# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 12:35:38 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N~4~-[4-(morpholin-4-yl)phenyl]-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCO1)c2ccc(Nc3ncnc4ccc(NCc5cccnc5)nc34)cc2
#
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
 31Y  31Y  N~4~-[4-(morpholin-4-yl)phenyl]-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine  ligand  54  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_31Y
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
 31Y  C2   C  CR66  0   0.170   1.8575  -3.5557   0.1163
 31Y  C3   C  CR16  0   0.022  -0.2340  -4.3831   0.1950
 31Y  N4   N  N     0  -0.426   7.0542   3.2890   0.7711
 31Y  C5   C  CR16  0  -0.324   4.0528  -2.5861   0.0693
 31Y  N6   N  NT    0  -0.446  -5.7649   1.2833   0.2169
 31Y  C7   C  CH2   0  -0.316   5.6133  -0.1339   0.1952
 31Y  C9   C  CR16  0  -0.045   6.5840   2.0601   0.9490
 31Y  C10  C  CR16  0  -0.071   7.1098   3.7557  -0.4692
 31Y  C11  C  CR16  0  -0.291   6.7077   3.0214  -1.5765
 31Y  C12  C  CR16  0  -0.163   6.2224   1.7406  -1.3783
 31Y  C13  C  CR6   0   0.343  -1.8850  -0.4119   0.0489
 31Y  C15  C  CR16  0  -0.378  -3.3440   1.5219   0.0886
 31Y  C18  C  CR16  0  -0.183  -3.0135  -1.2250   0.0916
 31Y  C20  C  CH2   0  -0.193  -8.1453   1.1438   0.7243
 31Y  C21  C  CH2   0  -0.196  -7.3630   3.0518  -0.3120
 31Y  C22  C  CH2   0  -0.321  -6.0770   2.3568  -0.7169
 31Y  O    O  O2    0  -0.540  -8.4395   2.1498  -0.2164
 31Y  C19  C  CH2   0  -0.347  -6.8872   0.3750   0.3639
 31Y  C16  C  CR6   0   0.321  -4.4912   0.7151   0.1335
 31Y  C14  C  CR16  0  -0.310  -2.0793   0.9725   0.0466
 31Y  C17  C  CR16  0  -0.410  -4.2848  -0.6660   0.1257
 31Y  C    C  CR6   0   0.430  -0.0694  -2.1161   0.0629
 31Y  N1   N  N     0  -0.521  -0.8360  -3.1835   0.1360
 31Y  N    N  N     0  -0.340   1.0413  -4.6404   0.1867
 31Y  C1   C  CR66  0   0.163   1.3666  -2.2507   0.0500
 31Y  N2   N  N     0  -0.492   2.1328  -1.1541  -0.0012
 31Y  C6   C  CR6   0   0.480   3.4444  -1.2973   0.0045
 31Y  C4   C  CR16  0  -0.199   3.2639  -3.6941   0.1219
 31Y  N3   N  NH1   0  -0.680   4.1906  -0.1682  -0.0716
 31Y  C8   C  CR6   0  -0.095   6.1549   1.2364  -0.0839
 31Y  H1   H  HCR6  0   0.258  -0.9071  -5.2326   0.2524
 31Y  H2   H  HCR6  0   0.300   5.1284  -2.6906   0.0857
 31Y  H3   H  HCH2  0   0.228   5.8423  -0.4231   1.2280
 31Y  H4   H  HCH2  0   0.275   6.1201  -0.8524  -0.4531
 31Y  H5   H  HCR6  0   0.284   6.5441   1.7016   1.9736
 31Y  H6   H  HCR6  0   0.271   7.4948   4.7618  -0.5930
 31Y  H7   H  HCR6  0   0.264   6.7777   3.4473  -2.5678
 31Y  H8   H  HCR6  0   0.256   5.9000   1.1378  -2.2187
 31Y  H9   H  HCR6  0   0.246  -3.4283   2.6003   0.1158
 31Y  H10  H  HCR6  0   0.285  -2.9146  -2.2981   0.0876
 31Y  H11  H  HCH2  0   0.227  -8.0253   1.5801   1.7256
 31Y  H12  H  HCH2  0   0.277  -8.9933   0.4599   0.7556
 31Y  H13  H  HCH2  0   0.239  -7.2121   3.5662   0.6482
 31Y  H14  H  HCH2  0   0.263  -7.6243   3.8002  -1.0608
 31Y  H15  H  HCH2  0   0.284  -5.2952   3.1192  -0.7387
 31Y  H16  H  HCH2  0   0.173  -6.1743   1.9644  -1.7400
 31Y  H17  H  HCH2  0   0.172  -7.0559  -0.2101  -0.5515
 31Y  H18  H  HCH2  0   0.286  -6.6871  -0.3323   1.1700
 31Y  H19  H  HCR6  0   0.266  -1.2239   1.6374   0.0220
 31Y  H20  H  HCR6  0   0.234  -5.1214  -1.3498   0.1359
 31Y  H21  H  HNH1  0   0.383   0.1494  -0.1562  -0.0458
 31Y  H22  H  HCR6  0   0.286   3.6994  -4.6839   0.1770
 31Y  H23  H  HNH1  0   0.380   3.6780   0.6868   0.0875
 31Y  N5   N  NH1   0  -0.780  -0.5677  -0.8692   0.0022

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
 31Y  C7   C8   single    1.500  0.020  1.500
 31Y  C7   N3   single    1.448  0.020  1.448
 31Y  C8   C9   aromatic  1.389  0.020  1.389
 31Y  C8   C12  aromatic  1.391  0.020  1.391
 31Y  C9   N4   aromatic  1.328  0.020  1.328
 31Y  C12  C11  aromatic  1.384  0.020  1.384
 31Y  N4   C10  aromatic  1.326  0.020  1.326
 31Y  N3   C6   single    1.356  0.020  1.356
 31Y  C11  C10  aromatic  1.388  0.020  1.388
 31Y  C6   N2   aromatic  1.319  0.020  1.319
 31Y  C6   C5   aromatic  1.427  0.020  1.427
 31Y  C22  C21  single    1.517  0.020  1.517
 31Y  C22  N6   single    1.457  0.020  1.457
 31Y  C21  O    single    1.408  0.020  1.408
 31Y  N2   C1   aromatic  1.339  0.020  1.339
 31Y  C18  C17  aromatic  1.389  0.020  1.389
 31Y  C18  C13  aromatic  1.392  0.020  1.392
 31Y  C17  C16  aromatic  1.396  0.020  1.396
 31Y  C5   C4   aromatic  1.361  0.020  1.361
 31Y  O    C20  single    1.408  0.020  1.408
 31Y  N5   C13  single    1.395  0.020  1.395
 31Y  N5   C    single    1.344  0.020  1.344
 31Y  C13  C14  aromatic  1.398  0.020  1.398
 31Y  N6   C16  single    1.397  0.020  1.397
 31Y  N6   C19  single    1.451  0.020  1.451
 31Y  C16  C15  aromatic  1.403  0.020  1.403
 31Y  C1   C    aromatic  1.442  0.020  1.442
 31Y  C1   C2   aromatic  1.396  0.020  1.396
 31Y  C    N1   aromatic  1.316  0.020  1.316
 31Y  C4   C2   aromatic  1.413  0.020  1.413
 31Y  C14  C15  aromatic  1.379  0.020  1.379
 31Y  C20  C19  single    1.518  0.020  1.518
 31Y  C2   N    aromatic  1.359  0.020  1.359
 31Y  N1   C3   aromatic  1.343  0.020  1.343
 31Y  N    C3   aromatic  1.301  0.020  1.301
 31Y  C3   H1   single    0.930  0.020  1.080
 31Y  C5   H2   single    0.930  0.020  1.080
 31Y  C7   H3   single    0.970  0.020  1.090
 31Y  C7   H4   single    0.970  0.020  1.090
 31Y  C9   H5   single    0.930  0.020  1.080
 31Y  C10  H6   single    0.930  0.020  1.080
 31Y  C11  H7   single    0.930  0.020  1.080
 31Y  C12  H8   single    0.930  0.020  1.080
 31Y  C15  H9   single    0.930  0.020  1.080
 31Y  C18  H10  single    0.930  0.020  1.080
 31Y  C20  H11  single    0.970  0.020  1.090
 31Y  C20  H12  single    0.970  0.020  1.090
 31Y  C21  H13  single    0.970  0.020  1.090
 31Y  C21  H14  single    0.970  0.020  1.090
 31Y  C22  H15  single    0.970  0.020  1.090
 31Y  C22  H16  single    0.970  0.020  1.090
 31Y  C19  H17  single    0.970  0.020  1.090
 31Y  C19  H18  single    0.970  0.020  1.090
 31Y  C14  H19  single    0.930  0.020  1.080
 31Y  C17  H20  single    0.930  0.020  1.080
 31Y  N5   H21  single    0.860  0.020  1.020
 31Y  C4   H22  single    0.930  0.020  1.080
 31Y  N3   H23  single    0.890  0.020  1.040

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
 31Y  C4   C2   C1   116.21  3.000
 31Y  C4   C2   N    121.28  3.000
 31Y  C1   C2   N    122.50  3.000
 31Y  H1   C3   N    116.96  3.000
 31Y  H1   C3   N1   115.05  3.000
 31Y  N    C3   N1   127.99  3.000
 31Y  C10  N4   C9   117.76  3.000
 31Y  H2   C5   C4   119.83  3.000
 31Y  H2   C5   C6   120.83  3.000
 31Y  C4   C5   C6   119.34  3.000
 31Y  C16  N6   C19  117.16  3.000
 31Y  C19  N6   C22  111.13  3.000
 31Y  C16  N6   C22  117.18  3.000
 31Y  H4   C7   H3   106.77  3.000
 31Y  H4   C7   C8   108.84  3.000
 31Y  H3   C7   C8   109.93  3.000
 31Y  H4   C7   N3   109.32  3.000
 31Y  H3   C7   N3   111.87  3.000
 31Y  C8   C7   N3   110.01  3.000
 31Y  H5   C9   C8   119.63  3.000
 31Y  H5   C9   N4   116.42  3.000
 31Y  C8   C9   N4   123.96  3.000
 31Y  H6   C10  C11  120.17  3.000
 31Y  H6   C10  N4   116.63  3.000
 31Y  C11  C10  N4   123.20  3.000
 31Y  H7   C11  C12  121.24  3.000
 31Y  H7   C11  C10  120.28  3.000
 31Y  C12  C11  C10  118.48  3.000
 31Y  H8   C12  C8   120.39  3.000
 31Y  H8   C12  C11  120.54  3.000
 31Y  C8   C12  C11  119.07  3.000
 31Y  N5   C13  C14  117.11  3.000
 31Y  C14  C13  C18  117.77  3.000
 31Y  N5   C13  C18  125.11  3.000
 31Y  H9   C15  C14  117.97  3.000
 31Y  H9   C15  C16  120.57  3.000
 31Y  C14  C15  C16  121.43  3.000
 31Y  H10  C18  C17  119.00  3.000
 31Y  H10  C18  C13  120.48  3.000
 31Y  C17  C18  C13  120.52  3.000
 31Y  H12  C20  H11  107.94  3.000
 31Y  H12  C20  C19  109.51  3.000
 31Y  H11  C20  C19  109.09  3.000
 31Y  H12  C20  O    107.75  3.000
 31Y  H11  C20  O    110.35  3.000
 31Y  C19  C20  O    112.11  3.000
 31Y  H14  C21  H13  108.14  3.000
 31Y  H14  C21  O    107.64  3.000
 31Y  H13  C21  O    110.20  3.000
 31Y  H14  C21  C22  109.53  3.000
 31Y  H13  C21  C22  109.34  3.000
 31Y  O    C21  C22  111.89  3.000
 31Y  H16  C22  H15  107.09  3.000
 31Y  H16  C22  C21  109.67  3.000
 31Y  H15  C22  C21  107.00  3.000
 31Y  H16  C22  N6   110.63  3.000
 31Y  H15  C22  N6   111.95  3.000
 31Y  C21  C22  N6   110.38  3.000
 31Y  C21  O    C20  110.08  3.000
 31Y  H18  C19  H17  107.36  3.000
 31Y  H18  C19  C20  107.76  3.000
 31Y  H17  C19  C20  109.89  3.000
 31Y  H18  C19  N6   109.80  3.000
 31Y  H17  C19  N6   111.55  3.000
 31Y  C20  C19  N6   110.37  3.000
 31Y  C17  C16  C15  116.60  3.000
 31Y  C15  C16  N6   120.89  3.000
 31Y  C17  C16  N6   122.50  3.000
 31Y  H19  C14  C15  118.69  3.000
 31Y  H19  C14  C13  119.86  3.000
 31Y  C15  C14  C13  121.45  3.000
 31Y  H20  C17  C16  120.76  3.000
 31Y  H20  C17  C18  117.01  3.000
 31Y  C16  C17  C18  122.23  3.000
 31Y  C1   C    N1   120.31  3.000
 31Y  N1   C    N5   122.61  3.000
 31Y  C1   C    N5   117.08  3.000
 31Y  C    N1   C3   117.75  3.000
 31Y  C3   N    C2   115.53  3.000
 31Y  N2   C1   C    119.58  3.000
 31Y  C    C1   C2   115.91  3.000
 31Y  N2   C1   C2   124.49  3.000
 31Y  C6   N2   C1   118.68  3.000
 31Y  N3   C6   N2   117.17  3.000
 31Y  N2   C6   C5   121.47  3.000
 31Y  N3   C6   C5   121.35  3.000
 31Y  H22  C4   C5   120.86  3.000
 31Y  H22  C4   C2   119.34  3.000
 31Y  C5   C4   C2   119.80  3.000
 31Y  H23  N3   C6   114.65  3.000
 31Y  H23  N3   C7   116.73  3.000
 31Y  C6   N3   C7   123.39  3.000
 31Y  C12  C8   C9   117.52  3.000
 31Y  C12  C8   C7   121.47  3.000
 31Y  C9   C8   C7   121.00  3.000
 31Y  H21  N5   C    113.14  3.000
 31Y  H21  N5   C13  116.07  3.000
 31Y  C    N5   C13  130.73  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
 31Y  CONST_01  C6   N2   C1   C2      0.00   0.0  0
 31Y  CONST_02  N1   C    C1   C2      0.00   0.0  0
 31Y  CONST_03  C6   C5   C4   C2      0.00   0.0  0
 31Y  CONST_04  N1   C3   N    C2      0.00   0.0  0
 31Y  CONST_05  C1   C    N1   C3      0.00   0.0  0
 31Y  CONST_06  C1   C2   N    C3      0.00   0.0  0
 31Y  CONST_07  C4   C2   N    C3    180.00   0.0  0
 31Y  CONST_08  C12  C8   C9   N4      0.00   0.0  0
 31Y  CONST_09  C12  C11  C10  N4      0.00   0.0  0
 31Y  CONST_10  C1   N2   C6   C5      0.00   0.0  0
 31Y  CONST_11  C1   C2   C4   C5      0.00   0.0  0
 31Y  CONST_12  N    C2   C4   C5    180.00   0.0  0
 31Y  CONST_13  C11  C12  C8   C9      0.00   0.0  0
 31Y  CONST_14  C11  C10  N4   C9      0.00   0.0  0
 31Y  CONST_15  C8   C9   N4   C10     0.00   0.0  0
 31Y  CONST_16  C8   C12  C11  C10     0.00   0.0  0
 31Y  CONST_17  C16  C17  C18  C13     0.00   0.0  0
 31Y  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 31Y  CONST_19  C18  C17  C16  C15     0.00   0.0  0
 31Y  CONST_20  C18  C13  C14  C15     0.00   0.0  0
 31Y  CONST_21  C17  C18  C13  C14     0.00   0.0  0
 31Y  CONST_22  C17  C16  C15  C14     0.00   0.0  0
 31Y  CONST_23  C6   N2   C1   C     180.00   0.0  0
 31Y  CONST_24  C4   C2   C1   C     180.00   0.0  0
 31Y  CONST_25  N    C2   C1   C       0.00   0.0  0
 31Y  CONST_26  N    C3   N1   C       0.00   0.0  0
 31Y  CONST_27  N2   C1   C    N1    180.00   0.0  0
 31Y  CONST_28  N2   C1   C2   N     180.00   0.0  0
 31Y  CONST_29  C4   C5   C6   N2      0.00   0.0  0
 31Y  CONST_30  C4   C2   C1   N2      0.00   0.0  0
 31Y  CONST_31  C18  C17  C16  N6    180.00   0.0  0
 31Y  CONST_32  C14  C15  C16  N6    180.00   0.0  0
 31Y  CONST_33  N5   C    C1   C2    180.00   0.0  0
 31Y  CONST_34  N5   C    N1   C3    180.00   0.0  0
 31Y  CONST_35  C7   C8   C9   N4    180.00   0.0  0
 31Y  CONST_36  C11  C12  C8   C7    180.00   0.0  0
 31Y  CONST_37  N5   C13  C14  C15   180.00   0.0  0
 31Y  CONST_38  N5   C13  C18  C17   180.00   0.0  0
 31Y  CONST_39  N2   C1   C    N5      0.00   0.0  0
 31Y  CONST_40  N3   C6   N2   C1    180.00   0.0  0
 31Y  CONST_41  N3   C6   C5   C4    180.00   0.0  0
 31Y  CONST_42  H2   C5   C4   C2    180.00   0.0  0
 31Y  CONST_43  H1   C3   N    C2    180.00   0.0  0
 31Y  CONST_44  H7   C11  C10  N4    180.00   0.0  0
 31Y  CONST_45  H20  C17  C16  N6      0.00   0.0  0
 31Y  CONST_46  H9   C15  C16  N6      0.00   0.0  0
 31Y  CONST_47  H8   C12  C8   C9    180.00   0.0  0
 31Y  CONST_48  H6   C10  N4   C9    180.00   0.0  0
 31Y  CONST_49  H5   C9   N4   C10   180.00   0.0  0
 31Y  CONST_50  H19  C14  C13  C18   180.00   0.0  0
 31Y  CONST_51  H10  C18  C17  C16   180.00   0.0  0
 31Y  CONST_52  H22  C4   C2   N       0.00   0.0  0
 31Y  CONST_53  C7   N3   C6   C5      0.00   0.0  0
 31Y  CONST_54  N2   C6   N3   C7    180.00   0.0  0
 31Y  CONST_55  H23  N3   C6   C5    180.00   0.0  0
 31Y  Var_01    O    C21  C22  N6    -56.37  30.0  1
 31Y  Var_02    O    C20  C19  N6     56.12  30.0  1
 31Y  Var_03    C22  N6   C16  C15    48.73  30.0  1
 31Y  Var_04    C22  C21  O    C20    58.59  30.0  1
 31Y  Var_05    C19  C20  O    C21   -58.50  30.0  1
 31Y  Var_06    C1   C    N5   C13  -177.13  30.0  2
 31Y  Var_07    C    N5   C13  C18    -4.28  30.0  1
 31Y  Var_08    N3   C7   C8   C9    110.22  30.0  2
 31Y  Var_09    C8   C7   N3   C6    175.41  30.0  1

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
 31Y  plan-1  N6   0.020
 31Y  plan-1  C13  0.020
 31Y  plan-1  C15  0.020
 31Y  plan-1  C18  0.020
 31Y  plan-1  C16  0.020
 31Y  plan-1  C14  0.020
 31Y  plan-1  C17  0.020
 31Y  plan-1  H9   0.020
 31Y  plan-1  H10  0.020
 31Y  plan-1  H19  0.020
 31Y  plan-1  H20  0.020
 31Y  plan-1  N5   0.020
 31Y  plan-2  N4   0.020
 31Y  plan-2  C7   0.020
 31Y  plan-2  C9   0.020
 31Y  plan-2  C10  0.020
 31Y  plan-2  C11  0.020
 31Y  plan-2  C12  0.020
 31Y  plan-2  C8   0.020
 31Y  plan-2  H5   0.020
 31Y  plan-2  H6   0.020
 31Y  plan-2  H7   0.020
 31Y  plan-2  H8   0.020
 31Y  plan-3  C2   0.020
 31Y  plan-3  C3   0.020
 31Y  plan-3  C5   0.020
 31Y  plan-3  C    0.020
 31Y  plan-3  N1   0.020
 31Y  plan-3  N    0.020
 31Y  plan-3  C1   0.020
 31Y  plan-3  N2   0.020
 31Y  plan-3  C6   0.020
 31Y  plan-3  C4   0.020
 31Y  plan-3  N3   0.020
 31Y  plan-3  H1   0.020
 31Y  plan-3  H2   0.020
 31Y  plan-3  H22  0.020
 31Y  plan-3  N5   0.020
 31Y  plan-4  C7   0.020
 31Y  plan-4  C6   0.020
 31Y  plan-4  N3   0.020
 31Y  plan-4  H23  0.020

