# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 15:10:40 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)c(OCc2ccccc2[N+]([O-])=O)c1)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
 BUU  BUU  '(2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid'  ligand  39  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BUU
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
 BUU  O1   O  O      0  -0.605  -6.2094   1.6077   0.4996
 BUU  C    C  C      0   0.403  -5.0053   1.8708   0.3150
 BUU  O    O  OC    -1  -0.621  -4.5341   2.9480  -0.1029
 BUU  C1   C  CH1    0  -0.198  -3.9863   0.7386   0.5684
 BUU  N    N  NH2    0  -0.793  -4.5261  -0.2583   1.4722
 BUU  C2   C  CH2    0  -0.526  -3.5435   0.1873  -0.8073
 BUU  C3   C  CR6    0   0.126  -2.5124  -0.8966  -0.6963
 BUU  C4   C  CR16   0  -0.336  -2.8561  -2.2391  -0.7583
 BUU  C5   C  CR16   0  -0.331  -1.8933  -3.2344  -0.6154
 BUU  C6   C  CR6    0   0.247  -0.5688  -2.9035  -0.3988
 BUU  O2   O  OH1    0  -0.633   0.3481  -3.8868  -0.2699
 BUU  C8   C  CR16   0  -0.426  -1.1725  -0.5642  -0.4716
 BUU  C7   C  CR6    0   0.337  -0.2100  -1.5478  -0.3233
 BUU  O3   O  O2     0  -0.508   1.1107  -1.3281  -0.1090
 BUU  C9   C  CH2    0  -0.194   1.5730   0.0022  -0.0747
 BUU  C10  C  CR6    0   0.065   3.0610  -0.0205   0.1708
 BUU  C15  C  CR6    0   0.217   3.9068   1.0626  -0.0926
 BUU  N1   N  N      1   0.326   3.3796   2.3226  -0.5918
 BUU  O4   O  O     -1  -0.370   4.1021   3.0130  -1.2698
 BUU  O5   O  O      0  -0.375   2.2476   2.6254  -0.2888
 BUU  C11  C  CR16   0  -0.311   3.6660  -1.1677   0.6783
 BUU  C12  C  CR16   0  -0.210   5.0315  -1.2297   0.9107
 BUU  C13  C  CR16   0  -0.264   5.8446  -0.1433   0.6291
 BUU  C14  C  CR16   0  -0.264   5.2787   1.0082   0.1161
 BUU  H1   H  HCH1   0   0.211  -3.0994   1.1773   1.0392
 BUU  HN1  H  HNH2   0   0.326  -5.4167  -0.5786   1.1129
 BUU  HN2  H  HNH2   0   0.334  -3.9165  -1.0669   1.5076
 BUU  H22  H  HCH2   0   0.234  -4.4243  -0.1962  -1.3326
 BUU  H21  H  HCH2   0   0.235  -3.1517   1.0142  -1.4044
 BUU  H4   H  HCR6   0   0.246  -3.8853  -2.5240  -0.9386
 BUU  H5   H  HCR6   0   0.262  -2.1717  -4.2791  -0.6783
 BUU  HO2  H  HOH1   0   0.472   1.2350  -3.5124  -0.2177
 BUU  H8   H  HCR6   0   0.277  -0.9000   0.4833  -0.4173
 BUU  H92  H  HCH2   0   0.253   1.3342   0.4984  -1.0196
 BUU  H91  H  HCH2   0   0.264   1.0764   0.5572   0.7279
 BUU  H11  H  HCR6   0   0.276   3.0650  -2.0364   0.9019
 BUU  H12  H  HCR6   0   0.279   5.4583  -2.1377   1.3144
 BUU  H13  H  HCR6   0   0.279   6.9096  -0.1866   0.8090
 BUU  H14  H  HCR6   0   0.299   5.8997   1.8647  -0.1030

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
 BUU  O5   N1   double    1.210  0.020  1.210
 BUU  O4   N1   single    1.208  0.020  1.208
 BUU  N1   C15  single    1.454  0.020  1.454
 BUU  C15  C14  aromatic  1.389  0.020  1.389
 BUU  C15  C10  aromatic  1.399  0.020  1.399
 BUU  O3   C9   single    1.409  0.020  1.409
 BUU  O3   C7   single    1.356  0.020  1.356
 BUU  C9   C10  single    1.508  0.020  1.508
 BUU  C14  C13  aromatic  1.382  0.020  1.382
 BUU  C10  C11  aromatic  1.393  0.020  1.393
 BUU  C7   C6   aromatic  1.404  0.020  1.404
 BUU  C7   C8   aromatic  1.384  0.020  1.384
 BUU  O2   C6   single    1.351  0.020  1.351
 BUU  C6   C5   aromatic  1.382  0.020  1.382
 BUU  C8   C3   aromatic  1.399  0.020  1.399
 BUU  C13  C12  aromatic  1.386  0.020  1.386
 BUU  C11  C12  aromatic  1.387  0.020  1.387
 BUU  C3   C2   single    1.500  0.020  1.500
 BUU  C3   C4   aromatic  1.387  0.020  1.387
 BUU  C5   C4   aromatic  1.392  0.020  1.392
 BUU  C2   C1   single    1.547  0.020  1.547
 BUU  O1   C    deloc     1.246  0.020  1.246
 BUU  C1   C    single    1.544  0.020  1.544
 BUU  C1   N    single    1.450  0.020  1.450
 BUU  C    O    deloc     1.248  0.020  1.248
 BUU  C1   H1   single    0.970  0.020  1.090
 BUU  N    HN1  single    0.890  0.020  1.040
 BUU  N    HN2  single    0.890  0.020  1.040
 BUU  C2   H22  single    0.970  0.020  1.090
 BUU  C2   H21  single    0.970  0.020  1.090
 BUU  C4   H4   single    0.930  0.020  1.080
 BUU  C5   H5   single    0.930  0.020  1.080
 BUU  O2   HO2  single    0.850  0.020  0.980
 BUU  C8   H8   single    0.930  0.020  1.080
 BUU  C9   H92  single    0.970  0.020  1.090
 BUU  C9   H91  single    0.970  0.020  1.090
 BUU  C11  H11  single    0.930  0.020  1.080
 BUU  C12  H12  single    0.930  0.020  1.080
 BUU  C13  H13  single    0.930  0.020  1.080
 BUU  C14  H14  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
 BUU  C1   C    O    116.03  3.000
 BUU  O    C    O1   126.64  3.000
 BUU  C1   C    O1   117.28  3.000
 BUU  H1   C1   C2   107.04  3.000
 BUU  H1   C1   N    107.99  3.000
 BUU  C2   C1   N    114.58  3.000
 BUU  H1   C1   C    108.12  3.000
 BUU  N    C1   C    111.15  3.000
 BUU  C2   C1   C    107.71  3.000
 BUU  HN2  N    HN1  106.81  3.000
 BUU  HN2  N    C1   110.28  3.000
 BUU  HN1  N    C1   108.90  3.000
 BUU  H21  C2   H22  106.95  3.000
 BUU  H21  C2   C3   109.93  3.000
 BUU  H22  C2   C3   109.59  3.000
 BUU  H21  C2   C1   108.60  3.000
 BUU  H22  C2   C1   108.74  3.000
 BUU  C3   C2   C1   112.85  3.000
 BUU  C8   C3   C4   118.33  3.000
 BUU  C4   C3   C2   121.72  3.000
 BUU  C8   C3   C2   119.91  3.000
 BUU  H4   C4   C5   119.09  3.000
 BUU  H4   C4   C3   119.83  3.000
 BUU  C5   C4   C3   121.07  3.000
 BUU  H5   C5   C6   119.09  3.000
 BUU  H5   C5   C4   120.40  3.000
 BUU  C6   C5   C4   120.51  3.000
 BUU  C7   C6   O2   121.61  3.000
 BUU  O2   C6   C5   119.42  3.000
 BUU  C7   C6   C5   118.97  3.000
 BUU  HO2  O2   C6   110.30  3.000
 BUU  H8   C8   C7   120.44  3.000
 BUU  H8   C8   C3   118.60  3.000
 BUU  C7   C8   C3   120.96  3.000
 BUU  O3   C7   C8   125.39  3.000
 BUU  C8   C7   C6   120.17  3.000
 BUU  O3   C7   C6   114.44  3.000
 BUU  C9   O3   C7   118.46  3.000
 BUU  H91  C9   H92  107.72  3.000
 BUU  H91  C9   C10  109.62  3.000
 BUU  H92  C9   C10  111.28  3.000
 BUU  H91  C9   O3   110.34  3.000
 BUU  H92  C9   O3   109.62  3.000
 BUU  C10  C9   O3   108.27  3.000
 BUU  C11  C10  C15  116.34  3.000
 BUU  C11  C10  C9   120.02  3.000
 BUU  C15  C10  C9   123.64  3.000
 BUU  C14  C15  N1   116.34  3.000
 BUU  C14  C15  C10  122.58  3.000
 BUU  N1   C15  C10  121.07  3.000
 BUU  O5   N1   O4   123.85  3.000
 BUU  O4   N1   C15  118.11  3.000
 BUU  O5   N1   C15  118.03  3.000
 BUU  H11  C11  C12  118.52  3.000
 BUU  H11  C11  C10  119.76  3.000
 BUU  C12  C11  C10  121.72  3.000
 BUU  H12  C12  C13  120.16  3.000
 BUU  H12  C12  C11  119.26  3.000
 BUU  C13  C12  C11  120.57  3.000
 BUU  H13  C13  C14  119.91  3.000
 BUU  H13  C13  C12  120.85  3.000
 BUU  C14  C13  C12  119.24  3.000
 BUU  H14  C14  C13  120.04  3.000
 BUU  H14  C14  C15  120.42  3.000
 BUU  C13  C14  C15  119.54  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
 BUU  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 BUU  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 BUU  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 BUU  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 BUU  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 BUU  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 BUU  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 BUU  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 BUU  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 BUU  CONST_10  C12  C11  C10  C15     0.00   0.0  0
 BUU  CONST_11  C14  C15  C10  C11     0.00   0.0  0
 BUU  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 BUU  CONST_13  C7   C8   C3   C2    180.00   0.0  0
 BUU  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 BUU  CONST_15  O3   C7   C8   C3    180.00   0.0  0
 BUU  CONST_16  O2   C6   C5   C4    180.00   0.0  0
 BUU  CONST_17  O3   C7   C6   C5    180.00   0.0  0
 BUU  CONST_18  C8   C7   C6   O2    180.00   0.0  0
 BUU  CONST_19  C14  C15  C10  C9    180.00   0.0  0
 BUU  CONST_20  C12  C11  C10  C9    180.00   0.0  0
 BUU  CONST_21  C13  C14  C15  N1    180.00   0.0  0
 BUU  CONST_22  C11  C10  C15  N1    180.00   0.0  0
 BUU  CONST_23  H5   C5   C4   C3    180.00   0.0  0
 BUU  CONST_24  H8   C8   C3   C4    180.00   0.0  0
 BUU  CONST_25  H4   C4   C5   C6    180.00   0.0  0
 BUU  CONST_26  H14  C14  C15  C10   180.00   0.0  0
 BUU  CONST_27  H12  C12  C11  C10   180.00   0.0  0
 BUU  CONST_28  H13  C13  C14  C15   180.00   0.0  0
 BUU  CONST_29  H11  C11  C10  C15   180.00   0.0  0
 BUU  Var_01    C8   C3   C2   C1    -79.40  30.0  3
 BUU  Var_02    C10  C9   O3   C7   -179.82  30.0  3
 BUU  Var_03    C15  C10  C9   O3    161.82  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
 BUU  chir_01  C1  C2  C  N  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
 BUU  plan-1  C2   0.020
 BUU  plan-1  C3   0.020
 BUU  plan-1  C4   0.020
 BUU  plan-1  C5   0.020
 BUU  plan-1  C6   0.020
 BUU  plan-1  O2   0.020
 BUU  plan-1  C8   0.020
 BUU  plan-1  C7   0.020
 BUU  plan-1  O3   0.020
 BUU  plan-1  H4   0.020
 BUU  plan-1  H5   0.020
 BUU  plan-1  H8   0.020
 BUU  plan-2  C9   0.020
 BUU  plan-2  C10  0.020
 BUU  plan-2  C15  0.020
 BUU  plan-2  N1   0.020
 BUU  plan-2  C11  0.020
 BUU  plan-2  C12  0.020
 BUU  plan-2  C13  0.020
 BUU  plan-2  C14  0.020
 BUU  plan-2  H11  0.020
 BUU  plan-2  H12  0.020
 BUU  plan-2  H13  0.020
 BUU  plan-2  H14  0.020
 BUU  plan-3  C15  0.020
 BUU  plan-3  N1   0.020
 BUU  plan-3  O4   0.020
 BUU  plan-3  O5   0.020
 BUU  plan-4  O1   0.020
 BUU  plan-4  C    0.020
 BUU  plan-4  O    0.020
 BUU  plan-4  C1   0.020

