# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:41:46 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: [(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(3~{S})-2-azanylidene-3-oxidanyl-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OCC(=N)[C@@H](O)C=C)[C@H](O)[C@@H](O[S](O)(=O)=O)[C@H]1O
#
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
 QAH  QAH  '[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(3~{S})-2-azanylidene-3-oxidanyl-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate'  ligand  42  23  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QAH
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
 QAH  C1   C  CH1   0   0.279   7.9095  -4.8721  12.8281
 QAH  C2   C  CH1   0   0.001   9.4263  -4.6782  12.9315
 QAH  C2'  C  CH2   0  -0.239   6.1272  -5.2012  14.3590
 QAH  C3   C  CH1   0  -0.054   9.9325  -4.2040  11.5823
 QAH  C3'  C  C     0   0.201   6.0558  -4.3264  15.5834
 QAH  C4   C  CH1   0  -0.003   9.4962  -5.1358  10.4532
 QAH  C4'  C  CH1   0  -0.063   6.7984  -4.7826  16.8330
 QAH  C5   C  CH1   0  -0.020   7.9776  -5.2669  10.5194
 QAH  C5'  C  C1    0  -0.216   8.1253  -4.0762  16.9303
 QAH  C6   C  CH2   0  -0.156   7.4404  -6.1988   9.4541
 QAH  C6'  C  C2    0  -0.565   9.3121  -4.6726  16.9599
 QAH  N1   N  N     0  -0.552   5.3931  -3.2524  15.5188
 QAH  O1   O  O2    0  -0.492   7.4812  -5.4338  14.0105
 QAH  O1S  O  OS    0  -0.625  12.1602  -3.3534   9.4732
 QAH  O2   O  OH1   0  -0.667   9.7473  -3.7063  13.8842
 QAH  O2S  O  OS    0  -0.625  11.7425  -1.7348  11.3241
 QAH  O3   O  OC2   0  -0.589  11.3770  -4.1635  11.6779
 QAH  O3S  O  OS    0  -0.691  13.5860  -3.2769  11.5106
 QAH  O4   O  OH1   0  -0.659  10.0679  -6.4104  10.5779
 QAH  O4'  O  OH1   0  -0.658   6.8926  -6.1763  16.8174
 QAH  O5   O  O2    0  -0.487   7.5790  -5.7473  11.7858
 QAH  O6   O  OH1   0  -0.669   6.0380  -6.0886   9.4326
 QAH  S    S  S     0   1.652  12.1644  -3.0347  10.8791
 QAH  H1   H  HCH1  0   0.196   7.4370  -3.8870  12.6539
 QAH  H2   H  HCH1  0   0.238   9.8796  -5.6525  13.1635
 QAH  H3   H  HCH2  0   0.251   5.5738  -4.7116  13.5536
 QAH  H4   H  HCH2  0   0.257   5.6451  -6.1625  14.5519
 QAH  H5   H  HCH1  0   0.280   9.5433  -3.1975  11.3899
 QAH  H6   H  HCH1  0   0.257   9.7478  -4.6723   9.4909
 QAH  H7   H  HCH1  0   0.262   6.1997  -4.4355  17.6897
 QAH  H8   H  HCH1  0   0.239   7.5572  -4.2637  10.3400
 QAH  H9   H  H     0   0.273   8.0598  -2.9965  17.0234
 QAH  H10  H  HCH2  0   0.212   7.7661  -7.2239   9.6607
 QAH  H11  H  HCH2  0   0.205   7.8864  -5.9046   8.4951
 QAH  H12  H  H     0   0.264  10.2188  -4.0957  17.0872
 QAH  H13  H  H     0   0.253   9.4261  -5.7457  16.8738
 QAH  H14  H  H     0   0.341   5.3865  -2.7618  16.4120
 QAH  H15  H  HOH1  0   0.467   9.4441  -4.0129  14.7497
 QAH  H16  H  HOH1  0   0.458  11.0007  -6.3594  10.3492
 QAH  H17  H  HOH1  0   0.465   7.2571  -6.4692  17.6594
 QAH  H18  H  HOH1  0   0.458   5.7003  -6.7306   8.8018
 QAH  H19  H  H     0   0.518  14.0728  -4.0063  11.0893

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
 QAH  O1S  S    double  1.442  0.020  1.442
 QAH  C6   O6   single  1.407  0.020  1.407
 QAH  C6   C5   single  1.514  0.020  1.514
 QAH  O2S  S    double  1.437  0.020  1.437
 QAH  S    O3S  single  1.574  0.020  1.574
 QAH  S    O3   single  1.591  0.020  1.591
 QAH  C4   C5   single  1.526  0.020  1.526
 QAH  C4   O4   single  1.402  0.020  1.402
 QAH  C4   C3   single  1.528  0.020  1.528
 QAH  C5   O5   single  1.412  0.020  1.412
 QAH  O3   C3   single  1.448  0.020  1.448
 QAH  C3   C2   single  1.517  0.020  1.517
 QAH  O5   C1   single  1.401  0.020  1.401
 QAH  C2   C1   single  1.533  0.020  1.533
 QAH  C2   O2   single  1.398  0.020  1.398
 QAH  C1   O1   single  1.377  0.020  1.377
 QAH  O1   C2'  single  1.417  0.020  1.417
 QAH  C2'  C3'  single  1.506  0.020  1.506
 QAH  C3'  N1   double  1.264  0.020  1.264
 QAH  C3'  C4'  single  1.523  0.020  1.523
 QAH  O4'  C4'  single  1.397  0.020  1.397
 QAH  C4'  C5'  single  1.506  0.020  1.506
 QAH  C5'  C6'  double  1.329  0.020  1.329
 QAH  C1   H1   single  0.970  0.020  1.090
 QAH  C2   H2   single  0.970  0.020  1.090
 QAH  C2'  H3   single  0.970  0.020  1.090
 QAH  C2'  H4   single  0.970  0.020  1.090
 QAH  C3   H5   single  0.970  0.020  1.090
 QAH  C4   H6   single  0.970  0.020  1.090
 QAH  C4'  H7   single  0.970  0.020  1.090
 QAH  C5   H8   single  0.970  0.020  1.090
 QAH  C5'  H9   single  0.930  0.020  1.080
 QAH  C6   H10  single  0.970  0.020  1.090
 QAH  C6   H11  single  0.970  0.020  1.090
 QAH  C6'  H12  single  0.930  0.020  1.080
 QAH  C6'  H13  single  0.930  0.020  1.080
 QAH  N1   H14  single  0.890  0.020  1.040
 QAH  O2   H15  single  0.850  0.020  0.980
 QAH  O4   H16  single  0.850  0.020  0.980
 QAH  O4'  H17  single  0.850  0.020  0.980
 QAH  O6   H18  single  0.850  0.020  0.980
 QAH  O3S  H19  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
 QAH  H1   C1   O5   109.78  3.000
 QAH  H1   C1   O1   111.44  3.000
 QAH  O5   C1   O1   108.10  3.000
 QAH  H1   C1   C2   108.70  3.000
 QAH  O1   C1   C2   107.54  3.000
 QAH  O5   C1   C2   111.28  3.000
 QAH  H2   C2   O2   112.18  3.000
 QAH  H2   C2   C3   109.09  3.000
 QAH  O2   C2   C3   108.18  3.000
 QAH  H2   C2   C1   108.07  3.000
 QAH  O2   C2   C1   111.17  3.000
 QAH  C3   C2   C1   108.04  3.000
 QAH  H4   C2'  H3   107.50  3.000
 QAH  H4   C2'  O1   108.70  3.000
 QAH  H3   C2'  O1   112.09  3.000
 QAH  H4   C2'  C3'  110.28  3.000
 QAH  H3   C2'  C3'  108.35  3.000
 QAH  O1   C2'  C3'  109.90  3.000
 QAH  H5   C3   O3   109.88  3.000
 QAH  H5   C3   C4   109.20  3.000
 QAH  O3   C3   C4   110.53  3.000
 QAH  H5   C3   C2   108.95  3.000
 QAH  O3   C3   C2   106.43  3.000
 QAH  C4   C3   C2   111.80  3.000
 QAH  N1   C3'  C4'  123.51  3.000
 QAH  C4'  C3'  C2'  118.01  3.000
 QAH  N1   C3'  C2'  118.48  3.000
 QAH  H6   C4   O4   111.61  3.000
 QAH  H6   C4   C5   107.60  3.000
 QAH  O4   C4   C5   108.89  3.000
 QAH  H6   C4   C3   108.97  3.000
 QAH  O4   C4   C3   111.86  3.000
 QAH  C5   C4   C3   107.74  3.000
 QAH  H7   C4'  O4'  111.08  3.000
 QAH  H7   C4'  C5'  106.31  3.000
 QAH  O4'  C4'  C5'  114.15  3.000
 QAH  H7   C4'  C3'  106.19  3.000
 QAH  C5'  C4'  C3'  110.00  3.000
 QAH  O4'  C4'  C3'  108.81  3.000
 QAH  H8   C5   O5   110.36  3.000
 QAH  H8   C5   C6   108.08  3.000
 QAH  O5   C5   C6   108.75  3.000
 QAH  H8   C5   C4   107.12  3.000
 QAH  O5   C5   C4   110.43  3.000
 QAH  C6   C5   C4   112.06  3.000
 QAH  H9   C5'  C6'  119.90  3.000
 QAH  H9   C5'  C4'  114.75  3.000
 QAH  C6'  C5'  C4'  125.30  3.000
 QAH  H11  C6   H10  107.15  3.000
 QAH  H11  C6   O6   111.75  3.000
 QAH  H10  C6   O6   111.88  3.000
 QAH  H11  C6   C5   107.79  3.000
 QAH  H10  C6   C5   109.75  3.000
 QAH  O6   C6   C5   108.44  3.000
 QAH  H13  C6'  H12  116.72  3.000
 QAH  H13  C6'  C5'  122.49  3.000
 QAH  H12  C6'  C5'  120.78  3.000
 QAH  H14  N1   C3'  111.58  3.000
 QAH  C2'  O1   C1   116.18  3.000
 QAH  H15  O2   C2   108.51  3.000
 QAH  S    O3   C3   118.70  3.000
 QAH  H19  O3S  S    113.17  3.000
 QAH  H16  O4   C4   109.03  3.000
 QAH  H17  O4'  C4'  108.62  3.000
 QAH  C5   O5   C1   112.85  3.000
 QAH  H18  O6   C6   107.93  3.000
 QAH  O3S  S    O3    97.84  3.000
 QAH  O3   S    O2S  109.93  3.000
 QAH  O3S  S    O2S  106.27  3.000
 QAH  O3   S    O1S  109.34  3.000
 QAH  O3S  S    O1S  111.09  3.000
 QAH  O2S  S    O1S  120.07  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
 QAH  Var_01  C3'  C2'  O1   C1   -112.69  30.0  3
 QAH  Var_02  O1S  S    O3   C3    -73.68  30.0  2
 QAH  Var_03  O1   C2'  C3'  C4'   -55.27  30.0  2
 QAH  Var_04  H12  C6'  C5'  C4'  -176.54   0.0  2

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
 QAH  chir_01  C1   O5   C2   O1   positiv
 QAH  chir_02  C2   O2   C1   C3   negativ
 QAH  chir_03  C3   O3   C4   C2   negativ
 QAH  chir_04  C4   O4   C3   C5   positiv
 QAH  chir_05  C4'  C3'  O4'  C5'  negativ
 QAH  chir_06  C5   O5   C4   C6   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
 QAH  plan-1  C2'  0.020
 QAH  plan-1  C3'  0.020
 QAH  plan-1  C4'  0.020
 QAH  plan-1  N1   0.020
 QAH  plan-1  H14  0.020
 QAH  plan-2  C4'  0.020
 QAH  plan-2  C5'  0.020
 QAH  plan-2  C6'  0.020
 QAH  plan-2  H9   0.020
 QAH  plan-2  H12  0.020
 QAH  plan-2  H13  0.020

