# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 15:28:07 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1S,2R,3R,5R)-3-(hydroxymethyl)-5-(quinazolin-4-ylamino)cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@@H](Nc2ncnc3ccccc23)[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
 5P7  5P7  (1S,2R,3R,5R)-3-(hydroxymethyl)-5-(quinazolin-4-ylamino)cyclopentane-1,2-diol  ligand  37  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5P7
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
 5P7  O2    O  OH1   0  -0.659  -1.3552   1.7163  -1.6536
 5P7  C1    C  CR15  0   0.025  -1.9758   0.6097  -1.0583
 5P7  C2    C  CR15  0   0.007  -3.4170   0.8529  -0.6016
 5P7  O1    O  OH1   0  -0.676  -3.5239   2.0830   0.0784
 5P7  C3    C  CR15  0  -0.294  -3.6784  -0.2904   0.3905
 5P7  C5    C  CH2   0  -0.148  -4.4800  -1.4016  -0.2647
 5P7  O     O  OH1   0  -0.670  -4.6604  -2.4416   0.6682
 5P7  C4    C  CH2   0  -0.453  -2.2830  -0.7638   0.8655
 5P7  C     C  CR15  0  -0.092  -1.2836   0.2138   0.2416
 5P7  N     N  NH1   0  -0.676   0.0241  -0.3587   0.0489
 5P7  C6    C  CR6   0   0.550   1.1847   0.2457   0.3207
 5P7  C9    C  CR66  0  -0.036   2.4389  -0.4053   0.0224
 5P7  C10   C  CR16  0  -0.305   2.5602  -1.6743  -0.5724
 5P7  C11   C  CR16  0  -0.256   3.7993  -2.2123  -0.8170
 5P7  C12   C  CR16  0  -0.246   4.9571  -1.4957  -0.4728
 5P7  C13   C  CR16  0  -0.311   4.8620  -0.2565   0.1068
 5P7  C8    C  CR66  0   0.239   3.6008   0.3153   0.3680
 5P7  N2    N  N     0  -0.469   3.5431   1.5459   0.9486
 5P7  C7    C  CR16  0   0.040   2.3469   2.0127   1.1653
 5P7  N1    N  N     0  -0.483   1.1709   1.4407   0.8857
 5P7  H2    H  HOH1  0   0.458  -1.6435   1.7752  -2.5699
 5P7  H1    H  HCR5  0   0.215  -1.9705  -0.2619  -1.7301
 5P7  HA    H  HCR5  0   0.222  -4.1131   0.8218  -1.4531
 5P7  H     H  HCR5  0   0.270  -1.1686   1.0955   0.8709
 5P7  HB    H  HOH1  0   0.442  -3.0853   2.7511  -0.4610
 5P7  H3    H  HCR5  0   0.255  -4.2613   0.0994   1.2295
 5P7  H51C  H  HCH2  0   0.208  -5.4421  -0.9962  -0.6048
 5P7  H52C  H  HCH2  0   0.191  -3.9488  -1.7532  -1.1613
 5P7  H41C  H  HCH2  0   0.256  -2.1939  -0.7969   1.9503
 5P7  H42C  H  HCH2  0   0.239  -2.0810  -1.7757   0.5020
 5P7  HC    H  HOH1  0   0.454  -5.1322  -3.1576   0.2338
 5P7  HD    H  HNH1  0   0.406   0.0477  -1.2570  -0.4054
 5P7  H10   H  HCR6  0   0.255   1.6861  -2.2514  -0.8476
 5P7  H11   H  HCR6  0   0.267   3.8844  -3.1883  -1.2754
 5P7  H12   H  HCR6  0   0.267   5.9303  -1.9270  -0.6673
 5P7  H13   H  HCR6  0   0.260   5.7481   0.3046   0.3746
 5P7  H7    H  HCR6  0   0.245   2.2828   2.9916   1.6317

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
 5P7  O2   C1    single    1.401  0.020  1.401
 5P7  C1   C2    single    1.531  0.020  1.531
 5P7  C1   C     single    1.525  0.020  1.525
 5P7  C2   O1    single    1.410  0.020  1.410
 5P7  C2   C3    single    1.536  0.020  1.536
 5P7  C3   C5    single    1.519  0.020  1.519
 5P7  C3   C4    single    1.548  0.020  1.548
 5P7  C5   O     single    1.409  0.020  1.409
 5P7  C4   C     single    1.531  0.020  1.531
 5P7  C    N     single    1.441  0.020  1.441
 5P7  N    C6    single    1.336  0.020  1.336
 5P7  C6   C9    aromatic  1.444  0.020  1.444
 5P7  C6   N1    aromatic  1.322  0.020  1.322
 5P7  C9   C10   aromatic  1.407  0.020  1.407
 5P7  C9   C8    aromatic  1.410  0.020  1.410
 5P7  C10  C11   aromatic  1.373  0.020  1.373
 5P7  C11  C12   aromatic  1.405  0.020  1.405
 5P7  C12  C13   aromatic  1.371  0.020  1.371
 5P7  C13  C8    aromatic  1.409  0.020  1.409
 5P7  C8   N2    aromatic  1.362  0.020  1.362
 5P7  N2   C7    aromatic  1.302  0.020  1.302
 5P7  C7   N1    aromatic  1.337  0.020  1.337
 5P7  O2   H2    single    0.850  0.020  0.980
 5P7  C1   H1    single    0.970  0.020  1.090
 5P7  C2   HA    single    0.970  0.020  1.090
 5P7  C    H     single    0.970  0.020  1.090
 5P7  O1   HB    single    0.850  0.020  0.980
 5P7  C3   H3    single    0.970  0.020  1.090
 5P7  C5   H51C  single    0.970  0.020  1.090
 5P7  C5   H52C  single    0.970  0.020  1.090
 5P7  C4   H41C  single    0.970  0.020  1.090
 5P7  C4   H42C  single    0.970  0.020  1.090
 5P7  O    HC    single    0.850  0.020  0.980
 5P7  N    HD    single    0.860  0.020  1.020
 5P7  C10  H10   single    0.930  0.020  1.080
 5P7  C11  H11   single    0.930  0.020  1.080
 5P7  C12  H12   single    0.930  0.020  1.080
 5P7  C13  H13   single    0.930  0.020  1.080
 5P7  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
 5P7  H2    O2   C1    108.67  3.000
 5P7  H1    C1   C     108.21  3.000
 5P7  H1    C1   C2    108.21  3.000
 5P7  C     C1   C2    102.37  3.000
 5P7  H1    C1   O2    111.34  3.000
 5P7  C     C1   O2    111.47  3.000
 5P7  C2    C1   O2    114.71  3.000
 5P7  HA    C2   C3    111.78  3.000
 5P7  HA    C2   O1    110.49  3.000
 5P7  C3    C2   O1    108.97  3.000
 5P7  HA    C2   C1    111.11  3.000
 5P7  C3    C2   C1    103.57  3.000
 5P7  O1    C2   C1    110.72  3.000
 5P7  HB    O1   C2    107.48  3.000
 5P7  H3    C3   C4    110.74  3.000
 5P7  H3    C3   C5    108.09  3.000
 5P7  C4    C3   C5    112.60  3.000
 5P7  H3    C3   C2    108.72  3.000
 5P7  C4    C3   C2    105.80  3.000
 5P7  C5    C3   C2    110.84  3.000
 5P7  H52C  C5   H51C  106.79  3.000
 5P7  H52C  C5   O     111.45  3.000
 5P7  H51C  C5   O     111.44  3.000
 5P7  H52C  C5   C3    109.31  3.000
 5P7  H51C  C5   C3    109.02  3.000
 5P7  O     C5   C3    108.78  3.000
 5P7  HC    O    C5    108.27  3.000
 5P7  H42C  C4   H41C  106.73  3.000
 5P7  H42C  C4   C     109.56  3.000
 5P7  H41C  C4   C     111.84  3.000
 5P7  H42C  C4   C3    110.32  3.000
 5P7  H41C  C4   C3    112.87  3.000
 5P7  C     C4   C3    105.55  3.000
 5P7  H     C    N     107.64  3.000
 5P7  H     C    C4    110.51  3.000
 5P7  N     C    C4    113.16  3.000
 5P7  H     C    C1    109.28  3.000
 5P7  N     C    C1    113.66  3.000
 5P7  C4    C    C1    102.52  3.000
 5P7  HD    N    C6    118.35  3.000
 5P7  HD    N    C     115.86  3.000
 5P7  C6    N    C     125.55  3.000
 5P7  N1    C6   C9    120.32  3.000
 5P7  N1    C6   N     119.12  3.000
 5P7  C9    C6   N     120.55  3.000
 5P7  C8    C9   C10   119.57  3.000
 5P7  C8    C9   C6    115.76  3.000
 5P7  C10   C9   C6    124.67  3.000
 5P7  H10   C10  C11   118.32  3.000
 5P7  H10   C10  C9    121.23  3.000
 5P7  C11   C10  C9    120.45  3.000
 5P7  H11   C11  C12   119.96  3.000
 5P7  H11   C11  C10   120.01  3.000
 5P7  C12   C11  C10   120.03  3.000
 5P7  H12   C12  C13   119.90  3.000
 5P7  H12   C12  C11   119.61  3.000
 5P7  C13   C12  C11   120.49  3.000
 5P7  H13   C13  C8    118.46  3.000
 5P7  H13   C13  C12   121.08  3.000
 5P7  C8    C13  C12   120.47  3.000
 5P7  N2    C8   C13   118.92  3.000
 5P7  N2    C8   C9    122.09  3.000
 5P7  C13   C8   C9    118.99  3.000
 5P7  C7    N2   C8    115.71  3.000
 5P7  H7    C7   N1    115.04  3.000
 5P7  H7    C7   N2    116.66  3.000
 5P7  N1    C7   N2    128.30  3.000
 5P7  C7    N1   C6    117.83  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
 5P7  CONST_01  C11  C10  C9   C6   180.00  0.0  0
 5P7  CONST_02  C13  C8   C9   C6   180.00  0.0  0
 5P7  CONST_03  N2   C8   C9   C6     0.00  0.0  0
 5P7  CONST_04  N2   C7   N1   C6     0.00  0.0  0
 5P7  CONST_05  C7   N1   C6   C9     0.00  0.0  0
 5P7  CONST_06  C12  C11  C10  C9     0.00  0.0  0
 5P7  CONST_07  C12  C13  C8   C9     0.00  0.0  0
 5P7  CONST_08  C7   N2   C8   C9     0.00  0.0  0
 5P7  CONST_09  N1   C6   C9   C10  180.00  0.0  0
 5P7  CONST_10  C13  C8   C9   C10    0.00  0.0  0
 5P7  CONST_11  N2   C8   C9   C10  180.00  0.0  0
 5P7  CONST_12  C13  C12  C11  C10    0.00  0.0  0
 5P7  CONST_13  C8   C9   C10  C11    0.00  0.0  0
 5P7  CONST_14  C8   C13  C12  C11    0.00  0.0  0
 5P7  CONST_15  N2   C8   C13  C12  180.00  0.0  0
 5P7  CONST_16  C7   N2   C8   C13  180.00  0.0  0
 5P7  CONST_17  N1   C6   C9   C8     0.00  0.0  0
 5P7  CONST_18  N1   C7   N2   C8     0.00  0.0  0
 5P7  CONST_19  C10  C9   C6   N      0.00  0.0  0
 5P7  CONST_20  C8   C9   C6   N    180.00  0.0  0
 5P7  CONST_21  C7   N1   C6   N    180.00  0.0  0
 5P7  CONST_22  C9   C6   N    C    180.00  0.0  0
 5P7  CONST_23  N1   C6   N    C      0.00  0.0  0
 5P7  CONST_24  H10  C10  C9   C6     0.00  0.0  0
 5P7  CONST_25  H7   C7   N1   C6   180.00  0.0  0
 5P7  CONST_26  H11  C11  C10  C9   180.00  0.0  0
 5P7  CONST_27  H13  C13  C8   C9   180.00  0.0  0
 5P7  CONST_28  H12  C12  C11  C10  180.00  0.0  0
 5P7  CONST_29  HD   N    C6   C9     0.00  0.0  0

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
 5P7  chir_01  C1  O2  C2  C   positiv
 5P7  chir_02  C2  O1  C3  C1  positiv
 5P7  chir_03  C3  C2  C5  C4  negativ
 5P7  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
 5P7  plan-1  N    0.020
 5P7  plan-1  C6   0.020
 5P7  plan-1  C9   0.020
 5P7  plan-1  C10  0.020
 5P7  plan-1  C11  0.020
 5P7  plan-1  C12  0.020
 5P7  plan-1  C13  0.020
 5P7  plan-1  C8   0.020
 5P7  plan-1  N2   0.020
 5P7  plan-1  C7   0.020
 5P7  plan-1  N1   0.020
 5P7  plan-1  H10  0.020
 5P7  plan-1  H11  0.020
 5P7  plan-1  H12  0.020
 5P7  plan-1  H13  0.020
 5P7  plan-1  H7   0.020
 5P7  plan-2  C    0.020
 5P7  plan-2  N    0.020
 5P7  plan-2  C6   0.020
 5P7  plan-2  HD   0.020

