# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:35:11 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (1S,2R,3R,5R)-3-(hydroxymethyl)-5-[(5-methoxyquinazolin-4-yl)amino]cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc2ncnc(N[C@@H]3C[C@H](CO)[C@@H](O)[C@H]3O)c12
#
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
 UX0  UX0  (1S,2R,3R,5R)-3-(hydroxymethyl)-5-[(5-methoxyquinazolin-4-yl)amino]cyclopentane-1,2-diol  ligand  41  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UX0
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
 UX0  O2    O  OH1   0  -0.660  -1.6079   1.6359  -1.8668
 UX0  C1    C  CR15  0   0.030  -2.1699   0.5750  -1.1436
 UX0  C2    C  CR15  0   0.008  -3.6315   0.7896  -0.7330
 UX0  O1    O  OH1   0  -0.676  -3.8341   2.1091  -0.2791
 UX0  C3    C  CR15  0  -0.287  -3.8344  -0.1827   0.4439
 UX0  C5    C  CH2   0  -0.148  -4.6991  -1.3628   0.0442
 UX0  O     O  OH1   0  -0.671  -4.8253  -2.2285   1.1487
 UX0  C4    C  CH2   0  -0.451  -2.4180  -0.6000   0.8999
 UX0  C     C  CR15  0  -0.094  -1.4768   0.3787   0.2000
 UX0  N     N  NH1   0  -0.682  -0.1260  -0.1058   0.0984
 UX0  C6    C  CR6   0   0.569   0.9725   0.6171   0.3349
 UX0  C9    C  CR66  0  -0.174   2.3029   0.0689   0.1740
 UX0  C10   C  CR6   0   0.417   2.6176  -1.2521  -0.2524
 UX0  O3    O  O2    0  -0.498   1.5836  -2.0664  -0.5240
 UX0  C14   C  CH3   0  -0.436   1.8354  -3.3898  -0.9669
 UX0  C11   C  CR16  0  -0.410   3.9329  -1.6510  -0.3715
 UX0  C12   C  CR16  0  -0.230   4.9659  -0.7549  -0.0699
 UX0  C13   C  CR16  0  -0.341   4.7009   0.5216   0.3456
 UX0  C8    C  CR66  0   0.251   3.3669   0.9532   0.4743
 UX0  N2    N  N     0  -0.477   3.1506   2.2297   0.8921
 UX0  C7    C  CR16  0   0.041   1.9038   2.5915   0.9987
 UX0  N1    N  N     0  -0.485   0.8150   1.8692   0.7444
 UX0  H2    H  HOH1  0   0.458  -1.8850   1.5619  -2.7855
 UX0  H1    H  HCR5  0   0.214  -2.1076  -0.3691  -1.7058
 UX0  HA    H  HCR5  0   0.219  -4.3113   0.5622  -1.5679
 UX0  H     H  HCR5  0   0.266  -1.4557   1.3289   0.7320
 UX0  HB    H  HOH1  0   0.441  -3.4203   2.7011  -0.9181
 UX0  H3    H  HCR5  0   0.254  -4.3432   0.3591   1.2460
 UX0  H51C  H  HCH2  0   0.206  -5.6780  -0.9936  -0.2899
 UX0  H52C  H  HCH2  0   0.192  -4.2421  -1.8733  -0.8160
 UX0  H41C  H  HCH2  0   0.255  -2.2985  -0.5848   1.9822
 UX0  H42C  H  HCH2  0   0.233  -2.1955  -1.6185   0.5660
 UX0  HC    H  HOH1  0   0.454  -5.3010  -3.0133   0.8626
 UX0  HD    H  HNH1  0   0.412   0.0046  -1.0541  -0.2170
 UX0  H11   H  HCR6  0   0.289   4.1884  -2.6494  -0.6952
 UX0  H141  H  HCH3  0   0.239   2.3851  -3.9640  -0.2187
 UX0  H142  H  HCH3  0   0.268   0.8629  -3.8476  -1.1237
 UX0  H143  H  HCH3  0   0.239   2.3900  -3.3977  -1.9072
 UX0  H12   H  HCR6  0   0.268   5.9899  -1.0899  -0.1712
 UX0  H13   H  HCR6  0   0.254   5.4953   1.2173   0.5802
 UX0  H7    H  HCR6  0   0.244   1.7177   3.6077   1.3351

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
 UX0  O2   C1    single    1.402  0.020  1.402
 UX0  C1   C2    single    1.533  0.020  1.533
 UX0  C1   C     single    1.525  0.020  1.525
 UX0  C2   O1    single    1.410  0.020  1.410
 UX0  C2   C3    single    1.540  0.020  1.540
 UX0  C3   C5    single    1.517  0.020  1.517
 UX0  C3   C4    single    1.545  0.020  1.545
 UX0  C5   O     single    1.409  0.020  1.409
 UX0  C4   C     single    1.528  0.020  1.528
 UX0  C    N     single    1.439  0.020  1.439
 UX0  N    C6    single    1.336  0.020  1.336
 UX0  C6   C9    aromatic  1.448  0.020  1.448
 UX0  C6   N1    aromatic  1.327  0.020  1.327
 UX0  C9   C10   aromatic  1.423  0.020  1.423
 UX0  C9   C8    aromatic  1.416  0.020  1.416
 UX0  C10  O3    single    1.344  0.020  1.344
 UX0  C10  C11   aromatic  1.380  0.020  1.380
 UX0  O3   C14   single    1.418  0.020  1.418
 UX0  C11  C12   aromatic  1.400  0.020  1.400
 UX0  C12  C13   aromatic  1.368  0.020  1.368
 UX0  C13  C8    aromatic  1.408  0.020  1.408
 UX0  C8   N2    aromatic  1.360  0.020  1.360
 UX0  N2   C7    aromatic  1.303  0.020  1.303
 UX0  C7   N1    aromatic  1.331  0.020  1.331
 UX0  O2   H2    single    0.850  0.020  0.980
 UX0  C1   H1    single    0.970  0.020  1.090
 UX0  C2   HA    single    0.970  0.020  1.090
 UX0  C    H     single    0.970  0.020  1.090
 UX0  O1   HB    single    0.850  0.020  0.980
 UX0  C3   H3    single    0.970  0.020  1.090
 UX0  C5   H51C  single    0.970  0.020  1.090
 UX0  C5   H52C  single    0.970  0.020  1.090
 UX0  C4   H41C  single    0.970  0.020  1.090
 UX0  C4   H42C  single    0.970  0.020  1.090
 UX0  O    HC    single    0.850  0.020  0.980
 UX0  N    HD    single    0.860  0.020  1.020
 UX0  C11  H11   single    0.930  0.020  1.080
 UX0  C14  H141  single    0.970  0.020  1.090
 UX0  C14  H142  single    0.970  0.020  1.090
 UX0  C14  H143  single    0.970  0.020  1.090
 UX0  C12  H12   single    0.930  0.020  1.080
 UX0  C13  H13   single    0.930  0.020  1.080
 UX0  C7   H7    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
 UX0  H2    O2   C1    108.59  3.000
 UX0  H1    C1   C     108.30  3.000
 UX0  H1    C1   C2    108.11  3.000
 UX0  C     C1   C2    102.44  3.000
 UX0  H1    C1   O2    111.29  3.000
 UX0  C     C1   O2    111.71  3.000
 UX0  C2    C1   O2    114.49  3.000
 UX0  HA    C2   C3    111.59  3.000
 UX0  HA    C2   O1    110.41  3.000
 UX0  C3    C2   O1    109.02  3.000
 UX0  HA    C2   C1    110.90  3.000
 UX0  C3    C2   C1    104.00  3.000
 UX0  O1    C2   C1    110.74  3.000
 UX0  HB    O1   C2    107.43  3.000
 UX0  H3    C3   C4    110.11  3.000
 UX0  H3    C3   C5    108.27  3.000
 UX0  C4    C3   C5    112.97  3.000
 UX0  H3    C3   C2    108.00  3.000
 UX0  C4    C3   C2    105.97  3.000
 UX0  C5    C3   C2    111.41  3.000
 UX0  H52C  C5   H51C  106.77  3.000
 UX0  H52C  C5   O     111.42  3.000
 UX0  H51C  C5   O     111.42  3.000
 UX0  H52C  C5   C3    109.30  3.000
 UX0  H51C  C5   C3    109.07  3.000
 UX0  O     C5   C3    108.82  3.000
 UX0  HC    O    C5    108.22  3.000
 UX0  H42C  C4   H41C  107.09  3.000
 UX0  H42C  C4   C     109.34  3.000
 UX0  H41C  C4   C     112.26  3.000
 UX0  H42C  C4   C3    110.33  3.000
 UX0  H41C  C4   C3    112.96  3.000
 UX0  C     C4   C3    104.87  3.000
 UX0  H     C    N     108.07  3.000
 UX0  H     C    C4    110.31  3.000
 UX0  N     C    C4    113.27  3.000
 UX0  H     C    C1    109.08  3.000
 UX0  N     C    C1    114.08  3.000
 UX0  C4    C    C1    101.89  3.000
 UX0  HD    N    C6    117.26  3.000
 UX0  HD    N    C     117.43  3.000
 UX0  C6    N    C     125.25  3.000
 UX0  N1    C6   C9    120.05  3.000
 UX0  N1    C6   N     117.88  3.000
 UX0  C9    C6   N     122.06  3.000
 UX0  C8    C9   C10   118.50  3.000
 UX0  C8    C9   C6    115.49  3.000
 UX0  C10   C9   C6    126.01  3.000
 UX0  C11   C10  O3    122.75  3.000
 UX0  C11   C10  C9    120.33  3.000
 UX0  O3    C10  C9    116.92  3.000
 UX0  C14   O3   C10   119.47  3.000
 UX0  H143  C14  H142  109.12  3.000
 UX0  H143  C14  H141  109.32  3.000
 UX0  H142  C14  H141  109.14  3.000
 UX0  H143  C14  O3    111.47  3.000
 UX0  H142  C14  O3    106.23  3.000
 UX0  H141  C14  O3    111.48  3.000
 UX0  H11   C11  C12   118.78  3.000
 UX0  H11   C11  C10   121.24  3.000
 UX0  C12   C11  C10   119.98  3.000
 UX0  H12   C12  C13   120.04  3.000
 UX0  H12   C12  C11   118.67  3.000
 UX0  C13   C12  C11   121.30  3.000
 UX0  H13   C13  C8    118.61  3.000
 UX0  H13   C13  C12   121.57  3.000
 UX0  C8    C13  C12   119.82  3.000
 UX0  N2    C8   C13   117.80  3.000
 UX0  N2    C8   C9    122.12  3.000
 UX0  C13   C8   C9    120.08  3.000
 UX0  C7    N2   C8    115.97  3.000
 UX0  H7    C7   N1    115.25  3.000
 UX0  H7    C7   N2    116.69  3.000
 UX0  N1    C7   N2    128.07  3.000
 UX0  C7    N1   C6    118.29  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
 UX0  CONST_01  C11   C10  C9   C6   180.00   0.0  0
 UX0  CONST_02  C13   C8   C9   C6   180.00   0.0  0
 UX0  CONST_03  N2    C8   C9   C6     0.00   0.0  0
 UX0  CONST_04  N2    C7   N1   C6     0.00   0.0  0
 UX0  CONST_05  C7    N1   C6   C9     0.00   0.0  0
 UX0  CONST_06  C12   C11  C10  C9     0.00   0.0  0
 UX0  CONST_07  C12   C13  C8   C9     0.00   0.0  0
 UX0  CONST_08  C7    N2   C8   C9     0.00   0.0  0
 UX0  CONST_09  N1    C6   C9   C10  180.00   0.0  0
 UX0  CONST_10  C13   C8   C9   C10    0.00   0.0  0
 UX0  CONST_11  N2    C8   C9   C10  180.00   0.0  0
 UX0  CONST_12  C13   C12  C11  C10    0.00   0.0  0
 UX0  CONST_13  C8    C9   C10  C11    0.00   0.0  0
 UX0  CONST_14  C8    C13  C12  C11    0.00   0.0  0
 UX0  CONST_15  N2    C8   C13  C12  180.00   0.0  0
 UX0  CONST_16  C7    N2   C8   C13  180.00   0.0  0
 UX0  CONST_17  N1    C6   C9   C8     0.00   0.0  0
 UX0  CONST_18  N1    C7   N2   C8     0.00   0.0  0
 UX0  CONST_19  C10   C9   C6   N      0.00   0.0  0
 UX0  CONST_20  C8    C9   C6   N    180.00   0.0  0
 UX0  CONST_21  C7    N1   C6   N    180.00   0.0  0
 UX0  CONST_22  O3    C10  C9   C6     0.00   0.0  0
 UX0  CONST_23  C8    C9   C10  O3   180.00   0.0  0
 UX0  CONST_24  C12   C11  C10  O3   180.00   0.0  0
 UX0  CONST_25  C9    C6   N    C    180.00   0.0  0
 UX0  CONST_26  N1    C6   N    C      0.00   0.0  0
 UX0  CONST_27  H7    C7   N1   C6   180.00   0.0  0
 UX0  CONST_28  H11   C11  C10  C9   180.00   0.0  0
 UX0  CONST_29  H13   C13  C8   C9   180.00   0.0  0
 UX0  CONST_30  H12   C12  C11  C10  180.00   0.0  0
 UX0  CONST_31  HD    N    C6   C9     0.00   0.0  0
 UX0  Var_01    C11   C10  O3   C14   -0.72  30.0  1
 UX0  Var_02    H141  C14  O3   C10   61.44  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
 UX0  chir_01  C1  O2  C2  C   positiv
 UX0  chir_02  C2  O1  C3  C1  positiv
 UX0  chir_03  C3  C2  C5  C4  negativ
 UX0  chir_04  C   N   C1  C4  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
 UX0  plan-1  N    0.020
 UX0  plan-1  C6   0.020
 UX0  plan-1  C9   0.020
 UX0  plan-1  C10  0.020
 UX0  plan-1  O3   0.020
 UX0  plan-1  C11  0.020
 UX0  plan-1  C12  0.020
 UX0  plan-1  C13  0.020
 UX0  plan-1  C8   0.020
 UX0  plan-1  N2   0.020
 UX0  plan-1  C7   0.020
 UX0  plan-1  N1   0.020
 UX0  plan-1  H11  0.020
 UX0  plan-1  H12  0.020
 UX0  plan-1  H13  0.020
 UX0  plan-1  H7   0.020
 UX0  plan-2  C    0.020
 UX0  plan-2  N    0.020
 UX0  plan-2  C6   0.020
 UX0  plan-2  HD   0.020

