# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:45:31 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: (1R,2R,3R,6R,7R,7aR)-3,7-bis(hydroxymethyl)hexahydro-1H-pyrrolizine-1,2,6-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)CN2[C@H](CO)[C@@H](O)[C@H](O)[C@@H]12
#
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
 LG9  LG9  (1R,2R,3R,6R,7R,7aR)-3,7-bis(hydroxymethyl)hexahydro-1H-pyrrolizine-1,2,6-triol  ligand  32  15  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LG9
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
 LG9  O4    O  OH1   0  -0.668   3.9683  -0.9092   0.1153
 LG9  C9    C  CH2   0  -0.135   2.6900  -1.0523   0.6887
 LG9  C1    C  CH1   0  -0.332   1.6844  -0.2002  -0.0582
 LG9  C5    C  CR15  0  -0.050   0.2656  -0.4080   0.4756
 LG9  C4    C  CR15  0   0.019  -0.6005  -1.4547  -0.2128
 LG9  O1    O  OH1   0  -0.672  -0.4475  -2.7109   0.3982
 LG9  C6    C  CR15  0   0.014  -1.9934  -0.8360  -0.0969
 LG9  O2    O  OH1   0  -0.673  -2.9484  -1.3373  -0.9970
 LG9  C7    C  CR15  0  -0.095  -1.7076   0.6338  -0.3914
 LG9  C8    C  CH2   0  -0.154  -2.7963   1.5995   0.0297
 LG9  O3    O  OH1   0  -0.669  -3.0426   1.4776   1.4100
 LG9  N4    N  NR5   0  -0.456  -0.4401   0.8667   0.2769
 LG9  C3    C  CH2   0  -0.293   0.4611   1.8206  -0.3317
 LG9  C2    C  CH1   0   0.058   1.8495   1.3138   0.0650
 LG9  OXT   O  OH1   0  -0.661   2.8835   1.7982  -0.7495
 LG9  H4    H  HOH1  0   0.451   4.5604  -1.5215   0.5605
 LG9  H91C  H  HCH2  0   0.204   2.3536  -2.0972   0.6565
 LG9  H92C  H  HCH2  0   0.185   2.6842  -0.7537   1.7476
 LG9  H1    H  HCH1  0   0.238   1.7106  -0.4607  -1.1248
 LG9  H5    H  HCR5  0   0.221   0.3102  -0.6492   1.5485
 LG9  H2    H  HCH1  0   0.200   2.0305   1.5624   1.1223
 LG9  HA    H  HCR5  0   0.207  -0.3384  -1.5032  -1.2808
 LG9  HB    H  HOH1  0   0.453  -0.8295  -3.3803  -0.1766
 LG9  H6    H  HCR5  0   0.216  -2.3327  -0.9454   0.9425
 LG9  HC    H  HOH1  0   0.455  -3.3166  -2.1488  -0.6366
 LG9  H7    H  HCR5  0   0.209  -1.6033   0.7469  -1.4859
 LG9  H81C  H  HCH2  0   0.202  -2.4808   2.6186  -0.2341
 LG9  H82C  H  HCH2  0   0.199  -3.6925   1.3851  -0.5668
 LG9  H3    H  HOH1  0   0.454  -3.7931   2.0367   1.6274
 LG9  H31C  H  HCH2  0   0.194   0.3843   1.8245  -1.4312
 LG9  H32C  H  HCH2  0   0.229   0.2752   2.8427   0.0122
 LG9  HXT   H  HOH1  0   0.450   2.9756   2.7420  -0.5872

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
 LG9  O4   C9    single  1.408  0.020  1.408
 LG9  C9   C1    single  1.515  0.020  1.515
 LG9  C1   C5    single  1.530  0.020  1.530
 LG9  C1   C2    single  1.528  0.020  1.528
 LG9  C5   C4    single  1.523  0.020  1.523
 LG9  C5   N4    single  1.470  0.020  1.470
 LG9  C4   O1    single  1.405  0.020  1.405
 LG9  C4   C6    single  1.529  0.020  1.529
 LG9  C6   O2    single  1.405  0.020  1.405
 LG9  C6   C7    single  1.526  0.020  1.526
 LG9  C7   C8    single  1.515  0.020  1.515
 LG9  C7   N4    single  1.452  0.020  1.452
 LG9  C8   O3    single  1.407  0.020  1.407
 LG9  N4   C3    single  1.447  0.020  1.447
 LG9  C3   C2    single  1.530  0.020  1.530
 LG9  C2   OXT   single  1.403  0.020  1.403
 LG9  O4   H4    single  0.850  0.020  0.980
 LG9  C9   H91C  single  0.970  0.020  1.090
 LG9  C9   H92C  single  0.970  0.020  1.090
 LG9  C1   H1    single  0.970  0.020  1.090
 LG9  C5   H5    single  0.970  0.020  1.090
 LG9  C2   H2    single  0.970  0.020  1.090
 LG9  C4   HA    single  0.970  0.020  1.090
 LG9  O1   HB    single  0.850  0.020  0.980
 LG9  C6   H6    single  0.970  0.020  1.090
 LG9  O2   HC    single  0.850  0.020  0.980
 LG9  C7   H7    single  0.970  0.020  1.090
 LG9  C8   H81C  single  0.970  0.020  1.090
 LG9  C8   H82C  single  0.970  0.020  1.090
 LG9  O3   H3    single  0.850  0.020  0.980
 LG9  C3   H31C  single  0.970  0.020  1.090
 LG9  C3   H32C  single  0.970  0.020  1.090
 LG9  OXT  HXT   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
 LG9  H4    O4   C9    107.80  3.000
 LG9  H92C  C9   H91C  106.55  3.000
 LG9  H92C  C9   C1    108.56  3.000
 LG9  H91C  C9   C1    108.51  3.000
 LG9  H92C  C9   O4    111.66  3.000
 LG9  H91C  C9   O4    111.27  3.000
 LG9  C1    C9   O4    110.15  3.000
 LG9  H1    C1   C2    108.11  3.000
 LG9  H1    C1   C5    109.19  3.000
 LG9  C2    C1   C5    101.93  3.000
 LG9  H1    C1   C9    109.24  3.000
 LG9  C2    C1   C9    116.48  3.000
 LG9  C5    C1   C9    111.53  3.000
 LG9  H5    C5   N4    109.95  3.000
 LG9  H5    C5   C4    108.24  3.000
 LG9  N4    C5   C4    105.17  3.000
 LG9  H5    C5   C1    109.41  3.000
 LG9  N4    C5   C1    106.27  3.000
 LG9  C4    C5   C1    117.58  3.000
 LG9  HA    C4   C6    107.97  3.000
 LG9  HA    C4   O1    110.88  3.000
 LG9  C6    C4   O1    115.34  3.000
 LG9  HA    C4   C5    109.47  3.000
 LG9  C6    C4   C5    101.88  3.000
 LG9  O1    C4   C5    110.85  3.000
 LG9  HB    O1   C4    108.61  3.000
 LG9  H6    C6   C7    109.65  3.000
 LG9  H6    C6   O2    111.14  3.000
 LG9  C7    C6   O2    110.33  3.000
 LG9  H6    C6   C4    108.23  3.000
 LG9  C7    C6   C4    101.80  3.000
 LG9  O2    C6   C4    115.24  3.000
 LG9  HC    O2   C6    108.75  3.000
 LG9  H7    C7   N4    110.92  3.000
 LG9  H7    C7   C8    106.13  3.000
 LG9  N4    C7   C8    113.40  3.000
 LG9  H7    C7   C6    107.90  3.000
 LG9  N4    C7   C6    103.25  3.000
 LG9  C8    C7   C6    115.19  3.000
 LG9  H82C  C8   H81C  106.56  3.000
 LG9  H82C  C8   O3    111.91  3.000
 LG9  H81C  C8   O3    111.47  3.000
 LG9  H82C  C8   C7    108.13  3.000
 LG9  H81C  C8   C7    108.54  3.000
 LG9  O3    C8   C7    110.07  3.000
 LG9  H3    O3   C8    107.95  3.000
 LG9  C3    N4   C7    117.13  3.000
 LG9  C3    N4   C5    109.23  3.000
 LG9  C7    N4   C5    110.01  3.000
 LG9  H32C  C3   H31C  107.35  3.000
 LG9  H32C  C3   C2    112.46  3.000
 LG9  H31C  C3   C2    108.85  3.000
 LG9  H32C  C3   N4    112.20  3.000
 LG9  H31C  C3   N4    112.25  3.000
 LG9  C2    C3   N4    103.76  3.000
 LG9  H2    C2   OXT   111.01  3.000
 LG9  H2    C2   C3    108.86  3.000
 LG9  OXT   C2   C3    113.82  3.000
 LG9  H2    C2   C1    108.60  3.000
 LG9  OXT   C2   C1    112.03  3.000
 LG9  C3    C2   C1    102.07  3.000
 LG9  HXT   OXT  C2    108.14  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
 LG9  Var_01  C2  C3  N4  C5  -24.30  30.0  1

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
 LG9  chir_01  C1  C9   C5  C2  negativ
 LG9  chir_02  C5  N4   C4  C1  negativ
 LG9  chir_03  C4  O1   C5  C6  positiv
 LG9  chir_04  C6  O2   C4  C7  negativ
 LG9  chir_05  C7  N4   C6  C8  negativ
 LG9  chir_06  C2  OXT  C3  C1  negativ

