# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 05:11:00 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]-N~4~-[5-(2-phenylethyl)-1H-pyrazol-3-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CNc2nccc(Nc3cc(CCc4ccccc4)[nH]n3)n2)on1
#
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
 2M2  2M2  N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]-N~4~-[5-(2-phenylethyl)-1H-pyrazol-3-yl]pyrimidine-2,4-diamine  ligand  49  28  .  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_2M2
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
 2M2  C1   C  CH3   0  -0.733   4.0155   5.9702  -0.4182
 2M2  C2   C  CR5   0   0.260   4.0357   4.5349  -0.0317
 2M2  C3   C  CR15  0  -0.517   3.8004   3.9731   1.2520
 2M2  C4   C  CR5   0   0.447   3.9365   2.6425   1.0544
 2M2  C5   C  CH2   0  -0.398   3.8150   1.4699   1.9710
 2M2  N6   N  NH1   0  -0.655   2.8489   0.5028   1.5292
 2M2  C7   C  CR6   0   0.614   3.1390  -0.5650   0.7499
 2M2  N8   N  N     0  -0.494   4.4154  -0.8255   0.4846
 2M2  C9   C  CR16  0  -0.019   4.6328  -1.9164  -0.2508
 2M2  C10  C  CR16  0  -0.464   3.6383  -2.7323  -0.7251
 2M2  C11  C  CR6   0   0.559   2.3225  -2.3523  -0.3886
 2M2  N12  N  NH1   0  -0.755   1.2838  -3.1059  -0.8209
 2M2  C13  C  CR5   0   0.457  -0.0711  -2.9184  -0.6019
 2M2  C14  C  CR15  0  -0.558  -0.7733  -1.8624   0.0140
 2M2  C15  C  CR5   0   0.438  -2.0984  -2.2337  -0.0834
 2M2  C16  C  CH2   0  -0.515  -3.3364  -1.5201   0.3344
 2M2  C17  C  CH2   0  -0.512  -4.0900  -0.9077  -0.8589
 2M2  C18  C  CR6   0   0.128  -5.2976  -0.1350  -0.4099
 2M2  C19  C  CR16  0  -0.304  -6.4886  -0.7919  -0.1054
 2M2  C20  C  CR16  0  -0.240  -7.5939  -0.0874   0.3515
 2M2  C21  C  CR16  0  -0.273  -7.5253   1.2912   0.5107
 2M2  C22  C  CR16  0  -0.240  -6.3448   1.9569   0.2088
 2M2  C23  C  CR16  0  -0.313  -5.2409   1.2469  -0.2462
 2M2  N24  N  NR15  0  -0.487  -2.1093  -3.4169  -0.7161
 2M2  N26  N  N     0  -0.328  -0.8911  -3.8570  -1.0393
 2M2  N27  N  N     0  -0.524   2.0826  -1.2756   0.3414
 2M2  O28  O  O     0  -0.340   4.2266   2.4141  -0.2282
 2M2  N29  N  N     0  -0.183   4.2836   3.6005  -0.9038
 2M2  H1   H  HCH3  0   0.259   3.0471   6.4143  -0.1883
 2M2  H2   H  HCH3  0   0.259   4.7698   6.5264   0.1384
 2M2  H3   H  HCH3  0   0.257   4.2095   6.0951  -1.4815
 2M2  H4   H  HCR5  0   0.277   3.5595   4.4857   2.1682
 2M2  H5   H  HCH2  0   0.284   4.7829   0.9805   2.0802
 2M2  H6   H  HCH2  0   0.290   3.5277   1.8418   2.9542
 2M2  H7   H  HNH1  0   0.397   1.8735   0.7287   1.6361
 2M2  H8   H  HCR6  0   0.264   5.6699  -2.1446  -0.4722
 2M2  H9   H  HCR6  0   0.272   3.8529  -3.6088  -1.3196
 2M2  H10  H  HNH1  0   0.409   1.5152  -3.9322  -1.3510
 2M2  H11  H  HCR5  0   0.273  -0.3787  -0.9685   0.4591
 2M2  H12  H  HCH2  0   0.264  -4.0016  -2.1990   0.8750
 2M2  H13  H  HCH2  0   0.267  -3.0624  -0.7294   1.0336
 2M2  H14  H  HCH2  0   0.256  -3.4099  -0.2560  -1.4114
 2M2  H15  H  HCH2  0   0.251  -4.3885  -1.7050  -1.5437
 2M2  H16  H  HCR6  0   0.247  -6.5536  -1.8669  -0.2307
 2M2  H17  H  HCR6  0   0.254  -8.5108  -0.6147   0.5823
 2M2  H18  H  HCR6  0   0.254  -8.3873   1.8417   0.8648
 2M2  H19  H  HCR6  0   0.253  -6.2821   3.0314   0.3252
 2M2  H20  H  HCR6  0   0.247  -4.3246   1.7754  -0.4833
 2M2  H21  H  HNR5  0   0.415  -2.9120  -3.9823  -0.9413

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
 2M2  C9   C10  aromatic  1.371  0.020  1.371
 2M2  C9   N8   aromatic  1.334  0.020  1.334
 2M2  C10  C11  aromatic  1.410  0.020  1.410
 2M2  N8   C7   aromatic  1.329  0.020  1.329
 2M2  C11  N12  single    1.354  0.020  1.354
 2M2  C11  N27  aromatic  1.323  0.020  1.323
 2M2  N12  C13  single    1.385  0.020  1.385
 2M2  C7   N27  aromatic  1.337  0.020  1.337
 2M2  C7   N6   single    1.353  0.020  1.353
 2M2  N6   C5   single    1.437  0.020  1.437
 2M2  C13  N26  aromatic  1.321  0.020  1.321
 2M2  C13  C14  aromatic  1.410  0.020  1.410
 2M2  N26  N24  aromatic  1.335  0.020  1.335
 2M2  C5   C4   single    1.493  0.020  1.493
 2M2  C14  C15  aromatic  1.380  0.020  1.380
 2M2  N24  C15  aromatic  1.342  0.020  1.342
 2M2  C15  C16  single    1.489  0.020  1.489
 2M2  C4   C3   aromatic  1.352  0.020  1.352
 2M2  C4   O28  aromatic  1.335  0.020  1.335
 2M2  C3   C2   aromatic  1.421  0.020  1.421
 2M2  C17  C16  single    1.538  0.020  1.538
 2M2  C17  C18  single    1.502  0.020  1.502
 2M2  O28  N29  aromatic  1.366  0.020  1.366
 2M2  C2   N29  aromatic  1.302  0.020  1.302
 2M2  C2   C1   single    1.487  0.020  1.487
 2M2  C19  C18  aromatic  1.394  0.020  1.394
 2M2  C19  C20  aromatic  1.388  0.020  1.388
 2M2  C18  C23  aromatic  1.393  0.020  1.393
 2M2  C20  C21  aromatic  1.389  0.020  1.389
 2M2  C23  C22  aromatic  1.389  0.020  1.389
 2M2  C21  C22  aromatic  1.388  0.020  1.388
 2M2  C1   H1   single    0.970  0.020  1.090
 2M2  C1   H2   single    0.970  0.020  1.090
 2M2  C1   H3   single    0.970  0.020  1.090
 2M2  C3   H4   single    0.930  0.020  1.080
 2M2  C5   H5   single    0.970  0.020  1.090
 2M2  C5   H6   single    0.970  0.020  1.090
 2M2  N6   H7   single    0.860  0.020  1.020
 2M2  C9   H8   single    0.930  0.020  1.080
 2M2  C10  H9   single    0.930  0.020  1.080
 2M2  N12  H10  single    0.860  0.020  1.020
 2M2  C14  H11  single    0.930  0.020  1.080
 2M2  C16  H12  single    0.970  0.020  1.090
 2M2  C16  H13  single    0.970  0.020  1.090
 2M2  C17  H14  single    0.970  0.020  1.090
 2M2  C17  H15  single    0.970  0.020  1.090
 2M2  C19  H16  single    0.930  0.020  1.080
 2M2  C20  H17  single    0.930  0.020  1.080
 2M2  C21  H18  single    0.930  0.020  1.080
 2M2  C22  H19  single    0.930  0.020  1.080
 2M2  C23  H20  single    0.930  0.020  1.080
 2M2  N24  H21  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
 2M2  H3   C1   H2   108.49  3.000
 2M2  H3   C1   H1   108.53  3.000
 2M2  H2   C1   H1   107.41  3.000
 2M2  H3   C1   C2   111.25  3.000
 2M2  H2   C1   C2   110.52  3.000
 2M2  H1   C1   C2   110.53  3.000
 2M2  N29  C2   C3   110.67  3.000
 2M2  N29  C2   C1   121.43  3.000
 2M2  C3   C2   C1   127.91  3.000
 2M2  H4   C3   C4   127.97  3.000
 2M2  H4   C3   C2   128.12  3.000
 2M2  C4   C3   C2   103.91  3.000
 2M2  O28  C4   C5   118.24  3.000
 2M2  O28  C4   C3   109.32  3.000
 2M2  C5   C4   C3   132.44  3.000
 2M2  H6   C5   H5   107.27  3.000
 2M2  H6   C5   N6   109.26  3.000
 2M2  H5   C5   N6   109.00  3.000
 2M2  H6   C5   C4   107.90  3.000
 2M2  H5   C5   C4   109.99  3.000
 2M2  N6   C5   C4   113.24  3.000
 2M2  H7   N6   C7   116.47  3.000
 2M2  H7   N6   C5   117.89  3.000
 2M2  C7   N6   C5   124.34  3.000
 2M2  N27  C7   N8   126.40  3.000
 2M2  N27  C7   N6   115.21  3.000
 2M2  N8   C7   N6   118.38  3.000
 2M2  C9   N8   C7   115.27  3.000
 2M2  H8   C9   C10  119.85  3.000
 2M2  H8   C9   N8   116.14  3.000
 2M2  C10  C9   N8   124.01  3.000
 2M2  H9   C10  C11  122.35  3.000
 2M2  H9   C10  C9   121.94  3.000
 2M2  C11  C10  C9   115.71  3.000
 2M2  N27  C11  N12  119.35  3.000
 2M2  N27  C11  C10  121.35  3.000
 2M2  N12  C11  C10  119.30  3.000
 2M2  H10  N12  C13  114.73  3.000
 2M2  H10  N12  C11  116.60  3.000
 2M2  C13  N12  C11  128.64  3.000
 2M2  N26  C13  C14  111.58  3.000
 2M2  C14  C13  N12  131.12  3.000
 2M2  N26  C13  N12  117.30  3.000
 2M2  H11  C14  C15  127.32  3.000
 2M2  H11  C14  C13  128.44  3.000
 2M2  C15  C14  C13  104.24  3.000
 2M2  N24  C15  C16  123.24  3.000
 2M2  C16  C15  C14  130.54  3.000
 2M2  N24  C15  C14  106.17  3.000
 2M2  H13  C16  H12  106.62  3.000
 2M2  H13  C16  C17  109.37  3.000
 2M2  H12  C16  C17  109.43  3.000
 2M2  H13  C16  C15  108.57  3.000
 2M2  H12  C16  C15  110.31  3.000
 2M2  C17  C16  C15  112.36  3.000
 2M2  H15  C17  H14  106.78  3.000
 2M2  H15  C17  C18  110.06  3.000
 2M2  H14  C17  C18  110.17  3.000
 2M2  H15  C17  C16  109.24  3.000
 2M2  H14  C17  C16  108.97  3.000
 2M2  C18  C17  C16  111.51  3.000
 2M2  C23  C18  C19  118.47  3.000
 2M2  C23  C18  C17  120.85  3.000
 2M2  C19  C18  C17  120.65  3.000
 2M2  H16  C19  C20  119.58  3.000
 2M2  H16  C19  C18  119.55  3.000
 2M2  C20  C19  C18  120.87  3.000
 2M2  H17  C20  C21  120.05  3.000
 2M2  H17  C20  C19  119.82  3.000
 2M2  C21  C20  C19  120.13  3.000
 2M2  H18  C21  C22  120.29  3.000
 2M2  H18  C21  C20  120.18  3.000
 2M2  C22  C21  C20  119.52  3.000
 2M2  H19  C22  C23  119.77  3.000
 2M2  H19  C22  C21  120.11  3.000
 2M2  C23  C22  C21  120.12  3.000
 2M2  H20  C23  C22  119.61  3.000
 2M2  H20  C23  C18  119.50  3.000
 2M2  C22  C23  C18  120.89  3.000
 2M2  H21  N24  N26  119.22  3.000
 2M2  H21  N24  C15  127.36  3.000
 2M2  N26  N24  C15  113.42  3.000
 2M2  N24  N26  C13  104.60  3.000
 2M2  C11  N27  C7   117.25  3.000
 2M2  N29  O28  C4   109.61  3.000
 2M2  O28  N29  C2   106.50  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
 2M2  CONST_01  O28  C4   C3   C2      0.00   0.0  0
 2M2  CONST_02  C4   O28  N29  C2      0.00   0.0  0
 2M2  CONST_03  N29  O28  C4   C3      0.00   0.0  0
 2M2  CONST_04  O28  N29  C2   C3      0.00   0.0  0
 2M2  CONST_05  N29  C2   C3   C4      0.00   0.0  0
 2M2  CONST_06  C10  C9   N8   C7      0.00   0.0  0
 2M2  CONST_07  C10  C11  N27  C7      0.00   0.0  0
 2M2  CONST_08  C11  C10  C9   N8      0.00   0.0  0
 2M2  CONST_09  C11  N27  C7   N8      0.00   0.0  0
 2M2  CONST_10  N27  C11  C10  C9      0.00   0.0  0
 2M2  CONST_11  N27  C7   N8   C9      0.00   0.0  0
 2M2  CONST_12  C15  N24  N26  C13     0.00   0.0  0
 2M2  CONST_13  N24  C15  C14  C13     0.00   0.0  0
 2M2  CONST_14  N24  N26  C13  C14     0.00   0.0  0
 2M2  CONST_15  N26  N24  C15  C14     0.00   0.0  0
 2M2  CONST_16  N26  C13  C14  C15     0.00   0.0  0
 2M2  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 2M2  CONST_18  C21  C22  C23  C18     0.00   0.0  0
 2M2  CONST_19  C22  C23  C18  C19     0.00   0.0  0
 2M2  CONST_20  C22  C21  C20  C19     0.00   0.0  0
 2M2  CONST_21  C23  C18  C19  C20     0.00   0.0  0
 2M2  CONST_22  C23  C22  C21  C20     0.00   0.0  0
 2M2  CONST_23  C4   C3   C2   C1    180.00   0.0  0
 2M2  CONST_24  O28  N29  C2   C1    180.00   0.0  0
 2M2  CONST_25  C5   C4   C3   C2    180.00   0.0  0
 2M2  CONST_26  N29  O28  C4   C5    180.00   0.0  0
 2M2  CONST_27  C9   N8   C7   N6    180.00   0.0  0
 2M2  CONST_28  C11  N27  C7   N6    180.00   0.0  0
 2M2  CONST_29  N12  C11  N27  C7    180.00   0.0  0
 2M2  CONST_30  N12  C11  C10  C9    180.00   0.0  0
 2M2  CONST_31  N24  N26  C13  N12   180.00   0.0  0
 2M2  CONST_32  C15  C14  C13  N12   180.00   0.0  0
 2M2  CONST_33  C16  C15  C14  C13   180.00   0.0  0
 2M2  CONST_34  N26  N24  C15  C16   180.00   0.0  0
 2M2  CONST_35  C20  C19  C18  C17   180.00   0.0  0
 2M2  CONST_36  C22  C23  C18  C17   180.00   0.0  0
 2M2  CONST_37  H8   C9   N8   C7    180.00   0.0  0
 2M2  CONST_38  H9   C10  C9   N8    180.00   0.0  0
 2M2  CONST_39  H21  N24  N26  C13   180.00   0.0  0
 2M2  CONST_40  H17  C20  C19  C18   180.00   0.0  0
 2M2  CONST_41  H19  C22  C23  C18   180.00   0.0  0
 2M2  CONST_42  H20  C23  C18  C19   180.00   0.0  0
 2M2  CONST_43  H18  C21  C20  C19   180.00   0.0  0
 2M2  CONST_44  H16  C19  C20  C21   180.00   0.0  0
 2M2  CONST_45  H11  C14  C15  N24   180.00   0.0  0
 2M2  CONST_46  H4   C3   C4   O28   180.00   0.0  0
 2M2  CONST_47  N8   C7   N6   C5      0.00   0.0  0
 2M2  CONST_48  N27  C7   N6   C5    180.00   0.0  0
 2M2  CONST_49  H7   N6   C7   N8    180.00   0.0  0
 2M2  Var_01    C13  N12  C11  C10   179.67  30.0  2
 2M2  Var_02    N26  C13  N12  C11  -174.58  30.0  2
 2M2  Var_03    N6   C5   C4   C3    123.42  30.0  1
 2M2  Var_04    C7   N6   C5   C4     91.97  30.0  2
 2M2  Var_05    C17  C16  C15  C14   104.07  30.0  2
 2M2  Var_06    C18  C17  C16  C15  -177.16  30.0  1
 2M2  Var_07    C19  C18  C17  C16   -80.98  30.0  2
 2M2  Var_08    H1   C1   C2   C3    -57.96  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
 2M2  plan-1  C1   0.020
 2M2  plan-1  C2   0.020
 2M2  plan-1  C3   0.020
 2M2  plan-1  C4   0.020
 2M2  plan-1  C5   0.020
 2M2  plan-1  O28  0.020
 2M2  plan-1  N29  0.020
 2M2  plan-1  H4   0.020
 2M2  plan-2  N12  0.020
 2M2  plan-2  C13  0.020
 2M2  plan-2  C14  0.020
 2M2  plan-2  C15  0.020
 2M2  plan-2  C16  0.020
 2M2  plan-2  N24  0.020
 2M2  plan-2  N26  0.020
 2M2  plan-2  H11  0.020
 2M2  plan-2  H21  0.020
 2M2  plan-3  N6   0.020
 2M2  plan-3  C7   0.020
 2M2  plan-3  N8   0.020
 2M2  plan-3  C9   0.020
 2M2  plan-3  C10  0.020
 2M2  plan-3  C11  0.020
 2M2  plan-3  N12  0.020
 2M2  plan-3  N27  0.020
 2M2  plan-3  H8   0.020
 2M2  plan-3  H9   0.020
 2M2  plan-4  C17  0.020
 2M2  plan-4  C18  0.020
 2M2  plan-4  C19  0.020
 2M2  plan-4  C20  0.020
 2M2  plan-4  C21  0.020
 2M2  plan-4  C22  0.020
 2M2  plan-4  C23  0.020
 2M2  plan-4  H16  0.020
 2M2  plan-4  H17  0.020
 2M2  plan-4  H18  0.020
 2M2  plan-4  H19  0.020
 2M2  plan-4  H20  0.020
 2M2  plan-5  C5   0.020
 2M2  plan-5  N6   0.020
 2M2  plan-5  C7   0.020
 2M2  plan-5  H7   0.020

