# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 12:56:13 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-methylidene-5,6-dihydro-2H-1,3-oxazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@](NC(=O)[C@H](C(O)=O)c1ccc(O)cc1)([C@H]2OCC(=C)C(=N2)C(O)=O)C(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
 MX1  MX1  '(2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-methylidene-5,6-dihydro-2H-1,3-oxazine-4-carboxylic acid'  ligand  48  30  .  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_MX1
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
 MX1  O4   O  OH1   0  -0.563   2.8267   2.7512  -1.0384
 MX1  C7   C  C     0   0.498   3.4829   2.5278   0.0802
 MX1  O3   O  O     0  -0.422   4.1429   3.3486   0.6644
 MX1  C4   C  C     0   0.124   3.2850   1.1206   0.5848
 MX1  N1   N  N     0  -0.329   2.1455   0.6104   0.3693
 MX1  C5   C  C     0   0.083   4.3336   0.4627   1.3795
 MX1  C8   C  C2    0  -0.556   5.6165   0.8155   1.4018
 MX1  C6   C  CH2   0  -0.238   3.7972  -0.7142   2.1392
 MX1  O2   O  O2    0  -0.492   2.9416  -1.4541   1.2911
 MX1  C3   C  CH1   0   0.140   1.8477  -0.6930   0.8654
 MX1  C2   C  CT    0   0.335   1.2237  -1.5207  -0.2840
 MX1  C1   C  C     0   0.544   0.9604  -2.9459   0.2588
 MX1  O32  O  OH1   0  -0.582   0.0096  -2.9283   1.1750
 MX1  O31  O  O     0  -0.413   1.5475  -3.9267  -0.1056
 MX1  O5   O  O2    0  -0.479   2.1961  -1.5593  -1.2639
 MX1  C9   C  CH3   0  -0.455   1.8526  -2.0360  -2.5523
 MX1  N2   N  NH1   0  -0.707  -0.0168  -0.9653  -0.7880
 MX1  C10  C  C     0   0.629  -0.9368  -0.1847  -0.1773
 MX1  O6   O  O     0  -0.446  -0.8797   0.2203   0.9627
 MX1  C11  C  CH1   0  -0.648  -2.1084   0.1685  -1.0995
 MX1  C12  C  C     0   0.579  -1.7510   1.4133  -1.8909
 MX1  O8   O  OH1   0  -0.582  -2.5749   1.5800  -2.9141
 MX1  O7   O  O     0  -0.410  -0.8523   2.1627  -1.6146
 MX1  C13  C  CR6   0   0.143  -3.3923   0.3808  -0.3379
 MX1  C14  C  CR16  0  -0.291  -4.4187  -0.5504  -0.4268
 MX1  C18  C  CR16  0  -0.268  -3.5823   1.4974   0.4740
 MX1  C17  C  CR16  0  -0.328  -4.7615   1.6797   1.1743
 MX1  C16  C  CR6   0   0.348  -5.7829   0.7352   1.0806
 MX1  O9   O  OH1   0  -0.630  -6.9105   0.9563   1.7827
 MX1  C15  C  CR16  0  -0.372  -5.6049  -0.3837   0.2732
 MX1  HO4  H  HOH1  0   0.488   2.9305   3.6783  -1.3021
 MX1  H81  H  H     0   0.264   6.0079   1.6632   0.8595
 MX1  H82  H  H     0   0.265   6.3288   0.2470   1.9865
 MX1  H61  H  HCH2  0   0.268   4.5965  -1.3797   2.4624
 MX1  H62  H  HCH2  0   0.241   3.2563  -0.3745   3.0329
 MX1  H3   H  HCH1  0   0.285   1.1242  -0.5670   1.6769
 MX1  H32  H  HOH1  0   0.492  -0.1353  -3.8180   1.5333
 MX1  H91  H  HCH3  0   0.229   1.2289  -2.9327  -2.5322
 MX1  H92  H  HCH3  0   0.229   1.3540  -1.2676  -3.1494
 MX1  H93  H  HCH3  0   0.260   2.7866  -2.2919  -3.0478
 MX1  HN2  H  HNH1  0   0.423  -0.2937  -1.3329  -1.6859
 MX1  H11  H  HCH1  0   0.326  -2.2718  -0.6412  -1.8171
 MX1  HO8  H  HOH1  0   0.486  -2.3591   2.3991  -3.3854
 MX1  H14  H  HCR6  0   0.262  -4.3017  -1.4259  -1.0541
 MX1  H18  H  HCR6  0   0.254  -2.8096   2.2502   0.5622
 MX1  H17  H  HCR6  0   0.265  -4.8953   2.5555   1.7971
 MX1  HO9  H  HOH1  0   0.475  -7.5507   0.2531   1.6247
 MX1  H15  H  HCR6  0   0.273  -6.3894  -1.1259   0.1830

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
 MX1  O4   C7   single    1.316  0.020  1.316
 MX1  O4   HO4  single    0.850  0.020  0.980
 MX1  C7   O3   double    1.204  0.020  1.204
 MX1  C7   C4   single    1.508  0.020  1.508
 MX1  C4   N1   double    1.267  0.020  1.267
 MX1  C4   C5   single    1.471  0.020  1.471
 MX1  N1   C3   single    1.426  0.020  1.426
 MX1  C5   C8   double    1.331  0.020  1.331
 MX1  C5   C6   single    1.500  0.020  1.500
 MX1  C8   H81  single    0.930  0.020  1.080
 MX1  C8   H82  single    0.930  0.020  1.080
 MX1  C6   O2   single    1.414  0.020  1.414
 MX1  C6   H61  single    0.970  0.020  1.090
 MX1  C6   H62  single    0.970  0.020  1.090
 MX1  O2   C3   single    1.399  0.020  1.399
 MX1  C3   C2   single    1.548  0.020  1.548
 MX1  C3   H3   single    0.970  0.020  1.090
 MX1  C2   C1   single    1.548  0.020  1.548
 MX1  C2   O5   single    1.381  0.020  1.381
 MX1  C2   N2   single    1.450  0.020  1.450
 MX1  C1   O32  single    1.321  0.020  1.321
 MX1  C1   O31  double    1.200  0.020  1.200
 MX1  O32  H32  single    0.850  0.020  0.980
 MX1  O5   C9   single    1.416  0.020  1.416
 MX1  C9   H91  single    0.970  0.020  1.090
 MX1  C9   H92  single    0.970  0.020  1.090
 MX1  C9   H93  single    0.970  0.020  1.090
 MX1  N2   C10  single    1.352  0.020  1.352
 MX1  N2   HN2  single    0.860  0.020  1.020
 MX1  C10  O6   double    1.211  0.020  1.211
 MX1  C10  C11  single    1.532  0.020  1.532
 MX1  C11  C12  single    1.518  0.020  1.518
 MX1  C11  C13  single    1.508  0.020  1.508
 MX1  C11  H11  single    0.970  0.020  1.090
 MX1  C12  O8   single    1.324  0.020  1.324
 MX1  C12  O7   double    1.202  0.020  1.202
 MX1  O8   HO8  single    0.850  0.020  0.980
 MX1  C13  C14  aromatic  1.389  0.020  1.389
 MX1  C13  C18  aromatic  1.394  0.020  1.394
 MX1  C14  C15  aromatic  1.387  0.020  1.387
 MX1  C14  H14  single    0.930  0.020  1.080
 MX1  C18  C17  aromatic  1.384  0.020  1.384
 MX1  C18  H18  single    0.930  0.020  1.080
 MX1  C17  C16  aromatic  1.394  0.020  1.394
 MX1  C17  H17  single    0.930  0.020  1.080
 MX1  C16  O9   single    1.347  0.020  1.347
 MX1  C16  C15  aromatic  1.391  0.020  1.391
 MX1  O9   HO9  single    0.850  0.020  0.980
 MX1  C15  H15  single    0.930  0.020  1.080

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
 MX1  HO4  O4   C7   109.89  3.000
 MX1  C4   C7   O3   123.06  3.000
 MX1  C4   C7   O4   112.18  3.000
 MX1  O3   C7   O4   124.75  3.000
 MX1  C5   C4   N1   123.57  3.000
 MX1  C5   C4   C7   120.30  3.000
 MX1  N1   C4   C7   115.91  3.000
 MX1  C3   N1   C4   119.78  3.000
 MX1  C6   C5   C8   122.97  3.000
 MX1  C6   C5   C4   111.69  3.000
 MX1  C8   C5   C4   125.29  3.000
 MX1  H82  C8   H81  116.42  3.000
 MX1  H82  C8   C5   120.27  3.000
 MX1  H81  C8   C5   123.31  3.000
 MX1  H62  C6   H61  107.99  3.000
 MX1  H62  C6   O2   110.60  3.000
 MX1  H61  C6   O2   107.60  3.000
 MX1  H62  C6   C5   110.21  3.000
 MX1  H61  C6   C5   111.55  3.000
 MX1  O2   C6   C5   108.86  3.000
 MX1  C3   O2   C6   111.78  3.000
 MX1  H3   C3   C2   110.22  3.000
 MX1  H3   C3   O2   110.73  3.000
 MX1  C2   C3   O2   104.50  3.000
 MX1  H3   C3   N1   106.90  3.000
 MX1  C2   C3   N1   108.34  3.000
 MX1  O2   C3   N1   116.09  3.000
 MX1  N2   C2   O5   111.50  3.000
 MX1  N2   C2   C1   109.22  3.000
 MX1  O5   C2   C1   110.05  3.000
 MX1  N2   C2   C3   113.47  3.000
 MX1  O5   C2   C3   104.95  3.000
 MX1  C1   C2   C3   107.49  3.000
 MX1  O31  C1   O32  125.03  3.000
 MX1  O31  C1   C2   124.27  3.000
 MX1  O32  C1   C2   110.70  3.000
 MX1  H32  O32  C1   110.59  3.000
 MX1  C9   O5   C2   118.96  3.000
 MX1  H93  C9   H92  107.94  3.000
 MX1  H93  C9   H91  107.78  3.000
 MX1  H92  C9   H91  109.05  3.000
 MX1  H93  C9   O5   106.58  3.000
 MX1  H92  C9   O5   111.77  3.000
 MX1  H91  C9   O5   113.46  3.000
 MX1  HN2  N2   C10  115.18  3.000
 MX1  HN2  N2   C2   113.87  3.000
 MX1  C10  N2   C2   130.27  3.000
 MX1  C11  C10  O6   121.70  3.000
 MX1  C11  C10  N2   112.42  3.000
 MX1  O6   C10  N2   125.88  3.000
 MX1  H11  C11  C13  107.96  3.000
 MX1  H11  C11  C12  107.46  3.000
 MX1  C13  C11  C12  110.39  3.000
 MX1  H11  C11  C10  109.78  3.000
 MX1  C13  C11  C10  112.31  3.000
 MX1  C12  C11  C10  108.83  3.000
 MX1  O7   C12  O8   124.34  3.000
 MX1  O7   C12  C11  124.56  3.000
 MX1  O8   C12  C11  111.08  3.000
 MX1  HO8  O8   C12  110.09  3.000
 MX1  C18  C13  C14  118.28  3.000
 MX1  C18  C13  C11  121.54  3.000
 MX1  C14  C13  C11  120.17  3.000
 MX1  H14  C14  C15  118.79  3.000
 MX1  H14  C14  C13  119.94  3.000
 MX1  C15  C14  C13  121.27  3.000
 MX1  H18  C18  C17  118.40  3.000
 MX1  H18  C18  C13  120.50  3.000
 MX1  C17  C18  C13  121.11  3.000
 MX1  H17  C17  C16  119.74  3.000
 MX1  H17  C17  C18  120.19  3.000
 MX1  C16  C17  C18  120.07  3.000
 MX1  C15  C16  O9   122.81  3.000
 MX1  C15  C16  C17  119.35  3.000
 MX1  O9   C16  C17  117.85  3.000
 MX1  HO9  O9   C16  110.55  3.000
 MX1  H15  C15  C16  120.42  3.000
 MX1  H15  C15  C14  119.65  3.000
 MX1  C16  C15  C14  119.92  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
 MX1  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 MX1  CONST_02  C16  C17  C18  C13    0.00   0.0  0
 MX1  CONST_03  C17  C18  C13  C14    0.00   0.0  0
 MX1  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 MX1  CONST_05  C15  C14  C13  C18    0.00   0.0  0
 MX1  CONST_06  C15  C16  C17  C18    0.00   0.0  0
 MX1  CONST_07  C15  C14  C13  C11  180.00   0.0  0
 MX1  CONST_08  C17  C18  C13  C11  180.00   0.0  0
 MX1  CONST_09  O9   C16  C15  C14  180.00   0.0  0
 MX1  CONST_10  O9   C16  C17  C18  180.00   0.0  0
 MX1  CONST_11  H15  C15  C14  C13  180.00   0.0  0
 MX1  CONST_12  H17  C17  C18  C13  180.00   0.0  0
 MX1  CONST_13  H18  C18  C13  C14  180.00   0.0  0
 MX1  CONST_14  H14  C14  C13  C18  180.00   0.0  0
 MX1  CONST_15  HO4  O4   C7   C4   180.00   0.0  0
 MX1  CONST_16  O6   C10  N2   C2     0.00   0.0  0
 MX1  CONST_17  C11  C10  N2   C2   180.00   0.0  0
 MX1  CONST_18  HN2  N2   C10  O6   180.00   0.0  0
 MX1  CONST_19  H32  O32  C1   C2   180.00   0.0  0
 MX1  CONST_20  HO8  O8   C12  C11  180.00   0.0  0
 MX1  Var_01    O2   C6   C5   C4    43.21  30.0  1
 MX1  Var_02    C6   C5   C4   N1   -12.53  30.0  1
 MX1  Var_03    N1   C4   C7   O4   -34.12  30.0  2
 MX1  Var_04    H81  C8   C5   C4     2.81  30.0  2
 MX1  Var_05    H91  C9   O5   C2   -43.23  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
 MX1  chir_01  C3   N1   O2   C2   positiv
 MX1  chir_02  C2   N2   C1   C3   positiv
 MX1  chir_03  C11  C13  C12  C10  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
 MX1  plan-1  C11  0.020
 MX1  plan-1  C13  0.020
 MX1  plan-1  C14  0.020
 MX1  plan-1  C18  0.020
 MX1  plan-1  C17  0.020
 MX1  plan-1  C16  0.020
 MX1  plan-1  O9   0.020
 MX1  plan-1  C15  0.020
 MX1  plan-1  H14  0.020
 MX1  plan-1  H18  0.020
 MX1  plan-1  H17  0.020
 MX1  plan-1  H15  0.020
 MX1  plan-2  C2   0.020
 MX1  plan-2  N2   0.020
 MX1  plan-2  C10  0.020
 MX1  plan-2  O6   0.020
 MX1  plan-2  C11  0.020
 MX1  plan-2  HN2  0.020
 MX1  plan-3  O4   0.020
 MX1  plan-3  C7   0.020
 MX1  plan-3  O3   0.020
 MX1  plan-3  C4   0.020
 MX1  plan-3  HO4  0.020
 MX1  plan-4  C2   0.020
 MX1  plan-4  C1   0.020
 MX1  plan-4  O32  0.020
 MX1  plan-4  O31  0.020
 MX1  plan-4  H32  0.020
 MX1  plan-5  C11  0.020
 MX1  plan-5  C12  0.020
 MX1  plan-5  O8   0.020
 MX1  plan-5  O7   0.020
 MX1  plan-5  HO8  0.020

