# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 23:09:59 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (3R)-4-{[(3,4-dihydroxyphenyl)acetyl]oxy}-N-(2-formylindolizin-3-yl)-3-sulfino-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](COC(=O)Cc1ccc(O)c(O)c1)([C@@H](Nc2n3ccccc3cc2C=O)C(O)=O)[S@](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
 LN1  LN1  (3R)-4-{[(3,4-dihydroxyphenyl)acetyl]oxy}-N-(2-formylindolizin-3-yl)-3-sulfino-D-valine  ligand  56  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LN1
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
 LN1  O8    O  O     0  -0.420  -5.1874   3.2393   0.4704
 LN1  C7    C  C1    0   0.110  -4.5973   2.3361  -0.0894
 LN1  C6    C  CR5   0  -0.103  -4.6775   0.9488   0.3104
 LN1  C9    C  CR15  0  -0.445  -5.4572   0.4262   1.3685
 LN1  CG    C  CR56  0   0.446  -5.2237  -0.9257   1.4144
 LN1  CD1   C  CR16  0  -0.379  -5.6800  -1.9792   2.2446
 LN1  CE1   C  CR16  0  -0.176  -5.2939  -3.2575   2.0009
 LN1  CZ    C  CR16  0  -0.392  -4.4464  -3.5403   0.8863
 LN1  CE2   C  CR16  0   0.015  -3.9911  -2.5446   0.0974
 LN1  ND2   N  N     0  -0.583  -4.3375  -1.2409   0.3709
 LN1  C5    C  CR5   0   0.542  -3.9786  -0.1003  -0.2788
 LN1  N4    N  NH1   0  -0.706  -3.1311  -0.1236  -1.3641
 LN1  C3    C  CH1   0  -0.168  -1.7720  -0.6109  -1.2994
 LN1  C3A   C  C     0   0.547  -1.5007  -1.2949  -2.6400
 LN1  O3A   O  OH1   0  -0.581  -0.8774  -2.4513  -2.4888
 LN1  O3B   O  O     0  -0.415  -1.8345  -0.8375  -3.7008
 LN1  C2    C  CT    0  -0.379  -0.6591   0.4358  -0.9978
 LN1  S1    S  S3    0   1.030  -0.8245   1.1793   0.7101
 LN1  O12   O  OH1   0  -0.733  -1.4096  -0.1821   1.4190
 LN1  O13   O  O     0  -0.690  -1.8958   2.1985   0.6431
 LN1  CG2   C  CH3   0  -0.664  -0.6620   1.6143  -1.9624
 LN1  CG1   C  CH2   0  -0.148   0.6962  -0.2761  -0.9784
 LN1  OAV   O  O2    0  -0.461   1.6725   0.6755  -0.5701
 LN1  CAX   C  C     0   0.615   2.9416   0.2735  -0.5055
 LN1  OAD   O  O     0  -0.430   3.2940  -0.8422  -0.7792
 LN1  CAS   C  CH2   0  -0.692   3.8364   1.3985  -0.0486
 LN1  CAY   C  CR6   0   0.129   5.2792   1.0006   0.0316
 LN1  CAQ   C  CR16  0  -0.406   5.7429   0.2514   1.1118
 LN1  CAM   C  CR16  0  -0.320   6.1765   1.3652  -0.9601
 LN1  CAN   C  CR16  0  -0.331   7.5133   0.9903  -0.8808
 LN1  CAZ   C  CR6   0   0.280   7.9735   0.2446   0.1910
 LN1  OAH   O  OH1   0  -0.635   9.2772  -0.1032   0.2444
 LN1  CBA   C  CR6   0   0.270   7.0712  -0.1266   1.1984
 LN1  OAI   O  OH1   0  -0.646   7.5852  -0.8511   2.2190
 LN1  H7    H  H     0   0.166  -3.9762   2.5448  -0.9755
 LN1  H9    H  HCR5  0   0.257  -6.1069   0.9782   2.0284
 LN1  HD1   H  HCR6  0   0.270  -6.3401  -1.7352   3.0662
 LN1  HE1   H  HCR6  0   0.265  -5.6330  -4.0657   2.6338
 LN1  HZ    H  HCR6  0   0.275  -4.1699  -4.5575   0.6500
 LN1  HE2   H  HCR6  0   0.297  -3.3824  -2.7232  -0.7748
 LN1  HN4   H  HNH1  0   0.398  -3.2984   0.5930  -2.0526
 LN1  H3    H  HCH1  0   0.315  -1.7065  -1.3726  -0.5240
 LN1  HO3A  H  HOH1  0   0.491  -0.7012  -2.8586  -3.3521
 LN1  HO12  H  HOH1  0   0.499  -1.1029  -0.2126   2.3376
 LN1  HG2   H  HCH3  0   0.258  -1.6359   2.0976  -2.0104
 LN1  HG2A  H  HCH3  0   0.266   0.0613   2.3777  -1.6768
 LN1  HG2B  H  HCH3  0   0.266  -0.3988   1.2825  -2.9658
 LN1  HG1   H  HCH2  0   0.274   0.6849  -1.1277  -0.2918
 LN1  HG1A  H  HCH2  0   0.276   0.9455  -0.6496  -1.9739
 LN1  HAS   H  HCH2  0   0.305   3.7059   2.2374  -0.7378
 LN1  HASA  H  HCH2  0   0.302   3.4681   1.7494   0.9202
 LN1  HAQ   H  HCR6  0   0.269   5.0586  -0.0396   1.9025
 LN1  HAM   H  HCR6  0   0.250   5.8404   1.9486  -1.8084
 LN1  HAN   H  HCR6  0   0.264   8.2096   1.2814  -1.6576
 LN1  HOAH  H  HOH1  0   0.472   9.4530  -0.6337   1.0302
 LN1  HOAI  H  HOH1  0   0.482   6.9006  -1.0770   2.8582

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
 LN1  O8   C7    double    1.215  0.020  1.215
 LN1  C7   H7    single    0.930  0.020  1.080
 LN1  C6   C7    single    1.446  0.020  1.446
 LN1  C6   C9    aromatic  1.414  0.020  1.414
 LN1  C9   H9    single    0.930  0.020  1.080
 LN1  CG   C9    aromatic  1.373  0.020  1.373
 LN1  CG   CD1   aromatic  1.417  0.020  1.417
 LN1  CD1  HD1   single    0.930  0.020  1.080
 LN1  CE1  CD1   aromatic  1.357  0.020  1.357
 LN1  CE1  HE1   single    0.930  0.020  1.080
 LN1  CZ   CE1   aromatic  1.429  0.020  1.429
 LN1  CZ   HZ    single    0.930  0.020  1.080
 LN1  CE2  CZ    aromatic  1.349  0.020  1.349
 LN1  CE2  ND2   aromatic  1.376  0.020  1.376
 LN1  CE2  HE2   single    0.930  0.020  1.080
 LN1  ND2  CG    aromatic  1.405  0.020  1.405
 LN1  C5   C6    aromatic  1.392  0.020  1.392
 LN1  C5   ND2   aromatic  1.361  0.020  1.361
 LN1  N4   C5    single    1.377  0.020  1.377
 LN1  N4   HN4   single    0.890  0.020  1.040
 LN1  C3   N4    single    1.445  0.020  1.445
 LN1  C3   C3A   single    1.529  0.020  1.529
 LN1  C3   H3    single    0.970  0.020  1.090
 LN1  C3A  O3A   single    1.322  0.020  1.322
 LN1  O3A  HO3A  single    0.850  0.020  0.980
 LN1  O3B  C3A   double    1.202  0.020  1.202
 LN1  C2   C3    single    1.557  0.020  1.557
 LN1  C2   CG2   single    1.523  0.020  1.523
 LN1  S1   C2    single    1.870  0.020  1.870
 LN1  O12  S1    single    1.643  0.020  1.643
 LN1  O12  HO12  single    0.850  0.020  0.980
 LN1  O13  S1    double    1.480  0.020  1.480
 LN1  CG2  HG2   single    0.970  0.020  1.090
 LN1  CG2  HG2A  single    0.970  0.020  1.090
 LN1  CG2  HG2B  single    0.970  0.020  1.090
 LN1  CG1  C2    single    1.531  0.020  1.531
 LN1  CG1  OAV   single    1.423  0.020  1.423
 LN1  CG1  HG1   single    0.970  0.020  1.090
 LN1  CG1  HG1A  single    0.970  0.020  1.090
 LN1  CAX  OAV   single    1.333  0.020  1.333
 LN1  OAD  CAX   double    1.202  0.020  1.202
 LN1  CAS  CAX   single    1.508  0.020  1.508
 LN1  CAS  HAS   single    0.970  0.020  1.090
 LN1  CAS  HASA  single    0.970  0.020  1.090
 LN1  CAY  CAS   single    1.499  0.020  1.499
 LN1  CAY  CAM   aromatic  1.386  0.020  1.386
 LN1  CAQ  CAY   aromatic  1.394  0.020  1.394
 LN1  CAQ  HAQ   single    0.930  0.020  1.080
 LN1  CAM  HAM   single    0.930  0.020  1.080
 LN1  CAN  CAM   aromatic  1.391  0.020  1.391
 LN1  CAN  HAN   single    0.930  0.020  1.080
 LN1  CAZ  CAN   aromatic  1.384  0.020  1.384
 LN1  OAH  CAZ   single    1.350  0.020  1.350
 LN1  OAH  HOAH  single    0.850  0.020  0.980
 LN1  CBA  CAQ   aromatic  1.384  0.020  1.384
 LN1  CBA  CAZ   aromatic  1.402  0.020  1.402
 LN1  OAI  CBA   single    1.353  0.020  1.353
 LN1  OAI  HOAI  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
 LN1  H7    C7   C6    115.81  3.000
 LN1  C6    C7   O8    123.96  3.000
 LN1  H7    C7   O8    120.22  3.000
 LN1  C5    C6   C9    108.36  3.000
 LN1  C5    C6   C7    125.34  3.000
 LN1  C9    C6   C7    126.30  3.000
 LN1  H9    C9   CG    125.90  3.000
 LN1  CG    C9   C6    107.17  3.000
 LN1  H9    C9   C6    126.93  3.000
 LN1  ND2   CG   CD1   118.14  3.000
 LN1  ND2   CG   C9    107.66  3.000
 LN1  CD1   CG   C9    134.19  3.000
 LN1  HD1   CD1  CE1   121.49  3.000
 LN1  CE1   CD1  CG    120.22  3.000
 LN1  HD1   CD1  CG    118.28  3.000
 LN1  HE1   CE1  CZ    119.66  3.000
 LN1  CZ    CE1  CD1   119.69  3.000
 LN1  HE1   CE1  CD1   120.64  3.000
 LN1  HZ    CZ   CE2   118.72  3.000
 LN1  CE2   CZ   CE1   120.68  3.000
 LN1  HZ    CZ   CE1   120.59  3.000
 LN1  HE2   CE2  ND2   117.36  3.000
 LN1  HE2   CE2  CZ    122.75  3.000
 LN1  ND2   CE2  CZ    119.86  3.000
 LN1  C5    ND2  CE2   129.24  3.000
 LN1  C5    ND2  CG    109.45  3.000
 LN1  CE2   ND2  CG    121.26  3.000
 LN1  N4    C5   ND2   121.63  3.000
 LN1  N4    C5   C6    130.96  3.000
 LN1  ND2   C5   C6    107.29  3.000
 LN1  HN4   N4   C3    115.25  3.000
 LN1  C3    N4   C5    123.30  3.000
 LN1  HN4   N4   C5    115.10  3.000
 LN1  H3    C3   C2    106.82  3.000
 LN1  C2    C3   C3A   110.10  3.000
 LN1  H3    C3   C3A   107.50  3.000
 LN1  C2    C3   N4    117.00  3.000
 LN1  H3    C3   N4    108.92  3.000
 LN1  C3A   C3   N4    106.16  3.000
 LN1  O3B   C3A  O3A   124.36  3.000
 LN1  O3B   C3A  C3    123.64  3.000
 LN1  O3A   C3A  C3    111.99  3.000
 LN1  HO3A  O3A  C3A   110.54  3.000
 LN1  CG1   C2   CG2   111.69  3.000
 LN1  CG1   C2   S1    104.57  3.000
 LN1  CG2   C2   S1    105.70  3.000
 LN1  CG1   C2   C3    108.81  3.000
 LN1  S1    C2   C3    112.39  3.000
 LN1  CG2   C2   C3    113.34  3.000
 LN1  O13   S1   O12   109.41  3.000
 LN1  O13   S1   C2    107.24  3.000
 LN1  O12   S1   C2     95.52  3.000
 LN1  HO12  O12  S1    108.81  3.000
 LN1  HG2B  CG2  HG2A  107.12  3.000
 LN1  HG2B  CG2  HG2   108.11  3.000
 LN1  HG2A  CG2  HG2   107.12  3.000
 LN1  HG2B  CG2  C2    110.33  3.000
 LN1  HG2A  CG2  C2    112.02  3.000
 LN1  HG2   CG2  C2    111.92  3.000
 LN1  HG1A  CG1  HG1   107.95  3.000
 LN1  HG1A  CG1  OAV   109.49  3.000
 LN1  HG1   CG1  OAV   110.34  3.000
 LN1  HG1A  CG1  C2    110.46  3.000
 LN1  HG1   CG1  C2    111.15  3.000
 LN1  OAV   CG1  C2    107.46  3.000
 LN1  CAX   OAV  CG1   117.74  3.000
 LN1  CAS   CAX  OAD   125.98  3.000
 LN1  CAS   CAX  OAV   110.77  3.000
 LN1  OAD   CAX  OAV   123.25  3.000
 LN1  HASA  CAS  HAS   105.78  3.000
 LN1  HASA  CAS  CAY   111.21  3.000
 LN1  HAS   CAS  CAY   110.62  3.000
 LN1  CAY   CAS  CAX   112.91  3.000
 LN1  HASA  CAS  CAX   107.92  3.000
 LN1  HAS   CAS  CAX   108.09  3.000
 LN1  CAM   CAY  CAQ   118.71  3.000
 LN1  CAQ   CAY  CAS   120.29  3.000
 LN1  CAM   CAY  CAS   121.00  3.000
 LN1  HAQ   CAQ  CBA   119.10  3.000
 LN1  CBA   CAQ  CAY   120.97  3.000
 LN1  HAQ   CAQ  CAY   119.93  3.000
 LN1  HAM   CAM  CAN   119.22  3.000
 LN1  CAN   CAM  CAY   120.70  3.000
 LN1  HAM   CAM  CAY   120.08  3.000
 LN1  HAN   CAN  CAZ   119.10  3.000
 LN1  CAZ   CAN  CAM   120.59  3.000
 LN1  HAN   CAN  CAM   120.31  3.000
 LN1  CBA   CAZ  OAH   121.64  3.000
 LN1  CBA   CAZ  CAN   119.00  3.000
 LN1  OAH   CAZ  CAN   119.36  3.000
 LN1  HOAH  OAH  CAZ   110.48  3.000
 LN1  OAI   CBA  CAZ   116.05  3.000
 LN1  OAI   CBA  CAQ   123.93  3.000
 LN1  CAZ   CBA  CAQ   120.02  3.000
 LN1  HOAI  OAI  CBA   110.86  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
 LN1  CONST_01  CD1   CG   C9   C6    180.00   0.0  0
 LN1  CONST_02  ND2   CG   C9   C6      0.00   0.0  0
 LN1  CONST_03  CE2   ND2  C5   C6    180.00   0.0  0
 LN1  CONST_04  CG    ND2  C5   C6      0.00   0.0  0
 LN1  CONST_05  ND2   C5   C6   C9      0.00   0.0  0
 LN1  CONST_06  CE1   CD1  CG   C9    180.00   0.0  0
 LN1  CONST_07  CE2   ND2  CG   C9    180.00   0.0  0
 LN1  CONST_08  C5    ND2  CG   C9      0.00   0.0  0
 LN1  CONST_09  C5    C6   C9   CG      0.00   0.0  0
 LN1  CONST_10  CZ    CE1  CD1  CG      0.00   0.0  0
 LN1  CONST_11  CZ    CE2  ND2  CG      0.00   0.0  0
 LN1  CONST_12  CE2   ND2  CG   CD1     0.00   0.0  0
 LN1  CONST_13  C5    ND2  CG   CD1   180.00   0.0  0
 LN1  CONST_14  CE2   CZ   CE1  CD1     0.00   0.0  0
 LN1  CONST_15  ND2   CG   CD1  CE1     0.00   0.0  0
 LN1  CONST_16  ND2   CE2  CZ   CE1     0.00   0.0  0
 LN1  CONST_17  C5    ND2  CE2  CZ    180.00   0.0  0
 LN1  CONST_18  CAZ   CAN  CAM  CAY     0.00   0.0  0
 LN1  CONST_19  CAZ   CBA  CAQ  CAY     0.00   0.0  0
 LN1  CONST_20  CAN   CAM  CAY  CAQ     0.00   0.0  0
 LN1  CONST_21  CAN   CAZ  CBA  CAQ     0.00   0.0  0
 LN1  CONST_22  CBA   CAQ  CAY  CAM     0.00   0.0  0
 LN1  CONST_23  CBA   CAZ  CAN  CAM     0.00   0.0  0
 LN1  CONST_24  CG    C9   C6   C7    180.00   0.0  0
 LN1  CONST_25  ND2   C5   C6   C7    180.00   0.0  0
 LN1  CONST_26  N4    C5   C6   C9    180.00   0.0  0
 LN1  CONST_27  N4    C5   ND2  CG    180.00   0.0  0
 LN1  CONST_28  N4    C5   ND2  CE2     0.00   0.0  0
 LN1  CONST_29  CAN   CAM  CAY  CAS   180.00   0.0  0
 LN1  CONST_30  CBA   CAQ  CAY  CAS   180.00   0.0  0
 LN1  CONST_31  OAI   CBA  CAQ  CAY   180.00   0.0  0
 LN1  CONST_32  OAH   CAZ  CBA  CAQ   180.00   0.0  0
 LN1  CONST_33  OAH   CAZ  CAN  CAM   180.00   0.0  0
 LN1  CONST_34  OAI   CBA  CAZ  CAN   180.00   0.0  0
 LN1  CONST_35  HD1   CD1  CG   C9      0.00   0.0  0
 LN1  CONST_36  HE1   CE1  CD1  CG    180.00   0.0  0
 LN1  CONST_37  HE2   CE2  ND2  CG    180.00   0.0  0
 LN1  CONST_38  H9    C9   CG   CD1     0.00   0.0  0
 LN1  CONST_39  HZ    CZ   CE1  CD1   180.00   0.0  0
 LN1  CONST_40  HAN   CAN  CAM  CAY   180.00   0.0  0
 LN1  CONST_41  HAM   CAM  CAY  CAQ   180.00   0.0  0
 LN1  CONST_42  HAQ   CAQ  CAY  CAM   180.00   0.0  0
 LN1  CONST_46  HO3A  O3A  C3A  C3    180.00   0.0  0
 LN1  Var_01    C9    C6   C7   O8      1.52  30.0  2
 LN1  Var_02    CAM   CAY  CAS  CAX   101.91  30.0  2
 LN1  Var_03    CAY   CAS  CAX  OAV  -179.58  30.0  1
 LN1  Var_04    OAD   CAX  OAV  CG1     0.33  30.0  2
 LN1  Var_05    HG1   CG1  OAV  CAX    59.83  30.0  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
 LN1  chir_01  C3  N4   C3A  C2  negativ
 LN1  chir_02  C2  CG1  CG2  C3  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
 LN1  plan-1  CAS   0.020
 LN1  plan-1  CAY   0.020
 LN1  plan-1  CAQ   0.020
 LN1  plan-1  CAM   0.020
 LN1  plan-1  CAN   0.020
 LN1  plan-1  CAZ   0.020
 LN1  plan-1  OAH   0.020
 LN1  plan-1  CBA   0.020
 LN1  plan-1  OAI   0.020
 LN1  plan-1  HAQ   0.020
 LN1  plan-1  HAM   0.020
 LN1  plan-1  HAN   0.020
 LN1  plan-2  OAV   0.020
 LN1  plan-2  CAX   0.020
 LN1  plan-2  OAD   0.020
 LN1  plan-2  CAS   0.020
 LN1  plan-3  C7    0.020
 LN1  plan-3  C6    0.020
 LN1  plan-3  C9    0.020
 LN1  plan-3  CG    0.020
 LN1  plan-3  CD1   0.020
 LN1  plan-3  CE1   0.020
 LN1  plan-3  CZ    0.020
 LN1  plan-3  CE2   0.020
 LN1  plan-3  ND2   0.020
 LN1  plan-3  C5    0.020
 LN1  plan-3  N4    0.020
 LN1  plan-3  H9    0.020
 LN1  plan-3  HD1   0.020
 LN1  plan-3  HE1   0.020
 LN1  plan-3  HZ    0.020
 LN1  plan-3  HE2   0.020
 LN1  plan-4  C5    0.020
 LN1  plan-4  N4    0.020
 LN1  plan-4  C3    0.020
 LN1  plan-4  HN4   0.020
 LN1  plan-5  C3    0.020
 LN1  plan-5  C3A   0.020
 LN1  plan-5  O3A   0.020
 LN1  plan-5  O3B   0.020
 LN1  plan-5  HO3A  0.020
 LN1  plan-6  O8    0.020
 LN1  plan-6  C7    0.020
 LN1  plan-6  C6    0.020
 LN1  plan-6  H7    0.020
 LN1  plan-7  C2    0.020
 LN1  plan-7  S1    0.020
 LN1  plan-7  O12   0.020
 LN1  plan-7  O13   0.020

