# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:40:24 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (1S,2S)-1-(2,4-diaminopteridin-6-yl)propane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@@H](O)c1cnc2nc(N)nc(N)c2n1
#
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
 7AP  7AP  (1S,2S)-1-(2,4-diaminopteridin-6-yl)propane-1,2-diol  ligand  29  17  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7AP
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
 7AP  N1    N  N     0  -0.511   2.2541  -7.3495  -4.5606
 7AP  C2    C  CR6   0   0.549   2.6258  -7.1039  -5.8090
 7AP  N2    N  NH2   0  -0.815   3.5524  -7.9084  -6.3462
 7AP  N3    N  N     0  -0.503   2.1733  -6.1232  -6.6236
 7AP  C4    C  CR6   0   0.481   1.2560  -5.3113  -6.1492
 7AP  N4    N  NH2   0  -0.804   0.7760  -4.3243  -6.8958
 7AP  C4A   C  CR66  0   0.001   0.7581  -5.4785  -4.8041
 7AP  C8A   C  CR66  0   0.388   1.3175  -6.5326  -4.0620
 7AP  N5    N  N     0  -0.372  -0.1758  -4.6622  -4.3222
 7AP  C6    C  CR6   0   0.166  -0.5833  -4.8688  -3.0921
 7AP  C7    C  CR16  0  -0.097  -0.0303  -5.9281  -2.3412
 7AP  N8    N  N     0  -0.395   0.8899  -6.7378  -2.7994
 7AP  C1'   C  CH1   0  -0.049  -1.6088  -3.9576  -2.4829
 7AP  O1'   O  OH1   0  -0.658  -2.4520  -3.4857  -3.4985
 7AP  C2'   C  CH1   0   0.005  -0.9468  -2.7951  -1.7077
 7AP  O2'   O  OH1   0  -0.662  -0.1902  -3.2959  -0.6279
 7AP  C3'   C  CH3   0  -0.679  -0.0365  -1.9388  -2.5632
 7AP  H77   H  HCR6  0   0.270  -0.3838  -6.1110  -1.3320
 7AP  H1''  H  HCH1  0   0.237  -2.1794  -4.5433  -1.7435
 7AP  H2''  H  HCH1  0   0.217  -1.7711  -2.1651  -1.3386
 7AP  H3'1  H  HCH3  0   0.229   0.8714  -2.4727  -2.8451
 7AP  H3'2  H  HCH3  0   0.234  -0.5433  -1.6320  -3.4763
 7AP  H3'3  H  HCH3  0   0.239   0.2564  -1.0381  -2.0229
 7AP  HO1   H  HOH1  0   0.453  -0.7897  -3.7136  -0.0009
 7AP  HO2   H  HOH1  0   0.456  -3.1323  -2.9418  -3.0879
 7AP  HN1   H  HNH2  0   0.400   3.8906  -7.7485  -7.2777
 7AP  HN2   H  HNH2  0   0.407   1.1013  -4.1848  -7.8369
 7AP  HN3   H  HNH2  0   0.399   3.9627  -8.6443  -5.8000
 7AP  HN4   H  HNH2  0   0.414   0.0754  -3.7057  -6.5237

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
 7AP  N1   C2    aromatic  1.325  0.020  1.325
 7AP  N1   C8A   aromatic  1.339  0.020  1.339
 7AP  C2   N2    single    1.340  0.020  1.340
 7AP  C2   N3    aromatic  1.353  0.020  1.353
 7AP  N3   C4    aromatic  1.314  0.020  1.314
 7AP  C4   N4    single    1.327  0.020  1.327
 7AP  C4   C4A   aromatic  1.444  0.020  1.444
 7AP  C4A  C8A   aromatic  1.405  0.020  1.405
 7AP  C4A  N5    aromatic  1.331  0.020  1.331
 7AP  C8A  N8    aromatic  1.349  0.020  1.349
 7AP  N5   C6    aromatic  1.312  0.020  1.312
 7AP  C6   C7    aromatic  1.411  0.020  1.411
 7AP  C6   C1'   single    1.501  0.020  1.501
 7AP  C7   N8    aromatic  1.309  0.020  1.309
 7AP  C7   H77   single    0.930  0.020  1.080
 7AP  C1'  O1'   single    1.402  0.020  1.402
 7AP  C1'  C2'   single    1.546  0.020  1.546
 7AP  C1'  H1''  single    0.970  0.020  1.090
 7AP  C2'  O2'   single    1.410  0.020  1.410
 7AP  C2'  C3'   single    1.515  0.020  1.515
 7AP  C2'  H2''  single    0.970  0.020  1.090
 7AP  C3'  H3'1  single    0.970  0.020  1.090
 7AP  C3'  H3'2  single    0.970  0.020  1.090
 7AP  C3'  H3'3  single    0.970  0.020  1.090
 7AP  HO1  O2'   single    0.850  0.020  0.980
 7AP  HO2  O1'   single    0.850  0.020  0.980
 7AP  HN1  N2    single    0.860  0.020  1.020
 7AP  HN2  N4    single    0.860  0.020  1.020
 7AP  HN3  N2    single    0.860  0.020  1.020
 7AP  HN4  N4    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
 7AP  C8A   N1   C2    115.71  3.000
 7AP  N3    C2   N2    115.17  3.000
 7AP  N3    C2   N1    127.42  3.000
 7AP  N2    C2   N1    117.41  3.000
 7AP  HN3   N2   HN1   118.94  3.000
 7AP  HN3   N2   C2    120.31  3.000
 7AP  HN1   N2   C2    120.63  3.000
 7AP  C4    N3   C2    117.66  3.000
 7AP  C4A   C4   N4    119.04  3.000
 7AP  C4A   C4   N3    120.37  3.000
 7AP  N4    C4   N3    120.59  3.000
 7AP  HN4   N4   HN2   119.09  3.000
 7AP  HN4   N4   C4    120.07  3.000
 7AP  HN2   N4   C4    120.84  3.000
 7AP  N5    C4A  C8A   123.25  3.000
 7AP  N5    C4A  C4    120.55  3.000
 7AP  C8A   C4A  C4    116.20  3.000
 7AP  N8    C8A  C4A   118.83  3.000
 7AP  N8    C8A  N1    118.52  3.000
 7AP  C4A   C8A  N1    122.64  3.000
 7AP  C6    N5   C4A   117.44  3.000
 7AP  C1'   C6   C7    120.49  3.000
 7AP  C1'   C6   N5    119.81  3.000
 7AP  C7    C6   N5    119.69  3.000
 7AP  H77   C7   N8    116.78  3.000
 7AP  H77   C7   C6    119.60  3.000
 7AP  N8    C7   C6    123.62  3.000
 7AP  C7    N8   C8A   117.17  3.000
 7AP  H1''  C1'  C2'   106.55  3.000
 7AP  H1''  C1'  O1'   110.69  3.000
 7AP  C2'   C1'  O1'   111.57  3.000
 7AP  H1''  C1'  C6    107.66  3.000
 7AP  C2'   C1'  C6    111.56  3.000
 7AP  O1'   C1'  C6    108.74  3.000
 7AP  HO2   O1'  C1'   107.82  3.000
 7AP  H2''  C2'  C3'   108.41  3.000
 7AP  H2''  C2'  O2'   110.37  3.000
 7AP  C3'   C2'  O2'   108.10  3.000
 7AP  H2''  C2'  C1'   106.13  3.000
 7AP  C3'   C2'  C1'   113.53  3.000
 7AP  O2'   C2'  C1'   110.28  3.000
 7AP  HO1   O2'  C2'   108.57  3.000
 7AP  H3'3  C3'  H3'2  107.93  3.000
 7AP  H3'3  C3'  H3'1  108.00  3.000
 7AP  H3'2  C3'  H3'1  107.99  3.000
 7AP  H3'3  C3'  C2'   110.40  3.000
 7AP  H3'2  C3'  C2'   110.69  3.000
 7AP  H3'1  C3'  C2'   111.69  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
 7AP  CONST_01  C4   N3   C2   N1     0.00  0.0  0
 7AP  CONST_02  C4   C4A  C8A  N1     0.00  0.0  0
 7AP  CONST_03  N5   C4A  C8A  N1   180.00  0.0  0
 7AP  CONST_04  C7   N8   C8A  N1   180.00  0.0  0
 7AP  CONST_05  C4A  C8A  N1   C2     0.00  0.0  0
 7AP  CONST_06  N8   C8A  N1   C2   180.00  0.0  0
 7AP  CONST_07  C4A  C4   N3   C2     0.00  0.0  0
 7AP  CONST_08  C8A  N1   C2   N3     0.00  0.0  0
 7AP  CONST_09  C8A  C4A  C4   N3     0.00  0.0  0
 7AP  CONST_10  N5   C4A  C4   N3   180.00  0.0  0
 7AP  CONST_11  N8   C8A  C4A  C4   180.00  0.0  0
 7AP  CONST_12  C6   N5   C4A  C4   180.00  0.0  0
 7AP  CONST_13  C7   N8   C8A  C4A    0.00  0.0  0
 7AP  CONST_14  C7   C6   N5   C4A    0.00  0.0  0
 7AP  CONST_15  C6   N5   C4A  C8A    0.00  0.0  0
 7AP  CONST_16  C6   C7   N8   C8A    0.00  0.0  0
 7AP  CONST_17  N8   C8A  C4A  N5     0.00  0.0  0
 7AP  CONST_18  N8   C7   C6   N5     0.00  0.0  0
 7AP  CONST_19  N4   C4   N3   C2   180.00  0.0  0
 7AP  CONST_20  C8A  N1   C2   N2   180.00  0.0  0
 7AP  CONST_21  C4   N3   C2   N2   180.00  0.0  0
 7AP  CONST_22  C8A  C4A  C4   N4   180.00  0.0  0
 7AP  CONST_23  N5   C4A  C4   N4     0.00  0.0  0
 7AP  CONST_24  C1'  C6   N5   C4A  180.00  0.0  0
 7AP  CONST_25  C1'  C6   C7   N8   180.00  0.0  0
 7AP  CONST_26  H77  C7   N8   C8A  180.00  0.0  0
 7AP  CONST_27  HN1  N2   C2   N1   180.00  0.0  0
 7AP  CONST_28  HN3  N2   C2   N1     0.00  0.0  0
 7AP  CONST_29  HN2  N4   C4   N3     0.00  0.0  0
 7AP  CONST_30  HN4  N4   C4   N3   180.00  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
 7AP  chir_01  C1'  C6   O1'  C2'  positiv
 7AP  chir_02  C2'  O2'  C1'  C3'  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
 7AP  plan-1  N1   0.020
 7AP  plan-1  C2   0.020
 7AP  plan-1  N2   0.020
 7AP  plan-1  N3   0.020
 7AP  plan-1  C4   0.020
 7AP  plan-1  N4   0.020
 7AP  plan-1  C4A  0.020
 7AP  plan-1  C8A  0.020
 7AP  plan-1  N5   0.020
 7AP  plan-1  C6   0.020
 7AP  plan-1  C7   0.020
 7AP  plan-1  N8   0.020
 7AP  plan-1  C1'  0.020
 7AP  plan-1  H77  0.020
 7AP  plan-2  C2   0.020
 7AP  plan-2  N2   0.020
 7AP  plan-2  HN1  0.020
 7AP  plan-2  HN3  0.020
 7AP  plan-3  C4   0.020
 7AP  plan-3  N4   0.020
 7AP  plan-3  HN2  0.020
 7AP  plan-3  HN4  0.020

