# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:57:17 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: [2-(aminomethyl)-4-chlorophenoxy]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cc(Cl)ccc1OCC(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
 01X  01X  '[2-(aminomethyl)-4-chlorophenoxy]acetic acid'  peptide  24  14  .  2022-03-07  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_01X
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
 01X  N'    N   NH2   0  -0.786  -0.2206  -2.9307  -0.8300
 01X  CA'   C   CH2   0  -0.351   0.1553  -2.3603   0.4571
 01X  CB'   C   CR6   0   0.005   0.7220  -0.9791   0.2696
 01X  CG'   C   CR6   0   0.379  -0.1106   0.1260   0.0357
 01X  CD'   C   CR16  0  -0.384   0.4410   1.3853  -0.1716
 01X  CE'   C   CR16  0  -0.213   1.8200   1.5603  -0.1568
 01X  CDB   C   CR6   0  -0.054   2.6381   0.4727   0.0702
 01X  CGB   C   CR16  0  -0.243   2.0936  -0.7871   0.2821
 01X  CL    CL  CL    0  -0.141   4.3620   0.6745   0.0949
 01X  OL    O   O2    0  -0.449  -1.4350  -0.1215   0.0449
 01X  CF    C   CH2   0  -0.296  -2.3202   0.9561  -0.0634
 01X  CH    C   C     0   0.512  -3.7201   0.4158   0.1048
 01X  OH    O   O     0  -0.419  -3.9955  -0.7299   0.3326
 01X  H'    H   HNH2  0   0.340   0.6187  -3.1539  -1.3509
 01X  HA'1  H   HCH2  0   0.240  -0.7373  -2.3144   1.0825
 01X  HA'2  H   HCH2  0   0.217   0.8901  -2.9614   1.0074
 01X  HD'   H   HCR6  0   0.290  -0.1794   2.2533  -0.3481
 01X  HE'   H   HCR6  0   0.282   2.2357   2.5452  -0.3209
 01X  HG'   H   HCR6  0   0.273   2.7425  -1.6355   0.4619
 01X  HF1   H   HCH2  0   0.275  -2.1425   1.7164   0.7076
 01X  HF2   H   HCH2  0   0.275  -2.2469   1.4574  -1.0363
 01X  H2    H   HNH2  0   0.350  -0.6891  -3.8143  -0.6733
 01X  OXT   O   OH1   0  -0.592  -4.6033   1.3940  -0.0303
 01X  HXT   H   HOH1  0   0.490  -5.5042   1.0536   0.0782

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
 01X  N'   CA'   single    1.457  0.020  1.457
 01X  N'   H'    single    0.890  0.020  1.040
 01X  CA'  CB'   single    1.505  0.020  1.505
 01X  CA'  HA'1  single    0.970  0.020  1.090
 01X  CA'  HA'2  single    0.970  0.020  1.090
 01X  CB'  CG'   aromatic  1.403  0.020  1.403
 01X  CB'  CGB   aromatic  1.385  0.020  1.385
 01X  CG'  CD'   aromatic  1.390  0.020  1.390
 01X  CG'  OL    single    1.347  0.020  1.347
 01X  CD'  CE'   aromatic  1.390  0.020  1.390
 01X  CD'  HD'   single    0.930  0.020  1.080
 01X  CE'  CDB   aromatic  1.380  0.020  1.380
 01X  CE'  HE'   single    0.930  0.020  1.080
 01X  CDB  CGB   aromatic  1.389  0.020  1.389
 01X  CDB  CL    single    1.736  0.020  1.736
 01X  CGB  HG'   single    0.930  0.020  1.080
 01X  OL   CF    single    1.399  0.020  1.399
 01X  CF   CH    single    1.510  0.020  1.510
 01X  CF   HF1   single    0.970  0.020  1.090
 01X  CF   HF2   single    0.970  0.020  1.090
 01X  CH   OH    double    1.200  0.020  1.200
 01X  N'   H2    single    0.890  0.020  1.040
 01X  CH   OXT   single    1.325  0.020  1.325
 01X  OXT  HXT   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
 01X  H2    N'   H'    105.72  3.000
 01X  H2    N'   CA'   108.93  3.000
 01X  H'    N'   CA'   109.08  3.000
 01X  HA'2  CA'  HA'1  106.47  3.000
 01X  HA'2  CA'  CB'   108.25  3.000
 01X  HA'1  CA'  CB'   109.94  3.000
 01X  HA'2  CA'  N'    113.66  3.000
 01X  HA'1  CA'  N'    108.16  3.000
 01X  CB'   CA'  N'    110.26  3.000
 01X  CGB   CB'  CG'   118.68  3.000
 01X  CGB   CB'  CA'   119.94  3.000
 01X  CG'   CB'  CA'   121.35  3.000
 01X  OL    CG'  CD'   123.87  3.000
 01X  OL    CG'  CB'   115.94  3.000
 01X  CD'   CG'  CB'   120.19  3.000
 01X  HD'   CD'  CE'   118.02  3.000
 01X  HD'   CD'  CG'   121.59  3.000
 01X  CE'   CD'  CG'   120.40  3.000
 01X  HE'   CE'  CDB   120.99  3.000
 01X  HE'   CE'  CD'   119.63  3.000
 01X  CDB   CE'  CD'   119.38  3.000
 01X  CL    CDB  CGB   119.52  3.000
 01X  CL    CDB  CE'   119.97  3.000
 01X  CGB   CDB  CE'   120.52  3.000
 01X  HG'   CGB  CDB   120.07  3.000
 01X  HG'   CGB  CB'   119.09  3.000
 01X  CDB   CGB  CB'   120.84  3.000
 01X  CF    OL   CG'   118.69  3.000
 01X  HF2   CF   HF1   107.20  3.000
 01X  HF2   CF   CH    108.93  3.000
 01X  HF1   CF   CH    108.65  3.000
 01X  HF2   CF   OL    112.24  3.000
 01X  HF1   CF   OL    112.14  3.000
 01X  CH    CF   OL    107.61  3.000
 01X  OXT   CH   OH    124.84  3.000
 01X  OXT   CH   CF    110.03  3.000
 01X  OH    CH   CF    125.14  3.000
 01X  HXT   OXT  CH    110.42  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
 01X  CONST_01  CE'  CD'  CG'  CB'     0.00   0.0  0
 01X  CONST_02  CE'  CDB  CGB  CB'     0.00   0.0  0
 01X  CONST_03  CDB  CGB  CB'  CG'     0.00   0.0  0
 01X  CONST_04  CDB  CE'  CD'  CG'     0.00   0.0  0
 01X  CONST_05  CGB  CB'  CG'  CD'     0.00   0.0  0
 01X  CONST_06  CGB  CDB  CE'  CD'     0.00   0.0  0
 01X  CONST_07  CD'  CG'  CB'  CA'   180.00   0.0  0
 01X  CONST_08  CDB  CGB  CB'  CA'   180.00   0.0  0
 01X  CONST_09  CL   CDB  CGB  CB'   180.00   0.0  0
 01X  CONST_10  CL   CDB  CE'  CD'   180.00   0.0  0
 01X  CONST_11  OL   CG'  CD'  CE'   180.00   0.0  0
 01X  CONST_12  OL   CG'  CB'  CGB   180.00   0.0  0
 01X  CONST_13  HD'  CD'  CG'  CB'   180.00   0.0  0
 01X  CONST_14  HG'  CGB  CB'  CG'   180.00   0.0  0
 01X  CONST_15  HE'  CE'  CD'  CG'   180.00   0.0  0
 01X  CONST_16  HXT  OXT  CH   CF    180.00   0.0  0
 01X  Var_01    CG'  CB'  CA'  N'     77.59  30.0  2
 01X  Var_02    CH   CF   OL   CG'  -174.73  30.0  3
 01X  Var_03    H'   N'   CA'  CB'    71.10  30.0  3
 01X  Var_04    OH   CH   CF   OL      2.16  30.0  3

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
 01X  plan-1  CA'  0.020
 01X  plan-1  CB'  0.020
 01X  plan-1  CG'  0.020
 01X  plan-1  CD'  0.020
 01X  plan-1  CE'  0.020
 01X  plan-1  CDB  0.020
 01X  plan-1  CGB  0.020
 01X  plan-1  CL   0.020
 01X  plan-1  OL   0.020
 01X  plan-1  HD'  0.020
 01X  plan-1  HE'  0.020
 01X  plan-1  HG'  0.020
 01X  plan-2  CF   0.020
 01X  plan-2  CH   0.020
 01X  plan-2  OH   0.020
 01X  plan-2  OXT  0.020
 01X  plan-2  HXT  0.020

