# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 08:58:02 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: N-{2-formyl-7-[(methoxycarbonyl)amino]indolizin-3-yl}-3-sulfino-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1ccn2c(N[C@@H](C(O)=O)C(C)(C)[S@@](O)=O)c(C=O)cc2c1
#
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
 MXS  MXS  N-{2-formyl-7-[(methoxycarbonyl)amino]indolizin-3-yl}-3-sulfino-D-valine  ligand  46  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MXS
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
 MXS  C1    C  CR6   0   0.455  -3.6673  -0.5862  -0.1385
 MXS  C2    C  CR16  0  -0.485  -3.0865  -1.6384   0.5020
 MXS  C3    C  CR56  0   0.480  -1.6889  -1.8443   0.4177
 MXS  C4    C  CR15  0  -0.443  -0.8270  -2.7819   0.9353
 MXS  C5    C  CR5   0  -0.091   0.4700  -2.4523   0.4729
 MXS  C6    C  CR5   0   0.507   0.3869  -1.2955  -0.2992
 MXS  C7    C  CR16  0   0.023  -1.5172   0.1100  -0.9859
 MXS  C8    C  CR16  0  -0.424  -2.8490   0.3053  -0.9090
 MXS  C9    C  C1    0   0.094   1.6714  -3.2263   0.7071
 MXS  C10   C  CH1   0  -0.188   2.5386  -0.0877  -0.3250
 MXS  C11   C  C     0   0.537   3.7307  -0.6608  -1.0829
 MXS  C12   C  CT    0  -0.290   2.5977   1.4745  -0.2441
 MXS  C13   C  CH3   0  -0.665   2.5684   2.1166  -1.6228
 MXS  C14   C  CH3   0  -0.647   1.4616   1.9639   0.6413
 MXS  C15   C  C     0   0.737  -5.7271   0.7398  -0.0635
 MXS  C16   C  CH3   0  -0.418  -7.8859   1.6533   0.1022
 MXS  N1    N  N     0  -0.586  -0.9322  -0.9383  -0.3258
 MXS  N2    N  NH1   0  -0.712   1.3166  -0.5165  -0.9602
 MXS  O6    O  O2    0  -0.474  -7.0342   0.5124   0.0292
 MXS  O1    O  O     0  -0.399   1.7114  -4.2316   1.3850
 MXS  O2    O  O     0  -0.415   3.6992  -0.9607  -2.2478
 MXS  O3    O  OH1   0  -0.578   4.7993  -0.7725  -0.3137
 MXS  O4    O  O     0  -0.725   4.1273   1.3806   1.9408
 MXS  O5    O  OH1   0  -0.735   3.9145   3.5301   0.6424
 MXS  N3    N  NH1   0  -0.756  -5.0561  -0.4430  -0.1032
 MXS  O7    O  O     0  -0.494  -5.2229   1.8385  -0.1112
 MXS  S1    S  S3    0   0.999   4.2122   1.9159   0.5585
 MXS  H2    H  HCR6  0   0.284  -3.6738  -2.3373   1.0833
 MXS  H4    H  HCR5  0   0.259  -1.0997  -3.6173   1.5595
 MXS  H7    H  HCR6  0   0.309  -0.8614   0.7370  -1.5703
 MXS  H8    H  HCR6  0   0.290  -3.2770   1.1295  -1.4554
 MXS  H9    H  H     0   0.172   2.5850  -2.8649   0.2055
 MXS  H10   H  HCH1  0   0.305   2.5629  -0.4547   0.7033
 MXS  H13   H  HCH3  0   0.259   1.7063   1.7472  -2.1786
 MXS  H13A  H  HCH3  0   0.263   2.4607   3.1966  -1.5440
 MXS  H13B  H  HCH3  0   0.250   3.4623   1.9100  -2.2139
 MXS  H14   H  HCH3  0   0.250   1.5439   1.5775   1.6571
 MXS  H14A  H  HCH3  0   0.261   1.4306   3.0510   0.6825
 MXS  H14B  H  HCH3  0   0.257   0.5086   1.6319   0.2331
 MXS  H16   H  HCH3  0   0.239  -7.6847   2.2474   0.9933
 MXS  H16A  H  HCH3  0   0.239  -7.7902   2.2835  -0.7815
 MXS  H16B  H  HCH3  0   0.253  -8.8976   1.2623   0.1549
 MXS  HN2   H  HNH1  0   0.397   1.3968  -0.6773  -1.9555
 MXS  HO3   H  HOH1  0   0.493   5.5637  -1.0777  -0.8284
 MXS  HO5   H  HOH1  0   0.494   4.7153   4.0022   0.3715
 MXS  HN3   H  HNH1  0   0.417  -5.5882  -1.2770   0.0973

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
 MXS  C1   C2    aromatic  1.362  0.020  1.362
 MXS  C1   C8    aromatic  1.435  0.020  1.435
 MXS  C1   N3    single    1.397  0.020  1.397
 MXS  C2   C3    aromatic  1.415  0.020  1.415
 MXS  C3   C4    aromatic  1.375  0.020  1.375
 MXS  C3   N1    aromatic  1.395  0.020  1.395
 MXS  C4   C5    aromatic  1.416  0.020  1.416
 MXS  C5   C6    aromatic  1.393  0.020  1.393
 MXS  C5   C9    single    1.448  0.020  1.448
 MXS  C6   N1    aromatic  1.367  0.020  1.367
 MXS  C6   N2    single    1.381  0.020  1.381
 MXS  C7   C8    aromatic  1.348  0.020  1.348
 MXS  C7   N1    aromatic  1.370  0.020  1.370
 MXS  C9   O1    double    1.213  0.020  1.213
 MXS  C10  C11   single    1.525  0.020  1.525
 MXS  C10  C12   single    1.565  0.020  1.565
 MXS  C10  N2    single    1.442  0.020  1.442
 MXS  C11  O2    double    1.203  0.020  1.203
 MXS  C11  O3    single    1.321  0.020  1.321
 MXS  C12  C13   single    1.521  0.020  1.521
 MXS  C12  C14   single    1.521  0.020  1.521
 MXS  C12  S1    single    1.856  0.020  1.856
 MXS  C15  O6    single    1.330  0.020  1.330
 MXS  C15  N3    single    1.360  0.020  1.360
 MXS  C15  O7    double    1.210  0.020  1.210
 MXS  C16  O6    single    1.426  0.020  1.426
 MXS  O4   S1    double    1.485  0.020  1.485
 MXS  O5   S1    single    1.644  0.020  1.644
 MXS  C2   H2    single    0.930  0.020  1.080
 MXS  C4   H4    single    0.930  0.020  1.080
 MXS  C7   H7    single    0.930  0.020  1.080
 MXS  C8   H8    single    0.930  0.020  1.080
 MXS  C9   H9    single    0.930  0.020  1.080
 MXS  C10  H10   single    0.970  0.020  1.090
 MXS  C13  H13   single    0.970  0.020  1.090
 MXS  C13  H13A  single    0.970  0.020  1.090
 MXS  C13  H13B  single    0.970  0.020  1.090
 MXS  C14  H14   single    0.970  0.020  1.090
 MXS  C14  H14A  single    0.970  0.020  1.090
 MXS  C14  H14B  single    0.970  0.020  1.090
 MXS  C16  H16   single    0.970  0.020  1.090
 MXS  C16  H16A  single    0.970  0.020  1.090
 MXS  C16  H16B  single    0.970  0.020  1.090
 MXS  N2   HN2   single    0.890  0.020  1.040
 MXS  O3   HO3   single    0.850  0.020  0.980
 MXS  O5   HO5   single    0.850  0.020  0.980
 MXS  N3   HN3   single    0.860  0.020  1.020

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
 MXS  N3    C1   C8    121.14  3.000
 MXS  N3    C1   C2    119.43  3.000
 MXS  C8    C1   C2    119.31  3.000
 MXS  H2    C2   C3    118.30  3.000
 MXS  H2    C2   C1    121.34  3.000
 MXS  C3    C2   C1    120.36  3.000
 MXS  N1    C3   C4    107.67  3.000
 MXS  N1    C3   C2    118.23  3.000
 MXS  C4    C3   C2    134.10  3.000
 MXS  H4    C4   C5    126.96  3.000
 MXS  H4    C4   C3    126.02  3.000
 MXS  C5    C4   C3    107.01  3.000
 MXS  C9    C5   C6    125.66  3.000
 MXS  C9    C5   C4    125.64  3.000
 MXS  C6    C5   C4    108.64  3.000
 MXS  N2    C6   N1    119.53  3.000
 MXS  N2    C6   C5    133.88  3.000
 MXS  N1    C6   C5    106.58  3.000
 MXS  H7    C7   N1    116.48  3.000
 MXS  H7    C7   C8    123.16  3.000
 MXS  N1    C7   C8    120.34  3.000
 MXS  H8    C8   C7    118.31  3.000
 MXS  H8    C8   C1    121.40  3.000
 MXS  C7    C8   C1    120.27  3.000
 MXS  H9    C9   O1    119.89  3.000
 MXS  H9    C9   C5    116.00  3.000
 MXS  O1    C9   C5    124.10  3.000
 MXS  H10   C10  N2    109.49  3.000
 MXS  H10   C10  C12   106.61  3.000
 MXS  N2    C10  C12   110.58  3.000
 MXS  H10   C10  C11   108.93  3.000
 MXS  N2    C10  C11   109.38  3.000
 MXS  C12   C10  C11   111.80  3.000
 MXS  O3    C11  O2    124.31  3.000
 MXS  O3    C11  C10   112.01  3.000
 MXS  O2    C11  C10   123.68  3.000
 MXS  S1    C12  C14   108.75  3.000
 MXS  S1    C12  C13   107.95  3.000
 MXS  C14   C12  C13   112.17  3.000
 MXS  S1    C12  C10   107.01  3.000
 MXS  C14   C12  C10   108.84  3.000
 MXS  C13   C12  C10   111.94  3.000
 MXS  H13B  C13  H13A  107.95  3.000
 MXS  H13B  C13  H13   107.90  3.000
 MXS  H13A  C13  H13   107.15  3.000
 MXS  H13B  C13  C12   113.28  3.000
 MXS  H13A  C13  C12   110.81  3.000
 MXS  H13   C13  C12   109.53  3.000
 MXS  H14B  C14  H14A  107.09  3.000
 MXS  H14B  C14  H14   107.91  3.000
 MXS  H14A  C14  H14   108.73  3.000
 MXS  H14B  C14  C12   109.72  3.000
 MXS  H14A  C14  C12   111.39  3.000
 MXS  H14   C14  C12   111.84  3.000
 MXS  O7    C15  N3    125.66  3.000
 MXS  O7    C15  O6    124.58  3.000
 MXS  N3    C15  O6    109.76  3.000
 MXS  H16B  C16  H16A  109.24  3.000
 MXS  H16B  C16  H16   109.18  3.000
 MXS  H16A  C16  H16   109.37  3.000
 MXS  H16B  C16  O6    105.72  3.000
 MXS  H16A  C16  O6    111.64  3.000
 MXS  H16   C16  O6    111.59  3.000
 MXS  C7    N1   C6    128.42  3.000
 MXS  C7    N1   C3    121.47  3.000
 MXS  C6    N1   C3    110.09  3.000
 MXS  HN2   N2   C10   114.42  3.000
 MXS  HN2   N2   C6    115.76  3.000
 MXS  C10   N2   C6    121.81  3.000
 MXS  C16   O6   C15   117.00  3.000
 MXS  HO3   O3   C11   110.78  3.000
 MXS  HO5   O5   S1    108.35  3.000
 MXS  HN3   N3   C15   116.91  3.000
 MXS  HN3   N3   C1    116.39  3.000
 MXS  C15   N3   C1    125.47  3.000
 MXS  O5    S1   O4    107.23  3.000
 MXS  O5    S1   C12    95.63  3.000
 MXS  O4    S1   C12   105.49  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
 MXS  CONST_01  C4   C3   C2   C1   180.00   0.0  0
 MXS  CONST_02  N1   C3   C2   C1     0.00   0.0  0
 MXS  CONST_03  N1   C7   C8   C1     0.00   0.0  0
 MXS  CONST_04  C7   C8   C1   C2     0.00   0.0  0
 MXS  CONST_05  C5   C4   C3   C2   180.00   0.0  0
 MXS  CONST_06  C6   N1   C3   C2   180.00   0.0  0
 MXS  CONST_07  C7   N1   C3   C2     0.00   0.0  0
 MXS  CONST_08  C8   C1   C2   C3     0.00   0.0  0
 MXS  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 MXS  CONST_10  C5   C6   N1   C3     0.00   0.0  0
 MXS  CONST_11  C8   C7   N1   C3     0.00   0.0  0
 MXS  CONST_12  C6   N1   C3   C4     0.00   0.0  0
 MXS  CONST_13  C7   N1   C3   C4   180.00   0.0  0
 MXS  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 MXS  CONST_15  N1   C3   C4   C5     0.00   0.0  0
 MXS  CONST_16  C7   N1   C6   C5   180.00   0.0  0
 MXS  CONST_17  C8   C7   N1   C6   180.00   0.0  0
 MXS  CONST_18  N3   C1   C2   C3   180.00   0.0  0
 MXS  CONST_19  C9   C5   C4   C3   180.00   0.0  0
 MXS  CONST_20  N2   C6   N1   C3   180.00   0.0  0
 MXS  CONST_21  N2   C6   C5   C4   180.00   0.0  0
 MXS  CONST_22  N3   C1   C8   C7   180.00   0.0  0
 MXS  CONST_23  N2   C6   N1   C7     0.00   0.0  0
 MXS  CONST_24  N1   C6   C5   C9   180.00   0.0  0
 MXS  CONST_25  H7   C7   C8   C1   180.00   0.0  0
 MXS  CONST_26  H8   C8   C1   C2   180.00   0.0  0
 MXS  CONST_27  H4   C4   C3   C2     0.00   0.0  0
 MXS  CONST_28  H2   C2   C3   C4     0.00   0.0  0
 MXS  CONST_35  O6   C15  N3   C1   180.00   0.0  0
 MXS  CONST_36  O7   C15  N3   C1     0.00   0.0  0
 MXS  CONST_37  HO3  O3   C11  C10  180.00   0.0  0
 MXS  Var_01    O1   C9   C5   C4    -3.30  30.0  2
 MXS  Var_02    O4   S1   C12  C10  -64.83  30.0  3
 MXS  Var_03    N3   C15  O6   C16  179.08  30.0  2
 MXS  Var_04    H13  C13  C12  C10   53.56  30.0  3
 MXS  Var_05    H14  C14  C12  C10   61.22  30.0  3
 MXS  Var_06    H16  C16  O6   C15  -62.34  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
 MXS  chir_01  C10  C11  C12  N2  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
 MXS  plan-1  C1   0.020
 MXS  plan-1  C2   0.020
 MXS  plan-1  C3   0.020
 MXS  plan-1  C4   0.020
 MXS  plan-1  C5   0.020
 MXS  plan-1  C6   0.020
 MXS  plan-1  C7   0.020
 MXS  plan-1  C8   0.020
 MXS  plan-1  C9   0.020
 MXS  plan-1  N1   0.020
 MXS  plan-1  N2   0.020
 MXS  plan-1  N3   0.020
 MXS  plan-1  H2   0.020
 MXS  plan-1  H4   0.020
 MXS  plan-1  H7   0.020
 MXS  plan-1  H8   0.020
 MXS  plan-2  C12  0.020
 MXS  plan-2  O4   0.020
 MXS  plan-2  O5   0.020
 MXS  plan-2  S1   0.020
 MXS  plan-3  C6   0.020
 MXS  plan-3  C10  0.020
 MXS  plan-3  N2   0.020
 MXS  plan-3  HN2  0.020
 MXS  plan-4  C1   0.020
 MXS  plan-4  C15  0.020
 MXS  plan-4  N3   0.020
 MXS  plan-4  HN3  0.020
 MXS  plan-5  C10  0.020
 MXS  plan-5  C11  0.020
 MXS  plan-5  O2   0.020
 MXS  plan-5  O3   0.020
 MXS  plan-5  HO3  0.020
 MXS  plan-6  C5   0.020
 MXS  plan-6  C9   0.020
 MXS  plan-6  O1   0.020
 MXS  plan-6  H9   0.020
 MXS  plan-7  C15  0.020
 MXS  plan-7  O6   0.020
 MXS  plan-7  N3   0.020
 MXS  plan-7  O7   0.020

