# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:19:07 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N~6~-methyl-N~6~-(3,4,5-trimethoxybenzyl)pyrido[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)c1OC
#
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
 DTM  DTM  N~6~-methyl-N~6~-(3,4,5-trimethoxybenzyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine  ligand  49  27  .  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_DTM
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
 DTM  C2B   C  CR6   0   0.532   1.3687   0.4672   4.7112
 DTM  C4B   C  CR6   0   0.483  -0.2966   1.3565   3.4278
 DTM  C4A   C  CR66  0  -0.123  -0.4264   0.0933   2.7469
 DTM  C5B   C  CR16  0  -0.273  -1.3135  -0.1669   1.6942
 DTM  C6B   C  CR6   0   0.265  -1.3475  -1.4222   1.1239
 DTM  C7'   C  CR16  0  -0.107  -0.4657  -2.3803   1.6763
 DTM  C8A   C  CR66  0   0.337   0.4373  -0.9237   3.1933
 DTM  C9'   C  CH2   0  -0.448  -1.5876  -2.3683  -1.1004
 DTM  C1'   C  CR6   0   0.168  -0.7946  -1.3625  -1.8994
 DTM  C2'   C  CR16  0  -0.454   0.5243  -1.0951  -1.5504
 DTM  C3'   C  CR6   0   0.343   1.2375  -0.1103  -2.2291
 DTM  C4'   C  CR6   0   0.165   0.6339   0.5932  -3.2747
 DTM  C5'   C  CR6   0   0.339  -0.6907   0.3187  -3.6233
 DTM  C6'   C  CR16  0  -0.472  -1.4015  -0.6637  -2.9355
 DTM  C31   C  CH3   0  -0.436   3.1575  -0.4145  -0.8784
 DTM  C41   C  CH3   0  -0.408   1.2577   2.8390  -3.4204
 DTM  C51   C  CH3   0  -0.437  -2.5279   0.8325  -5.0277
 DTM  CN'   C  CH3   0  -0.561  -3.3029  -0.8915  -0.1947
 DTM  N1'   N  N     0  -0.500   1.3337  -0.7387   4.1797
 DTM  N2'   N  NH2   0  -0.821   2.2891   0.7071   5.6682
 DTM  N3'   N  N     0  -0.508   0.5910   1.5199   4.3843
 DTM  N4'   N  NH2   0  -0.829  -1.0679   2.3974   3.1063
 DTM  N8'   N  N     0  -0.417   0.3861  -2.1533   2.6411
 DTM  N9'   N  NT    0  -0.486  -2.2124  -1.7960   0.0921
 DTM  O3'   O  O2    0  -0.464   2.5108   0.2274  -1.9588
 DTM  O4'   O  O2    0  -0.482   1.3405   1.5283  -3.9641
 DTM  O5'   O  O2    0  -0.464  -1.1877   1.0510  -4.6357
 DTM  H5'   H  HCR6  0   0.266  -1.9665   0.6118   1.3227
 DTM  H7'   H  HCR6  0   0.271  -0.4814  -3.3949   1.2887
 DTM  HC91  H  HCH2  0   0.269  -2.3847  -2.7939  -1.7125
 DTM  HC92  H  HCH2  0   0.267  -0.9474  -3.2016  -0.8091
 DTM  H2'   H  HCR6  0   0.273   0.9855  -1.6630  -0.7533
 DTM  H6'   H  HCR6  0   0.275  -2.4264  -0.8947  -3.1957
 DTM  H311  H  HCH3  0   0.262   4.1539   0.0158  -0.8146
 DTM  H312  H  HCH3  0   0.221   2.6389  -0.2411   0.0688
 DTM  H313  H  HCH3  0   0.230   3.2495  -1.4920  -1.0377
 DTM  H411  H  HCH3  0   0.236   1.8574   3.4894  -4.0548
 DTM  H412  H  HCH3  0   0.220   0.2297   3.2093  -3.4124
 DTM  H413  H  HCH3  0   0.221   1.6540   2.8820  -2.4029
 DTM  H511  H  HCH3  0   0.261  -2.7280   1.5260  -5.8409
 DTM  H512  H  HCH3  0   0.229  -2.6879  -0.1866  -5.3888
 DTM  H513  H  HCH3  0   0.227  -3.2304   1.0344  -4.2150
 DTM  HCN1  H  HCH3  0   0.254  -3.9665  -1.3623  -0.9197
 DTM  HCN2  H  HCH3  0   0.252  -3.8798  -0.7040   0.7117
 DTM  HCN3  H  HCH3  0   0.219  -2.9948   0.0766  -0.6094
 DTM  HN21  H  HNH2  0   0.392   2.2186   1.5458   6.2166
 DTM  HN22  H  HNH2  0   0.391   2.7794  -0.0702   6.0740
 DTM  HN41  H  HNH2  0   0.405  -0.9529   3.2687   3.5951
 DTM  HN42  H  HNH2  0   0.418  -1.7806   2.3530   2.4021

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
 DTM  C2B  N1'   aromatic  1.318  0.020  1.318
 DTM  C2B  N2'   single    1.349  0.020  1.349
 DTM  C2B  N3'   aromatic  1.349  0.020  1.349
 DTM  C4B  C4A   aromatic  1.441  0.020  1.441
 DTM  C4B  N3'   aromatic  1.315  0.020  1.315
 DTM  C4B  N4'   single    1.335  0.020  1.335
 DTM  C4A  C5B   aromatic  1.401  0.020  1.401
 DTM  C4A  C8A   aromatic  1.407  0.020  1.407
 DTM  C5B  C6B   aromatic  1.379  0.020  1.379
 DTM  C5B  H5'   single    0.930  0.020  1.080
 DTM  C6B  C7'   aromatic  1.414  0.020  1.414
 DTM  C6B  N9'   single    1.397  0.020  1.397
 DTM  C7'  N8'   aromatic  1.307  0.020  1.307
 DTM  C7'  H7'   single    0.930  0.020  1.080
 DTM  C8A  N1'   aromatic  1.346  0.020  1.346
 DTM  C8A  N8'   aromatic  1.349  0.020  1.349
 DTM  C9'  C1'   single    1.510  0.020  1.510
 DTM  C9'  N9'   single    1.463  0.020  1.463
 DTM  C9'  HC91  single    0.970  0.020  1.090
 DTM  C9'  HC92  single    0.970  0.020  1.090
 DTM  C1'  C2'   aromatic  1.390  0.020  1.390
 DTM  C1'  C6'   aromatic  1.389  0.020  1.389
 DTM  C2'  C3'   aromatic  1.393  0.020  1.393
 DTM  C2'  H2'   single    0.930  0.020  1.080
 DTM  C3'  C4'   aromatic  1.397  0.020  1.397
 DTM  C3'  O3'   single    1.345  0.020  1.345
 DTM  C4'  C5'   aromatic  1.397  0.020  1.397
 DTM  C4'  O4'   single    1.360  0.020  1.360
 DTM  C5'  C6'   aromatic  1.394  0.020  1.394
 DTM  C5'  O5'   single    1.345  0.020  1.345
 DTM  C6'  H6'   single    0.930  0.020  1.080
 DTM  C31  O3'   single    1.413  0.020  1.413
 DTM  C31  H311  single    0.970  0.020  1.090
 DTM  C31  H312  single    0.970  0.020  1.090
 DTM  C31  H313  single    0.970  0.020  1.090
 DTM  C41  O4'   single    1.421  0.020  1.421
 DTM  C41  H411  single    0.970  0.020  1.090
 DTM  C41  H412  single    0.970  0.020  1.090
 DTM  C41  H413  single    0.970  0.020  1.090
 DTM  C51  O5'   single    1.413  0.020  1.413
 DTM  C51  H511  single    0.970  0.020  1.090
 DTM  C51  H512  single    0.970  0.020  1.090
 DTM  C51  H513  single    0.970  0.020  1.090
 DTM  CN'  N9'   single    1.446  0.020  1.446
 DTM  CN'  HCN1  single    0.970  0.020  1.090
 DTM  CN'  HCN2  single    0.970  0.020  1.090
 DTM  CN'  HCN3  single    0.970  0.020  1.090
 DTM  N2'  HN21  single    0.890  0.020  1.040
 DTM  N2'  HN22  single    0.890  0.020  1.040
 DTM  N4'  HN41  single    0.860  0.020  1.020
 DTM  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
 DTM  N3'   C2B  N2'   115.24  3.000
 DTM  N3'   C2B  N1'   126.92  3.000
 DTM  N2'   C2B  N1'   117.82  3.000
 DTM  N4'   C4B  N3'   117.93  3.000
 DTM  N4'   C4B  C4A   121.18  3.000
 DTM  N3'   C4B  C4A   120.89  3.000
 DTM  C8A   C4A  C5B   119.53  3.000
 DTM  C8A   C4A  C4B   115.37  3.000
 DTM  C5B   C4A  C4B   125.09  3.000
 DTM  H5'   C5B  C6B   119.88  3.000
 DTM  H5'   C5B  C4A   120.43  3.000
 DTM  C6B   C5B  C4A   119.69  3.000
 DTM  N9'   C6B  C7'   119.54  3.000
 DTM  N9'   C6B  C5B   124.34  3.000
 DTM  C7'   C6B  C5B   116.08  3.000
 DTM  H7'   C7'  N8'   115.79  3.000
 DTM  H7'   C7'  C6B   118.97  3.000
 DTM  N8'   C7'  C6B   125.24  3.000
 DTM  N8'   C8A  N1'   116.79  3.000
 DTM  N8'   C8A  C4A   120.38  3.000
 DTM  N1'   C8A  C4A   122.83  3.000
 DTM  HC92  C9'  HC91  106.30  3.000
 DTM  HC92  C9'  N9'   109.39  3.000
 DTM  HC91  C9'  N9'   107.33  3.000
 DTM  HC92  C9'  C1'   110.00  3.000
 DTM  HC91  C9'  C1'   110.28  3.000
 DTM  N9'   C9'  C1'   113.28  3.000
 DTM  C6'   C1'  C2'   120.33  3.000
 DTM  C6'   C1'  C9'   120.02  3.000
 DTM  C2'   C1'  C9'   119.58  3.000
 DTM  H2'   C2'  C3'   120.79  3.000
 DTM  H2'   C2'  C1'   119.24  3.000
 DTM  C3'   C2'  C1'   119.97  3.000
 DTM  O3'   C3'  C4'   115.66  3.000
 DTM  O3'   C3'  C2'   124.38  3.000
 DTM  C4'   C3'  C2'   119.97  3.000
 DTM  O4'   C4'  C5'   120.09  3.000
 DTM  O4'   C4'  C3'   120.08  3.000
 DTM  C5'   C4'  C3'   119.83  3.000
 DTM  O5'   C5'  C6'   124.52  3.000
 DTM  O5'   C5'  C4'   115.55  3.000
 DTM  C6'   C5'  C4'   119.92  3.000
 DTM  H6'   C6'  C5'   120.97  3.000
 DTM  H6'   C6'  C1'   119.06  3.000
 DTM  C5'   C6'  C1'   119.98  3.000
 DTM  H313  C31  H312  108.81  3.000
 DTM  H313  C31  H311  108.76  3.000
 DTM  H312  C31  H311  108.72  3.000
 DTM  H313  C31  O3'   112.02  3.000
 DTM  H312  C31  O3'   111.90  3.000
 DTM  H311  C31  O3'   106.52  3.000
 DTM  H413  C41  H412  108.73  3.000
 DTM  H413  C41  H411  108.62  3.000
 DTM  H412  C41  H411  108.67  3.000
 DTM  H413  C41  O4'   111.80  3.000
 DTM  H412  C41  O4'   111.72  3.000
 DTM  H411  C41  O4'   107.21  3.000
 DTM  H513  C51  H512  108.89  3.000
 DTM  H513  C51  H511  108.66  3.000
 DTM  H512  C51  H511  108.71  3.000
 DTM  H513  C51  O5'   112.00  3.000
 DTM  H512  C51  O5'   112.00  3.000
 DTM  H511  C51  O5'   106.46  3.000
 DTM  HCN3  CN'  HCN2  108.11  3.000
 DTM  HCN3  CN'  HCN1  107.51  3.000
 DTM  HCN2  CN'  HCN1  107.76  3.000
 DTM  HCN3  CN'  N9'   114.53  3.000
 DTM  HCN2  CN'  N9'   109.98  3.000
 DTM  HCN1  CN'  N9'   108.72  3.000
 DTM  C8A   N1'  C2B   116.04  3.000
 DTM  HN22  N2'  HN21  117.37  3.000
 DTM  HN22  N2'  C2B   118.81  3.000
 DTM  HN21  N2'  C2B   119.19  3.000
 DTM  C4B   N3'  C2B   117.93  3.000
 DTM  HN42  N4'  HN41  117.44  3.000
 DTM  HN42  N4'  C4B   123.04  3.000
 DTM  HN41  N4'  C4B   119.51  3.000
 DTM  C8A   N8'  C7'   119.03  3.000
 DTM  CN'   N9'  C9'   113.90  3.000
 DTM  CN'   N9'  C6B   116.49  3.000
 DTM  C9'   N9'  C6B   116.25  3.000
 DTM  C31   O3'  C3'   118.22  3.000
 DTM  C41   O4'  C4'   114.20  3.000
 DTM  C51   O5'  C5'   118.37  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
 DTM  CONST_01  C4A   C8A  N1'  C2B     0.00   0.0  0
 DTM  CONST_02  N8'   C8A  N1'  C2B   180.00   0.0  0
 DTM  CONST_03  C4A   C4B  N3'  C2B     0.00   0.0  0
 DTM  CONST_04  C6B   C5B  C4A  C4B   180.00   0.0  0
 DTM  CONST_05  N1'   C8A  C4A  C4B     0.00   0.0  0
 DTM  CONST_06  N8'   C8A  C4A  C4B   180.00   0.0  0
 DTM  CONST_07  N1'   C2B  N3'  C4B     0.00   0.0  0
 DTM  CONST_08  C7'   C6B  C5B  C4A     0.00   0.0  0
 DTM  CONST_09  C7'   N8'  C8A  C4A     0.00   0.0  0
 DTM  CONST_10  N3'   C4B  C4A  C5B   180.00   0.0  0
 DTM  CONST_11  N1'   C8A  C4A  C5B   180.00   0.0  0
 DTM  CONST_12  N8'   C8A  C4A  C5B     0.00   0.0  0
 DTM  CONST_13  N8'   C7'  C6B  C5B     0.00   0.0  0
 DTM  CONST_14  C8A   C4A  C5B  C6B     0.00   0.0  0
 DTM  CONST_15  C8A   N8'  C7'  C6B     0.00   0.0  0
 DTM  CONST_16  N1'   C8A  N8'  C7'   180.00   0.0  0
 DTM  CONST_17  N3'   C4B  C4A  C8A     0.00   0.0  0
 DTM  CONST_18  N3'   C2B  N1'  C8A     0.00   0.0  0
 DTM  CONST_19  C4'   C3'  C2'  C1'     0.00   0.0  0
 DTM  CONST_20  C4'   C5'  C6'  C1'     0.00   0.0  0
 DTM  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 DTM  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 DTM  CONST_23  C6'   C1'  C2'  C3'     0.00   0.0  0
 DTM  CONST_24  C6'   C5'  C4'  C3'     0.00   0.0  0
 DTM  CONST_25  N4'   C4B  N3'  C2B   180.00   0.0  0
 DTM  CONST_26  N2'   C2B  N3'  C4B   180.00   0.0  0
 DTM  CONST_27  N9'   C6B  C5B  C4A   180.00   0.0  0
 DTM  CONST_28  N4'   C4B  C4A  C5B     0.00   0.0  0
 DTM  CONST_29  N4'   C4B  C4A  C8A   180.00   0.0  0
 DTM  CONST_30  N2'   C2B  N1'  C8A   180.00   0.0  0
 DTM  CONST_31  C3'   C2'  C1'  C9'   180.00   0.0  0
 DTM  CONST_32  C5'   C6'  C1'  C9'   180.00   0.0  0
 DTM  CONST_33  O3'   C3'  C2'  C1'   180.00   0.0  0
 DTM  CONST_34  O5'   C5'  C6'  C1'   180.00   0.0  0
 DTM  CONST_35  O4'   C4'  C3'  C2'   180.00   0.0  0
 DTM  CONST_36  O5'   C5'  C4'  C3'   180.00   0.0  0
 DTM  CONST_37  O3'   C3'  C4'  C5'   180.00   0.0  0
 DTM  CONST_38  O4'   C4'  C5'  C6'   180.00   0.0  0
 DTM  CONST_39  N9'   C6B  C7'  N8'   180.00   0.0  0
 DTM  CONST_40  H5'   C5B  C4A  C4B     0.00   0.0  0
 DTM  CONST_41  H7'   C7'  C6B  C5B   180.00   0.0  0
 DTM  CONST_42  H6'   C6'  C1'  C2'   180.00   0.0  0
 DTM  CONST_43  H2'   C2'  C3'  C4'   180.00   0.0  0
 DTM  CONST_45  CN'   N9'  C6B  C5B     0.00   0.0  0
 DTM  CONST_48  HN41  N4'  C4B  C4A   180.00   0.0  0
 DTM  CONST_49  HN42  N4'  C4B  C4A     0.00   0.0  0
 DTM  CONST_50  HN21  N2'  C2B  N1'   180.00   0.0  0
 DTM  CONST_51  HN22  N2'  C2B  N1'     0.00   0.0  0
 DTM  Var_01    C1'   C9'  N9'  C6B   -69.59  30.0  3
 DTM  Var_02    N9'   C9'  C1'  C2'    84.99  30.0  3
 DTM  Var_03    HCN1  CN'  N9'  C6B  -172.59  30.0  3
 DTM  Var_04    H311  C31  O3'  C3'  -178.47  30.0  3
 DTM  Var_05    H411  C41  O4'  C4'  -179.92  30.0  3
 DTM  Var_06    H511  C51  O5'  C5'   179.30  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
 DTM  plan-1  C9'   0.020
 DTM  plan-1  C1'   0.020
 DTM  plan-1  C2'   0.020
 DTM  plan-1  C3'   0.020
 DTM  plan-1  C4'   0.020
 DTM  plan-1  C5'   0.020
 DTM  plan-1  C6'   0.020
 DTM  plan-1  O3'   0.020
 DTM  plan-1  O4'   0.020
 DTM  plan-1  O5'   0.020
 DTM  plan-1  H2'   0.020
 DTM  plan-1  H6'   0.020
 DTM  plan-2  C2B   0.020
 DTM  plan-2  C4B   0.020
 DTM  plan-2  C4A   0.020
 DTM  plan-2  C5B   0.020
 DTM  plan-2  C6B   0.020
 DTM  plan-2  C7'   0.020
 DTM  plan-2  C8A   0.020
 DTM  plan-2  N1'   0.020
 DTM  plan-2  N2'   0.020
 DTM  plan-2  N3'   0.020
 DTM  plan-2  N4'   0.020
 DTM  plan-2  N8'   0.020
 DTM  plan-2  N9'   0.020
 DTM  plan-2  H5'   0.020
 DTM  plan-2  H7'   0.020
 DTM  plan-3  C2B   0.020
 DTM  plan-3  N2'   0.020
 DTM  plan-3  HN21  0.020
 DTM  plan-3  HN22  0.020
 DTM  plan-4  C4B   0.020
 DTM  plan-4  N4'   0.020
 DTM  plan-4  HN41  0.020
 DTM  plan-4  HN42  0.020
 DTM  plan-5  C6B   0.020
 DTM  plan-5  C9'   0.020
 DTM  plan-5  CN'   0.020
 DTM  plan-5  N9'   0.020

