# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 01:05:06 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3S,6R)-6-[(1S)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-3-chloro-3,4,5,6-tetrahydropyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C(=O)N[C@H](C=O)[C@H]1CC[C@H](Cl)C(=N1)C(O)=O)c2ccccc2
#
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
 LOR  LOR  '(3S,6R)-6-[(1S)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-3-chloro-3,4,5,6-tetrahydropyridine-2-carboxylic acid'  ligand  42  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LOR
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
 LOR  CL    CL  CL    0  -0.122   4.5905  -1.2163  -0.3341
 LOR  C1    C   C1    0   0.163  -0.1462   3.6755   0.1344
 LOR  O1    O   O     0  -0.361  -0.6890   4.2509  -0.7702
 LOR  C2    C   CH1   0  -0.148  -0.1256   2.1686   0.2885
 LOR  N2    N   NH1   0  -0.641  -1.2247   1.5424  -0.3896
 LOR  C3    C   CH1   0  -0.139   1.2109   1.6310  -0.2736
 LOR  C4    C   CH2   0  -0.492   2.4111   2.1079   0.5335
 LOR  C5    C   CH2   0  -0.435   3.6330   1.2871   0.1482
 LOR  C6    C   CH1   0  -0.352   3.3671  -0.1677   0.4772
 LOR  C7    C   C     0   0.181   2.0004  -0.5836   0.0036
 LOR  C8    C   C     0   0.524   1.6589  -2.0480   0.0627
 LOR  N8    N   N     0  -0.333   1.0767   0.1944  -0.3508
 LOR  C21   C   C     0   0.550  -2.4850   1.7084   0.0536
 LOR  O21   O   O     0  -0.476  -2.7788   2.5367   0.8985
 LOR  C22   C   CH1   0  -0.301  -3.5067   0.7620  -0.5775
 LOR  N22   N   NH2   0  -0.764  -4.8389   1.1165  -0.1384
 LOR  C23   C   CR6   0   0.104  -3.0934  -0.6764  -0.3121
 LOR  C24   C   CR16  0  -0.288  -2.9276  -1.1364   0.9941
 LOR  C25   C   CR16  0  -0.236  -2.5630  -2.4509   1.2376
 LOR  C26   C   CR16  0  -0.273  -2.3665  -3.3299   0.1776
 LOR  C27   C   CR16  0  -0.236  -2.5344  -2.8827  -1.1241
 LOR  C28   C   CR16  0  -0.307  -2.8947  -1.5619  -1.3649
 LOR  O81   O   O     0  -0.421   2.0832  -2.7623   0.9341
 LOR  O82   O   OH1   0  -0.562   0.8321  -2.4149  -0.8907
 LOR  H1    H   H     0   0.218   0.4065   4.2221   0.9172
 LOR  H2    H   HCH1  0   0.281  -0.1478   1.9495   1.3646
 LOR  HN2   H   HNH1  0   0.411  -1.0014   0.7035  -0.9083
 LOR  H3    H   HCH1  0   0.296   1.3033   1.9753  -1.3116
 LOR  H4    H   HCH2  0   0.277   2.6016   3.1650   0.3437
 LOR  H4A   H   HCH2  0   0.257   2.2088   2.0031   1.6041
 LOR  H5    H   HCH2  0   0.259   3.8236   1.3929  -0.9221
 LOR  H5A   H   HCH2  0   0.282   4.5209   1.6309   0.6768
 LOR  H6    H   HCH1  0   0.336   3.4665  -0.3578   1.5469
 LOR  H22   H   HCH1  0   0.283  -3.4618   0.9222  -1.6601
 LOR  HN22  H   HNH2  0   0.355  -5.5024   0.4811  -0.5631
 LOR  HN2A  H   HNH2  0   0.348  -4.9282   0.9907   0.8626
 LOR  H24   H   HCR6  0   0.250  -3.0750  -0.4647   1.8330
 LOR  H25   H   HCR6  0   0.256  -2.4310  -2.7926   2.2561
 LOR  H26   H   HCR6  0   0.259  -2.0864  -4.3577   0.3699
 LOR  H27   H   HCR6  0   0.256  -2.3870  -3.5600  -1.9555
 LOR  H28   H   HCR6  0   0.255  -3.0224  -1.2175  -2.3847
 LOR  HO82  H   HOH1  0   0.487   0.5651  -3.3388  -0.7714

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
 LOR  CL   C6    single    1.804  0.020  1.804
 LOR  O1   C1    double    1.202  0.020  1.202
 LOR  C1   C2    single    1.515  0.020  1.515
 LOR  C1   H1    single    0.930  0.020  1.080
 LOR  C3   C2    single    1.546  0.020  1.546
 LOR  C2   N2    single    1.435  0.020  1.435
 LOR  C2   H2    single    0.970  0.020  1.090
 LOR  N2   C21   single    1.346  0.020  1.346
 LOR  N2   HN2   single    0.890  0.020  1.040
 LOR  N8   C3    single    1.445  0.020  1.445
 LOR  C3   C4    single    1.523  0.020  1.523
 LOR  C3   H3    single    0.970  0.020  1.090
 LOR  C5   C4    single    1.522  0.020  1.522
 LOR  C4   H4    single    0.970  0.020  1.090
 LOR  C4   H4A   single    0.970  0.020  1.090
 LOR  C6   C5    single    1.515  0.020  1.515
 LOR  C5   H5    single    0.970  0.020  1.090
 LOR  C5   H5A   single    0.970  0.020  1.090
 LOR  C7   C6    single    1.505  0.020  1.505
 LOR  C6   H6    single    0.970  0.020  1.090
 LOR  C8   C7    single    1.505  0.020  1.505
 LOR  C7   N8    double    1.259  0.020  1.259
 LOR  O81  C8    double    1.204  0.020  1.204
 LOR  C8   O82   single    1.314  0.020  1.314
 LOR  C21  C22   single    1.529  0.020  1.529
 LOR  C21  O21   double    1.219  0.020  1.219
 LOR  C23  C22   single    1.520  0.020  1.520
 LOR  C22  N22   single    1.447  0.020  1.447
 LOR  C22  H22   single    0.970  0.020  1.090
 LOR  N22  HN22  single    0.890  0.020  1.040
 LOR  N22  HN2A  single    0.890  0.020  1.040
 LOR  C24  C23   aromatic  1.395  0.020  1.395
 LOR  C23  C28   aromatic  1.390  0.020  1.390
 LOR  C25  C24   aromatic  1.386  0.020  1.386
 LOR  C24  H24   single    0.930  0.020  1.080
 LOR  C25  C26   aromatic  1.391  0.020  1.391
 LOR  C25  H25   single    0.930  0.020  1.080
 LOR  C26  C27   aromatic  1.387  0.020  1.387
 LOR  C26  H26   single    0.930  0.020  1.080
 LOR  C27  C28   aromatic  1.390  0.020  1.390
 LOR  C27  H27   single    0.930  0.020  1.080
 LOR  C28  H28   single    0.930  0.020  1.080
 LOR  O82  HO82  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
 LOR  H1    C1   C2    114.45  3.000
 LOR  H1    C1   O1    121.55  3.000
 LOR  C2    C1   O1    123.98  3.000
 LOR  H2    C2   C3    107.72  3.000
 LOR  H2    C2   N2    111.13  3.000
 LOR  C3    C2   N2    109.78  3.000
 LOR  H2    C2   C1    107.32  3.000
 LOR  N2    C2   C1    112.06  3.000
 LOR  C3    C2   C1    108.69  3.000
 LOR  HN2   N2   C21   118.55  3.000
 LOR  HN2   N2   C2    115.79  3.000
 LOR  C21   N2   C2    120.50  3.000
 LOR  H3    C3   N8    105.62  3.000
 LOR  H3    C3   C4    109.67  3.000
 LOR  N8    C3   C4    114.38  3.000
 LOR  H3    C3   C2    107.91  3.000
 LOR  C4    C3   C2    112.31  3.000
 LOR  N8    C3   C2    106.54  3.000
 LOR  H4A   C4   H4    107.17  3.000
 LOR  H4A   C4   C5    110.15  3.000
 LOR  H4    C4   C5    109.79  3.000
 LOR  H4A   C4   C3    110.04  3.000
 LOR  H4    C4   C3    110.42  3.000
 LOR  C5    C4   C3    109.25  3.000
 LOR  H5A   C5   H5    107.62  3.000
 LOR  H5A   C5   C6    109.93  3.000
 LOR  H5    C5   C6    109.66  3.000
 LOR  H5A   C5   C4    111.19  3.000
 LOR  H5    C5   C4    109.64  3.000
 LOR  C6    C5   C4    108.79  3.000
 LOR  H6    C6   C7    110.06  3.000
 LOR  H6    C6   C5    111.37  3.000
 LOR  C7    C6   C5    110.88  3.000
 LOR  H6    C6   CL    106.13  3.000
 LOR  C7    C6   CL    108.28  3.000
 LOR  C5    C6   CL    109.97  3.000
 LOR  N8    C7   C8    116.49  3.000
 LOR  N8    C7   C6    125.75  3.000
 LOR  C8    C7   C6    117.55  3.000
 LOR  O82   C8   O81   125.53  3.000
 LOR  O82   C8   C7    112.70  3.000
 LOR  O81   C8   C7    121.72  3.000
 LOR  C7    N8   C3    122.10  3.000
 LOR  C22   C21  O21   123.06  3.000
 LOR  O21   C21  N2    122.51  3.000
 LOR  C22   C21  N2    114.42  3.000
 LOR  H22   C22  C23   107.45  3.000
 LOR  H22   C22  N22   107.57  3.000
 LOR  C23   C22  N22   115.42  3.000
 LOR  H22   C22  C21   106.86  3.000
 LOR  N22   C22  C21   109.78  3.000
 LOR  C23   C22  C21   109.39  3.000
 LOR  HN2A  N22  HN22  106.20  3.000
 LOR  HN2A  N22  C22   110.53  3.000
 LOR  HN22  N22  C22   108.81  3.000
 LOR  C28   C23  C24   118.83  3.000
 LOR  C28   C23  C22   120.63  3.000
 LOR  C24   C23  C22   120.53  3.000
 LOR  H24   C24  C25   119.17  3.000
 LOR  H24   C24  C23   120.25  3.000
 LOR  C25   C24  C23   120.58  3.000
 LOR  H25   C25  C26   120.03  3.000
 LOR  H25   C25  C24   119.79  3.000
 LOR  C26   C25  C24   120.18  3.000
 LOR  H26   C26  C27   120.29  3.000
 LOR  H26   C26  C25   120.07  3.000
 LOR  C27   C26  C25   119.64  3.000
 LOR  H27   C27  C28   119.78  3.000
 LOR  H27   C27  C26   120.19  3.000
 LOR  C28   C27  C26   120.03  3.000
 LOR  H28   C28  C27   119.70  3.000
 LOR  H28   C28  C23   119.57  3.000
 LOR  C27   C28  C23   120.74  3.000
 LOR  HO82  O82  C8    110.50  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
 LOR  CONST_01  C26   C25  C24  C23    0.00   0.0  0
 LOR  CONST_02  C26   C27  C28  C23    0.00   0.0  0
 LOR  CONST_03  C27   C28  C23  C24    0.00   0.0  0
 LOR  CONST_04  C27   C26  C25  C24    0.00   0.0  0
 LOR  CONST_05  C28   C23  C24  C25    0.00   0.0  0
 LOR  CONST_06  C28   C27  C26  C25    0.00   0.0  0
 LOR  CONST_07  C25   C24  C23  C22  180.00   0.0  0
 LOR  CONST_08  C27   C28  C23  C22  180.00   0.0  0
 LOR  CONST_09  H25   C25  C24  C23  180.00   0.0  0
 LOR  CONST_10  H27   C27  C28  C23  180.00   0.0  0
 LOR  CONST_11  H28   C28  C23  C24  180.00   0.0  0
 LOR  CONST_12  H26   C26  C25  C24  180.00   0.0  0
 LOR  CONST_13  H24   C24  C25  C26  180.00   0.0  0
 LOR  CONST_14  HO82  O82  C8   C7   180.00   0.0  0
 LOR  CONST_15  C22   C21  N2   C2   180.00   0.0  0
 LOR  CONST_16  O21   C21  N2   C2     0.00   0.0  0
 LOR  Var_01    C6    C7   N8   C3    -3.34  30.0  1
 LOR  Var_02    C6    C5   C4   C3   -61.24  30.0  1
 LOR  Var_03    O81   C8   C7   C6    33.75  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
 LOR  chir_01  C2   C1   C3   N2   positiv
 LOR  chir_02  C3   N8   C4   C2   positiv
 LOR  chir_03  C6   CL   C7   C5   positiv
 LOR  chir_04  C22  C21  C23  N22  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
 LOR  plan-1  C22   0.020
 LOR  plan-1  C23   0.020
 LOR  plan-1  C24   0.020
 LOR  plan-1  C25   0.020
 LOR  plan-1  C26   0.020
 LOR  plan-1  C27   0.020
 LOR  plan-1  C28   0.020
 LOR  plan-1  H24   0.020
 LOR  plan-1  H25   0.020
 LOR  plan-1  H26   0.020
 LOR  plan-1  H27   0.020
 LOR  plan-1  H28   0.020
 LOR  plan-2  C2    0.020
 LOR  plan-2  N2    0.020
 LOR  plan-2  C21   0.020
 LOR  plan-2  O21   0.020
 LOR  plan-2  C22   0.020
 LOR  plan-2  HN2   0.020
 LOR  plan-3  C7    0.020
 LOR  plan-3  C8    0.020
 LOR  plan-3  O81   0.020
 LOR  plan-3  O82   0.020
 LOR  plan-3  HO82  0.020
 LOR  plan-4  C1    0.020
 LOR  plan-4  O1    0.020
 LOR  plan-4  C2    0.020
 LOR  plan-4  H1    0.020

