# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:48:04 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S},3~{R},4~{R},5~{R})-2,3,4,5,6-pentakis(oxidanyl)hexyl]amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CC[C@H](NC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)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
 GOP  GOP  '(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S},3~{R},4~{R},5~{R})-2,3,4,5,6-pentakis(oxidanyl)hexyl]amino]pentanoic acid'  ligand  43  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOP
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
 GOP  OAN  O  OH1   0  -0.671  -6.9015   1.2538  -0.4028
 GOP  CAM  C  CH2   0  -0.158  -5.6499   1.4801   0.2035
 GOP  CAL  C  CH1   0  -0.020  -4.6761   0.4134  -0.2738
 GOP  OAT  O  OH1   0  -0.662  -4.5417   0.4271  -1.6776
 GOP  CAK  C  CH1   0  -0.040  -3.3083   0.5633   0.4148
 GOP  OAS  O  OH1   0  -0.661  -3.4384   0.5338   1.8196
 GOP  CAJ  C  CH1   0   0.011  -2.2739  -0.4367  -0.1170
 GOP  OAR  O  OH1   0  -0.669  -2.7132  -1.7755  -0.0371
 GOP  CAI  C  CH1   0  -0.011  -0.8964  -0.2513   0.5478
 GOP  OAQ  O  OH1   0  -0.665  -0.8265  -0.8968   1.8063
 GOP  CAH  C  CH2   0  -0.294   0.2295  -0.7088  -0.3687
 GOP  N    N  NH1   0  -0.589   1.5187  -0.3465   0.1833
 GOP  CA   C  CH1   0  -0.200   2.6557  -0.7602  -0.5934
 GOP  C    C  C     0   0.533   2.8848  -2.2674  -0.5664
 GOP  O    O  O     0  -0.439   2.4349  -3.0094   0.2706
 GOP  CB   C  CH2   0  -0.431   3.9305  -0.0621  -0.0947
 GOP  CG   C  CH2   0  -0.576   3.8268   1.4458  -0.2397
 GOP  CD   C  C     0   0.524   5.0335   2.1878   0.2958
 GOP  OE1  O  O     0  -0.496   5.9216   1.6393   0.9333
 GOP  NE2  N  NH2   0  -0.806   5.0437   3.5025   0.0212
 GOP  OXT  O  OH1   0  -0.592   3.6769  -2.6721  -1.5529
 GOP  H1   H  HOH1  0   0.454  -7.5194   1.9019  -0.0542
 GOP  H2   H  HCH2  0   0.187  -5.2485   2.4717  -0.0589
 GOP  H3   H  HCH2  0   0.205  -5.7191   1.4454   1.2954
 GOP  H4   H  HCH1  0   0.228  -5.0875  -0.5714  -0.0246
 GOP  H5   H  HOH1  0   0.444  -4.2359   1.3009  -1.9460
 GOP  H6   H  HCH1  0   0.232  -2.9191   1.5634   0.1826
 GOP  H7   H  HOH1  0   0.442  -3.7978  -0.3185   2.0874
 GOP  H8   H  HCH1  0   0.238  -2.1543  -0.2259  -1.1826
 GOP  H9   H  HOH1  0   0.436  -2.6908  -2.0561   0.8844
 GOP  H10  H  HCH1  0   0.232  -0.7476   0.8159   0.7419
 GOP  H11  H  HOH1  0   0.447  -0.6042  -1.8243   1.6681
 GOP  H12  H  HCH2  0   0.204   0.1145  -1.7873  -0.5668
 GOP  H13  H  HCH2  0   0.237   0.1161  -0.2051  -1.3324
 GOP  H14  H  HNH1  0   0.342   1.6096  -0.6877   1.1327
 GOP  H16  H  HCH1  0   0.267   2.4880  -0.4670  -1.6359
 GOP  H17  H  HCH2  0   0.241   4.0967  -0.3322   0.9515
 GOP  H18  H  HCH2  0   0.251   4.7923  -0.4309  -0.6532
 GOP  H19  H  HCH2  0   0.262   3.6820   1.7132  -1.2911
 GOP  H20  H  HCH2  0   0.278   2.9381   1.8090   0.2829
 GOP  H21  H  HNH2  0   0.405   4.2971   3.9431  -0.4876
 GOP  H22  H  HNH2  0   0.397   5.7789   4.0941   0.3716
 GOP  H23  H  HOH1  0   0.481   3.8458  -3.6236  -1.4784

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
 GOP  O    C    double  1.206  0.020  1.206
 GOP  CB   CA   single  1.537  0.020  1.537
 GOP  CB   CG   single  1.518  0.020  1.518
 GOP  CA   C    single  1.525  0.020  1.525
 GOP  CA   N    single  1.438  0.020  1.438
 GOP  C    OXT  single  1.328  0.020  1.328
 GOP  NE2  CD   single  1.343  0.020  1.343
 GOP  CAH  N    single  1.448  0.020  1.448
 GOP  CAH  CAI  single  1.522  0.020  1.522
 GOP  CG   CD   single  1.514  0.020  1.514
 GOP  CD   OE1  double  1.223  0.020  1.223
 GOP  OAR  CAJ  single  1.411  0.020  1.411
 GOP  CAJ  CAI  single  1.541  0.020  1.541
 GOP  CAJ  CAK  single  1.534  0.020  1.534
 GOP  CAI  OAQ  single  1.416  0.020  1.416
 GOP  OAS  CAK  single  1.411  0.020  1.411
 GOP  CAK  CAL  single  1.539  0.020  1.539
 GOP  OAT  CAL  single  1.410  0.020  1.410
 GOP  CAL  CAM  single  1.521  0.020  1.521
 GOP  CAM  OAN  single  1.409  0.020  1.409
 GOP  OAN  H1   single  0.850  0.020  0.980
 GOP  CAM  H2   single  0.970  0.020  1.090
 GOP  CAM  H3   single  0.970  0.020  1.090
 GOP  CAL  H4   single  0.970  0.020  1.090
 GOP  OAT  H5   single  0.850  0.020  0.980
 GOP  CAK  H6   single  0.970  0.020  1.090
 GOP  OAS  H7   single  0.850  0.020  0.980
 GOP  CAJ  H8   single  0.970  0.020  1.090
 GOP  OAR  H9   single  0.850  0.020  0.980
 GOP  CAI  H10  single  0.970  0.020  1.090
 GOP  OAQ  H11  single  0.850  0.020  0.980
 GOP  CAH  H12  single  0.970  0.020  1.090
 GOP  CAH  H13  single  0.970  0.020  1.090
 GOP  N    H14  single  0.890  0.020  1.040
 GOP  CA   H16  single  0.970  0.020  1.090
 GOP  CB   H17  single  0.970  0.020  1.090
 GOP  CB   H18  single  0.970  0.020  1.090
 GOP  CG   H19  single  0.970  0.020  1.090
 GOP  CG   H20  single  0.970  0.020  1.090
 GOP  NE2  H21  single  0.860  0.020  1.020
 GOP  NE2  H22  single  0.860  0.020  1.020
 GOP  OXT  H23  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
 GOP  H1   OAN  CAM  107.86  3.000
 GOP  H3   CAM  H2   106.81  3.000
 GOP  H3   CAM  CAL  109.34  3.000
 GOP  H2   CAM  CAL  108.86  3.000
 GOP  H3   CAM  OAN  111.59  3.000
 GOP  H2   CAM  OAN  111.45  3.000
 GOP  CAL  CAM  OAN  108.72  3.000
 GOP  H4   CAL  CAK  108.64  3.000
 GOP  H4   CAL  OAT  105.71  3.000
 GOP  CAK  CAL  OAT  111.09  3.000
 GOP  H4   CAL  CAM  108.57  3.000
 GOP  OAT  CAL  CAM  111.50  3.000
 GOP  CAK  CAL  CAM  111.12  3.000
 GOP  H5   OAT  CAL  108.43  3.000
 GOP  H6   CAK  CAJ  106.35  3.000
 GOP  H6   CAK  OAS  105.21  3.000
 GOP  CAJ  CAK  OAS  113.19  3.000
 GOP  H6   CAK  CAL  108.00  3.000
 GOP  OAS  CAK  CAL  111.19  3.000
 GOP  CAJ  CAK  CAL  112.38  3.000
 GOP  H7   OAS  CAK  109.25  3.000
 GOP  H8   CAJ  CAI  107.44  3.000
 GOP  H8   CAJ  OAR  105.80  3.000
 GOP  CAI  CAJ  OAR  111.59  3.000
 GOP  H8   CAJ  CAK  106.63  3.000
 GOP  CAI  CAJ  CAK  112.01  3.000
 GOP  OAR  CAJ  CAK  112.89  3.000
 GOP  H9   OAR  CAJ  108.86  3.000
 GOP  H10  CAI  CAH  107.41  3.000
 GOP  H10  CAI  OAQ  106.26  3.000
 GOP  CAH  CAI  OAQ  111.20  3.000
 GOP  H10  CAI  CAJ  108.38  3.000
 GOP  OAQ  CAI  CAJ  111.88  3.000
 GOP  CAH  CAI  CAJ  111.43  3.000
 GOP  H11  OAQ  CAI  108.83  3.000
 GOP  H13  CAH  H12  106.35  3.000
 GOP  H13  CAH  N    108.24  3.000
 GOP  H12  CAH  N    113.95  3.000
 GOP  H13  CAH  CAI  108.39  3.000
 GOP  H12  CAH  CAI  108.97  3.000
 GOP  N    CAH  CAI  110.71  3.000
 GOP  H14  N    CA   109.78  3.000
 GOP  H14  N    CAH  110.66  3.000
 GOP  CA   N    CAH  115.22  3.000
 GOP  H16  CA   CB   108.31  3.000
 GOP  H16  CA   C    107.72  3.000
 GOP  CB   CA   C    108.58  3.000
 GOP  H16  CA   N    108.42  3.000
 GOP  C    CA   N    113.18  3.000
 GOP  CB   CA   N    110.49  3.000
 GOP  OXT  C    O    123.41  3.000
 GOP  OXT  C    CA   112.19  3.000
 GOP  O    C    CA   124.37  3.000
 GOP  H18  CB   H17  106.64  3.000
 GOP  H18  CB   CG   109.93  3.000
 GOP  H17  CB   CG   110.31  3.000
 GOP  H18  CB   CA   109.60  3.000
 GOP  H17  CB   CA   108.93  3.000
 GOP  CG   CB   CA   111.32  3.000
 GOP  H20  CG   H19  105.70  3.000
 GOP  H20  CG   CD   108.42  3.000
 GOP  H19  CG   CD   108.99  3.000
 GOP  H20  CG   CB   109.87  3.000
 GOP  H19  CG   CB   110.09  3.000
 GOP  CD   CG   CB   113.48  3.000
 GOP  NE2  CD   OE1  122.69  3.000
 GOP  OE1  CD   CG   122.90  3.000
 GOP  NE2  CD   CG   114.41  3.000
 GOP  H22  NE2  H21  117.45  3.000
 GOP  H22  NE2  CD   120.64  3.000
 GOP  H21  NE2  CD   121.80  3.000
 GOP  H23  OXT  C    110.24  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
 GOP  CONST_01  H21  NE2  CD   CG     0.00   0.0  0
 GOP  CONST_02  H22  NE2  CD   CG   180.00   0.0  0
 GOP  CONST_03  H23  OXT  C    CA   180.00   0.0  0
 GOP  Var_01    CA   N    CAH  CAI  178.69  30.0  3
 GOP  Var_02    CD   CG   CB   CA   177.39  30.0  3
 GOP  Var_03    NE2  CD   CG   CB   171.68  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
 GOP  chir_01  CAL  CAK  OAT  CAM  positiv
 GOP  chir_02  CAK  OAS  CAL  CAJ  positiv
 GOP  chir_03  CAJ  OAR  CAK  CAI  negativ
 GOP  chir_04  CAI  OAQ  CAJ  CAH  positiv
 GOP  chir_05  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
 GOP  plan-1  CG   0.020
 GOP  plan-1  CD   0.020
 GOP  plan-1  OE1  0.020
 GOP  plan-1  NE2  0.020
 GOP  plan-1  H21  0.020
 GOP  plan-1  H22  0.020
 GOP  plan-2  CA   0.020
 GOP  plan-2  C    0.020
 GOP  plan-2  O    0.020
 GOP  plan-2  OXT  0.020
 GOP  plan-2  H23  0.020

