# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 05:33:40 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: ethyl (4R)-4-amino-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CC[C@@H](N)C[C@@H]1CCNC1=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
 CEV  CEV  'ethyl (4R)-4-amino-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate'  ligand  36  16  .  2021-08-07  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CEV
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
 CEV  O1    O  O2    0  -0.461   4.2350  -0.2881  -0.1140
 CEV  C3    C  CH2   0  -0.180   5.5679   0.2262   0.0279
 CEV  C5    C  CH3   0  -0.688   6.5295  -0.8978  -0.2740
 CEV  N49   N  NH2   0  -0.779  -0.8748  -1.0311   0.7891
 CEV  C57   C  CH1   0  -0.102  -0.6306   0.0254  -0.1834
 CEV  C59   C  CH2   0  -0.400  -1.7876   1.0215  -0.1226
 CEV  C61   C  CH1   0  -0.399  -3.0631   0.6270  -0.8814
 CEV  C63   C  CH2   0  -0.429   0.7013   0.7615   0.0072
 CEV  C65   C  C     0   0.564  -3.4898  -0.8192  -0.6640
 CEV  O66   O  O     0  -0.502  -3.0826  -1.8008  -1.2628
 CEV  N69   N  NH1   0  -0.624  -4.4502  -0.8127   0.2781
 CEV  C71   C  CH2   0  -0.257  -4.8251   0.5024   0.7492
 CEV  C73   C  CH2   0  -0.473  -4.2740   1.4056  -0.3592
 CEV  C82   C  CH2   0  -0.591   1.8968  -0.1764  -0.0205
 CEV  C84   C  C     0   0.606   3.2177   0.5271   0.1360
 CEV  O88   O  O     0  -0.457   3.3573   1.6808   0.4604
 CEV  H3    H  HCH2  0   0.233   5.7155   1.0611  -0.6603
 CEV  H3A   H  HCH2  0   0.233   5.7152   0.5989   1.0437
 CEV  H5    H  HCH3  0   0.235   6.4020  -1.7298   0.4187
 CEV  H5A   H  HCH3  0   0.235   6.4086  -1.2698  -1.2914
 CEV  H5B   H  HCH3  0   0.238   7.5506  -0.5313  -0.1720
 CEV  HN4A  H  HNH2  0   0.333  -0.6516  -0.6947   1.7197
 CEV  H57   H  HCH1  0   0.227  -0.6181  -0.4453  -1.1726
 CEV  H59   H  HCH2  0   0.224  -2.0236   1.2056   0.9317
 CEV  H59A  H  HCH2  0   0.238  -1.4704   1.9857  -0.5286
 CEV  H61   H  HCH1  0   0.263  -2.8962   0.7853  -1.9492
 CEV  H63   H  HCH2  0   0.230   0.8070   1.5108  -0.7817
 CEV  H63A  H  HCH2  0   0.224   0.6760   1.3093   0.9552
 CEV  HN69  H  HNH1  0   0.390  -4.8588  -1.6609   0.6373
 CEV  H71   H  HCH2  0   0.250  -5.9064   0.5874   0.8569
 CEV  H71A  H  HCH2  0   0.230  -4.3771   0.7258   1.7220
 CEV  H73   H  HCH2  0   0.249  -4.0168   2.4007   0.0035
 CEV  H73A  H  HCH2  0   0.252  -5.0237   1.5188  -1.1447
 CEV  H82   H  HCH2  0   0.271   1.8271  -0.9146   0.7852
 CEV  H82A  H  HCH2  0   0.270   1.9124  -0.7542  -0.9498
 CEV  HN49  H  HNH2  0   0.346  -0.2693  -1.8236   0.6185

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
 CEV  C3   O1    single  1.436  0.020  1.436
 CEV  O1   C84   single  1.327  0.020  1.327
 CEV  C5   C3    single  1.510  0.020  1.510
 CEV  C3   H3    single  0.970  0.020  1.090
 CEV  C3   H3A   single  0.970  0.020  1.090
 CEV  C5   H5    single  0.970  0.020  1.090
 CEV  C5   H5A   single  0.970  0.020  1.090
 CEV  C5   H5B   single  0.970  0.020  1.090
 CEV  C57  N49   single  1.457  0.020  1.457
 CEV  N49  HN49  single  0.890  0.020  1.040
 CEV  N49  HN4A  single  0.890  0.020  1.040
 CEV  C59  C57   single  1.528  0.020  1.528
 CEV  C57  C63   single  1.534  0.020  1.534
 CEV  C57  H57   single  0.970  0.020  1.090
 CEV  C61  C59   single  1.536  0.020  1.536
 CEV  C59  H59   single  0.970  0.020  1.090
 CEV  C59  H59A  single  0.970  0.020  1.090
 CEV  C73  C61   single  1.531  0.020  1.531
 CEV  C65  C61   single  1.523  0.020  1.523
 CEV  C61  H61   single  0.970  0.020  1.090
 CEV  C82  C63   single  1.520  0.020  1.520
 CEV  C63  H63   single  0.970  0.020  1.090
 CEV  C63  H63A  single  0.970  0.020  1.090
 CEV  N69  C65   single  1.345  0.020  1.345
 CEV  C65  O66   double  1.220  0.020  1.220
 CEV  C71  N69   single  1.446  0.020  1.446
 CEV  N69  HN69  single  0.860  0.020  1.020
 CEV  C71  C73   single  1.532  0.020  1.532
 CEV  C71  H71   single  0.970  0.020  1.090
 CEV  C71  H71A  single  0.970  0.020  1.090
 CEV  C73  H73   single  0.970  0.020  1.090
 CEV  C73  H73A  single  0.970  0.020  1.090
 CEV  C84  C82   single  1.505  0.020  1.505
 CEV  C82  H82   single  0.970  0.020  1.090
 CEV  C82  H82A  single  0.970  0.020  1.090
 CEV  O88  C84   double  1.207  0.020  1.207

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
 CEV  C84   O1   C3    118.22  3.000
 CEV  H3A   C3   H3    107.88  3.000
 CEV  H3A   C3   C5    110.74  3.000
 CEV  H3    C3   C5    110.92  3.000
 CEV  H3A   C3   O1    109.85  3.000
 CEV  H3    C3   O1    109.70  3.000
 CEV  C5    C3   O1    107.75  3.000
 CEV  H5B   C5   H5A   107.82  3.000
 CEV  H5B   C5   H5    107.87  3.000
 CEV  H5A   C5   H5    108.65  3.000
 CEV  H5B   C5   C3    109.13  3.000
 CEV  H5A   C5   C3    111.72  3.000
 CEV  H5    C5   C3    111.51  3.000
 CEV  HN4A  N49  HN49  106.42  3.000
 CEV  HN4A  N49  C57   109.57  3.000
 CEV  HN49  N49  C57   110.81  3.000
 CEV  H57   C57  C63   107.97  3.000
 CEV  H57   C57  C59   108.95  3.000
 CEV  C63   C57  C59   109.86  3.000
 CEV  H57   C57  N49   107.04  3.000
 CEV  C63   C57  N49   114.25  3.000
 CEV  C59   C57  N49   108.62  3.000
 CEV  H59A  C59  H59   105.76  3.000
 CEV  H59A  C59  C61   106.50  3.000
 CEV  H59   C59  C61   109.85  3.000
 CEV  H59A  C59  C57   109.90  3.000
 CEV  H59   C59  C57   108.12  3.000
 CEV  C61   C59  C57   116.22  3.000
 CEV  H61   C61  C73   112.36  3.000
 CEV  H61   C61  C65   108.65  3.000
 CEV  C73   C61  C65   102.27  3.000
 CEV  H61   C61  C59   108.60  3.000
 CEV  C65   C61  C59   113.95  3.000
 CEV  C73   C61  C59   110.95  3.000
 CEV  H63A  C63  H63   106.50  3.000
 CEV  H63A  C63  C82   110.04  3.000
 CEV  H63   C63  C82   109.50  3.000
 CEV  H63A  C63  C57   109.12  3.000
 CEV  H63   C63  C57   108.86  3.000
 CEV  C82   C63  C57   112.62  3.000
 CEV  N69   C65  O66   125.87  3.000
 CEV  O66   C65  C61   126.90  3.000
 CEV  N69   C65  C61   107.18  3.000
 CEV  HN69  N69  C71   122.96  3.000
 CEV  HN69  N69  C65   122.35  3.000
 CEV  C71   N69  C65   114.67  3.000
 CEV  H71A  C71  H71   107.61  3.000
 CEV  H71A  C71  C73   112.06  3.000
 CEV  H71   C71  C73   112.48  3.000
 CEV  H71A  C71  N69   111.66  3.000
 CEV  H71   C71  N69   111.11  3.000
 CEV  C73   C71  N69   101.95  3.000
 CEV  H73A  C73  H73   107.87  3.000
 CEV  H73A  C73  C71   109.55  3.000
 CEV  H73   C73  C71   112.48  3.000
 CEV  H73A  C73  C61   110.50  3.000
 CEV  H73   C73  C61   113.02  3.000
 CEV  C71   C73  C61   103.38  3.000
 CEV  H82A  C82  H82   105.65  3.000
 CEV  H82A  C82  C84   108.82  3.000
 CEV  H82   C82  C84   107.13  3.000
 CEV  H82A  C82  C63   110.64  3.000
 CEV  H82   C82  C63   110.65  3.000
 CEV  C84   C82  C63   113.58  3.000
 CEV  O88   C84  C82   125.22  3.000
 CEV  O88   C84  O1    123.31  3.000
 CEV  C82   C84  O1    111.47  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
 CEV  CONST_01  C71   N69  C65  C61     0.00   0.0  0
 CEV  CONST_02  C71   N69  C65  O66   180.00   0.0  0
 CEV  CONST_03  HN69  N69  C65  C61   180.00   0.0  0
 CEV  Var_01    N69   C71  C73  C61   -29.76  30.0  1
 CEV  Var_02    C73   C71  N69  C65    17.70  30.0  1
 CEV  Var_03    C63   C82  C84  O1   -169.61  30.0  3
 CEV  Var_04    C82   C84  O1   C3   -178.37  30.0  3
 CEV  Var_05    C84   C82  C63  C57   178.80  30.0  1
 CEV  Var_06    H5    C5   C3   O1    -60.90  30.0  3
 CEV  Var_07    H3    C3   O1   C84   -60.64  30.0  1

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
 CEV  chir_01  C57  N49  C59  C63  negativ
 CEV  chir_02  C61  C59  C73  C65  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
 CEV  plan-1  C61   0.020
 CEV  plan-1  C65   0.020
 CEV  plan-1  O66   0.020
 CEV  plan-1  N69   0.020
 CEV  plan-1  C71   0.020
 CEV  plan-1  HN69  0.020
 CEV  plan-2  O1    0.020
 CEV  plan-2  C82   0.020
 CEV  plan-2  C84   0.020
 CEV  plan-2  O88   0.020

