# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 23:34:22 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5-methyl-6-{[methyl(3,4,5-trimethoxyphenyl)amino]methyl}pyrido[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)N(C)Cc2cnc3nc(N)nc(N)c3c2C
#
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
 CO4  CO4  5-methyl-6-{[methyl(3,4,5-trimethoxyphenyl)amino]methyl}pyrido[2,3-d]pyrimidine-2,4-diamine  ligand  52  28  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CO4
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
 CO4  N2'   N  NH2    0  -0.819  -0.4036   2.5760  -6.1805
 CO4  C2D   C  CR6    0   0.541  -0.3138   1.6426  -5.2172
 CO4  N3'   N  N      0  -0.505  -0.9353   0.4776  -5.4770
 CO4  C4D   C  CR6    0   0.455  -0.8609  -0.4825  -4.5822
 CO4  N4'   N  NH2    0  -0.819  -1.5623  -1.5940  -4.8562
 CO4  C4A   C  CR66   0  -0.181  -0.0676  -0.3298  -3.3807
 CO4  C5D   C  CR6    0   0.186   0.2360  -1.3281  -2.4262
 CO4  C6D   C  CR6    0  -0.054   0.9091  -0.9417  -1.2748
 CO4  C7'   C  CR16   0  -0.076   1.2823   0.4004  -1.1533
 CO4  N8'   N  N      0  -0.433   1.0881   1.3253  -2.0616
 CO4  C8A   C  CR66   0   0.348   0.4380   0.9836  -3.1870
 CO4  N1'   N  N      0  -0.498   0.3178   1.9580  -4.1046
 CO4  C8'   C  CH2    0  -0.404   1.2528  -1.9350  -0.1797
 CO4  N9'   N  NT    -1  -0.522   1.7773  -1.3520   1.0264
 CO4  C1'   C  CR6    0   0.452   0.9432  -0.7455   1.9354
 CO4  C6'   C  CR16   0  -0.565   1.4683  -0.1826   3.1083
 CO4  C5'   C  CR6    0   0.375   0.6220   0.4117   4.0399
 CO4  O5'   O  O2     0  -0.467   1.0506   0.9611   5.1910
 CO4  C5B   C  CH3    0  -0.438   2.4339   0.9466   5.4774
 CO4  C4'   C  CR6    0   0.123  -0.7546   0.4764   3.8231
 CO4  O4'   O  O2     0  -0.484  -1.5735   1.0807   4.7312
 CO4  C4B   C  CH3    0  -0.406  -2.0872   0.1986   5.7174
 CO4  C3'   C  CR6    0   0.373  -1.2736  -0.0796   2.6527
 CO4  O3'   O  O2     0  -0.468  -2.6081   0.0208   2.5087
 CO4  C3B   C  CH3    0  -0.438  -3.2112  -0.5291   1.3560
 CO4  C2'   C  CR16   0  -0.531  -0.4409  -0.6756   1.7121
 CO4  C9'   C  CH3    0  -0.549   3.2097  -1.2661   1.1916
 CO4  C51   C  CH3    0  -0.823  -0.0958  -2.7810  -2.6207
 CO4  H2'1  H  HNH2   0   0.395  -0.7867   2.3347  -7.0768
 CO4  H2'2  H  HNH2   0   0.395   0.1313   3.4228  -6.1048
 CO4  H4'1  H  HNH2   0   0.401  -2.1752  -1.5537  -5.6548
 CO4  H4'2  H  HNH2   0   0.418  -1.8296  -2.2398  -4.1368
 CO4  H7'   H  HCR6   0   0.257   1.7925   0.7307  -0.2543
 CO4  H8'1  H  HCH2   0   0.286   1.9913  -2.6477  -0.5534
 CO4  H8'2  H  HCH2   0   0.262   0.3744  -2.5416   0.0603
 CO4  H6'   H  HCR6   0   0.288   2.5299  -0.2185   3.2985
 CO4  H5B1  H  HCH3   0   0.260   2.5539   1.4383   6.4398
 CO4  H5B2  H  HCH3   0   0.227   2.8270  -0.0708   5.5519
 CO4  H5B3  H  HCH3   0   0.227   3.0137   1.4935   4.7292
 CO4  H4B1  H  HCH3   0   0.232  -2.6930   0.7921   6.4009
 CO4  H4B2  H  HCH3   0   0.216  -2.7184  -0.5783   5.2781
 CO4  H4B3  H  HCH3   0   0.216  -1.2889  -0.2826   6.2885
 CO4  H3B1  H  HCH3   0   0.262  -4.2794  -0.3506   1.4528
 CO4  H3B2  H  HCH3   0   0.224  -2.8605  -0.0485   0.4384
 CO4  H3B3  H  HCH3   0   0.227  -3.0425  -1.6064   1.2787
 CO4  H2'   H  HCR6   0   0.268  -0.8648  -1.0663   0.8010
 CO4  H9'1  H  HCH3   0   0.233   3.5635  -0.2310   1.2251
 CO4  H9'2  H  HCH3   0   0.242   3.5483  -1.7666   2.1025
 CO4  H9'3  H  HCH3   0   0.264   3.6974  -1.7518   0.3507
 CO4  H511  H  HCH3   0   0.268  -1.1252  -3.0031  -2.3261
 CO4  H512  H  HCH3   0   0.274   0.0399  -3.0965  -3.6530
 CO4  H513  H  HCH3   0   0.286   0.5412  -3.4198  -2.0147

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
 CO4  N2'  C2D   single    1.344  0.020  1.344
 CO4  N2'  H2'1  single    0.860  0.020  1.020
 CO4  N2'  H2'2  single    0.860  0.020  1.020
 CO4  C2D  N3'   aromatic  1.346  0.020  1.346
 CO4  C2D  N1'   aromatic  1.318  0.020  1.318
 CO4  N3'  C4D   aromatic  1.315  0.020  1.315
 CO4  C4D  N4'   single    1.343  0.020  1.343
 CO4  C4D  C4A   aromatic  1.448  0.020  1.448
 CO4  N4'  H4'1  single    0.890  0.020  1.040
 CO4  N4'  H4'2  single    0.890  0.020  1.040
 CO4  C4A  C5D   aromatic  1.414  0.020  1.414
 CO4  C4A  C8A   aromatic  1.421  0.020  1.421
 CO4  C5D  C6D   aromatic  1.389  0.020  1.389
 CO4  C5D  C51   single    1.503  0.020  1.503
 CO4  C6D  C7'   aromatic  1.398  0.020  1.398
 CO4  C6D  C8'   single    1.518  0.020  1.518
 CO4  C7'  N8'   aromatic  1.311  0.020  1.311
 CO4  C7'  H7'   single    0.930  0.020  1.080
 CO4  N8'  C8A   aromatic  1.344  0.020  1.344
 CO4  C8A  N1'   aromatic  1.344  0.020  1.344
 CO4  C8'  N9'   single    1.439  0.020  1.439
 CO4  C8'  H8'1  single    0.970  0.020  1.090
 CO4  C8'  H8'2  single    0.970  0.020  1.090
 CO4  N9'  C1'   single    1.375  0.020  1.375
 CO4  N9'  C9'   single    1.444  0.020  1.444
 CO4  C1'  C6'   aromatic  1.403  0.020  1.403
 CO4  C1'  C2'   aromatic  1.404  0.020  1.404
 CO4  C6'  C5'   aromatic  1.392  0.020  1.392
 CO4  C6'  H6'   single    0.930  0.020  1.080
 CO4  C5'  O5'   single    1.346  0.020  1.346
 CO4  C5'  C4'   aromatic  1.395  0.020  1.395
 CO4  O5'  C5B   single    1.413  0.020  1.413
 CO4  C5B  H5B1  single    0.970  0.020  1.090
 CO4  C5B  H5B2  single    0.970  0.020  1.090
 CO4  C5B  H5B3  single    0.970  0.020  1.090
 CO4  C4'  O4'   single    1.364  0.020  1.364
 CO4  C4'  C3'   aromatic  1.396  0.020  1.396
 CO4  O4'  C4B   single    1.419  0.020  1.419
 CO4  C4B  H4B1  single    0.970  0.020  1.090
 CO4  C4B  H4B2  single    0.970  0.020  1.090
 CO4  C4B  H4B3  single    0.970  0.020  1.090
 CO4  C3'  O3'   single    1.346  0.020  1.346
 CO4  C3'  C2'   aromatic  1.390  0.020  1.390
 CO4  O3'  C3B   single    1.412  0.020  1.412
 CO4  C3B  H3B1  single    0.970  0.020  1.090
 CO4  C3B  H3B2  single    0.970  0.020  1.090
 CO4  C3B  H3B3  single    0.970  0.020  1.090
 CO4  C2'  H2'   single    0.930  0.020  1.080
 CO4  C9'  H9'1  single    0.970  0.020  1.090
 CO4  C9'  H9'2  single    0.970  0.020  1.090
 CO4  C9'  H9'3  single    0.970  0.020  1.090
 CO4  C51  H511  single    0.970  0.020  1.090
 CO4  C51  H512  single    0.970  0.020  1.090
 CO4  C51  H513  single    0.970  0.020  1.090

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
 CO4  H2'2  N2'  H2'1  118.23  3.000
 CO4  H2'2  N2'  C2D   119.72  3.000
 CO4  H2'1  N2'  C2D   119.88  3.000
 CO4  N1'   C2D  N3'   126.28  3.000
 CO4  N1'   C2D  N2'   118.09  3.000
 CO4  N3'   C2D  N2'   115.58  3.000
 CO4  C4D   N3'  C2D   118.34  3.000
 CO4  C4A   C4D  N4'   122.89  3.000
 CO4  C4A   C4D  N3'   121.25  3.000
 CO4  N4'   C4D  N3'   115.86  3.000
 CO4  H4'2  N4'  H4'1  115.61  3.000
 CO4  H4'2  N4'  C4D   121.72  3.000
 CO4  H4'1  N4'  C4D   116.52  3.000
 CO4  C8A   C4A  C5D   118.96  3.000
 CO4  C8A   C4A  C4D   113.93  3.000
 CO4  C5D   C4A  C4D   127.10  3.000
 CO4  C51   C5D  C6D   118.90  3.000
 CO4  C51   C5D  C4A   123.21  3.000
 CO4  C6D   C5D  C4A   117.86  3.000
 CO4  C8'   C6D  C7'   120.33  3.000
 CO4  C8'   C6D  C5D   121.73  3.000
 CO4  C7'   C6D  C5D   117.94  3.000
 CO4  H7'   C7'  N8'   115.40  3.000
 CO4  H7'   C7'  C6D   119.31  3.000
 CO4  N8'   C7'  C6D   125.27  3.000
 CO4  C8A   N8'  C7'   118.20  3.000
 CO4  N1'   C8A  N8'   115.52  3.000
 CO4  N1'   C8A  C4A   123.05  3.000
 CO4  N8'   C8A  C4A   121.43  3.000
 CO4  C8A   N1'  C2D   116.48  3.000
 CO4  H8'2  C8'  H8'1  104.84  3.000
 CO4  H8'2  C8'  N9'   109.48  3.000
 CO4  H8'1  C8'  N9'   107.74  3.000
 CO4  H8'2  C8'  C6D   109.84  3.000
 CO4  H8'1  C8'  C6D   109.47  3.000
 CO4  N9'   C8'  C6D   114.98  3.000
 CO4  C9'   N9'  C1'   119.99  3.000
 CO4  C9'   N9'  C8'   118.78  3.000
 CO4  C1'   N9'  C8'   120.79  3.000
 CO4  C2'   C1'  C6'   118.82  3.000
 CO4  C2'   C1'  N9'   121.00  3.000
 CO4  C6'   C1'  N9'   120.18  3.000
 CO4  H6'   C6'  C5'   119.63  3.000
 CO4  H6'   C6'  C1'   120.15  3.000
 CO4  C5'   C6'  C1'   120.22  3.000
 CO4  C4'   C5'  O5'   115.36  3.000
 CO4  C4'   C5'  C6'   121.05  3.000
 CO4  O5'   C5'  C6'   123.59  3.000
 CO4  C5B   O5'  C5'   118.76  3.000
 CO4  H5B3  C5B  H5B2  108.75  3.000
 CO4  H5B3  C5B  H5B1  108.72  3.000
 CO4  H5B2  C5B  H5B1  108.71  3.000
 CO4  H5B3  C5B  O5'   112.05  3.000
 CO4  H5B2  C5B  O5'   112.05  3.000
 CO4  H5B1  C5B  O5'   106.43  3.000
 CO4  C3'   C4'  O4'   120.76  3.000
 CO4  C3'   C4'  C5'   118.61  3.000
 CO4  O4'   C4'  C5'   120.63  3.000
 CO4  C4B   O4'  C4'   113.86  3.000
 CO4  H4B3  C4B  H4B2  108.59  3.000
 CO4  H4B3  C4B  H4B1  108.55  3.000
 CO4  H4B2  C4B  H4B1  108.56  3.000
 CO4  H4B3  C4B  O4'   111.86  3.000
 CO4  H4B2  C4B  O4'   111.80  3.000
 CO4  H4B1  C4B  O4'   107.38  3.000
 CO4  C2'   C3'  O3'   123.60  3.000
 CO4  C2'   C3'  C4'   121.02  3.000
 CO4  O3'   C3'  C4'   115.38  3.000
 CO4  C3B   O3'  C3'   118.79  3.000
 CO4  H3B3  C3B  H3B2  108.92  3.000
 CO4  H3B3  C3B  H3B1  108.64  3.000
 CO4  H3B2  C3B  H3B1  108.52  3.000
 CO4  H3B3  C3B  O3'   112.05  3.000
 CO4  H3B2  C3B  O3'   112.14  3.000
 CO4  H3B1  C3B  O3'   106.44  3.000
 CO4  H2'   C2'  C3'   119.44  3.000
 CO4  H2'   C2'  C1'   120.27  3.000
 CO4  C3'   C2'  C1'   120.28  3.000
 CO4  H9'3  C9'  H9'2  107.53  3.000
 CO4  H9'3  C9'  H9'1  107.54  3.000
 CO4  H9'2  C9'  H9'1  107.90  3.000
 CO4  H9'3  C9'  N9'   109.27  3.000
 CO4  H9'2  C9'  N9'   112.04  3.000
 CO4  H9'1  C9'  N9'   112.35  3.000
 CO4  H513  C51  H512  106.59  3.000
 CO4  H513  C51  H511  106.39  3.000
 CO4  H512  C51  H511  108.30  3.000
 CO4  H513  C51  C5D   111.51  3.000
 CO4  H512  C51  C5D   112.06  3.000
 CO4  H511  C51  C5D   111.68  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
 CO4  CONST_01  C4A   C4D  N3'  C2D     0.00   0.0  0
 CO4  CONST_02  C4A   C8A  N1'  C2D     0.00   0.0  0
 CO4  CONST_03  N8'   C8A  N1'  C2D   180.00   0.0  0
 CO4  CONST_04  C8A   N1'  C2D  N3'     0.00   0.0  0
 CO4  CONST_05  C5D   C4A  C4D  N3'   180.00   0.0  0
 CO4  CONST_06  C8A   C4A  C4D  N3'     0.00   0.0  0
 CO4  CONST_07  N1'   C2D  N3'  C4D     0.00   0.0  0
 CO4  CONST_08  C6D   C5D  C4A  C4D   180.00   0.0  0
 CO4  CONST_09  N8'   C8A  C4A  C4D   180.00   0.0  0
 CO4  CONST_10  N1'   C8A  C4A  C4D     0.00   0.0  0
 CO4  CONST_11  C7'   C6D  C5D  C4A     0.00   0.0  0
 CO4  CONST_12  C7'   N8'  C8A  C4A     0.00   0.0  0
 CO4  CONST_13  N8'   C8A  C4A  C5D     0.00   0.0  0
 CO4  CONST_14  N1'   C8A  C4A  C5D   180.00   0.0  0
 CO4  CONST_15  N8'   C7'  C6D  C5D     0.00   0.0  0
 CO4  CONST_16  C8A   C4A  C5D  C6D     0.00   0.0  0
 CO4  CONST_17  C8A   N8'  C7'  C6D     0.00   0.0  0
 CO4  CONST_18  N1'   C8A  N8'  C7'   180.00   0.0  0
 CO4  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 CO4  CONST_20  C4'   C3'  C2'  C1'     0.00   0.0  0
 CO4  CONST_21  C3'   C2'  C1'  C6'     0.00   0.0  0
 CO4  CONST_22  C3'   C4'  C5'  C6'     0.00   0.0  0
 CO4  CONST_23  C2'   C1'  C6'  C5'     0.00   0.0  0
 CO4  CONST_24  C2'   C3'  C4'  C5'     0.00   0.0  0
 CO4  CONST_25  C4D   N3'  C2D  N2'   180.00   0.0  0
 CO4  CONST_26  C8A   N1'  C2D  N2'   180.00   0.0  0
 CO4  CONST_27  N4'   C4D  N3'  C2D   180.00   0.0  0
 CO4  CONST_28  C51   C5D  C4A  C4D     0.00   0.0  0
 CO4  CONST_29  C5D   C4A  C4D  N4'     0.00   0.0  0
 CO4  CONST_30  C8A   C4A  C4D  N4'   180.00   0.0  0
 CO4  CONST_31  C8'   C6D  C5D  C4A   180.00   0.0  0
 CO4  CONST_32  C51   C5D  C6D  C7'   180.00   0.0  0
 CO4  CONST_33  C8'   C6D  C7'  N8'   180.00   0.0  0
 CO4  CONST_34  C51   C5D  C4A  C8A   180.00   0.0  0
 CO4  CONST_35  C5'   C6'  C1'  N9'   180.00   0.0  0
 CO4  CONST_36  C3'   C2'  C1'  N9'   180.00   0.0  0
 CO4  CONST_37  O5'   C5'  C6'  C1'   180.00   0.0  0
 CO4  CONST_38  O3'   C3'  C2'  C1'   180.00   0.0  0
 CO4  CONST_39  O4'   C4'  C5'  C6'   180.00   0.0  0
 CO4  CONST_40  O3'   C3'  C4'  C5'   180.00   0.0  0
 CO4  CONST_41  C3'   C4'  C5'  O5'   180.00   0.0  0
 CO4  CONST_42  C2'   C3'  C4'  O4'   180.00   0.0  0
 CO4  CONST_43  H7'   C7'  C6D  C5D   180.00   0.0  0
 CO4  CONST_44  H2'   C2'  C1'  C6'   180.00   0.0  0
 CO4  CONST_45  H6'   C6'  C5'  C4'   180.00   0.0  0
 CO4  CONST_46  H2'1  N2'  C2D  N3'     0.00   0.0  0
 CO4  CONST_47  H2'2  N2'  C2D  N3'   180.00   0.0  0
 CO4  CONST_48  H4'1  N4'  C4D  N3'     0.00   0.0  0
 CO4  Var_01    N9'   C8'  C6D  C5D  -171.54  30.0  2
 CO4  Var_02    C4'   C5'  O5'  C5B  -179.41  30.0  3
 CO4  Var_03    C3'   C4'  O4'  C4B    89.53  30.0  2
 CO4  Var_04    C2'   C3'  O3'  C3B     1.32  30.0  2
 CO4  Var_05    H511  C51  C5D  C4A   -84.15  30.0  2
 CO4  Var_06    H5B1  C5B  O5'  C5'   179.80  30.0  3
 CO4  Var_07    H4B1  C4B  O4'  C4'   178.07  30.0  3
 CO4  Var_08    H3B1  C3B  O3'  C3'   179.14  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
 CO4  chir_01  N9'  C8'  C1'  C9'  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
 CO4  plan-1  N9'   0.020
 CO4  plan-1  C1'   0.020
 CO4  plan-1  C6'   0.020
 CO4  plan-1  C5'   0.020
 CO4  plan-1  O5'   0.020
 CO4  plan-1  C4'   0.020
 CO4  plan-1  O4'   0.020
 CO4  plan-1  C3'   0.020
 CO4  plan-1  O3'   0.020
 CO4  plan-1  C2'   0.020
 CO4  plan-1  H6'   0.020
 CO4  plan-1  H2'   0.020
 CO4  plan-2  N2'   0.020
 CO4  plan-2  C2D   0.020
 CO4  plan-2  N3'   0.020
 CO4  plan-2  C4D   0.020
 CO4  plan-2  N4'   0.020
 CO4  plan-2  C4A   0.020
 CO4  plan-2  C5D   0.020
 CO4  plan-2  C6D   0.020
 CO4  plan-2  C7'   0.020
 CO4  plan-2  N8'   0.020
 CO4  plan-2  C8A   0.020
 CO4  plan-2  N1'   0.020
 CO4  plan-2  C8'   0.020
 CO4  plan-2  C51   0.020
 CO4  plan-2  H7'   0.020
 CO4  plan-3  N2'   0.020
 CO4  plan-3  C2D   0.020
 CO4  plan-3  H2'1  0.020
 CO4  plan-3  H2'2  0.020
 CO4  plan-4  C4D   0.020
 CO4  plan-4  N4'   0.020
 CO4  plan-4  H4'1  0.020
 CO4  plan-4  H4'2  0.020

