# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:13:36 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-(difluoromethyl)-5-{4-[(3S)-3-methylmorpholin-4-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1COCCN1c2nc(nc(n2)c3cnc(N)cc3C(F)F)N4CCOCC4
#
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
 M1J  M1J  4-(difluoromethyl)-5-{4-[(3S)-3-methylmorpholin-4-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}pyridin-2-amine  ligand  52  29  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M1J
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
 M1J  C10   C  CR6   0  -0.086  -2.0315  -1.0278   0.3418
 M1J  N12   N  N     0  -0.534  -0.7033   0.9499   0.0802
 M1J  C13   C  CR6   0   0.660   0.5106   1.4874  -0.1142
 M1J  C15   C  CH2   0  -0.328   1.8400   3.5175  -0.4800
 M1J  C21   C  CR6   0   0.657   1.4972  -0.5387  -0.1283
 M1J  C24   C  CH2   0  -0.188   4.9932  -1.4213   0.2675
 M1J  C26   C  CH2   0  -0.179   3.7057  -3.3177   0.5731
 M1J  C02   C  CR6   0   0.501  -4.3255  -2.4154   0.9685
 M1J  C03   C  CR16  0  -0.440  -4.4253  -1.1890   0.2781
 M1J  C04   C  CR6   0   0.017  -3.2826  -0.4949  -0.0335
 M1J  C05   C  CH1   0   0.533  -3.3926   0.7845  -0.8217
 M1J  C09   C  CR16  0  -0.072  -2.0555  -2.2556   0.9926
 M1J  C11   C  CR6   0   0.358  -0.7299  -0.3716   0.1286
 M1J  C16   C  CH2   0  -0.184   2.0186   4.6824   0.4773
 M1J  C18   C  CH2   0  -0.181  -0.2761   4.8658   0.8020
 M1J  C19   C  CH2   0  -0.331  -0.5550   3.7043  -0.1367
 M1J  C23   C  CH2   0  -0.326   3.9016  -0.7343  -0.5302
 M1J  C27   C  CH1   0  -0.136   2.5316  -2.7567  -0.2194
 M1J  F06   F  F     0  -0.341  -2.7174   0.6466  -1.9966
 M1J  F07   F  F     0  -0.336  -4.6881   1.0321  -1.1569
 M1J  N01   N  NH2   0  -0.831  -5.4303  -3.0959   1.3223
 M1J  N08   N  N     0  -0.456  -3.1458  -2.9353   1.3066
 M1J  N14   N  NT    0  -0.508   0.5991   2.8281  -0.1839
 M1J  N20   N  N     0  -0.541   1.6321   0.7812  -0.2327
 M1J  N22   N  NT    0  -0.506   2.6077  -1.2986  -0.1901
 M1J  N29   N  N     0  -0.512   0.3239  -1.1670   0.0324
 M1J  O17   O  O2    0  -0.483   0.9072   5.5502   0.4560
 M1J  O25   O  O2    0  -0.480   4.9442  -2.8221   0.1205
 M1J  H151  H  HCH2  0   0.240   1.8175   3.8833  -1.5132
 M1J  H152  H  HCH2  0   0.281   2.6770   2.8312  -0.3869
 M1J  H242  H  HCH2  0   0.244   5.9698  -1.0848  -0.0821
 M1J  H241  H  HCH2  0   0.207   4.8983  -1.1451   1.3272
 M1J  H261  H  HCH2  0   0.217   3.5671  -3.0808   1.6377
 M1J  H262  H  HCH2  0   0.240   3.7288  -4.4041   0.4729
 M1J  H031  H  HCR6  0   0.282  -5.4039  -0.8220   0.0040
 M1J  H051  H  HCH1  0   0.215  -3.0091   1.6518  -0.2925
 M1J  H091  H  HCR6  0   0.270  -1.1156  -2.7086   1.2863
 M1J  H162  H  HCH2  0   0.207   2.1871   4.2958   1.4924
 M1J  H161  H  HCH2  0   0.243   2.8956   5.2638   0.1898
 M1J  H181  H  HCH2  0   0.244  -1.0968   5.5820   0.7516
 M1J  H182  H  HCH2  0   0.208  -0.2159   4.4890   1.8328
 M1J  H192  H  HCH2  0   0.282  -1.4247   3.1584   0.2169
 M1J  H191  H  HCH2  0   0.239  -0.7766   4.0779  -1.1430
 M1J  H232  H  HCH2  0   0.279   3.9049   0.3294  -0.3074
 M1J  H231  H  HCH2  0   0.238   4.0929  -0.8433  -1.6039
 M1J  H271  H  HCH1  0   0.277   1.6222  -3.0545   0.2993
 M1J  H011  H  HNH2  0   0.405  -6.3318  -2.8327   0.9656
 M1J  H012  H  HNH2  0   0.396  -5.3362  -4.0261   1.6924
 M1J  C28   C  CH3   0  -0.660   2.4688  -3.2852  -1.6490
 M1J  H281  H  HCH3  0   0.234   2.3521  -4.3696  -1.6453
 M1J  H282  H  HCH3  0   0.236   1.6122  -2.8612  -2.1737
 M1J  H283  H  HCH3  0   0.228   3.3678  -3.0494  -2.2188

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
 M1J  N01  C02   single    1.345  0.020  1.345
 M1J  N08  C02   aromatic  1.333  0.020  1.333
 M1J  N08  C09   aromatic  1.323  0.020  1.323
 M1J  C02  C03   aromatic  1.411  0.020  1.411
 M1J  C09  C10   aromatic  1.390  0.020  1.390
 M1J  C03  C04   aromatic  1.373  0.020  1.373
 M1J  C10  C04   aromatic  1.411  0.020  1.411
 M1J  C10  C11   single    1.473  0.020  1.473
 M1J  C04  C05   single    1.507  0.020  1.507
 M1J  C11  N12   aromatic  1.323  0.020  1.323
 M1J  C11  N29   aromatic  1.324  0.020  1.324
 M1J  F06  C05   single    1.362  0.020  1.362
 M1J  N12  C13   aromatic  1.342  0.020  1.342
 M1J  N29  C21   aromatic  1.341  0.020  1.341
 M1J  C19  C18   single    1.519  0.020  1.519
 M1J  C19  N14   single    1.450  0.020  1.450
 M1J  C05  F07   single    1.361  0.020  1.361
 M1J  C18  O17   single    1.410  0.020  1.410
 M1J  C13  N20   aromatic  1.331  0.020  1.331
 M1J  C13  N14   single    1.345  0.020  1.345
 M1J  C21  N20   aromatic  1.331  0.020  1.331
 M1J  C21  N22   single    1.347  0.020  1.347
 M1J  C23  C24   single    1.517  0.020  1.517
 M1J  C23  N22   single    1.452  0.020  1.452
 M1J  N14  C15   single    1.450  0.020  1.450
 M1J  C24  O25   single    1.409  0.020  1.409
 M1J  N22  C27   single    1.460  0.020  1.460
 M1J  O17  C16   single    1.410  0.020  1.410
 M1J  C16  C15   single    1.518  0.020  1.518
 M1J  C27  C26   single    1.524  0.020  1.524
 M1J  C27  C28   single    1.525  0.020  1.525
 M1J  O25  C26   single    1.409  0.020  1.409
 M1J  C15  H151  single    0.970  0.020  1.090
 M1J  C15  H152  single    0.970  0.020  1.090
 M1J  C24  H242  single    0.970  0.020  1.090
 M1J  C24  H241  single    0.970  0.020  1.090
 M1J  C26  H261  single    0.970  0.020  1.090
 M1J  C26  H262  single    0.970  0.020  1.090
 M1J  C28  H281  single    0.970  0.020  1.090
 M1J  C28  H282  single    0.970  0.020  1.090
 M1J  C28  H283  single    0.970  0.020  1.090
 M1J  C03  H031  single    0.930  0.020  1.080
 M1J  C05  H051  single    0.970  0.020  1.090
 M1J  C09  H091  single    0.930  0.020  1.080
 M1J  C16  H162  single    0.970  0.020  1.090
 M1J  C16  H161  single    0.970  0.020  1.090
 M1J  C18  H181  single    0.970  0.020  1.090
 M1J  C18  H182  single    0.970  0.020  1.090
 M1J  C19  H192  single    0.970  0.020  1.090
 M1J  C19  H191  single    0.970  0.020  1.090
 M1J  C23  H232  single    0.970  0.020  1.090
 M1J  C23  H231  single    0.970  0.020  1.090
 M1J  C27  H271  single    0.970  0.020  1.090
 M1J  N01  H011  single    0.860  0.020  1.020
 M1J  N01  H012  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
 M1J  C11   C10  C09   118.46  3.000
 M1J  C11   C10  C04   125.23  3.000
 M1J  C09   C10  C04   116.29  3.000
 M1J  C11   N12  C13   115.07  3.000
 M1J  N20   C13  N14   117.95  3.000
 M1J  N14   C13  N12   117.79  3.000
 M1J  N20   C13  N12   124.26  3.000
 M1J  H152  C15  H151  107.90  3.000
 M1J  H152  C15  N14   109.97  3.000
 M1J  H151  C15  N14   109.48  3.000
 M1J  H152  C15  C16   109.88  3.000
 M1J  H151  C15  C16   109.91  3.000
 M1J  N14   C15  C16   109.67  3.000
 M1J  N29   C21  N22   117.56  3.000
 M1J  N22   C21  N20   118.18  3.000
 M1J  N29   C21  N20   124.26  3.000
 M1J  H241  C24  H242  107.99  3.000
 M1J  H241  C24  O25   110.33  3.000
 M1J  H242  C24  O25   107.72  3.000
 M1J  H241  C24  C23   109.33  3.000
 M1J  H242  C24  C23   109.64  3.000
 M1J  O25   C24  C23   111.74  3.000
 M1J  H262  C26  H261  107.82  3.000
 M1J  H262  C26  O25   107.58  3.000
 M1J  H261  C26  O25   110.25  3.000
 M1J  H262  C26  C27   109.58  3.000
 M1J  H261  C26  C27   109.10  3.000
 M1J  O25   C26  C27   112.39  3.000
 M1J  N08   C02  N01   117.58  3.000
 M1J  N08   C02  C03   121.72  3.000
 M1J  N01   C02  C03   120.69  3.000
 M1J  H031  C03  C04   121.64  3.000
 M1J  H031  C03  C02   118.91  3.000
 M1J  C04   C03  C02   119.45  3.000
 M1J  C05   C04  C03   119.16  3.000
 M1J  C05   C04  C10   121.64  3.000
 M1J  C03   C04  C10   119.13  3.000
 M1J  H051  C05  F07   108.11  3.000
 M1J  H051  C05  F06   109.03  3.000
 M1J  F07   C05  F06   106.13  3.000
 M1J  H051  C05  C04   113.42  3.000
 M1J  F07   C05  C04   110.66  3.000
 M1J  F06   C05  C04   109.21  3.000
 M1J  H091  C09  N08   115.83  3.000
 M1J  H091  C09  C10   118.76  3.000
 M1J  N08   C09  C10   125.40  3.000
 M1J  N29   C11  N12   125.57  3.000
 M1J  N29   C11  C10   116.50  3.000
 M1J  N12   C11  C10   117.91  3.000
 M1J  H161  C16  H162  107.92  3.000
 M1J  H161  C16  O17   107.56  3.000
 M1J  H162  C16  O17   110.56  3.000
 M1J  H161  C16  C15   109.71  3.000
 M1J  H162  C16  C15   109.30  3.000
 M1J  O17   C16  C15   111.71  3.000
 M1J  H182  C18  H181  108.04  3.000
 M1J  H182  C18  O17   110.52  3.000
 M1J  H181  C18  O17   107.55  3.000
 M1J  H182  C18  C19   109.11  3.000
 M1J  H181  C18  C19   109.59  3.000
 M1J  O17   C18  C19   111.93  3.000
 M1J  H191  C19  H192  107.96  3.000
 M1J  H191  C19  N14   109.69  3.000
 M1J  H192  C19  N14   110.14  3.000
 M1J  H191  C19  C18   110.11  3.000
 M1J  H192  C19  C18   109.28  3.000
 M1J  N14   C19  C18   109.63  3.000
 M1J  H231  C23  H232  107.32  3.000
 M1J  H231  C23  N22   110.26  3.000
 M1J  H232  C23  N22   109.58  3.000
 M1J  H231  C23  C24   110.16  3.000
 M1J  H232  C23  C24   109.47  3.000
 M1J  N22   C23  C24   110.01  3.000
 M1J  H271  C27  N22   107.89  3.000
 M1J  H271  C27  C28   108.51  3.000
 M1J  N22   C27  C28   111.52  3.000
 M1J  H271  C27  C26   107.17  3.000
 M1J  C28   C27  C26   113.05  3.000
 M1J  N22   C27  C26   108.48  3.000
 M1J  H012  N01  H011  117.19  3.000
 M1J  H012  N01  C02   119.21  3.000
 M1J  H011  N01  C02   120.74  3.000
 M1J  C09   N08  C02   117.97  3.000
 M1J  C19   N14  C15   113.62  3.000
 M1J  C15   N14  C13   122.72  3.000
 M1J  C19   N14  C13   123.24  3.000
 M1J  C21   N20  C13   115.71  3.000
 M1J  C27   N22  C23   115.46  3.000
 M1J  C27   N22  C21   121.41  3.000
 M1J  C23   N22  C21   121.74  3.000
 M1J  C11   N29  C21   115.07  3.000
 M1J  C18   O17  C16   111.04  3.000
 M1J  C26   O25  C24   110.28  3.000
 M1J  H283  C28  H282  108.19  3.000
 M1J  H283  C28  H281  107.76  3.000
 M1J  H282  C28  H281  107.71  3.000
 M1J  H283  C28  C27   112.39  3.000
 M1J  H282  C28  C27   110.40  3.000
 M1J  H281  C28  C27   110.23  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
 M1J  CONST_01  C02   N08  C09  C10     0.00   0.0  0
 M1J  CONST_02  C02   C03  C04  C10     0.00   0.0  0
 M1J  CONST_03  C13   N12  C11  C10   180.00   0.0  0
 M1J  CONST_04  C21   N29  C11  C10   180.00   0.0  0
 M1J  CONST_07  C21   N29  C11  N12     0.00   0.0  0
 M1J  CONST_08  C21   N20  C13  N12     0.00   0.0  0
 M1J  CONST_09  N29   C11  N12  C13     0.00   0.0  0
 M1J  CONST_10  N29   C21  N20  C13     0.00   0.0  0
 M1J  CONST_11  C09   N08  C02  C03     0.00   0.0  0
 M1J  CONST_12  C09   C10  C04  C03     0.00   0.0  0
 M1J  CONST_13  C11   C10  C04  C03   180.00   0.0  0
 M1J  CONST_14  N08   C02  C03  C04     0.00   0.0  0
 M1J  CONST_15  N08   C09  C10  C04     0.00   0.0  0
 M1J  CONST_18  N08   C09  C10  C11   180.00   0.0  0
 M1J  CONST_19  N20   C13  N12  C11     0.00   0.0  0
 M1J  CONST_20  N20   C21  N29  C11     0.00   0.0  0
 M1J  CONST_21  N22   C21  N20  C13   180.00   0.0  0
 M1J  CONST_22  N14   C13  N20  C21   180.00   0.0  0
 M1J  CONST_23  N14   C13  N12  C11   180.00   0.0  0
 M1J  CONST_24  N22   C21  N29  C11   180.00   0.0  0
 M1J  CONST_25  C05   C04  C03  C02   180.00   0.0  0
 M1J  CONST_26  N01   C02  C03  C04   180.00   0.0  0
 M1J  CONST_27  C09   C10  C04  C05   180.00   0.0  0
 M1J  CONST_28  C11   C10  C04  C05     0.00   0.0  0
 M1J  CONST_29  N01   C02  N08  C09   180.00   0.0  0
 M1J  CONST_30  H031  C03  C04  C10   180.00   0.0  0
 M1J  CONST_31  H091  C09  N08  C02   180.00   0.0  0
 M1J  CONST_32  H011  N01  C02  C03     0.00   0.0  0
 M1J  CONST_33  H012  N01  C02  C03   180.00   0.0  0
 M1J  Var_01    C19   N14  C13  N12    -3.66  30.0  2
 M1J  Var_02    C18   C19  N14  C13   135.07  30.0  1
 M1J  Var_03    C16   C15  N14  C13  -134.74  30.0  1
 M1J  Var_04    C24   C23  N22  C21   143.80  30.0  1
 M1J  Var_05    C27   C26  O25  C24    61.27  30.0  1
 M1J  Var_06    C23   C24  O25  C26   -60.21  30.0  1
 M1J  Var_07    C19   C18  O17  C16   -58.65  30.0  1
 M1J  Var_08    N29   C21  N22  C23   172.08  30.0  2
 M1J  Var_09    O17   C18  C19  N14    54.43  30.0  1
 M1J  Var_10    O17   C16  C15  N14   -54.88  30.0  1
 M1J  Var_11    O25   C24  C23  N22    53.47  30.0  1
 M1J  Var_12    H162  C16  O17  C18   -63.15  30.0  1
 M1J  Var_13    F06   C05  C04  C10    58.41  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M1J  chir_01  C27  N22  C26  C28  positiv

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
 M1J  plan-1  C10   0.020
 M1J  plan-1  N12   0.020
 M1J  plan-1  C13   0.020
 M1J  plan-1  C21   0.020
 M1J  plan-1  C11   0.020
 M1J  plan-1  N14   0.020
 M1J  plan-1  N20   0.020
 M1J  plan-1  N22   0.020
 M1J  plan-1  N29   0.020
 M1J  plan-2  C02   0.020
 M1J  plan-2  N01   0.020
 M1J  plan-2  H011  0.020
 M1J  plan-2  H012  0.020
 M1J  plan-3  C10   0.020
 M1J  plan-3  C02   0.020
 M1J  plan-3  C03   0.020
 M1J  plan-3  C04   0.020
 M1J  plan-3  C05   0.020
 M1J  plan-3  C09   0.020
 M1J  plan-3  C11   0.020
 M1J  plan-3  N01   0.020
 M1J  plan-3  N08   0.020
 M1J  plan-3  H031  0.020
 M1J  plan-3  H091  0.020

