# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:39:41 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[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
 H63  H63  "(2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide"  ligand  58  29  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_H63
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
 H63  C19  C  C     0   0.589   7.4576  25.6966   1.3590
 H63  O28  O  O     0  -0.491   8.1909  25.0037   2.0567
 H63  C20  C  C1    0  -0.425   7.3366  27.1620   1.5162
 H63  C21  C  C1    0  -0.228   8.0802  27.8126   2.4162
 H63  C22  C  CR6   0   0.150   8.0739  29.2454   2.6973
 H63  C23  C  CR16  0  -0.314   7.2196  30.1497   2.0568
 H63  C24  C  CR16  0  -0.231   7.2577  31.4971   2.3704
 H63  C25  C  CR16  0  -0.259   8.1490  31.9712   3.3284
 H63  C26  C  CR16  0  -0.238   9.0020  31.0860   3.9714
 H63  C27  C  CR16  0  -0.306   8.9625  29.7356   3.6576
 H63  N18  N  NH1   0  -0.663   6.6874  25.1613   0.3923
 H63  C13  C  CH1   0  -0.184   6.7376  23.7555   0.0915
 H63  C12  C  C     0   0.566   8.1213  23.3775  -0.4403
 H63  O29  O  O     0  -0.472   8.7574  24.1216  -1.1644
 H63  C14  C  CH2   0  -0.459   5.6726  23.3811  -0.9403
 H63  C15  C  CH2   0  -0.425   4.2507  23.5279  -0.4082
 H63  C16  C  CH2   0  -0.427   3.1794  23.1369  -1.4224
 H63  C17  C  CH3   0  -0.668   3.2105  21.6671  -1.8223
 H63  C09  C  CR5   0   0.570  11.6997  22.1426   2.9326
 H63  N08  N  NR15  0  -0.631  12.4696  23.2118   3.1980
 H63  C07  C  CH2   0  -0.260  12.2718  24.3297   2.2994
 H63  C06  C  CH2   0  -0.467  11.6305  23.6563   1.0861
 H63  C05  C  CR15  0  -0.421  10.8802  22.4720   1.6924
 H63  C04  C  CH2   0  -0.431  10.6773  21.2695   0.7876
 H63  C03  C  CH1   0  -0.215   9.8203  21.5921  -0.4321
 H63  N11  N  NH1   0  -0.641   8.5350  22.1460  -0.0796
 H63  C02  C  C1    0   0.192   9.6001  20.4027  -1.3440
 H63  O01  O  O     0  -0.359  10.2098  19.3685  -1.2820
 H63  H7   H  H     0   0.271   6.6293  27.6800   0.8780
 H63  H9   H  H     0   0.261   8.7718  27.2277   3.0155
 H63  H26  H  HCR6  0   0.255   6.5169  29.8033   1.3099
 H63  H11  H  HCR6  0   0.260   6.5888  32.1833   1.8673
 H63  H27  H  HCR6  0   0.261   8.1749  33.0255   3.5710
 H63  H12  H  HCR6  0   0.259   9.6977  31.4453   4.7183
 H63  H28  H  HCR6  0   0.259   9.6296  29.0477   4.1634
 H63  H31  H  HNH1  0   0.407   6.1639  25.7680  -0.2195
 H63  H1   H  HCH1  0   0.270   6.5405  23.1901   1.0087
 H63  H22  H  HCH2  0   0.256   5.8500  22.3455  -1.2380
 H63  H23  H  HCH2  0   0.239   5.8062  23.9901  -1.8405
 H63  H2   H  HCH2  0   0.230   4.0753  24.5598  -0.0928
 H63  H3   H  HCH2  0   0.219   4.1418  22.9106   0.4896
 H63  H24  H  HCH2  0   0.215   3.2748  23.7645  -2.3138
 H63  H25  H  HCH2  0   0.225   2.2007  23.3687  -0.9948
 H63  H4   H  HCH3  0   0.230   2.3707  21.4196  -2.4723
 H63  H5   H  HCH3  0   0.221   4.1225  21.4053  -2.3601
 H63  H6   H  HCH3  0   0.217   3.1503  21.0224  -0.9434
 H63  H20  H  HCH2  0   0.250  13.2172  24.8165   2.0618
 H63  H21  H  HCH2  0   0.233  11.6065  25.0795   2.7390
 H63  H18  H  HCH2  0   0.256  10.9904  24.3374   0.5294
 H63  H19  H  HCH2  0   0.244  12.4095  23.2956   0.4090
 H63  H17  H  HCR5  0   0.285   9.9062  22.8187   2.0601
 H63  H15  H  HCH2  0   0.249  10.2153  20.4587   1.3569
 H63  H16  H  HCH2  0   0.251  11.6465  20.9015   0.4423
 H63  H14  H  HCH1  0   0.302  10.3250  22.3426  -1.0523
 H63  H30  H  HNH1  0   0.408   7.9675  21.6212   0.5700
 H63  H13  H  H     0   0.208   8.8117  20.5669  -2.1018
 H63  H29  H  HNR5  0   0.394  13.0149  23.2820   4.0433
 H63  O10  O  O     0  -0.485  11.6533  21.1072   3.5756

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
 H63  C17  C16  single    1.523  0.020  1.523
 H63  C16  C15  single    1.526  0.020  1.526
 H63  O01  C02  double    1.202  0.020  1.202
 H63  C14  C15  single    1.525  0.020  1.525
 H63  C14  C13  single    1.529  0.020  1.529
 H63  O29  C12  double    1.218  0.020  1.218
 H63  C02  C03  single    1.515  0.020  1.515
 H63  C12  C13  single    1.530  0.020  1.530
 H63  C12  N11  single    1.348  0.020  1.348
 H63  C03  N11  single    1.443  0.020  1.443
 H63  C03  C04  single    1.525  0.020  1.525
 H63  C13  N18  single    1.439  0.020  1.439
 H63  N18  C19  single    1.347  0.020  1.347
 H63  C06  C07  single    1.529  0.020  1.529
 H63  C06  C05  single    1.527  0.020  1.527
 H63  C04  C05  single    1.518  0.020  1.518
 H63  C07  N08  single    1.448  0.020  1.448
 H63  C05  C09  single    1.523  0.020  1.523
 H63  C19  C20  single    1.479  0.020  1.479
 H63  C19  O28  double    1.227  0.020  1.227
 H63  C20  C21  double    1.336  0.020  1.336
 H63  C23  C24  aromatic  1.384  0.020  1.384
 H63  C23  C22  aromatic  1.399  0.020  1.399
 H63  C24  C25  aromatic  1.392  0.020  1.392
 H63  N08  C09  single    1.344  0.020  1.344
 H63  C21  C22  single    1.460  0.020  1.460
 H63  C09  O10  double    1.220  0.020  1.220
 H63  C22  C27  aromatic  1.397  0.020  1.397
 H63  C25  C26  aromatic  1.387  0.020  1.387
 H63  C27  C26  aromatic  1.387  0.020  1.387
 H63  C13  H1   single    0.970  0.020  1.090
 H63  C15  H2   single    0.970  0.020  1.090
 H63  C15  H3   single    0.970  0.020  1.090
 H63  C17  H4   single    0.970  0.020  1.090
 H63  C17  H5   single    0.970  0.020  1.090
 H63  C17  H6   single    0.970  0.020  1.090
 H63  C20  H7   single    0.930  0.020  1.080
 H63  C21  H9   single    0.930  0.020  1.080
 H63  C24  H11  single    0.930  0.020  1.080
 H63  C26  H12  single    0.930  0.020  1.080
 H63  C02  H13  single    0.930  0.020  1.080
 H63  C03  H14  single    0.970  0.020  1.090
 H63  C04  H15  single    0.970  0.020  1.090
 H63  C04  H16  single    0.970  0.020  1.090
 H63  C05  H17  single    0.970  0.020  1.090
 H63  C06  H18  single    0.970  0.020  1.090
 H63  C06  H19  single    0.970  0.020  1.090
 H63  C07  H20  single    0.970  0.020  1.090
 H63  C07  H21  single    0.970  0.020  1.090
 H63  C14  H22  single    0.970  0.020  1.090
 H63  C14  H23  single    0.970  0.020  1.090
 H63  C16  H24  single    0.970  0.020  1.090
 H63  C16  H25  single    0.970  0.020  1.090
 H63  C23  H26  single    0.930  0.020  1.080
 H63  C25  H27  single    0.930  0.020  1.080
 H63  C27  H28  single    0.930  0.020  1.080
 H63  N08  H29  single    0.860  0.020  1.020
 H63  N11  H30  single    0.860  0.020  1.020
 H63  N18  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
 H63  N18  C19  C20  115.04  3.000
 H63  C20  C19  O28  123.25  3.000
 H63  N18  C19  O28  121.71  3.000
 H63  H7   C20  C21  121.77  3.000
 H63  H7   C20  C19  117.66  3.000
 H63  C21  C20  C19  120.56  3.000
 H63  H9   C21  C22  115.15  3.000
 H63  H9   C21  C20  117.62  3.000
 H63  C22  C21  C20  127.23  3.000
 H63  C27  C22  C23  118.43  3.000
 H63  C27  C22  C21  118.29  3.000
 H63  C23  C22  C21  123.28  3.000
 H63  H26  C23  C24  119.07  3.000
 H63  H26  C23  C22  120.35  3.000
 H63  C24  C23  C22  120.58  3.000
 H63  H11  C24  C25  119.99  3.000
 H63  H11  C24  C23  119.66  3.000
 H63  C25  C24  C23  120.35  3.000
 H63  H27  C25  C26  120.20  3.000
 H63  H27  C25  C24  120.10  3.000
 H63  C26  C25  C24  119.70  3.000
 H63  H12  C26  C27  119.85  3.000
 H63  H12  C26  C25  120.22  3.000
 H63  C27  C26  C25  119.92  3.000
 H63  H28  C27  C26  119.67  3.000
 H63  H28  C27  C22  119.32  3.000
 H63  C26  C27  C22  121.01  3.000
 H63  H31  N18  C13  118.64  3.000
 H63  H31  N18  C19  119.56  3.000
 H63  C13  N18  C19  121.23  3.000
 H63  H1   C13  C14  108.26  3.000
 H63  H1   C13  C12  109.05  3.000
 H63  C14  C13  C12  109.57  3.000
 H63  H1   C13  N18  108.85  3.000
 H63  C12  C13  N18  110.22  3.000
 H63  C14  C13  N18  110.85  3.000
 H63  N11  C12  O29  123.84  3.000
 H63  N11  C12  C13  114.22  3.000
 H63  O29  C12  C13  121.89  3.000
 H63  H23  C14  H22  106.47  3.000
 H63  H23  C14  C15  110.31  3.000
 H63  H22  C14  C15  109.75  3.000
 H63  H23  C14  C13  109.48  3.000
 H63  H22  C14  C13  107.63  3.000
 H63  C15  C14  C13  112.97  3.000
 H63  H3   C15  H2   106.24  3.000
 H63  H3   C15  C16  109.31  3.000
 H63  H2   C15  C16  108.72  3.000
 H63  H3   C15  C14  108.94  3.000
 H63  H2   C15  C14  109.94  3.000
 H63  C16  C15  C14  113.44  3.000
 H63  H25  C16  H24  105.97  3.000
 H63  H25  C16  C17  109.00  3.000
 H63  H24  C16  C17  109.74  3.000
 H63  H25  C16  C15  108.31  3.000
 H63  H24  C16  C15  109.46  3.000
 H63  C17  C16  C15  114.04  3.000
 H63  H6   C17  H5   107.53  3.000
 H63  H6   C17  H4   107.66  3.000
 H63  H5   C17  H4   107.19  3.000
 H63  H6   C17  C16  110.93  3.000
 H63  H5   C17  C16  112.22  3.000
 H63  H4   C17  C16  111.09  3.000
 H63  C05  C09  N08  107.28  3.000
 H63  N08  C09  O10  126.37  3.000
 H63  C05  C09  O10  126.34  3.000
 H63  H29  N08  C07  122.71  3.000
 H63  H29  N08  C09  122.05  3.000
 H63  C07  N08  C09  114.42  3.000
 H63  H21  C07  H20  107.99  3.000
 H63  H21  C07  C06  111.44  3.000
 H63  H20  C07  C06  112.81  3.000
 H63  H21  C07  N08  111.26  3.000
 H63  H20  C07  N08  111.21  3.000
 H63  C06  C07  N08  102.11  3.000
 H63  H19  C06  H18  107.99  3.000
 H63  H19  C06  C05  109.88  3.000
 H63  H18  C06  C05  113.55  3.000
 H63  H19  C06  C07  109.75  3.000
 H63  H18  C06  C07  112.16  3.000
 H63  C05  C06  C07  103.45  3.000
 H63  H17  C05  C04  109.35  3.000
 H63  H17  C05  C06  108.91  3.000
 H63  C04  C05  C06  116.31  3.000
 H63  H17  C05  C09  105.85  3.000
 H63  C04  C05  C09  112.70  3.000
 H63  C06  C05  C09  103.10  3.000
 H63  H16  C04  H15  106.84  3.000
 H63  H16  C04  C03  108.47  3.000
 H63  H15  C04  C03  109.62  3.000
 H63  H16  C04  C05  109.67  3.000
 H63  H15  C04  C05  109.49  3.000
 H63  C03  C04  C05  112.58  3.000
 H63  H14  C03  C02  105.30  3.000
 H63  H14  C03  N11  106.57  3.000
 H63  C02  C03  N11  108.60  3.000
 H63  H14  C03  C04  109.78  3.000
 H63  N11  C03  C04  112.72  3.000
 H63  C02  C03  C04  113.39  3.000
 H63  H30  N11  C03  117.27  3.000
 H63  H30  N11  C12  118.32  3.000
 H63  C03  N11  C12  123.95  3.000
 H63  H13  C02  O01  121.65  3.000
 H63  H13  C02  C03  113.55  3.000
 H63  O01  C02  C03  124.80  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
 H63  CONST_01  C25  C24  C23  C22     0.00   0.0  0
 H63  CONST_02  C25  C26  C27  C22     0.00   0.0  0
 H63  CONST_03  C26  C25  C24  C23     0.00   0.0  0
 H63  CONST_04  C26  C27  C22  C23     0.00   0.0  0
 H63  CONST_05  C27  C22  C23  C24     0.00   0.0  0
 H63  CONST_06  C27  C26  C25  C24     0.00   0.0  0
 H63  CONST_07  C05  C09  N08  C07     0.00   0.0  0
 H63  CONST_08  C24  C23  C22  C21   180.00   0.0  0
 H63  CONST_09  C26  C27  C22  C21   180.00   0.0  0
 H63  CONST_10  C07  N08  C09  O10   180.00   0.0  0
 H63  CONST_11  H11  C24  C23  C22   180.00   0.0  0
 H63  CONST_12  H12  C26  C27  C22   180.00   0.0  0
 H63  CONST_13  H27  C25  C24  C23   180.00   0.0  0
 H63  CONST_14  H28  C27  C22  C23   180.00   0.0  0
 H63  CONST_15  H12  C26  C25  C24   180.00   0.0  0
 H63  CONST_16  H26  C23  C24  C25   180.00   0.0  0
 H63  CONST_17  H28  C27  C26  C25   180.00   0.0  0
 H63  CONST_18  H11  C24  C25  C26   180.00   0.0  0
 H63  CONST_19  H26  C23  C22  C27   180.00   0.0  0
 H63  CONST_20  H27  C25  C26  C27   180.00   0.0  0
 H63  CONST_21  H29  N08  C09  C05   180.00   0.0  0
 H63  CONST_22  H29  N08  C09  O10     0.00   0.0  0
 H63  CONST_23  C13  N18  C19  O28     0.00   0.0  0
 H63  CONST_24  C13  N18  C19  C20   180.00   0.0  0
 H63  CONST_25  C03  N11  C12  C13   180.00   0.0  0
 H63  CONST_26  C03  N11  C12  O29     0.00   0.0  0
 H63  CONST_27  H31  N18  C19  O28   180.00   0.0  0
 H63  CONST_28  H31  N18  C19  C20     0.00   0.0  0
 H63  CONST_29  H30  N11  C12  C13     0.00   0.0  0
 H63  CONST_30  H30  N11  C12  O29   180.00   0.0  0
 H63  Var_01    C06  C07  N08  C09   -20.44  30.0  1
 H63  Var_02    C05  C06  C07  N08    29.62  30.0  1
 H63  Var_03    H20  C07  N08  C09  -141.01  30.0  1
 H63  Var_04    H21  C07  N08  C09    98.55  30.0  1
 H63  Var_05    H18  C06  C07  N08   152.37  30.0  1
 H63  Var_06    H19  C06  C07  N08   -87.60  30.0  1
 H63  Var_07    H29  N08  C07  C06   169.73  30.0  1
 H63  Var_08    H20  C07  C06  C05   149.07  30.0  1
 H63  Var_09    H21  C07  C06  C05   -89.25  30.0  1
 H63  Var_10    C23  C22  C21  C20     2.09  30.0  2
 H63  Var_11    C27  C22  C21  C20  -178.15  30.0  2
 H63  Var_12    H9   C21  C22  C23  -177.87  30.0  3
 H63  Var_13    H9   C21  C22  C27     1.89  30.0  3
 H63  Var_14    C22  C21  C20  C19  -179.63   0.0  2
 H63  Var_15    H7   C20  C21  C22     0.44   0.0  2
 H63  Var_16    C21  C20  C19  O28     2.61  30.0  2
 H63  Var_17    N18  C19  C20  C21  -178.03  30.0  1
 H63  Var_18    C16  C15  C14  C13  -179.13  30.0  3
 H63  Var_19    C17  C16  C15  C14    64.14  30.0  1
 H63  Var_20    H9   C21  C20  C19     0.32   0.0  2
 H63  Var_21    H7   C20  C19  O28  -177.46  30.0  2
 H63  Var_22    H7   C20  C19  N18     1.91  30.0  2
 H63  Var_23    H2   C15  C14  C13    58.90  30.0  3
 H63  Var_24    H3   C15  C14  C13   -57.14  30.0  3
 H63  Var_25    H24  C16  C15  C14   -59.21  30.0  1
 H63  Var_26    H25  C16  C15  C14  -174.32  30.0  1
 H63  Var_27    H4   C17  C16  C15   174.60  30.0  3
 H63  Var_28    H5   C17  C16  C15   -65.41  30.0  3
 H63  Var_29    H6   C17  C16  C15    54.89  30.0  3
 H63  Var_30    H22  C14  C15  C16   -59.02  30.0  1
 H63  Var_31    H23  C14  C15  C16    57.98  30.0  1
 H63  Var_32    H2   C15  C16  C17  -173.21  30.0  3
 H63  Var_33    H3   C15  C16  C17   -57.64  30.0  3
 H63  Var_34    H9   C21  C20  H7   -179.61   0.0  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
 H63  chir_01  C13  C14  C12  N18  negativ
 H63  chir_02  C05  C06  C04  C09  negativ
 H63  chir_03  C03  N11  C02  C04  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
 H63  plan-1  C19  0.020
 H63  plan-1  C20  0.020
 H63  plan-1  C21  0.020
 H63  plan-1  C22  0.020
 H63  plan-1  H7   0.020
 H63  plan-1  H9   0.020
 H63  plan-2  C21  0.020
 H63  plan-2  C22  0.020
 H63  plan-2  C23  0.020
 H63  plan-2  C24  0.020
 H63  plan-2  C25  0.020
 H63  plan-2  C26  0.020
 H63  plan-2  C27  0.020
 H63  plan-2  H26  0.020
 H63  plan-2  H11  0.020
 H63  plan-2  H27  0.020
 H63  plan-2  H12  0.020
 H63  plan-2  H28  0.020
 H63  plan-3  C13  0.020
 H63  plan-3  C12  0.020
 H63  plan-3  O29  0.020
 H63  plan-3  C03  0.020
 H63  plan-3  N11  0.020
 H63  plan-3  H30  0.020
 H63  plan-4  C19  0.020
 H63  plan-4  O28  0.020
 H63  plan-4  C20  0.020
 H63  plan-4  N18  0.020
 H63  plan-4  C13  0.020
 H63  plan-4  H31  0.020
 H63  plan-5  C09  0.020
 H63  plan-5  N08  0.020
 H63  plan-5  C07  0.020
 H63  plan-5  C05  0.020
 H63  plan-5  H29  0.020
 H63  plan-5  O10  0.020
 H63  plan-6  C03  0.020
 H63  plan-6  C02  0.020
 H63  plan-6  O01  0.020
 H63  plan-6  H13  0.020

