# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 00:50:22 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)[C@@H]2[C@H]3CC[C@H](O3)[C@@H]2C(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
 LB1  LB1  '(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid'  ligand  39  19  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LB1
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
 LB1  C10  C  CH1   0  -0.356  -1.6800  -1.0253  -0.4986
 LB1  C13  C  C     0   0.591   0.0044   0.5885   0.6041
 LB1  C07  C  CH1   0  -0.388  -1.1151   0.4272  -0.4048
 LB1  C08  C  CH1   0  -0.012  -2.3882   1.1793   0.0707
 LB1  C09  C  CH1   0  -0.025  -3.1542  -0.7911  -0.1469
 LB1  C11  C  CH2   0  -0.453  -3.3141   1.3659  -1.1367
 LB1  C12  C  CH2   0  -0.454  -3.8421  -0.0750  -1.3181
 LB1  C14  C  C     0   0.561  -1.0077  -2.0232   0.4117
 LB1  O01  O  O2    0  -0.478  -3.0746   0.2161   0.8484
 LB1  O02  O  O     0  -0.502  -0.2254   0.3321   1.7803
 LB1  O04  O  O     0  -0.432  -1.5418  -2.6362   1.2999
 LB1  H1   H  HCH1  0   0.307  -1.5635  -1.3991  -1.5193
 LB1  H3   H  HCH1  0   0.287  -0.8380   0.7728  -1.3956
 LB1  H4   H  HCH1  0   0.256  -2.1943   2.0809   0.6504
 LB1  H5   H  HCH1  0   0.252  -3.6795  -1.6671   0.2288
 LB1  H6   H  HCH2  0   0.251  -4.1185   2.0627  -0.8998
 LB1  H7   H  HCH2  0   0.243  -2.7911   1.7510  -2.0113
 LB1  H8   H  HCH2  0   0.243  -3.5808  -0.5112  -2.2825
 LB1  H9   H  HCH2  0   0.253  -4.9262  -0.1245  -1.2166
 LB1  O1   O  OH1   0  -0.595   0.2633  -2.1986   0.0651
 LB1  N1   N  NT    0  -0.468   1.1995   1.0646   0.1961
 LB1  C2   C  CH2   0  -0.328   2.2839   1.2268   1.1513
 LB1  C3   C  CH2   0  -0.277   3.3926   0.2272   0.8678
 LB1  N2   N  NT    0  -0.416   3.8748   0.3714  -0.4916
 LB1  C5   C  CH2   0  -0.270   2.7930   0.2075  -1.4411
 LB1  C6   C  CH2   0  -0.327   1.6759   1.2021  -1.1691
 LB1  C1   C  CH3   0  -0.516   4.9673  -0.5324  -0.7708
 LB1  H2   H  HOH1  0   0.480   0.6899  -2.8334   0.6600
 LB1  H10  H  HCH2  0   0.245   2.6750   2.2446   1.0595
 LB1  H11  H  HCH2  0   0.268   1.9095   1.1000   2.1624
 LB1  H12  H  HCH2  0   0.242   4.2174   0.4082   1.5613
 LB1  H13  H  HCH2  0   0.197   3.0193  -0.7929   1.0666
 LB1  H14  H  HCH2  0   0.243   3.1749   0.3787  -2.4504
 LB1  H15  H  HCH2  0   0.199   2.3733  -0.8127  -1.4181
 LB1  H16  H  HCH2  0   0.267   0.8808   1.0532  -1.8914
 LB1  H17  H  HCH2  0   0.247   2.0492   2.2211  -1.3070
 LB1  H18  H  HCH3  0   0.193   4.6830  -1.5932  -0.6893
 LB1  H19  H  HCH3  0   0.234   5.3430  -0.3646  -1.7814
 LB1  H20  H  HCH3  0   0.234   5.7881  -0.3527  -0.0750

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
 LB1  O02  C13  double  1.226  0.020  1.226
 LB1  O04  C14  double  1.204  0.020  1.204
 LB1  O01  C08  single  1.416  0.020  1.416
 LB1  O01  C09  single  1.418  0.020  1.418
 LB1  C13  C07  single  1.516  0.020  1.516
 LB1  C14  C10  single  1.509  0.020  1.509
 LB1  C08  C07  single  1.553  0.020  1.553
 LB1  C08  C11  single  1.533  0.020  1.533
 LB1  C09  C10  single  1.534  0.020  1.534
 LB1  C09  C12  single  1.535  0.020  1.535
 LB1  C07  C10  single  1.561  0.020  1.561
 LB1  C11  C12  single  1.545  0.020  1.545
 LB1  C10  H1   single  0.970  0.020  1.090
 LB1  C07  H3   single  0.970  0.020  1.090
 LB1  C08  H4   single  0.970  0.020  1.090
 LB1  C09  H5   single  0.970  0.020  1.090
 LB1  C11  H6   single  0.970  0.020  1.090
 LB1  C11  H7   single  0.970  0.020  1.090
 LB1  C12  H8   single  0.970  0.020  1.090
 LB1  C12  H9   single  0.970  0.020  1.090
 LB1  C14  O1   single  1.329  0.020  1.329
 LB1  C13  N1   single  1.350  0.020  1.350
 LB1  N1   C2   single  1.454  0.020  1.454
 LB1  C2   C3   single  1.519  0.020  1.519
 LB1  C3   N2   single  1.450  0.020  1.450
 LB1  N2   C5   single  1.449  0.020  1.449
 LB1  C5   C6   single  1.520  0.020  1.520
 LB1  C6   N1   single  1.453  0.020  1.453
 LB1  N2   C1   single  1.445  0.020  1.445
 LB1  O1   H2   single  0.850  0.020  0.980
 LB1  C2   H10  single  0.970  0.020  1.090
 LB1  C2   H11  single  0.970  0.020  1.090
 LB1  C3   H12  single  0.970  0.020  1.090
 LB1  C3   H13  single  0.970  0.020  1.090
 LB1  C5   H14  single  0.970  0.020  1.090
 LB1  C5   H15  single  0.970  0.020  1.090
 LB1  C6   H16  single  0.970  0.020  1.090
 LB1  C6   H17  single  0.970  0.020  1.090
 LB1  C1   H18  single  0.970  0.020  1.090
 LB1  C1   H19  single  0.970  0.020  1.090
 LB1  C1   H20  single  0.970  0.020  1.090

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
 LB1  H1   C10  C14  106.84  3.000
 LB1  H1   C10  C09  111.64  3.000
 LB1  C14  C10  C09  113.02  3.000
 LB1  H1   C10  C07  109.61  3.000
 LB1  C09  C10  C07  101.07  3.000
 LB1  C14  C10  C07  114.69  3.000
 LB1  N1   C13  O02  122.00  3.000
 LB1  N1   C13  C07  119.37  3.000
 LB1  O02  C13  C07  118.56  3.000
 LB1  H3   C07  C08  109.54  3.000
 LB1  H3   C07  C13  112.66  3.000
 LB1  C08  C07  C13  110.50  3.000
 LB1  H3   C07  C10  109.50  3.000
 LB1  C08  C07  C10   99.92  3.000
 LB1  C13  C07  C10  113.97  3.000
 LB1  H4   C08  O01  110.92  3.000
 LB1  H4   C08  C11  115.21  3.000
 LB1  O01  C08  C11  102.87  3.000
 LB1  H4   C08  C07  114.69  3.000
 LB1  C11  C08  C07  108.24  3.000
 LB1  O01  C08  C07  103.66  3.000
 LB1  H5   C09  O01  110.88  3.000
 LB1  H5   C09  C12  114.99  3.000
 LB1  O01  C09  C12  103.25  3.000
 LB1  H5   C09  C10  114.85  3.000
 LB1  C12  C09  C10  109.09  3.000
 LB1  O01  C09  C10  102.44  3.000
 LB1  H7   C11  H6   107.62  3.000
 LB1  H7   C11  C12  113.54  3.000
 LB1  H6   C11  C12  111.68  3.000
 LB1  H7   C11  C08  112.67  3.000
 LB1  H6   C11  C08  110.63  3.000
 LB1  C12  C11  C08  100.68  3.000
 LB1  H9   C12  H8   107.62  3.000
 LB1  H9   C12  C11  111.79  3.000
 LB1  H8   C12  C11  113.27  3.000
 LB1  H9   C12  C09  110.69  3.000
 LB1  H8   C12  C09  112.38  3.000
 LB1  C11  C12  C09  101.08  3.000
 LB1  O1   C14  O04  123.33  3.000
 LB1  O1   C14  C10  110.86  3.000
 LB1  O04  C14  C10  125.73  3.000
 LB1  C09  O01  C08   97.17  3.000
 LB1  H2   O1   C14  110.32  3.000
 LB1  C6   N1   C2   111.24  3.000
 LB1  C6   N1   C13  127.44  3.000
 LB1  C2   N1   C13  120.08  3.000
 LB1  H11  C2   H10  108.07  3.000
 LB1  H11  C2   C3   110.40  3.000
 LB1  H10  C2   C3   109.60  3.000
 LB1  H11  C2   N1   109.97  3.000
 LB1  H10  C2   N1   108.37  3.000
 LB1  C3   C2   N1   110.37  3.000
 LB1  H13  C3   H12  107.09  3.000
 LB1  H13  C3   N2   111.92  3.000
 LB1  H12  C3   N2   109.12  3.000
 LB1  H13  C3   C2   109.12  3.000
 LB1  H12  C3   C2   108.86  3.000
 LB1  N2   C3   C2   110.63  3.000
 LB1  C1   N2   C5   111.54  3.000
 LB1  C1   N2   C3   111.74  3.000
 LB1  C5   N2   C3   110.79  3.000
 LB1  H15  C5   H14  107.29  3.000
 LB1  H15  C5   C6   108.76  3.000
 LB1  H14  C5   C6   108.64  3.000
 LB1  H15  C5   N2   112.03  3.000
 LB1  H14  C5   N2   109.07  3.000
 LB1  C6   C5   N2   110.94  3.000
 LB1  H17  C6   H16  107.11  3.000
 LB1  H17  C6   C5   109.64  3.000
 LB1  H16  C6   C5   109.25  3.000
 LB1  H17  C6   N1   108.58  3.000
 LB1  H16  C6   N1   111.88  3.000
 LB1  C5   C6   N1   110.32  3.000
 LB1  H20  C1   H19  107.83  3.000
 LB1  H20  C1   H18  107.80  3.000
 LB1  H19  C1   H18  107.80  3.000
 LB1  H20  C1   N2   110.03  3.000
 LB1  H19  C1   N2   110.06  3.000
 LB1  H18  C1   N2   113.14  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
 LB1  CONST_01  C2   N1   C13  C07  180.00   0.0  0
 LB1  CONST_02  C6   N1   C13  C07    0.00   0.0  0
 LB1  CONST_03  C2   N1   C13  O02    0.00   0.0  0
 LB1  CONST_04  C6   N1   C13  O02  180.00   0.0  0
 LB1  CONST_05  H2   O1   C14  C10  180.00   0.0  0
 LB1  Var_01    C09  C12  C11  C08    1.99  30.0  1
 LB1  Var_02    N2   C3   C2   N1    56.88  30.0  1
 LB1  Var_03    N2   C5   C6   N1   -56.41  30.0  1
 LB1  Var_04    C5   C6   N1   C2    56.44  30.0  1
 LB1  Var_05    C5   N2   C3   C2   -57.27  30.0  1
 LB1  Var_06    C6   N1   C2   C3   -56.80  30.0  1
 LB1  Var_07    C6   C5   N2   C3    57.12  30.0  1
 LB1  Var_08    H18  C1   N2   C3    62.32  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
 LB1  chir_01  C10  C14  C09  C07  negativ
 LB1  chir_02  C07  C10  C08  C13  negativ
 LB1  chir_03  C08  O01  C11  C07  positiv
 LB1  chir_04  C09  O01  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
 LB1  plan-1  C13  0.020
 LB1  plan-1  C07  0.020
 LB1  plan-1  O02  0.020
 LB1  plan-1  N1   0.020
 LB1  plan-1  C2   0.020
 LB1  plan-1  C6   0.020
 LB1  plan-2  C10  0.020
 LB1  plan-2  C14  0.020
 LB1  plan-2  O04  0.020
 LB1  plan-2  O1   0.020
 LB1  plan-2  H2   0.020

