# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 03:06:45 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (2~{S})-6-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@@H](CCCCN)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
 8LB  8LB  '(2~{S})-6-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]hexanoic acid'  ligand  66  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8LB
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
 8LB  C10  C  CH2    0  -0.424   0.7650  -3.4448  -0.5673
 8LB  C11  C  CH2    0  -0.268  -0.7180  -3.3728  -0.8926
 8LB  C12  C  C      0   0.404   4.8859  -1.1577   1.2274
 8LB  C13  C  CH2    0  -0.549  -0.2290   1.2144   0.5713
 8LB  C14  C  C      0   0.762  -2.1972  -0.1344   1.1335
 8LB  C15  C  CH2    0  -0.199  -4.0315  -1.6065   1.4007
 8LB  C16  C  CR6    0  -0.066  -4.8217  -2.5336   0.5270
 8LB  C19  C  CR16   0  -0.231  -6.2429  -4.2369  -1.1651
 8LB  C20  C  CR16   0  -0.254  -6.6773  -2.9329  -0.9648
 8LB  C21  C  CR16   0  -0.270  -5.9670  -2.0861  -0.1247
 8LB  O01  O  O      0  -0.835   0.5488   1.2667  -2.0220
 8LB  N01  N  NH1    0  -0.733   1.6578   3.0187  -0.4580
 8LB  C01  C  CH1    0  -0.246   2.9804   2.4876  -0.7060
 8LB  C02  C  CH2    0  -0.448   4.0201   3.6009  -0.7654
 8LB  C03  C  CH1    0  -0.256   3.6832   4.7283  -1.7427
 8LB  C04  C  CH3    0  -0.635   4.7986   5.7687  -1.7419
 8LB  C05  C  CH3    0  -0.670   3.4167   4.2180  -3.1547
 8LB  N02  N  NH1    0  -0.632   3.1935   0.1826  -0.0198
 8LB  C07  C  CH1    0  -0.130   3.3940  -0.9317   0.8740
 8LB  O04  O  O      0  -0.527   3.6767   1.7782   1.4952
 8LB  O05  O  OP    -1  -0.815  -0.8549   3.2721  -1.0800
 8LB  N04  N  NH1    0  -0.602  -1.3338   0.3489   0.2295
 8LB  O06  O  O2     0  -0.546  -3.0936  -0.9439   0.5495
 8LB  C17  C  CR16   0  -0.196  -4.3985  -3.8441   0.3259
 8LB  C18  C  CR16   0  -0.270  -5.1037  -4.6944  -0.5150
 8LB  O07  O  O      0  -0.539  -2.1913   0.1164   2.3234
 8LB  C08  C  CH2    0  -0.456   2.8119  -2.2007   0.2541
 8LB  C09  C  CH2    0  -0.437   1.3164  -2.1269  -0.0381
 8LB  H1   H  HCH2   0   0.202   0.9380  -4.2307   0.1771
 8LB  H2   H  HCH2   0   0.252   1.3135  -3.7428  -1.4664
 8LB  H3   H  HCH2   0   0.202  -1.2601  -3.0235  -0.0039
 8LB  H4   H  HCH2   0   0.216  -0.8789  -2.6122  -1.6623
 8LB  H6   H  HCH2   0   0.270   0.6341   0.6328   0.9092
 8LB  H7   H  HCH2   0   0.263  -0.5198   1.8692   1.3931
 8LB  H8   H  HCH2   0   0.231  -4.6853  -0.8767   1.8841
 8LB  H9   H  HCH2   0   0.278  -3.5104  -2.1639   2.1822
 8LB  H10  H  HCR6   0   0.267  -6.7930  -4.8967  -1.8227
 8LB  H11  H  HCR6   0   0.255  -7.5699  -2.5764  -1.4623
 8LB  H12  H  HCR6   0   0.259  -6.3101  -1.0695   0.0286
 8LB  H13  H  HNH1   0   0.377   1.6032   3.6630   0.3187
 8LB  H14  H  HCH1   0   0.291   2.9489   1.9880  -1.6757
 8LB  H15  H  HCH2   0   0.265   4.1522   4.0239   0.2356
 8LB  H16  H  HCH2   0   0.194   4.9859   3.1602  -1.0393
 8LB  H17  H  HCH1   0   0.189   2.7695   5.2141  -1.3877
 8LB  H18  H  HCH3   0   0.244   5.7352   5.3464  -2.1141
 8LB  H19  H  HCH3   0   0.190   4.5459   6.6194  -2.3777
 8LB  H20  H  HCH3   0   0.250   4.9854   6.1509  -0.7363
 8LB  H21  H  HCH3   0   0.206   4.2775   3.6702  -3.5472
 8LB  H22  H  HCH3   0   0.258   2.5499   3.5561  -3.1910
 8LB  H23  H  HCH3   0   0.218   3.2192   5.0484  -3.8357
 8LB  H24  H  HNH1   0   0.376   2.8882   0.0036  -0.9629
 8LB  H25  H  HCH1   0   0.221   2.8521  -0.7297   1.8046
 8LB  H28  H  HNH1   0   0.406  -1.3592  -0.0206  -0.7083
 8LB  H29  H  HCR6   0   0.257  -3.5130  -4.2051   0.8356
 8LB  H30  H  HCR6   0   0.223  -4.7697  -5.7143  -0.6563
 8LB  H31  H  HCH2   0   0.264   3.3553  -2.4383  -0.6682
 8LB  H32  H  HCH2   0   0.186   3.0032  -3.0225   0.9476
 8LB  H33  H  HCH2   0   0.236   1.1106  -1.3339  -0.7644
 8LB  H34  H  HCH2   0   0.261   0.7843  -1.8419   0.8760
 8LB  N1   N  NH2    0  -0.811  -1.2091  -4.6463  -1.4018
 8LB  H5   H  HNH2   0   0.290  -1.1806  -5.3339  -0.6586
 8LB  H35  H  HNH2   0   0.323  -2.1859  -4.5523  -1.6508
 8LB  O02  O  O      0  -0.641   5.7408  -0.6982   0.4528
 8LB  C06  C  C      0   0.610   3.3472   1.4541   0.3581
 8LB  O03  O  OC    -1  -0.670   5.0843  -1.8352   2.2567
 8LB  P01  P  P      0   1.158   0.2234   2.2334  -0.9053

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
 8LB  C20  C21  aromatic  1.388  0.020  1.388
 8LB  C20  C19  aromatic  1.389  0.020  1.389
 8LB  C21  C16  aromatic  1.392  0.020  1.392
 8LB  C19  C18  aromatic  1.389  0.020  1.389
 8LB  C16  C15  single    1.499  0.020  1.499
 8LB  C16  C17  aromatic  1.392  0.020  1.392
 8LB  C15  O06  single    1.429  0.020  1.429
 8LB  C18  C17  aromatic  1.388  0.020  1.388
 8LB  O06  C14  single    1.342  0.020  1.342
 8LB  O07  C14  double    1.216  0.020  1.216
 8LB  C14  N04  single    1.340  0.020  1.340
 8LB  N04  C13  single    1.444  0.020  1.444
 8LB  C13  P01  single    1.850  0.020  1.850
 8LB  O01  P01  deloc     1.512  0.020  1.512
 8LB  O05  P01  deloc     1.507  0.020  1.507
 8LB  P01  N01  single    1.695  0.020  1.695
 8LB  O02  C12  deloc     1.242  0.020  1.242
 8LB  O03  C12  deloc     1.248  0.020  1.248
 8LB  C12  C07  single    1.550  0.020  1.550
 8LB  N01  C01  single    1.447  0.020  1.447
 8LB  C07  N02  single    1.442  0.020  1.442
 8LB  C07  C08  single    1.528  0.020  1.528
 8LB  N02  C06  single    1.335  0.020  1.335
 8LB  C06  O04  double    1.227  0.020  1.227
 8LB  C06  C01  single    1.528  0.020  1.528
 8LB  C01  C02  single    1.524  0.020  1.524
 8LB  C08  C09  single    1.526  0.020  1.526
 8LB  C09  C10  single    1.523  0.020  1.523
 8LB  C02  C03  single    1.530  0.020  1.530
 8LB  C11  C10  single    1.520  0.020  1.520
 8LB  C05  C03  single    1.525  0.020  1.525
 8LB  C03  C04  single    1.525  0.020  1.525
 8LB  C10  H1   single    0.970  0.020  1.090
 8LB  C10  H2   single    0.970  0.020  1.090
 8LB  C11  H3   single    0.970  0.020  1.090
 8LB  C11  H4   single    0.970  0.020  1.090
 8LB  C13  H6   single    0.970  0.020  1.090
 8LB  C13  H7   single    0.970  0.020  1.090
 8LB  C15  H8   single    0.970  0.020  1.090
 8LB  C15  H9   single    0.970  0.020  1.090
 8LB  C19  H10  single    0.930  0.020  1.080
 8LB  C20  H11  single    0.930  0.020  1.080
 8LB  C21  H12  single    0.930  0.020  1.080
 8LB  N01  H13  single    0.890  0.020  1.040
 8LB  C01  H14  single    0.970  0.020  1.090
 8LB  C02  H15  single    0.970  0.020  1.090
 8LB  C02  H16  single    0.970  0.020  1.090
 8LB  C03  H17  single    0.970  0.020  1.090
 8LB  C04  H18  single    0.970  0.020  1.090
 8LB  C04  H19  single    0.970  0.020  1.090
 8LB  C04  H20  single    0.970  0.020  1.090
 8LB  C05  H21  single    0.970  0.020  1.090
 8LB  C05  H22  single    0.970  0.020  1.090
 8LB  C05  H23  single    0.970  0.020  1.090
 8LB  N02  H24  single    0.860  0.020  1.020
 8LB  C07  H25  single    0.970  0.020  1.090
 8LB  N04  H28  single    0.860  0.020  1.020
 8LB  C17  H29  single    0.930  0.020  1.080
 8LB  C18  H30  single    0.930  0.020  1.080
 8LB  C08  H31  single    0.970  0.020  1.090
 8LB  C08  H32  single    0.970  0.020  1.090
 8LB  C09  H33  single    0.970  0.020  1.090
 8LB  C09  H34  single    0.970  0.020  1.090
 8LB  C11  N1   single    1.457  0.020  1.457
 8LB  N1   H5   single    0.890  0.020  1.040
 8LB  N1   H35  single    0.890  0.020  1.040

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
 8LB  H2   C10  H1   106.47  3.000
 8LB  H2   C10  C09  109.85  3.000
 8LB  H1   C10  C09  109.10  3.000
 8LB  H2   C10  C11  109.02  3.000
 8LB  H1   C10  C11  109.47  3.000
 8LB  C09  C10  C11  112.74  3.000
 8LB  N1   C11  H4   108.20  3.000
 8LB  N1   C11  H3   113.24  3.000
 8LB  H4   C11  H3   106.00  3.000
 8LB  N1   C11  C10  111.24  3.000
 8LB  H4   C11  C10  109.09  3.000
 8LB  H3   C11  C10  108.88  3.000
 8LB  O03  C12  O02  127.29  3.000
 8LB  O03  C12  C07  114.85  3.000
 8LB  O02  C12  C07  117.81  3.000
 8LB  H7   C13  H6   107.26  3.000
 8LB  H7   C13  N04  109.52  3.000
 8LB  H6   C13  N04  110.97  3.000
 8LB  H7   C13  P01  109.64  3.000
 8LB  H6   C13  P01  110.26  3.000
 8LB  N04  C13  P01  109.16  3.000
 8LB  O07  C14  O06  123.61  3.000
 8LB  O07  C14  N04  125.62  3.000
 8LB  O06  C14  N04  110.76  3.000
 8LB  H9   C15  H8   108.04  3.000
 8LB  H9   C15  O06  110.47  3.000
 8LB  H8   C15  O06  110.27  3.000
 8LB  H9   C15  C16  110.67  3.000
 8LB  H8   C15  C16  110.83  3.000
 8LB  O06  C15  C16  106.59  3.000
 8LB  C17  C16  C21  119.04  3.000
 8LB  C17  C16  C15  120.41  3.000
 8LB  C21  C16  C15  120.53  3.000
 8LB  H10  C19  C18  120.04  3.000
 8LB  H10  C19  C20  120.08  3.000
 8LB  C18  C19  C20  119.88  3.000
 8LB  H11  C20  C21  119.95  3.000
 8LB  H11  C20  C19  120.06  3.000
 8LB  C21  C20  C19  120.00  3.000
 8LB  H12  C21  C20  119.72  3.000
 8LB  H12  C21  C16  119.72  3.000
 8LB  C20  C21  C16  120.55  3.000
 8LB  H13  N01  C01  114.53  3.000
 8LB  H13  N01  P01  116.89  3.000
 8LB  C01  N01  P01  123.93  3.000
 8LB  H14  C01  C06  108.43  3.000
 8LB  H14  C01  C02  108.63  3.000
 8LB  C06  C01  C02  110.94  3.000
 8LB  H14  C01  N01  107.10  3.000
 8LB  C02  C01  N01  111.23  3.000
 8LB  C06  C01  N01  110.39  3.000
 8LB  H16  C02  H15  106.11  3.000
 8LB  H16  C02  C03  109.31  3.000
 8LB  H15  C02  C03  109.03  3.000
 8LB  H16  C02  C01  108.48  3.000
 8LB  H15  C02  C01  109.20  3.000
 8LB  C03  C02  C01  114.39  3.000
 8LB  H17  C03  C05  107.65  3.000
 8LB  H17  C03  C04  107.92  3.000
 8LB  C05  C03  C04  110.88  3.000
 8LB  H17  C03  C02  107.70  3.000
 8LB  C04  C03  C02  109.96  3.000
 8LB  C05  C03  C02  112.55  3.000
 8LB  H20  C04  H19  107.65  3.000
 8LB  H20  C04  H18  107.60  3.000
 8LB  H19  C04  H18  107.53  3.000
 8LB  H20  C04  C03  111.37  3.000
 8LB  H19  C04  C03  111.22  3.000
 8LB  H18  C04  C03  111.28  3.000
 8LB  H23  C05  H22  107.27  3.000
 8LB  H23  C05  H21  107.43  3.000
 8LB  H22  C05  H21  108.03  3.000
 8LB  H23  C05  C03  110.78  3.000
 8LB  H22  C05  C03  111.88  3.000
 8LB  H21  C05  C03  111.26  3.000
 8LB  H24  N02  C07  119.01  3.000
 8LB  H24  N02  C06  117.97  3.000
 8LB  C07  N02  C06  122.97  3.000
 8LB  H25  C07  C08  108.02  3.000
 8LB  H25  C07  N02  108.37  3.000
 8LB  C08  C07  N02  109.71  3.000
 8LB  H25  C07  C12  108.02  3.000
 8LB  C08  C07  C12  109.77  3.000
 8LB  N02  C07  C12  112.82  3.000
 8LB  H28  N04  C14  118.62  3.000
 8LB  H28  N04  C13  117.31  3.000
 8LB  C14  N04  C13  123.32  3.000
 8LB  C15  O06  C14  117.32  3.000
 8LB  H29  C17  C18  119.73  3.000
 8LB  H29  C17  C16  119.62  3.000
 8LB  C18  C17  C16  120.65  3.000
 8LB  H30  C18  C17  119.97  3.000
 8LB  H30  C18  C19  120.15  3.000
 8LB  C17  C18  C19  119.88  3.000
 8LB  H32  C08  H31  106.51  3.000
 8LB  H32  C08  C09  109.25  3.000
 8LB  H31  C08  C09  109.59  3.000
 8LB  H32  C08  C07  107.50  3.000
 8LB  H31  C08  C07  109.42  3.000
 8LB  C09  C08  C07  114.28  3.000
 8LB  H34  C09  H33  105.89  3.000
 8LB  H34  C09  C08  109.21  3.000
 8LB  H33  C09  C08  110.26  3.000
 8LB  H34  C09  C10  109.83  3.000
 8LB  H33  C09  C10  109.16  3.000
 8LB  C08  C09  C10  112.30  3.000
 8LB  H35  N1   H5   105.70  3.000
 8LB  H35  N1   C11  109.28  3.000
 8LB  H5   N1   C11  109.12  3.000
 8LB  O04  C06  N02  122.99  3.000
 8LB  O04  C06  C01  122.08  3.000
 8LB  N02  C06  C01  114.79  3.000
 8LB  O05  P01  N01  108.46  3.000
 8LB  N01  P01  O01  107.99  3.000
 8LB  O05  P01  O01  120.58  3.000
 8LB  N01  P01  C13  104.56  3.000
 8LB  O05  P01  C13  107.28  3.000
 8LB  O01  P01  C13  106.85  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
 8LB  CONST_01  C19  C20  C21  C16     0.00   0.0  0
 8LB  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 8LB  CONST_03  C17  C16  C21  C20     0.00   0.0  0
 8LB  CONST_04  C17  C18  C19  C20     0.00   0.0  0
 8LB  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 8LB  CONST_06  C18  C17  C16  C21     0.00   0.0  0
 8LB  CONST_07  C20  C21  C16  C15   180.00   0.0  0
 8LB  CONST_08  C18  C17  C16  C15   180.00   0.0  0
 8LB  CONST_09  H11  C20  C21  C16   180.00   0.0  0
 8LB  CONST_10  H30  C18  C17  C16   180.00   0.0  0
 8LB  CONST_11  H12  C21  C20  C19   180.00   0.0  0
 8LB  CONST_12  H29  C17  C18  C19   180.00   0.0  0
 8LB  CONST_13  H10  C19  C20  C21   180.00   0.0  0
 8LB  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 8LB  CONST_15  O04  C06  N02  C07     0.00   0.0  0
 8LB  CONST_16  H24  N02  C06  C01     0.00   0.0  0
 8LB  Var_01    O06  C15  C16  C21   -87.71  30.0  2
 8LB  Var_02    C16  C15  O06  C14  -174.83  30.0  1
 8LB  Var_03    C07  C08  C09  C10  -176.16  30.0  1
 8LB  Var_04    C08  C09  C10  C11  -178.65  30.0  2
 8LB  Var_05    O06  C14  N04  C13  -177.93  30.0  1
 8LB  Var_06    C01  N01  P01  C13    91.27  30.0  3
 8LB  Var_07    P01  C13  N04  C14  -154.78  30.0  3
 8LB  Var_08    N04  C13  P01  O01   -57.31  30.0  1
 8LB  Var_09    C05  C03  C02  C01   -54.72  30.0  3
 8LB  Var_10    N1   C11  C10  C09   179.70  30.0  1
 8LB  Var_11    H5   N1   C11  C10    67.62  30.0  3
 8LB  Var_12    H21  C05  C03  C02   -58.29  30.0  3
 8LB  Var_13    H18  C04  C03  C02    64.29  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
 8LB  chir_02  C01  N01  C06  C02  positiv
 8LB  chir_03  C07  N02  C08  C12  negativ

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
 8LB  plan-1  C15  0.020
 8LB  plan-1  C16  0.020
 8LB  plan-1  C19  0.020
 8LB  plan-1  C20  0.020
 8LB  plan-1  C21  0.020
 8LB  plan-1  C17  0.020
 8LB  plan-1  C18  0.020
 8LB  plan-1  H10  0.020
 8LB  plan-1  H11  0.020
 8LB  plan-1  H12  0.020
 8LB  plan-1  H29  0.020
 8LB  plan-1  H30  0.020
 8LB  plan-2  C01  0.020
 8LB  plan-2  N02  0.020
 8LB  plan-2  C07  0.020
 8LB  plan-2  O04  0.020
 8LB  plan-2  H24  0.020
 8LB  plan-2  C06  0.020
 8LB  plan-3  C12  0.020
 8LB  plan-3  C07  0.020
 8LB  plan-3  O02  0.020
 8LB  plan-3  O03  0.020
 8LB  plan-4  C14  0.020
 8LB  plan-4  N04  0.020
 8LB  plan-4  O06  0.020
 8LB  plan-4  O07  0.020

