# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:01:43 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 6-(2,5-dimethoxybenzyl)-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(Cc2cnc3nc(N)nc(N)c3c2C)c1
#
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
 MXA  MXA  6-(2,5-dimethoxybenzyl)-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine  ligand  43  24  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MXA
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
 MXA  N1    N  N     0  -0.497  -1.4366  -0.0919  -4.0139
 MXA  C2    C  CR6   0   0.535  -0.4258  -0.5478  -4.7243
 MXA  N2    N  NH2   0  -0.819  -0.6616  -0.9108  -6.0013
 MXA  N3    N  N     0  -0.505   0.8288  -0.7488  -4.2859
 MXA  C4    C  CR6   0   0.454   1.1231  -0.3928  -3.0540
 MXA  N4    N  NH2   0  -0.818   2.3637  -0.6940  -2.6390
 MXA  C4A   C  CR66  0  -0.183   0.1521   0.2710  -2.2115
 MXA  C5    C  CR6   0   0.167   0.3832   0.8529  -0.9399
 MXA  C5M   C  CH3   0  -0.808   1.7623   1.0582  -0.3836
 MXA  C6    C  CR6   0   0.029  -0.7190   1.3017  -0.2264
 MXA  C7    C  CR16  0  -0.090  -1.9736   1.2187  -0.8448
 MXA  N8    N  N     0  -0.437  -2.2004   0.7782  -2.0559
 MXA  C8A   C  CR66  0   0.346  -1.1557   0.3099  -2.7621
 MXA  C9    C  CH2   0  -0.639  -0.6374   1.8719   1.1683
 MXA  C1'   C  CR6   0   0.098  -0.2478   0.8557   2.2135
 MXA  C2'   C  CR6   0   0.340  -1.0838  -0.2409   2.4847
 MXA  O2'   O  O2    0  -0.465  -2.2366  -0.2955   1.7836
 MXA  C21   C  CH3   0  -0.433  -3.1036  -1.3875   1.9939
 MXA  C3'   C  CR16  0  -0.371  -0.7027  -1.1746   3.4349
 MXA  C4'   C  CR16  0  -0.385   0.4937  -1.0341   4.1382
 MXA  C5'   C  CR6   0   0.372   1.3140   0.0550   3.8933
 MXA  O5'   O  O2    0  -0.479   2.4870   0.2962   4.5228
 MXA  C51   C  CH3   0  -0.434   2.9190  -0.6286   5.4973
 MXA  C6'   C  CR16  0  -0.413   0.9275   0.9888   2.9284
 MXA  HN21  H  HNH2  0   0.393   0.1196  -1.0944  -6.6060
 MXA  HN22  H  HNH2  0   0.392  -1.5224  -0.6262  -6.4347
 MXA  HN41  H  HNH2  0   0.401   2.9142  -1.2776  -3.2480
 MXA  HN42  H  HNH2  0   0.418   2.5949  -0.7445  -1.6642
 MXA  H5M1  H  HCH3  0   0.265   2.1273   0.1796   0.1546
 MXA  H5M2  H  HCH3  0   0.271   2.4786   1.3038  -1.1648
 MXA  H5M3  H  HCH3  0   0.272   1.7781   1.8812   0.3255
 MXA  H7    H  HCR6  0   0.254  -2.8427   1.5737  -0.2984
 MXA  H91   H  HCH2  0   0.276  -1.6106   2.2998   1.4220
 MXA  H92   H  HCH2  0   0.273   0.0676   2.7058   1.2049
 MXA  H211  H  HCH3  0   0.257  -3.9508  -1.2424   1.3278
 MXA  H212  H  HCH3  0   0.224  -2.6271  -2.3425   1.7546
 MXA  H213  H  HCH3  0   0.224  -3.4702  -1.4282   3.0237
 MXA  H3'   H  HCR6  0   0.279  -1.3265  -2.0301   3.6576
 MXA  H4'   H  HCR6  0   0.277   0.7499  -1.7893   4.8686
 MXA  H511  H  HCH3  0   0.257   3.8673  -0.2584   5.8795
 MXA  H512  H  HCH3  0   0.224   2.2137  -0.7097   6.3292
 MXA  H513  H  HCH3  0   0.224   3.0768  -1.6258   5.0764
 MXA  H6'   H  HCR6  0   0.255   1.5752   1.8373   2.7376

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
 MXA  N1   C2    aromatic  1.317  0.020  1.317
 MXA  N1   C8A   aromatic  1.344  0.020  1.344
 MXA  C2   N2    single    1.348  0.020  1.348
 MXA  C2   N3    aromatic  1.344  0.020  1.344
 MXA  N2   HN21  single    0.890  0.020  1.040
 MXA  N2   HN22  single    0.890  0.020  1.040
 MXA  N3   C4    aromatic  1.316  0.020  1.316
 MXA  C4   N4    single    1.342  0.020  1.342
 MXA  C4   C4A   aromatic  1.447  0.020  1.447
 MXA  N4   HN41  single    0.890  0.020  1.040
 MXA  N4   HN42  single    0.890  0.020  1.040
 MXA  C4A  C5    aromatic  1.417  0.020  1.417
 MXA  C4A  C8A   aromatic  1.420  0.020  1.420
 MXA  C5   C5M   single    1.501  0.020  1.501
 MXA  C5   C6    aromatic  1.387  0.020  1.387
 MXA  C5M  H5M1  single    0.970  0.020  1.090
 MXA  C5M  H5M2  single    0.970  0.020  1.090
 MXA  C5M  H5M3  single    0.970  0.020  1.090
 MXA  C6   C7    aromatic  1.401  0.020  1.401
 MXA  C6   C9    single    1.509  0.020  1.509
 MXA  C7   N8    aromatic  1.308  0.020  1.308
 MXA  C7   H7    single    0.930  0.020  1.080
 MXA  N8   C8A   aromatic  1.345  0.020  1.345
 MXA  C9   C1'   single    1.509  0.020  1.509
 MXA  C9   H91   single    0.970  0.020  1.090
 MXA  C9   H92   single    0.970  0.020  1.090
 MXA  C1'  C2'   aromatic  1.405  0.020  1.405
 MXA  C1'  C6'   aromatic  1.382  0.020  1.382
 MXA  C2'  O2'   single    1.350  0.020  1.350
 MXA  C2'  C3'   aromatic  1.386  0.020  1.386
 MXA  O2'  C21   single    1.410  0.020  1.410
 MXA  C21  H211  single    0.970  0.020  1.090
 MXA  C21  H212  single    0.970  0.020  1.090
 MXA  C21  H213  single    0.970  0.020  1.090
 MXA  C3'  C4'   aromatic  1.395  0.020  1.395
 MXA  C3'  H3'   single    0.930  0.020  1.080
 MXA  C4'  C5'   aromatic  1.385  0.020  1.385
 MXA  C4'  H4'   single    0.930  0.020  1.080
 MXA  C5'  O5'   single    1.353  0.020  1.353
 MXA  C5'  C6'   aromatic  1.397  0.020  1.397
 MXA  O5'  C51   single    1.411  0.020  1.411
 MXA  C51  H511  single    0.970  0.020  1.090
 MXA  C51  H512  single    0.970  0.020  1.090
 MXA  C51  H513  single    0.970  0.020  1.090
 MXA  C6'  H6'   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
 MXA  C8A   N1   C2    116.45  3.000
 MXA  N3    C2   N2    115.59  3.000
 MXA  N3    C2   N1    126.31  3.000
 MXA  N2    C2   N1    118.03  3.000
 MXA  HN22  N2   HN21  117.26  3.000
 MXA  HN22  N2   C2    118.82  3.000
 MXA  HN21  N2   C2    118.90  3.000
 MXA  C4    N3   C2    118.28  3.000
 MXA  C4A   C4   N4    122.90  3.000
 MXA  C4A   C4   N3    121.28  3.000
 MXA  N4    C4   N3    115.82  3.000
 MXA  HN42  N4   HN41  115.63  3.000
 MXA  HN42  N4   C4    121.65  3.000
 MXA  HN41  N4   C4    116.63  3.000
 MXA  C8A   C4A  C5    119.14  3.000
 MXA  C8A   C4A  C4    113.89  3.000
 MXA  C5    C4A  C4    126.97  3.000
 MXA  C6    C5   C5M   119.67  3.000
 MXA  C6    C5   C4A   117.68  3.000
 MXA  C5M   C5   C4A   122.57  3.000
 MXA  H5M3  C5M  H5M2  106.74  3.000
 MXA  H5M3  C5M  H5M1  106.42  3.000
 MXA  H5M2  C5M  H5M1  108.37  3.000
 MXA  H5M3  C5M  C5    111.03  3.000
 MXA  H5M2  C5M  C5    111.70  3.000
 MXA  H5M1  C5M  C5    112.29  3.000
 MXA  C9    C6   C7    118.60  3.000
 MXA  C9    C6   C5    123.68  3.000
 MXA  C7    C6   C5    117.72  3.000
 MXA  H7    C7   N8    115.91  3.000
 MXA  H7    C7   C6    118.36  3.000
 MXA  N8    C7   C6    125.70  3.000
 MXA  C8A   N8   C7    117.94  3.000
 MXA  N8    C8A  C4A   121.43  3.000
 MXA  N8    C8A  N1    115.51  3.000
 MXA  C4A   C8A  N1    123.06  3.000
 MXA  H92   C9   H91   105.54  3.000
 MXA  H92   C9   C1'   108.91  3.000
 MXA  H91   C9   C1'   109.44  3.000
 MXA  H92   C9   C6    110.75  3.000
 MXA  H91   C9   C6    108.33  3.000
 MXA  C1'   C9   C6    113.56  3.000
 MXA  C6'   C1'  C2'   118.76  3.000
 MXA  C6'   C1'  C9    120.87  3.000
 MXA  C2'   C1'  C9    120.37  3.000
 MXA  C3'   C2'  O2'   124.30  3.000
 MXA  C3'   C2'  C1'   119.65  3.000
 MXA  O2'   C2'  C1'   116.05  3.000
 MXA  C21   O2'  C2'   118.61  3.000
 MXA  H213  C21  H212  108.63  3.000
 MXA  H213  C21  H211  108.69  3.000
 MXA  H212  C21  H211  108.78  3.000
 MXA  H213  C21  O2'   112.04  3.000
 MXA  H212  C21  O2'   112.07  3.000
 MXA  H211  C21  O2'   106.52  3.000
 MXA  H3'   C3'  C4'   118.06  3.000
 MXA  H3'   C3'  C2'   121.03  3.000
 MXA  C4'   C3'  C2'   120.91  3.000
 MXA  H4'   C4'  C5'   121.88  3.000
 MXA  H4'   C4'  C3'   118.25  3.000
 MXA  C5'   C4'  C3'   119.87  3.000
 MXA  C6'   C5'  O5'   116.23  3.000
 MXA  C6'   C5'  C4'   118.92  3.000
 MXA  O5'   C5'  C4'   124.84  3.000
 MXA  C51   O5'  C5'   118.02  3.000
 MXA  H513  C51  H512  108.55  3.000
 MXA  H513  C51  H511  108.65  3.000
 MXA  H512  C51  H511  108.68  3.000
 MXA  H513  C51  O5'   112.08  3.000
 MXA  H512  C51  O5'   112.11  3.000
 MXA  H511  C51  O5'   106.65  3.000
 MXA  H6'   C6'  C5'   118.63  3.000
 MXA  H6'   C6'  C1'   119.49  3.000
 MXA  C5'   C6'  C1'   121.88  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
 MXA  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 MXA  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 MXA  CONST_03  C5    C4A  C8A  N1    180.00   0.0  0
 MXA  CONST_04  C7    N8   C8A  N1    180.00   0.0  0
 MXA  CONST_05  C4A   C8A  N1   C2      0.00   0.0  0
 MXA  CONST_06  N8    C8A  N1   C2    180.00   0.0  0
 MXA  CONST_07  C4A   C4   N3   C2      0.00   0.0  0
 MXA  CONST_08  C8A   N1   C2   N3      0.00   0.0  0
 MXA  CONST_09  C5    C4A  C4   N3    180.00   0.0  0
 MXA  CONST_10  C8A   C4A  C4   N3      0.00   0.0  0
 MXA  CONST_11  C6    C5   C4A  C4    180.00   0.0  0
 MXA  CONST_12  N8    C8A  C4A  C4    180.00   0.0  0
 MXA  CONST_13  C7    C6   C5   C4A     0.00   0.0  0
 MXA  CONST_14  C7    N8   C8A  C4A     0.00   0.0  0
 MXA  CONST_15  N8    C8A  C4A  C5      0.00   0.0  0
 MXA  CONST_16  N8    C7   C6   C5      0.00   0.0  0
 MXA  CONST_17  C8A   C4A  C5   C6      0.00   0.0  0
 MXA  CONST_18  C8A   N8   C7   C6      0.00   0.0  0
 MXA  CONST_19  C4'   C3'  C2'  C1'     0.00   0.0  0
 MXA  CONST_20  C4'   C5'  C6'  C1'     0.00   0.0  0
 MXA  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 MXA  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 MXA  CONST_23  C6'   C1'  C2'  C3'     0.00   0.0  0
 MXA  CONST_24  C6'   C5'  C4'  C3'     0.00   0.0  0
 MXA  CONST_25  N4    C4   N3   C2    180.00   0.0  0
 MXA  CONST_26  C8A   N1   C2   N2    180.00   0.0  0
 MXA  CONST_27  C4    N3   C2   N2    180.00   0.0  0
 MXA  CONST_28  C5M   C5   C4A  C4      0.00   0.0  0
 MXA  CONST_29  C5    C4A  C4   N4      0.00   0.0  0
 MXA  CONST_30  C8A   C4A  C4   N4    180.00   0.0  0
 MXA  CONST_31  C9    C6   C5   C4A   180.00   0.0  0
 MXA  CONST_32  C8A   C4A  C5   C5M   180.00   0.0  0
 MXA  CONST_33  C7    C6   C5   C5M   180.00   0.0  0
 MXA  CONST_34  C9    C6   C7   N8    180.00   0.0  0
 MXA  CONST_35  C3'   C2'  C1'  C9    180.00   0.0  0
 MXA  CONST_36  C5'   C6'  C1'  C9    180.00   0.0  0
 MXA  CONST_37  O5'   C5'  C6'  C1'   180.00   0.0  0
 MXA  CONST_38  C6'   C1'  C2'  O2'   180.00   0.0  0
 MXA  CONST_39  C4'   C3'  C2'  O2'   180.00   0.0  0
 MXA  CONST_40  O5'   C5'  C4'  C3'   180.00   0.0  0
 MXA  CONST_41  H7    C7   C6   C5    180.00   0.0  0
 MXA  CONST_42  H3'   C3'  C2'  C1'   180.00   0.0  0
 MXA  CONST_43  H6'   C6'  C1'  C2'   180.00   0.0  0
 MXA  CONST_44  H4'   C4'  C3'  C2'   180.00   0.0  0
 MXA  CONST_45  HN21  N2   C2   N1    180.00   0.0  0
 MXA  CONST_46  HN22  N2   C2   N1      0.00   0.0  0
 MXA  CONST_47  HN41  N4   C4   N3      0.00   0.0  0
 MXA  Var_01    C1'   C9   C6   C5    -67.78  30.0  2
 MXA  Var_02    C2'   C1'  C9   C6    -63.68  30.0  2
 MXA  Var_03    C3'   C2'  O2'  C21    -1.83  30.0  1
 MXA  Var_04    C6'   C5'  O5'  C51  -179.51  30.0  2
 MXA  Var_05    H5M1  C5M  C5   C4A   -87.21  30.0  2
 MXA  Var_06    H211  C21  O2'  C2'  -179.17  30.0  3
 MXA  Var_07    H511  C51  O5'  C5'  -179.94  30.0  3

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
 MXA  plan-1  C9    0.020
 MXA  plan-1  C1'   0.020
 MXA  plan-1  C2'   0.020
 MXA  plan-1  O2'   0.020
 MXA  plan-1  C3'   0.020
 MXA  plan-1  C4'   0.020
 MXA  plan-1  C5'   0.020
 MXA  plan-1  O5'   0.020
 MXA  plan-1  C6'   0.020
 MXA  plan-1  H3'   0.020
 MXA  plan-1  H4'   0.020
 MXA  plan-1  H6'   0.020
 MXA  plan-2  N1    0.020
 MXA  plan-2  C2    0.020
 MXA  plan-2  N2    0.020
 MXA  plan-2  N3    0.020
 MXA  plan-2  C4    0.020
 MXA  plan-2  N4    0.020
 MXA  plan-2  C4A   0.020
 MXA  plan-2  C5    0.020
 MXA  plan-2  C5M   0.020
 MXA  plan-2  C6    0.020
 MXA  plan-2  C7    0.020
 MXA  plan-2  N8    0.020
 MXA  plan-2  C8A   0.020
 MXA  plan-2  C9    0.020
 MXA  plan-2  H7    0.020
 MXA  plan-3  C2    0.020
 MXA  plan-3  N2    0.020
 MXA  plan-3  HN21  0.020
 MXA  plan-3  HN22  0.020
 MXA  plan-4  C4    0.020
 MXA  plan-4  N4    0.020
 MXA  plan-4  HN41  0.020
 MXA  plan-4  HN42  0.020

