# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:35:36 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: [(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)NCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(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
 5S4  5S4  '[(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate'  peptide  62  29  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_5S4
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
 5S4  C10  C  C     0   0.520    2.5271   1.5788   0.5098
 5S4  O27  O  O     0  -0.492    2.5035   2.0869   1.6226
 5S4  C08  C  CH1   0  -0.035    3.8456   1.3667  -0.2472
 5S4  O09  O  OH1   0  -0.660    3.6207   1.0034  -1.5909
 5S4  C05  C  CT    0  -0.209    4.8245   0.4014   0.4754
 5S4  C04  C  CH2   0  -0.125    6.0411   0.2736  -0.4544
 5S4  C06  C  CH3   0  -0.646    5.2863   0.9907   1.8106
 5S4  C07  C  CH3   0  -0.667    4.1798  -0.9676   0.7057
 5S4  P02  P  P     0   1.456    8.3794  -0.8851  -0.5964
 5S4  O03  O  O2    0  -0.589    7.0360  -0.5328   0.1858
 5S4  O01  O  O     0  -0.712    9.0688   0.2365  -1.2605
 5S4  O29  O  OH1   0  -0.731    9.1204  -1.6075   0.6155
 5S4  N11  N  NH1   0  -0.638    1.4218   1.1927  -0.1392
 5S4  C12  C  CH2   0  -0.238    0.0927   1.4359   0.3767
 5S4  C13  C  CH2   0  -0.620   -0.9135   0.5649  -0.3587
 5S4  C14  C  C     0   0.568   -2.3281   0.8388   0.1072
 5S4  O26  O  O     0  -0.500   -2.5763   1.1942   1.2512
 5S4  N18  N  NH1   0  -0.631   -6.7428  -0.1658   0.3312
 5S4  C17  C  CH2   0  -0.298   -5.3409  -0.3898   0.0734
 5S4  C16  C  CH2   0  -0.297   -4.6874   0.8415  -0.5575
 5S4  N15  N  NH1   0  -0.637   -3.2807   0.6564  -0.8217
 5S4  N24  N  NH2   0  -0.789   -9.9818   0.0435  -1.2562
 5S4  C20  C  CH1   0  -0.220   -9.1221  -0.0631  -0.0966
 5S4  C19  C  C     0   0.554   -7.7154  -0.4276  -0.5612
 5S4  O25  O  O     0  -0.494   -7.4997  -0.9517  -1.6439
 5S4  C21  C  CH1   0  -0.241   -9.5883  -1.0363   1.0161
 5S4  C22  C  CH3   0  -0.665  -10.9279  -0.5879   1.5905
 5S4  C23  C  CH3   0  -0.666   -9.6605  -2.4843   0.5439
 5S4  H19  H  HCH1  0   0.273    4.3226   2.3532  -0.2831
 5S4  H20  H  HOH1  0   0.454    3.5045   0.0491  -1.6608
 5S4  H11  H  HCH2  0   0.239    5.7650  -0.1853  -1.4058
 5S4  H21  H  HNH1  0   0.398    1.5121   0.9407  -1.1107
 5S4  H23  H  HCH2  0   0.248    0.0751   1.2110   1.4415
 5S4  H22  H  HCH2  0   0.242   -0.1705   2.4925   0.2656
 5S4  H1   H  HCH2  0   0.264   -0.8323   0.7157  -1.4383
 5S4  H2   H  HCH2  0   0.286   -0.6930  -0.4912  -0.1744
 5S4  H27  H  HNH1  0   0.401   -6.9844   0.3371   1.1700
 5S4  H3   H  HCH2  0   0.257   -4.8500  -0.6302   1.0164
 5S4  H4   H  HCH2  0   0.248   -5.2309  -1.2519  -0.5834
 5S4  H25  H  HCH2  0   0.259   -5.1784   1.0735  -1.5024
 5S4  H26  H  HCH2  0   0.245   -4.8199   1.7029   0.0984
 5S4  H24  H  HNH1  0   0.405   -3.0109   0.3430  -1.7394
 5S4  H32  H  HNH2  0   0.353  -10.9060   0.3400  -0.9722
 5S4  H5   H  HCH1  0   0.258   -9.0706   0.9328   0.3596
 5S4  H6   H  HCH1  0   0.223   -8.8508  -0.9790   1.8242
 5S4  H7   H  HCH3  0   0.215  -11.7322  -0.6739   0.8572
 5S4  H8   H  HCH3  0   0.236  -11.2078  -1.2064   2.4444
 5S4  H9   H  HCH3  0   0.230  -10.8922   0.4490   1.9297
 5S4  H28  H  HCH3  0   0.233   -8.7007  -2.8575   0.1845
 5S4  H29  H  HCH3  0   0.235   -9.9751  -3.1326   1.3631
 5S4  H30  H  HCH3  0   0.215  -10.3915  -2.6082  -0.2581
 5S4  OP3  O  OH1   0  -0.742    8.0118  -2.0016  -1.6808
 5S4  H10  H  HCH2  0   0.247    6.4528   1.2658  -0.6636
 5S4  H12  H  HCH3  0   0.248    4.4776   1.0359   2.5339
 5S4  H13  H  HCH3  0   0.235    6.0758   0.3757   2.2394
 5S4  H14  H  HCH3  0   0.227    5.6785   2.0019   1.6829
 5S4  H15  H  HCH3  0   0.224    3.8456  -1.4456  -0.2194
 5S4  H16  H  HCH3  0   0.254    4.8858  -1.6515   1.1762
 5S4  H17  H  HCH3  0   0.246    3.3170  -0.8911   1.3687
 5S4  H18  H  HOH1  0   0.504   10.0188  -1.8997   0.4105
 5S4  H33  H  HOH1  0   0.495    7.6034  -2.8065  -1.3350
 5S4  H31  H  HNH2  0   0.344  -10.0901  -0.8571  -1.7055

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
 5S4  O29  P02  single  1.594  0.020  1.594
 5S4  P02  O03  single  1.594  0.020  1.594
 5S4  P02  O01  double  1.475  0.020  1.475
 5S4  O03  C04  single  1.432  0.020  1.432
 5S4  C04  C05  single  1.537  0.020  1.537
 5S4  O09  C08  single  1.410  0.020  1.410
 5S4  C06  C05  single  1.531  0.020  1.531
 5S4  O27  C10  double  1.224  0.020  1.224
 5S4  C05  C08  single  1.553  0.020  1.553
 5S4  C05  C07  single  1.531  0.020  1.531
 5S4  C08  C10  single  1.535  0.020  1.535
 5S4  C10  N11  single  1.339  0.020  1.339
 5S4  N11  C12  single  1.446  0.020  1.446
 5S4  C13  C12  single  1.521  0.020  1.521
 5S4  C13  C14  single  1.514  0.020  1.514
 5S4  O26  C14  double  1.223  0.020  1.223
 5S4  C14  N15  single  1.343  0.020  1.343
 5S4  N15  C16  single  1.443  0.020  1.443
 5S4  C16  C17  single  1.530  0.020  1.530
 5S4  C17  N18  single  1.443  0.020  1.443
 5S4  N18  C19  single  1.346  0.020  1.346
 5S4  N24  C20  single  1.448  0.020  1.448
 5S4  C20  C19  single  1.526  0.020  1.526
 5S4  C20  C21  single  1.550  0.020  1.550
 5S4  C19  O25  double  1.222  0.020  1.222
 5S4  C22  C21  single  1.525  0.020  1.525
 5S4  C21  C23  single  1.525  0.020  1.525
 5S4  C13  H1   single  0.970  0.020  1.090
 5S4  C13  H2   single  0.970  0.020  1.090
 5S4  C17  H3   single  0.970  0.020  1.090
 5S4  C17  H4   single  0.970  0.020  1.090
 5S4  C20  H5   single  0.970  0.020  1.090
 5S4  C21  H6   single  0.970  0.020  1.090
 5S4  C22  H7   single  0.970  0.020  1.090
 5S4  C22  H8   single  0.970  0.020  1.090
 5S4  C22  H9   single  0.970  0.020  1.090
 5S4  C04  H11  single  0.970  0.020  1.090
 5S4  C08  H19  single  0.970  0.020  1.090
 5S4  O09  H20  single  0.850  0.020  0.980
 5S4  N11  H21  single  0.860  0.020  1.020
 5S4  C12  H22  single  0.970  0.020  1.090
 5S4  C12  H23  single  0.970  0.020  1.090
 5S4  N15  H24  single  0.860  0.020  1.020
 5S4  C16  H25  single  0.970  0.020  1.090
 5S4  C16  H26  single  0.970  0.020  1.090
 5S4  N18  H27  single  0.860  0.020  1.020
 5S4  C23  H28  single  0.970  0.020  1.090
 5S4  C23  H29  single  0.970  0.020  1.090
 5S4  C23  H30  single  0.970  0.020  1.090
 5S4  N24  H31  single  0.890  0.020  1.040
 5S4  N24  H32  single  0.890  0.020  1.040
 5S4  P02  OP3  single  1.599  0.020  1.599
 5S4  C04  H10  single  0.970  0.020  1.090
 5S4  C06  H12  single  0.970  0.020  1.090
 5S4  C06  H13  single  0.970  0.020  1.090
 5S4  C06  H14  single  0.970  0.020  1.090
 5S4  C07  H15  single  0.970  0.020  1.090
 5S4  C07  H16  single  0.970  0.020  1.090
 5S4  C07  H17  single  0.970  0.020  1.090
 5S4  O29  H18  single  0.850  0.020  0.980
 5S4  OP3  H33  single  0.850  0.020  0.980

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
 5S4  N11  C10  C08  115.48  3.000
 5S4  N11  C10  O27  123.01  3.000
 5S4  C08  C10  O27  121.50  3.000
 5S4  H19  C08  C05  107.48  3.000
 5S4  H19  C08  O09  105.67  3.000
 5S4  C05  C08  O09  112.57  3.000
 5S4  H19  C08  C10  105.39  3.000
 5S4  C05  C08  C10  113.44  3.000
 5S4  O09  C08  C10  111.62  3.000
 5S4  H20  O09  C08  110.09  3.000
 5S4  C07  C05  C06  109.88  3.000
 5S4  C07  C05  C04  110.50  3.000
 5S4  C06  C05  C04  108.72  3.000
 5S4  C07  C05  C08  111.13  3.000
 5S4  C06  C05  C08  110.89  3.000
 5S4  C04  C05  C08  105.62  3.000
 5S4  H10  C04  H11  108.04  3.000
 5S4  H10  C04  O03  109.56  3.000
 5S4  H11  C04  O03  109.18  3.000
 5S4  H10  C04  C05  109.76  3.000
 5S4  H11  C04  C05  111.22  3.000
 5S4  O03  C04  C05  109.06  3.000
 5S4  H14  C06  H13  107.98  3.000
 5S4  H14  C06  H12  107.87  3.000
 5S4  H13  C06  H12  107.53  3.000
 5S4  H14  C06  C05  111.27  3.000
 5S4  H13  C06  C05  110.17  3.000
 5S4  H12  C06  C05  111.86  3.000
 5S4  H17  C07  H16  107.10  3.000
 5S4  H17  C07  H15  107.65  3.000
 5S4  H16  C07  H15  106.79  3.000
 5S4  H17  C07  C05  111.22  3.000
 5S4  H16  C07  C05  110.69  3.000
 5S4  H15  C07  C05  113.10  3.000
 5S4  OP3  P02  O29  107.82  3.000
 5S4  OP3  P02  O01  109.46  3.000
 5S4  O29  P02  O01  118.03  3.000
 5S4  OP3  P02  O03  107.06  3.000
 5S4  O01  P02  O03  116.55  3.000
 5S4  O29  P02  O03   96.83  3.000
 5S4  P02  O03  C04  119.39  3.000
 5S4  H18  O29  P02  114.07  3.000
 5S4  H21  N11  C12  117.92  3.000
 5S4  H21  N11  C10  117.75  3.000
 5S4  C12  N11  C10  122.50  3.000
 5S4  H22  C12  H23  107.15  3.000
 5S4  H23  C12  C13  110.12  3.000
 5S4  H22  C12  C13  110.16  3.000
 5S4  H23  C12  N11  109.22  3.000
 5S4  H22  C12  N11  110.31  3.000
 5S4  C13  C12  N11  109.83  3.000
 5S4  H2   C13  H1   106.53  3.000
 5S4  H2   C13  C14  108.12  3.000
 5S4  H1   C13  C14  110.38  3.000
 5S4  H2   C13  C12  109.75  3.000
 5S4  H1   C13  C12  110.45  3.000
 5S4  C14  C13  C12  111.45  3.000
 5S4  N15  C14  O26  122.84  3.000
 5S4  N15  C14  C13  115.16  3.000
 5S4  O26  C14  C13  121.99  3.000
 5S4  H27  N18  C19  118.42  3.000
 5S4  H27  N18  C17  117.34  3.000
 5S4  C19  N18  C17  123.61  3.000
 5S4  H4   C17  H3   107.55  3.000
 5S4  H4   C17  C16  110.19  3.000
 5S4  H3   C17  C16  109.99  3.000
 5S4  H4   C17  N18  109.19  3.000
 5S4  H3   C17  N18  108.49  3.000
 5S4  C16  C17  N18  111.33  3.000
 5S4  H26  C16  H25  107.37  3.000
 5S4  H26  C16  N15  109.25  3.000
 5S4  H25  C16  N15  107.93  3.000
 5S4  H26  C16  C17  109.61  3.000
 5S4  H25  C16  C17  109.65  3.000
 5S4  N15  C16  C17  112.86  3.000
 5S4  H24  N15  C16  117.91  3.000
 5S4  H24  N15  C14  118.87  3.000
 5S4  C16  N15  C14  123.19  3.000
 5S4  H32  N24  H31  106.73  3.000
 5S4  H32  N24  C20  109.84  3.000
 5S4  H31  N24  C20  110.70  3.000
 5S4  H5   C20  C21  106.60  3.000
 5S4  H5   C20  C19  107.48  3.000
 5S4  C21  C20  C19  110.24  3.000
 5S4  H5   C20  N24  107.11  3.000
 5S4  C21  C20  N24  116.28  3.000
 5S4  C19  C20  N24  108.74  3.000
 5S4  O25  C19  C20  122.34  3.000
 5S4  O25  C19  N18  122.92  3.000
 5S4  C20  C19  N18  114.71  3.000
 5S4  H6   C21  C23  108.06  3.000
 5S4  H6   C21  C22  107.34  3.000
 5S4  C23  C21  C22  110.75  3.000
 5S4  H6   C21  C20  107.11  3.000
 5S4  C23  C21  C20  112.84  3.000
 5S4  C22  C21  C20  110.49  3.000
 5S4  H9   C22  H8   107.68  3.000
 5S4  H9   C22  H7   107.91  3.000
 5S4  H8   C22  H7   106.98  3.000
 5S4  H9   C22  C21  111.57  3.000
 5S4  H8   C22  C21  110.70  3.000
 5S4  H7   C22  C21  111.78  3.000
 5S4  H30  C23  H29  106.92  3.000
 5S4  H30  C23  H28  107.95  3.000
 5S4  H29  C23  H28  107.32  3.000
 5S4  H30  C23  C21  111.52  3.000
 5S4  H29  C23  C21  110.21  3.000
 5S4  H28  C23  C21  112.66  3.000
 5S4  H33  OP3  P02  115.85  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
 5S4  CONST_01  C12  N11  C10  O27     0.00   0.0  0
 5S4  CONST_02  C12  N11  C10  C08   180.00   0.0  0
 5S4  CONST_03  C16  N15  C14  C13   180.00   0.0  0
 5S4  CONST_04  C16  N15  C14  O26     0.00   0.0  0
 5S4  CONST_05  C20  C19  N18  C17   180.00   0.0  0
 5S4  CONST_06  O25  C19  N18  C17     0.00   0.0  0
 5S4  CONST_07  H21  N11  C10  O27   180.00   0.0  0
 5S4  CONST_08  H24  N15  C14  C13     0.00   0.0  0
 5S4  CONST_09  H27  N18  C19  C20     0.00   0.0  0
 5S4  Var_01    C13  C12  N11  C10  -164.32  30.0  3
 5S4  Var_02    O03  C04  C05  C08   176.06  30.0  1
 5S4  Var_03    O29  P02  O03  C04   173.81  30.0  1
 5S4  Var_04    C14  C13  C12  N11  -177.26  30.0  1
 5S4  Var_05    O26  C14  C13  C12   -30.78  30.0  3
 5S4  Var_06    C17  C16  N15  C14   -83.63  30.0  3
 5S4  Var_07    N15  C16  C17  N18   179.62  30.0  1
 5S4  Var_08    C19  N18  C17  C16    89.30  30.0  3
 5S4  Var_09    H12  C06  C05  C08    68.47  30.0  3
 5S4  Var_10    H15  C07  C05  C08    57.90  30.0  3
 5S4  Var_11    H7   C22  C21  C20    66.92  30.0  3
 5S4  Var_12    H28  C23  C21  C20    59.16  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
 5S4  chir_01  C08  O09  C05  C10  positiv
 5S4  chir_02  C20  N24  C19  C21  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
 5S4  plan-1  C10  0.020
 5S4  plan-1  O27  0.020
 5S4  plan-1  C08  0.020
 5S4  plan-1  N11  0.020
 5S4  plan-1  C12  0.020
 5S4  plan-1  H21  0.020
 5S4  plan-2  C13  0.020
 5S4  plan-2  C14  0.020
 5S4  plan-2  O26  0.020
 5S4  plan-2  C16  0.020
 5S4  plan-2  N15  0.020
 5S4  plan-2  H24  0.020
 5S4  plan-3  N18  0.020
 5S4  plan-3  C17  0.020
 5S4  plan-3  C20  0.020
 5S4  plan-3  C19  0.020
 5S4  plan-3  O25  0.020
 5S4  plan-3  H27  0.020

