# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:41:03 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 6-{[(2,5-diethoxyphenyl)amino]methyl}-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc(OCC)c(NCc2cnc3nc(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
 VG9  VG9  6-{[(2,5-diethoxyphenyl)amino]methyl}-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine  ligand  51  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VG9
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
 VG9  N2    N  NH2   0  -0.819   0.7864  27.9364  -6.9956
 VG9  C2    C  CR6   0   0.538   1.2417  28.3253  -5.7901
 VG9  N3    N  N     0  -0.505   0.9527  27.5043  -4.7659
 VG9  C4    C  CR6   0   0.455   1.2995  27.8728  -3.5515
 VG9  N4    N  NH2   0  -0.819   1.0555  26.9769  -2.5828
 VG9  N1    N  N     0  -0.498   1.9226  29.4507  -5.7177
 VG9  C8A   C  CR66  0   0.351   2.2525  29.8712  -4.4851
 VG9  N8    N  N     0  -0.433   2.9394  31.0263  -4.4347
 VG9  C7    C  CR16  0  -0.072   3.2182  31.5272  -3.2575
 VG9  C6    C  CR6   0  -0.087   2.8286  30.9798  -2.0286
 VG9  C5    C  CR6   0   0.183   2.1517  29.7674  -2.0438
 VG9  C5A   C  CH3   0  -0.816   1.6807  29.1558  -0.7551
 VG9  C4A   C  CR66  0  -0.175   1.9017  29.1665  -3.3032
 VG9  C9    C  CH2   0  -0.359   3.1559  31.7314  -0.7484
 VG9  N10   N  NH1   0  -0.696   3.4731  33.1164  -0.9403
 VG9  C11   C  CR6   0   0.351   2.5384  34.0657  -1.2381
 VG9  C12   C  CR6   0   0.236   2.8961  35.4259  -1.2479
 VG9  O2    O  O2    0  -0.504   4.1831  35.7705  -0.9300
 VG9  C21   C  CH2   0  -0.170   4.3686  36.1344   0.4389
 VG9  C22   C  CH3   0  -0.690   5.8395  36.3737   0.6803
 VG9  C13   C  CR16  0  -0.316   1.9561  36.3838  -1.5764
 VG9  C14   C  CR16  0  -0.392   0.6557  36.0386  -1.9196
 VG9  C15   C  CR6   0   0.411   0.2912  34.6949  -1.9143
 VG9  C16   C  CR16  0  -0.485   1.2218  33.7198  -1.5671
 VG9  O5    O  O2    0  -0.490  -0.9880  34.4166  -2.2511
 VG9  C51   C  CH2   0  -0.211  -1.3730  33.0799  -2.5457
 VG9  C52   C  CH3   0  -0.697  -0.7951  32.5622  -3.8491
 VG9  H21N  H  HNH2  0   0.393   1.1000  28.4218  -7.8172
 VG9  H22N  H  HNH2  0   0.394   0.4295  27.0047  -7.1114
 VG9  H41N  H  HNH2  0   0.401   0.7365  26.0684  -2.8784
 VG9  H42N  H  HNH2  0   0.418   1.5237  27.0074  -1.6970
 VG9  H7    H  HCR6  0   0.263   3.7795  32.4562  -3.2570
 VG9  H91C  H  HCH2  0   0.244   2.3251  31.6417  -0.0419
 VG9  H92C  H  HCH2  0   0.289   4.0122  31.2657  -0.2574
 VG9  H5A1  H  HCH3  0   0.271   0.6795  28.7394  -0.8434
 VG9  H5A2  H  HCH3  0   0.268   2.3535  28.3639  -0.4158
 VG9  H5A3  H  HCH3  0   0.276   1.6462  29.8822   0.0512
 VG9  H10   H  HNH1  0   0.389   4.4013  33.4253  -0.7151
 VG9  H16   H  HCR6  0   0.272   0.9398  32.6775  -1.5666
 VG9  H13   H  HCR6  0   0.258   2.2499  37.4271  -1.5792
 VG9  H211  H  HCH2  0   0.221   3.7919  37.0376   0.6663
 VG9  H212  H  HCH2  0   0.213   3.9952  35.3392   1.0941
 VG9  H221  H  HCH3  0   0.233   6.2192  37.1801   0.0524
 VG9  H222  H  HCH3  0   0.236   5.9981  36.6573   1.7204
 VG9  H223  H  HCH3  0   0.231   6.4280  35.4768   0.4838
 VG9  H14   H  HCR6  0   0.251  -0.0647  36.7995  -2.1904
 VG9  H511  H  HCH2  0   0.219  -1.1300  32.4083  -1.7157
 VG9  H512  H  HCH2  0   0.254  -2.4602  33.1140  -2.6090
 VG9  H521  H  HCH3  0   0.237  -1.0907  33.1944  -4.6867
 VG9  H522  H  HCH3  0   0.239   0.2932  32.5054  -3.8289
 VG9  H523  H  HCH3  0   0.239  -1.1724  31.5567  -4.0383

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
 VG9  N2   C2    single    1.346  0.020  1.346
 VG9  C2   N3    aromatic  1.344  0.020  1.344
 VG9  C2   N1    aromatic  1.317  0.020  1.317
 VG9  N3   C4    aromatic  1.316  0.020  1.316
 VG9  C4   N4    single    1.342  0.020  1.342
 VG9  C4   C4A   aromatic  1.448  0.020  1.448
 VG9  N1   C8A   aromatic  1.344  0.020  1.344
 VG9  C8A  N8    aromatic  1.345  0.020  1.345
 VG9  C8A  C4A   aromatic  1.420  0.020  1.420
 VG9  N8   C7    aromatic  1.309  0.020  1.309
 VG9  C7   C6    aromatic  1.401  0.020  1.401
 VG9  C6   C5    aromatic  1.389  0.020  1.389
 VG9  C6   C9    single    1.520  0.020  1.520
 VG9  C5   C5A   single    1.502  0.020  1.502
 VG9  C5   C4A   aromatic  1.418  0.020  1.418
 VG9  C9   N10   single    1.434  0.020  1.434
 VG9  N10  C11   single    1.365  0.020  1.365
 VG9  C11  C12   aromatic  1.406  0.020  1.406
 VG9  C11  C16   aromatic  1.400  0.020  1.400
 VG9  C12  O2    single    1.370  0.020  1.370
 VG9  C12  C13   aromatic  1.382  0.020  1.382
 VG9  O2   C21   single    1.428  0.020  1.428
 VG9  C21  C22   single    1.510  0.020  1.510
 VG9  C13  C14   aromatic  1.388  0.020  1.388
 VG9  C14  C15   aromatic  1.392  0.020  1.392
 VG9  C15  C16   aromatic  1.392  0.020  1.392
 VG9  C15  O5    single    1.352  0.020  1.352
 VG9  O5   C51   single    1.422  0.020  1.422
 VG9  C51  C52   single    1.517  0.020  1.517
 VG9  N2   H21N  single    0.890  0.020  1.040
 VG9  N2   H22N  single    0.890  0.020  1.040
 VG9  N4   H41N  single    0.890  0.020  1.040
 VG9  N4   H42N  single    0.890  0.020  1.040
 VG9  C7   H7    single    0.930  0.020  1.080
 VG9  C9   H91C  single    0.970  0.020  1.090
 VG9  C9   H92C  single    0.970  0.020  1.090
 VG9  C5A  H5A1  single    0.970  0.020  1.090
 VG9  C5A  H5A2  single    0.970  0.020  1.090
 VG9  C5A  H5A3  single    0.970  0.020  1.090
 VG9  N10  H10   single    0.860  0.020  1.020
 VG9  C16  H16   single    0.930  0.020  1.080
 VG9  C13  H13   single    0.930  0.020  1.080
 VG9  C21  H211  single    0.970  0.020  1.090
 VG9  C21  H212  single    0.970  0.020  1.090
 VG9  C22  H221  single    0.970  0.020  1.090
 VG9  C22  H222  single    0.970  0.020  1.090
 VG9  C22  H223  single    0.970  0.020  1.090
 VG9  C14  H14   single    0.930  0.020  1.080
 VG9  C51  H511  single    0.970  0.020  1.090
 VG9  C51  H512  single    0.970  0.020  1.090
 VG9  C52  H521  single    0.970  0.020  1.090
 VG9  C52  H522  single    0.970  0.020  1.090
 VG9  C52  H523  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
 VG9  H22N  N2   H21N  117.70  3.000
 VG9  H22N  N2   C2    119.44  3.000
 VG9  H21N  N2   C2    119.17  3.000
 VG9  N1    C2   N3    126.24  3.000
 VG9  N1    C2   N2    118.09  3.000
 VG9  N3    C2   N2    115.67  3.000
 VG9  C4    N3   C2    118.40  3.000
 VG9  C4A   C4   N4    123.25  3.000
 VG9  C4A   C4   N3    121.20  3.000
 VG9  N4    C4   N3    115.55  3.000
 VG9  H42N  N4   H41N  115.77  3.000
 VG9  H42N  N4   C4    122.18  3.000
 VG9  H41N  N4   C4    116.61  3.000
 VG9  C8A   N1   C2    116.41  3.000
 VG9  C4A   C8A  N8    121.42  3.000
 VG9  C4A   C8A  N1    123.20  3.000
 VG9  N8    C8A  N1    115.38  3.000
 VG9  C7    N8   C8A   118.10  3.000
 VG9  H7    C7   C6    118.55  3.000
 VG9  H7    C7   N8    115.98  3.000
 VG9  C6    C7   N8    125.46  3.000
 VG9  C9    C6   C5    123.08  3.000
 VG9  C9    C6   C7    119.07  3.000
 VG9  C5    C6   C7    117.85  3.000
 VG9  C4A   C5   C5A   122.29  3.000
 VG9  C4A   C5   C6    117.76  3.000
 VG9  C5A   C5   C6    119.93  3.000
 VG9  H5A3  C5A  H5A2  105.89  3.000
 VG9  H5A3  C5A  H5A1  106.68  3.000
 VG9  H5A2  C5A  H5A1  108.32  3.000
 VG9  H5A3  C5A  C5    112.00  3.000
 VG9  H5A2  C5A  C5    111.61  3.000
 VG9  H5A1  C5A  C5    112.01  3.000
 VG9  C5    C4A  C8A   119.04  3.000
 VG9  C5    C4A  C4    127.17  3.000
 VG9  C8A   C4A  C4    113.79  3.000
 VG9  H92C  C9   H91C  105.68  3.000
 VG9  H92C  C9   N10   107.39  3.000
 VG9  H91C  C9   N10   109.48  3.000
 VG9  H92C  C9   C6    109.68  3.000
 VG9  H91C  C9   C6    109.86  3.000
 VG9  N10   C9   C6    114.36  3.000
 VG9  H10   N10  C11   117.91  3.000
 VG9  H10   N10  C9    118.15  3.000
 VG9  C11   N10  C9    123.33  3.000
 VG9  C16   C11  C12   118.44  3.000
 VG9  C16   C11  N10   121.55  3.000
 VG9  C12   C11  N10   119.99  3.000
 VG9  C13   C12  O2    121.33  3.000
 VG9  C13   C12  C11   119.95  3.000
 VG9  O2    C12  C11   118.73  3.000
 VG9  C21   O2   C12   114.11  3.000
 VG9  H212  C21  H211  107.14  3.000
 VG9  H212  C21  C22   110.57  3.000
 VG9  H211  C21  C22   110.43  3.000
 VG9  H212  C21  O2    110.11  3.000
 VG9  H211  C21  O2    109.91  3.000
 VG9  C22   C21  O2    108.67  3.000
 VG9  H223  C22  H222  107.91  3.000
 VG9  H223  C22  H221  108.46  3.000
 VG9  H222  C22  H221  107.84  3.000
 VG9  H223  C22  C21   111.51  3.000
 VG9  H222  C22  C21   109.61  3.000
 VG9  H221  C22  C21   111.38  3.000
 VG9  H13   C13  C14   119.51  3.000
 VG9  H13   C13  C12   118.92  3.000
 VG9  C14   C13  C12   121.57  3.000
 VG9  H14   C14  C15   120.34  3.000
 VG9  H14   C14  C13   120.69  3.000
 VG9  C15   C14  C13   118.96  3.000
 VG9  O5    C15  C16   123.41  3.000
 VG9  O5    C15  C14   116.46  3.000
 VG9  C16   C15  C14   120.13  3.000
 VG9  H16   C16  C15   120.11  3.000
 VG9  H16   C16  C11   118.94  3.000
 VG9  C15   C16  C11   120.94  3.000
 VG9  C51   O5   C15   120.09  3.000
 VG9  H512  C51  H511  106.54  3.000
 VG9  H512  C51  C52   109.93  3.000
 VG9  H511  C51  C52   110.95  3.000
 VG9  H512  C51  O5    104.64  3.000
 VG9  H511  C51  O5    111.07  3.000
 VG9  C52   C51  O5    113.31  3.000
 VG9  H523  C52  H522  107.50  3.000
 VG9  H523  C52  H521  107.91  3.000
 VG9  H522  C52  H521  108.37  3.000
 VG9  H523  C52  C51   109.38  3.000
 VG9  H522  C52  C51   112.47  3.000
 VG9  H521  C52  C51   111.04  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
 VG9  CONST_01  C4A   C4   N3   C2     0.00   0.0  0
 VG9  CONST_02  N8    C8A  N1   C2   180.00   0.0  0
 VG9  CONST_03  C4A   C8A  N1   C2     0.00   0.0  0
 VG9  CONST_04  C8A   N1   C2   N3     0.00   0.0  0
 VG9  CONST_05  C8A   C4A  C4   N3     0.00   0.0  0
 VG9  CONST_06  C5    C4A  C4   N3   180.00   0.0  0
 VG9  CONST_07  N1    C2   N3   C4     0.00   0.0  0
 VG9  CONST_08  N1    C8A  C4A  C4     0.00   0.0  0
 VG9  CONST_09  N8    C8A  C4A  C4   180.00   0.0  0
 VG9  CONST_10  C6    C5   C4A  C4   180.00   0.0  0
 VG9  CONST_11  C7    N8   C8A  N1   180.00   0.0  0
 VG9  CONST_12  C5    C4A  C8A  N1   180.00   0.0  0
 VG9  CONST_13  C6    C7   N8   C8A    0.00   0.0  0
 VG9  CONST_14  C6    C5   C4A  C8A    0.00   0.0  0
 VG9  CONST_15  C5    C4A  C8A  N8     0.00   0.0  0
 VG9  CONST_16  C5    C6   C7   N8     0.00   0.0  0
 VG9  CONST_17  C4A   C8A  N8   C7     0.00   0.0  0
 VG9  CONST_18  C4A   C5   C6   C7     0.00   0.0  0
 VG9  CONST_19  C14   C13  C12  C11    0.00   0.0  0
 VG9  CONST_20  C14   C15  C16  C11    0.00   0.0  0
 VG9  CONST_21  C15   C16  C11  C12    0.00   0.0  0
 VG9  CONST_22  C15   C14  C13  C12    0.00   0.0  0
 VG9  CONST_23  C16   C11  C12  C13    0.00   0.0  0
 VG9  CONST_24  C16   C15  C14  C13    0.00   0.0  0
 VG9  CONST_25  C4    N3   C2   N2   180.00   0.0  0
 VG9  CONST_26  C8A   N1   C2   N2   180.00   0.0  0
 VG9  CONST_27  N4    C4   N3   C2   180.00   0.0  0
 VG9  CONST_28  C5A   C5   C4A  C4     0.00   0.0  0
 VG9  CONST_29  C8A   C4A  C4   N4   180.00   0.0  0
 VG9  CONST_30  C5    C4A  C4   N4     0.00   0.0  0
 VG9  CONST_31  C5A   C5   C4A  C8A  180.00   0.0  0
 VG9  CONST_32  C9    C6   C7   N8   180.00   0.0  0
 VG9  CONST_33  C5A   C5   C6   C7   180.00   0.0  0
 VG9  CONST_34  C9    C6   C5   C4A  180.00   0.0  0
 VG9  CONST_35  C13   C12  C11  N10  180.00   0.0  0
 VG9  CONST_36  C15   C16  C11  N10  180.00   0.0  0
 VG9  CONST_37  O5    C15  C16  C11  180.00   0.0  0
 VG9  CONST_38  C16   C11  C12  O2   180.00   0.0  0
 VG9  CONST_39  C14   C13  C12  O2   180.00   0.0  0
 VG9  CONST_40  O5    C15  C14  C13  180.00   0.0  0
 VG9  CONST_41  H7    C7   N8   C8A  180.00   0.0  0
 VG9  CONST_42  H13   C13  C12  C11  180.00   0.0  0
 VG9  CONST_43  H16   C16  C11  C12  180.00   0.0  0
 VG9  CONST_44  H14   C14  C13  C12  180.00   0.0  0
 VG9  CONST_45  C12   C11  N10  C9   180.00   0.0  0
 VG9  CONST_46  C16   C11  N10  C9     0.00   0.0  0
 VG9  CONST_47  H21N  N2   C2   N3   180.00   0.0  0
 VG9  CONST_48  H22N  N2   C2   N3     0.00   0.0  0
 VG9  CONST_49  H41N  N4   C4   N3     0.00   0.0  0
 VG9  CONST_51  H10   N10  C11  C12    0.00   0.0  0
 VG9  Var_01    N10   C9   C6   C7    18.08  30.0  2
 VG9  Var_02    C11   N10  C9   C6    73.67  30.0  3
 VG9  Var_03    C13   C12  O2   C21   84.64  30.0  2
 VG9  Var_04    H5A1  C5A  C5   C6   137.96  30.0  2
 VG9  Var_05    C22   C21  O2   C12  175.20  30.0  3
 VG9  Var_06    C52   C51  O5   C15  -69.79  30.0  3
 VG9  Var_07    H221  C22  C21  O2    60.47  30.0  3
 VG9  Var_08    H521  C52  C51  O5   -57.97  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
 VG9  plan-1  N10   0.020
 VG9  plan-1  C11   0.020
 VG9  plan-1  C12   0.020
 VG9  plan-1  O2    0.020
 VG9  plan-1  C13   0.020
 VG9  plan-1  C14   0.020
 VG9  plan-1  C15   0.020
 VG9  plan-1  C16   0.020
 VG9  plan-1  O5    0.020
 VG9  plan-1  H16   0.020
 VG9  plan-1  H13   0.020
 VG9  plan-1  H14   0.020
 VG9  plan-2  N2    0.020
 VG9  plan-2  C2    0.020
 VG9  plan-2  N3    0.020
 VG9  plan-2  C4    0.020
 VG9  plan-2  N4    0.020
 VG9  plan-2  N1    0.020
 VG9  plan-2  C8A   0.020
 VG9  plan-2  N8    0.020
 VG9  plan-2  C7    0.020
 VG9  plan-2  C6    0.020
 VG9  plan-2  C5    0.020
 VG9  plan-2  C5A   0.020
 VG9  plan-2  C4A   0.020
 VG9  plan-2  C9    0.020
 VG9  plan-2  H7    0.020
 VG9  plan-3  N2    0.020
 VG9  plan-3  C2    0.020
 VG9  plan-3  H21N  0.020
 VG9  plan-3  H22N  0.020
 VG9  plan-4  C4    0.020
 VG9  plan-4  N4    0.020
 VG9  plan-4  H41N  0.020
 VG9  plan-4  H42N  0.020
 VG9  plan-5  C9    0.020
 VG9  plan-5  N10   0.020
 VG9  plan-5  C11   0.020
 VG9  plan-5  H10   0.020

