# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:46:25 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: methyl (3S)-3-[(tert-butoxycarbonyl)amino]-4-oxopentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C[C@H](NC(=O)OC(C)(C)C)C(C)=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
 DZE  DZE  'methyl (3S)-3-[(tert-butoxycarbonyl)amino]-4-oxopentanoate'  ligand  36  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZE
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
 DZE  C15   C  CH3   0  -0.672  -4.1494   0.4686   0.3601
 DZE  C14   C  CT    0   0.188  -3.3701  -0.7944   0.0130
 DZE  C16   C  CH3   0  -0.671  -3.3445  -1.7913   1.1650
 DZE  C17   C  CH3   0  -0.659  -3.9783  -1.4506  -1.2203
 DZE  O13   O  O2    0  -0.502  -2.0195  -0.4758  -0.4203
 DZE  C11   C  C     0   0.764  -1.1392   0.1390   0.3638
 DZE  O12   O  O     0  -0.515  -1.3411   0.5272   1.4957
 DZE  N10   N  NH1   0  -0.647   0.0518   0.2496  -0.2726
 DZE  C4    C  CH1   0  -0.209   1.1083   1.0581   0.2605
 DZE  C2    C  C     0   0.415   0.9331   2.5354  -0.0899
 DZE  C1    C  CH3   0  -0.796   1.9994   3.4729   0.3995
 DZE  O3    O  O     0  -0.382  -0.0276   2.9126  -0.7153
 DZE  C5    C  CH2   0  -0.612   2.4577   0.5259  -0.2106
 DZE  C6    C  C     0   0.621   2.7201  -0.8626   0.3190
 DZE  O8    O  O2    0  -0.450   3.5174  -1.5474  -0.4848
 DZE  C9    C  CH3   0  -0.427   3.9069  -2.8579  -0.0680
 DZE  O7    O  O     0  -0.444   2.2921  -1.2877   1.3615
 DZE  H15   H  HCH3  0   0.247  -3.8018   0.9391   1.2768
 DZE  H15A  H  HCH3  0   0.235  -4.0910   1.1964  -0.4506
 DZE  H15B  H  HCH3  0   0.234  -5.2007   0.2120   0.4956
 DZE  H16   H  HCH3  0   0.235  -4.3632  -2.1099   1.3882
 DZE  H16A  H  HCH3  0   0.235  -2.7742  -2.6815   0.8938
 DZE  H16B  H  HCH3  0   0.246  -2.9226  -1.3697   2.0743
 DZE  H17   H  HCH3  0   0.238  -3.9976  -0.7645  -2.0685
 DZE  H17A  H  HCH3  0   0.238  -3.4214  -2.3431  -1.5095
 DZE  H17B  H  HCH3  0   0.231  -5.0042  -1.7519  -1.0103
 DZE  HN10  H  HNH1  0   0.397   0.0775   0.0437  -1.2600
 DZE  H4    H  HCH1  0   0.298   1.0794   0.9977   1.3523
 DZE  H1    H  HCH3  0   0.280   2.8221   3.4963  -0.3194
 DZE  H1A   H  HCH3  0   0.277   1.6082   4.4840   0.4922
 DZE  H1B   H  HCH3  0   0.264   2.4170   3.1563   1.3553
 DZE  H5    H  HCH2  0   0.291   2.5289   0.5429  -1.3001
 DZE  H5A   H  HCH2  0   0.315   3.2678   1.1605   0.1590
 DZE  H9    H  HCH3  0   0.254   4.5745  -3.2291  -0.8397
 DZE  H9A   H  HCH3  0   0.241   4.4341  -2.8332   0.8853
 DZE  H9B   H  HCH3  0   0.241   3.0450  -3.5193   0.0138

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
 DZE  C15  C14   single  1.524  0.020  1.524
 DZE  C15  H15   single  0.970  0.020  1.090
 DZE  C15  H15A  single  0.970  0.020  1.090
 DZE  C15  H15B  single  0.970  0.020  1.090
 DZE  C17  C14   single  1.524  0.020  1.524
 DZE  C14  C16   single  1.524  0.020  1.524
 DZE  C14  O13   single  1.454  0.020  1.454
 DZE  C16  H16   single  0.970  0.020  1.090
 DZE  C16  H16A  single  0.970  0.020  1.090
 DZE  C16  H16B  single  0.970  0.020  1.090
 DZE  C17  H17   single  0.970  0.020  1.090
 DZE  C17  H17A  single  0.970  0.020  1.090
 DZE  C17  H17B  single  0.970  0.020  1.090
 DZE  O13  C11   single  1.330  0.020  1.330
 DZE  O12  C11   double  1.213  0.020  1.213
 DZE  C11  N10   single  1.355  0.020  1.355
 DZE  N10  C4    single  1.433  0.020  1.433
 DZE  N10  HN10  single  0.890  0.020  1.040
 DZE  C4   C5    single  1.525  0.020  1.525
 DZE  C4   C2    single  1.528  0.020  1.528
 DZE  C4   H4    single  0.970  0.020  1.090
 DZE  C1   C2    single  1.502  0.020  1.502
 DZE  C2   O3    double  1.207  0.020  1.207
 DZE  C1   H1    single  0.970  0.020  1.090
 DZE  C1   H1A   single  0.970  0.020  1.090
 DZE  C1   H1B   single  0.970  0.020  1.090
 DZE  C6   C5    single  1.509  0.020  1.509
 DZE  C5   H5    single  0.970  0.020  1.090
 DZE  C5   H5A   single  0.970  0.020  1.090
 DZE  O7   C6    double  1.204  0.020  1.204
 DZE  C6   O8    single  1.323  0.020  1.323
 DZE  O8   C9    single  1.429  0.020  1.429
 DZE  C9   H9    single  0.970  0.020  1.090
 DZE  C9   H9A   single  0.970  0.020  1.090
 DZE  C9   H9B   single  0.970  0.020  1.090

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
 DZE  H15B  C15  H15A  107.50  3.000
 DZE  H15B  C15  H15   107.76  3.000
 DZE  H15A  C15  H15   108.70  3.000
 DZE  H15B  C15  C14   109.04  3.000
 DZE  H15A  C15  C14   110.87  3.000
 DZE  H15   C15  C14   112.78  3.000
 DZE  O13   C14  C17   102.94  3.000
 DZE  O13   C14  C16   110.68  3.000
 DZE  C17   C14  C16   109.69  3.000
 DZE  O13   C14  C15   111.18  3.000
 DZE  C16   C14  C15   112.25  3.000
 DZE  C17   C14  C15   109.70  3.000
 DZE  H16B  C16  H16A  108.74  3.000
 DZE  H16B  C16  H16   107.73  3.000
 DZE  H16A  C16  H16   107.50  3.000
 DZE  H16B  C16  C14   112.65  3.000
 DZE  H16A  C16  C14   110.77  3.000
 DZE  H16   C16  C14   109.28  3.000
 DZE  H17B  C17  H17A  107.79  3.000
 DZE  H17B  C17  H17   107.88  3.000
 DZE  H17A  C17  H17   108.50  3.000
 DZE  H17B  C17  C14   109.81  3.000
 DZE  H17A  C17  C14   111.29  3.000
 DZE  H17   C17  C14   111.44  3.000
 DZE  C11   O13  C14   122.73  3.000
 DZE  N10   C11  O12   123.94  3.000
 DZE  N10   C11  O13   110.04  3.000
 DZE  O12   C11  O13   126.00  3.000
 DZE  HN10  N10  C4    117.41  3.000
 DZE  HN10  N10  C11   117.74  3.000
 DZE  C4    N10  C11   121.29  3.000
 DZE  H4    C4   C5    108.20  3.000
 DZE  H4    C4   C2    106.21  3.000
 DZE  C5    C4   C2    111.58  3.000
 DZE  H4    C4   N10   108.70  3.000
 DZE  C2    C4   N10   112.05  3.000
 DZE  C5    C4   N10   109.91  3.000
 DZE  O3    C2   C1    122.62  3.000
 DZE  O3    C2   C4    120.81  3.000
 DZE  C1    C2   C4    116.57  3.000
 DZE  H1B   C1   H1A   109.45  3.000
 DZE  H1B   C1   H1    107.14  3.000
 DZE  H1A   C1   H1    107.87  3.000
 DZE  H1B   C1   C2    112.11  3.000
 DZE  H1A   C1   C2    110.64  3.000
 DZE  H1    C1   C2    109.48  3.000
 DZE  H5A   C5   H5    106.25  3.000
 DZE  H5A   C5   C6    106.65  3.000
 DZE  H5    C5   C6    110.68  3.000
 DZE  H5A   C5   C4    110.40  3.000
 DZE  H5    C5   C4    111.13  3.000
 DZE  C6    C5   C4    111.50  3.000
 DZE  O7    C6   O8    123.87  3.000
 DZE  O8    C6   C5    111.58  3.000
 DZE  O7    C6   C5    124.52  3.000
 DZE  C9    O8   C6    117.49  3.000
 DZE  H9B   C9   H9A   109.31  3.000
 DZE  H9B   C9   H9    109.40  3.000
 DZE  H9A   C9   H9    109.39  3.000
 DZE  H9B   C9   O8    111.28  3.000
 DZE  H9A   C9   O8    111.48  3.000
 DZE  H9    C9   O8    105.89  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
 DZE  Var_01  O12  C11  O13  C14    -1.47  30.0  3
 DZE  Var_02  C4   N10  C11  O13   169.87  30.0  2
 DZE  Var_03  O7   C6   C5   C4    -29.63  30.0  1
 DZE  Var_04  H17  C17  C14  C15    57.07  30.0  3
 DZE  Var_05  H16  C16  C14  C15    62.22  30.0  3
 DZE  Var_06  H15  C15  C14  C16    53.62  30.0  3
 DZE  Var_07  H1   C1   C2   C4     85.65  30.0  3
 DZE  Var_08  H9   C9   O8   C6   -178.24  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
 DZE  chir_01  C4  N10  C5  C2  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
 DZE  plan-1  C4   0.020
 DZE  plan-1  C2   0.020
 DZE  plan-1  C1   0.020
 DZE  plan-1  O3   0.020
 DZE  plan-2  O13  0.020
 DZE  plan-2  C11  0.020
 DZE  plan-2  O12  0.020
 DZE  plan-2  N10  0.020
 DZE  plan-3  C5   0.020
 DZE  plan-3  C6   0.020
 DZE  plan-3  O8   0.020
 DZE  plan-3  O7   0.020

