# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:21:29 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N~6~-[(1R)-2-{[(1R)-1-carboxy-2-methylprop-2-en-1-yl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxolysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCCC(N)C(O)=O)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
 CDH  CDH  N~6~-[(1R)-2-{[(1R)-1-carboxy-2-methylprop-2-en-1-yl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxolysine  ligand  47  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CDH
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
 CDH  O43   O  O     0  -0.425   1.9701  -3.9514  -0.7875
 CDH  C31   C  C     0   0.559   3.1514  -3.7282  -0.8324
 CDH  O42   O  OH1   0  -0.578   4.0841  -4.5458  -0.3793
 CDH  C30   C  CH1   0  -0.307   3.7180  -2.4754  -1.4814
 CDH  C32   C  C     0   0.181   2.7878  -1.2940  -1.3133
 CDH  C37   C  C2    0  -0.568   2.2482  -0.7187  -2.3826
 CDH  C33   C  CH3   0  -0.723   2.5727  -0.7897   0.0816
 CDH  N29   N  NH1   0  -0.637   5.0513  -2.1663  -1.0227
 CDH  C13   C  C     0   0.558   5.9883  -1.6573  -1.8432
 CDH  O18   O  O     0  -0.460   5.8460  -1.5554  -3.0479
 CDH  C12   C  CH1   0  -0.196   7.2366  -1.1551  -1.1247
 CDH  C16   C  CH2   0  -0.580   6.8807   0.0173  -0.1999
 CDH  S     S  S2    0  -0.221   6.1154   1.4236  -1.0576
 CDH  N30   N  NH1   0  -0.636   8.2280  -0.8004  -2.0968
 CDH  C25   C  C     0   0.573   9.5506  -0.8685  -1.8506
 CDH  O25   O  O     0  -0.496   9.9989  -1.1971  -0.7623
 CDH  C24   C  CH2   0  -0.580  10.4276  -0.5403  -3.0396
 CDH  C23   C  CH2   0  -0.439  11.8552  -0.1757  -2.6640
 CDH  C22   C  CH2   0  -0.423  12.6952   0.0846  -3.9098
 CDH  C21   C  CH1   0  -0.225  14.1703   0.3993  -3.6238
 CDH  N31   N  NH2   0  -0.782  14.8320  -0.7277  -3.0096
 CDH  C20   C  C     0   0.516  14.2945   1.6891  -2.8224
 CDH  O20   O  O     0  -0.441  14.7256   1.7617  -1.6988
 CDH  O21   O  OH1   0  -0.593  13.8642   2.7453  -3.5048
 CDH  H42   H  HOH1  0   0.490   3.6775  -5.3425  -0.0043
 CDH  H30   H  HCH1  0   0.328   3.7874  -2.7161  -2.5472
 CDH  H371  H  H     0   0.246   2.4296  -1.0888  -3.3837
 CDH  H372  H  H     0   0.245   1.5984   0.1424  -2.2922
 CDH  H331  H  HCH3  0   0.251   2.1500  -1.5604   0.7290
 CDH  H332  H  HCH3  0   0.257   1.8949   0.0621   0.0909
 CDH  H333  H  HCH3  0   0.233   3.5090  -0.4682   0.5445
 CDH  H29   H  HNH1  0   0.415   5.2547  -2.2373  -0.0378
 CDH  H121  H  HCH1  0   0.308   7.6296  -1.9594  -0.4946
 CDH  H161  H  HCH2  0   0.284   6.2445  -0.3032   0.6253
 CDH  H162  H  HCH2  0   0.310   7.7961   0.4045   0.2458
 CDH  HS    H  HSH1  0   0.212   4.8949   0.8963  -1.2281
 CDH  H30N  H  HNH1  0   0.401   7.9052  -0.5084  -3.0058
 CDH  H241  H  HCH2  0   0.259   9.9698   0.2638  -3.6221
 CDH  H242  H  HCH2  0   0.275  10.4294  -1.4186  -3.6949
 CDH  H231  H  HCH2  0   0.231  12.2912  -0.9888  -2.0806
 CDH  H232  H  HCH2  0   0.234  11.8481   0.7066  -2.0172
 CDH  H221  H  HCH2  0   0.242  12.6761  -0.7998  -4.5513
 CDH  H222  H  HCH2  0   0.238  12.2539   0.8970  -4.4913
 CDH  H211  H  HCH1  0   0.284  14.6501   0.5838  -4.5901
 CDH  H311  H  HNH2  0   0.347  14.5315  -0.8396  -2.0494
 CDH  H312  H  HNH2  0   0.355  15.8303  -0.5677  -2.9691
 CDH  H21   H  HOH1  0   0.480  13.9405   3.5441  -2.9619

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
 CDH  O43  C31   double  1.203  0.020  1.203
 CDH  C31  O42   single  1.320  0.020  1.320
 CDH  C31  C30   single  1.520  0.020  1.520
 CDH  O42  H42   single  0.850  0.020  0.980
 CDH  C30  C32   single  1.513  0.020  1.513
 CDH  C30  N29   single  1.443  0.020  1.443
 CDH  C30  H30   single  0.970  0.020  1.090
 CDH  C32  C37   double  1.329  0.020  1.329
 CDH  C32  C33   single  1.499  0.020  1.499
 CDH  C37  H371  single  0.930  0.020  1.080
 CDH  C37  H372  single  0.930  0.020  1.080
 CDH  C33  H331  single  0.970  0.020  1.090
 CDH  C33  H332  single  0.970  0.020  1.090
 CDH  C33  H333  single  0.970  0.020  1.090
 CDH  N29  C13   single  1.345  0.020  1.345
 CDH  N29  H29   single  0.860  0.020  1.020
 CDH  C13  O18   double  1.217  0.020  1.217
 CDH  C13  C12   single  1.525  0.020  1.525
 CDH  C12  C16   single  1.535  0.020  1.535
 CDH  C12  N30   single  1.433  0.020  1.433
 CDH  C12  H121  single  0.970  0.020  1.090
 CDH  C16  S     single  1.816  0.020  1.816
 CDH  C16  H161  single  0.970  0.020  1.090
 CDH  C16  H162  single  0.970  0.020  1.090
 CDH  S    HS    single  1.200  0.020  1.300
 CDH  N30  C25   single  1.347  0.020  1.347
 CDH  N30  H30N  single  0.860  0.020  1.020
 CDH  C25  O25   double  1.222  0.020  1.222
 CDH  C25  C24   single  1.513  0.020  1.513
 CDH  C24  C23   single  1.521  0.020  1.521
 CDH  C24  H241  single  0.970  0.020  1.090
 CDH  C24  H242  single  0.970  0.020  1.090
 CDH  C23  C22   single  1.525  0.020  1.525
 CDH  C23  H231  single  0.970  0.020  1.090
 CDH  C23  H232  single  0.970  0.020  1.090
 CDH  C22  C21   single  1.535  0.020  1.535
 CDH  C22  H221  single  0.970  0.020  1.090
 CDH  C22  H222  single  0.970  0.020  1.090
 CDH  C21  N31   single  1.444  0.020  1.444
 CDH  C21  C20   single  1.524  0.020  1.524
 CDH  C21  H211  single  0.970  0.020  1.090
 CDH  N31  H311  single  0.890  0.020  1.040
 CDH  N31  H312  single  0.890  0.020  1.040
 CDH  C20  O20   double  1.206  0.020  1.206
 CDH  C20  O21   single  1.329  0.020  1.329
 CDH  O21  H21   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
 CDH  C30   C31  O42   113.17  3.000
 CDH  C30   C31  O43   122.32  3.000
 CDH  O42   C31  O43   124.47  3.000
 CDH  H42   O42  C31   110.19  3.000
 CDH  H30   C30  N29   107.33  3.000
 CDH  H30   C30  C32   108.59  3.000
 CDH  N29   C30  C32   111.43  3.000
 CDH  H30   C30  C31   104.95  3.000
 CDH  N29   C30  C31   112.64  3.000
 CDH  C32   C30  C31   111.52  3.000
 CDH  C33   C32  C37   123.02  3.000
 CDH  C33   C32  C30   117.03  3.000
 CDH  C37   C32  C30   119.89  3.000
 CDH  H372  C37  H371  116.72  3.000
 CDH  H372  C37  C32   121.40  3.000
 CDH  H371  C37  C32   121.88  3.000
 CDH  H333  C33  H332  107.43  3.000
 CDH  H333  C33  H331  106.76  3.000
 CDH  H332  C33  H331  107.83  3.000
 CDH  H333  C33  C32   111.73  3.000
 CDH  H332  C33  C32   111.14  3.000
 CDH  H331  C33  C32   111.71  3.000
 CDH  H29   N29  C13   118.80  3.000
 CDH  H29   N29  C30   118.80  3.000
 CDH  C13   N29  C30   122.04  3.000
 CDH  C12   C13  O18   122.29  3.000
 CDH  C12   C13  N29   114.03  3.000
 CDH  O18   C13  N29   123.62  3.000
 CDH  H121  C12  N30   108.90  3.000
 CDH  H121  C12  C16   107.31  3.000
 CDH  N30   C12  C16   112.34  3.000
 CDH  H121  C12  C13   108.85  3.000
 CDH  N30   C12  C13   109.15  3.000
 CDH  C16   C12  C13   110.21  3.000
 CDH  H162  C16  H161  106.57  3.000
 CDH  H162  C16  S     105.79  3.000
 CDH  H161  C16  S     109.83  3.000
 CDH  H162  C16  C12   108.85  3.000
 CDH  H161  C16  C12   111.52  3.000
 CDH  S     C16  C12   113.86  3.000
 CDH  HS    S    C16    98.00  3.000
 CDH  H30N  N30  C25   119.60  3.000
 CDH  H30N  N30  C12   117.52  3.000
 CDH  C25   N30  C12   122.87  3.000
 CDH  C24   C25  O25   123.05  3.000
 CDH  C24   C25  N30   114.49  3.000
 CDH  O25   C25  N30   122.45  3.000
 CDH  H242  C24  H241  105.76  3.000
 CDH  H242  C24  C23   109.77  3.000
 CDH  H241  C24  C23   110.39  3.000
 CDH  H242  C24  C25   107.27  3.000
 CDH  H241  C24  C25   109.60  3.000
 CDH  C23   C24  C25   113.70  3.000
 CDH  H232  C23  H231  106.70  3.000
 CDH  H232  C23  C22   110.42  3.000
 CDH  H231  C23  C22   110.11  3.000
 CDH  H232  C23  C24   109.47  3.000
 CDH  H231  C23  C24   109.17  3.000
 CDH  C22   C23  C24   110.87  3.000
 CDH  H222  C22  H221  106.40  3.000
 CDH  H222  C22  C21   109.57  3.000
 CDH  H221  C22  C21   106.98  3.000
 CDH  H222  C22  C23   109.84  3.000
 CDH  H221  C22  C23   109.38  3.000
 CDH  C21   C22  C23   114.34  3.000
 CDH  H211  C21  C20   106.62  3.000
 CDH  H211  C21  N31   107.83  3.000
 CDH  C20   C21  N31   113.55  3.000
 CDH  H211  C21  C22   106.93  3.000
 CDH  C20   C21  C22   110.48  3.000
 CDH  N31   C21  C22   111.07  3.000
 CDH  H312  N31  H311  105.81  3.000
 CDH  H312  N31  C21   110.23  3.000
 CDH  H311  N31  C21   110.72  3.000
 CDH  O21   C20  O20   123.12  3.000
 CDH  O21   C20  C21   112.11  3.000
 CDH  O20   C20  C21   124.77  3.000
 CDH  H21   O21  C20   110.00  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
 CDH  CONST_01  O18   C13  N29  C30     0.00   0.0  0
 CDH  CONST_02  C12   C13  N29  C30   180.00   0.0  0
 CDH  CONST_03  O25   C25  N30  C12     0.00   0.0  0
 CDH  CONST_04  C24   C25  N30  C12   180.00   0.0  0
 CDH  CONST_05  H29   N29  C13  O18   180.00   0.0  0
 CDH  CONST_06  H30N  N30  C25  O25   180.00   0.0  0
 CDH  CONST_07  H42   O42  C31  O43     0.00   0.0  0
 CDH  CONST_08  H21   O21  C20  C21   180.00   0.0  0
 CDH  Var_01    C23   C24  C25  N30   161.08  30.0  3
 CDH  Var_02    C22   C23  C24  C25   177.61  30.0  3
 CDH  Var_03    C21   C22  C23  C24  -177.42  30.0  3
 CDH  Var_04    H371  C37  C32  C30     1.87   0.0  2
 CDH  Var_05    H331  C33  C32  C30   -59.88  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
 CDH  chir_01  C30  C31  C32  N29  negativ
 CDH  chir_02  C12  N30  C13  C16  positiv
 CDH  chir_03  C21  C22  N31  C20  positiv

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
 CDH  plan-1  C30   0.020
 CDH  plan-1  N29   0.020
 CDH  plan-1  C13   0.020
 CDH  plan-1  O18   0.020
 CDH  plan-1  C12   0.020
 CDH  plan-1  H29   0.020
 CDH  plan-2  C12   0.020
 CDH  plan-2  N30   0.020
 CDH  plan-2  C25   0.020
 CDH  plan-2  O25   0.020
 CDH  plan-2  C24   0.020
 CDH  plan-2  H30N  0.020
 CDH  plan-3  O43   0.020
 CDH  plan-3  C31   0.020
 CDH  plan-3  O42   0.020
 CDH  plan-3  C30   0.020
 CDH  plan-3  H42   0.020
 CDH  plan-4  C21   0.020
 CDH  plan-4  C20   0.020
 CDH  plan-4  O20   0.020
 CDH  plan-4  O21   0.020
 CDH  plan-4  H21   0.020
 CDH  plan-5  C30   0.020
 CDH  plan-5  C32   0.020
 CDH  plan-5  C37   0.020
 CDH  plan-5  C33   0.020
 CDH  plan-5  H371  0.020
 CDH  plan-5  H372  0.020

