# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 12:17:22 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 6-(4-methoxyphenyl)-N~4~,N~4~-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2cc(nc(N)n2)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
 6GF  6GF  6-(4-methoxyphenyl)-N~4~,N~4~-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine  ligand  52  30  .  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_6GF
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
 6GF  C10  C  CR6   0   0.590  -1.0596  -0.2881  -0.3486
 6GF  C13  C  CR6   0   0.270  -4.0680  -1.1287   0.1296
 6GF  C15  C  CR16  0  -0.152  -5.5024  -3.0398   0.0387
 6GF  C17  C  CR16  0  -0.079  -4.3884  -2.3584   2.0247
 6GF  C20  C  CR16  0  -0.079  -1.4290   4.2502  -1.2214
 6GF  C21  C  CR16  0  -0.329  -0.6190   5.1221  -0.5090
 6GF  C22  C  CR16  0  -0.150  -0.2529   4.7653   0.7798
 6GF  C01  C  CH3   0  -0.438   7.7027  -0.4043   0.4372
 6GF  C02  C  CR6   0   0.378   5.3737  -0.0393   0.6982
 6GF  C07  C  CR16  0  -0.323   4.3466   0.6231   1.3761
 6GF  C06  C  CR16  0  -0.311   3.0283   0.3912   1.0427
 6GF  C03  C  CR16  0  -0.365   5.0449  -0.9407  -0.3120
 6GF  C04  C  CR16  0  -0.266   3.7137  -1.1637  -0.6312
 6GF  C05  C  CR6   0   0.029   2.6782  -0.5052   0.0274
 6GF  C08  C  CR6   0   0.298   1.2736  -0.7595  -0.3572
 6GF  C11  C  CR16  0  -0.478   0.2369   0.0335   0.1006
 6GF  N01  N  N     0  -0.521   1.0660  -1.7850  -1.1876
 6GF  C09  C  CR6   0   0.518  -0.1930  -2.0008  -1.5612
 6GF  N02  N  NH2   0  -0.826  -0.4172  -3.0598  -2.3765
 6GF  N03  N  N     0  -0.514  -1.2620  -1.3048  -1.1838
 6GF  N04  N  NT    0  -0.462  -2.1491   0.4148   0.0299
 6GF  C18  C  CH2   0  -0.409  -2.0586   1.4478   1.0286
 6GF  C19  C  CR6   0   0.247  -1.5160   2.7550   0.4980
 6GF  N06  N  N     0  -0.404  -1.8693   3.0962  -0.7356
 6GF  C23  C  CR16  0  -0.337  -0.7088   3.5612   1.2928
 6GF  C12  C  CH2   0  -0.379  -3.4383   0.0798  -0.5197
 6GF  N05  N  N     0  -0.414  -3.8175  -1.3236   1.4182
 6GF  C16  C  CR16  0  -0.333  -5.2398  -3.2456   1.3859
 6GF  C14  C  CR16  0  -0.336  -4.9045  -1.9669  -0.6006
 6GF  H1   H  HCR6  0   0.272  -6.1553  -3.7091  -0.5062
 6GF  H2   H  HCR6  0   0.259  -4.1567  -2.4873   3.0765
 6GF  H3   H  HCR6  0   0.262  -1.7363   4.4953  -2.2322
 6GF  H4   H  HCR6  0   0.270  -0.2845   6.0481  -0.9559
 6GF  H5   H  HCR6  0   0.275   0.3833   5.4087   1.3730
 6GF  H6   H  HCH3  0   0.262   8.6126  -0.0326   0.9014
 6GF  H7   H  HCH3  0   0.231   7.6571  -1.4881   0.5685
 6GF  H8   H  HCH3  0   0.231   7.7353  -0.1791  -0.6315
 6GF  H9   H  HCR6  0   0.266   4.5907   1.3177   2.1700
 6GF  H10  H  HCR6  0   0.246   2.2696   0.9198   1.6048
 6GF  H11  H  HCR6  0   0.280   5.8064  -1.4769  -0.8616
 6GF  H12  H  HCR6  0   0.258   3.4777  -1.8653  -1.4194
 6GF  H13  H  HCR6  0   0.249   0.4205   0.8797   0.7408
 6GF  H14  H  HNH2  0   0.387   0.3707  -3.4467  -2.8669
 6GF  H15  H  HNH2  0   0.387  -1.3002  -3.0999  -2.8559
 6GF  H16  H  HCH2  0   0.295  -3.0605   1.6178   1.4258
 6GF  H17  H  HCH2  0   0.267  -1.4658   1.1106   1.8829
 6GF  H18  H  HCR6  0   0.270  -0.4368   3.2471   2.2926
 6GF  H19  H  HCH2  0   0.268  -3.3618  -0.0796  -1.5951
 6GF  H20  H  HCH2  0   0.278  -4.0947   0.9414  -0.3815
 6GF  H21  H  HCR6  0   0.268  -5.6787  -4.0713   1.9287
 6GF  H22  H  HCR6  0   0.262  -5.0773  -1.7804  -1.6528
 6GF  O01  O  O2    0  -0.466   6.6267   0.2501   1.0825

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
 6GF  N02  C09  single    1.355  0.020  1.355
 6GF  C01  O01  single    1.415  0.020  1.415
 6GF  C03  C04  aromatic  1.387  0.020  1.387
 6GF  C03  C02  aromatic  1.393  0.020  1.393
 6GF  C04  C05  aromatic  1.393  0.020  1.393
 6GF  N01  C09  aromatic  1.331  0.020  1.331
 6GF  N01  C08  aromatic  1.336  0.020  1.336
 6GF  C09  N03  aromatic  1.330  0.020  1.330
 6GF  O01  C02  single    1.342  0.020  1.342
 6GF  C02  C07  aromatic  1.398  0.020  1.398
 6GF  C05  C08  single    1.478  0.020  1.478
 6GF  C05  C06  aromatic  1.399  0.020  1.399
 6GF  C08  C11  aromatic  1.383  0.020  1.383
 6GF  N03  C10  aromatic  1.331  0.020  1.331
 6GF  C07  C06  aromatic  1.379  0.020  1.379
 6GF  C11  C10  aromatic  1.409  0.020  1.409
 6GF  C10  N04  single    1.351  0.020  1.351
 6GF  C22  C23  aromatic  1.386  0.020  1.386
 6GF  C22  C21  aromatic  1.387  0.020  1.387
 6GF  C23  C19  aromatic  1.390  0.020  1.390
 6GF  C21  C20  aromatic  1.387  0.020  1.387
 6GF  C19  C18  single    1.511  0.020  1.511
 6GF  C19  N06  aromatic  1.328  0.020  1.328
 6GF  N04  C18  single    1.440  0.020  1.440
 6GF  N04  C12  single    1.441  0.020  1.441
 6GF  C20  N06  aromatic  1.327  0.020  1.327
 6GF  C12  C13  single    1.510  0.020  1.510
 6GF  N05  C13  aromatic  1.327  0.020  1.327
 6GF  N05  C17  aromatic  1.328  0.020  1.328
 6GF  C13  C14  aromatic  1.391  0.020  1.391
 6GF  C17  C16  aromatic  1.386  0.020  1.386
 6GF  C14  C15  aromatic  1.385  0.020  1.385
 6GF  C16  C15  aromatic  1.388  0.020  1.388
 6GF  C15  H1   single    0.930  0.020  1.080
 6GF  C17  H2   single    0.930  0.020  1.080
 6GF  C20  H3   single    0.930  0.020  1.080
 6GF  C21  H4   single    0.930  0.020  1.080
 6GF  C22  H5   single    0.930  0.020  1.080
 6GF  C01  H6   single    0.970  0.020  1.090
 6GF  C01  H7   single    0.970  0.020  1.090
 6GF  C01  H8   single    0.970  0.020  1.090
 6GF  C07  H9   single    0.930  0.020  1.080
 6GF  C06  H10  single    0.930  0.020  1.080
 6GF  C03  H11  single    0.930  0.020  1.080
 6GF  C04  H12  single    0.930  0.020  1.080
 6GF  C11  H13  single    0.930  0.020  1.080
 6GF  N02  H14  single    0.890  0.020  1.040
 6GF  N02  H15  single    0.890  0.020  1.040
 6GF  C18  H16  single    0.970  0.020  1.090
 6GF  C18  H17  single    0.970  0.020  1.090
 6GF  C23  H18  single    0.930  0.020  1.080
 6GF  C12  H19  single    0.970  0.020  1.090
 6GF  C12  H20  single    0.970  0.020  1.090
 6GF  C16  H21  single    0.930  0.020  1.080
 6GF  C14  H22  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
 6GF  N04  C10  N03  116.79  3.000
 6GF  N04  C10  C11  122.28  3.000
 6GF  N03  C10  C11  120.93  3.000
 6GF  C14  C13  N05  122.32  3.000
 6GF  C14  C13  C12  120.49  3.000
 6GF  N05  C13  C12  117.16  3.000
 6GF  H1   C15  C14  120.48  3.000
 6GF  H1   C15  C16  120.74  3.000
 6GF  C14  C15  C16  118.77  3.000
 6GF  H2   C17  C16  120.14  3.000
 6GF  H2   C17  N05  116.33  3.000
 6GF  C16  C17  N05  123.52  3.000
 6GF  H3   C20  N06  116.33  3.000
 6GF  H3   C20  C21  120.14  3.000
 6GF  N06  C20  C21  123.53  3.000
 6GF  H4   C21  C22  121.53  3.000
 6GF  H4   C21  C20  120.45  3.000
 6GF  C22  C21  C20  118.02  3.000
 6GF  H5   C22  C23  120.47  3.000
 6GF  H5   C22  C21  120.78  3.000
 6GF  C23  C22  C21  118.74  3.000
 6GF  H8   C01  H7   108.85  3.000
 6GF  H8   C01  H6   108.80  3.000
 6GF  H7   C01  H6   108.83  3.000
 6GF  H8   C01  O01  111.93  3.000
 6GF  H7   C01  O01  111.85  3.000
 6GF  H6   C01  O01  106.47  3.000
 6GF  C03  C02  C07  119.00  3.000
 6GF  C07  C02  O01  116.42  3.000
 6GF  C03  C02  O01  124.57  3.000
 6GF  H9   C07  C06  120.04  3.000
 6GF  H9   C07  C02  119.60  3.000
 6GF  C06  C07  C02  120.36  3.000
 6GF  H10  C06  C05  120.97  3.000
 6GF  H10  C06  C07  117.54  3.000
 6GF  C05  C06  C07  121.49  3.000
 6GF  H11  C03  C04  118.63  3.000
 6GF  H11  C03  C02  121.54  3.000
 6GF  C04  C03  C02  119.83  3.000
 6GF  H12  C04  C05  119.29  3.000
 6GF  H12  C04  C03  118.79  3.000
 6GF  C05  C04  C03  121.92  3.000
 6GF  C08  C05  C04  120.14  3.000
 6GF  C08  C05  C06  122.47  3.000
 6GF  C04  C05  C06  117.39  3.000
 6GF  N01  C08  C11  121.97  3.000
 6GF  C11  C08  C05  121.83  3.000
 6GF  N01  C08  C05  116.19  3.000
 6GF  H13  C11  C08  121.31  3.000
 6GF  H13  C11  C10  121.71  3.000
 6GF  C08  C11  C10  116.95  3.000
 6GF  C09  N01  C08  116.49  3.000
 6GF  N03  C09  N02  116.53  3.000
 6GF  N03  C09  N01  126.56  3.000
 6GF  N02  C09  N01  116.88  3.000
 6GF  H15  N02  H14  116.12  3.000
 6GF  H15  N02  C09  117.60  3.000
 6GF  H14  N02  C09  117.68  3.000
 6GF  C09  N03  C10  117.10  3.000
 6GF  C12  N04  C18  119.19  3.000
 6GF  C12  N04  C10  119.59  3.000
 6GF  C18  N04  C10  121.14  3.000
 6GF  H17  C18  H16  105.16  3.000
 6GF  H17  C18  C19  110.27  3.000
 6GF  H16  C18  C19  108.83  3.000
 6GF  H17  C18  N04  110.79  3.000
 6GF  H16  C18  N04  107.86  3.000
 6GF  C19  C18  N04  113.55  3.000
 6GF  C23  C19  N06  122.45  3.000
 6GF  N06  C19  C18  116.93  3.000
 6GF  C23  C19  C18  120.61  3.000
 6GF  C19  N06  C20  118.37  3.000
 6GF  H18  C23  C19  120.37  3.000
 6GF  H18  C23  C22  120.74  3.000
 6GF  C19  C23  C22  118.89  3.000
 6GF  H20  C12  H19  106.41  3.000
 6GF  H20  C12  N04  107.83  3.000
 6GF  H19  C12  N04  110.34  3.000
 6GF  H20  C12  C13  109.05  3.000
 6GF  H19  C12  C13  109.67  3.000
 6GF  N04  C12  C13  113.28  3.000
 6GF  C17  N05  C13  118.47  3.000
 6GF  H21  C16  C17  120.46  3.000
 6GF  H21  C16  C15  121.59  3.000
 6GF  C17  C16  C15  117.96  3.000
 6GF  H22  C14  C15  120.89  3.000
 6GF  H22  C14  C13  120.16  3.000
 6GF  C15  C14  C13  118.96  3.000
 6GF  C02  O01  C01  118.66  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
 6GF  CONST_01  N01  C09  N03  C10     0.00   0.0  0
 6GF  CONST_02  N01  C08  C11  C10     0.00   0.0  0
 6GF  CONST_03  C05  C08  C11  C10   180.00   0.0  0
 6GF  CONST_04  C16  C17  N05  C13     0.00   0.0  0
 6GF  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 6GF  CONST_06  N05  C13  C14  C15     0.00   0.0  0
 6GF  CONST_07  N05  C17  C16  C15     0.00   0.0  0
 6GF  CONST_08  C14  C13  N05  C17     0.00   0.0  0
 6GF  CONST_09  C14  C15  C16  C17     0.00   0.0  0
 6GF  CONST_10  C23  C22  C21  C20     0.00   0.0  0
 6GF  CONST_11  C23  C19  N06  C20     0.00   0.0  0
 6GF  CONST_12  C19  C23  C22  C21     0.00   0.0  0
 6GF  CONST_13  C19  N06  C20  C21     0.00   0.0  0
 6GF  CONST_14  N06  C19  C23  C22     0.00   0.0  0
 6GF  CONST_15  N06  C20  C21  C22     0.00   0.0  0
 6GF  CONST_16  C05  C04  C03  C02     0.00   0.0  0
 6GF  CONST_17  C05  C06  C07  C02     0.00   0.0  0
 6GF  CONST_18  C04  C03  C02  C07     0.00   0.0  0
 6GF  CONST_19  C04  C05  C06  C07     0.00   0.0  0
 6GF  CONST_20  C08  C05  C06  C07   180.00   0.0  0
 6GF  CONST_21  C03  C04  C05  C06     0.00   0.0  0
 6GF  CONST_22  N01  C08  C05  C06   180.00   0.0  0
 6GF  CONST_23  C11  C08  C05  C06     0.00   0.0  0
 6GF  CONST_24  C03  C02  C07  C06     0.00   0.0  0
 6GF  CONST_25  C08  C05  C04  C03   180.00   0.0  0
 6GF  CONST_26  N01  C08  C05  C04     0.00   0.0  0
 6GF  CONST_27  C11  C08  C05  C04   180.00   0.0  0
 6GF  CONST_28  C09  N01  C08  C05   180.00   0.0  0
 6GF  CONST_29  N03  C09  N01  C08     0.00   0.0  0
 6GF  CONST_30  N03  C10  C11  C08     0.00   0.0  0
 6GF  CONST_31  C09  N01  C08  C11     0.00   0.0  0
 6GF  CONST_32  C09  N03  C10  C11     0.00   0.0  0
 6GF  CONST_33  N02  C09  N03  C10   180.00   0.0  0
 6GF  CONST_34  C12  C13  C14  C15   180.00   0.0  0
 6GF  CONST_35  C12  C13  N05  C17   180.00   0.0  0
 6GF  CONST_36  C18  C19  N06  C20   180.00   0.0  0
 6GF  CONST_37  C18  C19  C23  C22   180.00   0.0  0
 6GF  CONST_38  C04  C03  C02  O01   180.00   0.0  0
 6GF  CONST_39  C06  C07  C02  O01   180.00   0.0  0
 6GF  CONST_40  N02  C09  N01  C08   180.00   0.0  0
 6GF  CONST_41  N04  C10  C11  C08   180.00   0.0  0
 6GF  CONST_42  N04  C10  N03  C09   180.00   0.0  0
 6GF  CONST_43  H2   C17  N05  C13   180.00   0.0  0
 6GF  CONST_44  H1   C15  C14  C13   180.00   0.0  0
 6GF  CONST_45  H5   C22  C21  C20   180.00   0.0  0
 6GF  CONST_46  H18  C23  C22  C21   180.00   0.0  0
 6GF  CONST_47  H3   C20  C21  C22   180.00   0.0  0
 6GF  CONST_48  H12  C04  C03  C02   180.00   0.0  0
 6GF  CONST_49  H10  C06  C07  C02   180.00   0.0  0
 6GF  CONST_50  H11  C03  C02  C07   180.00   0.0  0
 6GF  CONST_51  H9   C07  C02  C03   180.00   0.0  0
 6GF  CONST_52  H13  C11  C08  C05     0.00   0.0  0
 6GF  CONST_53  H4   C21  C20  N06   180.00   0.0  0
 6GF  CONST_54  H22  C14  C13  N05   180.00   0.0  0
 6GF  CONST_55  H21  C16  C17  N05   180.00   0.0  0
 6GF  CONST_56  C18  N04  C10  C11     0.00   0.0  0
 6GF  CONST_57  C12  N04  C10  C11   180.00   0.0  0
 6GF  CONST_58  C18  N04  C10  N03   180.00   0.0  0
 6GF  CONST_59  C12  N04  C10  N03     0.00   0.0  0
 6GF  Var_01    C19  C18  N04  C10    79.38  30.0  3
 6GF  Var_02    C13  C12  N04  C10    78.83  30.0  3
 6GF  Var_03    C03  C02  O01  C01    -0.59  30.0  2
 6GF  Var_04    C23  C19  C18  N04  -144.91  30.0  2
 6GF  Var_05    N05  C13  C12  N04    32.99  30.0  2
 6GF  Var_06    H6   C01  O01  C02  -179.60  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
 6GF  plan-1  C20  0.020
 6GF  plan-1  C21  0.020
 6GF  plan-1  C22  0.020
 6GF  plan-1  C18  0.020
 6GF  plan-1  C19  0.020
 6GF  plan-1  N06  0.020
 6GF  plan-1  C23  0.020
 6GF  plan-1  H3   0.020
 6GF  plan-1  H4   0.020
 6GF  plan-1  H5   0.020
 6GF  plan-1  H18  0.020
 6GF  plan-2  C02  0.020
 6GF  plan-2  C07  0.020
 6GF  plan-2  C06  0.020
 6GF  plan-2  C03  0.020
 6GF  plan-2  C04  0.020
 6GF  plan-2  C05  0.020
 6GF  plan-2  C08  0.020
 6GF  plan-2  H9   0.020
 6GF  plan-2  H10  0.020
 6GF  plan-2  H11  0.020
 6GF  plan-2  H12  0.020
 6GF  plan-2  O01  0.020
 6GF  plan-3  C10  0.020
 6GF  plan-3  C05  0.020
 6GF  plan-3  C08  0.020
 6GF  plan-3  C11  0.020
 6GF  plan-3  N01  0.020
 6GF  plan-3  C09  0.020
 6GF  plan-3  N02  0.020
 6GF  plan-3  N03  0.020
 6GF  plan-3  N04  0.020
 6GF  plan-3  H13  0.020
 6GF  plan-4  C13  0.020
 6GF  plan-4  C15  0.020
 6GF  plan-4  C17  0.020
 6GF  plan-4  C12  0.020
 6GF  plan-4  N05  0.020
 6GF  plan-4  C16  0.020
 6GF  plan-4  C14  0.020
 6GF  plan-4  H1   0.020
 6GF  plan-4  H2   0.020
 6GF  plan-4  H21  0.020
 6GF  plan-4  H22  0.020
 6GF  plan-5  C09  0.020
 6GF  plan-5  N02  0.020
 6GF  plan-5  H14  0.020
 6GF  plan-5  H15  0.020
 6GF  plan-6  C10  0.020
 6GF  plan-6  N04  0.020
 6GF  plan-6  C18  0.020
 6GF  plan-6  C12  0.020

