# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:49:38 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: {[4-(aminomethyl)phenyl]amino}(oxo)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(NC(=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
 LO1  LO1  '{[4-(aminomethyl)phenyl]amino}(oxo)acetic acid'  ligand  23  14  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LO1
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
 LO1  C1    C  C      0   0.351  -0.2927  -0.0218  -3.6758
 LO1  O1    O  O      0  -0.586  -1.5224  -0.2196  -3.6762
 LO1  OXT   O  OC    -1  -0.569   0.4803   0.0785  -4.6326
 LO1  C2    C  C      0   0.338   0.3692   0.1188  -2.2687
 LO1  O2    O  O      0  -0.470   1.5634   0.3088  -2.1229
 LO1  C1'   C  CR6    0   0.359  -0.3600   0.0707   0.1127
 LO1  C2'   C  CR16   0  -0.336  -1.5050  -0.0536   0.9031
 LO1  C3'   C  CR16   0  -0.296  -1.4198  -0.0107   2.2835
 LO1  C4'   C  CR6    0   0.070  -0.1983   0.1644   2.9282
 LO1  C5'   C  CR16   0  -0.279   0.9370   0.2840   2.1336
 LO1  C6'   C  CR16   0  -0.307   0.8724   0.2401   0.7476
 LO1  C     C  CH2    0  -0.335  -0.1281   0.2438   4.4318
 LO1  N1    N  NH2    0  -0.793   1.0829  -0.3655   4.9546
 LO1  N7    N  NH1    0  -0.722  -0.5324   0.0062  -1.2684
 LO1  H2'   H  HCR6   0   0.263  -2.4705  -0.1962   0.4310
 LO1  H3'   H  HCR6   0   0.248  -2.3254  -0.1220   2.8689
 LO1  H5'   H  HCR6   0   0.246   1.9031   0.4087   2.6061
 LO1  H6'   H  HCR6   0   0.271   1.7788   0.3362   0.1718
 LO1  HC1   H  HCH2   0   0.212  -1.0537  -0.1798   4.8456
 LO1  HC2   H  HCH2   0   0.236  -0.1243   1.2968   4.7309
 LO1  H1N1  H  HNH2   0   0.353   1.1215  -0.2238   5.9556
 LO1  H1N2  H  HNH2   0   0.342   1.0445  -1.3673   4.8146
 LO1  H7    H  HNH1   0   0.403  -1.4746  -0.1462  -1.6057

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
 LO1  C1   O1    deloc     1.246  0.020  1.246
 LO1  C1   OXT   deloc     1.234  0.020  1.234
 LO1  C1   C2    single    1.561  0.020  1.561
 LO1  C2   O2    double    1.218  0.020  1.218
 LO1  C2   N7    single    1.351  0.020  1.351
 LO1  C1'  C2'   aromatic  1.397  0.020  1.397
 LO1  C1'  C6'   aromatic  1.397  0.020  1.397
 LO1  C1'  N7    single    1.393  0.020  1.393
 LO1  C2'  C3'   aromatic  1.384  0.020  1.384
 LO1  C2'  H2'   single    0.930  0.020  1.080
 LO1  C3'  C4'   aromatic  1.392  0.020  1.392
 LO1  C3'  H3'   single    0.930  0.020  1.080
 LO1  C4'  C5'   aromatic  1.391  0.020  1.391
 LO1  C4'  C     single    1.507  0.020  1.507
 LO1  C5'  C6'   aromatic  1.388  0.020  1.388
 LO1  C5'  H5'   single    0.930  0.020  1.080
 LO1  C6'  H6'   single    0.930  0.020  1.080
 LO1  C    N1    single    1.453  0.020  1.453
 LO1  C    HC1   single    0.970  0.020  1.090
 LO1  C    HC2   single    0.970  0.020  1.090
 LO1  N1   H1N1  single    0.890  0.020  1.040
 LO1  N1   H1N2  single    0.890  0.020  1.040
 LO1  N7   H7    single    0.860  0.020  1.020

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
 LO1  C2    C1   OXT   115.21  3.000
 LO1  C2    C1   O1    115.67  3.000
 LO1  OXT   C1   O1    129.13  3.000
 LO1  N7    C2   O2    125.35  3.000
 LO1  N7    C2   C1    112.13  3.000
 LO1  O2    C2   C1    122.51  3.000
 LO1  N7    C1'  C6'   124.43  3.000
 LO1  N7    C1'  C2'   117.09  3.000
 LO1  C6'   C1'  C2'   118.48  3.000
 LO1  H2'   C2'  C3'   119.57  3.000
 LO1  H2'   C2'  C1'   119.68  3.000
 LO1  C3'   C2'  C1'   120.75  3.000
 LO1  H3'   C3'  C4'   119.72  3.000
 LO1  H3'   C3'  C2'   118.95  3.000
 LO1  C4'   C3'  C2'   121.33  3.000
 LO1  C     C4'  C5'   121.82  3.000
 LO1  C     C4'  C3'   120.63  3.000
 LO1  C5'   C4'  C3'   117.54  3.000
 LO1  H5'   C5'  C6'   118.74  3.000
 LO1  H5'   C5'  C4'   119.27  3.000
 LO1  C6'   C5'  C4'   121.99  3.000
 LO1  H6'   C6'  C5'   119.43  3.000
 LO1  H6'   C6'  C1'   120.65  3.000
 LO1  C5'   C6'  C1'   119.92  3.000
 LO1  HC2   C    HC1   105.71  3.000
 LO1  HC2   C    N1    107.59  3.000
 LO1  HC1   C    N1    113.89  3.000
 LO1  HC2   C    C4'   108.87  3.000
 LO1  HC1   C    C4'   108.43  3.000
 LO1  N1    C    C4'   112.07  3.000
 LO1  H1N2  N1   H1N1  106.07  3.000
 LO1  H1N2  N1   C     109.49  3.000
 LO1  H1N1  N1   C     109.21  3.000
 LO1  H7    N7   C1'   116.90  3.000
 LO1  H7    N7   C2    112.76  3.000
 LO1  C1'   N7   C2    130.34  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
 LO1  CONST_01  C4'   C3'  C2'  C1'    0.00   0.0  0
 LO1  CONST_02  C4'   C5'  C6'  C1'    0.00   0.0  0
 LO1  CONST_03  C5'   C6'  C1'  C2'    0.00   0.0  0
 LO1  CONST_04  C5'   C4'  C3'  C2'    0.00   0.0  0
 LO1  CONST_05  C6'   C1'  C2'  C3'    0.00   0.0  0
 LO1  CONST_06  C6'   C5'  C4'  C3'    0.00   0.0  0
 LO1  CONST_07  C     C4'  C3'  C2'  180.00   0.0  0
 LO1  CONST_08  N7    C1'  C2'  C3'  180.00   0.0  0
 LO1  CONST_09  N7    C1'  C6'  C5'  180.00   0.0  0
 LO1  CONST_10  C     C4'  C5'  C6'  180.00   0.0  0
 LO1  CONST_11  H3'   C3'  C2'  C1'  180.00   0.0  0
 LO1  CONST_12  H5'   C5'  C6'  C1'  180.00   0.0  0
 LO1  CONST_13  H6'   C6'  C1'  C2'  180.00   0.0  0
 LO1  CONST_14  H2'   C2'  C3'  C4'  180.00   0.0  0
 LO1  CONST_15  C2'   C1'  N7   C2   180.00   0.0  0
 LO1  CONST_16  C6'   C1'  N7   C2     0.00   0.0  0
 LO1  CONST_17  H7    N7   C1'  C2'    0.00   0.0  0
 LO1  CONST_18  C1'   N7   C2   C1   180.00   0.0  0
 LO1  CONST_19  C1'   N7   C2   O2     0.00   0.0  0
 LO1  Var_01    N1    C    C4'  C3'  145.07  30.0  2
 LO1  Var_02    H1N1  N1   C    C4'  175.55  30.0  3
 LO1  Var_03    O2    C2   C1   O1   179.69  30.0  2

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
 LO1  plan-1  C1'  0.020
 LO1  plan-1  C2'  0.020
 LO1  plan-1  C3'  0.020
 LO1  plan-1  C4'  0.020
 LO1  plan-1  C5'  0.020
 LO1  plan-1  C6'  0.020
 LO1  plan-1  C    0.020
 LO1  plan-1  N7   0.020
 LO1  plan-1  H2'  0.020
 LO1  plan-1  H3'  0.020
 LO1  plan-1  H5'  0.020
 LO1  plan-1  H6'  0.020
 LO1  plan-2  C1   0.020
 LO1  plan-2  C2   0.020
 LO1  plan-2  O2   0.020
 LO1  plan-2  C1'  0.020
 LO1  plan-2  N7   0.020
 LO1  plan-2  H7   0.020
 LO1  plan-3  C1   0.020
 LO1  plan-3  O1   0.020
 LO1  plan-3  OXT  0.020
 LO1  plan-3  C2   0.020

