# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:12:23 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1nccnc1C(=O)NC2Cc3ccccc3C2)N4CCCCC4
#
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
 MU5  MU5  ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide  ligand  50  27  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MU5
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
 MU5  N1   N  N     0  -0.381  10.0591  81.7623   8.5139
 MU5  N3   N  NH1   0  -0.628   5.3153  81.5563   8.1645
 MU5  C4   C  CR6   0  -0.017   7.6995  81.6384   8.2673
 MU5  C5   C  C     0   0.593   6.4191  82.0406   7.6032
 MU5  C6   C  CR15  0  -0.129   3.9818  81.8607   7.6805
 MU5  C7   C  CH2   0  -0.482   3.5877  80.9507   6.4993
 MU5  C8   C  CR56  0   0.106   2.9750  79.7585   7.1791
 MU5  C10  C  CH2   0  -0.509   2.9627  81.5154   8.7775
 MU5  C13  C  CR16  0  -0.260   2.1312  77.5423   7.5004
 MU5  C15  C  CH2   0  -0.313  11.1589  84.8031   4.4181
 MU5  C17  C  CH2   0  -0.445  10.6738  87.1585   5.1176
 MU5  N    N  NH1   0  -0.800   9.0575  82.9282   6.7528
 MU5  C    C  C     0   0.715  10.2105  83.3085   6.0735
 MU5  O    O  O     0  -0.495  11.2725  82.7273   6.2049
 MU5  C1   C  CR6   0   0.530   8.9691  82.1000   7.8354
 MU5  C11  C  CR16  0  -0.325   2.0143  79.1419   9.3063
 MU5  C12  C  CR16  0  -0.260   1.7740  77.8661   8.8051
 MU5  C14  C  CR16  0  -0.326   2.7343  78.4894   6.6777
 MU5  C16  C  CH2   0  -0.434  11.7481  86.0820   5.0003
 MU5  C18  C  CH2   0  -0.426   9.4635  86.6345   5.8833
 MU5  C19  C  CH2   0  -0.328   8.9567  85.3291   5.2803
 MU5  C2   C  CR16  0  -0.085   9.9237  80.9627   9.5553
 MU5  C3   C  CR16  0  -0.136   8.6888  80.4784   9.9622
 MU5  C9   C  CR56  0   0.084   2.6168  80.0816   8.4859
 MU5  N2   N  N     0  -0.376   7.5967  80.8397   9.3141
 MU5  N4   N  NT    0  -0.487  10.0279  84.3423   5.2113
 MU5  O1   O  O     0  -0.514   6.4048  82.7843   6.6184
 MU5  H1   H  HNH1  0   0.412   5.4321  80.9402   8.9568
 MU5  H2   H  HCR5  0   0.270   3.9443  82.9149   7.4072
 MU5  H3   H  HCH2  0   0.261   4.4322  80.7097   5.8527
 MU5  H4   H  HCH2  0   0.259   2.8440  81.4581   5.8766
 MU5  H5   H  HCH2  0   0.264   3.3507  81.6851   9.7837
 MU5  H6   H  HCH2  0   0.274   2.0798  82.1519   8.6706
 MU5  H7   H  HCR6  0   0.252   1.9431  76.5445   7.1247
 MU5  H8   H  HCH2  0   0.238  10.7979  84.9919   3.4019
 MU5  H9   H  HCH2  0   0.263  11.9053  84.0166   4.3522
 MU5  H10  H  HCH2  0   0.239  11.0727  88.0507   5.6039
 MU5  H11  H  HCH2  0   0.217  10.3585  87.4626   4.1139
 MU5  H12  H  HNH1  0   0.445   8.1451  83.1404   6.3536
 MU5  H13  H  HCR6  0   0.249   1.7371  79.3904  10.3237
 MU5  H14  H  HCR6  0   0.252   1.3105  77.1184   9.4361
 MU5  H15  H  HCR6  0   0.248   3.0156  78.2332   5.6634
 MU5  H16  H  HCH2  0   0.224  12.1750  85.8662   5.9844
 MU5  H17  H  HCH2  0   0.238  12.5684  86.4237   4.3652
 MU5  H18  H  HCH2  0   0.225   9.7274  86.4632   6.9313
 MU5  H19  H  HCH2  0   0.241   8.6537  87.3672   5.8737
 MU5  H20  H  HCH2  0   0.245   8.5946  85.5050   4.2631
 MU5  H21  H  HCH2  0   0.251   8.1060  84.9658   5.8504
 MU5  H22  H  HCR6  0   0.282  10.8253  80.7013  10.0966
 MU5  H23  H  HCR6  0   0.280   8.5860  79.8174  10.8124

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
 MU5  C15  C16  single    1.524  0.020  1.524
 MU5  C15  N4   single    1.456  0.020  1.456
 MU5  C16  C17  single    1.525  0.020  1.525
 MU5  N4   C19  single    1.458  0.020  1.458
 MU5  N4   C    single    1.358  0.020  1.358
 MU5  C17  C18  single    1.525  0.020  1.525
 MU5  C19  C18  single    1.525  0.020  1.525
 MU5  C    O    double    1.218  0.020  1.218
 MU5  C    N    single    1.391  0.020  1.391
 MU5  C7   C8   single    1.503  0.020  1.503
 MU5  C7   C6   single    1.542  0.020  1.542
 MU5  O1   C5   double    1.234  0.020  1.234
 MU5  C14  C8   aromatic  1.386  0.020  1.386
 MU5  C14  C13  aromatic  1.392  0.020  1.392
 MU5  N    C1   single    1.366  0.020  1.366
 MU5  C8   C9   aromatic  1.393  0.020  1.393
 MU5  C5   N3   single    1.330  0.020  1.330
 MU5  C5   C4   single    1.497  0.020  1.497
 MU5  C13  C12  aromatic  1.391  0.020  1.391
 MU5  C6   N3   single    1.451  0.020  1.451
 MU5  C6   C10  single    1.537  0.020  1.537
 MU5  C1   C4   aromatic  1.418  0.020  1.418
 MU5  C1   N1   aromatic  1.328  0.020  1.328
 MU5  C4   N2   aromatic  1.321  0.020  1.321
 MU5  C9   C10  single    1.503  0.020  1.503
 MU5  C9   C11  aromatic  1.385  0.020  1.385
 MU5  N1   C2   aromatic  1.320  0.020  1.320
 MU5  C12  C11  aromatic  1.392  0.020  1.392
 MU5  N2   C3   aromatic  1.320  0.020  1.320
 MU5  C2   C3   aromatic  1.387  0.020  1.387
 MU5  N3   H1   single    0.860  0.020  1.020
 MU5  C6   H2   single    0.970  0.020  1.090
 MU5  C7   H3   single    0.970  0.020  1.090
 MU5  C7   H4   single    0.970  0.020  1.090
 MU5  C10  H5   single    0.970  0.020  1.090
 MU5  C10  H6   single    0.970  0.020  1.090
 MU5  C13  H7   single    0.930  0.020  1.080
 MU5  C15  H8   single    0.970  0.020  1.090
 MU5  C15  H9   single    0.970  0.020  1.090
 MU5  C17  H10  single    0.970  0.020  1.090
 MU5  C17  H11  single    0.970  0.020  1.090
 MU5  N    H12  single    0.860  0.020  1.020
 MU5  C11  H13  single    0.930  0.020  1.080
 MU5  C12  H14  single    0.930  0.020  1.080
 MU5  C14  H15  single    0.930  0.020  1.080
 MU5  C16  H16  single    0.970  0.020  1.090
 MU5  C16  H17  single    0.970  0.020  1.090
 MU5  C18  H18  single    0.970  0.020  1.090
 MU5  C18  H19  single    0.970  0.020  1.090
 MU5  C19  H20  single    0.970  0.020  1.090
 MU5  C19  H21  single    0.970  0.020  1.090
 MU5  C2   H22  single    0.930  0.020  1.080
 MU5  C3   H23  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
 MU5  C2   N1   C1   118.24  3.000
 MU5  H1   N3   C6   119.72  3.000
 MU5  H1   N3   C5   117.20  3.000
 MU5  C6   N3   C5   123.07  3.000
 MU5  N2   C4   C1   120.52  3.000
 MU5  N2   C4   C5   116.58  3.000
 MU5  C1   C4   C5   122.89  3.000
 MU5  O1   C5   C4   121.71  3.000
 MU5  C4   C5   N3   115.14  3.000
 MU5  O1   C5   N3   123.14  3.000
 MU5  H2   C6   C10  111.94  3.000
 MU5  H2   C6   C7   111.71  3.000
 MU5  C10  C6   C7   104.16  3.000
 MU5  H2   C6   N3   108.56  3.000
 MU5  C10  C6   N3   108.92  3.000
 MU5  C7   C6   N3   111.50  3.000
 MU5  H4   C7   H3   106.93  3.000
 MU5  H4   C7   C8   110.37  3.000
 MU5  H3   C7   C8   114.11  3.000
 MU5  H4   C7   C6   109.62  3.000
 MU5  H3   C7   C6   112.74  3.000
 MU5  C8   C7   C6   103.05  3.000
 MU5  C9   C8   C14  120.48  3.000
 MU5  C9   C8   C7   110.19  3.000
 MU5  C14  C8   C7   129.33  3.000
 MU5  H6   C10  H5   106.65  3.000
 MU5  H6   C10  C9   110.51  3.000
 MU5  H5   C10  C9   114.13  3.000
 MU5  H6   C10  C6   109.56  3.000
 MU5  H5   C10  C6   112.79  3.000
 MU5  C9   C10  C6   103.20  3.000
 MU5  H7   C13  C14  119.82  3.000
 MU5  H7   C13  C12  119.70  3.000
 MU5  C14  C13  C12  120.48  3.000
 MU5  H9   C15  H8   107.17  3.000
 MU5  H9   C15  N4   109.73  3.000
 MU5  H8   C15  N4   107.70  3.000
 MU5  H9   C15  C16  111.42  3.000
 MU5  H8   C15  C16  109.72  3.000
 MU5  N4   C15  C16  110.96  3.000
 MU5  H11  C17  H10  106.65  3.000
 MU5  H11  C17  C18  109.09  3.000
 MU5  H10  C17  C18  110.31  3.000
 MU5  H11  C17  C16  109.16  3.000
 MU5  H10  C17  C16  110.72  3.000
 MU5  C18  C17  C16  110.80  3.000
 MU5  H12  N    C1   112.28  3.000
 MU5  H12  N    C    119.61  3.000
 MU5  C1   N    C    127.33  3.000
 MU5  N4   C    O    123.29  3.000
 MU5  O    C    N    122.66  3.000
 MU5  N4   C    N    113.99  3.000
 MU5  N    C1   C4   119.77  3.000
 MU5  C4   C1   N1   119.77  3.000
 MU5  N    C1   N1   120.41  3.000
 MU5  H13  C11  C9   120.79  3.000
 MU5  H13  C11  C12  120.29  3.000
 MU5  C9   C11  C12  118.92  3.000
 MU5  H14  C12  C11  119.81  3.000
 MU5  H14  C12  C13  119.73  3.000
 MU5  C11  C12  C13  120.46  3.000
 MU5  H15  C14  C13  120.33  3.000
 MU5  H15  C14  C8   120.68  3.000
 MU5  C13  C14  C8   118.99  3.000
 MU5  H17  C16  H16  106.95  3.000
 MU5  H17  C16  C17  110.66  3.000
 MU5  H16  C16  C17  110.17  3.000
 MU5  H17  C16  C15  109.32  3.000
 MU5  H16  C16  C15  109.21  3.000
 MU5  C17  C16  C15  110.45  3.000
 MU5  H19  C18  H18  107.00  3.000
 MU5  H19  C18  C19  108.94  3.000
 MU5  H18  C18  C19  108.96  3.000
 MU5  H19  C18  C17  110.71  3.000
 MU5  H18  C18  C17  110.07  3.000
 MU5  C19  C18  C17  111.06  3.000
 MU5  H21  C19  H20  106.40  3.000
 MU5  H21  C19  N4   111.95  3.000
 MU5  H20  C19  N4   107.94  3.000
 MU5  H21  C19  C18  109.81  3.000
 MU5  H20  C19  C18  109.88  3.000
 MU5  N4   C19  C18  110.73  3.000
 MU5  H22  C2   C3   120.65  3.000
 MU5  H22  C2   N1   117.06  3.000
 MU5  C3   C2   N1   122.29  3.000
 MU5  H23  C3   N2   118.32  3.000
 MU5  H23  C3   C2   121.90  3.000
 MU5  N2   C3   C2   119.78  3.000
 MU5  C11  C9   C10  129.20  3.000
 MU5  C11  C9   C8   120.67  3.000
 MU5  C10  C9   C8   110.12  3.000
 MU5  C3   N2   C4   119.35  3.000
 MU5  C19  N4   C    125.71  3.000
 MU5  C    N4   C15  118.83  3.000
 MU5  C19  N4   C15  112.47  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
 MU5  CONST_01  N2   C4   C1   N1      0.00   0.0  0
 MU5  CONST_02  N2   C3   C2   N1      0.00   0.0  0
 MU5  CONST_03  C2   N1   C1   C4      0.00   0.0  0
 MU5  CONST_04  C2   C3   N2   C4      0.00   0.0  0
 MU5  CONST_05  C12  C13  C14  C8      0.00   0.0  0
 MU5  CONST_06  C12  C11  C9   C8      0.00   0.0  0
 MU5  CONST_07  C9   C8   C14  C13     0.00   0.0  0
 MU5  CONST_08  C9   C11  C12  C13     0.00   0.0  0
 MU5  CONST_09  C3   N2   C4   C1      0.00   0.0  0
 MU5  CONST_10  C3   C2   N1   C1      0.00   0.0  0
 MU5  CONST_11  C14  C8   C9   C11     0.00   0.0  0
 MU5  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 MU5  CONST_13  C5   C4   C1   N1    180.00   0.0  0
 MU5  CONST_14  C3   N2   C4   C5    180.00   0.0  0
 MU5  CONST_15  N2   C4   C1   N     180.00   0.0  0
 MU5  CONST_16  C2   N1   C1   N     180.00   0.0  0
 MU5  CONST_17  H23  C3   C2   N1    180.00   0.0  0
 MU5  CONST_18  H15  C14  C8   C7      0.00   0.0  0
 MU5  CONST_19  H7   C13  C14  C8    180.00   0.0  0
 MU5  CONST_20  H13  C11  C9   C8    180.00   0.0  0
 MU5  CONST_21  H22  C2   N1   C1    180.00   0.0  0
 MU5  CONST_22  H14  C12  C13  C14   180.00   0.0  0
 MU5  CONST_23  C6   N3   C5   C4    180.00   0.0  0
 MU5  CONST_24  O    C    N4   C15     0.00   0.0  0
 MU5  CONST_26  C    N    C1   N1      0.00   0.0  0
 MU5  CONST_27  C    N    C1   C4    180.00   0.0  0
 MU5  CONST_28  N4   C    N    C1    180.00   0.0  0
 MU5  CONST_29  N    C    N4   C15   180.00   0.0  0
 MU5  CONST_31  H12  N    C1   N1    180.00   0.0  0
 MU5  CONST_32  O1   C5   N3   C6      0.00   0.0  0
 MU5  CONST_34  H1   N3   C5   C4      0.00   0.0  0
 MU5  Var_01    C14  C8   C7   C6   -162.53  30.0  1
 MU5  Var_02    C8   C9   C10  C6    -18.54  30.0  1
 MU5  Var_03    C18  C17  C16  C15    52.97  30.0  1
 MU5  Var_04    C18  C19  N4   C15   -58.70  30.0  1
 MU5  Var_05    N4   C15  C16  C17   -55.90  30.0  1
 MU5  Var_06    N4   C19  C18  C17    54.92  30.0  1
 MU5  Var_07    C19  N4   C15  C16    59.44  30.0  1
 MU5  Var_08    C19  C18  C17  C16   -52.73  30.0  1
 MU5  Var_09    C1   C4   C5   N3   -177.63  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
 MU5  chir_01  C6  C7  N3  C10  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
 MU5  plan-1  N1   0.020
 MU5  plan-1  C4   0.020
 MU5  plan-1  C5   0.020
 MU5  plan-1  N    0.020
 MU5  plan-1  C1   0.020
 MU5  plan-1  C2   0.020
 MU5  plan-1  C3   0.020
 MU5  plan-1  N2   0.020
 MU5  plan-1  H22  0.020
 MU5  plan-1  H23  0.020
 MU5  plan-2  C7   0.020
 MU5  plan-2  C8   0.020
 MU5  plan-2  C10  0.020
 MU5  plan-2  C13  0.020
 MU5  plan-2  C11  0.020
 MU5  plan-2  C12  0.020
 MU5  plan-2  C14  0.020
 MU5  plan-2  C9   0.020
 MU5  plan-2  H7   0.020
 MU5  plan-2  H13  0.020
 MU5  plan-2  H14  0.020
 MU5  plan-2  H15  0.020
 MU5  plan-3  N3   0.020
 MU5  plan-3  C4   0.020
 MU5  plan-3  C5   0.020
 MU5  plan-3  C6   0.020
 MU5  plan-3  O1   0.020
 MU5  plan-3  H1   0.020
 MU5  plan-4  C15  0.020
 MU5  plan-4  N    0.020
 MU5  plan-4  C    0.020
 MU5  plan-4  O    0.020
 MU5  plan-4  C1   0.020
 MU5  plan-4  C19  0.020
 MU5  plan-4  N4   0.020
 MU5  plan-4  H12  0.020

