# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:00:41 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 2-amino-6-[(1S,2S)-1,2,3-trihydroxypropyl]pteridin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2ncc(nc2C(=O)N1)[C@H](O)[C@@H](O)CO
#
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
 MPU  MPU  2-amino-6-[(1S,2S)-1,2,3-trihydroxypropyl]pteridin-4(3H)-one  ligand  29  18  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MPU
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
 MPU  N2    N  NR16  0  -0.715   3.4988  -0.9632   0.5597
 MPU  C1    C  CR6   0   0.540   2.2059  -1.1495   0.9985
 MPU  O11   O  OC    0  -0.435   1.9126  -2.0402   1.7670
 MPU  C10   C  CR66  0  -0.023   1.2785  -0.1713   0.4350
 MPU  N9    N  N     0  -0.419  -0.0051  -0.2380   0.7751
 MPU  C8    C  CR6   0   0.165  -0.8276   0.6445   0.2674
 MPU  C7    C  CR16  0  -0.075  -0.3416   1.6362  -0.6039
 MPU  N6    N  N     0  -0.383   0.9177   1.7197  -0.9507
 MPU  C5    C  CR66  0   0.389   1.7681   0.8094  -0.4410
 MPU  N4    N  N     0  -0.505   3.0639   0.9026  -0.8055
 MPU  C3    C  CR6   0   0.703   3.8899   0.0244  -0.3030
 MPU  N13   N  NH2   0  -0.822   5.1818   0.0644  -0.6176
 MPU  C16   C  CH1   0  -0.048  -2.2800   0.5436   0.6605
 MPU  O21   O  OH1   0  -0.675  -2.4366  -0.3604   1.7208
 MPU  C26   C  CH1   0  -0.012  -3.1283   0.1128  -0.5475
 MPU  O22   O  OH1   0  -0.659  -2.7152  -1.1390  -1.0337
 MPU  C28   C  CH2   0  -0.164  -4.6091   0.1496  -0.2044
 MPU  O24   O  OH1   0  -0.670  -5.3482  -0.1103  -1.3738
 MPU  HN2   H  HNR6  0   0.433   4.1926  -1.6111   0.9121
 MPU  H7    H  HCR6  0   0.283  -1.0157   2.3809  -1.0152
 MPU  H131  H  HNH2  0   0.420   5.5033   0.7598  -1.2689
 MPU  H132  H  HNH2  0   0.423   5.8442  -0.6159  -0.2868
 MPU  H16   H  HCH1  0   0.250  -2.6195   1.5397   0.9750
 MPU  H21   H  HOH1  0   0.454  -1.5951  -0.8328   1.8195
 MPU  H26   H  HCH1  0   0.246  -2.9522   0.8307  -1.3566
 MPU  H22   H  HOH1  0   0.441  -2.8286  -1.7870  -0.3287
 MPU  H281  H  HCH2  0   0.202  -4.8242  -0.5859   0.5823
 MPU  H282  H  HCH2  0   0.199  -4.8434   1.1388   0.2111
 MPU  H24   H  HOH1  0   0.456  -6.2813  -0.1031  -1.1434

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
 MPU  N2   C1    aromatic  1.378  0.020  1.378
 MPU  N2   C3    aromatic  1.368  0.020  1.368
 MPU  N2   HN2   single    0.860  0.020  1.020
 MPU  C1   O11   double    1.212  0.020  1.212
 MPU  C1   C10   aromatic  1.461  0.020  1.461
 MPU  C10  N9    aromatic  1.330  0.020  1.330
 MPU  C10  C5    aromatic  1.403  0.020  1.403
 MPU  N9   C8    aromatic  1.309  0.020  1.309
 MPU  C8   C7    aromatic  1.407  0.020  1.407
 MPU  C8   C16   single    1.508  0.020  1.508
 MPU  C7   N6    aromatic  1.309  0.020  1.309
 MPU  C7   H7    single    0.930  0.020  1.080
 MPU  N6   C5    aromatic  1.346  0.020  1.346
 MPU  C5   N4    aromatic  1.349  0.020  1.349
 MPU  N4   C3    aromatic  1.306  0.020  1.306
 MPU  C3   N13   single    1.330  0.020  1.330
 MPU  N13  H131  single    0.860  0.020  1.020
 MPU  N13  H132  single    0.860  0.020  1.020
 MPU  C16  O21   single    1.402  0.020  1.402
 MPU  C16  C26   single    1.538  0.020  1.538
 MPU  C16  H16   single    0.970  0.020  1.090
 MPU  O21  H21   single    0.850  0.020  0.980
 MPU  C26  O22   single    1.405  0.020  1.405
 MPU  C26  C28   single    1.521  0.020  1.521
 MPU  C26  H26   single    0.970  0.020  1.090
 MPU  O22  H22   single    0.850  0.020  0.980
 MPU  C28  O24   single    1.408  0.020  1.408
 MPU  C28  H281  single    0.970  0.020  1.090
 MPU  C28  H282  single    0.970  0.020  1.090
 MPU  O24  H24   single    0.850  0.020  0.980

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
 MPU  HN2   N2   C3    119.04  3.000
 MPU  HN2   N2   C1    116.46  3.000
 MPU  C3    N2   C1    124.50  3.000
 MPU  C10   C1   O11   125.65  3.000
 MPU  C10   C1   N2    112.48  3.000
 MPU  O11   C1   N2    121.87  3.000
 MPU  C5    C10  N9    122.11  3.000
 MPU  C5    C10  C1    119.16  3.000
 MPU  N9    C10  C1    118.73  3.000
 MPU  C8    N9   C10   118.28  3.000
 MPU  C16   C8   C7    122.77  3.000
 MPU  C16   C8   N9    117.33  3.000
 MPU  C7    C8   N9    119.90  3.000
 MPU  H7    C7   N6    116.96  3.000
 MPU  H7    C7   C8    120.25  3.000
 MPU  N6    C7   C8    122.78  3.000
 MPU  C5    N6   C7    117.68  3.000
 MPU  N4    C5   N6    117.24  3.000
 MPU  N4    C5   C10   123.50  3.000
 MPU  N6    C5   C10   119.25  3.000
 MPU  C3    N4   C5    117.20  3.000
 MPU  N13   C3   N4    120.20  3.000
 MPU  N13   C3   N2    116.63  3.000
 MPU  N4    C3   N2    123.16  3.000
 MPU  H132  N13  H131  118.05  3.000
 MPU  H132  N13  C3    122.80  3.000
 MPU  H131  N13  C3    118.98  3.000
 MPU  H16   C16  C26   107.97  3.000
 MPU  H16   C16  O21   109.49  3.000
 MPU  C26   C16  O21   110.60  3.000
 MPU  H16   C16  C8    108.16  3.000
 MPU  C26   C16  C8    110.20  3.000
 MPU  O21   C16  C8    110.35  3.000
 MPU  H21   O21  C16   107.10  3.000
 MPU  H26   C26  C28   107.89  3.000
 MPU  H26   C26  O22   106.32  3.000
 MPU  C28   C26  O22   112.71  3.000
 MPU  H26   C26  C16   107.93  3.000
 MPU  C28   C26  C16   110.68  3.000
 MPU  O22   C26  C16   111.05  3.000
 MPU  H22   O22  C26   108.13  3.000
 MPU  H282  C28  H281  106.88  3.000
 MPU  H282  C28  O24   111.63  3.000
 MPU  H281  C28  O24   111.63  3.000
 MPU  H282  C28  C26   108.36  3.000
 MPU  H281  C28  C26   109.65  3.000
 MPU  O24   C28  C26   108.63  3.000
 MPU  H24   O24  C28   108.01  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
 MPU  CONST_01  N9    C10  C1   N2   180.00  0.0  0
 MPU  CONST_02  C5    C10  C1   N2     0.00  0.0  0
 MPU  CONST_03  C5    N4   C3   N2     0.00  0.0  0
 MPU  CONST_04  N4    C3   N2   C1     0.00  0.0  0
 MPU  CONST_05  C8    N9   C10  C1   180.00  0.0  0
 MPU  CONST_06  N6    C5   C10  C1   180.00  0.0  0
 MPU  CONST_07  N4    C5   C10  C1     0.00  0.0  0
 MPU  CONST_08  C3    N2   C1   C10    0.00  0.0  0
 MPU  CONST_09  C7    C8   N9   C10    0.00  0.0  0
 MPU  CONST_10  C7    N6   C5   C10    0.00  0.0  0
 MPU  CONST_11  C3    N4   C5   C10    0.00  0.0  0
 MPU  CONST_12  N6    C5   C10  N9     0.00  0.0  0
 MPU  CONST_13  N4    C5   C10  N9   180.00  0.0  0
 MPU  CONST_14  N6    C7   C8   N9     0.00  0.0  0
 MPU  CONST_15  C5    C10  N9   C8     0.00  0.0  0
 MPU  CONST_16  C5    N6   C7   C8     0.00  0.0  0
 MPU  CONST_17  N4    C5   N6   C7   180.00  0.0  0
 MPU  CONST_18  C3    N4   C5   N6   180.00  0.0  0
 MPU  CONST_19  N13   C3   N2   C1   180.00  0.0  0
 MPU  CONST_20  C3    N2   C1   O11  180.00  0.0  0
 MPU  CONST_21  N9    C10  C1   O11    0.00  0.0  0
 MPU  CONST_22  C5    C10  C1   O11  180.00  0.0  0
 MPU  CONST_23  C16   C8   N9   C10  180.00  0.0  0
 MPU  CONST_24  C16   C8   C7   N6   180.00  0.0  0
 MPU  CONST_25  N13   C3   N4   C5   180.00  0.0  0
 MPU  CONST_26  HN2   N2   C1   C10  180.00  0.0  0
 MPU  CONST_27  H7    C7   C8   N9   180.00  0.0  0
 MPU  CONST_28  H131  N13  C3   N2   180.00  0.0  0
 MPU  CONST_29  H132  N13  C3   N2     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
 MPU  chir_01  C16  C8   O21  C26  positiv
 MPU  chir_02  C26  O22  C16  C28  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
 MPU  plan-1  N2    0.020
 MPU  plan-1  C1    0.020
 MPU  plan-1  O11   0.020
 MPU  plan-1  C10   0.020
 MPU  plan-1  N9    0.020
 MPU  plan-1  C8    0.020
 MPU  plan-1  C7    0.020
 MPU  plan-1  N6    0.020
 MPU  plan-1  C5    0.020
 MPU  plan-1  N4    0.020
 MPU  plan-1  C3    0.020
 MPU  plan-1  N13   0.020
 MPU  plan-1  C16   0.020
 MPU  plan-1  HN2   0.020
 MPU  plan-1  H7    0.020
 MPU  plan-2  C3    0.020
 MPU  plan-2  N13   0.020
 MPU  plan-2  H131  0.020
 MPU  plan-2  H132  0.020

