# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:57:56 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-4-(morpholin-4-yl)-2-[(quinolin-3-ylmethyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](NCc2cnc3ccccc3c2)[C@H]4CO[C@H](O4)[C@@H]1N5CCOCC5
#
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
 D97  D97  '(1S,2S,3S,4R,5R)-4-(morpholin-4-yl)-2-[(quinolin-3-ylmethyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  52  27  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D97
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
 D97  O3   O  O2    0  -0.496  15.7402  -15.8979   -9.1595
 D97  C4   C  CR66  0   0.091   7.1225  -14.1842   -3.8215
 D97  C5   C  CR16  0  -0.312   6.5034  -15.4409   -4.0145
 D97  C6   C  CR16  0  -0.219   7.6842  -13.4381   -4.8772
 D97  N1   N  NH1   0  -0.614   9.6931  -12.1730   -6.6101
 D97  C7   C  CR6   0   0.009   8.2689  -12.2271   -4.6215
 D97  C8   C  CR16  0  -0.119   8.2817  -11.7833   -3.2793
 D97  N2   N  NT    0  -0.440  13.5096  -15.0385   -7.5192
 D97  C9   C  CH2   0  -0.361   8.8798  -11.3817   -5.7071
 D97  C10  C  CH1   0  -0.127  10.9379  -12.6561   -6.0416
 D97  C11  C  CR15  0  -0.102  12.0221  -11.5840   -5.7710
 D97  C12  C  CH2   0  -0.162  12.7234  -11.7857   -4.4316
 D97  C13  C  CR15  0   0.242  13.7100  -12.9244   -6.1476
 D97  C14  C  CH1   0  -0.140  12.8816  -14.1821   -6.5365
 D97  C15  C  CH1   0   0.064  11.4925  -13.7310   -6.9813
 D97  O2   O  OH1   0  -0.669  10.6345  -14.8421   -7.0313
 D97  C19  C  CH2   0  -0.355  13.8016  -14.4433   -8.8112
 D97  C18  C  CH2   0  -0.160  14.5000  -15.4620   -9.6897
 D97  C17  C  CH2   0  -0.188  15.8938  -15.6469   -7.7783
 D97  C16  C  CH2   0  -0.323  14.6049  -15.8634   -7.0062
 D97  O    O  O     0  -0.507  13.7303  -12.7381   -4.7469
 D97  O1   O  O     0  -0.484  13.1161  -11.7671   -6.6648
 D97  C    C  CR16  0  -0.255   5.9817  -16.1243   -2.9508
 D97  N    N  N     0  -0.426   7.7737  -12.4404   -2.2717
 D97  C3   C  CR66  0   0.202   7.1928  -13.6381   -2.5153
 D97  C2   C  CR16  0  -0.290   6.6461  -14.3668   -1.4340
 D97  C1   C  CR16  0  -0.260   6.0555  -15.5819   -1.6492
 D97  H2   H  HCR6  0   0.260   7.6468  -13.8294   -5.8874
 D97  H3   H  HNH1  0   0.362   9.8742  -11.6454   -7.4560
 D97  H5   H  HCR6  0   0.258   8.7458  -10.8278   -3.0477
 D97  H7   H  HCH2  0   0.224   9.4261  -10.5490   -5.2409
 D97  H8   H  HCH2  0   0.271   8.0839  -10.9200   -6.2960
 D97  H9   H  HCH1  0   0.254  10.6782  -13.1458   -5.0960
 D97  H10  H  HCR5  0   0.271  11.6357  -10.5718   -5.9007
 D97  H11  H  HCH2  0   0.234  13.1756  -10.8581   -4.0689
 D97  H12  H  HCH2  0   0.228  12.0586  -12.1725   -3.6561
 D97  H13  H  HCR5  0   0.250  14.7400  -12.9905   -6.5125
 D97  H14  H  HCH1  0   0.266  12.7563  -14.7866   -5.6319
 D97  H15  H  HCH1  0   0.211  11.5675  -13.2705   -7.9775
 D97  H16  H  HOH1  0   0.443   9.7496  -14.4857   -7.1786
 D97  H17  H  HCH2  0   0.211  14.4136  -13.5287   -8.7569
 D97  H18  H  HCH2  0   0.257  12.8746  -14.1610   -9.3144
 D97  H19  H  HCH2  0   0.231  14.6838  -15.0249  -10.6741
 D97  H20  H  HCH2  0   0.205  13.8304  -16.3201   -9.8308
 D97  H21  H  HCH2  0   0.241  16.6630  -16.3271   -7.4071
 D97  H22  H  HCH2  0   0.202  16.2603  -14.6256   -7.6048
 D97  H23  H  HCH2  0   0.241  14.8060  -15.6379   -5.9554
 D97  H24  H  HCH2  0   0.232  14.3341  -16.9253   -7.0467
 D97  H25  H  HCR6  0   0.263   5.5087  -17.0854   -3.1029
 D97  H26  H  HCR6  0   0.261   6.7086  -13.9428   -0.4400
 D97  H27  H  HCR6  0   0.264   5.6410  -16.1363   -0.8173
 D97  H1   H  HCR6  0   0.262   6.4470  -15.8530   -5.0147

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
 D97  C18  O3   single    1.418  0.020  1.418
 D97  C18  C19  single    1.516  0.020  1.516
 D97  O3   C17  single    1.412  0.020  1.412
 D97  C19  N2   single    1.452  0.020  1.452
 D97  N2   C16  single    1.464  0.020  1.464
 D97  N2   C14  single    1.447  0.020  1.447
 D97  C17  C16  single    1.518  0.020  1.518
 D97  O2   C15  single    1.405  0.020  1.405
 D97  C15  C14  single    1.527  0.020  1.527
 D97  C15  C10  single    1.532  0.020  1.532
 D97  N1   C10  single    1.451  0.020  1.451
 D97  N1   C9   single    1.450  0.020  1.450
 D97  C14  C13  single    1.555  0.020  1.555
 D97  O1   C13  single    1.400  0.020  1.400
 D97  O1   C11  single    1.424  0.020  1.424
 D97  C10  C11  single    1.549  0.020  1.549
 D97  C9   C7   single    1.505  0.020  1.505
 D97  C13  O    single    1.413  0.020  1.413
 D97  C11  C12  single    1.525  0.020  1.525
 D97  C6   C7   aromatic  1.369  0.020  1.369
 D97  C6   C4   aromatic  1.409  0.020  1.409
 D97  C7   C8   aromatic  1.414  0.020  1.414
 D97  O    C12  single    1.421  0.020  1.421
 D97  C5   C4   aromatic  1.414  0.020  1.414
 D97  C5   C    aromatic  1.368  0.020  1.368
 D97  C4   C3   aromatic  1.418  0.020  1.418
 D97  C8   N    aromatic  1.306  0.020  1.306
 D97  C    C1   aromatic  1.412  0.020  1.412
 D97  C3   N    aromatic  1.353  0.020  1.353
 D97  C3   C2   aromatic  1.414  0.020  1.414
 D97  C1   C2   aromatic  1.368  0.020  1.368
 D97  C5   H1   single    0.930  0.020  1.080
 D97  C6   H2   single    0.930  0.020  1.080
 D97  N1   H3   single    0.890  0.020  1.040
 D97  C8   H5   single    0.930  0.020  1.080
 D97  C9   H7   single    0.970  0.020  1.090
 D97  C9   H8   single    0.970  0.020  1.090
 D97  C10  H9   single    0.970  0.020  1.090
 D97  C11  H10  single    0.970  0.020  1.090
 D97  C12  H11  single    0.970  0.020  1.090
 D97  C12  H12  single    0.970  0.020  1.090
 D97  C13  H13  single    0.970  0.020  1.090
 D97  C14  H14  single    0.970  0.020  1.090
 D97  C15  H15  single    0.970  0.020  1.090
 D97  O2   H16  single    0.850  0.020  0.980
 D97  C19  H17  single    0.970  0.020  1.090
 D97  C19  H18  single    0.970  0.020  1.090
 D97  C18  H19  single    0.970  0.020  1.090
 D97  C18  H20  single    0.970  0.020  1.090
 D97  C17  H21  single    0.970  0.020  1.090
 D97  C17  H22  single    0.970  0.020  1.090
 D97  C16  H23  single    0.970  0.020  1.090
 D97  C16  H24  single    0.970  0.020  1.090
 D97  C    H25  single    0.930  0.020  1.080
 D97  C2   H26  single    0.930  0.020  1.080
 D97  C1   H27  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
 D97  C17  O3   C18  113.97  3.000
 D97  C3   C4   C6   117.81  3.000
 D97  C3   C4   C5   119.33  3.000
 D97  C6   C4   C5   122.87  3.000
 D97  H1   C5   C    120.54  3.000
 D97  H1   C5   C4   119.13  3.000
 D97  C    C5   C4   120.32  3.000
 D97  H2   C6   C7   120.55  3.000
 D97  H2   C6   C4   119.54  3.000
 D97  C7   C6   C4   119.91  3.000
 D97  H3   N1   C10  110.30  3.000
 D97  H3   N1   C9   109.63  3.000
 D97  C10  N1   C9   114.75  3.000
 D97  C9   C7   C8   120.31  3.000
 D97  C8   C7   C6   117.32  3.000
 D97  C9   C7   C6   122.37  3.000
 D97  H5   C8   N    116.35  3.000
 D97  H5   C8   C7   118.82  3.000
 D97  N    C8   C7   124.83  3.000
 D97  C16  N2   C19  113.10  3.000
 D97  C16  N2   C14  114.85  3.000
 D97  C19  N2   C14  116.67  3.000
 D97  H8   C9   H7   105.70  3.000
 D97  H8   C9   C7   109.29  3.000
 D97  H7   C9   C7   108.73  3.000
 D97  H8   C9   N1   107.67  3.000
 D97  H7   C9   N1   113.50  3.000
 D97  C7   C9   N1   111.72  3.000
 D97  H9   C10  C15  107.55  3.000
 D97  H9   C10  C11  108.93  3.000
 D97  C15  C10  C11  109.85  3.000
 D97  H9   C10  N1   106.47  3.000
 D97  C11  C10  N1   116.01  3.000
 D97  C15  C10  N1   107.69  3.000
 D97  H10  C11  O1   108.46  3.000
 D97  H10  C11  C12  112.94  3.000
 D97  O1   C11  C12  100.42  3.000
 D97  H10  C11  C10  111.93  3.000
 D97  C12  C11  C10  112.57  3.000
 D97  O1   C11  C10  109.82  3.000
 D97  H12  C12  H11  108.45  3.000
 D97  H12  C12  O    110.57  3.000
 D97  H11  C12  O    110.42  3.000
 D97  H12  C12  C11  112.99  3.000
 D97  H11  C12  C11  111.66  3.000
 D97  O    C12  C11  102.68  3.000
 D97  H13  C13  O1   109.03  3.000
 D97  H13  C13  O    108.96  3.000
 D97  O1   C13  O    105.26  3.000
 D97  H13  C13  C14  111.65  3.000
 D97  O    C13  C14  111.22  3.000
 D97  O1   C13  C14  110.50  3.000
 D97  H14  C14  C15  107.43  3.000
 D97  H14  C14  C13  107.50  3.000
 D97  C15  C14  C13  108.57  3.000
 D97  H14  C14  N2   106.50  3.000
 D97  C13  C14  N2   114.66  3.000
 D97  C15  C14  N2   111.84  3.000
 D97  H15  C15  O2   109.91  3.000
 D97  H15  C15  C14  108.99  3.000
 D97  O2   C15  C14  109.41  3.000
 D97  H15  C15  C10  106.65  3.000
 D97  C14  C15  C10  110.99  3.000
 D97  O2   C15  C10  110.84  3.000
 D97  H16  O2   C15  105.87  3.000
 D97  H18  C19  H17  106.24  3.000
 D97  H18  C19  C18  107.33  3.000
 D97  H17  C19  C18  109.30  3.000
 D97  H18  C19  N2   110.20  3.000
 D97  H17  C19  N2   114.08  3.000
 D97  C18  C19  N2   109.44  3.000
 D97  H20  C18  H19  107.44  3.000
 D97  H20  C18  C19  108.59  3.000
 D97  H19  C18  C19  109.32  3.000
 D97  H20  C18  O3   109.96  3.000
 D97  H19  C18  O3   108.23  3.000
 D97  C19  C18  O3   113.14  3.000
 D97  H22  C17  H21  106.87  3.000
 D97  H22  C17  C16  109.60  3.000
 D97  H21  C17  C16  109.66  3.000
 D97  H22  C17  O3   110.85  3.000
 D97  H21  C17  O3   107.36  3.000
 D97  C16  C17  O3   112.32  3.000
 D97  H24  C16  H23  106.30  3.000
 D97  H24  C16  C17  109.21  3.000
 D97  H23  C16  C17  107.66  3.000
 D97  H24  C16  N2   110.35  3.000
 D97  H23  C16  N2   110.99  3.000
 D97  C17  C16  N2   112.13  3.000
 D97  C13  O    C12  107.34  3.000
 D97  C13  O1   C11  101.56  3.000
 D97  H25  C    C1   119.58  3.000
 D97  H25  C    C5   120.08  3.000
 D97  C1   C    C5   120.34  3.000
 D97  C3   N    C8   118.26  3.000
 D97  C2   C3   N    118.98  3.000
 D97  C2   C3   C4   119.14  3.000
 D97  N    C3   C4   121.88  3.000
 D97  H26  C2   C1   121.15  3.000
 D97  H26  C2   C3   118.56  3.000
 D97  C1   C2   C3   120.29  3.000
 D97  H27  C1   C2   119.96  3.000
 D97  H27  C1   C    119.46  3.000
 D97  C2   C1   C    120.58  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
 D97  CONST_01  C8   C7   C6   C4      0.00   0.0  0
 D97  CONST_02  C1   C    C5   C4      0.00   0.0  0
 D97  CONST_03  C8   N    C3   C4      0.00   0.0  0
 D97  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 D97  CONST_05  C7   C6   C4   C5    180.00   0.0  0
 D97  CONST_06  N    C3   C4   C5    180.00   0.0  0
 D97  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 D97  CONST_08  C2   C1   C    C5      0.00   0.0  0
 D97  CONST_09  N    C8   C7   C6      0.00   0.0  0
 D97  CONST_10  C    C5   C4   C6    180.00   0.0  0
 D97  CONST_11  N    C3   C4   C6      0.00   0.0  0
 D97  CONST_12  C2   C3   C4   C6    180.00   0.0  0
 D97  CONST_13  C3   C4   C6   C7      0.00   0.0  0
 D97  CONST_14  C3   N    C8   C7      0.00   0.0  0
 D97  CONST_15  C2   C3   N    C8    180.00   0.0  0
 D97  CONST_16  C3   C4   C5   C       0.00   0.0  0
 D97  CONST_17  C3   C2   C1   C       0.00   0.0  0
 D97  CONST_18  C1   C2   C3   N     180.00   0.0  0
 D97  CONST_19  C9   C7   C6   C4    180.00   0.0  0
 D97  CONST_20  N    C8   C7   C9    180.00   0.0  0
 D97  CONST_21  H25  C    C5   C4    180.00   0.0  0
 D97  CONST_22  H26  C2   C3   C4    180.00   0.0  0
 D97  CONST_23  H2   C6   C4   C5      0.00   0.0  0
 D97  CONST_24  H27  C1   C    C5    180.00   0.0  0
 D97  CONST_25  H5   C8   C7   C6    180.00   0.0  0
 D97  CONST_26  H1   C5   C4   C6      0.00   0.0  0
 D97  Var_01    N2   C19  C18  O3    -61.50  30.0  1
 D97  Var_02    N2   C16  C17  O3    -56.98  30.0  1
 D97  Var_03    C18  C19  N2   C14   177.89  30.0  1
 D97  Var_04    C17  C16  N2   C14  -124.10  30.0  1
 D97  Var_05    C16  C17  O3   C18    38.33  30.0  1
 D97  Var_06    H11  C12  O    C13  -112.50  30.0  3
 D97  Var_07    N1   C9   C7   C6    -44.69  30.0  2
 D97  Var_08    C10  N1   C9   C7    -70.88  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
 D97  chir_01  C10  C15  N1   C11  positiv
 D97  chir_02  C11  O1   C10  C12  negativ
 D97  chir_03  C13  O    O1   C14  positiv
 D97  chir_04  C14  N2   C15  C13  positiv
 D97  chir_05  C15  O2   C14  C10  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
 D97  plan-1  C4   0.020
 D97  plan-1  C5   0.020
 D97  plan-1  C6   0.020
 D97  plan-1  C7   0.020
 D97  plan-1  C8   0.020
 D97  plan-1  C9   0.020
 D97  plan-1  C    0.020
 D97  plan-1  N    0.020
 D97  plan-1  C3   0.020
 D97  plan-1  C2   0.020
 D97  plan-1  C1   0.020
 D97  plan-1  H2   0.020
 D97  plan-1  H5   0.020
 D97  plan-1  H25  0.020
 D97  plan-1  H26  0.020
 D97  plan-1  H27  0.020
 D97  plan-1  H1   0.020

