# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:57:41 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: (2~{S})-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)\C=C\c1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C=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
 EOF  EOF  (2~{S})-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pentanamide  ligand  58  29  .  2022-03-18  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EOF
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
 EOF  C09  C  C     0   0.595  -24.0562  -15.2527   4.0332
 EOF  O18  O  O     0  -0.488  -22.8348  -15.2095   3.9480
 EOF  C10  C  C1    0  -0.428  -24.9293  -14.0747   3.8454
 EOF  C11  C  C1    0  -0.228  -24.4107  -12.8776   3.5563
 EOF  C12  C  CR6   0   0.150  -25.1432  -11.6324   3.3447
 EOF  C13  C  CR16  0  -0.315  -26.5390  -11.5499   3.3920
 EOF  C14  C  CR16  0  -0.233  -27.1802  -10.3413   3.1839
 EOF  C15  C  CR16  0  -0.260  -26.4429   -9.1900   2.9236
 EOF  C16  C  CR16  0  -0.240  -25.0579   -9.2573   2.8728
 EOF  C17  C  CR16  0  -0.307  -24.4158  -10.4691   3.0816
 EOF  N08  N  NH1   0  -0.663  -24.7093  -16.3961   4.3231
 EOF  C03  C  CH1   0  -0.208  -24.0088  -17.6444   4.4564
 EOF  C02  C  C     0   0.584  -23.4033  -18.0517   3.1123
 EOF  O01  O  O     0  -0.478  -24.0068  -17.8870   2.0672
 EOF  C04  C  CH2   0  -0.445  -24.9616  -18.7452   4.9244
 EOF  C05  C  CH1   0  -0.238  -25.5908  -18.5162   6.3016
 EOF  C06  C  CH3   0  -0.652  -26.5407  -19.6681   6.6158
 EOF  C07  C  CH3   0  -0.665  -24.5391  -18.3760   7.3967
 EOF  C28  C  CR5   0   0.571  -19.1015  -16.0371   1.5083
 EOF  N27  N  NR15  0  -0.629  -19.3110  -15.0892   0.5816
 EOF  C26  C  CH2   0  -0.259  -20.6587  -15.0511   0.0545
 EOF  C25  C  CH2   0  -0.471  -21.1853  -16.4432   0.4082
 EOF  C24  C  CR15  0  -0.429  -20.3950  -16.8230   1.6603
 EOF  C23  C  CH2   0  -0.428  -20.1460  -18.3078   1.8674
 EOF  C20  C  CH1   0  -0.220  -21.4349  -19.0962   2.0602
 EOF  N19  N  NH1   0  -0.642  -22.2000  -18.6507   3.2002
 EOF  C21  C  C1    0   0.196  -21.2188  -20.5890   2.1844
 EOF  O22  O  O     0  -0.366  -20.1895  -21.1567   1.9306
 EOF  H1   H  H     0   0.272  -25.9985  -14.2204   3.9527
 EOF  H21  H  H     0   0.261  -23.3311  -12.8019   3.4667
 EOF  H3   H  HCR6  0   0.257  -27.1329  -12.4331   3.5899
 EOF  H23  H  HCR6  0   0.263  -28.2605  -10.2941   3.2230
 EOF  H4   H  HCR6  0   0.263  -26.9486   -8.2474   2.7593
 EOF  H24  H  HCR6  0   0.262  -24.4765   -8.3677   2.6689
 EOF  H5   H  HCR6  0   0.260  -23.3342  -10.5170   3.0413
 EOF  H29  H  HNH1  0   0.406  -25.7162  -16.4120   4.2800
 EOF  H11  H  HCH1  0   0.273  -23.2080  -17.5243   5.1913
 EOF  H12  H  HCH2  0   0.248  -25.7501  -18.8665   4.1749
 EOF  H13  H  HCH2  0   0.247  -24.4057  -19.6881   4.9444
 EOF  H14  H  HCH1  0   0.225  -26.1834  -17.5952   6.2724
 EOF  H15  H  HCH3  0   0.230  -27.0321  -19.5206   7.5784
 EOF  H16  H  HCH3  0   0.228  -27.3191  -19.7661   5.8572
 EOF  H17  H  HCH3  0   0.216  -26.0007  -20.6169   6.6630
 EOF  H18  H  HCH3  0   0.234  -25.0106  -18.2972   8.3773
 EOF  H19  H  HCH3  0   0.218  -23.8795  -19.2472   7.4153
 EOF  H20  H  HCH3  0   0.231  -23.9165  -17.4896   7.2691
 EOF  H10  H  HCH2  0   0.251  -20.6563  -14.8617  -1.0184
 EOF  H9   H  HCH2  0   0.233  -21.2477  -14.2634   0.5340
 EOF  H27  H  HCH2  0   0.261  -22.2616  -16.4495   0.5651
 EOF  H28  H  HCH2  0   0.243  -20.9601  -17.1413  -0.4026
 EOF  H8   H  HCR5  0   0.296  -20.9026  -16.4103   2.5411
 EOF  H25  H  HCH2  0   0.250  -19.6167  -18.7152   1.0028
 EOF  H26  H  HCH2  0   0.250  -19.4939  -18.4522   2.7327
 EOF  H6   H  HCH1  0   0.305  -22.0811  -18.9743   1.1828
 EOF  H30  H  HNH1  0   0.407  -21.7458  -18.6821   4.1008
 EOF  H7   H  H     0   0.211  -22.1131  -21.1392   2.5299
 EOF  H31  H  HNR5  0   0.396  -18.6288  -14.3735   0.3838
 EOF  O29  O  O     0  -0.498  -18.0652  -16.2253   2.1264

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
 EOF  C26  N27  single    1.448  0.020  1.448
 EOF  C26  C25  single    1.530  0.020  1.530
 EOF  N27  C28  single    1.342  0.020  1.342
 EOF  C25  C24  single    1.529  0.020  1.529
 EOF  C28  C24  single    1.521  0.020  1.521
 EOF  C28  O29  double    1.221  0.020  1.221
 EOF  C24  C23  single    1.520  0.020  1.520
 EOF  O22  C21  double    1.203  0.020  1.203
 EOF  C23  C20  single    1.523  0.020  1.523
 EOF  O01  C02  double    1.218  0.020  1.218
 EOF  C20  C21  single    1.513  0.020  1.513
 EOF  C20  N19  single    1.443  0.020  1.443
 EOF  C16  C17  aromatic  1.387  0.020  1.387
 EOF  C16  C15  aromatic  1.388  0.020  1.388
 EOF  C17  C12  aromatic  1.397  0.020  1.397
 EOF  C15  C14  aromatic  1.392  0.020  1.392
 EOF  C02  N19  single    1.347  0.020  1.347
 EOF  C02  C03  single    1.529  0.020  1.529
 EOF  C12  C11  single    1.460  0.020  1.460
 EOF  C12  C13  aromatic  1.399  0.020  1.399
 EOF  C14  C13  aromatic  1.384  0.020  1.384
 EOF  C10  C11  double    1.336  0.020  1.336
 EOF  C10  C09  single    1.478  0.020  1.478
 EOF  C09  O18  double    1.225  0.020  1.225
 EOF  C09  N08  single    1.348  0.020  1.348
 EOF  N08  C03  single    1.438  0.020  1.438
 EOF  C03  C04  single    1.529  0.020  1.529
 EOF  C04  C05  single    1.531  0.020  1.531
 EOF  C05  C06  single    1.526  0.020  1.526
 EOF  C05  C07  single    1.525  0.020  1.525
 EOF  C10  H1   single    0.930  0.020  1.080
 EOF  C13  H3   single    0.930  0.020  1.080
 EOF  C15  H4   single    0.930  0.020  1.080
 EOF  C17  H5   single    0.930  0.020  1.080
 EOF  C20  H6   single    0.970  0.020  1.090
 EOF  C21  H7   single    0.930  0.020  1.080
 EOF  C24  H8   single    0.970  0.020  1.090
 EOF  C26  H9   single    0.970  0.020  1.090
 EOF  C26  H10  single    0.970  0.020  1.090
 EOF  C03  H11  single    0.970  0.020  1.090
 EOF  C04  H12  single    0.970  0.020  1.090
 EOF  C04  H13  single    0.970  0.020  1.090
 EOF  C05  H14  single    0.970  0.020  1.090
 EOF  C06  H15  single    0.970  0.020  1.090
 EOF  C06  H16  single    0.970  0.020  1.090
 EOF  C06  H17  single    0.970  0.020  1.090
 EOF  C07  H18  single    0.970  0.020  1.090
 EOF  C07  H19  single    0.970  0.020  1.090
 EOF  C07  H20  single    0.970  0.020  1.090
 EOF  C11  H21  single    0.930  0.020  1.080
 EOF  C14  H23  single    0.930  0.020  1.080
 EOF  C16  H24  single    0.930  0.020  1.080
 EOF  C23  H25  single    0.970  0.020  1.090
 EOF  C23  H26  single    0.970  0.020  1.090
 EOF  C25  H27  single    0.970  0.020  1.090
 EOF  C25  H28  single    0.970  0.020  1.090
 EOF  N08  H29  single    0.860  0.020  1.020
 EOF  N19  H30  single    0.860  0.020  1.020
 EOF  N27  H31  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
 EOF  N08  C09  C10  114.64  3.000
 EOF  N08  C09  O18  121.86  3.000
 EOF  C10  C09  O18  123.49  3.000
 EOF  H1   C10  C11  121.63  3.000
 EOF  H1   C10  C09  117.56  3.000
 EOF  C11  C10  C09  120.81  3.000
 EOF  H21  C11  C12  115.30  3.000
 EOF  H21  C11  C10  117.78  3.000
 EOF  C12  C11  C10  126.92  3.000
 EOF  C17  C12  C13  118.47  3.000
 EOF  C13  C12  C11  123.09  3.000
 EOF  C17  C12  C11  118.44  3.000
 EOF  H3   C13  C14  119.07  3.000
 EOF  H3   C13  C12  120.36  3.000
 EOF  C14  C13  C12  120.57  3.000
 EOF  H23  C14  C15  119.98  3.000
 EOF  H23  C14  C13  119.68  3.000
 EOF  C15  C14  C13  120.34  3.000
 EOF  H4   C15  C16  120.20  3.000
 EOF  H4   C15  C14  120.09  3.000
 EOF  C16  C15  C14  119.71  3.000
 EOF  H24  C16  C17  119.86  3.000
 EOF  H24  C16  C15  120.22  3.000
 EOF  C17  C16  C15  119.92  3.000
 EOF  H5   C17  C16  119.68  3.000
 EOF  H5   C17  C12  119.33  3.000
 EOF  C16  C17  C12  120.99  3.000
 EOF  H29  N08  C03  118.49  3.000
 EOF  H29  N08  C09  119.22  3.000
 EOF  C03  N08  C09  121.35  3.000
 EOF  H11  C03  C04  109.25  3.000
 EOF  H11  C03  C02  109.27  3.000
 EOF  C04  C03  C02  108.90  3.000
 EOF  H11  C03  N08  108.89  3.000
 EOF  C04  C03  N08  110.47  3.000
 EOF  C02  C03  N08  110.04  3.000
 EOF  N19  C02  O01  123.97  3.000
 EOF  N19  C02  C03  114.50  3.000
 EOF  O01  C02  C03  121.46  3.000
 EOF  H13  C04  H12  106.43  3.000
 EOF  H13  C04  C05  108.73  3.000
 EOF  H12  C04  C05  109.66  3.000
 EOF  H13  C04  C03  108.00  3.000
 EOF  H12  C04  C03  108.60  3.000
 EOF  C05  C04  C03  115.06  3.000
 EOF  H14  C05  C07  108.35  3.000
 EOF  H14  C05  C06  107.66  3.000
 EOF  C07  C05  C06  110.54  3.000
 EOF  H14  C05  C04  108.91  3.000
 EOF  C07  C05  C04  112.10  3.000
 EOF  C06  C05  C04  109.15  3.000
 EOF  H17  C06  H16  107.73  3.000
 EOF  H17  C06  H15  107.58  3.000
 EOF  H16  C06  H15  107.71  3.000
 EOF  H17  C06  C05  110.90  3.000
 EOF  H16  C06  C05  111.63  3.000
 EOF  H15  C06  C05  111.11  3.000
 EOF  H20  C07  H19  107.78  3.000
 EOF  H20  C07  H18  107.05  3.000
 EOF  H19  C07  H18  107.65  3.000
 EOF  H20  C07  C05  112.61  3.000
 EOF  H19  C07  C05  110.81  3.000
 EOF  H18  C07  C05  110.74  3.000
 EOF  C24  C28  N27  107.52  3.000
 EOF  C24  C28  O29  126.26  3.000
 EOF  N27  C28  O29  126.21  3.000
 EOF  H31  N27  C26  122.67  3.000
 EOF  H31  N27  C28  122.08  3.000
 EOF  C26  N27  C28  114.54  3.000
 EOF  H9   C26  H10  107.91  3.000
 EOF  H10  C26  C25  112.74  3.000
 EOF  H9   C26  C25  111.62  3.000
 EOF  H10  C26  N27  111.17  3.000
 EOF  H9   C26  N27  111.13  3.000
 EOF  C25  C26  N27  102.26  3.000
 EOF  H28  C25  H27  107.89  3.000
 EOF  H28  C25  C24  110.02  3.000
 EOF  H27  C25  C24  113.08  3.000
 EOF  H28  C25  C26  109.79  3.000
 EOF  H27  C25  C26  112.29  3.000
 EOF  C24  C25  C26  103.74  3.000
 EOF  H8   C24  C23  109.51  3.000
 EOF  H8   C24  C25  108.96  3.000
 EOF  C23  C24  C25  116.05  3.000
 EOF  H8   C24  C28  106.21  3.000
 EOF  C23  C24  C28  112.27  3.000
 EOF  C25  C24  C28  103.27  3.000
 EOF  H26  C23  H25  106.75  3.000
 EOF  H26  C23  C20  109.65  3.000
 EOF  H25  C23  C20  108.49  3.000
 EOF  H26  C23  C24  109.56  3.000
 EOF  H25  C23  C24  109.63  3.000
 EOF  C20  C23  C24  112.60  3.000
 EOF  H6   C20  C21  105.04  3.000
 EOF  H6   C20  N19  106.58  3.000
 EOF  C21  C20  N19  108.38  3.000
 EOF  H6   C20  C23  109.87  3.000
 EOF  N19  C20  C23  112.88  3.000
 EOF  C21  C20  C23  113.58  3.000
 EOF  H30  N19  C20  117.17  3.000
 EOF  H30  N19  C02  118.30  3.000
 EOF  C20  N19  C02  124.00  3.000
 EOF  H7   C21  O22  121.56  3.000
 EOF  H7   C21  C20  113.65  3.000
 EOF  O22  C21  C20  124.79  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
 EOF  CONST_01  C15  C16  C17  C12     0.00   0.0  0
 EOF  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 EOF  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 EOF  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 EOF  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 EOF  CONST_06  C17  C12  C13  C14     0.00   0.0  0
 EOF  CONST_07  C24  C28  N27  C26     0.00   0.0  0
 EOF  CONST_08  C16  C17  C12  C11   180.00   0.0  0
 EOF  CONST_09  C14  C13  C12  C11   180.00   0.0  0
 EOF  CONST_10  C26  N27  C28  O29   180.00   0.0  0
 EOF  CONST_11  H24  C16  C17  C12   180.00   0.0  0
 EOF  CONST_12  H23  C14  C13  C12   180.00   0.0  0
 EOF  CONST_13  H5   C17  C12  C13   180.00   0.0  0
 EOF  CONST_14  H4   C15  C14  C13   180.00   0.0  0
 EOF  CONST_15  H3   C13  C14  C15   180.00   0.0  0
 EOF  CONST_16  H31  N27  C28  C24   180.00   0.0  0
 EOF  CONST_17  C03  N08  C09  O18     0.00   0.0  0
 EOF  CONST_18  C03  N08  C09  C10   180.00   0.0  0
 EOF  CONST_19  C20  N19  C02  C03   180.00   0.0  0
 EOF  CONST_20  C20  N19  C02  O01     0.00   0.0  0
 EOF  CONST_21  H29  N08  C09  O18   180.00   0.0  0
 EOF  CONST_22  H30  N19  C02  C03     0.00   0.0  0
 EOF  Var_01    C25  C26  N27  C28   -19.72  30.0  1
 EOF  Var_02    C24  C25  C26  N27    28.20  30.0  1
 EOF  Var_03    C17  C12  C11  C10   178.47  30.0  3
 EOF  Var_04    C12  C11  C10  C09  -179.99   0.0  2
 EOF  Var_05    C11  C10  C09  O18     0.51  30.0  2
 EOF  Var_06    C06  C05  C04  C03   178.44  30.0  3
 EOF  Var_07    H15  C06  C05  C04  -178.17  30.0  3
 EOF  Var_08    H18  C07  C05  C04  -175.28  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
 EOF  chir_01  C03  C02  N08  C04  negativ
 EOF  chir_02  C24  C25  C28  C23  positiv
 EOF  chir_03  C20  N19  C21  C23  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
 EOF  plan-1  C09  0.020
 EOF  plan-1  C10  0.020
 EOF  plan-1  C11  0.020
 EOF  plan-1  C12  0.020
 EOF  plan-1  H1   0.020
 EOF  plan-1  H21  0.020
 EOF  plan-2  C11  0.020
 EOF  plan-2  C12  0.020
 EOF  plan-2  C13  0.020
 EOF  plan-2  C14  0.020
 EOF  plan-2  C15  0.020
 EOF  plan-2  C16  0.020
 EOF  plan-2  C17  0.020
 EOF  plan-2  H3   0.020
 EOF  plan-2  H23  0.020
 EOF  plan-2  H4   0.020
 EOF  plan-2  H24  0.020
 EOF  plan-2  H5   0.020
 EOF  plan-3  C03  0.020
 EOF  plan-3  C02  0.020
 EOF  plan-3  O01  0.020
 EOF  plan-3  C20  0.020
 EOF  plan-3  N19  0.020
 EOF  plan-3  H30  0.020
 EOF  plan-4  C09  0.020
 EOF  plan-4  O18  0.020
 EOF  plan-4  C10  0.020
 EOF  plan-4  N08  0.020
 EOF  plan-4  C03  0.020
 EOF  plan-4  H29  0.020
 EOF  plan-5  C28  0.020
 EOF  plan-5  N27  0.020
 EOF  plan-5  C26  0.020
 EOF  plan-5  C24  0.020
 EOF  plan-5  H31  0.020
 EOF  plan-5  O29  0.020
 EOF  plan-6  C20  0.020
 EOF  plan-6  C21  0.020
 EOF  plan-6  O22  0.020
 EOF  plan-6  H7   0.020

