# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 18:29:58 2022
#   Inital geometry file: a 171 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-4-methyl-2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]pentanoyl]amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)[C@@H](Cc1ccccc1)NC(=O)OCc2ccccc2)C(=O)N[C@@H](C)C(O)=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
 ORK  ORK  '(2~{S})-2-[[(2~{S})-4-methyl-2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]pentanoyl]amino]propanoic acid'  ligand  68  36  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ORK
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
 ORK  N    N  NH1    0  -0.817  34.6770  41.2033   -4.2373
 ORK  C    C  CH3    0  -0.654  37.9325  42.5599   -1.4929
 ORK  O    O  O      0  -0.791  35.2688  42.6326   -6.3480
 ORK  C1   C  CH1    0  -0.245  37.4575  41.1140   -1.5920
 ORK  C10  C  CR16   0  -0.265  30.8699  36.7346   -8.7534
 ORK  C11  C  CR16   0  -0.235  30.1721  37.9120   -8.5228
 ORK  C12  C  CR16   0  -0.322  30.6788  38.8610   -7.6441
 ORK  C14  C  CH2    0  -0.246  33.5422  40.9361  -11.4884
 ORK  C15  C  CR6    0   0.068  33.0600  39.5640  -11.8718
 ORK  C16  C  CR16   0  -0.294  33.9514  38.5936  -12.3151
 ORK  C17  C  CR16   0  -0.240  33.4979  37.3378  -12.6983
 ORK  C18  C  CR16   0  -0.268  32.1448  37.0362  -12.6282
 ORK  C19  C  CR16   0  -0.229  31.2485  37.9976  -12.1778
 ORK  C2   C  CH3    0  -0.646  37.3688  40.4865   -0.2038
 ORK  C20  C  CR16   0  -0.282  31.7035  39.2536  -11.8049
 ORK  C21  C  C      0   0.527  37.0846  40.7765   -4.5740
 ORK  C22  C  CH1    0  -0.195  37.6561  38.6169   -5.6269
 ORK  C23  C  CH3    0  -0.658  38.7766  38.0909   -4.7282
 ORK  C24  C  C      0   0.427  36.8263  37.4306   -6.1770
 ORK  C3   C  CH2    0  -0.439  36.1027  40.9862   -2.2898
 ORK  C4   C  CH1    0  -0.141  36.0147  41.4786   -3.7412
 ORK  C5   C  CH1    0  -0.335  33.5582  40.5349   -6.7025
 ORK  C6   C  CH2    0  -0.532  32.4400  39.7048   -6.0567
 ORK  C7   C  CR6    0   0.146  31.8855  38.6544   -6.9791
 ORK  C8   C  CR16   0  -0.336  32.5775  37.4683   -7.2196
 ORK  C9   C  CR16   0  -0.248  32.0740  36.5166   -8.0966
 ORK  N1   N  NH1    0  -0.650  33.1430  41.0465   -7.9907
 ORK  N2   N  NH1    0  -0.620  36.7830  39.5248   -4.9220
 ORK  O2   O  O      0  -0.510  34.6716  39.9559   -9.2791
 ORK  O3   O  O2     0  -0.487  33.1162  41.3149  -10.1832
 ORK  O4   O  O      0  -0.516  38.1594  41.3163   -4.8230
 ORK  O5   O  OC    -1  -0.591  37.4208  36.6696   -6.9569
 ORK  O6   O  O      0  -0.587  35.6501  37.3298   -5.7650
 ORK  P    P  P      0   1.261  34.0977  41.9769   -5.6602
 ORK  H1   H  HNH1   0   0.364  33.9922  41.1862   -3.4936
 ORK  H2   H  HCH3   0   0.223  38.8744  42.6196   -0.9449
 ORK  H3   H  HCH3   0   0.227  38.0957  43.0076   -2.4728
 ORK  H4   H  HCH3   0   0.211  37.2022  43.1739   -0.9599
 ORK  H5   H  HCH1   0   0.222  38.2029  40.5474   -2.1598
 ORK  H6   H  HCR6   0   0.244  30.4799  35.9949   -9.4407
 ORK  H7   H  HCR6   0   0.245  29.2332  38.0954   -9.0301
 ORK  H8   H  HCR6   0   0.239  30.1248  39.7763   -7.4695
 ORK  H9   H  HCH2   0   0.248  34.6274  41.0061  -11.5852
 ORK  H10  H  HCH2   0   0.258  33.1031  41.6878  -12.1451
 ORK  H11  H  HCR6   0   0.250  35.0099  38.8203  -12.3614
 ORK  H12  H  HCR6   0   0.253  34.2034  36.5925  -13.0424
 ORK  H13  H  HCR6   0   0.253  31.7899  36.0565  -12.9214
 ORK  H14  H  HCR6   0   0.251  30.1924  37.7683  -12.1168
 ORK  H15  H  HCH3   0   0.224  38.3299  40.5301    0.3114
 ORK  H16  H  HCH3   0   0.212  36.6364  41.0093    0.4162
 ORK  H17  H  HCH3   0   0.223  37.0683  39.4388   -0.2593
 ORK  H18  H  HCR6   0   0.251  30.9946  39.9959  -11.4579
 ORK  H19  H  HCH1   0   0.228  38.1078  39.1392   -6.4761
 ORK  H20  H  HCH3   0   0.228  39.3798  38.9071   -4.3320
 ORK  H21  H  HCH3   0   0.215  38.3670  37.5317   -3.8847
 ORK  H22  H  HCH3   0   0.224  39.4366  37.4283   -5.2865
 ORK  H23  H  HCH2   0   0.227  35.3587  41.5411   -1.7054
 ORK  H24  H  HCH2   0   0.227  35.7892  39.9371   -2.2677
 ORK  H25  H  HCH1   0   0.227  36.2576  42.5463   -3.7693
 ORK  H26  H  HCH1   0   0.252  34.4208  39.8886   -6.8689
 ORK  H27  H  HCH2   0   0.238  31.6343  40.3708   -5.7387
 ORK  H28  H  HCH2   0   0.247  32.8426  39.2424   -5.1525
 ORK  H29  H  HCR6   0   0.274  33.5219  37.2858   -6.7196
 ORK  H30  H  HCR6   0   0.244  32.6255  35.6003   -8.2672
 ORK  H31  H  HNH1   0   0.390  32.3582  41.6798   -8.0130
 ORK  H32  H  HNH1   0   0.382  35.8469  39.1832   -4.7497
 ORK  O1   O  OP    -1  -0.795  32.8508  42.7630   -5.3299
 ORK  C13  C  C      0   0.744  33.7227  40.7026   -9.1494

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
 ORK  C17  C18  aromatic  1.388  0.020  1.388
 ORK  C17  C16  aromatic  1.389  0.020  1.389
 ORK  C18  C19  aromatic  1.389  0.020  1.389
 ORK  C16  C15  aromatic  1.390  0.020  1.390
 ORK  C19  C20  aromatic  1.387  0.020  1.387
 ORK  C15  C20  aromatic  1.393  0.020  1.393
 ORK  C15  C14  single    1.504  0.020  1.504
 ORK  C14  O3   single    1.424  0.020  1.424
 ORK  O3   C13  single    1.346  0.020  1.346
 ORK  O2   C13  double    1.214  0.020  1.214
 ORK  C13  N1   single    1.340  0.020  1.340
 ORK  C10  C11  aromatic  1.388  0.020  1.388
 ORK  C10  C9   aromatic  1.389  0.020  1.389
 ORK  C11  C12  aromatic  1.389  0.020  1.389
 ORK  N1   C5   single    1.447  0.020  1.447
 ORK  C9   C8   aromatic  1.389  0.020  1.389
 ORK  C12  C7   aromatic  1.393  0.020  1.393
 ORK  C8   C7   aromatic  1.394  0.020  1.394
 ORK  C7   C6   single    1.504  0.020  1.504
 ORK  C5   C6   single    1.535  0.020  1.535
 ORK  C5   P    single    1.859  0.020  1.859
 ORK  O    P    deloc     1.508  0.020  1.508
 ORK  O1   P    deloc     1.511  0.020  1.511
 ORK  P    N    single    1.720  0.020  1.720
 ORK  O6   C24  deloc     1.250  0.020  1.250
 ORK  O5   C24  deloc     1.241  0.020  1.241
 ORK  C24  C22  single    1.549  0.020  1.549
 ORK  N    C4   single    1.453  0.020  1.453
 ORK  N2   C22  single    1.444  0.020  1.444
 ORK  N2   C21  single    1.334  0.020  1.334
 ORK  C22  C23  single    1.530  0.020  1.530
 ORK  O4   C21  double    1.228  0.020  1.228
 ORK  C21  C4   single    1.527  0.020  1.527
 ORK  C4   C3   single    1.535  0.020  1.535
 ORK  C3   C1   single    1.529  0.020  1.529
 ORK  C    C1   single    1.525  0.020  1.525
 ORK  C1   C2   single    1.526  0.020  1.526
 ORK  N    H1   single    0.890  0.020  1.040
 ORK  C    H2   single    0.970  0.020  1.090
 ORK  C    H3   single    0.970  0.020  1.090
 ORK  C    H4   single    0.970  0.020  1.090
 ORK  C1   H5   single    0.970  0.020  1.090
 ORK  C10  H6   single    0.930  0.020  1.080
 ORK  C11  H7   single    0.930  0.020  1.080
 ORK  C12  H8   single    0.930  0.020  1.080
 ORK  C14  H9   single    0.970  0.020  1.090
 ORK  C14  H10  single    0.970  0.020  1.090
 ORK  C16  H11  single    0.930  0.020  1.080
 ORK  C17  H12  single    0.930  0.020  1.080
 ORK  C18  H13  single    0.930  0.020  1.080
 ORK  C19  H14  single    0.930  0.020  1.080
 ORK  C2   H15  single    0.970  0.020  1.090
 ORK  C2   H16  single    0.970  0.020  1.090
 ORK  C2   H17  single    0.970  0.020  1.090
 ORK  C20  H18  single    0.930  0.020  1.080
 ORK  C22  H19  single    0.970  0.020  1.090
 ORK  C23  H20  single    0.970  0.020  1.090
 ORK  C23  H21  single    0.970  0.020  1.090
 ORK  C23  H22  single    0.970  0.020  1.090
 ORK  C3   H23  single    0.970  0.020  1.090
 ORK  C3   H24  single    0.970  0.020  1.090
 ORK  C4   H25  single    0.970  0.020  1.090
 ORK  C5   H26  single    0.970  0.020  1.090
 ORK  C6   H27  single    0.970  0.020  1.090
 ORK  C6   H28  single    0.970  0.020  1.090
 ORK  C8   H29  single    0.930  0.020  1.080
 ORK  C9   H30  single    0.930  0.020  1.080
 ORK  N1   H31  single    0.860  0.020  1.020
 ORK  N2   H32  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
 ORK  H1   N    P    112.82  3.000
 ORK  H1   N    C4   112.07  3.000
 ORK  P    N    C4   120.48  3.000
 ORK  H4   C    H3   107.93  3.000
 ORK  H4   C    H2   107.53  3.000
 ORK  H3   C    H2   107.44  3.000
 ORK  H4   C    C1   110.87  3.000
 ORK  H3   C    C1   112.19  3.000
 ORK  H2   C    C1   110.69  3.000
 ORK  H5   C1   C3   108.86  3.000
 ORK  H5   C1   C2   107.37  3.000
 ORK  C3   C1   C2   109.22  3.000
 ORK  H5   C1   C    108.19  3.000
 ORK  C2   C1   C    110.41  3.000
 ORK  C3   C1   C    112.63  3.000
 ORK  H6   C10  C9   120.36  3.000
 ORK  H6   C10  C11  120.27  3.000
 ORK  C9   C10  C11  119.37  3.000
 ORK  H7   C11  C12  119.80  3.000
 ORK  H7   C11  C10  120.12  3.000
 ORK  C12  C11  C10  120.09  3.000
 ORK  H8   C12  C7   119.41  3.000
 ORK  H8   C12  C11  119.49  3.000
 ORK  C7   C12  C11  121.10  3.000
 ORK  H10  C14  H9   107.62  3.000
 ORK  H10  C14  O3   104.36  3.000
 ORK  H9   C14  O3   111.19  3.000
 ORK  H10  C14  C15  110.25  3.000
 ORK  H9   C14  C15  110.77  3.000
 ORK  O3   C14  C15  112.35  3.000
 ORK  C20  C15  C16  118.95  3.000
 ORK  C20  C15  C14  120.22  3.000
 ORK  C16  C15  C14  120.83  3.000
 ORK  H11  C16  C17  119.76  3.000
 ORK  H11  C16  C15  119.60  3.000
 ORK  C17  C16  C15  120.64  3.000
 ORK  H12  C17  C18  120.12  3.000
 ORK  H12  C17  C16  119.82  3.000
 ORK  C18  C17  C16  120.06  3.000
 ORK  H13  C18  C19  120.17  3.000
 ORK  H13  C18  C17  120.17  3.000
 ORK  C19  C18  C17  119.66  3.000
 ORK  H14  C19  C20  119.79  3.000
 ORK  H14  C19  C18  120.07  3.000
 ORK  C20  C19  C18  120.14  3.000
 ORK  H17  C2   H16  107.67  3.000
 ORK  H17  C2   H15  107.75  3.000
 ORK  H16  C2   H15  107.66  3.000
 ORK  H17  C2   C1   111.37  3.000
 ORK  H16  C2   C1   111.00  3.000
 ORK  H15  C2   C1   111.21  3.000
 ORK  H18  C20  C19  119.46  3.000
 ORK  H18  C20  C15  119.98  3.000
 ORK  C19  C20  C15  120.55  3.000
 ORK  O4   C21  N2   123.88  3.000
 ORK  O4   C21  C4   121.45  3.000
 ORK  N2   C21  C4   114.54  3.000
 ORK  H19  C22  N2   109.17  3.000
 ORK  H19  C22  C24  108.13  3.000
 ORK  N2   C22  C24  109.34  3.000
 ORK  H19  C22  C23  108.52  3.000
 ORK  N2   C22  C23  111.86  3.000
 ORK  C24  C22  C23  109.74  3.000
 ORK  H22  C23  H21  108.17  3.000
 ORK  H22  C23  H20  107.86  3.000
 ORK  H21  C23  H20  108.09  3.000
 ORK  H22  C23  C22  110.60  3.000
 ORK  H21  C23  C22  110.80  3.000
 ORK  H20  C23  C22  111.20  3.000
 ORK  O6   C24  O5   127.45  3.000
 ORK  O5   C24  C22  115.86  3.000
 ORK  O6   C24  C22  116.67  3.000
 ORK  H24  C3   H23  106.24  3.000
 ORK  H24  C3   C4   108.05  3.000
 ORK  H23  C3   C4   107.61  3.000
 ORK  H24  C3   C1   108.93  3.000
 ORK  H23  C3   C1   108.40  3.000
 ORK  C4   C3   C1   117.09  3.000
 ORK  H25  C4   C3   108.92  3.000
 ORK  H25  C4   C21  106.19  3.000
 ORK  C3   C4   C21  109.15  3.000
 ORK  H25  C4   N    112.33  3.000
 ORK  C3   C4   N    108.35  3.000
 ORK  C21  C4   N    111.83  3.000
 ORK  H26  C5   P    108.40  3.000
 ORK  H26  C5   N1   107.50  3.000
 ORK  P    C5   N1   107.95  3.000
 ORK  H26  C5   C6   108.65  3.000
 ORK  P    C5   C6   113.26  3.000
 ORK  N1   C5   C6   110.90  3.000
 ORK  H28  C6   H27  106.78  3.000
 ORK  H28  C6   C7   110.36  3.000
 ORK  H27  C6   C7   109.41  3.000
 ORK  H28  C6   C5   107.98  3.000
 ORK  H27  C6   C5   109.27  3.000
 ORK  C7   C6   C5   112.85  3.000
 ORK  C8   C7   C6   121.13  3.000
 ORK  C6   C7   C12  120.57  3.000
 ORK  C8   C7   C12  118.28  3.000
 ORK  H29  C8   C9   119.46  3.000
 ORK  H29  C8   C7   119.74  3.000
 ORK  C9   C8   C7   120.80  3.000
 ORK  H30  C9   C8   119.65  3.000
 ORK  H30  C9   C10  119.99  3.000
 ORK  C8   C9   C10  120.36  3.000
 ORK  H31  N1   C5   117.70  3.000
 ORK  H31  N1   C13  118.58  3.000
 ORK  C5   N1   C13  123.70  3.000
 ORK  H32  N2   C22  115.51  3.000
 ORK  H32  N2   C21  118.82  3.000
 ORK  C22  N2   C21  125.51  3.000
 ORK  C14  O3   C13  116.62  3.000
 ORK  O1   P    C5   106.66  3.000
 ORK  O1   P    O    120.96  3.000
 ORK  C5   P    O    107.87  3.000
 ORK  O1   P    N    109.34  3.000
 ORK  O    P    N    108.14  3.000
 ORK  C5   P    N    102.28  3.000
 ORK  O3   C13  O2   123.35  3.000
 ORK  O2   C13  N1   126.01  3.000
 ORK  O3   C13  N1   110.63  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
 ORK  CONST_01  C7   C12  C11  C10     0.00   0.0  0
 ORK  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 ORK  CONST_03  C8   C9   C10  C11     0.00   0.0  0
 ORK  CONST_04  C8   C7   C12  C11     0.00   0.0  0
 ORK  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 ORK  CONST_06  C9   C8   C7   C12     0.00   0.0  0
 ORK  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 ORK  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 ORK  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 ORK  CONST_10  C19  C20  C15  C16     0.00   0.0  0
 ORK  CONST_11  C20  C19  C18  C17     0.00   0.0  0
 ORK  CONST_12  C20  C15  C16  C17     0.00   0.0  0
 ORK  CONST_13  C6   C7   C12  C11   180.00   0.0  0
 ORK  CONST_14  C17  C16  C15  C14   180.00   0.0  0
 ORK  CONST_15  C19  C20  C15  C14   180.00   0.0  0
 ORK  CONST_16  C9   C8   C7   C6    180.00   0.0  0
 ORK  CONST_17  H8   C12  C11  C10   180.00   0.0  0
 ORK  CONST_18  H29  C8   C9   C10   180.00   0.0  0
 ORK  CONST_19  H30  C9   C10  C11   180.00   0.0  0
 ORK  CONST_20  H6   C10  C11  C12   180.00   0.0  0
 ORK  CONST_21  H12  C17  C16  C15   180.00   0.0  0
 ORK  CONST_22  H14  C19  C20  C15   180.00   0.0  0
 ORK  CONST_23  H13  C18  C17  C16   180.00   0.0  0
 ORK  CONST_24  H18  C20  C15  C16   180.00   0.0  0
 ORK  CONST_25  H11  C16  C17  C18   180.00   0.0  0
 ORK  CONST_26  H7   C11  C12  C7    180.00   0.0  0
 ORK  CONST_27  O4   C21  N2   C22     0.00   0.0  0
 ORK  CONST_28  C4   C21  N2   C22   180.00   0.0  0
 ORK  CONST_29  H32  N2   C21  C4      0.00   0.0  0
 ORK  Var_01    C5   C6   C7   C12  -101.08  30.0  2
 ORK  Var_02    O3   C14  C15  C16  -126.71  30.0  2
 ORK  Var_03    C15  C14  O3   C13    72.75  30.0  3
 ORK  Var_04    C4   C3   C1   C      60.87  30.0  2
 ORK  Var_05    C4   N    P    O      12.53  30.0  3
 ORK  Var_06    O2   C13  O3   C14     6.80  30.0  3
 ORK  Var_07    O3   C13  N1   C5    179.00  30.0  2
 ORK  Var_08    H15  C2   C1   C     -57.53  30.0  3
 ORK  Var_09    H2   C    C1   C2     54.64  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
 ORK  chir_01  C22  C24  N2   C23  negativ
 ORK  chir_02  C4   N    C21  C3   positiv
 ORK  chir_03  C5   P    N1   C6   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
 ORK  plan-1  C10  0.020
 ORK  plan-1  C11  0.020
 ORK  plan-1  C12  0.020
 ORK  plan-1  C6   0.020
 ORK  plan-1  C7   0.020
 ORK  plan-1  C8   0.020
 ORK  plan-1  C9   0.020
 ORK  plan-1  H6   0.020
 ORK  plan-1  H7   0.020
 ORK  plan-1  H8   0.020
 ORK  plan-1  H29  0.020
 ORK  plan-1  H30  0.020
 ORK  plan-2  C14  0.020
 ORK  plan-2  C15  0.020
 ORK  plan-2  C16  0.020
 ORK  plan-2  C17  0.020
 ORK  plan-2  C18  0.020
 ORK  plan-2  C19  0.020
 ORK  plan-2  C20  0.020
 ORK  plan-2  H11  0.020
 ORK  plan-2  H12  0.020
 ORK  plan-2  H13  0.020
 ORK  plan-2  H14  0.020
 ORK  plan-2  H18  0.020
 ORK  plan-3  C21  0.020
 ORK  plan-3  C22  0.020
 ORK  plan-3  C4   0.020
 ORK  plan-3  N2   0.020
 ORK  plan-3  O4   0.020
 ORK  plan-3  H32  0.020
 ORK  plan-4  C22  0.020
 ORK  plan-4  C24  0.020
 ORK  plan-4  O5   0.020
 ORK  plan-4  O6   0.020
 ORK  plan-5  N1   0.020
 ORK  plan-5  O2   0.020
 ORK  plan-5  O3   0.020
 ORK  plan-5  C13  0.020

