090
 AQ0  C18  H13  single    0.970  0.020  1.090
 AQ0  C5   H15  single    0.930  0.020  1.080
 AQ0  C    H16  single    0.930  0.020  1.080
 AQ0  C11  H17  single    0.930  0.020  1.080
 AQ0  C7   H18  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
 AQ0  H1   C1   C    120.41  3.000
 AQ0  H1   C1   C2   118.87  3.000
 AQ0  C    C1   C2   120.71  3.000
 AQ0  C6   C2   C3   119.81  3.000
 AQ0  C6   C2   C1   121.42  3.000
 AQ0  C3   C2   C1   118.77  3.000
 AQ0  C4   C3   C9   122.90  3.000
 AQ0  C9   C3   C2   117.45  3.000
 AQ0  C4   C3   C2   119.66  3.000
 AQ0  C8   C9   O    121.76  3.000
 AQ0  C8   C9   C3   122.27  3.000
 AQ0  O    C9   C3   115.97  3.000
 AQ0  C8   C10  O1   122.44  3.000
 AQ0  O1   C10  C11  123.51  3.000
 AQ0  C8   C10  C11  114.05  3.000
 AQ0  H2   C13  C12  105.86  3.000
 AQ0  H2   C13  C18  107.94  3.000
 AQ0  C12  C13  C18  112.48  3.000
 AQ0  H2   C13  C14  107.93  3.000
 AQ0  C18  C13  C14  110.66  3.000
 AQ0  C12  C13  C14  111.69  3.000
 AQ0  H4   C14  H3   106.94  3.000
 AQ0  H4   C14  C15  109.81  3.000
 AQ0  H3   C14  C15  109.56  3.000
 AQ0  H4   C14  C13  110.16  3.000
 AQ0  H3   C14  C13  109.94  3.000
 AQ0  C15  C14  C13  110.37  3.000
 AQ0  H6   C15  H5   106.75  3.000
 AQ0  H6   C15  C16  109.87  3.000
 AQ0  H5   C15  C16  107.91  3.000
 AQ0  H6   C15  C14  110.24  3.000
 AQ0  H5   C15  C14  109.57  3.000
 AQ0  C16  C15  C14  112.32  3.000
 AQ0  H7   C16  N    108.70  3.000
 AQ0  H7   C16  C17  109.44  3.000
 AQ0  N    C16  C17  111.67  3.000
 AQ0  H7   C16  C15  109.20  3.000
 AQ0  C17  C16  C15  110.95  3.000
 AQ0  N    C16  C15  106.81  3.000
 AQ0  H8   C4   C5   119.57  3.000
 AQ0  H8   C4   C3   120.35  3.000
 AQ0  C5   C4   C3   120.09  3.000
 AQ0  H9   C6   C7   120.43  3.000
 AQ0  H9   C6   C2   118.76  3.000
 AQ0  C7   C6   C2   120.81  3.000
 AQ0  H11  C17  H10  105.88  3.000
 AQ0  H11  C17  C18  110.20  3.000
 AQ0  H10  C17  C18  109.82  3.000
 AQ0  H11  C17  C16  110.70  3.000
 AQ0  H10  C17  C16  107.74  3.000
 AQ0  C18  C17  C16  112.27  3.000
 AQ0  H13  C18  H12  106.91  3.000
 AQ0  H13  C18  C17  109.59  3.000
 AQ0  H12  C18  C17  109.72  3.000
 AQ0  H13  C18  C13  110.09  3.000
 AQ0  H12  C18  C13  110.18  3.000
 AQ0  C17  C18  C13  110.30  3.000
 AQ0  N1   N    C16  116.57  3.000
 AQ0  C11  C12  O    121.81  3.000
 AQ0  C11  C12  C13  124.94  3.000
 AQ0  O    C12  C13  113.25  3.000
 AQ0  C12  O    C9   120.90  3.000
 AQ0  H15  C5   C    119.76  3.000
 AQ0  H15  C5   C4   119.72  3.000
 AQ0  C    C5   C4   120.52  3.000
 AQ0  H16  C    C5   119.68  3.000
 AQ0  H16  C    C1   120.07  3.000
 AQ0  C5   C    C1   120.25  3.000
 AQ0  H17  C11  C12  118.79  3.000
 AQ0  H17  C11  C10  119.47  3.000
 AQ0  C12  C11  C10  121.74  3.000
 AQ0  C7   C8   C10  121.30  3.000
 AQ0  C10  C8   C9   119.75  3.000
 AQ0  C7   C8   C9   118.95  3.000
 AQ0  H18  C7   C8   118.70  3.000
 AQ0  H18  C7   C6   120.59  3.000
 AQ0  C8   C7   C6   120.71  3.000
 AQ0  N    N1   N2   175.00  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
 AQ0  CONST_01  C4   C5   C    C1     0.00   0.0  0
 AQ0  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 AQ0  CONST_03  C9   C3   C2   C1   180.00   0.0  0
 AQ0  CONST_04  C7   C6   C2   C1   180.00   0.0  0
 AQ0  CONST_05  C5   C    C1   C2     0.00   0.0  0
 AQ0  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 AQ0  CONST_07  C8   C9   C3   C2     0.00   0.0  0
 AQ0  CONST_08  C8   C7   C6   C2     0.00   0.0  0
 AQ0  CONST_09  C    C5   C4   C3     0.00   0.0  0
 AQ0  CONST_10  C    C1   C2   C3     0.00   0.0  0
 AQ0  CONST_11  C7   C6   C2   C3     0.00   0.0  0
 AQ0  CONST_12  C7   C8   C9   C3     0.00   0.0  0
 AQ0  CONST_13  C5   C4   C3   C9   180.00   0.0  0
 AQ0  CONST_14  C6   C2   C3   C9     0.00   0.0  0
 AQ0  CONST_15  C6   C7   C8   C9     0.00   0.0  0
 AQ0  CONST_16  C6   C2   C3   C4   180.00   0.0  0
 AQ0  CONST_17  C8   C9   C3   C4   180.00   0.0  0
 AQ0  CONST_18  C    C1   C2   C6   180.00   0.0  0
 AQ0  CONST_19  H15  C5   C    C1   180.00   0.0  0
 AQ0  CONST_20  H9   C6   C2   C1     0.00   0.0  0
 AQ0  CONST_21  H16  C    C1   C2   180.00   0.0  0
 AQ0  CONST_22  H8   C4   C3   C2   180.00   0.0  0
 AQ0  CONST_23  H18  C7   C6   C2   180.00   0.0  0
 AQ0  CONST_24  H1   C1   C2   C3   180.00   0.0  0
 AQ0  Var_01    C13  C12  O    C9   179.67  30.0  1
 AQ0  Var_02    C11  C10  C8   C9     0.13  30.0  1
 AQ0  Var_03    O    C12  C11  C10    0.29  30.0  1
 AQ0  Var_04    C16  C15  C14  C13  -55.78  30.0  1
 AQ0  Var_05    C16  C17  C18  C13   55.83  30.0  1
 AQ0  Var_06    C8   C9   O    C12   -0.76  30.0  1
 AQ0  Var_07    C8   C10  C11  C12   -0.51  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
 AQ0  chir_01  C13  C14  C12  C18  positiv
 AQ0  chir_02  C16  N    C15  C17  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
 AQ0  plan-1  C1   0.020
 AQ0  plan-1  C2   0.020
 AQ0  plan-1  C3   0.020
 AQ0  plan-1  C9   0.020
 AQ0  plan-1  C10  0.020
 AQ0  plan-1  C4   0.020
 AQ0  plan-1  C6   0.020
 AQ0  plan-1  O    0.020
 AQ0  plan-1  C5   0.020
 AQ0  plan-1  C    0.020
 AQ0  plan-1  C8   0.020
 AQ0  plan-1  C7   0.020
 AQ0  plan-1  H1   0.020
 AQ0  plan-1  H8   0.020
 AQ0  plan-1  H9   0.020
 AQ0  plan-1  H15  0.020
 AQ0  plan-1  H16  0.020
 AQ0  plan-1  H18  0.020
 AQ0  plan-2  C10  0.020
 AQ0  plan-2  C11  0.020
 AQ0  plan-2  O1   0.020
 AQ0  plan-2  C8   0.020
 AQ0  plan-3  C15  0.020
 AQ0  plan-3  C16  0.020
 AQ0  plan-3  C17  0.020
 AQ0  plan-3  N2   0.020
 AQ0  plan-3  N    0.020
 AQ0  plan-3  H7   0.020
 AQ0  plan-3  N1   0.020

