# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:44:39 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: (2S)-2-amino-4-(L-serylamino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(=O)NCC[C@H](N)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
 UU4  UU4  '(2S)-2-amino-4-(L-serylamino)butanoic acid'  L-peptide  28  14  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_UU4
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
 UU4  N     N  NH2    0  -0.793  -18.3528  -6.5033  34.6814
 UU4  CA    C  CH1    0  -0.222  -19.0560  -5.2506  34.4327
 UU4  C     C  C      0   0.411  -18.8297  -4.6270  33.0288
 UU4  O     O  O      0  -0.624  -19.4656  -3.5764  32.7936
 UU4  C3    C  CH2    0  -0.440  -18.7582  -4.2527  35.5567
 UU4  C4    C  CH2    0  -0.278  -17.2903  -3.8928  35.7334
 UU4  N2    N  NH1    0  -0.623  -16.7843  -3.0534  34.6671
 UU4  C5    C  C      0   0.525  -15.5158  -3.0764  34.2319
 UU4  C6    C  CH1    0  -0.238  -15.1980  -2.0432  33.1448
 UU4  O2    O  O      0  -0.487  -14.6741  -3.8492  34.6649
 UU4  OXT   O  OC    -1  -0.602  -18.0549  -5.2203  32.2540
 UU4  H1    H  HNH2   0   0.334  -18.7887  -7.2314  34.1291
 UU4  H2    H  HNH2   0   0.326  -17.4242  -6.4233  34.2835
 UU4  HA    H  HCH1   0   0.223  -20.1289  -5.4647  34.5037
 UU4  H5    H  HCH2   0   0.222  -19.3496  -3.3454  35.4142
 UU4  H6    H  HCH2   0   0.225  -19.0918  -4.6897  36.5013
 UU4  H7    H  HCH2   0   0.234  -17.1631  -3.3830  36.6941
 UU4  H8    H  HCH2   0   0.235  -16.6847  -4.7969  35.7818
 UU4  H9    H  HNH1   0   0.390  -17.4178  -2.3712  34.2800
 UU4  H10   H  HCH1   0   0.230  -15.7242  -1.1133  33.4164
 UU4  N3    N  NH2    0  -0.793  -13.7646  -1.8770  33.0316
 UU4  C7    C  CH2    0  -0.140  -15.7653  -2.5120  31.8082
 UU4  O4    O  OH1    0  -0.667  -15.4666  -1.5285  30.8422
 UU4  H11   H  HNH2   0   0.347  -13.5717  -1.1882  32.3167
 UU4  H12   H  HNH2   0   0.345  -13.3888  -1.5010  33.8926
 UU4  H131  H  HCH2   0   0.196  -15.3138  -3.4796  31.5552
 UU4  H14   H  HCH2   0   0.211  -16.8451  -2.6653  31.8998
 UU4  H15   H  HOH1   0   0.455  -15.7262  -1.8645  29.9797

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
 UU4  N   H1    single  0.890  0.020  1.040
 UU4  N   H2    single  0.890  0.020  1.040
 UU4  CA  N     single  1.458  0.019  1.458
 UU4  CA  C3    single  1.532  0.020  1.532
 UU4  CA  HA    single  0.970  0.020  0.970
 UU4  C   CA    single  1.525  0.021  1.525
 UU4  C   OXT   deloc   1.246  0.020  1.246
 UU4  O   C     deloc   1.231  0.020  1.231
 UU4  C3  C4    single  1.522  0.020  1.522
 UU4  C3  H5    single  0.970  0.020  1.090
 UU4  C3  H6    single  0.970  0.020  1.090
 UU4  C4  H7    single  0.970  0.020  1.090
 UU4  C4  H8    single  0.970  0.020  1.090
 UU4  N2  C4    single  1.448  0.020  1.448
 UU4  N2  H9    single  0.860  0.020  1.020
 UU4  C5  O2    double  1.222  0.020  1.222
 UU4  C5  N2    single  1.341  0.020  1.341
 UU4  C6  C5    single  1.533  0.020  1.533
 UU4  C6  H10   single  0.970  0.020  1.090
 UU4  C6  N3    single  1.448  0.020  1.448
 UU4  C6  C7    single  1.526  0.020  1.526
 UU4  C7  O4    single  1.411  0.020  1.411
 UU4  N3  H11   single  0.890  0.020  1.040
 UU4  N3  H12   single  0.890  0.020  1.040
 UU4  C7  H131  single  0.970  0.020  1.090
 UU4  C7  H14   single  0.970  0.020  1.090
 UU4  O4  H15   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
 UU4  H2    N   H1    103.72  3.000
 UU4  H2    N   CA    107.89  3.000
 UU4  H1    N   CA    108.49  3.000
 UU4  HA    CA  C3    105.65  3.000
 UU4  HA    CA  C     110.00  3.000
 UU4  C3    CA  C     111.92  3.000
 UU4  C     CA  N     111.00  2.800
 UU4  HA    CA  N     110.00  3.000
 UU4  C3    CA  N     109.92  3.000
 UU4  OXT   C   O     126.82  3.000
 UU4  O     C   CA    120.80  1.700
 UU4  OXT   C   CA    120.80  1.700
 UU4  H6    C3  H5    106.23  3.000
 UU4  H6    C3  C4    106.78  3.000
 UU4  H5    C3  C4    109.94  3.000
 UU4  H6    C3  CA    108.32  3.000
 UU4  H5    C3  CA    109.88  3.000
 UU4  C4    C3  CA    115.26  3.000
 UU4  H8    C4  H7    106.43  3.000
 UU4  H8    C4  N2    108.64  3.000
 UU4  H7    C4  N2    109.60  3.000
 UU4  N2    C4  C3    112.87  3.000
 UU4  H8    C4  C3    110.19  3.000
 UU4  H7    C4  C3    108.91  3.000
 UU4  H9    N2  C5    118.77  3.000
 UU4  C5    N2  C4    124.01  3.000
 UU4  H9    N2  C4    117.09  3.000
 UU4  O2    C5  C6    122.32  3.000
 UU4  C6    C5  N2    114.49  3.000
 UU4  O2    C5  N2    123.18  3.000
 UU4  C7    C6  N3    109.57  3.000
 UU4  C7    C6  H10   107.31  3.000
 UU4  N3    C6  H10   113.27  3.000
 UU4  C7    C6  C5    109.70  3.000
 UU4  N3    C6  C5    109.76  3.000
 UU4  H10   C6  C5    107.14  3.000
 UU4  H12   N3  H11   106.12  3.000
 UU4  H12   N3  C6    110.11  3.000
 UU4  H11   N3  C6    108.80  3.000
 UU4  H14   C7  H131  107.56  3.000
 UU4  H14   C7  O4    111.34  3.000
 UU4  H131  C7  O4    111.70  3.000
 UU4  H14   C7  C6    109.67  3.000
 UU4  H131  C7  C6    108.66  3.000
 UU4  O4    C7  C6    107.88  3.000
 UU4  H15   O4  C7    108.27  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
 UU4  CONST_01  O2  C5  N2  C4     0.00   0.0  0
 UU4  CONST_02  C6  C5  N2  C4   180.00   0.0  0
 UU4  CONST_03  H9  N2  C5  C6     0.00   0.0  0
 UU4  Var_01    N2  C4  C3  CA    71.79  30.0  3
 UU4  Var_02    C5  N2  C4  C3  -148.79  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
 UU4  chir_01  CA  N   C3  C   negativ
 UU4  chir_02  C6  C5  N3  C7  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
 UU4  plan-1  C4   0.020
 UU4  plan-1  N2   0.020
 UU4  plan-1  C5   0.020
 UU4  plan-1  C6   0.020
 UU4  plan-1  O2   0.020
 UU4  plan-1  H9   0.020
 UU4  plan-2  CA   0.020
 UU4  plan-2  C    0.020
 UU4  plan-2  O    0.020
 UU4  plan-2  OXT  0.020

