# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:43:56 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3S,4S)-1-{3-[2-amino-6-(propan-2-yl)pyrimidin-4-yl]-4-hydroxyphenyl}pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1cc(nc(N)n1)c2cc(ccc2O)N3C[C@H](O)[C@@H](O)C3
#
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
 PMU  PMU  (3S,4S)-1-{3-[2-amino-6-(propan-2-yl)pyrimidin-4-yl]-4-hydroxyphenyl}pyrrolidine-3,4-diol  ligand  46  24  .  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_PMU
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
 PMU  C1    C  CH2   0  -0.301   2.7275   1.2776   0.6392
 PMU  N1    N  NT    0  -0.552   2.8714  -0.0899   0.1970
 PMU  C2    C  CR6   0   0.311  -0.3776  -2.7065  -0.3284
 PMU  O2    O  OH1   0  -0.665   6.3233   0.7636   0.5351
 PMU  C3    C  CR16  0  -0.329   0.9407  -3.1620  -0.3886
 PMU  O3    O  OH1   0  -0.665   4.4368   3.0339   0.9234
 PMU  C4    C  CR16  0  -0.352   2.0120  -2.3116  -0.2210
 PMU  C5    C  CR6   0   0.442   1.8130  -0.9398   0.0147
 PMU  C6    C  CR16  0  -0.490   0.4974  -0.4845   0.0554
 PMU  C7    C  CR6   0  -0.072  -0.6052  -1.3341  -0.1099
 PMU  C8    C  CH2   0  -0.298   4.2522  -0.4881   0.0543
 PMU  C9    C  CH1   0   0.009   4.1508   1.6685   1.0419
 PMU  C10   C  CH1   0   0.010   4.9990   0.8462   0.0882
 PMU  C12   C  CH3   0  -0.650  -3.5811   2.9331   1.6197
 PMU  C15   C  CR6   0   0.439  -1.9716  -0.7823  -0.0577
 PMU  N16   N  N     0  -0.630  -2.9772  -1.6625  -0.1291
 PMU  C17   C  CR6   0   0.583  -4.2304  -1.2057  -0.0816
 PMU  C18   C  CH3   0  -0.655  -3.3520   3.2696  -0.8693
 PMU  N18   N  N     0  -0.481  -4.5743   0.0811   0.0293
 PMU  C19   C  CR6   0   0.333  -3.5860   0.9609   0.0938
 PMU  C20   C  CR16  0  -0.428  -2.2499   0.5752   0.0534
 PMU  N21   N  NH2   0  -0.829  -5.2212  -2.1070  -0.1337
 PMU  H1    H  HCH2  0   0.223   2.3649   1.9393  -0.1589
 PMU  H1A   H  HCH2  0   0.239   2.0306   1.3627   1.4790
 PMU  HO1   H  HOH1  0   0.470  -2.2132  -3.1258  -0.3834
 PMU  HO2   H  HOH1  0   0.457   6.8573   0.3768  -0.1650
 PMU  H3    H  HCR6  0   0.260   1.1181  -4.2164  -0.5613
 PMU  HO3   H  HOH1  0   0.457   3.9891   3.5030   1.6337
 PMU  H4    H  HCR6  0   0.272   3.0120  -2.7225  -0.2640
 PMU  H6    H  HCR6  0   0.266   0.3245   0.5691   0.2180
 PMU  H8    H  HCH2  0   0.221   4.5956  -1.1298   0.8776
 PMU  H8A   H  HCH2  0   0.242   4.4266  -1.0293  -0.8804
 PMU  H9    H  HCH1  0   0.221   4.3389   1.3075   2.0634
 PMU  H10   H  HCH1  0   0.220   4.9420   1.3089  -0.9079
 PMU  H11   H  HCH1  0   0.250  -5.0564   2.4576   0.1428
 PMU  H12   H  HCH3  0   0.238  -3.9223   3.9615   1.7447
 PMU  H12A  H  HCH3  0   0.237  -4.0299   2.3347   2.4132
 PMU  H12B  H  HCH3  0   0.224  -2.4990   2.9252   1.7619
 PMU  H18   H  HCH3  0   0.223  -2.2622   3.2719  -0.8165
 PMU  H18A  H  HCH3  0   0.238  -3.6408   2.9178  -1.8600
 PMU  H18B  H  HCH3  0   0.238  -3.6854   4.3034  -0.7713
 PMU  H20   H  HCR6  0   0.263  -1.4722   1.3203   0.0961
 PMU  HN21  H  HNH2  0   0.404  -5.0226  -3.0782  -0.2940
 PMU  HN2A  H  HNH2  0   0.402  -6.1752  -1.7985  -0.1908
 PMU  O1    O  OH1   0  -0.652  -1.3549  -3.6125  -0.4860
 PMU  C11   C  CH1   0  -0.342  -3.9685   2.4123   0.2347

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
 PMU  C1   N1    single    1.444  0.020  1.444
 PMU  C1   C9    single    1.530  0.020  1.530
 PMU  N1   C5    single    1.370  0.020  1.370
 PMU  N1   C8    single    1.444  0.020  1.444
 PMU  O1   C2    single    1.342  0.020  1.342
 PMU  C2   C3    aromatic  1.396  0.020  1.396
 PMU  C2   C7    aromatic  1.408  0.020  1.408
 PMU  O2   C10   single    1.400  0.020  1.400
 PMU  C3   C4    aromatic  1.378  0.020  1.378
 PMU  O3   C9    single    1.400  0.020  1.400
 PMU  C4   C5    aromatic  1.406  0.020  1.406
 PMU  C5   C6    aromatic  1.393  0.020  1.393
 PMU  C6   C7    aromatic  1.402  0.020  1.402
 PMU  C7   C15   single    1.475  0.020  1.475
 PMU  C8   C10   single    1.529  0.020  1.529
 PMU  C9   C10   single    1.518  0.020  1.518
 PMU  C11  C12   single    1.530  0.020  1.530
 PMU  C11  C18   single    1.528  0.020  1.528
 PMU  C11  C19   single    1.508  0.020  1.508
 PMU  C15  N16   aromatic  1.338  0.020  1.338
 PMU  C15  C20   aromatic  1.390  0.020  1.390
 PMU  N16  C17   aromatic  1.335  0.020  1.335
 PMU  C17  N18   aromatic  1.337  0.020  1.337
 PMU  C17  N21   single    1.340  0.020  1.340
 PMU  N18  C19   aromatic  1.325  0.020  1.325
 PMU  C19  C20   aromatic  1.391  0.020  1.391
 PMU  C1   H1    single    0.970  0.020  1.090
 PMU  C1   H1A   single    0.970  0.020  1.090
 PMU  O1   HO1   single    0.850  0.020  0.980
 PMU  O2   HO2   single    0.850  0.020  0.980
 PMU  C3   H3    single    0.930  0.020  1.080
 PMU  O3   HO3   single    0.850  0.020  0.980
 PMU  C4   H4    single    0.930  0.020  1.080
 PMU  C6   H6    single    0.930  0.020  1.080
 PMU  C8   H8    single    0.970  0.020  1.090
 PMU  C8   H8A   single    0.970  0.020  1.090
 PMU  C9   H9    single    0.970  0.020  1.090
 PMU  C10  H10   single    0.970  0.020  1.090
 PMU  C11  H11   single    0.970  0.020  1.090
 PMU  C12  H12   single    0.970  0.020  1.090
 PMU  C12  H12A  single    0.970  0.020  1.090
 PMU  C12  H12B  single    0.970  0.020  1.090
 PMU  C18  H18   single    0.970  0.020  1.090
 PMU  C18  H18A  single    0.970  0.020  1.090
 PMU  C18  H18B  single    0.970  0.020  1.090
 PMU  C20  H20   single    0.930  0.020  1.080
 PMU  N21  HN21  single    0.860  0.020  1.020
 PMU  N21  HN2A  single    0.860  0.020  1.020

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
 PMU  H1A   C1   H1    107.49  3.000
 PMU  H1A   C1   C9    111.75  3.000
 PMU  H1    C1   C9    110.15  3.000
 PMU  H1A   C1   N1    111.83  3.000
 PMU  H1    C1   N1    112.38  3.000
 PMU  C9    C1   N1    103.29  3.000
 PMU  C8    N1   C5    123.68  3.000
 PMU  C8    N1   C1    112.74  3.000
 PMU  C5    N1   C1    123.46  3.000
 PMU  C7    C2   C3    118.51  3.000
 PMU  C7    C2   O1    123.95  3.000
 PMU  C3    C2   O1    117.54  3.000
 PMU  HO2   O2   C10   108.46  3.000
 PMU  H3    C3   C4    119.52  3.000
 PMU  H3    C3   C2    118.63  3.000
 PMU  C4    C3   C2    121.84  3.000
 PMU  HO3   O3   C9    108.54  3.000
 PMU  H4    C4   C5    120.53  3.000
 PMU  H4    C4   C3    118.64  3.000
 PMU  C5    C4   C3    120.82  3.000
 PMU  C6    C5   C4    117.23  3.000
 PMU  C6    C5   N1    121.55  3.000
 PMU  C4    C5   N1    121.23  3.000
 PMU  H6    C6   C7    118.89  3.000
 PMU  H6    C6   C5    118.32  3.000
 PMU  C7    C6   C5    122.78  3.000
 PMU  C15   C7   C6    119.86  3.000
 PMU  C15   C7   C2    121.33  3.000
 PMU  C6    C7   C2    118.80  3.000
 PMU  H8A   C8   H8    107.54  3.000
 PMU  H8A   C8   C10   111.88  3.000
 PMU  H8    C8   C10   109.90  3.000
 PMU  H8A   C8   N1    111.91  3.000
 PMU  H8    C8   N1    112.70  3.000
 PMU  C10   C8   N1    102.95  3.000
 PMU  H9    C9   C10   108.07  3.000
 PMU  H9    C9   O3    111.34  3.000
 PMU  C10   C9   O3    111.15  3.000
 PMU  H9    C9   C1    108.65  3.000
 PMU  C10   C9   C1    102.47  3.000
 PMU  O3    C9   C1    114.64  3.000
 PMU  H10   C10  C9    108.19  3.000
 PMU  H10   C10  C8    108.77  3.000
 PMU  C9    C10  C8    102.33  3.000
 PMU  H10   C10  O2    111.28  3.000
 PMU  C9    C10  O2    111.09  3.000
 PMU  C8    C10  O2    114.67  3.000
 PMU  H12B  C12  H12A  108.02  3.000
 PMU  H12B  C12  H12   107.58  3.000
 PMU  H12A  C12  H12   107.78  3.000
 PMU  H12B  C12  C11   111.50  3.000
 PMU  H12A  C12  C11   111.58  3.000
 PMU  H12   C12  C11   110.21  3.000
 PMU  C20   C15  N16   119.74  3.000
 PMU  C20   C15  C7    123.62  3.000
 PMU  N16   C15  C7    116.64  3.000
 PMU  C17   N16  C15   118.59  3.000
 PMU  N21   C17  N18   117.41  3.000
 PMU  N21   C17  N16   117.55  3.000
 PMU  N18   C17  N16   125.04  3.000
 PMU  H18B  C18  H18A  107.85  3.000
 PMU  H18B  C18  H18   107.40  3.000
 PMU  H18A  C18  H18   108.02  3.000
 PMU  H18B  C18  C11   110.10  3.000
 PMU  H18A  C18  C11   111.64  3.000
 PMU  H18   C18  C11   111.67  3.000
 PMU  C19   N18  C17   116.84  3.000
 PMU  C20   C19  N18   122.07  3.000
 PMU  C20   C19  C11   120.88  3.000
 PMU  N18   C19  C11   117.04  3.000
 PMU  H20   C20  C19   120.01  3.000
 PMU  H20   C20  C15   122.26  3.000
 PMU  C19   C20  C15   117.73  3.000
 PMU  HN2A  N21  HN21  118.42  3.000
 PMU  HN2A  N21  C17   119.86  3.000
 PMU  HN21  N21  C17   120.68  3.000
 PMU  HO1   O1   C2    106.66  3.000
 PMU  H11   C11  C19   106.54  3.000
 PMU  H11   C11  C18   108.53  3.000
 PMU  C19   C11  C18   111.74  3.000
 PMU  H11   C11  C12   108.31  3.000
 PMU  C19   C11  C12   110.38  3.000
 PMU  C18   C11  C12   111.17  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
 PMU  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 PMU  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 PMU  CONST_03  N16   C15  C7   C2      0.00   0.0  0
 PMU  CONST_04  C20   C15  C7   C2    180.00   0.0  0
 PMU  CONST_05  C6    C7   C2   C3      0.00   0.0  0
 PMU  CONST_06  C15   C7   C2   C3    180.00   0.0  0
 PMU  CONST_07  C6    C5   C4   C3      0.00   0.0  0
 PMU  CONST_08  C7    C2   C3   C4      0.00   0.0  0
 PMU  CONST_09  C7    C6   C5   C4      0.00   0.0  0
 PMU  CONST_10  C15   C7   C6   C5    180.00   0.0  0
 PMU  CONST_11  N16   C15  C7   C6    180.00   0.0  0
 PMU  CONST_12  C20   C15  C7   C6      0.00   0.0  0
 PMU  CONST_13  C17   N16  C15  C7    180.00   0.0  0
 PMU  CONST_14  C19   C20  C15  C7    180.00   0.0  0
 PMU  CONST_15  N18   C17  N16  C15     0.00   0.0  0
 PMU  CONST_16  N18   C19  C20  C15     0.00   0.0  0
 PMU  CONST_17  C19   C20  C15  N16     0.00   0.0  0
 PMU  CONST_18  C19   N18  C17  N16     0.00   0.0  0
 PMU  CONST_19  C20   C15  N16  C17     0.00   0.0  0
 PMU  CONST_20  C20   C19  N18  C17     0.00   0.0  0
 PMU  CONST_21  C3    C4   C5   N1    180.00   0.0  0
 PMU  CONST_22  C7    C6   C5   N1    180.00   0.0  0
 PMU  CONST_23  C4    C3   C2   O1    180.00   0.0  0
 PMU  CONST_24  C6    C7   C2   O1    180.00   0.0  0
 PMU  CONST_25  C15   C7   C2   O1      0.00   0.0  0
 PMU  CONST_26  C17   N18  C19  C11   180.00   0.0  0
 PMU  CONST_27  C15   C20  C19  C11   180.00   0.0  0
 PMU  CONST_28  N21   C17  N16  C15   180.00   0.0  0
 PMU  CONST_29  N21   C17  N18  C19   180.00   0.0  0
 PMU  CONST_30  H4    C4   C5   N1      0.00   0.0  0
 PMU  CONST_31  H6    C6   C5   N1      0.00   0.0  0
 PMU  CONST_32  H3    C3   C4   C5    180.00   0.0  0
 PMU  CONST_33  H20   C20  C15  C7      0.00   0.0  0
 PMU  CONST_34  HN21  N21  C17  N16     0.00   0.0  0
 PMU  CONST_35  HN2A  N21  C17  N16   180.00   0.0  0
 PMU  Var_01    C4    C5   N1   C1   -170.33  30.0  2
 PMU  Var_02    C10   C8   N1   C1    -14.36  30.0  1
 PMU  Var_03    C9    C1   N1   C5    165.41  30.0  1
 PMU  Var_04    N18   C19  C11  C12   111.12  30.0  2
 PMU  Var_05    H12   C12  C11  C19  -175.98  30.0  3
 PMU  Var_06    H18   C18  C11  C19   -63.62  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
 PMU  chir_01  C9   C1  O3  C10  positiv
 PMU  chir_02  C10  O2  C9  C8   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
 PMU  plan-1  N1    0.020
 PMU  plan-1  C2    0.020
 PMU  plan-1  C3    0.020
 PMU  plan-1  C4    0.020
 PMU  plan-1  C5    0.020
 PMU  plan-1  C6    0.020
 PMU  plan-1  C7    0.020
 PMU  plan-1  C15   0.020
 PMU  plan-1  H3    0.020
 PMU  plan-1  H4    0.020
 PMU  plan-1  H6    0.020
 PMU  plan-1  O1    0.020
 PMU  plan-2  C7    0.020
 PMU  plan-2  C15   0.020
 PMU  plan-2  N16   0.020
 PMU  plan-2  C17   0.020
 PMU  plan-2  N18   0.020
 PMU  plan-2  C19   0.020
 PMU  plan-2  C20   0.020
 PMU  plan-2  N21   0.020
 PMU  plan-2  H20   0.020
 PMU  plan-2  C11   0.020
 PMU  plan-3  C17   0.020
 PMU  plan-3  N21   0.020
 PMU  plan-3  HN21  0.020
 PMU  plan-3  HN2A  0.020

