# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:45:15 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: (2R)-2-[(1R)-2-[(2S)-2-amino-2-carboxyethoxy]-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N[C@H](SC1)[C@H](NC(=O)[C@H](N)c2ccccc2)C(=O)OC[C@H](N)C(O)=O)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
 4OV  4OV  '(2R)-2-[(1R)-2-[(2S)-2-amino-2-carboxyethoxy]-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  L-peptide  53  31  .  2016-04-22  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_4OV
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
 4OV  C14  C  C      0   0.393  -16.7367  11.3834  -19.6871
 4OV  C16  C  C      0   0.606  -15.1587   7.2338  -17.4192
 4OV  C13  C  CH3    0  -0.734  -19.4852  10.3444  -20.8275
 4OV  C8   C  C      0   0.558  -18.1820   6.3086  -17.0678
 4OV  C3   C  CR16   0  -0.237  -22.1255   8.1266  -18.9565
 4OV  C2   C  CR16   0  -0.267  -22.4147   6.9913  -19.6987
 4OV  S1   S  S2     0  -0.010  -17.0839   7.0798  -21.0909
 4OV  C6   C  CR16   0  -0.284  -20.8278   5.7424  -18.3882
 4OV  C4   C  CR16   0  -0.309  -21.1828   8.0701  -17.9365
 4OV  C7   C  CH1    0  -0.314  -19.5114   6.8176  -16.5125
 4OV  C11  C  C      0   0.014  -18.3222   9.4835  -20.4247
 4OV  O2   O  OC    -1  -0.565  -17.6140  12.2562  -19.6004
 4OV  O3   O  O      0  -0.595  -15.5023  11.5617  -19.6099
 4OV  C12  C  C      0   0.097  -17.1520   9.9134  -19.9090
 4OV  N3   N  NH1    0  -0.664  -16.1078   9.0793  -19.5328
 4OV  C10  C  CH2    0  -0.624  -18.5785   8.0318  -20.7081
 4OV  C9   C  CH1    0  -0.262  -16.0211   7.6695  -19.7382
 4OV  C15  C  CH1    0  -0.170  -16.2545   6.8924  -18.4295
 4OV  CB   C  CH2    0  -0.184  -12.8473   6.8565  -16.9762
 4OV  CA   C  CH1    0  -0.246  -12.6311   5.5058  -16.3047
 4OV  C    C  C      0   0.383  -11.3207   5.5962  -15.4703
 4OV  O    O  O      0  -0.609  -10.2867   5.8398  -16.1248
 4OV  N    N  NH2    0  -0.783  -13.8239   5.1058  -15.5820
 4OV  N2   N  NH1    0  -0.622  -17.5413   7.1795  -17.8714
 4OV  O1   O  O      0  -0.473  -17.7717   5.1829  -16.8433
 4OV  N1   N  NH2    0  -0.765  -19.9006   6.0045  -15.3791
 4OV  C5   C  CR6    0   0.120  -20.5252   6.8812  -17.6420
 4OV  C1   C  CR16   0  -0.239  -21.7609   5.7982  -19.4118
 4OV  H1   H  HCH3   0   0.259  -19.3637  11.3784  -20.5330
 4OV  H2   H  HCH3   0   0.216  -19.6346  10.3035  -21.9113
 4OV  H3   H  HCH3   0   0.222  -20.4092   9.9650  -20.3805
 4OV  H5   H  HCR6   0   0.255  -23.1447   7.0331  -20.4967
 4OV  H6   H  HCR6   0   0.252  -20.3253   4.8049  -18.1781
 4OV  H7   H  HCR6   0   0.255  -20.9534   8.9635  -17.3670
 4OV  H8   H  HCH1   0   0.275  -19.3545   7.8388  -16.1492
 4OV  H11  H  HCH2   0   0.274  -19.1996   7.9429  -21.6035
 4OV  H12  H  HCH2   0   0.289  -19.1338   7.5434  -19.9050
 4OV  H13  H  HCH1   0   0.311  -15.0113   7.4273  -20.0769
 4OV  H14  H  HCH1   0   0.291  -16.1892   5.8246  -18.6488
 4OV  H15  H  HCH2   0   0.246  -11.9986   7.1056  -17.6087
 4OV  H16  H  HCH2   0   0.231  -12.9743   7.6501  -16.2375
 4OV  H17  H  HCH1   0   0.228  -12.4624   4.7702  -17.0990
 4OV  H    H  HNH2   0   0.341  -13.7596   4.1179  -15.3709
 4OV  HN   H  HNH2   0   0.327  -13.8138   5.5629  -14.6773
 4OV  H22  H  HNH1   0   0.409  -17.8496   8.1414  -17.8852
 4OV  H23  H  HNH2   0   0.353  -20.7932   6.3311  -15.0307
 4OV  H24  H  HNH2   0   0.348  -20.0414   5.0445  -15.6692
 4OV  H26  H  HCR6   0   0.254  -21.9795   4.9084  -19.9882
 4OV  OXT  O  OC    -1  -0.589  -11.4168   5.4359  -14.2406
 4OV  H9   H  HNH1   0   0.381  -15.2344   9.5891  -19.5413
 4OV  O4   O  O      0  -0.435  -15.3551   7.8400  -16.4000
 4OV  H4   H  HCR6   0   0.256  -22.6301   9.0601  -19.1709
 4OV  OG   O  O2     0  -0.461  -13.9859   6.8016  -17.8465

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
 4OV  S1   C10  single    1.813  0.020  1.813
 4OV  S1   C9   single    1.819  0.020  1.819
 4OV  C13  C11  single    1.502  0.020  1.502
 4OV  C11  C10  single    1.501  0.020  1.501
 4OV  C11  C12  double    1.349  0.020  1.349
 4OV  O3   C14  deloc     1.250  0.020  1.250
 4OV  C12  C14  single    1.544  0.020  1.544
 4OV  C12  N3   single    1.388  0.020  1.388
 4OV  C14  O2   deloc     1.241  0.020  1.241
 4OV  N3   C9   single    1.427  0.020  1.427
 4OV  C9   C15  single    1.540  0.020  1.540
 4OV  C1   C6   aromatic  1.386  0.020  1.386
 4OV  C1   C2   aromatic  1.390  0.020  1.390
 4OV  C6   C5   aromatic  1.395  0.020  1.395
 4OV  C2   C3   aromatic  1.387  0.020  1.387
 4OV  O1   C8   double    1.219  0.020  1.219
 4OV  C15  N2   single    1.432  0.020  1.432
 4OV  C15  C16  single    1.529  0.020  1.529
 4OV  OG   CB   single    1.434  0.020  1.434
 4OV  OG   C16  single    1.321  0.020  1.321
 4OV  C8   N2   single    1.347  0.020  1.347
 4OV  C8   C7   single    1.528  0.020  1.528
 4OV  C5   C7   single    1.519  0.020  1.519
 4OV  C5   C4   aromatic  1.390  0.020  1.390
 4OV  C3   C4   aromatic  1.390  0.020  1.390
 4OV  CB   CA   single    1.530  0.020  1.530
 4OV  C16  O4   double    1.202  0.020  1.202
 4OV  C7   N1   single    1.448  0.020  1.448
 4OV  O    C    deloc     1.231  0.020  1.231
 4OV  CA   C    single    1.525  0.021  1.525
 4OV  CA   N    single    1.458  0.019  1.458
 4OV  C13  H1   single    0.970  0.020  1.090
 4OV  C13  H2   single    0.970  0.020  1.090
 4OV  C13  H3   single    0.970  0.020  1.090
 4OV  C3   H4   single    0.930  0.020  1.080
 4OV  C2   H5   single    0.930  0.020  1.080
 4OV  C6   H6   single    0.930  0.020  1.080
 4OV  C4   H7   single    0.930  0.020  1.080
 4OV  C7   H8   single    0.970  0.020  1.090
 4OV  C10  H11  single    0.970  0.020  1.090
 4OV  C10  H12  single    0.970  0.020  1.090
 4OV  C9   H13  single    0.970  0.020  1.090
 4OV  C15  H14  single    0.970  0.020  1.090
 4OV  CB   H15  single    0.970  0.020  1.090
 4OV  CB   H16  single    0.970  0.020  1.090
 4OV  CA   H17  single    0.970  0.020  1.090
 4OV  N    H    single    0.860  0.020  0.860
 4OV  N    HN   single    0.890  0.020  1.040
 4OV  N2   H22  single    0.860  0.020  1.020
 4OV  N1   H23  single    0.890  0.020  1.040
 4OV  N1   H24  single    0.890  0.020  1.040
 4OV  C1   H26  single    0.930  0.020  1.080
 4OV  C    OXT  deloc     1.244  0.020  1.244
 4OV  N3   H9   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
 4OV  C12  C14  O3   114.24  3.000
 4OV  C12  C14  O2   119.33  3.000
 4OV  O3   C14  O2   126.43  3.000
 4OV  OG   C16  O4   125.76  3.000
 4OV  O4   C16  C15  123.76  3.000
 4OV  OG   C16  C15  110.46  3.000
 4OV  H3   C13  H2   106.04  3.000
 4OV  H3   C13  H1   108.36  3.000
 4OV  H2   C13  H1   108.69  3.000
 4OV  H3   C13  C11  110.22  3.000
 4OV  H2   C13  C11  110.47  3.000
 4OV  H1   C13  C11  112.81  3.000
 4OV  O1   C8   N2   123.15  3.000
 4OV  N2   C8   C7   114.53  3.000
 4OV  O1   C8   C7   122.24  3.000
 4OV  H4   C3   C4   119.77  3.000
 4OV  H4   C3   C2   120.18  3.000
 4OV  C4   C3   C2   120.05  3.000
 4OV  H5   C2   C1   120.16  3.000
 4OV  H5   C2   C3   120.24  3.000
 4OV  C1   C2   C3   119.60  3.000
 4OV  C9   S1   C10   98.89  3.000
 4OV  H6   C6   C1   119.33  3.000
 4OV  H6   C6   C5   120.12  3.000
 4OV  C1   C6   C5   120.55  3.000
 4OV  H7   C4   C5   119.57  3.000
 4OV  H7   C4   C3   119.70  3.000
 4OV  C5   C4   C3   120.73  3.000
 4OV  H8   C7   C5   107.64  3.000
 4OV  H8   C7   N1   107.60  3.000
 4OV  C5   C7   N1   115.22  3.000
 4OV  H8   C7   C8   107.85  3.000
 4OV  N1   C7   C8   109.35  3.000
 4OV  C5   C7   C8   108.93  3.000
 4OV  C10  C11  C12  121.90  3.000
 4OV  C12  C11  C13  126.27  3.000
 4OV  C10  C11  C13  111.80  3.000
 4OV  N3   C12  C11  124.37  3.000
 4OV  N3   C12  C14  109.32  3.000
 4OV  C11  C12  C14  126.28  3.000
 4OV  H9   N3   C9   116.38  3.000
 4OV  H9   N3   C12  110.15  3.000
 4OV  C9   N3   C12  126.88  3.000
 4OV  H12  C10  H11  106.09  3.000
 4OV  H12  C10  C11  112.37  3.000
 4OV  H11  C10  C11  109.29  3.000
 4OV  H12  C10  S1   109.86  3.000
 4OV  H11  C10  S1   104.64  3.000
 4OV  C11  C10  S1   114.01  3.000
 4OV  H13  C9   C15  106.96  3.000
 4OV  H13  C9   N3   108.65  3.000
 4OV  C15  C9   N3   111.53  3.000
 4OV  H13  C9   S1   103.75  3.000
 4OV  C15  C9   S1   112.33  3.000
 4OV  N3   C9   S1   113.07  3.000
 4OV  H14  C15  N2   109.15  3.000
 4OV  H14  C15  C9   108.29  3.000
 4OV  N2   C15  C9   111.49  3.000
 4OV  H14  C15  C16  107.94  3.000
 4OV  N2   C15  C16  109.99  3.000
 4OV  C9   C15  C16  109.89  3.000
 4OV  H16  CB   H15  108.53  3.000
 4OV  H16  CB   CA   111.27  3.000
 4OV  H15  CB   CA   110.41  3.000
 4OV  H16  CB   OG   110.25  3.000
 4OV  H15  CB   OG   105.98  3.000
 4OV  CA   CB   OG   110.25  3.000
 4OV  H17  CA   N    107.61  3.000
 4OV  H17  CA   C    107.34  3.000
 4OV  N    CA   C    111.00  2.800
 4OV  H17  CA   CB   107.31  3.000
 4OV  N    CA   CB   110.50  1.700
 4OV  C    CA   CB   110.10  1.900
 4OV  OXT  C    O    127.43  3.000
 4OV  OXT  C    CA   117.23  3.000
 4OV  O    C    CA   120.80  1.700
 4OV  HN   N    H    104.67  3.000
 4OV  HN   N    CA   108.18  3.000
 4OV  H    N    CA   114.00  3.000
 4OV  H22  N2   C15  117.38  3.000
 4OV  H22  N2   C8   118.59  3.000
 4OV  C15  N2   C8   122.03  3.000
 4OV  H24  N1   H23  106.37  3.000
 4OV  H24  N1   C7   110.20  3.000
 4OV  H23  N1   C7   108.98  3.000
 4OV  C7   C5   C4   120.60  3.000
 4OV  C4   C5   C6   118.84  3.000
 4OV  C7   C5   C6   120.56  3.000
 4OV  H26  C1   C6   119.74  3.000
 4OV  H26  C1   C2   120.03  3.000
 4OV  C6   C1   C2   120.23  3.000
 4OV  CB   OG   C16  119.74  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
 4OV  CONST_01  C6   C1   C2   C3      0.00   0.0  0
 4OV  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 4OV  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 4OV  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 4OV  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 4OV  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 4OV  CONST_07  C7   C5   C4   C3    180.00   0.0  0
 4OV  CONST_08  C1   C6   C5   C7    180.00   0.0  0
 4OV  CONST_09  H26  C1   C2   C3    180.00   0.0  0
 4OV  CONST_10  H6   C6   C1   C2    180.00   0.0  0
 4OV  CONST_11  H7   C4   C3   C2    180.00   0.0  0
 4OV  CONST_12  H5   C2   C1   C6    180.00   0.0  0
 4OV  CONST_13  H4   C3   C4   C5    180.00   0.0  0
 4OV  CONST_14  C15  N2   C8   C7    180.00   0.0  0
 4OV  CONST_15  O1   C8   N2   C15     0.00   0.0  0
 4OV  CONST_16  H22  N2   C8   C7      0.00   0.0  0
 4OV  Var_01    C12  C11  C10  S1    -28.42  30.0  1
 4OV  Var_02    C9   N3   C12  C11     6.68  30.0  1
 4OV  Var_03    C10  C11  C12  N3     -3.18  30.0  1
 4OV  Var_04    O3   C14  C12  C11  -158.31  30.0  2
 4OV  Var_05    H1   C13  C11  C12    -8.33  30.0  3
 4OV  Var_06    CA   CB   OG   C16    97.17  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
 4OV  chir_01  C7   C8  C5  N1   negativ
 4OV  chir_02  C9   S1  N3  C15  negativ
 4OV  chir_03  C15  N2  C9  C16  negativ
 4OV  chir_04  CA   N   CB  C    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
 4OV  plan-1  C3   0.020
 4OV  plan-1  C2   0.020
 4OV  plan-1  C6   0.020
 4OV  plan-1  C4   0.020
 4OV  plan-1  C7   0.020
 4OV  plan-1  C5   0.020
 4OV  plan-1  C1   0.020
 4OV  plan-1  H5   0.020
 4OV  plan-1  H6   0.020
 4OV  plan-1  H7   0.020
 4OV  plan-1  H26  0.020
 4OV  plan-1  H4   0.020
 4OV  plan-2  C8   0.020
 4OV  plan-2  C7   0.020
 4OV  plan-2  C15  0.020
 4OV  plan-2  N2   0.020
 4OV  plan-2  O1   0.020
 4OV  plan-2  H22  0.020
 4OV  plan-3  C12  0.020
 4OV  plan-3  N3   0.020
 4OV  plan-3  C9   0.020
 4OV  plan-3  H9   0.020
 4OV  plan-4  C14  0.020
 4OV  plan-4  O2   0.020
 4OV  plan-4  O3   0.020
 4OV  plan-4  C12  0.020
 4OV  plan-5  CA   0.020
 4OV  plan-5  C    0.020
 4OV  plan-5  O    0.020
 4OV  plan-5  OXT  0.020
 4OV  plan-6  C16  0.020
 4OV  plan-6  C15  0.020
 4OV  plan-6  O4   0.020
 4OV  plan-6  OG   0.020

