# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 08:24:27 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (1S,2R,3R,5R)-3-(hydroxymethyl)-5-[(5-phenylmethoxyquinazolin-4-yl)amino]cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@@H](Nc2ncnc3cccc(OCc4ccccc4)c23)[C@H](O)[C@@H]1O
#
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
 KC7  KC7  (1S,2R,3R,5R)-3-(hydroxymethyl)-5-[(5-phenylmethoxyquinazolin-4-yl)amino]cyclopentane-1,2-diol  ligand  51  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KC7
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
 KC7  O2    O  OH1   0  -0.657  -0.5095   2.7469  -1.8456
 KC7  C1    C  CR15  0   0.031  -1.3566   1.9418  -1.0729
 KC7  C2    C  CR15  0   0.006  -2.7066   2.5799  -0.7326
 KC7  O1    O  OH1   0  -0.677  -2.5341   3.9201  -0.3300
 KC7  C3    C  CR15  0  -0.288  -3.2087   1.7555   0.4635
 KC7  C5    C  CH2   0  -0.150  -4.2916   0.7780   0.0429
 KC7  O     O  OH1   0  -0.668  -4.6903   0.0327   1.1700
 KC7  C4    C  CH2   0  -0.459  -1.9629   1.0438   1.0391
 KC7  C     C  CR15  0  -0.091  -0.7667   1.6551   0.3056
 KC7  N     N  NH1   0  -0.684   0.3635   0.7651   0.2798
 KC7  C6    C  CR6   0   0.564   1.6498   1.1191   0.3411
 KC7  N2    N  N     0  -0.480   1.9433   2.4005   0.5167
 KC7  C13   C  CR16  0   0.038   3.2284   2.7470   0.5688
 KC7  N1    N  N     0  -0.477   4.2762   1.9802   0.4545
 KC7  C12   C  CR66  0   0.253   4.0280   0.6540   0.2814
 KC7  C7    C  CR66  0  -0.181   2.7120   0.1401   0.2310
 KC7  C11   C  CR16  0  -0.340   5.1263  -0.2186   0.1496
 KC7  C10   C  CR16  0  -0.231   4.9158  -1.5606  -0.0238
 KC7  C9    C  CR16  0  -0.407   3.6219  -2.0974  -0.0641
 KC7  C8    C  CR6   0   0.429   2.5352  -1.2611   0.0684
 KC7  O3    O  O2    0  -0.506   1.2656  -1.6964   0.0649
 KC7  C14   C  CH2   0  -0.261   0.9356  -3.0562  -0.2089
 KC7  C15   C  CR6   0   0.080  -0.5627  -3.0971  -0.2223
 KC7  C20   C  CR16  0  -0.288  -1.2607  -2.5859  -1.3143
 KC7  C19   C  CR16  0  -0.240  -2.6466  -2.5348  -1.3005
 KC7  C18   C  CR16  0  -0.257  -3.3487  -2.9917  -0.1915
 KC7  C17   C  CR16  0  -0.238  -2.6600  -3.5060   0.8978
 KC7  C16   C  CR16  0  -0.292  -1.2717  -3.5537   0.8828
 KC7  H2    H  HOH1  0   0.458  -0.7914   2.6975  -2.7646
 KC7  H1    H  HCR5  0   0.205  -1.5487   0.9762  -1.5647
 KC7  HA    H  HCR5  0   0.221  -3.3985   2.5205  -1.5860
 KC7  H     H  HCR5  0   0.264  -0.4603   2.5913   0.7718
 KC7  HB    H  HOH1  0   0.441  -1.9325   4.3346  -0.9597
 KC7  H3    H  HCR5  0   0.255  -3.6370   2.4404   1.2005
 KC7  H51C  H  HCH2  0   0.207  -5.1338   1.3350  -0.3901
 KC7  H52C  H  HCH2  0   0.194  -3.9020   0.1233  -0.7488
 KC7  H41C  H  HCH2  0   0.258  -1.8769   1.1426   2.1202
 KC7  H42C  H  HCH2  0   0.236  -2.0148  -0.0296   0.8221
 KC7  HC    H  HOH1  0   0.451  -5.2104  -0.7167   0.8690
 KC7  HD    H  HNH1  0   0.416   0.1727  -0.2130   0.1266
 KC7  H13   H  HCR6  0   0.244   3.4161   3.8064   0.7196
 KC7  H11   H  HCR6  0   0.255   6.1251   0.1950   0.1899
 KC7  H10   H  HCR6  0   0.268   5.7589  -2.2310  -0.1273
 KC7  H9    H  HCR6  0   0.291   3.4953  -3.1636  -0.1906
 KC7  H141  H  HCH2  0   0.255   1.3584  -3.3555  -1.1726
 KC7  H142  H  HCH2  0   0.255   1.3459  -3.7095   0.5661
 KC7  H20   H  HCR6  0   0.259  -0.7196  -2.2261  -2.1816
 KC7  H16   H  HCR6  0   0.258  -0.7379  -3.9478   1.7392
 KC7  H19   H  HCR6  0   0.262  -3.1783  -2.1377  -2.1555
 KC7  H18   H  HCR6  0   0.258  -4.4306  -2.9585  -0.1836
 KC7  H17   H  HCR6  0   0.260  -3.2007  -3.8672   1.7628

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
 KC7  O2   C1    single    1.401  0.020  1.401
 KC7  C1   C2    single    1.531  0.020  1.531
 KC7  C1   C     single    1.527  0.020  1.527
 KC7  C2   O1    single    1.410  0.020  1.410
 KC7  C2   C3    single    1.537  0.020  1.537
 KC7  C3   C5    single    1.518  0.020  1.518
 KC7  C3   C4    single    1.546  0.020  1.546
 KC7  C5   O     single    1.409  0.020  1.409
 KC7  C4   C     single    1.531  0.020  1.531
 KC7  C    N     single    1.439  0.020  1.439
 KC7  N    C6    single    1.336  0.020  1.336
 KC7  C6   N2    aromatic  1.326  0.020  1.326
 KC7  C6   C7    aromatic  1.449  0.020  1.449
 KC7  N2   C13   aromatic  1.332  0.020  1.332
 KC7  C13  N1    aromatic  1.303  0.020  1.303
 KC7  N1   C12   aromatic  1.360  0.020  1.360
 KC7  C12  C7    aromatic  1.414  0.020  1.414
 KC7  C12  C11   aromatic  1.409  0.020  1.409
 KC7  C7   C8    aromatic  1.422  0.020  1.422
 KC7  C11  C10   aromatic  1.369  0.020  1.369
 KC7  C10  C9    aromatic  1.401  0.020  1.401
 KC7  C9   C8    aromatic  1.378  0.020  1.378
 KC7  C8   O3    single    1.342  0.020  1.342
 KC7  O3   C14   single    1.426  0.020  1.426
 KC7  C14  C15   single    1.499  0.020  1.499
 KC7  C15  C20   aromatic  1.393  0.020  1.393
 KC7  C15  C16   aromatic  1.390  0.020  1.390
 KC7  C20  C19   aromatic  1.387  0.020  1.387
 KC7  C19  C18   aromatic  1.390  0.020  1.390
 KC7  C18  C17   aromatic  1.388  0.020  1.388
 KC7  C17  C16   aromatic  1.389  0.020  1.389
 KC7  O2   H2    single    0.850  0.020  0.980
 KC7  C1   H1    single    0.970  0.020  1.090
 KC7  C2   HA    single    0.970  0.020  1.090
 KC7  C    H     single    0.970  0.020  1.090
 KC7  O1   HB    single    0.850  0.020  0.980
 KC7  C3   H3    single    0.970  0.020  1.090
 KC7  C5   H51C  single    0.970  0.020  1.090
 KC7  C5   H52C  single    0.970  0.020  1.090
 KC7  C4   H41C  single    0.970  0.020  1.090
 KC7  C4   H42C  single    0.970  0.020  1.090
 KC7  O    HC    single    0.850  0.020  0.980
 KC7  N    HD    single    0.860  0.020  1.020
 KC7  C13  H13   single    0.930  0.020  1.080
 KC7  C11  H11   single    0.930  0.020  1.080
 KC7  C10  H10   single    0.930  0.020  1.080
 KC7  C9   H9    single    0.930  0.020  1.080
 KC7  C14  H141  single    0.970  0.020  1.090
 KC7  C14  H142  single    0.970  0.020  1.090
 KC7  C20  H20   single    0.930  0.020  1.080
 KC7  C16  H16   single    0.930  0.020  1.080
 KC7  C19  H19   single    0.930  0.020  1.080
 KC7  C18  H18   single    0.930  0.020  1.080
 KC7  C17  H17   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
 KC7  H2    O2   C1    108.66  3.000
 KC7  H1    C1   C     107.83  3.000
 KC7  H1    C1   C2    108.12  3.000
 KC7  C     C1   C2    102.60  3.000
 KC7  H1    C1   O2    111.30  3.000
 KC7  C     C1   O2    111.85  3.000
 KC7  C2    C1   O2    114.59  3.000
 KC7  HA    C2   C3    111.67  3.000
 KC7  HA    C2   O1    110.47  3.000
 KC7  C3    C2   O1    109.12  3.000
 KC7  HA    C2   C1    111.07  3.000
 KC7  C3    C2   C1    103.73  3.000
 KC7  O1    C2   C1    110.59  3.000
 KC7  HB    O1   C2    107.36  3.000
 KC7  H3    C3   C4    110.68  3.000
 KC7  H3    C3   C5    108.09  3.000
 KC7  C4    C3   C5    112.43  3.000
 KC7  H3    C3   C2    108.45  3.000
 KC7  C4    C3   C2    105.87  3.000
 KC7  C5    C3   C2    111.27  3.000
 KC7  H52C  C5   H51C  106.86  3.000
 KC7  H52C  C5   O     111.20  3.000
 KC7  H51C  C5   O     111.50  3.000
 KC7  H52C  C5   C3    109.29  3.000
 KC7  H51C  C5   C3    109.24  3.000
 KC7  O     C5   C3    108.71  3.000
 KC7  HC    O    C5    108.37  3.000
 KC7  H42C  C4   H41C  106.80  3.000
 KC7  H42C  C4   C     109.47  3.000
 KC7  H41C  C4   C     112.20  3.000
 KC7  H42C  C4   C3    109.81  3.000
 KC7  H41C  C4   C3    113.04  3.000
 KC7  C     C4   C3    105.51  3.000
 KC7  H     C    N     108.56  3.000
 KC7  H     C    C4    110.97  3.000
 KC7  N     C    C4    112.05  3.000
 KC7  H     C    C1    109.49  3.000
 KC7  N     C    C1    113.80  3.000
 KC7  C4    C    C1    101.87  3.000
 KC7  HD    N    C6    116.52  3.000
 KC7  HD    N    C     117.01  3.000
 KC7  C6    N    C     126.28  3.000
 KC7  C7    C6   N2    120.05  3.000
 KC7  C7    C6   N     121.57  3.000
 KC7  N2    C6   N     118.38  3.000
 KC7  C13   N2   C6    118.04  3.000
 KC7  H13   C13  N1    116.55  3.000
 KC7  H13   C13  N2    115.20  3.000
 KC7  N1    C13  N2    128.25  3.000
 KC7  C12   N1   C13   115.98  3.000
 KC7  C11   C12  C7    119.82  3.000
 KC7  C11   C12  N1    118.26  3.000
 KC7  C7    C12  N1    121.92  3.000
 KC7  C8    C7   C12   118.56  3.000
 KC7  C8    C7   C6    125.70  3.000
 KC7  C12   C7   C6    115.74  3.000
 KC7  H11   C11  C10   121.42  3.000
 KC7  H11   C11  C12   118.65  3.000
 KC7  C10   C11  C12   119.93  3.000
 KC7  H10   C10  C9    118.64  3.000
 KC7  H10   C10  C11   119.97  3.000
 KC7  C9    C10  C11   121.40  3.000
 KC7  H9    C9   C8    121.17  3.000
 KC7  H9    C9   C10   119.30  3.000
 KC7  C8    C9   C10   119.53  3.000
 KC7  O3    C8   C9    123.30  3.000
 KC7  O3    C8   C7    115.95  3.000
 KC7  C9    C8   C7    120.75  3.000
 KC7  C14   O3   C8    121.92  3.000
 KC7  H142  C14  H141  108.41  3.000
 KC7  H142  C14  C15   111.41  3.000
 KC7  H141  C14  C15   111.77  3.000
 KC7  H142  C14  O3    110.29  3.000
 KC7  H141  C14  O3    109.92  3.000
 KC7  C15   C14  O3    105.02  3.000
 KC7  C16   C15  C20   119.21  3.000
 KC7  C16   C15  C14   120.78  3.000
 KC7  C20   C15  C14   119.85  3.000
 KC7  H20   C20  C19   119.65  3.000
 KC7  H20   C20  C15   119.93  3.000
 KC7  C19   C20  C15   120.42  3.000
 KC7  H19   C19  C18   120.18  3.000
 KC7  H19   C19  C20   119.77  3.000
 KC7  C18   C19  C20   120.04  3.000
 KC7  H18   C18  C17   120.12  3.000
 KC7  H18   C18  C19   120.04  3.000
 KC7  C17   C18  C19   119.84  3.000
 KC7  H17   C17  C16   119.77  3.000
 KC7  H17   C17  C18   120.21  3.000
 KC7  C16   C17  C18   120.02  3.000
 KC7  H16   C16  C17   119.76  3.000
 KC7  H16   C16  C15   119.77  3.000
 KC7  C17   C16  C15   120.47  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
 KC7  CONST_01  N1   C13  N2   C6      0.00   0.0  0
 KC7  CONST_02  N1   C12  C7   C6      0.00   0.0  0
 KC7  CONST_03  C11  C12  C7   C6    180.00   0.0  0
 KC7  CONST_04  C9   C8   C7   C6    180.00   0.0  0
 KC7  CONST_05  C12  C7   C6   N2      0.00   0.0  0
 KC7  CONST_06  C8   C7   C6   N2    180.00   0.0  0
 KC7  CONST_07  C12  N1   C13  N2      0.00   0.0  0
 KC7  CONST_08  C7   C6   N2   C13     0.00   0.0  0
 KC7  CONST_09  C7   C12  N1   C13     0.00   0.0  0
 KC7  CONST_10  C11  C12  N1   C13   180.00   0.0  0
 KC7  CONST_11  C8   C7   C12  N1    180.00   0.0  0
 KC7  CONST_12  C10  C11  C12  N1    180.00   0.0  0
 KC7  CONST_13  C9   C8   C7   C12     0.00   0.0  0
 KC7  CONST_14  C9   C10  C11  C12     0.00   0.0  0
 KC7  CONST_15  C10  C11  C12  C7      0.00   0.0  0
 KC7  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 KC7  CONST_17  C8   C7   C12  C11     0.00   0.0  0
 KC7  CONST_18  C8   C9   C10  C11     0.00   0.0  0
 KC7  CONST_19  C18  C19  C20  C15     0.00   0.0  0
 KC7  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 KC7  CONST_21  C17  C16  C15  C20     0.00   0.0  0
 KC7  CONST_22  C17  C18  C19  C20     0.00   0.0  0
 KC7  CONST_23  C16  C15  C20  C19     0.00   0.0  0
 KC7  CONST_24  C16  C17  C18  C19     0.00   0.0  0
 KC7  CONST_25  C13  N2   C6   N     180.00   0.0  0
 KC7  CONST_26  C12  C7   C6   N     180.00   0.0  0
 KC7  CONST_27  C8   C7   C6   N       0.00   0.0  0
 KC7  CONST_28  O3   C8   C7   C6      0.00   0.0  0
 KC7  CONST_29  O3   C8   C7   C12   180.00   0.0  0
 KC7  CONST_30  O3   C8   C9   C10   180.00   0.0  0
 KC7  CONST_31  C19  C20  C15  C14   180.00   0.0  0
 KC7  CONST_32  C17  C16  C15  C14   180.00   0.0  0
 KC7  CONST_33  N2   C6   N    C       0.00   0.0  0
 KC7  CONST_34  C7   C6   N    C     180.00   0.0  0
 KC7  CONST_35  H13  C13  N2   C6    180.00   0.0  0
 KC7  CONST_36  H11  C11  C12  N1      0.00   0.0  0
 KC7  CONST_37  H10  C10  C11  C12   180.00   0.0  0
 KC7  CONST_38  H9   C9   C8   C7    180.00   0.0  0
 KC7  CONST_39  H19  C19  C20  C15   180.00   0.0  0
 KC7  CONST_40  H17  C17  C16  C15   180.00   0.0  0
 KC7  CONST_41  H16  C16  C15  C20   180.00   0.0  0
 KC7  CONST_42  H18  C18  C19  C20   180.00   0.0  0
 KC7  CONST_43  H20  C20  C19  C18   180.00   0.0  0
 KC7  CONST_44  HD   N    C6   N2    180.00   0.0  0
 KC7  Var_01    C15  C14  O3   C8   -175.65  30.0  3
 KC7  Var_02    C20  C15  C14  O3     75.31  30.0  2

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
 KC7  chir_01  C1  O2  C2  C   positiv
 KC7  chir_02  C2  O1  C3  C1  positiv
 KC7  chir_03  C3  C2  C5  C4  negativ
 KC7  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
 KC7  plan-1  C14  0.020
 KC7  plan-1  C15  0.020
 KC7  plan-1  C20  0.020
 KC7  plan-1  C19  0.020
 KC7  plan-1  C18  0.020
 KC7  plan-1  C17  0.020
 KC7  plan-1  C16  0.020
 KC7  plan-1  H20  0.020
 KC7  plan-1  H16  0.020
 KC7  plan-1  H19  0.020
 KC7  plan-1  H18  0.020
 KC7  plan-1  H17  0.020
 KC7  plan-2  N    0.020
 KC7  plan-2  C6   0.020
 KC7  plan-2  N2   0.020
 KC7  plan-2  C13  0.020
 KC7  plan-2  N1   0.020
 KC7  plan-2  C12  0.020
 KC7  plan-2  C7   0.020
 KC7  plan-2  C11  0.020
 KC7  plan-2  C10  0.020
 KC7  plan-2  C9   0.020
 KC7  plan-2  C8   0.020
 KC7  plan-2  O3   0.020
 KC7  plan-2  H13  0.020
 KC7  plan-2  H11  0.020
 KC7  plan-2  H10  0.020
 KC7  plan-2  H9   0.020
 KC7  plan-3  C    0.020
 KC7  plan-3  N    0.020
 KC7  plan-3  C6   0.020
 KC7  plan-3  HD   0.020

