# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:21:53 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: methyl 6-[(5-cyanopyrazin-2-yl)amino]-4-[[(2~{R})-morpholin-2-yl]methylamino]pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cnc(Nc2cnc(cn2)C#N)cc1NC[C@H]3CNCCO3
#
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
 5UY  5UY  'methyl 6-[(5-cyanopyrazin-2-yl)amino]-4-[[(2~{R})-morpholin-2-yl]methylamino]pyridine-3-carboxylate'  ligand  46  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5UY
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
 5UY  C1   C  CR16  0  -0.069  -0.7113   2.0780   0.2444
 5UY  O1   O  O     0  -0.477   2.8418   2.7073   0.0593
 5UY  C2   C  CR6   0   0.538  -1.3077  -0.0933   0.3260
 5UY  O2   O  O2    0  -0.460   1.0969   4.0871   0.1194
 5UY  C3   C  CR16  0  -0.526   0.0089  -0.5202   0.2849
 5UY  C4   C  CR6   0   0.518   1.0449   0.4255   0.2337
 5UY  C5   C  CH2   0  -0.285   2.7743  -1.3219   0.1469
 5UY  C6   C  CH1   0   0.004   4.2762  -1.3939   0.3337
 5UY  C7   C  CH2   0  -0.187   6.2848  -0.5592  -0.5476
 5UY  C8   C  CH2   0  -0.333   6.8436  -1.9658  -0.6857
 5UY  N1   N  NH1   0  -0.701   2.3278   0.0483   0.2154
 5UY  C9   C  CH2   0  -0.312   4.7970  -2.8239   0.2216
 5UY  C13  C  CR16  0  -0.165  -4.4320  -2.0880   0.5719
 5UY  C10  C  CR6   0   0.500  -3.6194  -0.9969   0.1646
 5UY  C11  C  CR16  0  -0.042  -5.4487   0.0062  -0.7064
 5UY  C12  C  CR6   0   0.123  -6.2388  -1.0549  -0.2972
 5UY  C14  C  CSP   0   0.059  -7.6449  -1.0630  -0.5446
 5UY  C16  C  CH3   0  -0.421   1.9768   5.2079   0.0388
 5UY  N2   N  NH1   0  -0.589   6.2484  -2.8970   0.2621
 5UY  C    C  CR6   0  -0.284   0.6510   1.7985   0.2014
 5UY  O    O  O2    0  -0.497   4.8736  -0.5714  -0.6504
 5UY  N    N  N     0  -0.448  -1.6804   1.1843   0.3128
 5UY  N3   N  NH1   0  -0.759  -2.2891  -1.0679   0.4294
 5UY  N5   N  N     0  -0.346  -5.7139  -2.1093   0.3414
 5UY  N4   N  N     0  -0.383  -4.1454   0.0320  -0.4804
 5UY  N6   N  NS    0  -0.243  -8.7786  -1.0561  -0.7489
 5UY  H1   H  HCR6  0   0.272  -1.0406   3.1100   0.2304
 5UY  H2   H  HCR6  0   0.293   0.2241  -1.5797   0.2824
 5UY  H3   H  HCH2  0   0.241   2.4928  -1.7808  -0.8090
 5UY  H4   H  HCH2  0   0.249   2.3077  -1.9143   0.9384
 5UY  H5   H  HCH1  0   0.216   4.5295  -1.0078   1.3357
 5UY  H6   H  HCH2  0   0.200   6.5921  -0.1335   0.4194
 5UY  H7   H  HCH2  0   0.235   6.6594   0.0960  -1.3363
 5UY  H8   H  HCH2  0   0.227   6.6559  -2.3337  -1.6996
 5UY  H9   H  HCH2  0   0.241   7.9262  -1.9506  -0.5452
 5UY  H10  H  HNH1  0   0.409   3.0111   0.7777   0.0695
 5UY  H11  H  HCH2  0   0.246   4.3843  -3.4336   1.0282
 5UY  H12  H  HCH2  0   0.225   4.4529  -3.2592  -0.7238
 5UY  H13  H  HCR6  0   0.298  -3.9968  -2.9368   1.0881
 5UY  H14  H  HCR6  0   0.296  -5.8779   0.8488  -1.2355
 5UY  H15  H  HCH3  0   0.240   2.6508   5.2477   0.8941
 5UY  H16  H  HCH3  0   0.240   2.5613   5.1913  -0.8806
 5UY  H17  H  HCH3  0   0.253   1.3379   6.0858   0.0433
 5UY  H18  H  HNH1  0   0.345   6.5669  -2.6664   1.1967
 5UY  H20  H  HNH1  0   0.430  -1.9616  -1.9727   0.7330
 5UY  C15  C  C     0   0.627   1.6393   2.8790   0.1208

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
 5UY  C16  O2   single    1.427  0.020  1.427
 5UY  O2   C15  single    1.324  0.020  1.324
 5UY  C1   N    aromatic  1.320  0.020  1.320
 5UY  C1   C    aromatic  1.391  0.020  1.391
 5UY  C15  C    single    1.467  0.020  1.467
 5UY  C15  O1   double    1.216  0.020  1.216
 5UY  N    C2   aromatic  1.331  0.020  1.331
 5UY  C    C4   aromatic  1.429  0.020  1.429
 5UY  C2   N3   single    1.387  0.020  1.387
 5UY  C2   C3   aromatic  1.385  0.020  1.385
 5UY  C4   C3   aromatic  1.404  0.020  1.404
 5UY  C4   N1   single    1.337  0.020  1.337
 5UY  N3   C10  single    1.358  0.020  1.358
 5UY  N1   C5   single    1.443  0.020  1.443
 5UY  C10  C13  aromatic  1.420  0.020  1.420
 5UY  C10  N4   aromatic  1.323  0.020  1.323
 5UY  C5   C6   single    1.515  0.020  1.515
 5UY  C13  N5   aromatic  1.303  0.020  1.303
 5UY  N4   C11  aromatic  1.323  0.020  1.323
 5UY  N5   C12  aromatic  1.340  0.020  1.340
 5UY  C11  C12  aromatic  1.385  0.020  1.385
 5UY  C12  C14  single    1.428  0.020  1.428
 5UY  C6   O    single    1.415  0.020  1.415
 5UY  C6   C9   single    1.526  0.020  1.526
 5UY  O    C7   single    1.415  0.020  1.415
 5UY  C9   N2   single    1.454  0.020  1.454
 5UY  C14  N6   triple    1.152  0.020  1.152
 5UY  C7   C8   single    1.520  0.020  1.520
 5UY  N2   C8   single    1.456  0.020  1.456
 5UY  C1   H1   single    0.930  0.020  1.080
 5UY  C3   H2   single    0.930  0.020  1.080
 5UY  C5   H3   single    0.970  0.020  1.090
 5UY  C5   H4   single    0.970  0.020  1.090
 5UY  C6   H5   single    0.970  0.020  1.090
 5UY  C7   H6   single    0.970  0.020  1.090
 5UY  C7   H7   single    0.970  0.020  1.090
 5UY  C8   H8   single    0.970  0.020  1.090
 5UY  C8   H9   single    0.970  0.020  1.090
 5UY  N1   H10  single    0.860  0.020  1.020
 5UY  C9   H11  single    0.970  0.020  1.090
 5UY  C9   H12  single    0.970  0.020  1.090
 5UY  C13  H13  single    0.930  0.020  1.080
 5UY  C11  H14  single    0.930  0.020  1.080
 5UY  C16  H15  single    0.970  0.020  1.090
 5UY  C16  H16  single    0.970  0.020  1.090
 5UY  C16  H17  single    0.970  0.020  1.090
 5UY  N2   H18  single    0.890  0.020  1.040
 5UY  N3   H20  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
 5UY  H1   C1   N    114.99  3.000
 5UY  H1   C1   C    119.25  3.000
 5UY  N    C1   C    125.75  3.000
 5UY  N3   C2   N    118.50  3.000
 5UY  N3   C2   C3   117.28  3.000
 5UY  N    C2   C3   124.19  3.000
 5UY  C16  O2   C15  117.64  3.000
 5UY  H2   C3   C4   120.88  3.000
 5UY  H2   C3   C2   119.44  3.000
 5UY  C4   C3   C2   119.68  3.000
 5UY  C    C4   N1   122.36  3.000
 5UY  N1   C4   C3   121.23  3.000
 5UY  C    C4   C3   116.41  3.000
 5UY  H4   C5   H3   107.13  3.000
 5UY  H4   C5   N1   110.38  3.000
 5UY  H3   C5   N1   111.05  3.000
 5UY  H4   C5   C6   107.94  3.000
 5UY  H3   C5   C6   109.99  3.000
 5UY  N1   C5   C6   110.25  3.000
 5UY  H5   C6   O    109.35  3.000
 5UY  H5   C6   C9   108.44  3.000
 5UY  O    C6   C9   110.46  3.000
 5UY  H5   C6   C5   108.84  3.000
 5UY  C9   C6   C5   111.95  3.000
 5UY  O    C6   C5   107.77  3.000
 5UY  H7   C7   H6   107.87  3.000
 5UY  H7   C7   O    107.15  3.000
 5UY  H6   C7   O    110.23  3.000
 5UY  H7   C7   C8   111.32  3.000
 5UY  H6   C7   C8   109.59  3.000
 5UY  O    C7   C8   110.62  3.000
 5UY  H9   C8   H8   107.10  3.000
 5UY  H9   C8   N2   109.30  3.000
 5UY  H8   C8   N2   108.53  3.000
 5UY  H9   C8   C7   109.88  3.000
 5UY  H8   C8   C7   109.40  3.000
 5UY  N2   C8   C7   112.48  3.000
 5UY  H10  N1   C5   118.00  3.000
 5UY  H10  N1   C4   116.58  3.000
 5UY  C5   N1   C4   124.43  3.000
 5UY  H12  C9   H11  107.26  3.000
 5UY  H12  C9   N2   108.51  3.000
 5UY  H11  C9   N2   109.18  3.000
 5UY  H12  C9   C6   109.17  3.000
 5UY  H11  C9   C6   109.87  3.000
 5UY  N2   C9   C6   112.69  3.000
 5UY  H13  C13  N5   117.80  3.000
 5UY  H13  C13  C10  120.54  3.000
 5UY  N5   C13  C10  121.66  3.000
 5UY  N4   C10  N3   121.67  3.000
 5UY  N4   C10  C13  120.64  3.000
 5UY  N3   C10  C13  117.67  3.000
 5UY  H14  C11  N4   117.28  3.000
 5UY  H14  C11  C12  120.95  3.000
 5UY  N4   C11  C12  121.77  3.000
 5UY  N5   C12  C14  117.64  3.000
 5UY  C14  C12  C11  121.00  3.000
 5UY  N5   C12  C11  121.36  3.000
 5UY  N6   C14  C12  180.00  3.000
 5UY  H17  C16  H16  109.36  3.000
 5UY  H17  C16  H15  109.34  3.000
 5UY  H16  C16  H15  109.33  3.000
 5UY  H17  C16  O2   105.78  3.000
 5UY  H16  C16  O2   111.49  3.000
 5UY  H15  C16  O2   111.45  3.000
 5UY  H18  N2   C9   109.13  3.000
 5UY  H18  N2   C8   109.04  3.000
 5UY  C9   N2   C8   110.97  3.000
 5UY  C15  C    C4   121.57  3.000
 5UY  C4   C    C1   117.54  3.000
 5UY  C15  C    C1   120.89  3.000
 5UY  C7   O    C6   112.06  3.000
 5UY  C2   N    C1   116.42  3.000
 5UY  H20  N3   C10  115.05  3.000
 5UY  H20  N3   C2   115.02  3.000
 5UY  C10  N3   C2   129.92  3.000
 5UY  C12  N5   C13  117.19  3.000
 5UY  C11  N4   C10  117.36  3.000
 5UY  C    C15  O2   113.34  3.000
 5UY  C    C15  O1   124.40  3.000
 5UY  O2   C15  O1   122.26  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
 5UY  CONST_01  C3   C2   N    C1      0.00   0.0  0
 5UY  CONST_02  C3   C4   C    C1      0.00   0.0  0
 5UY  CONST_03  C    C1   N    C2      0.00   0.0  0
 5UY  CONST_04  C    C4   C3   C2      0.00   0.0  0
 5UY  CONST_05  N    C1   C    C4      0.00   0.0  0
 5UY  CONST_06  N    C2   C3   C4      0.00   0.0  0
 5UY  CONST_07  C11  N4   C10  C13     0.00   0.0  0
 5UY  CONST_08  C11  C12  N5   C13     0.00   0.0  0
 5UY  CONST_09  C12  N5   C13  C10     0.00   0.0  0
 5UY  CONST_10  C12  C11  N4   C10     0.00   0.0  0
 5UY  CONST_11  N4   C10  C13  N5      0.00   0.0  0
 5UY  CONST_12  N4   C11  C12  N5      0.00   0.0  0
 5UY  CONST_13  N3   C2   N    C1    180.00   0.0  0
 5UY  CONST_14  N1   C4   C    C1    180.00   0.0  0
 5UY  CONST_15  N1   C4   C3   C2    180.00   0.0  0
 5UY  CONST_16  C15  C    C4   C3    180.00   0.0  0
 5UY  CONST_17  N3   C2   C3   C4    180.00   0.0  0
 5UY  CONST_18  C14  C12  N5   C13   180.00   0.0  0
 5UY  CONST_19  N3   C10  N4   C11   180.00   0.0  0
 5UY  CONST_20  N4   C11  C12  C14   180.00   0.0  0
 5UY  CONST_21  N    C1   C    C15   180.00   0.0  0
 5UY  CONST_22  N5   C13  C10  N3    180.00   0.0  0
 5UY  CONST_23  H1   C1   N    C2    180.00   0.0  0
 5UY  CONST_24  H14  C11  N4   C10   180.00   0.0  0
 5UY  CONST_25  H13  C13  N5   C12   180.00   0.0  0
 5UY  CONST_26  H2   C3   C4   C     180.00   0.0  0
 5UY  CONST_27  C5   N1   C4   C3      0.00   0.0  0
 5UY  CONST_28  C    C4   N1   C5    180.00   0.0  0
 5UY  CONST_29  H10  N1   C4   C3    180.00   0.0  0
 5UY  Var_01    C8   C7   O    C6     58.62  30.0  1
 5UY  Var_02    C8   N2   C9   C6    -50.32  30.0  1
 5UY  Var_03    C9   N2   C8   C7     50.57  30.0  1
 5UY  Var_04    O    C7   C8   N2    -54.63  30.0  1
 5UY  Var_05    C13  C10  N3   C2   -169.65  30.0  2
 5UY  Var_06    C10  N3   C2   C3   -161.78  30.0  2
 5UY  Var_07    O2   C15  C    C1      1.12  30.0  3
 5UY  Var_08    C6   C5   N1   C4   -172.34  30.0  3
 5UY  Var_09    C    C15  O2   C16  -179.78  30.0  3
 5UY  Var_10    H15  C16  O2   C15   -61.73  30.0  3

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
 5UY  chir_01  C6  C5  O  C9  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
 5UY  plan-1  C1   0.020
 5UY  plan-1  C2   0.020
 5UY  plan-1  C3   0.020
 5UY  plan-1  C4   0.020
 5UY  plan-1  N1   0.020
 5UY  plan-1  C    0.020
 5UY  plan-1  N    0.020
 5UY  plan-1  N3   0.020
 5UY  plan-1  H1   0.020
 5UY  plan-1  H2   0.020
 5UY  plan-1  C15  0.020
 5UY  plan-2  C13  0.020
 5UY  plan-2  C10  0.020
 5UY  plan-2  C11  0.020
 5UY  plan-2  C12  0.020
 5UY  plan-2  C14  0.020
 5UY  plan-2  N3   0.020
 5UY  plan-2  N5   0.020
 5UY  plan-2  N4   0.020
 5UY  plan-2  N6   0.020
 5UY  plan-2  H13  0.020
 5UY  plan-2  H14  0.020
 5UY  plan-3  C4   0.020
 5UY  plan-3  C5   0.020
 5UY  plan-3  N1   0.020
 5UY  plan-3  H10  0.020
 5UY  plan-4  O1   0.020
 5UY  plan-4  O2   0.020
 5UY  plan-4  C    0.020
 5UY  plan-4  C15  0.020

