# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:17:24 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{S})-5-oxidanylidene-1-[(2~{R},3~{R},4~{R},5~{R})-2,3,4,5,6-pentakis(oxidanyl)hexyl]-2~{H}-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CN1[C@@H](C=CC1=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
 G9Z  G9Z  '(2~{S})-5-oxidanylidene-1-[(2~{R},3~{R},4~{R},5~{R})-2,3,4,5,6-pentakis(oxidanyl)hexyl]-2~{H}-pyrrole-2-carboxylic acid'  ligand  36  20  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G9Z
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
 G9Z  OAM  O  O      0  -0.518  -2.1596  -2.5522   1.0132
 G9Z  CAB  C  CR5    0   0.518  -2.7074  -1.6722   0.3597
 G9Z  CAC  C  CR15   0  -0.374  -3.9888  -1.7468  -0.3716
 G9Z  CB   C  CR15   0  -0.201  -4.2146  -0.5706  -0.9557
 G9Z  CA   C  CR15   0  -0.224  -3.1213   0.3880  -0.6280
 G9Z  C    C  C      0   0.425  -3.7360   1.6285   0.1025
 G9Z  O    O  O      0  -0.573  -3.5330   1.7323   1.3187
 G9Z  N    N  NR5    0  -0.469  -2.2344  -0.4190   0.1643
 G9Z  CAG  C  CH2    0  -0.314  -0.9791   0.0392   0.6941
 G9Z  CAH  C  CH1    0   0.004   0.1999  -0.2840  -0.2239
 G9Z  OAP  O  OH1    0  -0.657   0.0765   0.3745  -1.4640
 G9Z  CAI  C  CH1    0  -0.013   1.5379   0.0339   0.4640
 G9Z  OAQ  O  OH1    0  -0.668   1.6853  -0.7308   1.6436
 G9Z  CAJ  C  CH1    0  -0.020   2.7309  -0.1473  -0.4815
 G9Z  OAR  O  OH1    0  -0.667   2.7661  -1.4486  -1.0315
 G9Z  CAK  C  CH1    0  -0.018   4.0704   0.2020   0.1913
 G9Z  OAT  O  OH1    0  -0.661   4.0112   1.4447   0.8536
 G9Z  CAL  C  CH2    0  -0.158   5.2049   0.1635  -0.8213
 G9Z  OAS  O  OH1    0  -0.671   6.4249   0.3671  -0.1475
 G9Z  OXT  O  OC    -1  -0.598  -4.3937   2.3704  -0.6453
 G9Z  H1   H  HCR5   0   0.263  -4.6075  -2.6314  -0.4019
 G9Z  H2   H  HCR5   0   0.273  -5.0615  -0.2943  -1.5662
 G9Z  H3   H  HCR5   0   0.271  -2.6274   0.7377  -1.5410
 G9Z  H4   H  HCH2   0   0.251  -1.0421   1.1174   0.8573
 G9Z  H5   H  HCH2   0   0.250  -0.8246  -0.4129   1.6740
 G9Z  H6   H  HCH1   0   0.233   0.1762  -1.3539  -0.4576
 G9Z  H7   H  HOH1   0   0.445   0.0553   1.3253  -1.3074
 G9Z  H8   H  HCH1   0   0.233   1.5193   1.0801   0.7864
 G9Z  H9   H  HOH1   0   0.443   1.4785  -1.6522   1.4534
 G9Z  H10  H  HCH1   0   0.232   2.5921   0.5314  -1.3299
 G9Z  H11  H  HOH1   0   0.443   3.0530  -2.0706  -0.3538
 G9Z  H12  H  HCH1   0   0.227   4.2719  -0.5388   0.9734
 G9Z  H13  H  HOH1   0   0.444   3.9021   2.1402   0.1953
 G9Z  H14  H  HCH2   0   0.206   5.1897  -0.7974  -1.3463
 G9Z  H15  H  HCH2   0   0.189   5.0259   0.9422  -1.5791
 G9Z  H16  H  HOH1   0   0.455   7.1359   0.2717  -0.7872

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
 G9Z  O    C    deloc   1.237  0.020  1.237
 G9Z  CB   CAC  double  1.333  0.020  1.333
 G9Z  CB   CA   single  1.490  0.020  1.490
 G9Z  CAC  CAB  single  1.477  0.020  1.477
 G9Z  C    OXT  deloc   1.242  0.020  1.242
 G9Z  C    CA   single  1.565  0.020  1.565
 G9Z  CA   N    single  1.437  0.020  1.437
 G9Z  CAB  OAM  double  1.225  0.020  1.225
 G9Z  CAB  N    single  1.354  0.020  1.354
 G9Z  N    CAG  single  1.437  0.020  1.437
 G9Z  CAG  CAH  single  1.529  0.020  1.529
 G9Z  CAH  OAP  single  1.409  0.020  1.409
 G9Z  CAH  CAI  single  1.538  0.020  1.538
 G9Z  OAQ  CAI  single  1.413  0.020  1.413
 G9Z  CAI  CAJ  single  1.533  0.020  1.533
 G9Z  CAJ  CAK  single  1.539  0.020  1.539
 G9Z  CAJ  OAR  single  1.413  0.020  1.413
 G9Z  CAK  CAL  single  1.521  0.020  1.521
 G9Z  CAK  OAT  single  1.409  0.020  1.409
 G9Z  CAL  OAS  single  1.408  0.020  1.408
 G9Z  CAC  H1   single  0.930  0.020  1.080
 G9Z  CB   H2   single  0.930  0.020  1.080
 G9Z  CA   H3   single  0.970  0.020  1.090
 G9Z  CAG  H4   single  0.970  0.020  1.090
 G9Z  CAG  H5   single  0.970  0.020  1.090
 G9Z  CAH  H6   single  0.970  0.020  1.090
 G9Z  OAP  H7   single  0.850  0.020  0.980
 G9Z  CAI  H8   single  0.970  0.020  1.090
 G9Z  OAQ  H9   single  0.850  0.020  0.980
 G9Z  CAJ  H10  single  0.970  0.020  1.090
 G9Z  OAR  H11  single  0.850  0.020  0.980
 G9Z  CAK  H12  single  0.970  0.020  1.090
 G9Z  OAT  H13  single  0.850  0.020  0.980
 G9Z  CAL  H14  single  0.970  0.020  1.090
 G9Z  CAL  H15  single  0.970  0.020  1.090
 G9Z  OAS  H16  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
 G9Z  N    CAB  CAC  106.17  3.000
 G9Z  N    CAB  OAM  125.85  3.000
 G9Z  CAC  CAB  OAM  127.99  3.000
 G9Z  H1   CAC  CB   127.86  3.000
 G9Z  H1   CAC  CAB  123.52  3.000
 G9Z  CB   CAC  CAB  108.62  3.000
 G9Z  H2   CB   CA   122.34  3.000
 G9Z  H2   CB   CAC  127.33  3.000
 G9Z  CA   CB   CAC  110.31  3.000
 G9Z  H3   CA   N    111.13  3.000
 G9Z  H3   CA   C    108.24  3.000
 G9Z  N    CA   C    115.47  3.000
 G9Z  H3   CA   CB   110.66  3.000
 G9Z  N    CA   CB   102.28  3.000
 G9Z  C    CA   CB   108.92  3.000
 G9Z  OXT  C    O    128.95  3.000
 G9Z  OXT  C    CA   113.60  3.000
 G9Z  O    C    CA   117.43  3.000
 G9Z  CAG  N    CA   124.27  3.000
 G9Z  CAG  N    CAB  123.16  3.000
 G9Z  CA   N    CAB  112.57  3.000
 G9Z  H5   CAG  H4   106.45  3.000
 G9Z  H5   CAG  CAH  110.05  3.000
 G9Z  H4   CAG  CAH  110.05  3.000
 G9Z  H5   CAG  N    108.83  3.000
 G9Z  H4   CAG  N    108.62  3.000
 G9Z  CAH  CAG  N    112.63  3.000
 G9Z  H6   CAH  CAI  108.43  3.000
 G9Z  H6   CAH  OAP  105.47  3.000
 G9Z  CAI  CAH  OAP  111.92  3.000
 G9Z  H6   CAH  CAG  108.53  3.000
 G9Z  CAI  CAH  CAG  111.02  3.000
 G9Z  OAP  CAH  CAG  111.22  3.000
 G9Z  H7   OAP  CAH  108.65  3.000
 G9Z  H8   CAI  CAJ  107.92  3.000
 G9Z  H8   CAI  OAQ  105.84  3.000
 G9Z  CAJ  CAI  OAQ  111.69  3.000
 G9Z  H8   CAI  CAH  108.33  3.000
 G9Z  CAJ  CAI  CAH  112.13  3.000
 G9Z  OAQ  CAI  CAH  110.63  3.000
 G9Z  H9   OAQ  CAI  109.28  3.000
 G9Z  H10  CAJ  CAK  107.95  3.000
 G9Z  H10  CAJ  OAR  105.81  3.000
 G9Z  CAK  CAJ  OAR  110.95  3.000
 G9Z  H10  CAJ  CAI  107.81  3.000
 G9Z  OAR  CAJ  CAI  111.61  3.000
 G9Z  CAK  CAJ  CAI  112.38  3.000
 G9Z  H11  OAR  CAJ  109.16  3.000
 G9Z  H12  CAK  CAL  108.70  3.000
 G9Z  H12  CAK  OAT  105.57  3.000
 G9Z  CAL  CAK  OAT  111.50  3.000
 G9Z  H12  CAK  CAJ  108.58  3.000
 G9Z  OAT  CAK  CAJ  111.66  3.000
 G9Z  CAL  CAK  CAJ  110.63  3.000
 G9Z  H13  OAT  CAK  108.66  3.000
 G9Z  H15  CAL  H14  106.75  3.000
 G9Z  H15  CAL  OAS  111.58  3.000
 G9Z  H14  CAL  OAS  111.61  3.000
 G9Z  H15  CAL  CAK  108.60  3.000
 G9Z  H14  CAL  CAK  109.33  3.000
 G9Z  OAS  CAL  CAK  108.90  3.000
 G9Z  H16  OAS  CAL  107.94  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
 G9Z  CONST_01  CA   N    CAB  CAC    0.00   0.0  0
 G9Z  CONST_02  CA   N    CAB  OAM  180.00   0.0  0
 G9Z  CONST_03  CAG  N    CAB  CAC  180.00   0.0  0
 G9Z  CONST_04  CAG  N    CAB  OAM    0.00   0.0  0
 G9Z  Var_01    CA   CB   CAC  CAB   -1.56  30.0  1
 G9Z  Var_02    N    CAB  CAC  CB     0.14  30.0  1
 G9Z  Var_03    CAH  CAG  N    CAB   86.29  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
 G9Z  chir_01  CA   CB   C    N    negativ
 G9Z  chir_02  CAH  OAP  CAI  CAG  negativ
 G9Z  chir_03  CAI  OAQ  CAH  CAJ  positiv
 G9Z  chir_04  CAJ  OAR  CAI  CAK  negativ
 G9Z  chir_05  CAK  OAT  CAJ  CAL  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
 G9Z  plan-1  OAM  0.020
 G9Z  plan-1  CAB  0.020
 G9Z  plan-1  CAC  0.020
 G9Z  plan-1  CA   0.020
 G9Z  plan-1  N    0.020
 G9Z  plan-1  CAG  0.020
 G9Z  plan-2  CA   0.020
 G9Z  plan-2  C    0.020
 G9Z  plan-2  O    0.020
 G9Z  plan-2  OXT  0.020

