# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:35:42 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[[(~{Z})-~{C}-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-~{N}-[(2~{R})-1-oxidanyl-1-oxidanylidene-3-sulfanyl-propan-2-yl]carbonimidoyl]amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(c1O)C(NCCCC[C@H](N)C(O)=O)=N[C@@H](CS)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
 5OW  5OW  '(2~{S})-2-azanyl-6-[[(~{Z})-~{C}-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-~{N}-[(2~{R})-1-oxidanyl-1-oxidanylidene-3-sulfanyl-propan-2-yl]carbonimidoyl]amino]hexanoic acid'  L-peptide  55  32  .  2017-07-04  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_5OW
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
 5OW  N1   N  N      0  -0.408  54.1891  30.2009  39.4596
 5OW  C2   C  CR6    0   0.116  55.0150  31.0912  38.9262
 5OW  C3   C  CR6    0   0.301  56.0919  31.6214  39.6548
 5OW  C7   C  C      0   0.474  59.8592  33.4450  40.8444
 5OW  O8   O  OC    -1  -0.557  60.8583  34.1402  41.0699
 5OW  CA   C  CH1    0  -0.210  53.2451  35.4247  40.4647
 5OW  CB   C  CH2    0  -0.437  54.6132  34.7482  40.4139
 5OW  CD   C  CH2    0  -0.442  55.6380  34.8368  42.8086
 5OW  CE   C  CH2    0  -0.297  55.8062  33.3353  43.0011
 5OW  CG   C  CH2    0  -0.430  55.6859  35.3026  41.3542
 5OW  O9   O  O      0  -0.589  58.9917  33.6652  39.9614
 5OW  C1   C  CH1    0  -0.260  59.7047  32.1793  41.7343
 5OW  C10  C  CH2    0  -0.550  60.9169  31.2626  41.5602
 5OW  S11  S  S2     0  -0.250  62.4706  32.0265  42.1451
 5OW  N4   N  N      0  -0.441  58.5421  31.4273  41.3650
 5OW  C4   C  CR6    0  -0.072  56.2440  31.2318  40.9899
 5OW  C5   C  CR6    0   0.003  55.3735  30.2960  41.5380
 5OW  C5'  C  CH2    0  -0.210  55.4625  29.8263  42.9665
 5OW  OP4  O  O2     0  -0.652  54.3038  30.2070  43.6436
 5OW  P    P  P      0   1.232  54.2910  30.0434  45.3570
 5OW  OP3  O  OP    -1  -0.899  54.6504  28.5806  45.6031
 5OW  OP2  O  OP    -1  -0.890  55.3412  31.0371  45.8542
 5OW  OP1  O  O      0  -0.886  52.8492  30.4250  45.6594
 5OW  C6   C  CR16   0  -0.141  54.3688  29.8078  40.7137
 5OW  C2'  C  CH3    0  -0.722  54.7562  31.5465  37.5224
 5OW  O3   O  OH1    0  -0.668  56.8827  32.4954  39.0355
 5OW  NZ   N  NH1    0  -0.625  57.1076  32.8651  42.5677
 5OW  N    N  NH2    0  -0.782  52.6506  35.3105  41.7907
 5OW  C    C  C      0   0.392  52.3391  34.9189  39.3038
 5OW  O    O  O      0  -0.600  51.1801  34.5659  39.5968
 5OW  H2   H  HCH1   0   0.200  53.4106  36.4957  40.2734
 5OW  H3   H  HCH2   0   0.222  54.9769  34.8381  39.3914
 5OW  H4   H  HCH2   0   0.208  54.4807  33.6730  40.5809
 5OW  H5   H  HCH2   0   0.216  56.4223  35.3527  43.3733
 5OW  H6   H  HCH2   0   0.229  54.6906  35.1298  43.2632
 5OW  H7   H  HCH2   0   0.244  55.0382  32.7923  42.4543
 5OW  H8   H  HCH2   0   0.238  55.6606  33.0740  44.0529
 5OW  H9   H  HCH2   0   0.211  56.6665  35.0457  40.9434
 5OW  H10  H  HCH2   0   0.211  55.6401  36.3964  41.3358
 5OW  H11  H  HCH1   0   0.216  59.7136  32.5127  42.7853
 5OW  H12  H  HCH2   0   0.271  60.7546  30.3589  42.1457
 5OW  H13  H  HCH2   0   0.254  61.0152  30.9680  40.5141
 5OW  H14  H  HSH1   0   0.188  63.0529  30.8814  42.5279
 5OW  H15  H  HCH2   0   0.185  55.5899  28.7334  42.9645
 5OW  H16  H  HCH2   0   0.185  56.3687  30.2329  43.4352
 5OW  H19  H  HCR6   0   0.238  53.6724  29.0654  41.0909
 5OW  H20  H  HCH3   0   0.237  53.9536  30.9578  37.0820
 5OW  H21  H  HCH3   0   0.236  54.4555  32.5972  37.4990
 5OW  H22  H  HCH3   0   0.237  55.6399  31.4545  36.8895
 5OW  H23  H  HOH1   0   0.489  57.6943  32.8094  39.5442
 5OW  H24  H  HNH1   0   0.390  57.8890  33.2957  43.0375
 5OW  H25  H  HNH2   0   0.328  51.6703  35.5549  41.7116
 5OW  H26  H  HNH2   0   0.323  52.6396  34.3298  42.0504
 5OW  OXT  O  OC    -1  -0.612  52.8402  34.9365  38.1580
 5OW  C4'  C  C      0   0.356  57.3859  31.8511  41.7179

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
 5OW  C2'  C2   single    1.498  0.020  1.498
 5OW  O3   C3   single    1.331  0.020  1.331
 5OW  C2   C3   aromatic  1.404  0.020  1.404
 5OW  C2   N1   aromatic  1.326  0.020  1.326
 5OW  C3   C4   aromatic  1.399  0.020  1.399
 5OW  N1   C6   aromatic  1.327  0.020  1.327
 5OW  O9   C7   deloc     1.257  0.020  1.257
 5OW  C4   C4'  single    1.489  0.020  1.489
 5OW  C4   C5   aromatic  1.391  0.020  1.391
 5OW  C6   C5   aromatic  1.388  0.020  1.388
 5OW  CB   CG   single    1.530  0.020  1.530
 5OW  CB   CA   single    1.530  0.020  1.530
 5OW  CG   CD   single    1.528  0.020  1.528
 5OW  C7   O8   deloc     1.238  0.020  1.238
 5OW  C7   C1   single    1.555  0.020  1.555
 5OW  C4'  N4   double    1.281  0.020  1.281
 5OW  C4'  NZ   single    1.352  0.020  1.352
 5OW  N4   C1   single    1.433  0.020  1.433
 5OW  C5   C5'  single    1.506  0.020  1.506
 5OW  C    CA   single    1.525  0.021  1.525
 5OW  C    O    deloc     1.231  0.020  1.231
 5OW  CE   NZ   single    1.450  0.020  1.450
 5OW  CE   CD   single    1.523  0.020  1.523
 5OW  C1   C10  single    1.530  0.020  1.530
 5OW  CA   N    single    1.458  0.019  1.458
 5OW  C5'  OP4  single    1.395  0.020  1.395
 5OW  C10  S11  single    1.827  0.020  1.827
 5OW  OP4  P    single    1.721  0.020  1.721
 5OW  P    OP1  deloc     1.522  0.020  1.522
 5OW  P    OP2  deloc     1.529  0.020  1.529
 5OW  P    OP3  deloc     1.526  0.020  1.526
 5OW  CA   H2   single    0.970  0.020  1.090
 5OW  CB   H3   single    0.970  0.020  1.090
 5OW  CB   H4   single    0.970  0.020  1.090
 5OW  CD   H5   single    0.970  0.020  1.090
 5OW  CD   H6   single    0.970  0.020  1.090
 5OW  CE   H7   single    0.970  0.020  1.090
 5OW  CE   H8   single    0.970  0.020  1.090
 5OW  CG   H9   single    0.970  0.020  1.090
 5OW  CG   H10  single    0.970  0.020  1.090
 5OW  C1   H11  single    0.970  0.020  1.090
 5OW  C10  H12  single    0.970  0.020  1.090
 5OW  C10  H13  single    0.970  0.020  1.090
 5OW  S11  H14  single    1.200  0.020  1.300
 5OW  C5'  H15  single    0.970  0.020  1.090
 5OW  C5'  H16  single    0.970  0.020  1.090
 5OW  C6   H19  single    0.930  0.020  1.080
 5OW  C2'  H20  single    0.970  0.020  1.090
 5OW  C2'  H21  single    0.970  0.020  1.090
 5OW  C2'  H22  single    0.970  0.020  1.090
 5OW  O3   H23  single    0.850  0.020  0.980
 5OW  NZ   H24  single    0.860  0.020  1.020
 5OW  N    H25  single    0.890  0.020  1.040
 5OW  N    H26  single    0.890  0.020  1.040
 5OW  C    OXT  deloc     1.251  0.020  1.251

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
 5OW  C6   N1   C2   119.65  3.000
 5OW  C2'  C2   C3   120.26  3.000
 5OW  C3   C2   N1   121.49  3.000
 5OW  C2'  C2   N1   118.24  3.000
 5OW  O3   C3   C4   124.20  3.000
 5OW  C4   C3   C2   118.25  3.000
 5OW  O3   C3   C2   117.51  3.000
 5OW  C1   C7   O9   118.42  3.000
 5OW  C1   C7   O8   115.67  3.000
 5OW  O9   C7   O8   125.90  3.000
 5OW  H2   CA   C    105.90  3.000
 5OW  H2   CA   N    107.20  3.000
 5OW  C    CA   N    111.00  2.800
 5OW  H2   CA   CB   106.90  3.000
 5OW  N    CA   CB   110.50  1.700
 5OW  C    CA   CB   110.10  1.900
 5OW  H4   CB   H3   105.33  3.000
 5OW  H4   CB   CG   110.27  3.000
 5OW  H3   CB   CG   108.23  3.000
 5OW  H4   CB   CA   108.74  3.000
 5OW  H3   CB   CA   107.09  3.000
 5OW  CG   CB   CA   116.55  3.000
 5OW  H6   CD   H5   106.29  3.000
 5OW  H6   CD   CG   110.00  3.000
 5OW  H5   CD   CG   108.95  3.000
 5OW  H6   CD   CE   107.94  3.000
 5OW  H5   CD   CE   108.66  3.000
 5OW  CG   CD   CE   114.67  3.000
 5OW  H8   CE   H7   105.67  3.000
 5OW  H8   CE   NZ   109.24  3.000
 5OW  H7   CE   NZ   108.76  3.000
 5OW  H8   CE   CD   110.02  3.000
 5OW  H7   CE   CD   110.52  3.000
 5OW  NZ   CE   CD   112.40  3.000
 5OW  H10  CG   H9   105.42  3.000
 5OW  H10  CG   CD   108.62  3.000
 5OW  H9   CG   CD   108.30  3.000
 5OW  H10  CG   CB   108.80  3.000
 5OW  H9   CG   CB   108.21  3.000
 5OW  CD   CG   CB   116.90  3.000
 5OW  H11  C1   N4   114.25  3.000
 5OW  H11  C1   C10  106.46  3.000
 5OW  N4   C1   C10  107.40  3.000
 5OW  H11  C1   C7   107.37  3.000
 5OW  C10  C1   C7   110.12  3.000
 5OW  N4   C1   C7   111.12  3.000
 5OW  H13  C10  H12  107.75  3.000
 5OW  H13  C10  S11  110.06  3.000
 5OW  H12  C10  S11  107.55  3.000
 5OW  H13  C10  C1   110.01  3.000
 5OW  H12  C10  C1   108.55  3.000
 5OW  S11  C10  C1   112.76  3.000
 5OW  H14  S11  C10   95.95  3.000
 5OW  C4'  N4   C1   119.19  3.000
 5OW  C5   C4   C4'  124.55  3.000
 5OW  C5   C4   C3   119.70  3.000
 5OW  C4'  C4   C3   115.73  3.000
 5OW  C6   C5   C5'  119.75  3.000
 5OW  C5'  C5   C4   123.13  3.000
 5OW  C6   C5   C4   117.11  3.000
 5OW  H16  C5'  H15  105.84  3.000
 5OW  H16  C5'  OP4  112.16  3.000
 5OW  H15  C5'  OP4  111.60  3.000
 5OW  H16  C5'  C5   109.76  3.000
 5OW  H15  C5'  C5   108.35  3.000
 5OW  OP4  C5'  C5   109.03  3.000
 5OW  P    OP4  C5'  117.61  3.000
 5OW  OP1  P    OP2  115.03  3.000
 5OW  OP2  P    OP3  114.13  3.000
 5OW  OP1  P    OP3  115.56  3.000
 5OW  OP3  P    OP4  104.47  3.000
 5OW  OP2  P    OP4  104.88  3.000
 5OW  OP1  P    OP4  100.43  3.000
 5OW  H19  C6   C5   119.90  3.000
 5OW  H19  C6   N1   116.38  3.000
 5OW  C5   C6   N1   123.73  3.000
 5OW  H22  C2'  H21  106.95  3.000
 5OW  H22  C2'  H20  108.48  3.000
 5OW  H21  C2'  H20  107.96  3.000
 5OW  H22  C2'  C2   112.21  3.000
 5OW  H21  C2'  C2   111.08  3.000
 5OW  H20  C2'  C2   110.00  3.000
 5OW  H23  O3   C3   116.61  3.000
 5OW  H24  NZ   C4'  116.98  3.000
 5OW  H24  NZ   CE   114.69  3.000
 5OW  C4'  NZ   CE   128.01  3.000
 5OW  H26  N    H25  104.05  3.000
 5OW  H26  N    CA   108.24  3.000
 5OW  H25  N    CA   107.74  3.000
 5OW  OXT  C    O    126.29  3.000
 5OW  OXT  C    CA   116.45  3.000
 5OW  O    C    CA   120.80  1.700
 5OW  NZ   C4'  C4   117.48  3.000
 5OW  NZ   C4'  N4   127.38  3.000
 5OW  C4   C4'  N4   114.83  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
 5OW  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 5OW  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 5OW  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 5OW  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 5OW  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 5OW  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 5OW  CONST_07  O3   C3   C2   N1    180.00   0.0  0
 5OW  CONST_08  C5'  C5   C6   N1    180.00   0.0  0
 5OW  CONST_09  C4'  C4   C3   C2    180.00   0.0  0
 5OW  CONST_10  C5'  C5   C4   C3    180.00   0.0  0
 5OW  CONST_11  C6   C5   C4   C4'   180.00   0.0  0
 5OW  CONST_12  C2'  C2   C3   C4    180.00   0.0  0
 5OW  CONST_13  O3   C3   C4   C5    180.00   0.0  0
 5OW  CONST_14  C2'  C2   N1   C6    180.00   0.0  0
 5OW  CONST_15  H19  C6   N1   C2    180.00   0.0  0
 5OW  CONST_16  C4   C4'  NZ   CE      0.00   0.0  0
 5OW  CONST_18  H24  NZ   C4'  C4    180.00   0.0  0
 5OW  CONST_19  N4   C4'  NZ   CE    180.00   0.0  0
 5OW  CONST_20  NZ   C4'  N4   C1      0.00   0.0  0
 5OW  Var_01    N4   C4'  C4   C3    -71.83  30.0  2
 5OW  Var_02    OP4  C5'  C5   C4    116.19  30.0  2
 5OW  Var_03    H20  C2'  C2   N1     -7.14  30.0  2
 5OW  Var_04    CD   CG   CB   CA     80.85  30.0  3
 5OW  Var_05    CE   CD   CG   CB     61.16  30.0  3
 5OW  Var_06    C4'  NZ   CE   CD   -127.96  30.0  3
 5OW  Var_07    NZ   CE   CD   CG     63.66  30.0  1
 5OW  Var_08    OP1  P    OP4  C5'  -174.83  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
 5OW  chir_01  CA  CB  C   N    negativ
 5OW  chir_02  C1  C7  N4  C10  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
 5OW  plan-1  N1   0.020
 5OW  plan-1  C2   0.020
 5OW  plan-1  C3   0.020
 5OW  plan-1  C4   0.020
 5OW  plan-1  C5   0.020
 5OW  plan-1  C5'  0.020
 5OW  plan-1  C6   0.020
 5OW  plan-1  C2'  0.020
 5OW  plan-1  O3   0.020
 5OW  plan-1  H19  0.020
 5OW  plan-1  C4'  0.020
 5OW  plan-2  CE   0.020
 5OW  plan-2  C1   0.020
 5OW  plan-2  N4   0.020
 5OW  plan-2  C4   0.020
 5OW  plan-2  NZ   0.020
 5OW  plan-2  H24  0.020
 5OW  plan-2  C4'  0.020
 5OW  plan-3  C7   0.020
 5OW  plan-3  O8   0.020
 5OW  plan-3  O9   0.020
 5OW  plan-3  C1   0.020
 5OW  plan-4  CA   0.020
 5OW  plan-4  C    0.020
 5OW  plan-4  O    0.020
 5OW  plan-4  OXT  0.020

