# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 19:48:24 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N~6~-(2,5-dimethoxybenzyl)-N~6~-methylquinazoline-2,4,6-triamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(CN(C)c2ccc3nc(N)nc(N)c3c2)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
 COG  COG  N~6~-(2,5-dimethoxybenzyl)-N~6~-methylquinazoline-2,4,6-triamine  ligand  46  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_COG
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
 COG  C2B   C  CR6   0   0.496   0.2272   1.1616  -5.0417
 COG  C4B   C  CR6   0   0.467   0.1226  -0.9689  -4.2205
 COG  C4A   C  CR66  0   0.005  -0.2512  -0.4496  -2.9280
 COG  C5B   C  CR16  0  -0.450  -0.4977  -1.2506  -1.7997
 COG  C6B   C  CR6   0   0.407  -0.8675  -0.6892  -0.5841
 COG  C7B   C  CR16  0  -0.319  -0.9593   0.7276  -0.5275
 COG  C8A   C  CR66  0   0.213  -0.3537   0.9496  -2.8647
 COG  C21   C  CH3   0  -0.434  -2.5777   1.0501   5.2813
 COG  C7'   C  CH2   0  -0.369  -1.5814  -0.8851   1.7565
 COG  C61   C  CH3   0  -0.548  -0.8496  -2.8797   0.4788
 COG  C1'   C  CR6   0  -0.005  -0.4875  -0.3193   2.6389
 COG  C2'   C  CR6   0   0.340  -0.8375   0.3288   3.8352
 COG  C3'   C  CR16  0  -0.371   0.1544   0.8448   4.6522
 COG  C4'   C  CR16  0  -0.384   1.5000   0.7268   4.3025
 COG  C5'   C  CR6   0   0.381   1.8525   0.0880   3.1251
 COG  C51   C  CH3   0  -0.434   4.1682   0.4514   3.4715
 COG  C6'   C  CR16  0  -0.370   0.8469  -0.4300   2.3036
 COG  N1'   N  N     0  -0.524  -0.1104   1.7610  -3.9258
 COG  N2'   N  NH2   0  -0.829   0.4361   1.9284  -6.1481
 COG  N3'   N  N     0  -0.508   0.3521  -0.1683  -5.2375
 COG  N4'   N  NH2   0  -0.829   0.2686  -2.2857  -4.4221
 COG  C8'   C  CR16  0  -0.316  -0.7162   1.5102  -1.6232
 COG  O2'   O  O2    0  -0.475  -2.1625   0.3970   4.1011
 COG  O5'   O  O2    0  -0.478   3.1218  -0.0822   2.6894
 COG  N6'   N  NT    0  -0.517  -1.1292  -1.4654   0.5208
 COG  H5'   H  HCR6  0   0.256  -0.3998  -2.3239  -1.8798
 COG  H7'   H  HCR6  0   0.267  -1.2122   1.2223   0.4000
 COG  H211  H  HCH3  0   0.258  -3.6634   0.9936   5.3022
 COG  H212  H  HCH3  0   0.225  -2.1842   0.5651   6.1789
 COG  H213  H  HCH3  0   0.225  -2.2804   2.1024   5.2932
 COG  H7'1  H  HCH2  0   0.279  -2.1252  -1.6546   2.3096
 COG  H7'2  H  HCH2  0   0.260  -2.3284  -0.1120   1.5558
 COG  H611  H  HCH3  0   0.262  -1.0333  -3.3122   1.4588
 COG  H612  H  HCH3  0   0.237  -1.4866  -3.4057  -0.2389
 COG  H613  H  HCH3  0   0.233   0.1918  -3.0870   0.2150
 COG  H3'   H  HCR6  0   0.280  -0.0899   1.3469   5.5785
 COG  H4'   H  HCR6  0   0.278   2.2427   1.1432   4.9694
 COG  H511  H  HCH3  0   0.257   5.0950   0.2258   2.9490
 COG  H512  H  HCH3  0   0.224   4.0833   1.5361   3.5840
 COG  H513  H  HCH3  0   0.224   4.2080  -0.0004   4.4668
 COG  H6'   H  HCR6  0   0.258   1.1343  -0.9236   1.3832
 COG  HN21  H  HNH2  0   0.383   0.9726   1.5162  -6.8922
 COG  HN22  H  HNH2  0   0.382   0.6029   2.9086  -5.9945
 COG  HN41  H  HNH2  0   0.399   0.4423  -2.6155  -5.3563
 COG  HN42  H  HNH2  0   0.414  -0.0375  -2.9673  -3.7524
 COG  H8'   H  HCR6  0   0.251  -0.7905   2.5873  -1.5413

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
 COG  C2B  N1'   aromatic  1.311  0.020  1.311
 COG  C2B  N2'   single    1.362  0.020  1.362
 COG  C2B  N3'   aromatic  1.350  0.020  1.350
 COG  C4B  C4A   aromatic  1.442  0.020  1.442
 COG  C4B  N3'   aromatic  1.315  0.020  1.315
 COG  C4B  N4'   single    1.340  0.020  1.340
 COG  C4A  C5B   aromatic  1.406  0.020  1.406
 COG  C4A  C8A   aromatic  1.404  0.020  1.404
 COG  C5B  C6B   aromatic  1.389  0.020  1.389
 COG  C5B  H5'   single    0.930  0.020  1.080
 COG  C6B  C7B   aromatic  1.421  0.020  1.421
 COG  C6B  N6'   single    1.375  0.020  1.375
 COG  C7B  C8'   aromatic  1.368  0.020  1.368
 COG  C7B  H7'   single    0.930  0.020  1.080
 COG  C8A  N1'   aromatic  1.358  0.020  1.358
 COG  C8A  C8'   aromatic  1.410  0.020  1.410
 COG  C21  O2'   single    1.411  0.020  1.411
 COG  C21  H211  single    0.970  0.020  1.090
 COG  C21  H212  single    0.970  0.020  1.090
 COG  C21  H213  single    0.970  0.020  1.090
 COG  C7'  C1'   single    1.515  0.020  1.515
 COG  C7'  N6'   single    1.438  0.020  1.438
 COG  C7'  H7'1  single    0.970  0.020  1.090
 COG  C7'  H7'2  single    0.970  0.020  1.090
 COG  C61  N6'   single    1.442  0.020  1.442
 COG  C61  H611  single    0.970  0.020  1.090
 COG  C61  H612  single    0.970  0.020  1.090
 COG  C61  H613  single    0.970  0.020  1.090
 COG  C1'  C2'   aromatic  1.405  0.020  1.405
 COG  C1'  C6'   aromatic  1.380  0.020  1.380
 COG  C2'  C3'   aromatic  1.385  0.020  1.385
 COG  C2'  O2'   single    1.353  0.020  1.353
 COG  C3'  C4'   aromatic  1.395  0.020  1.395
 COG  C3'  H3'   single    0.930  0.020  1.080
 COG  C4'  C5'   aromatic  1.385  0.020  1.385
 COG  C4'  H4'   single    0.930  0.020  1.080
 COG  C5'  C6'   aromatic  1.398  0.020  1.398
 COG  C5'  O5'   single    1.353  0.020  1.353
 COG  C51  O5'   single    1.411  0.020  1.411
 COG  C51  H511  single    0.970  0.020  1.090
 COG  C51  H512  single    0.970  0.020  1.090
 COG  C51  H513  single    0.970  0.020  1.090
 COG  C6'  H6'   single    0.930  0.020  1.080
 COG  N2'  HN21  single    0.890  0.020  1.040
 COG  N2'  HN22  single    0.890  0.020  1.040
 COG  N4'  HN41  single    0.860  0.020  1.020
 COG  N4'  HN42  single    0.860  0.020  1.020
 COG  C8'  H8'   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
 COG  N3'   C2B  N2'   114.99  3.000
 COG  N3'   C2B  N1'   126.71  3.000
 COG  N2'   C2B  N1'   118.26  3.000
 COG  N4'   C4B  N3'   117.58  3.000
 COG  N4'   C4B  C4A   121.12  3.000
 COG  N3'   C4B  C4A   121.28  3.000
 COG  C8A   C4A  C5B   121.25  3.000
 COG  C8A   C4A  C4B   114.71  3.000
 COG  C5B   C4A  C4B   124.04  3.000
 COG  H5'   C5B  C6B   119.37  3.000
 COG  H5'   C5B  C4A   119.37  3.000
 COG  C6B   C5B  C4A   121.26  3.000
 COG  N6'   C6B  C7B   121.22  3.000
 COG  N6'   C6B  C5B   121.70  3.000
 COG  C7B   C6B  C5B   117.07  3.000
 COG  H7'   C7B  C8'   117.83  3.000
 COG  H7'   C7B  C6B   120.37  3.000
 COG  C8'   C7B  C6B   121.80  3.000
 COG  C8'   C8A  N1'   119.78  3.000
 COG  C8'   C8A  C4A   117.05  3.000
 COG  N1'   C8A  C4A   123.16  3.000
 COG  H213  C21  H212  108.67  3.000
 COG  H213  C21  H211  108.74  3.000
 COG  H212  C21  H211  108.69  3.000
 COG  H213  C21  O2'   111.99  3.000
 COG  H212  C21  O2'   112.04  3.000
 COG  H211  C21  O2'   106.60  3.000
 COG  H7'2  C7'  H7'1  104.52  3.000
 COG  H7'2  C7'  N6'   110.02  3.000
 COG  H7'1  C7'  N6'   107.90  3.000
 COG  H7'2  C7'  C1'   109.64  3.000
 COG  H7'1  C7'  C1'   109.12  3.000
 COG  N6'   C7'  C1'   115.10  3.000
 COG  H613  C61  H612  107.75  3.000
 COG  H613  C61  H611  107.63  3.000
 COG  H612  C61  H611  107.56  3.000
 COG  H613  C61  N6'   112.17  3.000
 COG  H612  C61  N6'   112.18  3.000
 COG  H611  C61  N6'   109.34  3.000
 COG  C6'   C1'  C2'   118.99  3.000
 COG  C6'   C1'  C7'   121.77  3.000
 COG  C2'   C1'  C7'   119.23  3.000
 COG  O2'   C2'  C3'   124.52  3.000
 COG  O2'   C2'  C1'   115.76  3.000
 COG  C3'   C2'  C1'   119.73  3.000
 COG  H3'   C3'  C4'   118.15  3.000
 COG  H3'   C3'  C2'   121.10  3.000
 COG  C4'   C3'  C2'   120.75  3.000
 COG  H4'   C4'  C5'   121.79  3.000
 COG  H4'   C4'  C3'   118.37  3.000
 COG  C5'   C4'  C3'   119.84  3.000
 COG  O5'   C5'  C6'   116.04  3.000
 COG  O5'   C5'  C4'   124.79  3.000
 COG  C6'   C5'  C4'   119.17  3.000
 COG  H513  C51  H512  108.59  3.000
 COG  H513  C51  H511  108.69  3.000
 COG  H512  C51  H511  108.74  3.000
 COG  H513  C51  O5'   112.03  3.000
 COG  H512  C51  O5'   111.98  3.000
 COG  H511  C51  O5'   106.69  3.000
 COG  H6'   C6'  C5'   118.51  3.000
 COG  H6'   C6'  C1'   119.96  3.000
 COG  C5'   C6'  C1'   121.53  3.000
 COG  C8A   N1'  C2B   115.99  3.000
 COG  HN22  N2'  HN21  115.08  3.000
 COG  HN22  N2'  C2B   116.73  3.000
 COG  HN21  N2'  C2B   116.87  3.000
 COG  C4B   N3'  C2B   118.14  3.000
 COG  HN42  N4'  HN41  116.73  3.000
 COG  HN42  N4'  C4B   122.27  3.000
 COG  HN41  N4'  C4B   118.74  3.000
 COG  H8'   C8'  C8A   118.69  3.000
 COG  H8'   C8'  C7B   119.74  3.000
 COG  C8A   C8'  C7B   121.57  3.000
 COG  C2'   O2'  C21   118.41  3.000
 COG  C51   O5'  C5'   118.02  3.000
 COG  C61   N6'  C7'   118.79  3.000
 COG  C61   N6'  C6B   119.55  3.000
 COG  C7'   N6'  C6B   121.49  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
 COG  CONST_01  C4A   C8A  N1'  C2B     0.00   0.0  0
 COG  CONST_02  C8'   C8A  N1'  C2B   180.00   0.0  0
 COG  CONST_03  C4A   C4B  N3'  C2B     0.00   0.0  0
 COG  CONST_04  C6B   C5B  C4A  C4B   180.00   0.0  0
 COG  CONST_05  N1'   C8A  C4A  C4B     0.00   0.0  0
 COG  CONST_06  C8'   C8A  C4A  C4B   180.00   0.0  0
 COG  CONST_07  N1'   C2B  N3'  C4B     0.00   0.0  0
 COG  CONST_08  C7B   C6B  C5B  C4A     0.00   0.0  0
 COG  CONST_09  C7B   C8'  C8A  C4A     0.00   0.0  0
 COG  CONST_10  N3'   C4B  C4A  C5B   180.00   0.0  0
 COG  CONST_11  N1'   C8A  C4A  C5B   180.00   0.0  0
 COG  CONST_12  C8'   C8A  C4A  C5B     0.00   0.0  0
 COG  CONST_13  C8'   C7B  C6B  C5B     0.00   0.0  0
 COG  CONST_14  C8A   C4A  C5B  C6B     0.00   0.0  0
 COG  CONST_15  C8A   C8'  C7B  C6B     0.00   0.0  0
 COG  CONST_16  N1'   C8A  C8'  C7B   180.00   0.0  0
 COG  CONST_17  N3'   C4B  C4A  C8A     0.00   0.0  0
 COG  CONST_18  N3'   C2B  N1'  C8A     0.00   0.0  0
 COG  CONST_19  C4'   C3'  C2'  C1'     0.00   0.0  0
 COG  CONST_20  C4'   C5'  C6'  C1'     0.00   0.0  0
 COG  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 COG  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 COG  CONST_23  C6'   C1'  C2'  C3'     0.00   0.0  0
 COG  CONST_24  C6'   C5'  C4'  C3'     0.00   0.0  0
 COG  CONST_25  N4'   C4B  N3'  C2B   180.00   0.0  0
 COG  CONST_26  N2'   C2B  N3'  C4B   180.00   0.0  0
 COG  CONST_27  N6'   C6B  C5B  C4A   180.00   0.0  0
 COG  CONST_28  N4'   C4B  C4A  C5B     0.00   0.0  0
 COG  CONST_29  N4'   C4B  C4A  C8A   180.00   0.0  0
 COG  CONST_30  N2'   C2B  N1'  C8A   180.00   0.0  0
 COG  CONST_31  C3'   C2'  C1'  C7'   180.00   0.0  0
 COG  CONST_32  C5'   C6'  C1'  C7'   180.00   0.0  0
 COG  CONST_33  O5'   C5'  C6'  C1'   180.00   0.0  0
 COG  CONST_34  O5'   C5'  C4'  C3'   180.00   0.0  0
 COG  CONST_35  O2'   C2'  C3'  C4'   180.00   0.0  0
 COG  CONST_36  O2'   C2'  C1'  C6'   180.00   0.0  0
 COG  CONST_37  N6'   C6B  C7B  C8'   180.00   0.0  0
 COG  CONST_38  H5'   C5B  C4A  C4B     0.00   0.0  0
 COG  CONST_39  H8'   C8'  C8A  C4A   180.00   0.0  0
 COG  CONST_40  H7'   C7B  C6B  C5B   180.00   0.0  0
 COG  CONST_41  H3'   C3'  C2'  C1'   180.00   0.0  0
 COG  CONST_42  H6'   C6'  C1'  C2'   180.00   0.0  0
 COG  CONST_43  H4'   C4'  C3'  C2'   180.00   0.0  0
 COG  CONST_44  C7'   N6'  C6B  C5B   180.00   0.0  0
 COG  CONST_45  C61   N6'  C6B  C5B     0.00   0.0  0
 COG  CONST_46  C7'   N6'  C6B  C7B     0.00   0.0  0
 COG  CONST_47  C61   N6'  C6B  C7B   180.00   0.0  0
 COG  CONST_48  HN41  N4'  C4B  C4A   180.00   0.0  0
 COG  CONST_49  HN42  N4'  C4B  C4A     0.00   0.0  0
 COG  Var_01    C1'   C7'  N6'  C6B   -82.42  30.0  2
 COG  Var_02    C1'   C2'  O2'  C21  -179.27  30.0  2
 COG  Var_03    N6'   C7'  C1'  C2'   176.81  30.0  1
 COG  Var_04    C6'   C5'  O5'  C51   178.59  30.0  1
 COG  Var_05    H611  C61  N6'  C6B   175.03  30.0  3
 COG  Var_06    H211  C21  O2'  C2'   179.95  30.0  3
 COG  Var_07    H511  C51  O5'  C5'  -179.09  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
 COG  plan-1  C7'   0.020
 COG  plan-1  C1'   0.020
 COG  plan-1  C2'   0.020
 COG  plan-1  C3'   0.020
 COG  plan-1  C4'   0.020
 COG  plan-1  C5'   0.020
 COG  plan-1  C6'   0.020
 COG  plan-1  O2'   0.020
 COG  plan-1  O5'   0.020
 COG  plan-1  H3'   0.020
 COG  plan-1  H4'   0.020
 COG  plan-1  H6'   0.020
 COG  plan-2  C2B   0.020
 COG  plan-2  C4B   0.020
 COG  plan-2  C4A   0.020
 COG  plan-2  C5B   0.020
 COG  plan-2  C6B   0.020
 COG  plan-2  C7B   0.020
 COG  plan-2  C8A   0.020
 COG  plan-2  N1'   0.020
 COG  plan-2  N2'   0.020
 COG  plan-2  N3'   0.020
 COG  plan-2  N4'   0.020
 COG  plan-2  C8'   0.020
 COG  plan-2  N6'   0.020
 COG  plan-2  H5'   0.020
 COG  plan-2  H7'   0.020
 COG  plan-2  H8'   0.020
 COG  plan-3  C2B   0.020
 COG  plan-3  N2'   0.020
 COG  plan-3  HN21  0.020
 COG  plan-3  HN22  0.020
 COG  plan-4  C4B   0.020
 COG  plan-4  N4'   0.020
 COG  plan-4  HN41  0.020
 COG  plan-4  HN42  0.020
 COG  plan-5  C6B   0.020
 COG  plan-5  C7'   0.020
 COG  plan-5  C61   0.020
 COG  plan-5  N6'   0.020

