# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:17:17 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  45  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   0.454  -3.6109  -0.5367  -0.0882
 MXS  C2    C  CR16   0  -0.489  -3.0411  -1.5587   0.6100
 MXS  C3    C  CR56   0   0.471  -1.6547  -1.8200   0.4937
 MXS  C4    C  CR15   0  -0.447  -0.8059  -2.7568   1.0368
 MXS  C5    C  CR5    0  -0.092   0.4838  -2.4945   0.5137
 MXS  C6    C  CR5    0   0.477   0.4132  -1.3842  -0.3234
 MXS  C7    C  CR16   0   0.015  -1.4704   0.0228  -1.0516
 MXS  C8    C  CR16   0  -0.429  -2.7925   0.2669  -0.9502
 MXS  C9    C  C1     0   0.078   1.6824  -3.2763   0.7354
 MXS  C10   C  CH1    0  -0.218   2.5486  -0.1671  -0.4302
 MXS  C11   C  C      0   0.455   3.7950  -0.5852  -1.2459
 MXS  C12   C  CT     0  -0.263   2.4583   1.3684  -0.2414
 MXS  C13   C  CH3    0  -0.663   2.3091   2.0967  -1.5680
 MXS  C14   C  CH3    0  -0.649   1.3215   1.6997   0.7157
 MXS  C15   C  C      0   0.738  -5.6438   0.8417  -0.1110
 MXS  C16   C  CH3    0  -0.418  -7.7878   1.8024  -0.0455
 MXS  N1    N  N      0  -0.580  -0.8959  -0.9914  -0.3336
 MXS  N2    N  NH1    0  -0.696   1.3523  -0.6928  -1.0723
 MXS  O6    O  O2     0  -0.474  -6.9528   0.6499   0.0310
 MXS  O1    O  O      0  -0.406   1.7491  -4.2278   1.4872
 MXS  O2    O  O      0  -0.575   3.6350  -1.3903  -2.1786
 MXS  O3    O  OC    -1  -0.574   4.8669  -0.0741  -0.8680
 MXS  O4    O  O      0  -0.755   4.1586   1.2150   1.8183
 MXS  O5    O  OH1    0  -0.757   3.4990   3.4595   0.9255
 MXS  N3    N  NH1    0  -0.757  -4.9932  -0.3485  -0.0179
 MXS  O7    O  O      0  -0.495  -5.1258   1.9183  -0.3019
 MXS  S1    S  S3     0   0.993   4.0580   1.9394   0.5204
 MXS  H2    H  HCR6   0   0.282  -3.6307  -2.1930   1.2596
 MXS  H4    H  HCR5   0   0.256  -1.0853  -3.5476   1.7141
 MXS  H7    H  HCR6   0   0.315  -0.8088   0.5779  -1.6988
 MXS  H8    H  HCR6   0   0.288  -3.2142   1.0606  -1.5443
 MXS  H9    H  H      0   0.182   2.5617  -2.9711   0.1418
 MXS  H10   H  HCH1   0   0.256   2.6685  -0.5961   0.5720
 MXS  H13   H  HCH3   0   0.254   1.4373   1.7092  -2.0956
 MXS  H13A  H  HCH3   0   0.245   2.1561   3.1655  -1.4200
 MXS  H13B  H  HCH3   0   0.241   3.1779   1.9658  -2.2158
 MXS  H14   H  HCH3   0   0.238   1.4736   1.2415   1.6939
 MXS  H14A  H  HCH3   0   0.252   1.1950   2.7723   0.8484
 MXS  H14B  H  HCH3   0   0.248   0.3819   1.3227   0.3164
 MXS  H16   H  HCH3   0   0.239  -7.5796   2.5036   0.7624
 MXS  H16A  H  HCH3   0   0.239  -7.6823   2.3131  -1.0023
 MXS  H16B  H  HCH3   0   0.253  -8.8051   1.4358   0.0536
 MXS  HN2   H  HNH1   0   0.376   1.6459  -1.1983  -1.9045
 MXS  HO5   H  HOH1   0   0.477   4.1685   4.0961   0.6418
 MXS  HN3   H  HNH1   0   0.417  -5.5390  -1.1458   0.2743

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  1.363  0.020  1.363
 MXS  C1   C8    aromatic  1.435  0.020  1.435
 MXS  C1   N3    single    1.397  0.020  1.397
 MXS  C2   C3    aromatic  1.416  0.020  1.416
 MXS  C3   C4    aromatic  1.376  0.020  1.376
 MXS  C3   N1    aromatic  1.395  0.020  1.395
 MXS  C4   C5    aromatic  1.416  0.020  1.416
 MXS  C5   C6    aromatic  1.392  0.020  1.392
 MXS  C5   C9    single    1.448  0.020  1.448
 MXS  C6   N1    aromatic  1.367  0.020  1.367
 MXS  C6   N2    single    1.386  0.020  1.386
 MXS  C7   C8    aromatic  1.348  0.020  1.348
 MXS  C7   N1    aromatic  1.369  0.020  1.369
 MXS  C9   O1    double    1.214  0.020  1.214
 MXS  C10  C11   single    1.547  0.020  1.547
 MXS  C10  C12   single    1.550  0.020  1.550
 MXS  C10  N2    single    1.456  0.020  1.456
 MXS  C11  O2    deloc     1.242  0.020  1.242
 MXS  C11  O3    deloc     1.246  0.020  1.246
 MXS  C12  C13   single    1.521  0.020  1.521
 MXS  C12  C14   single    1.523  0.020  1.523
 MXS  C12  S1    single    1.862  0.020  1.862
 MXS  C15  O6    single    1.331  0.020  1.331
 MXS  C15  N3    single    1.360  0.020  1.360
 MXS  C15  O7    double    1.210  0.020  1.210
 MXS  C16  O6    single    1.425  0.020  1.425
 MXS  O4   S1    double    1.490  0.020  1.490
 MXS  O5   S1    single    1.670  0.020  1.670
 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  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    121.28  3.000
 MXS  N3    C1   C2    119.28  3.000
 MXS  C8    C1   C2    119.30  3.000
 MXS  H2    C2   C3    118.33  3.000
 MXS  H2    C2   C1    121.28  3.000
 MXS  C3    C2   C1    120.39  3.000
 MXS  N1    C3   C4    107.63  3.000
 MXS  N1    C3   C2    118.15  3.000
 MXS  C4    C3   C2    134.22  3.000
 MXS  H4    C4   C5    127.15  3.000
 MXS  H4    C4   C3    125.99  3.000
 MXS  C5    C4   C3    106.85  3.000
 MXS  C9    C5   C6    124.37  3.000
 MXS  C9    C5   C4    126.67  3.000
 MXS  C6    C5   C4    108.88  3.000
 MXS  N2    C6   N1    120.11  3.000
 MXS  N2    C6   C5    133.50  3.000
 MXS  N1    C6   C5    106.40  3.000
 MXS  H7    C7   N1    116.00  3.000
 MXS  H7    C7   C8    123.58  3.000
 MXS  N1    C7   C8    120.41  3.000
 MXS  H8    C8   C7    118.41  3.000
 MXS  H8    C8   C1    121.38  3.000
 MXS  C7    C8   C1    120.20  3.000
 MXS  H9    C9   O1    120.38  3.000
 MXS  H9    C9   C5    115.32  3.000
 MXS  O1    C9   C5    124.28  3.000
 MXS  H10   C10  N2    110.58  3.000
 MXS  H10   C10  C12   106.42  3.000
 MXS  N2    C10  C12   111.32  3.000
 MXS  H10   C10  C11   106.74  3.000
 MXS  N2    C10  C11   109.38  3.000
 MXS  C12   C10  C11   112.27  3.000
 MXS  O3    C11  O2    127.17  3.000
 MXS  O3    C11  C10   114.97  3.000
 MXS  O2    C11  C10   117.85  3.000
 MXS  S1    C12  C14   108.52  3.000
 MXS  S1    C12  C13   107.12  3.000
 MXS  C14   C12  C13   111.78  3.000
 MXS  S1    C12  C10   107.68  3.000
 MXS  C14   C12  C10   109.62  3.000
 MXS  C13   C12  C10   111.96  3.000
 MXS  H13B  C13  H13A  108.06  3.000
 MXS  H13B  C13  H13   107.86  3.000
 MXS  H13A  C13  H13   107.58  3.000
 MXS  H13B  C13  C12   112.47  3.000
 MXS  H13A  C13  C12   111.40  3.000
 MXS  H13   C13  C12   109.29  3.000
 MXS  H14B  C14  H14A  106.61  3.000
 MXS  H14B  C14  H14   107.69  3.000
 MXS  H14A  C14  H14   108.72  3.000
 MXS  H14B  C14  C12   109.79  3.000
 MXS  H14A  C14  C12   112.21  3.000
 MXS  H14   C14  C12   111.61  3.000
 MXS  O7    C15  N3    125.79  3.000
 MXS  O7    C15  O6    124.49  3.000
 MXS  N3    C15  O6    109.71  3.000
 MXS  H16B  C16  H16A  109.22  3.000
 MXS  H16B  C16  H16   109.18  3.000
 MXS  H16A  C16  H16   109.32  3.000
 MXS  H16B  C16  O6    105.72  3.000
 MXS  H16A  C16  O6    111.68  3.000
 MXS  H16   C16  O6    111.62  3.000
 MXS  C7    N1   C6    128.23  3.000
 MXS  C7    N1   C3    121.51  3.000
 MXS  C6    N1   C3    110.23  3.000
 MXS  HN2   N2   C10   107.65  3.000
 MXS  HN2   N2   C6    112.94  3.000
 MXS  C10   N2   C6    119.91  3.000
 MXS  C16   O6   C15   117.00  3.000
 MXS  HO5   O5   S1    107.25  3.000
 MXS  HN3   N3   C15   116.90  3.000
 MXS  HN3   N3   C1    116.31  3.000
 MXS  C15   N3   C1    126.02  3.000
 MXS  O5    S1   O4    104.71  3.000
 MXS  O5    S1   C12    95.21  3.000
 MXS  O4    S1   C12   105.39  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  Var_01    O1   C9   C5   C4     -5.19  30.0  2
 MXS  Var_02    O4   S1   C12  C10   -59.94  30.0  3
 MXS  Var_03    N3   C15  O6   C16  -179.78  30.0  2
 MXS  Var_04    H13  C13  C12  C10    56.12  30.0  3
 MXS  Var_05    H14  C14  C12  C10    59.93  30.0  3
 MXS  Var_06    H16  C16  O6   C15   -63.55  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-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

