# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 01:21:00 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(2-azanylpyridin-4-yl)methyl]pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccnc(N)c3
#
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
 M6Q  M6Q  (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(2-azanylpyridin-4-yl)methyl]pyrrolidine-2-carboxamide  ligand  52  27  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M6Q
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
 M6Q  C4   C  CR16  0  -0.241  -4.0679   -8.8295  15.5584
 M6Q  C5   C  CR16  0  -0.267  -4.3049   -7.6164  14.9254
 M6Q  C6   C  CR16  0  -0.241  -3.4529   -6.5445  15.1582
 M6Q  N1   N  NT    0  -0.471  -0.1615   -9.8665  14.7273
 M6Q  C7   C  CR16  0  -0.309  -2.3699   -6.6897  16.0147
 M6Q  C8   C  C     0   0.588   0.0809   -9.8281  16.0431
 M6Q  N2   N  NH1   0  -0.636   0.1141  -13.4292  14.3397
 M6Q  C9   C  CH1   0  -0.179  -0.5327  -11.1264  14.1107
 M6Q  C10  C  C     0   0.566   0.5687  -12.1680  14.2460
 M6Q  C11  C  CH2   0  -0.342   0.9597  -14.5893  14.4317
 M6Q  C12  C  CR6   0   0.187   1.0008  -15.2028  15.8093
 M6Q  N3   N  N     0  -0.464   1.1544  -16.3832  18.3308
 M6Q  C13  C  CR16  0  -0.425   0.8258  -14.4378  16.9647
 M6Q  C14  C  CR16  0  -0.058   0.9131  -15.0844  18.1821
 M6Q  C15  C  CR6   0   0.458   1.3235  -17.1140  17.2306
 M6Q  N4   N  NH2   0  -0.836   1.6130  -18.4373  17.3995
 M6Q  N    N  NH2   0  -0.783   1.5506   -8.6355  17.5254
 M6Q  C    C  CH1   0  -0.208   0.3570   -8.4884  16.7138
 M6Q  O    O  O     0  -0.484   1.7487  -11.8671  14.1921
 M6Q  C16  C  CR16  0  -0.441   1.2485  -16.5537  15.9446
 M6Q  C17  C  CH2   0  -0.478  -0.7645  -10.7631  12.6367
 M6Q  C18  C  CH2   0  -0.471  -1.1296   -9.2847  12.6895
 M6Q  C19  C  CH2   0  -0.279  -0.2273   -8.7488  13.7904
 M6Q  C2   C  CR6   0   0.104  -2.1172   -7.9042  16.6505
 M6Q  C3   C  CR16  0  -0.287  -2.9839   -8.9697  16.4146
 M6Q  H1   H  HCR6  0   0.253  -4.7296   -9.6691  15.3874
 M6Q  H2   H  HCR6  0   0.253  -5.1500   -7.5061  14.2581
 M6Q  H3   H  HCR6  0   0.253  -3.6319   -5.5930  14.6738
 M6Q  H4   H  HCR6  0   0.250  -1.7075   -5.8489  16.1892
 M6Q  H5   H  HNH1  0   0.404  -0.8785  -13.5742  14.4333
 M6Q  H6   H  HCH1  0   0.272  -1.4613  -11.4960  14.5599
 M6Q  H7   H  HCH2  0   0.271   0.6288  -15.3376  13.7091
 M6Q  H8   H  HCH2  0   0.277   1.9697  -14.2989  14.1399
 M6Q  H9   H  HCR6  0   0.273   0.6160  -13.3780  16.9216
 M6Q  H10  H  HCR6  0   0.254   0.7765  -14.5217  19.1000
 M6Q  H11  H  HNH2  0   0.381   1.3750  -18.8318  18.2950
 M6Q  H12  H  HNH2  0   0.389   1.4344  -19.0523  16.6233
 M6Q  H13  H  HNH2  0   0.353   1.7208   -7.7704  18.0231
 M6Q  H14  H  HNH2  0   0.343   1.3916   -9.3423  18.2332
 M6Q  H16  H  HCH1  0   0.260   0.5598   -7.7139  15.9726
 M6Q  H17  H  HCH2  0   0.256  -0.6679   -7.1388  18.0272
 M6Q  H18  H  HCH2  0   0.248  -1.0788   -8.8295  18.2847
 M6Q  H19  H  HCR6  0   0.260   1.3767  -17.1833  15.0717
 M6Q  H20  H  HCH2  0   0.266  -1.5344  -11.3867  12.1863
 M6Q  H21  H  HCH2  0   0.251   0.1544  -10.8959  12.0613
 M6Q  H22  H  HCH2  0   0.256  -0.9693   -8.7753  11.7404
 M6Q  H23  H  HCH2  0   0.246  -2.1754   -9.1534  12.9751
 M6Q  H24  H  HCH2  0   0.247   0.7683   -8.5063  13.4082
 M6Q  H25  H  HCH2  0   0.264  -0.6428   -7.8590  14.2556
 M6Q  H26  H  HCR6  0   0.246  -2.8072   -9.9216  16.9024
 M6Q  C1   C  CH2   0  -0.524  -0.8995   -8.0755  17.5141
 M6Q  O1   O  O     0  -0.505   0.0461  -10.8470  16.7276

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
 M6Q  C17  C18  single    1.524  0.020  1.524
 M6Q  C17  C9   single    1.536  0.020  1.536
 M6Q  C18  C19  single    1.521  0.020  1.521
 M6Q  O    C10  double    1.219  0.020  1.219
 M6Q  C9   C10  single    1.522  0.020  1.522
 M6Q  C9   N1   single    1.451  0.020  1.451
 M6Q  C10  N2   single    1.344  0.020  1.344
 M6Q  N2   C11  single    1.439  0.020  1.439
 M6Q  C19  N1   single    1.460  0.020  1.460
 M6Q  C11  C12  single    1.509  0.020  1.509
 M6Q  C5   C4   aromatic  1.389  0.020  1.389
 M6Q  C5   C6   aromatic  1.389  0.020  1.389
 M6Q  N1   C8   single    1.338  0.020  1.338
 M6Q  C4   C3   aromatic  1.388  0.020  1.388
 M6Q  C6   C7   aromatic  1.388  0.020  1.388
 M6Q  C12  C16  aromatic  1.380  0.020  1.380
 M6Q  C12  C13  aromatic  1.397  0.020  1.397
 M6Q  C3   C2   aromatic  1.394  0.020  1.394
 M6Q  C8   O1   double    1.228  0.020  1.228
 M6Q  C8   C    single    1.523  0.020  1.523
 M6Q  C16  C15  aromatic  1.405  0.020  1.405
 M6Q  C13  C14  aromatic  1.381  0.020  1.381
 M6Q  C7   C2   aromatic  1.394  0.020  1.394
 M6Q  C2   C1   single    1.503  0.020  1.503
 M6Q  C    C1   single    1.546  0.020  1.546
 M6Q  C    N    single    1.451  0.020  1.451
 M6Q  C15  N4   single    1.365  0.020  1.365
 M6Q  C15  N3   aromatic  1.332  0.020  1.332
 M6Q  C14  N3   aromatic  1.329  0.020  1.329
 M6Q  C4   H1   single    0.930  0.020  1.080
 M6Q  C5   H2   single    0.930  0.020  1.080
 M6Q  C6   H3   single    0.930  0.020  1.080
 M6Q  C7   H4   single    0.930  0.020  1.080
 M6Q  N2   H5   single    0.860  0.020  1.020
 M6Q  C9   H6   single    0.970  0.020  1.090
 M6Q  C11  H7   single    0.970  0.020  1.090
 M6Q  C11  H8   single    0.970  0.020  1.090
 M6Q  C13  H9   single    0.930  0.020  1.080
 M6Q  C14  H10  single    0.930  0.020  1.080
 M6Q  N4   H11  single    0.890  0.020  1.040
 M6Q  N4   H12  single    0.890  0.020  1.040
 M6Q  N    H13  single    0.890  0.020  1.040
 M6Q  N    H14  single    0.890  0.020  1.040
 M6Q  C    H16  single    0.970  0.020  1.090
 M6Q  C1   H17  single    0.970  0.020  1.090
 M6Q  C1   H18  single    0.970  0.020  1.090
 M6Q  C16  H19  single    0.930  0.020  1.080
 M6Q  C17  H20  single    0.970  0.020  1.090
 M6Q  C17  H21  single    0.970  0.020  1.090
 M6Q  C18  H22  single    0.970  0.020  1.090
 M6Q  C18  H23  single    0.970  0.020  1.090
 M6Q  C19  H24  single    0.970  0.020  1.090
 M6Q  C19  H25  single    0.970  0.020  1.090
 M6Q  C3   H26  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
 M6Q  H1   C4   C3   119.76  3.000
 M6Q  H1   C4   C5   120.07  3.000
 M6Q  C3   C4   C5   120.17  3.000
 M6Q  H2   C5   C6   120.24  3.000
 M6Q  H2   C5   C4   120.22  3.000
 M6Q  C6   C5   C4   119.54  3.000
 M6Q  H3   C6   C7   119.79  3.000
 M6Q  H3   C6   C5   120.13  3.000
 M6Q  C7   C6   C5   120.08  3.000
 M6Q  C19  N1   C9   112.37  3.000
 M6Q  C19  N1   C8   128.10  3.000
 M6Q  C9   N1   C8   119.27  3.000
 M6Q  H4   C7   C2   119.43  3.000
 M6Q  H4   C7   C6   119.64  3.000
 M6Q  C2   C7   C6   120.93  3.000
 M6Q  O1   C8   C    119.30  3.000
 M6Q  C    C8   N1   119.39  3.000
 M6Q  O1   C8   N1   121.28  3.000
 M6Q  H5   N2   C11  117.20  3.000
 M6Q  H5   N2   C10  118.34  3.000
 M6Q  C11  N2   C10  124.23  3.000
 M6Q  H6   C9   C17  110.21  3.000
 M6Q  H6   C9   C10  110.24  3.000
 M6Q  C17  C9   C10  110.88  3.000
 M6Q  H6   C9   N1   109.60  3.000
 M6Q  C10  C9   N1   111.80  3.000
 M6Q  C17  C9   N1   103.95  3.000
 M6Q  O    C10  C9   121.85  3.000
 M6Q  C9   C10  N2   113.81  3.000
 M6Q  O    C10  N2   124.20  3.000
 M6Q  H8   C11  H7   106.63  3.000
 M6Q  H8   C11  C12  109.11  3.000
 M6Q  H7   C11  C12  109.51  3.000
 M6Q  H8   C11  N2   108.21  3.000
 M6Q  H7   C11  N2   109.40  3.000
 M6Q  C12  C11  N2   113.73  3.000
 M6Q  C16  C12  C13  118.52  3.000
 M6Q  C13  C12  C11  121.96  3.000
 M6Q  C16  C12  C11  119.51  3.000
 M6Q  C15  N3   C14  117.83  3.000
 M6Q  H9   C13  C14  120.42  3.000
 M6Q  H9   C13  C12  121.88  3.000
 M6Q  C14  C13  C12  117.70  3.000
 M6Q  H10  C14  C13  119.65  3.000
 M6Q  H10  C14  N3   115.77  3.000
 M6Q  C13  C14  N3   124.57  3.000
 M6Q  C16  C15  N4   120.75  3.000
 M6Q  N4   C15  N3   117.18  3.000
 M6Q  C16  C15  N3   122.05  3.000
 M6Q  H12  N4   H11  113.86  3.000
 M6Q  H12  N4   C15  117.34  3.000
 M6Q  H11  N4   C15  116.08  3.000
 M6Q  H14  N    H13  106.21  3.000
 M6Q  H14  N    C    109.43  3.000
 M6Q  H13  N    C    109.06  3.000
 M6Q  H16  C    C1   108.25  3.000
 M6Q  H16  C    N    107.40  3.000
 M6Q  C1   C    N    113.96  3.000
 M6Q  H16  C    C8   111.03  3.000
 M6Q  N    C    C8   107.83  3.000
 M6Q  C1   C    C8   108.39  3.000
 M6Q  H19  C16  C15  119.95  3.000
 M6Q  H19  C16  C12  120.72  3.000
 M6Q  C15  C16  C12  119.33  3.000
 M6Q  H21  C17  H20  107.90  3.000
 M6Q  H21  C17  C18  109.75  3.000
 M6Q  H20  C17  C18  113.63  3.000
 M6Q  H21  C17  C9   110.48  3.000
 M6Q  H20  C17  C9   111.61  3.000
 M6Q  C18  C17  C9   103.44  3.000
 M6Q  H23  C18  H22  108.22  3.000
 M6Q  H23  C18  C19  109.66  3.000
 M6Q  H22  C18  C19  112.25  3.000
 M6Q  H23  C18  C17  110.81  3.000
 M6Q  H22  C18  C17  112.85  3.000
 M6Q  C19  C18  C17  102.99  3.000
 M6Q  H25  C19  H24  108.43  3.000
 M6Q  H25  C19  C18  111.81  3.000
 M6Q  H24  C19  C18  111.43  3.000
 M6Q  H25  C19  N1   111.68  3.000
 M6Q  H24  C19  N1   110.67  3.000
 M6Q  C18  C19  N1   102.79  3.000
 M6Q  C3   C2   C1   120.94  3.000
 M6Q  C1   C2   C7   120.55  3.000
 M6Q  C3   C2   C7   118.44  3.000
 M6Q  H26  C3   C2   119.59  3.000
 M6Q  H26  C3   C4   119.57  3.000
 M6Q  C2   C3   C4   120.85  3.000
 M6Q  H18  C1   H17  107.16  3.000
 M6Q  H18  C1   C2   110.54  3.000
 M6Q  H17  C1   C2   110.11  3.000
 M6Q  H18  C1   C    108.31  3.000
 M6Q  H17  C1   C    107.45  3.000
 M6Q  C2   C1   C    113.05  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
 M6Q  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 M6Q  CONST_02  C7   C2   C3   C4     0.00   0.0  0
 M6Q  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 M6Q  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 M6Q  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 M6Q  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 M6Q  CONST_07  N3   C15  C16  C12    0.00   0.0  0
 M6Q  CONST_08  N3   C14  C13  C12    0.00   0.0  0
 M6Q  CONST_09  C15  C16  C12  C13    0.00   0.0  0
 M6Q  CONST_10  C15  N3   C14  C13    0.00   0.0  0
 M6Q  CONST_11  C16  C12  C13  C14    0.00   0.0  0
 M6Q  CONST_12  C16  C15  N3   C14    0.00   0.0  0
 M6Q  CONST_13  C1   C2   C3   C4   180.00   0.0  0
 M6Q  CONST_14  C1   C2   C7   C6   180.00   0.0  0
 M6Q  CONST_15  C15  C16  C12  C11  180.00   0.0  0
 M6Q  CONST_16  C14  C13  C12  C11  180.00   0.0  0
 M6Q  CONST_17  N4   C15  C16  C12  180.00   0.0  0
 M6Q  CONST_18  N4   C15  N3   C14  180.00   0.0  0
 M6Q  CONST_19  H3   C6   C5   C4   180.00   0.0  0
 M6Q  CONST_20  H26  C3   C4   C5   180.00   0.0  0
 M6Q  CONST_21  H4   C7   C6   C5   180.00   0.0  0
 M6Q  CONST_22  H1   C4   C5   C6   180.00   0.0  0
 M6Q  CONST_23  H2   C5   C6   C7   180.00   0.0  0
 M6Q  CONST_24  H10  C14  C13  C12  180.00   0.0  0
 M6Q  CONST_25  H19  C16  C15  N3   180.00   0.0  0
 M6Q  CONST_26  H9   C13  C14  N3   180.00   0.0  0
 M6Q  CONST_27  O1   C8   N1   C9     0.00   0.0  0
 M6Q  CONST_28  C    C8   N1   C9   180.00   0.0  0
 M6Q  CONST_29  C19  N1   C8   C      0.00   0.0  0
 M6Q  CONST_30  O1   C8   N1   C19  180.00   0.0  0
 M6Q  CONST_33  C11  N2   C10  C9   180.00   0.0  0
 M6Q  CONST_34  H5   N2   C10  C9     0.00   0.0  0
 M6Q  CONST_35  O    C10  N2   C11    0.00   0.0  0
 M6Q  Var_01    C17  C18  C19  N1   -34.71  30.0  1
 M6Q  Var_02    C19  C18  C17  C9    37.38  30.0  1
 M6Q  Var_03    C18  C19  N1   C9    19.60  30.0  1
 M6Q  Var_04    C    C1   C2   C7   -86.01  30.0  2
 M6Q  Var_05    C16  C12  C11  N2   151.93  30.0  2
 M6Q  Var_06    C12  C11  N2   C10  106.08  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
 M6Q  chir_01  C9  C17  C10  N1  negativ
 M6Q  chir_02  C   N    C1   C8  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
 M6Q  plan-1  C4   0.020
 M6Q  plan-1  C5   0.020
 M6Q  plan-1  C6   0.020
 M6Q  plan-1  C7   0.020
 M6Q  plan-1  C2   0.020
 M6Q  plan-1  C3   0.020
 M6Q  plan-1  H1   0.020
 M6Q  plan-1  H2   0.020
 M6Q  plan-1  H3   0.020
 M6Q  plan-1  H4   0.020
 M6Q  plan-1  H26  0.020
 M6Q  plan-1  C1   0.020
 M6Q  plan-2  C11  0.020
 M6Q  plan-2  C12  0.020
 M6Q  plan-2  N3   0.020
 M6Q  plan-2  C13  0.020
 M6Q  plan-2  C14  0.020
 M6Q  plan-2  C15  0.020
 M6Q  plan-2  N4   0.020
 M6Q  plan-2  C16  0.020
 M6Q  plan-2  H9   0.020
 M6Q  plan-2  H10  0.020
 M6Q  plan-2  H19  0.020
 M6Q  plan-3  N2   0.020
 M6Q  plan-3  C9   0.020
 M6Q  plan-3  C10  0.020
 M6Q  plan-3  C11  0.020
 M6Q  plan-3  O    0.020
 M6Q  plan-3  H5   0.020
 M6Q  plan-4  C15  0.020
 M6Q  plan-4  N4   0.020
 M6Q  plan-4  H11  0.020
 M6Q  plan-4  H12  0.020
 M6Q  plan-5  N1   0.020
 M6Q  plan-5  C8   0.020
 M6Q  plan-5  C9   0.020
 M6Q  plan-5  C    0.020
 M6Q  plan-5  C19  0.020
 M6Q  plan-5  O1   0.020

