# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 05:35:51 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(cc(n1)c2ccc(O)cc2)N(Cc3ccccn3)Cc4ccccn4
#
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
 6GM  6GM  4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol  ligand  49  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6GM
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
 6GM  C10  C  CR16  0  -0.309  -3.4100   1.1074   0.0855
 6GM  C13  C  CR16  0  -0.303   3.3046  -1.2724   0.7400
 6GM  C15  C  CR16  0  -0.318   5.5863  -0.7581   1.2200
 6GM  C17  C  CH2   0  -0.428   1.3843   0.8987  -1.8419
 6GM  C20  C  CR16  0  -0.328   1.5411   3.6621   1.3748
 6GM  C21  C  CR16  0  -0.148   2.7055   2.9895   1.0341
 6GM  C22  C  CR16  0  -0.323   2.6744   2.0914  -0.0192
 6GM  C06  C  CR16  0  -0.270  -4.4891  -1.0185   0.2563
 6GM  C07  C  CR16  0  -0.323  -5.7048  -0.3958   0.4678
 6GM  C08  C  CR6   0   0.353  -5.7791   0.9963   0.4918
 6GM  O01  O  OH1   0  -0.626  -6.9813   1.5603   0.7008
 6GM  C09  C  CR16  0  -0.369  -4.6188   1.7449   0.3045
 6GM  C05  C  CR6   0   0.033  -3.3188  -0.2844   0.0510
 6GM  C04  C  CR6   0   0.285  -2.0353  -0.9758  -0.1835
 6GM  C03  C  CR16  0  -0.476  -0.9654  -0.3198  -0.7641
 6GM  N03  N  N     0  -0.517  -1.9703  -2.2559   0.1910
 6GM  C01  C  CR6   0   0.521  -0.8062  -2.8684  -0.0136
 6GM  N01  N  NH2   0  -0.826  -0.7402  -4.1832   0.3102
 6GM  N02  N  N     0  -0.533   0.2955  -2.3232  -0.5231
 6GM  C02  C  CR6   0   0.595   0.2285  -1.0492  -0.9063
 6GM  N04  N  NT    0  -0.487   1.3502  -0.4980  -1.4383
 6GM  C18  C  CR6   0   0.276   1.4756   1.8848  -0.6969
 6GM  N06  N  N     0  -0.421   0.3672   2.5488  -0.3822
 6GM  C19  C  CR16  0  -0.067   0.4019   3.4113   0.6274
 6GM  C11  C  CH2   0  -0.406   2.5371  -1.2979  -1.6700
 6GM  C12  C  CR6   0   0.235   3.6019  -1.1285  -0.6137
 6GM  N05  N  N     0  -0.425   4.8226  -0.8283  -1.0438
 6GM  C16  C  CR16  0  -0.086   5.7880  -0.6523  -0.1455
 6GM  C14  C  CR16  0  -0.156   4.3120  -1.0804   1.6681
 6GM  H1   H  HCR6  0   0.256  -2.5258   1.7200  -0.0407
 6GM  H2   H  HCR6  0   0.271   2.3033  -1.5314   1.0559
 6GM  H3   H  HCR6  0   0.269   6.4029  -0.5944   1.9093
 6GM  H4   H  HCH2  0   0.289   2.2498   1.0226  -2.4931
 6GM  H5   H  HCH2  0   0.276   0.5090   1.1389  -2.4495
 6GM  H7   H  HCR6  0   0.274   3.6256   3.1669   1.5751
 6GM  H8   H  HCR6  0   0.268   3.5739   1.5727  -0.3216
 6GM  H9   H  HCR6  0   0.254  -4.4454  -2.0991   0.2428
 6GM  H10  H  HCR6  0   0.265  -6.6011  -0.9853   0.6149
 6GM  H11  H  HOH1  0   0.477  -6.9107   2.5216   0.6867
 6GM  H12  H  HCR6  0   0.274  -4.6562   2.8279   0.3337
 6GM  H13  H  HCR6  0   0.271  -1.0421   0.7100  -1.0675
 6GM  H14  H  HNH2  0   0.387  -1.4551  -4.5435   0.9188
 6GM  H15  H  HNH2  0   0.387   0.1730  -4.5901   0.4203
 6GM  H16  H  HCR6  0   0.263  -0.5238   3.9306   0.8487
 6GM  H17  H  HCH2  0   0.284   2.2432  -2.3451  -1.7280
 6GM  H18  H  HCH2  0   0.272   2.9637  -1.0240  -2.6362
 6GM  H19  H  HCR6  0   0.263   6.7693  -0.4068  -0.5360
 6GM  H20  H  HCR6  0   0.273   4.1083  -1.1795   2.7263
 6GM  H6   H  HCR6  0   0.272   1.5161   4.3717   2.1900

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
 6GM  C11  C12  single    1.509  0.020  1.509
 6GM  C11  N04  single    1.450  0.020  1.450
 6GM  C13  C12  aromatic  1.393  0.020  1.393
 6GM  C13  C14  aromatic  1.383  0.020  1.383
 6GM  C12  N05  aromatic  1.329  0.020  1.329
 6GM  C14  C15  aromatic  1.389  0.020  1.389
 6GM  C17  N04  single    1.454  0.020  1.454
 6GM  C17  C18  single    1.514  0.020  1.514
 6GM  N05  C16  aromatic  1.330  0.020  1.330
 6GM  N04  C02  single    1.358  0.020  1.358
 6GM  C15  C16  aromatic  1.384  0.020  1.384
 6GM  C18  C22  aromatic  1.392  0.020  1.392
 6GM  C18  N06  aromatic  1.330  0.020  1.330
 6GM  C22  C21  aromatic  1.385  0.020  1.385
 6GM  N06  C19  aromatic  1.328  0.020  1.328
 6GM  C02  C03  aromatic  1.406  0.020  1.406
 6GM  C02  N02  aromatic  1.332  0.020  1.332
 6GM  C21  C20  aromatic  1.387  0.020  1.387
 6GM  C03  C04  aromatic  1.383  0.020  1.383
 6GM  C19  C20  aromatic  1.385  0.020  1.385
 6GM  N02  C01  aromatic  1.331  0.020  1.331
 6GM  C06  C07  aromatic  1.382  0.020  1.382
 6GM  C06  C05  aromatic  1.397  0.020  1.397
 6GM  C04  C05  single    1.477  0.020  1.477
 6GM  C04  N03  aromatic  1.335  0.020  1.335
 6GM  C07  C08  aromatic  1.394  0.020  1.394
 6GM  C05  C10  aromatic  1.395  0.020  1.395
 6GM  C01  N03  aromatic  1.331  0.020  1.331
 6GM  C01  N01  single    1.356  0.020  1.356
 6GM  C08  O01  single    1.344  0.020  1.344
 6GM  C08  C09  aromatic  1.394  0.020  1.394
 6GM  C10  C09  aromatic  1.384  0.020  1.384
 6GM  C10  H1   single    0.930  0.020  1.080
 6GM  C13  H2   single    0.930  0.020  1.080
 6GM  C15  H3   single    0.930  0.020  1.080
 6GM  C17  H4   single    0.970  0.020  1.090
 6GM  C17  H5   single    0.970  0.020  1.090
 6GM  C20  H6   single    0.930  0.020  1.080
 6GM  C21  H7   single    0.930  0.020  1.080
 6GM  C22  H8   single    0.930  0.020  1.080
 6GM  C06  H9   single    0.930  0.020  1.080
 6GM  C07  H10  single    0.930  0.020  1.080
 6GM  O01  H11  single    0.850  0.020  0.980
 6GM  C09  H12  single    0.930  0.020  1.080
 6GM  C03  H13  single    0.930  0.020  1.080
 6GM  N01  H14  single    0.890  0.020  1.040
 6GM  N01  H15  single    0.890  0.020  1.040
 6GM  C19  H16  single    0.930  0.020  1.080
 6GM  C11  H17  single    0.970  0.020  1.090
 6GM  C11  H18  single    0.970  0.020  1.090
 6GM  C16  H19  single    0.930  0.020  1.080
 6GM  C14  H20  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
 6GM  H1   C10  C05  120.53  3.000
 6GM  H1   C10  C09  118.09  3.000
 6GM  C05  C10  C09  121.37  3.000
 6GM  H2   C13  C14  120.77  3.000
 6GM  H2   C13  C12  120.40  3.000
 6GM  C14  C13  C12  118.83  3.000
 6GM  H3   C15  C14  121.50  3.000
 6GM  H3   C15  C16  120.48  3.000
 6GM  C14  C15  C16  118.02  3.000
 6GM  H5   C17  H4   106.20  3.000
 6GM  H5   C17  C18  109.01  3.000
 6GM  H4   C17  C18  109.26  3.000
 6GM  H5   C17  N04  110.29  3.000
 6GM  H4   C17  N04  107.08  3.000
 6GM  C18  C17  N04  114.65  3.000
 6GM  H6   C20  C19  120.44  3.000
 6GM  H6   C20  C21  121.53  3.000
 6GM  C19  C20  C21  118.03  3.000
 6GM  H7   C21  C22  120.38  3.000
 6GM  H7   C21  C20  120.76  3.000
 6GM  C22  C21  C20  118.85  3.000
 6GM  H8   C22  C18  120.59  3.000
 6GM  H8   C22  C21  120.34  3.000
 6GM  C18  C22  C21  119.06  3.000
 6GM  H9   C06  C05  119.30  3.000
 6GM  H9   C06  C07  119.18  3.000
 6GM  C05  C06  C07  121.51  3.000
 6GM  H10  C07  C08  119.81  3.000
 6GM  H10  C07  C06  120.23  3.000
 6GM  C08  C07  C06  119.96  3.000
 6GM  C09  C08  O01  122.69  3.000
 6GM  C09  C08  C07  119.32  3.000
 6GM  O01  C08  C07  117.99  3.000
 6GM  H11  O01  C08  110.53  3.000
 6GM  H12  C09  C08  120.29  3.000
 6GM  H12  C09  C10  119.64  3.000
 6GM  C08  C09  C10  120.06  3.000
 6GM  C04  C05  C06  120.37  3.000
 6GM  C04  C05  C10  121.86  3.000
 6GM  C06  C05  C10  117.76  3.000
 6GM  N03  C04  C03  122.33  3.000
 6GM  N03  C04  C05  116.53  3.000
 6GM  C03  C04  C05  121.14  3.000
 6GM  H13  C03  C02  121.89  3.000
 6GM  H13  C03  C04  121.14  3.000
 6GM  C02  C03  C04  116.95  3.000
 6GM  C01  N03  C04  116.14  3.000
 6GM  N02  C01  N01  116.65  3.000
 6GM  N01  C01  N03  116.88  3.000
 6GM  N02  C01  N03  126.47  3.000
 6GM  H15  N01  H14  115.74  3.000
 6GM  H15  N01  C01  117.56  3.000
 6GM  H14  N01  C01  117.22  3.000
 6GM  C02  N02  C01  117.41  3.000
 6GM  N04  C02  N02  117.33  3.000
 6GM  N02  C02  C03  120.65  3.000
 6GM  N04  C02  C03  122.02  3.000
 6GM  C11  N04  C02  120.98  3.000
 6GM  C02  N04  C17  121.19  3.000
 6GM  C11  N04  C17  117.79  3.000
 6GM  N06  C18  C22  121.89  3.000
 6GM  N06  C18  C17  117.00  3.000
 6GM  C22  C18  C17  121.11  3.000
 6GM  C19  N06  C18  118.83  3.000
 6GM  H16  C19  N06  116.35  3.000
 6GM  H16  C19  C20  120.35  3.000
 6GM  N06  C19  C20  123.31  3.000
 6GM  H18  C11  H17  107.44  3.000
 6GM  H18  C11  C12  108.41  3.000
 6GM  H17  C11  C12  109.60  3.000
 6GM  H18  C11  N04  108.85  3.000
 6GM  H17  C11  N04  108.54  3.000
 6GM  C12  C11  N04  113.81  3.000
 6GM  N05  C12  C11  116.55  3.000
 6GM  N05  C12  C13  122.26  3.000
 6GM  C11  C12  C13  121.19  3.000
 6GM  C16  N05  C12  118.55  3.000
 6GM  H19  C16  N05  116.32  3.000
 6GM  H19  C16  C15  120.29  3.000
 6GM  N05  C16  C15  123.38  3.000
 6GM  H20  C14  C15  120.63  3.000
 6GM  H20  C14  C13  120.42  3.000
 6GM  C15  C14  C13  118.95  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
 6GM  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 6GM  CONST_04  C07  C08  C09  C10     0.00   0.0  0
 6GM  CONST_05  C16  N05  C12  C13     0.00   0.0  0
 6GM  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 6GM  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 6GM  CONST_08  C12  N05  C16  C15     0.00   0.0  0
 6GM  CONST_09  C18  C22  C21  C20     0.00   0.0  0
 6GM  CONST_10  C18  N06  C19  C20     0.00   0.0  0
 6GM  CONST_11  N06  C18  C22  C21     0.00   0.0  0
 6GM  CONST_12  N06  C19  C20  C21     0.00   0.0  0
 6GM  CONST_13  C19  N06  C18  C22     0.00   0.0  0
 6GM  CONST_14  C19  C20  C21  C22     0.00   0.0  0
 6GM  CONST_15  C09  C08  C07  C06     0.00   0.0  0
 6GM  CONST_18  C09  C10  C05  C06     0.00   0.0  0
 6GM  CONST_19  C04  C05  C06  C07   180.00   0.0  0
 6GM  CONST_20  C05  C06  C07  C08     0.00   0.0  0
 6GM  CONST_21  C05  C10  C09  C08     0.00   0.0  0
 6GM  CONST_22  C04  C05  C10  C09   180.00   0.0  0
 6GM  CONST_23  C02  C03  C04  C05   180.00   0.0  0
 6GM  CONST_24  C01  N03  C04  C05   180.00   0.0  0
 6GM  CONST_25  N02  C02  C03  C04     0.00   0.0  0
 6GM  CONST_26  N02  C01  N03  C04     0.00   0.0  0
 6GM  CONST_27  C01  N02  C02  C03     0.00   0.0  0
 6GM  CONST_28  C01  N03  C04  C03     0.00   0.0  0
 6GM  CONST_29  C02  C03  C04  N03     0.00   0.0  0
 6GM  CONST_30  C02  N02  C01  N03     0.00   0.0  0
 6GM  CONST_31  C14  C13  C12  N05     0.00   0.0  0
 6GM  CONST_32  C14  C15  C16  N05     0.00   0.0  0
 6GM  CONST_33  O01  C08  C09  C10   180.00   0.0  0
 6GM  CONST_34  C21  C22  C18  C17   180.00   0.0  0
 6GM  CONST_35  C19  N06  C18  C17   180.00   0.0  0
 6GM  CONST_36  O01  C08  C07  C06   180.00   0.0  0
 6GM  CONST_37  N04  C02  C03  C04   180.00   0.0  0
 6GM  CONST_38  N01  C01  N03  C04   180.00   0.0  0
 6GM  CONST_39  N04  C02  N02  C01   180.00   0.0  0
 6GM  CONST_40  C02  N02  C01  N01   180.00   0.0  0
 6GM  CONST_41  C14  C13  C12  C11   180.00   0.0  0
 6GM  CONST_42  C16  N05  C12  C11   180.00   0.0  0
 6GM  CONST_43  H9   C06  C05  C10   180.00   0.0  0
 6GM  CONST_44  H3   C15  C14  C13   180.00   0.0  0
 6GM  CONST_45  H2   C13  C14  C15   180.00   0.0  0
 6GM  CONST_46  H8   C22  C21  C20   180.00   0.0  0
 6GM  CONST_47  H16  C19  C20  C21   180.00   0.0  0
 6GM  CONST_48  H6   C20  C21  C22   180.00   0.0  0
 6GM  CONST_49  H1   C10  C05  C06   180.00   0.0  0
 6GM  CONST_50  H12  C09  C08  C07   180.00   0.0  0
 6GM  CONST_51  H10  C07  C08  C09   180.00   0.0  0
 6GM  CONST_52  H13  C03  C04  C05     0.00   0.0  0
 6GM  CONST_53  H7   C21  C22  C18   180.00   0.0  0
 6GM  CONST_54  H20  C14  C13  C12   180.00   0.0  0
 6GM  CONST_55  H19  C16  N05  C12   180.00   0.0  0
 6GM  CONST_56  C03  C02  N04  C17     0.00   0.0  0
 6GM  CONST_57  N02  C02  N04  C17   180.00   0.0  0
 6GM  CONST_58  C11  N04  C02  C03   180.00   0.0  0
 6GM  CONST_59  C11  N04  C02  N02     0.00   0.0  0
 6GM  Var_01    N04  C11  C12  C13    51.99  30.0  1
 6GM  Var_02    N04  C17  C18  C22    76.03  30.0  1
 6GM  Var_03    C12  C11  N04  C02  -100.73  30.0  2
 6GM  Var_04    C18  C17  N04  C02    75.24  30.0  2

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
 6GM  plan-1  C13  0.020
 6GM  plan-1  C15  0.020
 6GM  plan-1  C11  0.020
 6GM  plan-1  C12  0.020
 6GM  plan-1  N05  0.020
 6GM  plan-1  C16  0.020
 6GM  plan-1  C14  0.020
 6GM  plan-1  H2   0.020
 6GM  plan-1  H3   0.020
 6GM  plan-1  H19  0.020
 6GM  plan-1  H20  0.020
 6GM  plan-2  C10  0.020
 6GM  plan-2  C06  0.020
 6GM  plan-2  C07  0.020
 6GM  plan-2  C08  0.020
 6GM  plan-2  O01  0.020
 6GM  plan-2  C09  0.020
 6GM  plan-2  C05  0.020
 6GM  plan-2  C04  0.020
 6GM  plan-2  H1   0.020
 6GM  plan-2  H9   0.020
 6GM  plan-2  H10  0.020
 6GM  plan-2  H12  0.020
 6GM  plan-3  C05  0.020
 6GM  plan-3  C04  0.020
 6GM  plan-3  C03  0.020
 6GM  plan-3  N03  0.020
 6GM  plan-3  C01  0.020
 6GM  plan-3  N01  0.020
 6GM  plan-3  N02  0.020
 6GM  plan-3  C02  0.020
 6GM  plan-3  N04  0.020
 6GM  plan-3  H13  0.020
 6GM  plan-4  C17  0.020
 6GM  plan-4  C20  0.020
 6GM  plan-4  C21  0.020
 6GM  plan-4  C22  0.020
 6GM  plan-4  C18  0.020
 6GM  plan-4  N06  0.020
 6GM  plan-4  C19  0.020
 6GM  plan-4  H7   0.020
 6GM  plan-4  H8   0.020
 6GM  plan-4  H16  0.020
 6GM  plan-4  H6   0.020
 6GM  plan-5  C01  0.020
 6GM  plan-5  N01  0.020
 6GM  plan-5  H14  0.020
 6GM  plan-5  H15  0.020
 6GM  plan-6  C17  0.020
 6GM  plan-6  C02  0.020
 6GM  plan-6  N04  0.020
 6GM  plan-6  C11  0.020

