# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 18:30:56 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (3R)-N-(7-carbamoyl-2-formylindolizin-3-yl)-4-(carbamoyloxy)-3-sulfino-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](COC(N)=O)([C@@H](Nc1n2ccc(cc2cc1C=O)C(N)=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
 MXC  MXC  (3R)-N-(7-carbamoyl-2-formylindolizin-3-yl)-4-(carbamoyloxy)-3-sulfino-D-valine  ligand  47  29  .  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_MXC
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
 MXC  C1    C  CR6   0   0.040  -4.1374   1.5793  -0.6845
 MXC  C2    C  CR16  0  -0.409  -4.0357   0.3028  -1.1523
 MXC  C3    C  CR56  0   0.476  -3.0349  -0.5650  -0.6741
 MXC  C4    C  CR15  0  -0.416  -2.7187  -1.8814  -0.9216
 MXC  C5    C  CR5   0  -0.118  -1.5910  -2.1912  -0.1334
 MXC  C6    C  CR5   0   0.516  -1.2345  -1.0517   0.5924
 MXC  C7    C  CR16  0   0.030  -2.2431   1.1956   0.7794
 MXC  C8    C  CR16  0  -0.421  -3.2111   2.0132   0.3217
 MXC  C9    C  C     0   0.519  -5.2238   2.4409  -1.2383
 MXC  C10   C  C1    0   0.101  -0.9000  -3.4645  -0.0770
 MXC  C11   C  CH1   0  -0.201   0.8338   0.1337   1.2715
 MXC  C12   C  C     0   0.561   1.1504   0.7555   2.6315
 MXC  C13   C  CT    0  -0.353   2.1228  -0.4374   0.6061
 MXC  C14   C  CH3   0  -0.673   2.8299  -1.4624   1.4871
 MXC  C15   C  CH2   0  -0.115   3.0355   0.7159   0.1865
 MXC  C16   C  C     0   0.721   5.2156   1.0758  -0.6023
 MXC  N1    N  N     0  -0.583  -2.1277  -0.0794   0.2777
 MXC  N2    N  NH2   0  -0.829  -5.3029   3.6952  -0.7717
 MXC  N3    N  NH1   0  -0.706  -0.2174  -0.8371   1.4932
 MXC  N4    N  NH2   0  -0.832   6.3715   0.4599  -0.8906
 MXC  O1    O  O     0  -0.396  -1.2042  -4.4310  -0.7433
 MXC  O2    O  O     0  -0.485  -6.0022   2.0077  -2.0789
 MXC  O3    O  O     0  -0.413   1.2175   0.1187   3.6487
 MXC  O4    O  OH1   0  -0.579   1.3180   2.0639   2.5551
 MXC  O7    O  O2    0  -0.464   4.3067   0.2004  -0.1558
 MXC  O8    O  O     0  -0.519   5.0065   2.2674  -0.7085
 MXC  S1    S  S3    0   0.997   1.5851  -1.4103  -0.8921
 MXC  H2    H  HCR6  0   0.280  -4.7223  -0.0761  -1.8969
 MXC  H4    H  HCR5  0   0.270  -3.2403  -2.5386  -1.5983
 MXC  H7    H  HCR6  0   0.310  -1.5560   1.4867   1.5580
 MXC  H8    H  HCR6  0   0.270  -3.2564   2.9979   0.7629
 MXC  H10   H  H     0   0.170  -0.0578  -3.5172   0.6340
 MXC  H11   H  HCH1  0   0.319   0.4489   0.9212   0.6218
 MXC  H14   H  HCH3  0   0.248   2.1291  -2.1829   1.9105
 MXC  H14A  H  HCH3  0   0.273   3.5743  -2.0251   0.9270
 MXC  H14B  H  HCH3  0   0.274   3.3487  -0.9772   2.3132
 MXC  H15   H  HCH2  0   0.265   2.5962   1.2756  -0.6433
 MXC  H15A  H  HCH2  0   0.261   3.1407   1.4173   1.0181
 MXC  HN2   H  HNH2  0   0.416  -4.6771   4.0823  -0.0895
 MXC  HN2A  H  HNH2  0   0.407  -6.0163   4.3101  -1.1275
 MXC  HN3   H  HNH1  0   0.406  -0.0036  -1.5972   2.1201
 MXC  HN4   H  HNH2  0   0.407   6.4576  -0.5417  -0.8738
 MXC  HN4A  H  HNH2  0   0.409   7.1169   0.9880  -1.3090
 MXC  HO4   H  HOH1  0   0.492   1.5416   2.4305   3.4257
 MXC  HO6   H  HOH1  0   0.496   0.0394  -0.5285  -2.1257
 MXC  O5    O  O     0  -0.687   2.7999  -1.6566  -1.6966
 MXC  O6    O  OH1   0  -0.735   0.7578  -0.1665  -1.5847

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
 MXC  C1   C2    aromatic  1.363  0.020  1.363
 MXC  C1   C8    aromatic  1.435  0.020  1.435
 MXC  C1   C9    single    1.493  0.020  1.493
 MXC  C2   C3    aromatic  1.408  0.020  1.408
 MXC  C3   C4    aromatic  1.376  0.020  1.376
 MXC  C3   N1    aromatic  1.402  0.020  1.402
 MXC  C4   C5    aromatic  1.410  0.020  1.410
 MXC  C5   C6    aromatic  1.397  0.020  1.397
 MXC  C5   C10   single    1.450  0.020  1.450
 MXC  C6   N1    aromatic  1.357  0.020  1.357
 MXC  C6   N3    single    1.376  0.020  1.376
 MXC  C7   C8    aromatic  1.347  0.020  1.347
 MXC  C7   N1    aromatic  1.375  0.020  1.375
 MXC  C9   N2    single    1.341  0.020  1.341
 MXC  C9   O2    double    1.225  0.020  1.225
 MXC  C10  O1    double    1.213  0.020  1.213
 MXC  C11  C12   single    1.528  0.020  1.528
 MXC  C11  C13   single    1.559  0.020  1.559
 MXC  C11  N3    single    1.448  0.020  1.448
 MXC  C12  O3    double    1.202  0.020  1.202
 MXC  C12  O4    single    1.321  0.020  1.321
 MXC  C13  C14   single    1.525  0.020  1.525
 MXC  C13  C15   single    1.529  0.020  1.529
 MXC  C13  S1    single    1.866  0.020  1.866
 MXC  C15  O7    single    1.414  0.020  1.414
 MXC  C16  N4    single    1.341  0.020  1.341
 MXC  C16  O7    single    1.339  0.020  1.339
 MXC  C16  O8    double    1.214  0.020  1.214
 MXC  O5   S1    double    1.478  0.020  1.478
 MXC  O6   S1    single    1.647  0.020  1.647
 MXC  C2   H2    single    0.930  0.020  1.080
 MXC  C4   H4    single    0.930  0.020  1.080
 MXC  C7   H7    single    0.930  0.020  1.080
 MXC  C8   H8    single    0.930  0.020  1.080
 MXC  C10  H10   single    0.930  0.020  1.080
 MXC  C11  H11   single    0.970  0.020  1.090
 MXC  C14  H14   single    0.970  0.020  1.090
 MXC  C14  H14A  single    0.970  0.020  1.090
 MXC  C14  H14B  single    0.970  0.020  1.090
 MXC  C15  H15   single    0.970  0.020  1.090
 MXC  C15  H15A  single    0.970  0.020  1.090
 MXC  N2   HN2   single    0.860  0.020  1.020
 MXC  N2   HN2A  single    0.860  0.020  1.020
 MXC  N3   HN3   single    0.890  0.020  1.040
 MXC  N4   HN4   single    0.860  0.020  1.020
 MXC  N4   HN4A  single    0.860  0.020  1.020
 MXC  O4   HO4   single    0.850  0.020  0.980
 MXC  O6   HO6   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
 MXC  C9    C1   C8    123.73  3.000
 MXC  C9    C1   C2    117.86  3.000
 MXC  C8    C1   C2    118.40  3.000
 MXC  H2    C2   C3    117.97  3.000
 MXC  H2    C2   C1    121.13  3.000
 MXC  C3    C2   C1    120.89  3.000
 MXC  N1    C3   C4    107.74  3.000
 MXC  N1    C3   C2    118.49  3.000
 MXC  C4    C3   C2    133.76  3.000
 MXC  H4    C4   C5    127.15  3.000
 MXC  H4    C4   C3    125.79  3.000
 MXC  C5    C4   C3    107.06  3.000
 MXC  C10   C5   C6    125.06  3.000
 MXC  C10   C5   C4    126.57  3.000
 MXC  C6    C5   C4    108.37  3.000
 MXC  N3    C6   N1    121.79  3.000
 MXC  N3    C6   C5    131.00  3.000
 MXC  N1    C6   C5    107.21  3.000
 MXC  H7    C7   N1    117.40  3.000
 MXC  H7    C7   C8    122.63  3.000
 MXC  N1    C7   C8    119.94  3.000
 MXC  H8    C8   C7    116.41  3.000
 MXC  H8    C8   C1    122.35  3.000
 MXC  C7    C8   C1    121.23  3.000
 MXC  O2    C9   N2    122.16  3.000
 MXC  O2    C9   C1    120.86  3.000
 MXC  N2    C9   C1    116.99  3.000
 MXC  H10   C10  O1    120.50  3.000
 MXC  H10   C10  C5    115.51  3.000
 MXC  O1    C10  C5    123.99  3.000
 MXC  H11   C11  N3    108.60  3.000
 MXC  H11   C11  C13   107.57  3.000
 MXC  N3    C11  C13   114.83  3.000
 MXC  H11   C11  C12   108.02  3.000
 MXC  N3    C11  C12   106.67  3.000
 MXC  C13   C11  C12   110.95  3.000
 MXC  O4    C12  O3    124.50  3.000
 MXC  O4    C12  C11   112.19  3.000
 MXC  O3    C12  C11   123.30  3.000
 MXC  S1    C13  C15   110.18  3.000
 MXC  S1    C13  C14   104.30  3.000
 MXC  C15   C13  C14   112.87  3.000
 MXC  S1    C13  C11   107.19  3.000
 MXC  C15   C13  C11   109.52  3.000
 MXC  C14   C13  C11   112.52  3.000
 MXC  H14B  C14  H14A  107.14  3.000
 MXC  H14B  C14  H14   107.81  3.000
 MXC  H14A  C14  H14   107.32  3.000
 MXC  H14B  C14  C13   111.07  3.000
 MXC  H14A  C14  C13   111.55  3.000
 MXC  H14   C14  C13   111.73  3.000
 MXC  H15A  C15  H15   106.72  3.000
 MXC  H15A  C15  O7    109.37  3.000
 MXC  H15   C15  O7    111.36  3.000
 MXC  H15A  C15  C13   109.43  3.000
 MXC  H15   C15  C13   110.77  3.000
 MXC  O7    C15  C13   109.15  3.000
 MXC  O8    C16  O7    123.64  3.000
 MXC  O8    C16  N4    125.47  3.000
 MXC  O7    C16  N4    110.89  3.000
 MXC  C7    N1   C6    129.41  3.000
 MXC  C7    N1   C3    120.97  3.000
 MXC  C6    N1   C3    109.59  3.000
 MXC  HN2A  N2   HN2   116.52  3.000
 MXC  HN2A  N2   C9    119.36  3.000
 MXC  HN2   N2   C9    124.11  3.000
 MXC  HN3   N3   C11   116.54  3.000
 MXC  HN3   N3   C6    116.51  3.000
 MXC  C11   N3   C6    122.76  3.000
 MXC  HN4A  N4   HN4   117.84  3.000
 MXC  HN4A  N4   C16   119.18  3.000
 MXC  HN4   N4   C16   121.85  3.000
 MXC  HO4   O4   C12   110.57  3.000
 MXC  C16   O7   C15   116.93  3.000
 MXC  O6    S1   O5    108.05  3.000
 MXC  O6    S1   C13    95.09  3.000
 MXC  O5    S1   C13   106.69  3.000
 MXC  HO6   O6   S1    108.96  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
 MXC  CONST_01  C4    C3   C2   C1    180.00   0.0  0
 MXC  CONST_02  N1    C3   C2   C1      0.00   0.0  0
 MXC  CONST_03  N1    C7   C8   C1      0.00   0.0  0
 MXC  CONST_04  C7    C8   C1   C2      0.00   0.0  0
 MXC  CONST_05  C5    C4   C3   C2    180.00   0.0  0
 MXC  CONST_06  C6    N1   C3   C2    180.00   0.0  0
 MXC  CONST_07  C7    N1   C3   C2      0.00   0.0  0
 MXC  CONST_08  C8    C1   C2   C3      0.00   0.0  0
 MXC  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 MXC  CONST_10  C5    C6   N1   C3      0.00   0.0  0
 MXC  CONST_11  C8    C7   N1   C3      0.00   0.0  0
 MXC  CONST_12  C6    N1   C3   C4      0.00   0.0  0
 MXC  CONST_13  C7    N1   C3   C4    180.00   0.0  0
 MXC  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 MXC  CONST_15  N1    C3   C4   C5      0.00   0.0  0
 MXC  CONST_16  C7    N1   C6   C5    180.00   0.0  0
 MXC  CONST_17  C8    C7   N1   C6    180.00   0.0  0
 MXC  CONST_18  C9    C1   C2   C3    180.00   0.0  0
 MXC  CONST_19  C10   C5   C4   C3    180.00   0.0  0
 MXC  CONST_20  N3    C6   N1   C3    180.00   0.0  0
 MXC  CONST_21  N3    C6   C5   C4    180.00   0.0  0
 MXC  CONST_22  C9    C1   C8   C7    180.00   0.0  0
 MXC  CONST_23  N3    C6   N1   C7      0.00   0.0  0
 MXC  CONST_24  N1    C6   C5   C10   180.00   0.0  0
 MXC  CONST_25  H7    C7   C8   C1    180.00   0.0  0
 MXC  CONST_26  H8    C8   C1   C2    180.00   0.0  0
 MXC  CONST_27  H4    C4   C3   C2      0.00   0.0  0
 MXC  CONST_28  H2    C2   C3   C4      0.00   0.0  0
 MXC  CONST_32  HN2   N2   C9   C1      0.00   0.0  0
 MXC  CONST_33  HN2A  N2   C9   C1    180.00   0.0  0
 MXC  CONST_34  HO4   O4   C12  C11   180.00   0.0  0
 MXC  Var_01    N2    C9   C1   C2   -179.62  30.0  2
 MXC  Var_02    O1    C10  C5   C4      1.70  30.0  2
 MXC  Var_03    N4    C16  O7   C15  -179.96  30.0  1
 MXC  Var_04    H15   C15  O7   C16    54.67  30.0  1
 MXC  Var_05    HN4   N4   C16  O7      7.32  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
 MXC  chir_01  C11  C12  C13  N3   negativ
 MXC  chir_02  C13  C15  C14  C11  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
 MXC  plan-1  C1    0.020
 MXC  plan-1  C2    0.020
 MXC  plan-1  C3    0.020
 MXC  plan-1  C4    0.020
 MXC  plan-1  C5    0.020
 MXC  plan-1  C6    0.020
 MXC  plan-1  C7    0.020
 MXC  plan-1  C8    0.020
 MXC  plan-1  C9    0.020
 MXC  plan-1  C10   0.020
 MXC  plan-1  N1    0.020
 MXC  plan-1  N3    0.020
 MXC  plan-1  H2    0.020
 MXC  plan-1  H4    0.020
 MXC  plan-1  H7    0.020
 MXC  plan-1  H8    0.020
 MXC  plan-2  C16   0.020
 MXC  plan-2  N4    0.020
 MXC  plan-2  O7    0.020
 MXC  plan-2  O8    0.020
 MXC  plan-3  C13   0.020
 MXC  plan-3  S1    0.020
 MXC  plan-3  O5    0.020
 MXC  plan-3  O6    0.020
 MXC  plan-4  C1    0.020
 MXC  plan-4  C9    0.020
 MXC  plan-4  N2    0.020
 MXC  plan-4  O2    0.020
 MXC  plan-4  HN2   0.020
 MXC  plan-4  HN2A  0.020
 MXC  plan-5  C6    0.020
 MXC  plan-5  C11   0.020
 MXC  plan-5  N3    0.020
 MXC  plan-5  HN3   0.020
 MXC  plan-6  C11   0.020
 MXC  plan-6  C12   0.020
 MXC  plan-6  O3    0.020
 MXC  plan-6  O4    0.020
 MXC  plan-6  HO4   0.020
 MXC  plan-7  C5    0.020
 MXC  plan-7  C10   0.020
 MXC  plan-7  O1    0.020
 MXC  plan-7  H10   0.020

