# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:37:28 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  60  29  .  2022-09-22  2022-09-22
;
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   0.518    2.5477   1.7781   0.3648
 5S4  O27  O  O      0  -0.499    2.5084   2.4375   1.3960
 5S4  C08  C  CH1    0  -0.020    3.8703   1.4935  -0.3545
 5S4  O09  O  OH1    0  -0.669    3.6378   1.1042  -1.6920
 5S4  C05  C  CT     0  -0.207    4.7855   0.5089   0.4191
 5S4  C04  C  CH2    0  -0.064    6.0470   0.2907  -0.4435
 5S4  C06  C  CH3    0  -0.643    5.2090   1.1190   1.7568
 5S4  C07  C  CH3    0  -0.661    4.0796  -0.8260   0.6691
 5S4  P02  P  P      0   1.219    8.2723  -1.1341  -0.6595
 5S4  O03  O  O2     0  -0.652    6.9800  -0.4807   0.2433
 5S4  O01  O  O      0  -0.908    8.9542   0.0729  -1.2962
 5S4  O29  O  OP    -1  -0.899    9.0664  -1.8191   0.4450
 5S4  N11  N  NH1    0  -0.635    1.4515   1.2678  -0.2110
 5S4  C12  C  CH2    0  -0.235    0.1203   1.5254   0.2903
 5S4  C13  C  CH2    0  -0.620   -0.8718   0.5771  -0.3656
 5S4  C14  C  C      0   0.566   -2.2832   0.8427   0.1139
 5S4  O26  O  O      0  -0.501   -2.5218   1.1758   1.2669
 5S4  N18  N  NH1    0  -0.631   -6.6922  -0.1777   0.3590
 5S4  C17  C  CH2    0  -0.298   -5.2916  -0.3877   0.0821
 5S4  C16  C  CH2    0  -0.297   -4.6483   0.8582  -0.5303
 5S4  N15  N  NH1    0  -0.636   -3.2436   0.6798  -0.8103
 5S4  N24  N  NH2    0  -0.788   -9.9500   0.0659  -1.1838
 5S4  C20  C  CH1    0  -0.220   -9.0767  -0.0863  -0.0392
 5S4  C19  C  C      0   0.554   -7.6708  -0.4092  -0.5350
 5S4  O25  O  O      0  -0.494   -7.4601  -0.8779  -1.6438
 5S4  C21  C  CH1    0  -0.240   -9.5188  -1.1208   1.0268
 5S4  C22  C  CH3    0  -0.665  -10.8607  -0.7228   1.6330
 5S4  C23  C  CH3    0  -0.666   -9.5701  -2.5445   0.4836
 5S4  H19  H  HCH1   0   0.253    4.3944   2.4559  -0.3985
 5S4  H20  H  HOH1   0   0.452    3.6965   0.1468  -1.7727
 5S4  H11  H  HCH2   0   0.170    5.7736  -0.1960  -1.3891
 5S4  H21  H  HNH1   0   0.396    1.5461   0.8748  -1.1337
 5S4  H23  H  HCH2   0   0.245    0.1078   1.3878   1.3704
 5S4  H22  H  HCH2   0   0.239   -0.1683   2.5631   0.0936
 5S4  H1   H  HCH2   0   0.263   -0.8120   0.6568  -1.4541
 5S4  H2   H  HCH2   0   0.284   -0.6161  -0.4565  -0.1124
 5S4  H27  H  HNH1   0   0.402   -6.9303   0.2852   1.2213
 5S4  H3   H  HCH2   0   0.257   -4.7913  -0.6438   1.0159
 5S4  H4   H  HCH2   0   0.248   -5.1822  -1.2361  -0.5927
 5S4  H25  H  HCH2   0   0.259   -5.1476   1.1067  -1.4665
 5S4  H26  H  HCH2   0   0.245   -4.7769   1.7066   0.1430
 5S4  H24  H  HNH1   0   0.405   -2.9813   0.3861  -1.7365
 5S4  H5   H  HCH1   0   0.258   -9.0335   0.8857   0.4670
 5S4  H6   H  HCH1   0   0.223   -8.7767  -1.0912   1.8323
 5S4  H7   H  HCH3   0   0.215  -11.6707  -0.7848   0.9034
 5S4  H8   H  HCH3   0   0.236  -11.1223  -1.3868   2.4579
 5S4  H9   H  HCH3   0   0.229  -10.8375   0.2969   2.0223
 5S4  H28  H  HCH3   0   0.233   -8.6038  -2.8848   0.1091
 5S4  H29  H  HCH3   0   0.235   -9.8761  -3.2369   1.2691
 5S4  H30  H  HCH3   0   0.215  -10.2969  -2.6396  -0.3260
 5S4  OP3  O  OP    -1  -0.904    7.6178  -2.0782  -1.6624
 5S4  H10  H  HCH2   0   0.171    6.4579   1.2789  -0.7081
 5S4  H12  H  HCH3   0   0.231    4.3768   1.2176   2.4499
 5S4  H13  H  HCH3   0   0.229    5.9588   0.4842   2.2253
 5S4  H14  H  HCH3   0   0.215    5.6465   2.1106   1.6178
 5S4  H15  H  HCH3   0   0.213    3.7367  -1.3099  -0.2501
 5S4  H16  H  HCH3   0   0.244    4.7636  -1.5230   1.1522
 5S4  H17  H  HCH3   0   0.232    3.2128  -0.7118   1.3224
 5S4  H31  H  HNH2   0   0.344  -10.0430  -0.8114  -1.6802
 5S4  H32  H  HNH2   0   0.353  -10.8779   0.3234  -0.8745

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  deloc   1.523  0.020  1.523
 5S4  P02  O03  single  1.707  0.020  1.707
 5S4  P02  O01  deloc   1.525  0.020  1.525
 5S4  O03  C04  single  1.392  0.020  1.392
 5S4  C04  C05  single  1.544  0.020  1.544
 5S4  O09  C08  single  1.412  0.020  1.412
 5S4  C06  C05  single  1.530  0.020  1.530
 5S4  O27  C10  double  1.225  0.020  1.225
 5S4  C05  C08  single  1.551  0.020  1.551
 5S4  C05  C07  single  1.531  0.020  1.531
 5S4  C08  C10  single  1.532  0.020  1.532
 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  1.224  0.020  1.224
 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  1.525  0.020  1.525
 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  deloc   1.525  0.020  1.525
 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

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  115.72  3.000
 5S4  N11  C10  O27  122.75  3.000
 5S4  C08  C10  O27  121.53  3.000
 5S4  H19  C08  C05  107.16  3.000
 5S4  H19  C08  O09  106.41  3.000
 5S4  C05  C08  O09  113.24  3.000
 5S4  H19  C08  C10  105.57  3.000
 5S4  C05  C08  C10  113.15  3.000
 5S4  O09  C08  C10  110.71  3.000
 5S4  H20  O09  C08  110.09  3.000
 5S4  C07  C05  C06  109.43  3.000
 5S4  C07  C05  C04  110.18  3.000
 5S4  C06  C05  C04  108.58  3.000
 5S4  C07  C05  C08  111.28  3.000
 5S4  C06  C05  C08  110.26  3.000
 5S4  C04  C05  C08  107.05  3.000
 5S4  H10  C04  H11  106.47  3.000
 5S4  H10  C04  O03  111.43  3.000
 5S4  H11  C04  O03  110.25  3.000
 5S4  H10  C04  C05  108.18  3.000
 5S4  H11  C04  C05  109.90  3.000
 5S4  O03  C04  C05  110.51  3.000
 5S4  H14  C06  H13  107.95  3.000
 5S4  H14  C06  H12  107.77  3.000
 5S4  H13  C06  H12  107.80  3.000
 5S4  H14  C06  C05  111.19  3.000
 5S4  H13  C06  C05  109.54  3.000
 5S4  H12  C06  C05  112.43  3.000
 5S4  H17  C07  H16  107.47  3.000
 5S4  H17  C07  H15  107.48  3.000
 5S4  H16  C07  H15  106.64  3.000
 5S4  H17  C07  C05  111.89  3.000
 5S4  H16  C07  C05  109.93  3.000
 5S4  H15  C07  C05  113.14  3.000
 5S4  OP3  P02  O29  114.98  3.000
 5S4  OP3  P02  O01  114.03  3.000
 5S4  O29  P02  O01  115.18  3.000
 5S4  OP3  P02  O03  105.07  3.000
 5S4  O01  P02  O03  104.85  3.000
 5S4  O29  P02  O03  100.57  3.000
 5S4  P02  O03  C04  117.31  3.000
 5S4  H21  N11  C12  118.27  3.000
 5S4  H21  N11  C10  117.74  3.000
 5S4  C12  N11  C10  122.46  3.000
 5S4  H22  C12  H23  107.15  3.000
 5S4  H23  C12  C13  109.97  3.000
 5S4  H22  C12  C13  109.97  3.000
 5S4  H23  C12  N11  109.39  3.000
 5S4  H22  C12  N11  110.45  3.000
 5S4  C13  C12  N11  109.88  3.000
 5S4  H2   C13  H1   106.64  3.000
 5S4  H2   C13  C14  108.07  3.000
 5S4  H1   C13  C14  110.71  3.000
 5S4  H2   C13  C12  109.67  3.000
 5S4  H1   C13  C12  110.38  3.000
 5S4  C14  C13  C12  111.23  3.000
 5S4  N15  C14  O26  122.83  3.000
 5S4  N15  C14  C13  115.31  3.000
 5S4  O26  C14  C13  121.86  3.000
 5S4  H27  N18  C19  118.42  3.000
 5S4  H27  N18  C17  117.43  3.000
 5S4  C19  N18  C17  123.60  3.000
 5S4  H4   C17  H3   107.55  3.000
 5S4  H4   C17  C16  110.12  3.000
 5S4  H3   C17  C16  109.95  3.000
 5S4  H4   C17  N18  109.25  3.000
 5S4  H3   C17  N18  108.38  3.000
 5S4  C16  C17  N18  111.49  3.000
 5S4  H26  C16  H25  107.39  3.000
 5S4  H26  C16  N15  109.31  3.000
 5S4  H25  C16  N15  107.91  3.000
 5S4  H26  C16  C17  109.68  3.000
 5S4  H25  C16  C17  109.68  3.000
 5S4  N15  C16  C17  112.72  3.000
 5S4  H24  N15  C16  117.92  3.000
 5S4  H24  N15  C14  118.84  3.000
 5S4  C16  N15  C14  123.20  3.000
 5S4  H32  N24  H31  106.64  3.000
 5S4  H32  N24  C20  109.78  3.000
 5S4  H31  N24  C20  110.61  3.000
 5S4  H5   C20  C21  106.58  3.000
 5S4  H5   C20  C19  107.54  3.000
 5S4  C21  C20  C19  110.20  3.000
 5S4  H5   C20  N24  107.19  3.000
 5S4  C21  C20  N24  116.22  3.000
 5S4  C19  C20  N24  108.74  3.000
 5S4  O25  C19  C20  122.35  3.000
 5S4  O25  C19  N18  122.92  3.000
 5S4  C20  C19  N18  114.70  3.000
 5S4  H6   C21  C23  108.06  3.000
 5S4  H6   C21  C22  107.26  3.000
 5S4  C23  C21  C22  110.84  3.000
 5S4  H6   C21  C20  107.12  3.000
 5S4  C23  C21  C20  112.82  3.000
 5S4  C22  C21  C20  110.50  3.000
 5S4  H9   C22  H8   107.70  3.000
 5S4  H9   C22  H7   107.88  3.000
 5S4  H8   C22  H7   107.03  3.000
 5S4  H9   C22  C21  111.51  3.000
 5S4  H8   C22  C21  110.65  3.000
 5S4  H7   C22  C21  111.86  3.000
 5S4  H30  C23  H29  106.96  3.000
 5S4  H30  C23  H28  107.93  3.000
 5S4  H29  C23  H28  107.32  3.000
 5S4  H30  C23  C21  111.58  3.000
 5S4  H29  C23  C21  110.21  3.000
 5S4  H28  C23  C21  112.58  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  -167.38  30.0  3
 5S4  Var_02    O03  C04  C05  C08   174.15  30.0  2
 5S4  Var_03    O29  P02  O03  C04   177.24  30.0  3
 5S4  Var_04    C14  C13  C12  N11  -178.66  30.0  2
 5S4  Var_05    O26  C14  C13  C12   -36.05  30.0  3
 5S4  Var_06    C17  C16  N15  C14   -83.49  30.0  3
 5S4  Var_07    N15  C16  C17  N18   179.63  30.0  1
 5S4  Var_08    C19  N18  C17  C16    88.32  30.0  3
 5S4  Var_09    H12  C06  C05  C08    68.10  30.0  3
 5S4  Var_10    H15  C07  C05  C08    57.06  30.0  3
 5S4  Var_11    H7   C22  C21  C20    66.95  30.0  3
 5S4  Var_12    H28  C23  C21  C20    59.69  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

