# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 23:49:14 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N~6~-(3,5-dimethoxybenzyl)-N~6~-methylpyrido[2,3-d]pyrimidine-2,4,6-triamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CN(C)c2cnc3nc(N)nc(N)c3c2)cc(OC)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
 COQ  COQ  N~6~-(3,5-dimethoxybenzyl)-N~6~-methylpyrido[2,3-d]pyrimidine-2,4,6-triamine  ligand  45  25  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_COQ
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
 COQ  C2B   C  CR6   0   0.530   1.4194  -0.4151  -4.5144
 COQ  C4B   C  CR6   0   0.482  -0.2069  -1.3858  -3.2406
 COQ  C4A   C  CR66  0  -0.121  -0.3578  -0.1497  -2.5167
 COQ  C5B   C  CR16  0  -0.277  -1.2319   0.0524  -1.4399
 COQ  C6B   C  CR6   0   0.271  -1.2887   1.2878  -0.8290
 COQ  C7'   C  CR16  0  -0.108  -0.4433   2.2870  -1.3676
 COQ  C8A   C  CR66  0   0.336   0.4716   0.9031  -2.9433
 COQ  C9'   C  CH2   0  -0.446  -1.5454   2.1991   1.4132
 COQ  C1'   C  CR6   0   0.171  -0.7407   1.2157   2.2298
 COQ  C2'   C  CR16  0  -0.417   0.5828   0.9564   1.8953
 COQ  C3'   C  CR6   0   0.429   1.3043   0.0033   2.6094
 COQ  C4'   C  CR16  0  -0.544   0.7106  -0.6926   3.6626
 COQ  C5'   C  CR6   0   0.428  -0.6159  -0.4194   3.9935
 COQ  C6'   C  CR16  0  -0.431  -1.3401   0.5332   3.2799
 COQ  C31   C  CH3   0  -0.439   3.3735  -1.1276   2.9167
 COQ  C51   C  CH3   0  -0.439  -0.5969  -2.0204   5.7506
 COQ  CN'   C  CH3   0  -0.559  -3.2029   0.6590   0.5083
 COQ  N1'   N  N     0  -0.499   1.3594   0.7722  -3.9468
 COQ  N2'   N  NH2   0  -0.821   2.3378  -0.6038  -5.4870
 COQ  N3'   N  N     0  -0.507   0.6719  -1.4961  -4.2128
 COQ  N4'   N  NH2   0  -0.829  -0.9423  -2.4591  -2.9405
 COQ  N8'   N  N     0  -0.417   0.3963   2.1135  -2.3533
 COQ  N9'   N  NT    0  -0.487  -2.1493   1.6055   0.2224
 COQ  O3'   O  O2    0  -0.474   2.5798  -0.1874   2.2223
 COQ  O5'   O  O2    0  -0.474  -1.2713  -1.0352   4.9954
 COQ  H5'   H  HCR6  0   0.266  -1.8557  -0.7560  -1.0819
 COQ  H7'   H  HCR6  0   0.272  -0.4807   3.2890  -0.9501
 COQ  H9'1  H  HCH2  0   0.269  -2.3553   2.6128   2.0167
 COQ  H9'2  H  HCH2  0   0.269  -0.9184   3.0417   1.1211
 COQ  H2'   H  HCR6  0   0.251   1.0665   1.4920   1.0873
 COQ  H4'   H  HCR6  0   0.301   1.2743  -1.4278   4.2182
 COQ  H6'   H  HCR6  0   0.254  -2.3694   0.7360   3.5520
 COQ  H311  H  HCH3  0   0.261   4.3532  -1.1126   2.4452
 COQ  H312  H  HCH3  0   0.229   3.4888  -0.8667   3.9721
 COQ  H313  H  HCH3  0   0.229   2.9669  -2.1400   2.8460
 COQ  H511  H  HCH3  0   0.261  -1.3084  -2.3863   6.4870
 COQ  H512  H  HCH3  0   0.229  -0.2712  -2.8600   5.1307
 COQ  H513  H  HCH3  0   0.229   0.2709  -1.6123   6.2758
 COQ  HCN1  H  HCH3  0   0.255  -3.8727   1.0955   1.2485
 COQ  HCN2  H  HCH3  0   0.252  -3.7849   0.4646  -0.3935
 COQ  HCN3  H  HCH3  0   0.219  -2.8550  -0.3035   0.9038
 COQ  HN21  H  HNH2  0   0.391   2.2672  -1.4203  -6.0679
 COQ  HN22  H  HNH2  0   0.390   2.7878   0.2015  -5.8850
 COQ  HN41  H  HNH2  0   0.405  -0.8340  -3.2985  -3.4833
 COQ  HN42  H  HNH2  0   0.417  -1.6862  -2.4399  -2.2681

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
 COQ  C2B  N1'   aromatic  1.317  0.020  1.317
 COQ  C2B  N2'   single    1.351  0.020  1.351
 COQ  C2B  N3'   aromatic  1.348  0.020  1.348
 COQ  C4B  C4A   aromatic  1.440  0.020  1.440
 COQ  C4B  N3'   aromatic  1.315  0.020  1.315
 COQ  C4B  N4'   single    1.335  0.020  1.335
 COQ  C4A  C5B   aromatic  1.402  0.020  1.402
 COQ  C4A  C8A   aromatic  1.407  0.020  1.407
 COQ  C5B  C6B   aromatic  1.379  0.020  1.379
 COQ  C5B  H5'   single    0.930  0.020  1.080
 COQ  C6B  C7'   aromatic  1.415  0.020  1.415
 COQ  C6B  N9'   single    1.395  0.020  1.395
 COQ  C7'  N8'   aromatic  1.306  0.020  1.306
 COQ  C7'  H7'   single    0.930  0.020  1.080
 COQ  C8A  N1'   aromatic  1.346  0.020  1.346
 COQ  C8A  N8'   aromatic  1.349  0.020  1.349
 COQ  C9'  C1'   single    1.510  0.020  1.510
 COQ  C9'  N9'   single    1.461  0.020  1.461
 COQ  C9'  H9'1  single    0.970  0.020  1.090
 COQ  C9'  H9'2  single    0.970  0.020  1.090
 COQ  C1'  C2'   aromatic  1.389  0.020  1.389
 COQ  C1'  C6'   aromatic  1.388  0.020  1.388
 COQ  C2'  C3'   aromatic  1.392  0.020  1.392
 COQ  C2'  H2'   single    0.930  0.020  1.080
 COQ  C3'  C4'   aromatic  1.395  0.020  1.395
 COQ  C3'  O3'   single    1.346  0.020  1.346
 COQ  C4'  C5'   aromatic  1.394  0.020  1.394
 COQ  C4'  H4'   single    0.930  0.020  1.080
 COQ  C5'  C6'   aromatic  1.393  0.020  1.393
 COQ  C5'  O5'   single    1.346  0.020  1.346
 COQ  C6'  H6'   single    0.930  0.020  1.080
 COQ  C31  O3'   single    1.413  0.020  1.413
 COQ  C31  H311  single    0.970  0.020  1.090
 COQ  C31  H312  single    0.970  0.020  1.090
 COQ  C31  H313  single    0.970  0.020  1.090
 COQ  C51  O5'   single    1.413  0.020  1.413
 COQ  C51  H511  single    0.970  0.020  1.090
 COQ  C51  H512  single    0.970  0.020  1.090
 COQ  C51  H513  single    0.970  0.020  1.090
 COQ  CN'  N9'   single    1.445  0.020  1.445
 COQ  CN'  HCN1  single    0.970  0.020  1.090
 COQ  CN'  HCN2  single    0.970  0.020  1.090
 COQ  CN'  HCN3  single    0.970  0.020  1.090
 COQ  N2'  HN21  single    0.890  0.020  1.040
 COQ  N2'  HN22  single    0.890  0.020  1.040
 COQ  N4'  HN41  single    0.860  0.020  1.020
 COQ  N4'  HN42  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
 COQ  N3'   C2B  N2'   115.21  3.000
 COQ  N3'   C2B  N1'   126.93  3.000
 COQ  N2'   C2B  N1'   117.84  3.000
 COQ  N4'   C4B  N3'   117.82  3.000
 COQ  N4'   C4B  C4A   121.28  3.000
 COQ  N3'   C4B  C4A   120.90  3.000
 COQ  C8A   C4A  C5B   119.53  3.000
 COQ  C8A   C4A  C4B   115.35  3.000
 COQ  C5B   C4A  C4B   125.11  3.000
 COQ  H5'   C5B  C6B   119.92  3.000
 COQ  H5'   C5B  C4A   120.40  3.000
 COQ  C6B   C5B  C4A   119.68  3.000
 COQ  N9'   C6B  C7'   119.63  3.000
 COQ  N9'   C6B  C5B   124.27  3.000
 COQ  C7'   C6B  C5B   116.05  3.000
 COQ  H7'   C7'  N8'   115.76  3.000
 COQ  H7'   C7'  C6B   118.98  3.000
 COQ  N8'   C7'  C6B   125.26  3.000
 COQ  N8'   C8A  N1'   116.75  3.000
 COQ  N8'   C8A  C4A   120.41  3.000
 COQ  N1'   C8A  C4A   122.84  3.000
 COQ  H9'2  C9'  H9'1  106.38  3.000
 COQ  H9'2  C9'  N9'   109.48  3.000
 COQ  H9'1  C9'  N9'   107.33  3.000
 COQ  H9'2  C9'  C1'   109.98  3.000
 COQ  H9'1  C9'  C1'   110.06  3.000
 COQ  N9'   C9'  C1'   113.35  3.000
 COQ  C6'   C1'  C2'   120.10  3.000
 COQ  C6'   C1'  C9'   119.93  3.000
 COQ  C2'   C1'  C9'   119.92  3.000
 COQ  H2'   C2'  C3'   119.31  3.000
 COQ  H2'   C2'  C1'   120.84  3.000
 COQ  C3'   C2'  C1'   119.86  3.000
 COQ  O3'   C3'  C4'   123.34  3.000
 COQ  O3'   C3'  C2'   116.13  3.000
 COQ  C4'   C3'  C2'   120.54  3.000
 COQ  H4'   C4'  C5'   120.52  3.000
 COQ  H4'   C4'  C3'   120.38  3.000
 COQ  C5'   C4'  C3'   119.10  3.000
 COQ  O5'   C5'  C6'   116.16  3.000
 COQ  O5'   C5'  C4'   123.38  3.000
 COQ  C6'   C5'  C4'   120.46  3.000
 COQ  H6'   C6'  C5'   119.54  3.000
 COQ  H6'   C6'  C1'   120.52  3.000
 COQ  C5'   C6'  C1'   119.94  3.000
 COQ  H313  C31  H312  108.82  3.000
 COQ  H313  C31  H311  108.65  3.000
 COQ  H312  C31  H311  108.69  3.000
 COQ  H313  C31  O3'   112.06  3.000
 COQ  H312  C31  O3'   112.02  3.000
 COQ  H311  C31  O3'   106.49  3.000
 COQ  H513  C51  H512  108.81  3.000
 COQ  H513  C51  H511  108.64  3.000
 COQ  H512  C51  H511  108.70  3.000
 COQ  H513  C51  O5'   112.05  3.000
 COQ  H512  C51  O5'   112.00  3.000
 COQ  H511  C51  O5'   106.52  3.000
 COQ  HCN3  CN'  HCN2  108.11  3.000
 COQ  HCN3  CN'  HCN1  107.55  3.000
 COQ  HCN2  CN'  HCN1  107.76  3.000
 COQ  HCN3  CN'  N9'   114.50  3.000
 COQ  HCN2  CN'  N9'   110.02  3.000
 COQ  HCN1  CN'  N9'   108.68  3.000
 COQ  C8A   N1'  C2B   116.03  3.000
 COQ  HN22  N2'  HN21  117.00  3.000
 COQ  HN22  N2'  C2B   118.54  3.000
 COQ  HN21  N2'  C2B   118.81  3.000
 COQ  C4B   N3'  C2B   117.94  3.000
 COQ  HN42  N4'  HN41  117.24  3.000
 COQ  HN42  N4'  C4B   122.94  3.000
 COQ  HN41  N4'  C4B   119.37  3.000
 COQ  C8A   N8'  C7'   119.02  3.000
 COQ  CN'   N9'  C9'   113.97  3.000
 COQ  CN'   N9'  C6B   116.72  3.000
 COQ  C9'   N9'  C6B   116.85  3.000
 COQ  C31   O3'  C3'   119.02  3.000
 COQ  C51   O5'  C5'   118.97  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
 COQ  CONST_01  C4A   C8A  N1'  C2B     0.00   0.0  0
 COQ  CONST_02  N8'   C8A  N1'  C2B   180.00   0.0  0
 COQ  CONST_03  C4A   C4B  N3'  C2B     0.00   0.0  0
 COQ  CONST_04  C6B   C5B  C4A  C4B   180.00   0.0  0
 COQ  CONST_05  N1'   C8A  C4A  C4B     0.00   0.0  0
 COQ  CONST_06  N8'   C8A  C4A  C4B   180.00   0.0  0
 COQ  CONST_07  N1'   C2B  N3'  C4B     0.00   0.0  0
 COQ  CONST_08  C7'   C6B  C5B  C4A     0.00   0.0  0
 COQ  CONST_09  C7'   N8'  C8A  C4A     0.00   0.0  0
 COQ  CONST_10  N3'   C4B  C4A  C5B   180.00   0.0  0
 COQ  CONST_11  N1'   C8A  C4A  C5B   180.00   0.0  0
 COQ  CONST_12  N8'   C8A  C4A  C5B     0.00   0.0  0
 COQ  CONST_13  N8'   C7'  C6B  C5B     0.00   0.0  0
 COQ  CONST_14  C8A   C4A  C5B  C6B     0.00   0.0  0
 COQ  CONST_15  C8A   N8'  C7'  C6B     0.00   0.0  0
 COQ  CONST_16  N1'   C8A  N8'  C7'   180.00   0.0  0
 COQ  CONST_17  N3'   C4B  C4A  C8A     0.00   0.0  0
 COQ  CONST_18  N3'   C2B  N1'  C8A     0.00   0.0  0
 COQ  CONST_19  C4'   C3'  C2'  C1'     0.00   0.0  0
 COQ  CONST_20  C4'   C5'  C6'  C1'     0.00   0.0  0
 COQ  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 COQ  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 COQ  CONST_23  C6'   C1'  C2'  C3'     0.00   0.0  0
 COQ  CONST_24  C6'   C5'  C4'  C3'     0.00   0.0  0
 COQ  CONST_25  N4'   C4B  N3'  C2B   180.00   0.0  0
 COQ  CONST_26  N2'   C2B  N3'  C4B   180.00   0.0  0
 COQ  CONST_27  N9'   C6B  C5B  C4A   180.00   0.0  0
 COQ  CONST_28  N4'   C4B  C4A  C5B     0.00   0.0  0
 COQ  CONST_29  N4'   C4B  C4A  C8A   180.00   0.0  0
 COQ  CONST_30  N2'   C2B  N1'  C8A   180.00   0.0  0
 COQ  CONST_31  C3'   C2'  C1'  C9'   180.00   0.0  0
 COQ  CONST_32  C5'   C6'  C1'  C9'   180.00   0.0  0
 COQ  CONST_33  O3'   C3'  C2'  C1'   180.00   0.0  0
 COQ  CONST_34  O5'   C5'  C6'  C1'   180.00   0.0  0
 COQ  CONST_35  O5'   C5'  C4'  C3'   180.00   0.0  0
 COQ  CONST_36  O3'   C3'  C4'  C5'   180.00   0.0  0
 COQ  CONST_37  N9'   C6B  C7'  N8'   180.00   0.0  0
 COQ  CONST_38  H5'   C5B  C4A  C4B     0.00   0.0  0
 COQ  CONST_39  H7'   C7'  C6B  C5B   180.00   0.0  0
 COQ  CONST_40  H6'   C6'  C1'  C2'   180.00   0.0  0
 COQ  CONST_41  H4'   C4'  C3'  C2'   180.00   0.0  0
 COQ  CONST_42  H2'   C2'  C3'  C4'   180.00   0.0  0
 COQ  CONST_44  CN'   N9'  C6B  C5B     0.00   0.0  0
 COQ  CONST_46  CN'   N9'  C6B  C7'   180.00   0.0  0
 COQ  CONST_47  HN41  N4'  C4B  C4A   180.00   0.0  0
 COQ  CONST_48  HN42  N4'  C4B  C4A     0.00   0.0  0
 COQ  CONST_49  HN21  N2'  C2B  N1'   180.00   0.0  0
 COQ  CONST_50  HN22  N2'  C2B  N1'     0.00   0.0  0
 COQ  Var_01    C1'   C9'  N9'  C6B   -72.35  30.0  1
 COQ  Var_02    N9'   C9'  C1'  C2'    84.52  30.0  2
 COQ  Var_03    HCN1  CN'  N9'  C6B  -172.18  30.0  3
 COQ  Var_04    H311  C31  O3'  C3'  -179.67  30.0  3
 COQ  Var_05    H511  C51  O5'  C5'  -179.39  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
 COQ  plan-1  C9'   0.020
 COQ  plan-1  C1'   0.020
 COQ  plan-1  C2'   0.020
 COQ  plan-1  C3'   0.020
 COQ  plan-1  C4'   0.020
 COQ  plan-1  C5'   0.020
 COQ  plan-1  C6'   0.020
 COQ  plan-1  O3'   0.020
 COQ  plan-1  O5'   0.020
 COQ  plan-1  H2'   0.020
 COQ  plan-1  H4'   0.020
 COQ  plan-1  H6'   0.020
 COQ  plan-2  C2B   0.020
 COQ  plan-2  C4B   0.020
 COQ  plan-2  C4A   0.020
 COQ  plan-2  C5B   0.020
 COQ  plan-2  C6B   0.020
 COQ  plan-2  C7'   0.020
 COQ  plan-2  C8A   0.020
 COQ  plan-2  N1'   0.020
 COQ  plan-2  N2'   0.020
 COQ  plan-2  N3'   0.020
 COQ  plan-2  N4'   0.020
 COQ  plan-2  N8'   0.020
 COQ  plan-2  N9'   0.020
 COQ  plan-2  H5'   0.020
 COQ  plan-2  H7'   0.020
 COQ  plan-3  C2B   0.020
 COQ  plan-3  N2'   0.020
 COQ  plan-3  HN21  0.020
 COQ  plan-3  HN22  0.020
 COQ  plan-4  C4B   0.020
 COQ  plan-4  N4'   0.020
 COQ  plan-4  HN41  0.020
 COQ  plan-4  HN42  0.020
 COQ  plan-5  C6B   0.020
 COQ  plan-5  C9'   0.020
 COQ  plan-5  CN'   0.020
 COQ  plan-5  N9'   0.020

