# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:28:12 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (2R)-2-[(1R)-1-{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-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=O)[C@H]2OCC(=C)C(=N2)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
 3P7  3P7  '(2R)-2-[(1R)-1-{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3-oxazine-4-carboxylic acid'  ligand  47  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3P7
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
 3P7  C1   C  C1    0   0.159  -1.0004   1.5708   2.3129
 3P7  O1   O  O     0  -0.365  -1.1661   1.0001   3.3553
 3P7  C2   C  CT    0   0.307  -1.1828   0.8746   0.9490
 3P7  N2   N  NH1   0  -0.680  -0.1319  -0.0750   0.7141
 3P7  C3   C  CH1   0   0.177  -2.5089   0.0835   0.9962
 3P7  O4   O  O2    0  -0.486  -3.5205   1.0051   1.2460
 3P7  C5   C  CH2   0  -0.241  -4.8051   0.4567   1.0178
 3P7  C6   C  C     0   0.079  -4.9123   0.0515  -0.4226
 3P7  C7   C  C     0   0.146  -3.6989  -0.6357  -0.8860
 3P7  C8   C  C     0   0.505  -3.7173  -1.4648  -2.1460
 3P7  N8   N  N     0  -0.380  -2.6172  -0.6509  -0.2255
 3P7  C9   C  C2    0  -0.551  -5.9679   0.3439  -1.1787
 3P7  C21  C  C     0   0.623   1.1248   0.0845   1.1708
 3P7  O21  O  O     0  -0.454   1.4555   1.0175   1.8778
 3P7  C22  C  CH1   0  -0.655   2.1218  -0.9717   0.7124
 3P7  C23  C  CR6   0   0.144   3.2762  -0.3299  -0.0137
 3P7  C24  C  CR16  0  -0.286   3.3968  -0.4745  -1.3891
 3P7  C25  C  CR16  0  -0.372   4.4330   0.1262  -2.0899
 3P7  C26  C  CR6   0   0.348   5.3741   0.8925  -1.4108
 3P7  O26  O  OH1   0  -0.629   6.4043   1.5002  -2.0291
 3P7  C27  C  CR16  0  -0.328   5.2644   1.0443  -0.0283
 3P7  C28  C  CR16  0  -0.266   4.2259   0.4402   0.6559
 3P7  C29  C  C     0   0.602   2.5148  -1.8193   1.9086
 3P7  O30  O  O     0  -0.422   1.8586  -1.8972   2.9141
 3P7  O31  O  OH1   0  -0.577   3.6245  -2.5000   1.6874
 3P7  O61  O  O2    0  -0.485  -1.3384   1.8189  -0.0631
 3P7  C62  C  CH3   0  -0.428  -0.1773   2.4508  -0.5680
 3P7  O81  O  O     0  -0.416  -4.7045  -2.0164  -2.5574
 3P7  O82  O  OH1   0  -0.570  -2.5293  -1.5303  -2.7110
 3P7  H1   H  HNH1  0   0.416  -0.3522  -0.8384   0.0878
 3P7  H2   H  HCH1  0   0.276  -2.4299  -0.6611   1.8035
 3P7  H3   H  HCH2  0   0.244  -4.9771  -0.4087   1.6714
 3P7  H4   H  HCH2  0   0.270  -5.5375   1.2211   1.2727
 3P7  H6   H  H     0   0.268  -6.8000   0.8954  -0.7594
 3P7  H7   H  H     0   0.267  -6.0549   0.0592  -2.2163
 3P7  H9   H  HCH1  0   0.340   1.6300  -1.6669   0.0220
 3P7  H10  H  HCR6  0   0.261   2.6743  -1.0692  -1.9350
 3P7  H11  H  HCR6  0   0.273   4.5052  -0.0087  -3.1630
 3P7  H12  H  HOH1  0   0.475   6.3784   1.3252  -2.9765
 3P7  H13  H  HCR6  0   0.266   5.9979   1.6348   0.5062
 3P7  H14  H  HCR6  0   0.255   4.1652   0.5756   1.7280
 3P7  H15  H  HOH1  0   0.488   3.8214  -3.0716   2.4456
 3P7  H16  H  HCH3  0   0.221   0.3939   2.9739   0.2020
 3P7  H17  H  HCH3  0   0.219   0.4852   1.7482  -1.0797
 3P7  H18  H  HCH3  0   0.253  -0.5208   3.1832  -1.2955
 3P7  H19  H  HOH1  0   0.492  -2.5682  -2.0989  -3.4956
 3P7  H20  H  H     0   0.221  -0.8134   2.6556   2.2561

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
 3P7  O81  C8   double    1.203  0.020  1.203
 3P7  O82  C8   single    1.317  0.020  1.317
 3P7  C8   C7   single    1.508  0.020  1.508
 3P7  C9   C6   double    1.331  0.020  1.331
 3P7  C7   C6   single    1.469  0.020  1.469
 3P7  C7   N8   double    1.267  0.020  1.267
 3P7  C6   C5   single    1.500  0.020  1.500
 3P7  N8   C3   single    1.430  0.020  1.430
 3P7  C5   O4   single    1.415  0.020  1.415
 3P7  C3   O4   single    1.391  0.020  1.391
 3P7  C3   C2   single    1.545  0.020  1.545
 3P7  O1   C1   double    1.200  0.020  1.200
 3P7  C1   C2   single    1.542  0.020  1.542
 3P7  C2   O61  single    1.393  0.020  1.393
 3P7  C2   N2   single    1.436  0.020  1.436
 3P7  O61  C62  single    1.415  0.020  1.415
 3P7  N2   C21  single    1.347  0.020  1.347
 3P7  O26  C26  single    1.346  0.020  1.346
 3P7  C25  C26  aromatic  1.391  0.020  1.391
 3P7  C25  C24  aromatic  1.388  0.020  1.388
 3P7  C26  C27  aromatic  1.395  0.020  1.395
 3P7  C21  O21  double    1.216  0.020  1.216
 3P7  C21  C22  single    1.523  0.020  1.523
 3P7  C24  C23  aromatic  1.388  0.020  1.388
 3P7  C27  C28  aromatic  1.383  0.020  1.383
 3P7  C28  C23  aromatic  1.394  0.020  1.394
 3P7  C23  C22  single    1.507  0.020  1.507
 3P7  C22  C29  single    1.518  0.020  1.518
 3P7  O30  C29  double    1.203  0.020  1.203
 3P7  C29  O31  single    1.320  0.020  1.320
 3P7  N2   H1   single    0.860  0.020  1.020
 3P7  C3   H2   single    0.970  0.020  1.090
 3P7  C5   H3   single    0.970  0.020  1.090
 3P7  C5   H4   single    0.970  0.020  1.090
 3P7  C9   H6   single    0.930  0.020  1.080
 3P7  C9   H7   single    0.930  0.020  1.080
 3P7  C22  H9   single    0.970  0.020  1.090
 3P7  C24  H10  single    0.930  0.020  1.080
 3P7  C25  H11  single    0.930  0.020  1.080
 3P7  O26  H12  single    0.850  0.020  0.980
 3P7  C27  H13  single    0.930  0.020  1.080
 3P7  C28  H14  single    0.930  0.020  1.080
 3P7  O31  H15  single    0.850  0.020  0.980
 3P7  C62  H16  single    0.970  0.020  1.090
 3P7  C62  H17  single    0.970  0.020  1.090
 3P7  C62  H18  single    0.970  0.020  1.090
 3P7  O82  H19  single    0.850  0.020  0.980
 3P7  C1   H20  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
 3P7  H20  C1   C2   114.76  3.000
 3P7  H20  C1   O1   122.43  3.000
 3P7  C2   C1   O1   122.50  3.000
 3P7  O61  C2   C3   105.87  3.000
 3P7  O61  C2   N2   114.29  3.000
 3P7  C3   C2   N2   107.13  3.000
 3P7  N2   C2   C1   110.90  3.000
 3P7  O61  C2   C1   110.47  3.000
 3P7  C3   C2   C1   107.80  3.000
 3P7  H1   N2   C21  120.16  3.000
 3P7  H1   N2   C2   116.17  3.000
 3P7  C21  N2   C2   123.32  3.000
 3P7  H2   C3   N8   106.54  3.000
 3P7  H2   C3   O4   111.62  3.000
 3P7  N8   C3   O4   116.02  3.000
 3P7  H2   C3   C2   107.89  3.000
 3P7  O4   C3   C2   106.89  3.000
 3P7  N8   C3   C2   107.58  3.000
 3P7  C5   O4   C3   111.99  3.000
 3P7  H4   C5   H3   107.98  3.000
 3P7  H4   C5   C6   111.49  3.000
 3P7  H3   C5   C6   110.33  3.000
 3P7  H4   C5   O4   107.50  3.000
 3P7  H3   C5   O4   110.58  3.000
 3P7  C6   C5   O4   108.92  3.000
 3P7  C9   C6   C7   125.34  3.000
 3P7  C7   C6   C5   111.73  3.000
 3P7  C9   C6   C5   122.87  3.000
 3P7  N8   C7   C8   116.05  3.000
 3P7  N8   C7   C6   123.08  3.000
 3P7  C8   C7   C6   120.69  3.000
 3P7  O82  C8   O81  124.79  3.000
 3P7  O82  C8   C7   112.00  3.000
 3P7  O81  C8   C7   123.20  3.000
 3P7  C7   N8   C3   120.26  3.000
 3P7  H7   C9   H6   116.39  3.000
 3P7  H7   C9   C6   123.51  3.000
 3P7  H6   C9   C6   120.10  3.000
 3P7  C22  C21  O21  121.93  3.000
 3P7  C22  C21  N2   115.26  3.000
 3P7  O21  C21  N2   122.80  3.000
 3P7  H9   C22  C29  104.97  3.000
 3P7  H9   C22  C23  108.07  3.000
 3P7  C29  C22  C23  114.78  3.000
 3P7  H9   C22  C21  109.62  3.000
 3P7  C29  C22  C21  108.64  3.000
 3P7  C23  C22  C21  110.56  3.000
 3P7  C28  C23  C24  118.31  3.000
 3P7  C28  C23  C22  121.71  3.000
 3P7  C24  C23  C22  119.97  3.000
 3P7  H10  C24  C25  118.76  3.000
 3P7  H10  C24  C23  119.90  3.000
 3P7  C25  C24  C23  121.34  3.000
 3P7  H11  C25  C26  120.46  3.000
 3P7  H11  C25  C24  119.72  3.000
 3P7  C26  C25  C24  119.82  3.000
 3P7  C27  C26  O26  117.78  3.000
 3P7  C27  C26  C25  119.38  3.000
 3P7  O26  C26  C25  122.83  3.000
 3P7  H12  O26  C26  110.42  3.000
 3P7  H13  C27  C28  120.19  3.000
 3P7  H13  C27  C26  119.69  3.000
 3P7  C28  C27  C26  120.13  3.000
 3P7  H14  C28  C27  118.53  3.000
 3P7  H14  C28  C23  120.44  3.000
 3P7  C27  C28  C23  121.03  3.000
 3P7  O31  C29  O30  124.39  3.000
 3P7  O31  C29  C22  111.93  3.000
 3P7  O30  C29  C22  123.61  3.000
 3P7  H15  O31  C29  110.09  3.000
 3P7  C62  O61  C2   118.05  3.000
 3P7  H18  C62  H17  108.12  3.000
 3P7  H18  C62  H16  108.31  3.000
 3P7  H17  C62  H16  108.73  3.000
 3P7  H18  C62  O61  106.26  3.000
 3P7  H17  C62  O61  112.17  3.000
 3P7  H16  C62  O61  113.05  3.000
 3P7  H19  O82  C8   109.88  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
 3P7  CONST_01  C26  C25  C24  C23    0.00   0.0  0
 3P7  CONST_02  C26  C27  C28  C23    0.00   0.0  0
 3P7  CONST_03  C27  C26  C25  C24    0.00   0.0  0
 3P7  CONST_04  C27  C28  C23  C24    0.00   0.0  0
 3P7  CONST_05  C28  C27  C26  C25    0.00   0.0  0
 3P7  CONST_06  C28  C23  C24  C25    0.00   0.0  0
 3P7  CONST_07  C25  C24  C23  C22  180.00   0.0  0
 3P7  CONST_08  C27  C28  C23  C22  180.00   0.0  0
 3P7  CONST_09  O26  C26  C25  C24  180.00   0.0  0
 3P7  CONST_10  C28  C27  C26  O26  180.00   0.0  0
 3P7  CONST_11  H11  C25  C24  C23  180.00   0.0  0
 3P7  CONST_12  H13  C27  C28  C23  180.00   0.0  0
 3P7  CONST_13  H14  C28  C23  C24  180.00   0.0  0
 3P7  CONST_14  H10  C24  C25  C26  180.00   0.0  0
 3P7  CONST_15  H19  O82  C8   C7   180.00   0.0  0
 3P7  CONST_16  O21  C21  N2   C2     0.00   0.0  0
 3P7  CONST_17  C22  C21  N2   C2   180.00   0.0  0
 3P7  CONST_18  H1   N2   C21  O21  180.00   0.0  0
 3P7  CONST_19  H15  O31  C29  C22  180.00   0.0  0
 3P7  Var_01    C6   C7   N8   C3    -3.60  30.0  1
 3P7  Var_02    C6   C5   O4   C3   -61.33  30.0  1
 3P7  Var_03    C7   C6   C5   O4    43.49  30.0  1
 3P7  Var_04    N8   C7   C6   C5   -12.40  30.0  1
 3P7  Var_05    O81  C8   C7   C6   -28.11  30.0  2
 3P7  Var_06    H6   C9   C6   C5    -0.15  30.0  2
 3P7  Var_07    H16  C62  O61  C2   -58.02  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
 3P7  chir_01  C2   C3   O61  N2   positiv
 3P7  chir_02  C3   O4   N8   C2   negativ
 3P7  chir_03  C22  C21  C23  C29  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
 3P7  plan-1  C22  0.020
 3P7  plan-1  C23  0.020
 3P7  plan-1  C24  0.020
 3P7  plan-1  C25  0.020
 3P7  plan-1  C26  0.020
 3P7  plan-1  O26  0.020
 3P7  plan-1  C27  0.020
 3P7  plan-1  C28  0.020
 3P7  plan-1  H10  0.020
 3P7  plan-1  H11  0.020
 3P7  plan-1  H13  0.020
 3P7  plan-1  H14  0.020
 3P7  plan-2  C2   0.020
 3P7  plan-2  N2   0.020
 3P7  plan-2  C21  0.020
 3P7  plan-2  O21  0.020
 3P7  plan-2  C22  0.020
 3P7  plan-2  H1   0.020
 3P7  plan-3  C7   0.020
 3P7  plan-3  C8   0.020
 3P7  plan-3  O81  0.020
 3P7  plan-3  O82  0.020
 3P7  plan-3  H19  0.020
 3P7  plan-4  C22  0.020
 3P7  plan-4  C29  0.020
 3P7  plan-4  O30  0.020
 3P7  plan-4  O31  0.020
 3P7  plan-4  H15  0.020
 3P7  plan-5  C1   0.020
 3P7  plan-5  O1   0.020
 3P7  plan-5  C2   0.020
 3P7  plan-5  H20  0.020

