# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 03:57:23 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (4Z)-4-imino-4-[(4Z)-4-(1H-indol-3-ylmethylidene)-5-oxo-1-(2-oxoethyl)-4,5-dihydro-1H-imidazol-2-yl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CCC(=N)C1=NC(=C\c2c[nH]c3ccccc23)/C(=O)N1CC=O
#
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
 4M9  4M9  (4Z)-4-imino-4-[(4Z)-4-(1H-indol-3-ylmethylidene)-5-oxo-1-(2-oxoethyl)-4,5-dihydro-1H-imidazol-2-yl]butanamide  ligand  43  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4M9
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
 4M9  O2   O  O     0  -0.459   0.2182  -3.7215  -0.4694
 4M9  C2   C  CR5   0   0.529  -0.1988  -2.5870  -0.3311
 4M9  N3   N  NR5   0  -0.592  -1.5347  -2.2117  -0.3132
 4M9  CA3  C  CH2   0  -0.404  -2.6146  -3.1342  -0.5531
 4M9  C    C  C1    0   0.189  -3.5171  -3.3096   0.6437
 4M9  O    O  O     0  -0.394  -4.5603  -3.9074   0.5867
 4M9  CA2  C  CR5   0   0.072   0.5069  -1.3139  -0.1616
 4M9  N2   N  N     0  -0.468  -0.4172  -0.2909  -0.0608
 4M9  C1   C  CR5   0   0.524  -1.5803  -0.8384  -0.1499
 4M9  CA1  C  C     0   0.180  -2.8324  -0.0676  -0.0427
 4M9  N    N  N     0  -0.576  -3.9007  -0.7265   0.1293
 4M9  CB1  C  CH2   0  -0.494  -2.6789   1.4247  -0.1301
 4M9  CG1  C  CH2   0  -0.628  -3.9683   2.1906   0.0973
 4M9  CB2  C  C1    0  -0.399   1.8571  -1.1836  -0.1245
 4M9  CG2  C  CR5   0   0.024   2.6166   0.0070   0.0171
 4M9  CD1  C  CR15  0  -0.015   2.1558   1.3103   0.1492
 4M9  NE1  N  NR15  0  -0.668   3.1976   2.1508   0.2491
 4M9  CE2  C  CR56  0   0.358   4.3813   1.4544   0.1879
 4M9  CD2  C  CR56  0   0.060   4.0573   0.0942   0.0418
 4M9  CZ2  C  CR16  0  -0.290   5.6930   1.9121   0.2494
 4M9  CH2  C  CR16  0  -0.282   6.6960   0.9649   0.1588
 4M9  CZ3  C  CR16  0  -0.258   6.3965  -0.3980   0.0129
 4M9  CE3  C  CR16  0  -0.373   5.0889  -0.8426  -0.0458
 4M9  C3   C  C     0   0.541  -3.7475   3.6917   0.1084
 4M9  N4   N  NH2   0  -0.805  -4.8120   4.4161  -0.2643
 4M9  O5   O  O     0  -0.490  -2.6885   4.1937   0.4556
 4M9  H1   H  HCH2  0   0.299  -3.1981  -2.8500  -1.4282
 4M9  H2   H  HCH2  0   0.300  -2.1612  -4.1055  -0.7708
 4M9  H3   H  H     0   0.199  -3.1120  -2.9254   1.5958
 4M9  H4   H  H     0   0.374  -4.7228  -0.1339   0.2085
 4M9  H5   H  HCH2  0   0.277  -1.9204   1.7319   0.5911
 4M9  H6   H  HCH2  0   0.279  -2.2618   1.6634  -1.1122
 4M9  H7   H  HCH2  0   0.270  -4.7164   1.9338  -0.6566
 4M9  H8   H  HCH2  0   0.288  -4.4021   1.9251   1.0676
 4M9  H9   H  H     0   0.267   2.4204  -2.1061  -0.2215
 4M9  H10  H  HCR5  0   0.303   1.1417   1.6723   0.1754
 4M9  H11  H  HNR5  0   0.425   3.1129   3.1502   0.3481
 4M9  H12  H  HCR6  0   0.269   5.9194   2.9642   0.3632
 4M9  H13  H  HCR6  0   0.257   7.7303   1.2795   0.2027
 4M9  H14  H  HCR6  0   0.256   7.2062  -1.1126  -0.0538
 4M9  H15  H  HCR6  0   0.248   4.8785  -1.8995  -0.1562
 4M9  H16  H  HNH2  0   0.406  -5.6767   3.9869  -0.5432
 4M9  H17  H  HNH2  0   0.401  -4.7855   5.4219  -0.2256

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
 4M9  O    C    double    1.204  0.020  1.204
 4M9  C    CA3  single    1.509  0.020  1.509
 4M9  CA3  N3   single    1.440  0.020  1.440
 4M9  O2   C2   double    1.217  0.020  1.217
 4M9  N3   C2   single    1.388  0.020  1.388
 4M9  N3   C1   single    1.384  0.020  1.384
 4M9  C2   CA2  single    1.465  0.020  1.465
 4M9  N    CA1  double    1.267  0.020  1.267
 4M9  CA1  C1   single    1.474  0.020  1.474
 4M9  CA1  CB1  single    1.503  0.020  1.503
 4M9  C1   N2   double    1.289  0.020  1.289
 4M9  CG1  CB1  single    1.517  0.020  1.517
 4M9  CG1  C3   single    1.517  0.020  1.517
 4M9  CA2  N2   single    1.382  0.020  1.382
 4M9  CA2  CB2  double    1.357  0.020  1.357
 4M9  N4   C3   single    1.341  0.020  1.341
 4M9  CB2  CG2  single    1.419  0.020  1.419
 4M9  C3   O5   double    1.222  0.020  1.222
 4M9  CG2  CD1  aromatic  1.389  0.020  1.389
 4M9  CG2  CD2  aromatic  1.444  0.020  1.444
 4M9  CE3  CD2  aromatic  1.396  0.020  1.396
 4M9  CE3  CZ3  aromatic  1.382  0.020  1.382
 4M9  CD1  NE1  aromatic  1.342  0.020  1.342
 4M9  CD2  CE2  aromatic  1.406  0.020  1.406
 4M9  CZ3  CH2  aromatic  1.403  0.020  1.403
 4M9  NE1  CE2  aromatic  1.375  0.020  1.375
 4M9  CE2  CZ2  aromatic  1.391  0.020  1.391
 4M9  CH2  CZ2  aromatic  1.382  0.020  1.382
 4M9  CA3  H1   single    0.970  0.020  1.090
 4M9  CA3  H2   single    0.970  0.020  1.090
 4M9  C    H3   single    0.930  0.020  1.080
 4M9  N    H4   single    0.890  0.020  1.040
 4M9  CB1  H5   single    0.970  0.020  1.090
 4M9  CB1  H6   single    0.970  0.020  1.090
 4M9  CG1  H7   single    0.970  0.020  1.090
 4M9  CG1  H8   single    0.970  0.020  1.090
 4M9  CB2  H9   single    0.930  0.020  1.080
 4M9  CD1  H10  single    0.930  0.020  1.080
 4M9  NE1  H11  single    0.860  0.020  1.020
 4M9  CZ2  H12  single    0.930  0.020  1.080
 4M9  CH2  H13  single    0.930  0.020  1.080
 4M9  CZ3  H14  single    0.930  0.020  1.080
 4M9  CE3  H15  single    0.930  0.020  1.080
 4M9  N4   H16  single    0.860  0.020  1.020
 4M9  N4   H17  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
 4M9  CA2  C2   N3   103.13  3.000
 4M9  CA2  C2   O2   131.17  3.000
 4M9  N3   C2   O2   125.71  3.000
 4M9  C1   N3   CA3  129.09  3.000
 4M9  C1   N3   C2   107.56  3.000
 4M9  CA3  N3   C2   123.12  3.000
 4M9  H2   CA3  H1   107.08  3.000
 4M9  H2   CA3  C    107.61  3.000
 4M9  H1   CA3  C    110.30  3.000
 4M9  H2   CA3  N3   106.92  3.000
 4M9  H1   CA3  N3   111.61  3.000
 4M9  C    CA3  N3   113.00  3.000
 4M9  H3   C    O    122.13  3.000
 4M9  H3   C    CA3  115.09  3.000
 4M9  O    C    CA3  122.58  3.000
 4M9  CB2  CA2  N2   126.31  3.000
 4M9  CB2  CA2  C2   124.45  3.000
 4M9  N2   CA2  C2   109.24  3.000
 4M9  C1   N2   CA2  106.49  3.000
 4M9  CA1  C1   N2   122.64  3.000
 4M9  N2   C1   N3   113.58  3.000
 4M9  CA1  C1   N3   123.75  3.000
 4M9  CB1  CA1  N    127.63  3.000
 4M9  CB1  CA1  C1   115.36  3.000
 4M9  N    CA1  C1   117.01  3.000
 4M9  H4   N    CA1  112.91  3.000
 4M9  H6   CB1  H5   105.49  3.000
 4M9  H6   CB1  CG1  110.41  3.000
 4M9  H5   CB1  CG1  110.48  3.000
 4M9  H6   CB1  CA1  107.94  3.000
 4M9  H5   CB1  CA1  108.19  3.000
 4M9  CG1  CB1  CA1  113.95  3.000
 4M9  H8   CG1  H7   106.44  3.000
 4M9  H8   CG1  C3   106.91  3.000
 4M9  H7   CG1  C3   109.71  3.000
 4M9  H8   CG1  CB1  110.30  3.000
 4M9  H7   CG1  CB1  111.09  3.000
 4M9  C3   CG1  CB1  112.14  3.000
 4M9  H9   CB2  CG2  116.37  3.000
 4M9  H9   CB2  CA2  115.62  3.000
 4M9  CG2  CB2  CA2  128.01  3.000
 4M9  CD2  CG2  CD1  105.84  3.000
 4M9  CD2  CG2  CB2  125.91  3.000
 4M9  CD1  CG2  CB2  128.25  3.000
 4M9  H10  CD1  NE1  121.23  3.000
 4M9  H10  CD1  CG2  129.06  3.000
 4M9  NE1  CD1  CG2  109.70  3.000
 4M9  H11  NE1  CE2  125.39  3.000
 4M9  H11  NE1  CD1  124.26  3.000
 4M9  CE2  NE1  CD1  110.35  3.000
 4M9  CZ2  CE2  CD2  122.71  3.000
 4M9  CZ2  CE2  NE1  130.05  3.000
 4M9  CD2  CE2  NE1  107.24  3.000
 4M9  CE3  CD2  CE2  119.04  3.000
 4M9  CE2  CD2  CG2  106.87  3.000
 4M9  CE3  CD2  CG2  134.09  3.000
 4M9  H12  CZ2  CH2  121.42  3.000
 4M9  H12  CZ2  CE2  121.46  3.000
 4M9  CH2  CZ2  CE2  117.12  3.000
 4M9  H13  CH2  CZ3  119.39  3.000
 4M9  H13  CH2  CZ2  119.45  3.000
 4M9  CZ3  CH2  CZ2  121.17  3.000
 4M9  H14  CZ3  CE3  119.52  3.000
 4M9  H14  CZ3  CH2  119.23  3.000
 4M9  CE3  CZ3  CH2  121.25  3.000
 4M9  H15  CE3  CZ3  120.13  3.000
 4M9  H15  CE3  CD2  121.17  3.000
 4M9  CZ3  CE3  CD2  118.71  3.000
 4M9  O5   C3   N4   123.03  3.000
 4M9  O5   C3   CG1  122.31  3.000
 4M9  N4   C3   CG1  114.65  3.000
 4M9  H17  N4   H16  117.39  3.000
 4M9  H17  N4   C3   120.54  3.000
 4M9  H16  N4   C3   121.99  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
 4M9  CONST_01  CE2  NE1  CD1  CG2     0.00   0.0  0
 4M9  CONST_02  CZ3  CE3  CD2  CG2   180.00   0.0  0
 4M9  CONST_03  NE1  CE2  CD2  CG2     0.00   0.0  0
 4M9  CONST_04  CZ2  CE2  CD2  CG2   180.00   0.0  0
 4M9  CONST_05  CE3  CD2  CG2  CD1   180.00   0.0  0
 4M9  CONST_06  CE2  CD2  CG2  CD1     0.00   0.0  0
 4M9  CONST_07  CD2  CE2  NE1  CD1     0.00   0.0  0
 4M9  CONST_08  CZ2  CE2  NE1  CD1   180.00   0.0  0
 4M9  CONST_09  CD2  CG2  CD1  NE1     0.00   0.0  0
 4M9  CONST_10  CE3  CD2  CE2  NE1   180.00   0.0  0
 4M9  CONST_11  CH2  CZ2  CE2  NE1   180.00   0.0  0
 4M9  CONST_12  CZ3  CE3  CD2  CE2     0.00   0.0  0
 4M9  CONST_13  CZ3  CH2  CZ2  CE2     0.00   0.0  0
 4M9  CONST_14  CH2  CZ3  CE3  CD2     0.00   0.0  0
 4M9  CONST_15  CH2  CZ2  CE2  CD2     0.00   0.0  0
 4M9  CONST_16  CE3  CD2  CE2  CZ2     0.00   0.0  0
 4M9  CONST_17  CE3  CZ3  CH2  CZ2     0.00   0.0  0
 4M9  CONST_18  N2   C1   N3   C2      0.00   0.0  0
 4M9  CONST_19  C1   N2   CA2  C2      0.00   0.0  0
 4M9  CONST_20  N2   CA2  C2   N3      0.00   0.0  0
 4M9  CONST_21  CA2  N2   C1   N3      0.00   0.0  0
 4M9  CONST_22  C1   N3   C2   CA2     0.00   0.0  0
 4M9  CONST_23  NE1  CD1  CG2  CB2   180.00   0.0  0
 4M9  CONST_24  CE3  CD2  CG2  CB2     0.00   0.0  0
 4M9  CONST_25  CE2  CD2  CG2  CB2   180.00   0.0  0
 4M9  CONST_26  C1   N3   C2   O2    180.00   0.0  0
 4M9  CONST_27  CA1  C1   N3   C2    180.00   0.0  0
 4M9  CONST_28  CA2  C2   N3   CA3   180.00   0.0  0
 4M9  CONST_29  N2   C1   N3   CA3   180.00   0.0  0
 4M9  CONST_30  CA1  C1   N2   CA2   180.00   0.0  0
 4M9  CONST_31  H11  NE1  CD1  CG2   180.00   0.0  0
 4M9  CONST_32  H15  CE3  CD2  CG2     0.00   0.0  0
 4M9  CONST_33  H12  CZ2  CE2  NE1     0.00   0.0  0
 4M9  CONST_34  H10  CD1  NE1  CE2   180.00   0.0  0
 4M9  CONST_35  H13  CH2  CZ2  CE2   180.00   0.0  0
 4M9  CONST_36  H14  CZ3  CE3  CD2   180.00   0.0  0
 4M9  CONST_37  CA3  N3   C2   O2      0.00   0.0  0
 4M9  CONST_38  CA1  C1   N3   CA3     0.00   0.0  0
 4M9  CONST_39  H16  N4   C3   CG1     0.00   0.0  0
 4M9  CONST_40  H17  N4   C3   CG1   180.00   0.0  0
 4M9  Var_01    CG2  CB2  CA2  C2    179.06  30.0  2
 4M9  Var_02    CD1  CG2  CB2  CA2    -0.03  30.0  2
 4M9  Var_03    C    CA3  N3   C2    116.25  30.0  1
 4M9  Var_04    N    CA1  C1   N3     12.01  30.0  2
 4M9  Var_05    O    C    CA3  N3    170.64  30.0  2
 4M9  Var_06    CG1  CB1  CA1  C1   -175.25  30.0  3
 4M9  Var_07    C3   CG1  CB1  CA1   175.51  30.0  2
 4M9  Var_08    N4   C3   CG1  CB1   152.84  30.0  3

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
 4M9  plan-1  O2   0.020
 4M9  plan-1  C2   0.020
 4M9  plan-1  N3   0.020
 4M9  plan-1  CA3  0.020
 4M9  plan-1  CA2  0.020
 4M9  plan-1  N2   0.020
 4M9  plan-1  C1   0.020
 4M9  plan-1  CA1  0.020
 4M9  plan-1  CB2  0.020
 4M9  plan-2  CB2  0.020
 4M9  plan-2  CG2  0.020
 4M9  plan-2  CD1  0.020
 4M9  plan-2  NE1  0.020
 4M9  plan-2  CE2  0.020
 4M9  plan-2  CD2  0.020
 4M9  plan-2  CZ2  0.020
 4M9  plan-2  CH2  0.020
 4M9  plan-2  CZ3  0.020
 4M9  plan-2  CE3  0.020
 4M9  plan-2  H10  0.020
 4M9  plan-2  H11  0.020
 4M9  plan-2  H12  0.020
 4M9  plan-2  H13  0.020
 4M9  plan-2  H14  0.020
 4M9  plan-2  H15  0.020
 4M9  plan-3  CG1  0.020
 4M9  plan-3  C3   0.020
 4M9  plan-3  N4   0.020
 4M9  plan-3  O5   0.020
 4M9  plan-3  H16  0.020
 4M9  plan-3  H17  0.020
 4M9  plan-4  CA3  0.020
 4M9  plan-4  C    0.020
 4M9  plan-4  O    0.020
 4M9  plan-4  H3   0.020
 4M9  plan-5  C1   0.020
 4M9  plan-5  CA1  0.020
 4M9  plan-5  N    0.020
 4M9  plan-5  CB1  0.020
 4M9  plan-5  H4   0.020

