# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 16:12:22 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(C[C@H](O)C(O)=O)cc1
#
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
 APA  APA  '(2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid'  ligand  27  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_APA
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
 APA  C1    C  C     0   0.504   3.8863   0.1594  -0.1947
 APA  O1    O  O     0  -0.433   4.6459  -0.7724  -0.2570
 APA  OXT   O  OH1   0  -0.589   4.2447   1.3916   0.1337
 APA  C2    C  CH1   0  -0.055   2.3918   0.0578  -0.4589
 APA  O2    O  OH1   0  -0.643   2.0834  -1.1238  -1.1298
 APA  C3    C  CH2   0  -0.584   1.6197   0.2196   0.8635
 APA  C1'   C  CR6   0   0.151   0.1376   0.1583   0.6382
 APA  C2'   C  CR16  0  -0.298  -0.5577  -1.0458   0.7219
 APA  C3'   C  CR16  0  -0.261  -1.9208  -1.0983   0.4848
 APA  C4'   C  CR6   0   0.032  -2.6280   0.0514   0.1395
 APA  C5'   C  CR16  0  -0.277  -1.9364   1.2584   0.0572
 APA  C6'   C  CR16  0  -0.287  -0.5729   1.3072   0.3061
 APA  C     C  C     0   0.331  -4.0935  -0.0345  -0.1078
 APA  N1    N  NH2   0  -0.822  -4.6139   0.9635  -0.8825
 APA  N2    N  N     0  -0.652  -4.7544  -0.9795   0.4430
 APA  HXT   H  HOH1  0   0.486   5.1938   1.4271   0.3276
 APA  H31   H  HCH2  0   0.270   1.9284  -0.5642   1.5617
 APA  H32   H  HCH2  0   0.275   1.8870   1.1747   1.3184
 APA  H2'   H  HCR6  0   0.247  -0.0310  -1.9540   0.9884
 APA  H3'   H  HCR6  0   0.253  -2.4463  -2.0410   0.5589
 APA  H5'   H  HCR6  0   0.257  -2.4564   2.1782  -0.1777
 APA  H6'   H  HCR6  0   0.252  -0.0570   2.2588   0.2492
 APA  HN11  H  HNH2  0   0.394  -4.0192   1.3923  -1.5726
 APA  HN12  H  HNH2  0   0.391  -5.5686   0.8583  -1.1877
 APA  HN2   H  H     0   0.323  -5.7338  -0.9481   0.1724
 APA  H11   H  HCH1  0   0.286   2.1108   0.8785  -1.1258
 APA  H12   H  HOH1  0   0.448   2.3372  -1.8750  -0.5822

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
 APA  C1   O1    double    1.204  0.020  1.204
 APA  C1   OXT   single    1.325  0.020  1.325
 APA  C1   C2    single    1.521  0.020  1.521
 APA  OXT  HXT   single    0.850  0.020  0.980
 APA  C2   O2    single    1.393  0.020  1.393
 APA  C2   C3    single    1.540  0.020  1.540
 APA  C3   C1'   single    1.500  0.020  1.500
 APA  C3   H31   single    0.970  0.020  1.090
 APA  C3   H32   single    0.970  0.020  1.090
 APA  C1'  C2'   aromatic  1.393  0.020  1.393
 APA  C1'  C6'   aromatic  1.391  0.020  1.391
 APA  C2'  C3'   aromatic  1.385  0.020  1.385
 APA  C2'  H2'   single    0.930  0.020  1.080
 APA  C3'  C4'   aromatic  1.393  0.020  1.393
 APA  C3'  H3'   single    0.930  0.020  1.080
 APA  C4'  C5'   aromatic  1.393  0.020  1.393
 APA  C4'  C     single    1.489  0.020  1.489
 APA  C5'  C6'   aromatic  1.387  0.020  1.387
 APA  C5'  H5'   single    0.930  0.020  1.080
 APA  C6'  H6'   single    0.930  0.020  1.080
 APA  C    N1    single    1.366  0.020  1.366
 APA  C    N2    double    1.278  0.020  1.278
 APA  N1   HN11  single    0.890  0.020  1.040
 APA  N1   HN12  single    0.890  0.020  1.040
 APA  N2   HN2   single    0.890  0.020  1.040
 APA  C2   H11   single    0.970  0.020  1.090
 APA  O2   H12   single    0.850  0.020  0.980

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
 APA  C2    C1   OXT   111.78  3.000
 APA  C2    C1   O1    124.01  3.000
 APA  OXT   C1   O1    124.20  3.000
 APA  HXT   OXT  C1    110.40  3.000
 APA  H11   C2   C3    108.41  3.000
 APA  H11   C2   O2    106.61  3.000
 APA  C3    C2   O2    113.06  3.000
 APA  H11   C2   C1    107.94  3.000
 APA  C3    C2   C1    109.66  3.000
 APA  O2    C2   C1    110.96  3.000
 APA  H12   O2   C2    109.22  3.000
 APA  H32   C3   H31   106.97  3.000
 APA  H32   C3   C1'   109.90  3.000
 APA  H31   C3   C1'   110.19  3.000
 APA  H32   C3   C2    109.10  3.000
 APA  H31   C3   C2    109.35  3.000
 APA  C1'   C3   C2    111.23  3.000
 APA  C6'   C1'  C2'   118.25  3.000
 APA  C6'   C1'  C3    120.43  3.000
 APA  C2'   C1'  C3    121.29  3.000
 APA  H2'   C2'  C3'   119.28  3.000
 APA  H2'   C2'  C1'   119.79  3.000
 APA  C3'   C2'  C1'   120.93  3.000
 APA  H3'   C3'  C4'   119.31  3.000
 APA  H3'   C3'  C2'   119.97  3.000
 APA  C4'   C3'  C2'   120.72  3.000
 APA  C     C4'  C5'   121.92  3.000
 APA  C     C4'  C3'   119.55  3.000
 APA  C5'   C4'  C3'   118.52  3.000
 APA  H5'   C5'  C6'   118.77  3.000
 APA  H5'   C5'  C4'   120.69  3.000
 APA  C6'   C5'  C4'   120.52  3.000
 APA  H6'   C6'  C5'   119.30  3.000
 APA  H6'   C6'  C1'   119.64  3.000
 APA  C5'   C6'  C1'   121.05  3.000
 APA  N2    C    N1    125.98  3.000
 APA  N2    C    C4'   118.70  3.000
 APA  N1    C    C4'   115.27  3.000
 APA  HN12  N1   HN11  113.35  3.000
 APA  HN12  N1   C     117.15  3.000
 APA  HN11  N1   C     118.34  3.000
 APA  HN2   N2   C     111.14  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
 APA  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 APA  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 APA  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 APA  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 APA  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 APA  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 APA  CONST_07  C3'   C2'  C1'  C3    180.00   0.0  0
 APA  CONST_08  C5'   C6'  C1'  C3    180.00   0.0  0
 APA  CONST_09  C     C4'  C3'  C2'   180.00   0.0  0
 APA  CONST_10  C     C4'  C5'  C6'   180.00   0.0  0
 APA  CONST_11  H3'   C3'  C2'  C1'   180.00   0.0  0
 APA  CONST_12  H5'   C5'  C6'  C1'   180.00   0.0  0
 APA  CONST_13  H6'   C6'  C1'  C2'   180.00   0.0  0
 APA  CONST_14  H2'   C2'  C3'  C4'   180.00   0.0  0
 APA  CONST_16  HN12  N1   C    C4'   180.00   0.0  0
 APA  CONST_17  HN2   N2   C    C4'   180.00   0.0  0
 APA  CONST_18  HXT   OXT  C1   O1      0.00   0.0  0
 APA  Var_01    C2'   C1'  C3   C2     91.65  30.0  2
 APA  Var_02    N1    C    C4'  C3'  -157.35  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
 APA  chir_01  C2  C1  O2  C3  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
 APA  plan-1  C3    0.020
 APA  plan-1  C1'   0.020
 APA  plan-1  C2'   0.020
 APA  plan-1  C3'   0.020
 APA  plan-1  C4'   0.020
 APA  plan-1  C5'   0.020
 APA  plan-1  C6'   0.020
 APA  plan-1  C     0.020
 APA  plan-1  H2'   0.020
 APA  plan-1  H3'   0.020
 APA  plan-1  H5'   0.020
 APA  plan-1  H6'   0.020
 APA  plan-2  C4'   0.020
 APA  plan-2  C     0.020
 APA  plan-2  N1    0.020
 APA  plan-2  N2    0.020
 APA  plan-2  HN11  0.020
 APA  plan-2  HN12  0.020
 APA  plan-2  HN2   0.020
 APA  plan-3  C1    0.020
 APA  plan-3  O1    0.020
 APA  plan-3  OXT   0.020
 APA  plan-3  C2    0.020
 APA  plan-3  HXT   0.020

