# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:23:24 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: (2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](Cc1ccc(OCc2coc(CN)c2)cc1)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
 L6K  L6K  '(2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid'  ligand  41  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L6K
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
 L6K  C1   C  CH2    0  -0.334   7.2502   0.0418   0.9542
 L6K  O1   O  O      0  -0.463   5.9460   0.7658  -0.9624
 L6K  C2   C  CR5    0   0.346   5.9707   0.0677   0.1983
 L6K  O2   O  O2     0  -0.520   1.7479   0.0299   0.1902
 L6K  C3   C  CR15   0  -0.410   4.7544  -0.4826   0.4218
 L6K  C4   C  CR5    0   0.095   3.9228  -0.0967  -0.6788
 L6K  C5   C  CR15   0  -0.048   4.7066   0.6602  -1.4807
 L6K  C6   C  CR6    0   0.058  -2.3433  -0.6867   0.4986
 L6K  N2   N  NH1    0  -0.595  -4.3331   1.4674   0.2443
 L6K  C15  C  CH1    0  -0.138  -4.6557   0.1223  -0.1805
 L6K  C12  C  CH2    0  -0.577  -3.8267  -0.8951   0.6211
 L6K  C11  C  CR16   0  -0.281  -1.6157  -0.0382   1.4971
 L6K  C10  C  CR16   0  -0.293  -0.2554   0.1860   1.3743
 L6K  C7   C  CR16   0  -0.236  -1.6483  -1.1013  -0.6319
 L6K  C8   C  CR16   0  -0.406  -0.2825  -0.8867  -0.7763
 L6K  C9   C  CR6    0   0.369   0.4243  -0.2354   0.2317
 L6K  C13  C  CH2    0  -0.285   2.5015  -0.4593  -0.9083
 L6K  N1   N  NH2    0  -0.863   8.2899  -0.6792   0.2266
 L6K  C35  C  C      0   0.395  -6.1472  -0.2358   0.0260
 L6K  O36  O  O      0  -0.698  -6.7431   0.2943   0.9808
 L6K  O37  O  OC    -1  -0.624  -6.6098  -1.0821  -0.7671
 L6K  H1   H  HCH2   0   0.240   7.5340   1.0684   1.2239
 L6K  H2   H  HCH2   0   0.285   7.0564  -0.4795   1.8924
 L6K  H3   H  HCR5   0   0.248   4.4788  -1.0927   1.2679
 L6K  H4   H  HCR5   0   0.287   4.5210   1.1631  -2.4170
 L6K  H5   H  HCH3   0   0.262  -4.8026   2.3712  -1.6449
 L6K  H6   H  HCH3   0   0.219  -6.0445   2.4880  -0.3938
 L6K  H7   H  HCH3   0   0.191  -4.5912   3.4701  -0.2772
 L6K  H10  H  HCH1   0   0.210  -4.4226  -0.0305  -1.2497
 L6K  H11  H  HCH2   0   0.259  -4.0897  -1.8947   0.2683
 L6K  H12  H  HCH2   0   0.261  -4.1229  -0.8348   1.6718
 L6K  H13  H  HCR6   0   0.262  -2.1225   0.2971   2.3943
 L6K  H14  H  HCR6   0   0.269   0.2889   0.6886   2.1645
 L6K  H15  H  HCR6   0   0.258  -2.1783  -1.6099  -1.4294
 L6K  H16  H  HCR6   0   0.278   0.2064  -1.2348  -1.6763
 L6K  H17  H  HCH2   0   0.222   2.3899  -1.5468  -0.9843
 L6K  H18  H  HCH2   0   0.267   2.1497  -0.0253  -1.8506
 L6K  H19  H  HNH2   0   0.351   8.5980  -0.1209  -0.5597
 L6K  H20  H  HNH2   0   0.342   9.1006  -0.7655   0.8265
 L6K  C16  C  CH3    0  -0.521  -4.9678   2.4872  -0.5631
 L6K  H8   H  HNH1   0   0.317  -3.3302   1.5931   0.1776

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
 L6K  N1   C1   single    1.459  0.020  1.459
 L6K  O1   C5   aromatic  1.348  0.020  1.348
 L6K  O1   C2   aromatic  1.355  0.020  1.355
 L6K  C1   C2   single    1.486  0.020  1.486
 L6K  C5   C4   aromatic  1.353  0.020  1.353
 L6K  C2   C3   aromatic  1.354  0.020  1.354
 L6K  C4   C3   aromatic  1.432  0.020  1.432
 L6K  C4   C13  single    1.485  0.020  1.485
 L6K  C13  O2   single    1.419  0.020  1.419
 L6K  O2   C9   single    1.351  0.020  1.351
 L6K  C9   C10  aromatic  1.395  0.020  1.395
 L6K  C9   C8   aromatic  1.393  0.020  1.393
 L6K  C10  C11  aromatic  1.384  0.020  1.384
 L6K  C8   C7   aromatic  1.390  0.020  1.390
 L6K  C11  C6   aromatic  1.395  0.020  1.395
 L6K  C7   C6   aromatic  1.390  0.020  1.390
 L6K  C6   C12  single    1.503  0.020  1.503
 L6K  C12  C15  single    1.538  0.020  1.538
 L6K  N2   C16  single    1.447  0.020  1.447
 L6K  N2   C15  single    1.447  0.020  1.447
 L6K  C15  C35  single    1.548  0.020  1.548
 L6K  C35  O36  deloc     1.244  0.020  1.244
 L6K  C35  O37  deloc     1.249  0.020  1.249
 L6K  C1   H1   single    0.970  0.020  1.090
 L6K  C1   H2   single    0.970  0.020  1.090
 L6K  C3   H3   single    0.930  0.020  1.080
 L6K  C5   H4   single    0.930  0.020  1.080
 L6K  C16  H5   single    0.970  0.020  1.090
 L6K  C16  H6   single    0.970  0.020  1.090
 L6K  C16  H7   single    0.970  0.020  1.090
 L6K  N2   H8   single    0.890  0.020  1.040
 L6K  C15  H10  single    0.970  0.020  1.090
 L6K  C12  H11  single    0.970  0.020  1.090
 L6K  C12  H12  single    0.970  0.020  1.090
 L6K  C11  H13  single    0.930  0.020  1.080
 L6K  C10  H14  single    0.930  0.020  1.080
 L6K  C7   H15  single    0.930  0.020  1.080
 L6K  C8   H16  single    0.930  0.020  1.080
 L6K  C13  H17  single    0.970  0.020  1.090
 L6K  C13  H18  single    0.970  0.020  1.090
 L6K  N1   H19  single    0.890  0.020  1.040
 L6K  N1   H20  single    0.890  0.020  1.040

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
 L6K  H2   C1   H1   106.34  3.000
 L6K  H2   C1   N1   108.62  3.000
 L6K  H1   C1   N1   113.57  3.000
 L6K  H2   C1   C2   107.03  3.000
 L6K  H1   C1   C2   109.32  3.000
 L6K  N1   C1   C2   111.61  3.000
 L6K  C5   O1   C2   107.81  3.000
 L6K  C3   C2   O1   109.55  3.000
 L6K  C3   C2   C1   133.04  3.000
 L6K  O1   C2   C1   117.41  3.000
 L6K  C13  O2   C9   118.45  3.000
 L6K  H3   C3   C4   127.34  3.000
 L6K  H3   C3   C2   126.08  3.000
 L6K  C4   C3   C2   106.57  3.000
 L6K  C13  C4   C5   126.84  3.000
 L6K  C13  C4   C3   127.50  3.000
 L6K  C5   C4   C3   105.66  3.000
 L6K  H4   C5   C4   132.49  3.000
 L6K  H4   C5   O1   117.10  3.000
 L6K  C4   C5   O1   110.41  3.000
 L6K  C7   C6   C11  117.38  3.000
 L6K  C7   C6   C12  121.22  3.000
 L6K  C11  C6   C12  121.38  3.000
 L6K  H8   N2   C15  108.46  3.000
 L6K  H8   N2   C16  108.06  3.000
 L6K  C15  N2   C16  113.17  3.000
 L6K  H10  C15  C35  107.48  3.000
 L6K  H10  C15  C12  107.41  3.000
 L6K  C35  C15  C12  107.27  3.000
 L6K  H10  C15  N2   111.44  3.000
 L6K  C35  C15  N2   113.00  3.000
 L6K  C12  C15  N2   109.99  3.000
 L6K  H12  C12  H11  107.20  3.000
 L6K  H12  C12  C15  108.57  3.000
 L6K  H11  C12  C15  107.90  3.000
 L6K  H12  C12  C6   109.76  3.000
 L6K  H11  C12  C6   109.77  3.000
 L6K  C15  C12  C6   113.44  3.000
 L6K  H13  C11  C10  118.88  3.000
 L6K  H13  C11  C6   119.50  3.000
 L6K  C10  C11  C6   121.62  3.000
 L6K  H14  C10  C9   119.53  3.000
 L6K  H14  C10  C11  120.28  3.000
 L6K  C9   C10  C11  120.18  3.000
 L6K  H15  C7   C8   118.44  3.000
 L6K  H15  C7   C6   119.58  3.000
 L6K  C8   C7   C6   121.98  3.000
 L6K  H16  C8   C9   121.55  3.000
 L6K  H16  C8   C7   118.74  3.000
 L6K  C9   C8   C7   119.71  3.000
 L6K  C8   C9   C10  119.14  3.000
 L6K  C8   C9   O2   124.54  3.000
 L6K  C10  C9   O2   116.32  3.000
 L6K  H18  C13  H17  107.50  3.000
 L6K  H18  C13  C4   110.10  3.000
 L6K  H17  C13  C4   110.53  3.000
 L6K  H18  C13  O2   111.02  3.000
 L6K  H17  C13  O2   109.98  3.000
 L6K  C4   C13  O2   107.73  3.000
 L6K  H20  N1   H19  105.28  3.000
 L6K  H20  N1   C1   108.50  3.000
 L6K  H19  N1   C1   109.36  3.000
 L6K  O37  C35  O36  126.79  3.000
 L6K  O37  C35  C15  115.41  3.000
 L6K  O36  C35  C15  117.74  3.000
 L6K  H7   C16  H6   107.44  3.000
 L6K  H7   C16  H5   107.51  3.000
 L6K  H6   C16  H5   107.52  3.000
 L6K  H7   C16  N2   109.72  3.000
 L6K  H6   C16  N2   110.31  3.000
 L6K  H5   C16  N2   114.10  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
 L6K  CONST_01  C3   C4   C5   O1      0.00   0.0  0
 L6K  CONST_02  C4   C3   C2   O1      0.00   0.0  0
 L6K  CONST_03  C4   C5   O1   C2      0.00   0.0  0
 L6K  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 L6K  CONST_05  C5   O1   C2   C3      0.00   0.0  0
 L6K  CONST_06  C9   C10  C11  C6      0.00   0.0  0
 L6K  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 L6K  CONST_08  C8   C9   C10  C11     0.00   0.0  0
 L6K  CONST_09  C8   C7   C6   C11     0.00   0.0  0
 L6K  CONST_10  C7   C8   C9   C10     0.00   0.0  0
 L6K  CONST_11  C7   C6   C11  C10     0.00   0.0  0
 L6K  CONST_12  C5   O1   C2   C1    180.00   0.0  0
 L6K  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 L6K  CONST_14  C13  C4   C5   O1    180.00   0.0  0
 L6K  CONST_15  C13  C4   C3   C2    180.00   0.0  0
 L6K  CONST_16  C11  C10  C9   O2    180.00   0.0  0
 L6K  CONST_17  C7   C8   C9   O2    180.00   0.0  0
 L6K  CONST_18  C10  C11  C6   C12   180.00   0.0  0
 L6K  CONST_19  C8   C7   C6   C12   180.00   0.0  0
 L6K  CONST_20  H3   C3   C2   O1    180.00   0.0  0
 L6K  CONST_21  H4   C5   O1   C2    180.00   0.0  0
 L6K  CONST_22  H14  C10  C11  C6    180.00   0.0  0
 L6K  CONST_23  H16  C8   C7   C6    180.00   0.0  0
 L6K  CONST_24  H15  C7   C6   C11   180.00   0.0  0
 L6K  CONST_25  H13  C11  C6   C7    180.00   0.0  0
 L6K  Var_01    N1   C1   C2   O1    -66.49  30.0  1
 L6K  Var_02    C5   C4   C13  O2   -120.86  30.0  2
 L6K  Var_03    C11  C6   C12  C15   100.25  30.0  2
 L6K  Var_04    H19  N1   C1   C2     72.43  30.0  3
 L6K  Var_05    H5   C16  N2   C15   -52.25  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
 L6K  chir_01  C15  C12  N2  C35  positiv

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
 L6K  plan-1  C1   0.020
 L6K  plan-1  O1   0.020
 L6K  plan-1  C2   0.020
 L6K  plan-1  C3   0.020
 L6K  plan-1  C4   0.020
 L6K  plan-1  C5   0.020
 L6K  plan-1  C13  0.020
 L6K  plan-1  H3   0.020
 L6K  plan-1  H4   0.020
 L6K  plan-2  O2   0.020
 L6K  plan-2  C6   0.020
 L6K  plan-2  C12  0.020
 L6K  plan-2  C11  0.020
 L6K  plan-2  C10  0.020
 L6K  plan-2  C7   0.020
 L6K  plan-2  C8   0.020
 L6K  plan-2  C9   0.020
 L6K  plan-2  H13  0.020
 L6K  plan-2  H14  0.020
 L6K  plan-2  H15  0.020
 L6K  plan-2  H16  0.020
 L6K  plan-3  C15  0.020
 L6K  plan-3  C35  0.020
 L6K  plan-3  O36  0.020
 L6K  plan-3  O37  0.020

