# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:13 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: N~6~-[(1R)-2-{[(1R)-1-carboxy-2-methylpropyl]oxy}-2-oxo-1-(sulfanylcarbonyl)ethyl]-6-oxo-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](OC(=O)[C@@H](NC(=O)CCC[C@H](N)C(O)=O)C(S)=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
 SCV  SCV  N~6~-[(1R)-2-{[(1R)-1-carboxy-2-methylpropyl]oxy}-2-oxo-1-(sulfanylcarbonyl)ethyl]-6-oxo-L-lysine  ligand  45  25  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SCV
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
 SCV  C1    C  C      0   0.384  -8.6883   5.1320  -5.6443
 SCV  C2    C  CH1    0  -0.225  -8.6322   3.7777  -4.8959
 SCV  C3    C  CH2    0  -0.406  -7.4469   3.7775  -3.9244
 SCV  C4    C  CH2    0  -0.432  -6.0836   3.8225  -4.6062
 SCV  C7    C  CH1    0  -0.258  -1.2196   4.0469  -3.7967
 SCV  C10   C  CH1    0  -0.087  -1.1094   0.4455  -3.0675
 SCV  C12   C  CH1    0  -0.270  -2.2525  -0.3094  -2.3947
 SCV  C13   C  CH3    0  -0.658  -3.4675  -0.4136  -3.3132
 SCV  C5    C  CH2    0  -0.589  -4.9542   3.8120  -3.5877
 SCV  N1    N  NH2    0  -0.796  -8.5890   2.5943  -5.7458
 SCV  O1    O  O      0  -0.611  -8.4209   5.1322  -6.8629
 SCV  O2    O  OC    -1  -0.622  -8.9766   6.1284  -4.9487
 SCV  O5    O  O2     0  -0.436  -1.5565   1.7886  -3.2668
 SCV  C11   C  C      0   0.405   0.1914   0.4517  -2.2293
 SCV  O6    O  OC    -1  -0.610   0.6802  -0.6773  -2.0336
 SCV  O7    O  O      0  -0.572   0.6164   1.5502  -1.8393
 SCV  C6    C  C      0   0.588  -3.5769   3.7723  -4.2031
 SCV  O3    O  O      0  -0.490  -3.3483   3.3367  -5.3206
 SCV  N2    N  NH1    0  -0.657  -2.5834   4.2309  -3.4122
 SCV  C8    C  C      0   0.608  -0.8449   2.5779  -4.0260
 SCV  C9    C  C      0   0.226  -0.3069   4.5739  -2.6909
 SCV  O8    O  O      0  -0.354  -0.6998   4.8199  -1.5846
 SCV  S     S  S2     0  -0.145   1.3502   4.8212  -3.2367
 SCV  HC2   H  HCH1   0   0.219  -9.5377   3.7060  -4.2832
 SCV  HC31  H  HCH2   0   0.210  -7.5020   2.8777  -3.3024
 SCV  HC32  H  HCH2   0   0.213  -7.5483   4.6299  -3.2479
 SCV  HC41  H  HCH2   0   0.223  -5.9765   2.9661  -5.2754
 SCV  HC42  H  HCH2   0   0.228  -6.0007   4.7168  -5.2301
 SCV  HC7   H  HCH1   0   0.328  -0.9929   4.5897  -4.7195
 SCV  HC01  H  HCH1   0   0.245  -0.9048  -0.0209  -4.0379
 SCV  H131  H  HCH3   0   0.225  -3.2047  -0.8692  -4.2699
 SCV  H132  H  HCH3   0   0.222  -3.9035   0.5654  -3.5212
 SCV  H133  H  HCH3   0   0.228  -4.2451  -1.0281  -2.8571
 SCV  HC51  H  HCH2   0   0.260  -5.0370   4.6706  -2.9158
 SCV  HC52  H  HCH2   0   0.268  -5.0399   2.9264  -2.9460
 SCV  HN11  H  HNH2   0   0.327  -7.9413   2.7814  -6.5027
 SCV  HN12  H  HNH2   0   0.335  -9.4838   2.5039  -6.2120
 SCV  H141  H  HCH3   0   0.222  -3.0085   1.3020  -1.1372
 SCV  H142  H  HCH3   0   0.225  -3.4251  -0.3149  -0.5806
 SCV  H143  H  HCH3   0   0.229  -1.7943   0.2959  -0.3464
 SCV  HN2   H  HNH1   0   0.406  -2.7822   4.4853  -2.4563
 SCV  HS1   H  HSH1   0   0.261   1.8314   5.2111  -2.0504
 SCV  O4    O  O      0  -0.442   0.0130   2.2490  -4.8034
 SCV  C14   C  CH3    0  -0.658  -2.6356   0.2812  -1.0403
 SCV  HC21  H  HCH1   0   0.233  -1.8679  -1.3196  -2.2304

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
 SCV  C1   C2    single  1.548  0.020  1.548
 SCV  C1   O1    deloc   1.248  0.020  1.248
 SCV  C1   O2    deloc   1.249  0.020  1.249
 SCV  C2   C3    single  1.533  0.020  1.533
 SCV  C2   N1    single  1.458  0.020  1.458
 SCV  C2   HC2   single  0.970  0.020  1.090
 SCV  C3   C4    single  1.525  0.020  1.525
 SCV  C3   HC31  single  0.970  0.020  1.090
 SCV  C3   HC32  single  0.970  0.020  1.090
 SCV  C4   C5    single  1.521  0.020  1.521
 SCV  C4   HC41  single  0.970  0.020  1.090
 SCV  C4   HC42  single  0.970  0.020  1.090
 SCV  C7   N2    single  1.429  0.020  1.429
 SCV  C7   C8    single  1.533  0.020  1.533
 SCV  C7   C9    single  1.528  0.020  1.528
 SCV  C7   HC7   single  0.970  0.020  1.090
 SCV  C10  C12   single  1.526  0.020  1.526
 SCV  C10  O5    single  1.430  0.020  1.430
 SCV  C10  C11   single  1.547  0.020  1.547
 SCV  C10  HC01  single  0.970  0.020  1.090
 SCV  C12  C13   single  1.527  0.020  1.527
 SCV  C12  C14   single  1.526  0.020  1.526
 SCV  C12  HC21  single  0.970  0.020  1.090
 SCV  C13  H131  single  0.970  0.020  1.090
 SCV  C13  H132  single  0.970  0.020  1.090
 SCV  C13  H133  single  0.970  0.020  1.090
 SCV  C5   C6    single  1.509  0.020  1.509
 SCV  C5   HC51  single  0.970  0.020  1.090
 SCV  C5   HC52  single  0.970  0.020  1.090
 SCV  N1   HN11  single  0.890  0.020  1.040
 SCV  N1   HN12  single  0.890  0.020  1.040
 SCV  O5   C8    single  1.306  0.020  1.306
 SCV  C11  O6    deloc   1.246  0.020  1.246
 SCV  C11  O7    deloc   1.241  0.020  1.241
 SCV  C14  H141  single  0.970  0.020  1.090
 SCV  C14  H142  single  0.970  0.020  1.090
 SCV  C14  H143  single  0.970  0.020  1.090
 SCV  C6   O3    double  1.221  0.020  1.221
 SCV  C6   N2    single  1.350  0.020  1.350
 SCV  N2   HN2   single  0.860  0.020  1.020
 SCV  O4   C8    double  1.204  0.020  1.204
 SCV  C9   O8    double  1.199  0.020  1.199
 SCV  C9   S     single  1.762  0.020  1.762
 SCV  HS1  S     single  1.200  0.020  1.300

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
 SCV  O2    C1   O1    126.39  3.000
 SCV  O2    C1   C2    115.91  3.000
 SCV  O1    C1   C2    117.68  3.000
 SCV  HC2   C2   N1    107.31  3.000
 SCV  HC2   C2   C3    106.54  3.000
 SCV  N1    C2   C3    110.28  3.000
 SCV  HC2   C2   C1    107.31  3.000
 SCV  N1    C2   C1    115.43  3.000
 SCV  C3    C2   C1    109.54  3.000
 SCV  HC32  C3   HC31  106.53  3.000
 SCV  HC32  C3   C4    109.68  3.000
 SCV  HC31  C3   C4    108.85  3.000
 SCV  HC32  C3   C2    108.69  3.000
 SCV  HC31  C3   C2    108.73  3.000
 SCV  C4    C3   C2    114.08  3.000
 SCV  HC42  C4   HC41  106.51  3.000
 SCV  HC42  C4   C5    109.35  3.000
 SCV  HC41  C4   C5    109.40  3.000
 SCV  HC42  C4   C3    110.30  3.000
 SCV  HC41  C4   C3    109.79  3.000
 SCV  C5    C4   C3    111.36  3.000
 SCV  HC7   C7   C9    108.40  3.000
 SCV  HC7   C7   C8    107.36  3.000
 SCV  C9    C7   C8    107.03  3.000
 SCV  HC7   C7   N2    111.14  3.000
 SCV  C9    C7   N2    109.34  3.000
 SCV  C8    C7   N2    113.38  3.000
 SCV  HC01  C10  C11   108.93  3.000
 SCV  HC01  C10  O5    109.56  3.000
 SCV  C11   C10  O5    109.55  3.000
 SCV  HC01  C10  C12   108.64  3.000
 SCV  C11   C10  C12   113.13  3.000
 SCV  O5    C10  C12   106.97  3.000
 SCV  HC21  C12  C14   108.21  3.000
 SCV  HC21  C12  C13   107.90  3.000
 SCV  C14   C12  C13   111.13  3.000
 SCV  HC21  C12  C10   105.05  3.000
 SCV  C14   C12  C10   112.81  3.000
 SCV  C13   C12  C10   111.38  3.000
 SCV  H133  C13  H132  107.46  3.000
 SCV  H133  C13  H131  107.63  3.000
 SCV  H132  C13  H131  107.66  3.000
 SCV  H133  C13  C12   110.74  3.000
 SCV  H132  C13  C12   111.80  3.000
 SCV  H131  C13  C12   111.36  3.000
 SCV  HC52  C5   HC51  105.58  3.000
 SCV  HC52  C5   C6    106.77  3.000
 SCV  HC51  C5   C6    109.90  3.000
 SCV  HC52  C5   C4    109.83  3.000
 SCV  HC51  C5   C4    110.48  3.000
 SCV  C6    C5   C4    113.88  3.000
 SCV  HN12  N1   HN11  103.72  3.000
 SCV  HN12  N1   C2    108.33  3.000
 SCV  HN11  N1   C2    107.73  3.000
 SCV  C8    O5   C10   118.58  3.000
 SCV  O7    C11  O6    128.22  3.000
 SCV  O7    C11  C10   117.50  3.000
 SCV  O6    C11  C10   114.28  3.000
 SCV  N2    C6   O3    121.30  3.000
 SCV  N2    C6   C5    115.07  3.000
 SCV  O3    C6   C5    123.61  3.000
 SCV  HN2   N2   C6    119.71  3.000
 SCV  HN2   N2   C7    118.39  3.000
 SCV  C6    N2   C7    120.06  3.000
 SCV  O4    C8   O5    126.78  3.000
 SCV  O4    C8   C7    122.18  3.000
 SCV  O5    C8   C7    111.03  3.000
 SCV  S     C9   O8    124.40  3.000
 SCV  S     C9   C7    112.71  3.000
 SCV  O8    C9   C7    122.87  3.000
 SCV  HS1   S    C9     95.99  3.000
 SCV  H143  C14  H142  107.31  3.000
 SCV  H143  C14  H141  107.91  3.000
 SCV  H142  C14  H141  107.54  3.000
 SCV  H143  C14  C12   112.09  3.000
 SCV  H142  C14  C12   110.13  3.000
 SCV  H141  C14  C12   111.65  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
 SCV  CONST_01  C5    C6   N2   C7    180.00   0.0  0
 SCV  CONST_02  O3    C6   N2   C7      0.00   0.0  0
 SCV  CONST_03  HN2   N2   C6   C5      0.00   0.0  0
 SCV  Var_01    C5    C4   C3   C2   -179.68  30.0  3
 SCV  Var_02    C6    C5   C4   C3    176.55  30.0  3
 SCV  Var_03    O3    C6   C5   C4    -24.03  30.0  3
 SCV  Var_04    O4    C8   O5   C10    16.01  30.0  3
 SCV  Var_05    H131  C13  C12  C10    55.36  30.0  3
 SCV  Var_06    H141  C14  C12  C10    62.99  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
 SCV  chir_01  C2   C1  C3   N1   positiv
 SCV  chir_02  C7   N2  C8   C9   positiv
 SCV  chir_03  C10  O5  C12  C11  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
 SCV  plan-1  C7   0.020
 SCV  plan-1  C5   0.020
 SCV  plan-1  C6   0.020
 SCV  plan-1  O3   0.020
 SCV  plan-1  N2   0.020
 SCV  plan-1  HN2  0.020
 SCV  plan-2  C1   0.020
 SCV  plan-2  C2   0.020
 SCV  plan-2  O1   0.020
 SCV  plan-2  O2   0.020
 SCV  plan-3  C10  0.020
 SCV  plan-3  C11  0.020
 SCV  plan-3  O6   0.020
 SCV  plan-3  O7   0.020
 SCV  plan-4  C7   0.020
 SCV  plan-4  O5   0.020
 SCV  plan-4  C8   0.020
 SCV  plan-4  O4   0.020
 SCV  plan-5  C7   0.020
 SCV  plan-5  C9   0.020
 SCV  plan-5  O8   0.020
 SCV  plan-5  S    0.020

