# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 00:19:17 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: glycyl-D-alanyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@@H](C)NC(=O)CN)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
 UM1  UM1  glycyl-D-alanyl-D-alanine  D-peptide  30  15  .  2022-03-23  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UM1
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
 UM1  NCF   N  NH2   0  -0.793   5.5185  -0.6768  -0.5963
 UM1  CCG   C  CH2   0  -0.410   4.4321  -0.6261   0.3582
 UM1  CCR   C  C     0   0.542   3.2693   0.1832  -0.1873
 UM1  OCS   O  O     0  -0.500   3.4145   1.0279  -1.0583
 UM1  NCT   N  NH1   0  -0.638   2.0862  -0.0802   0.3922
 UM1  CCU   C  CH1   0  -0.200   0.8822   0.6585   0.1061
 UM1  CCV   C  CH3   0  -0.649   0.7817   1.9481   0.9251
 UM1  CCW   C  C     0   0.564  -0.3121  -0.2366   0.4168
 UM1  OCX   O  O     0  -0.488  -0.2415  -1.1422   1.2346
 UM1  NCY   N  NH1   0  -0.633  -1.4374   0.0896  -0.2326
 UM1  CCZ   C  CH1   0  -0.207  -2.6853  -0.6029  -0.0290
 UM1  CDA   C  CH3   0  -0.652  -2.8437  -1.7933  -0.9792
 UM1  CDB   C  C     0   0.552  -3.8267   0.3808  -0.1945
 UM1  ODC   O  O     0  -0.432  -3.7064   1.5074  -0.6023
 UM1  ODB   O  OH1   0  -0.586  -4.9819  -0.1645   0.1477
 UM1  HNCF  H  HNH2  0   0.345   5.8907   0.2534  -0.7356
 UM1  HNCA  H  HNH2  0   0.354   6.2737  -1.2219  -0.2019
 UM1  HCG   H  HCH2  0   0.252   4.0973  -1.6424   0.5775
 UM1  HCGA  H  HCH2  0   0.241   4.6951  -0.1793   1.3292
 UM1  HNCT  H  HNH1  0   0.398   2.0337  -0.7733   1.1233
 UM1  HCU   H  HCH1  0   0.277   0.8759   0.9114  -0.9563
 UM1  HCV   H  HCH3  0   0.236   0.7573   1.7285   1.9928
 UM1  HCVA  H  HCH3  0   0.252   1.6426   2.5840   0.7246
 UM1  HCVB  H  HCH3  0   0.238  -0.1159   2.5102   0.6685
 UM1  HNCY  H  HNH1  0   0.407  -1.4069   0.8073  -0.9403
 UM1  HCZ   H  HCH1  0   0.299  -2.7079  -0.9695   0.9999
 UM1  HDA   H  HCH3  0   0.254  -2.0027  -2.4719  -0.8474
 UM1  HDAA  H  HCH3  0   0.248  -3.7574  -2.3483  -0.7757
 UM1  HDAB  H  HCH3  0   0.240  -2.8589  -1.4643  -2.0183
 UM1  HODB  H  HOH1  0   0.488  -5.7064   0.4636   0.0057

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
 UM1  NCF  CCG   single  1.447  0.020  1.447
 UM1  CCG  CCR   single  1.518  0.020  1.518
 UM1  CCR  OCS   double  1.222  0.020  1.222
 UM1  CCR  NCT   single  1.343  0.020  1.343
 UM1  NCT  CCU   single  1.441  0.020  1.441
 UM1  CCU  CCV   single  1.531  0.020  1.531
 UM1  CCU  CCW   single  1.525  0.020  1.525
 UM1  CCW  OCX   double  1.222  0.020  1.222
 UM1  CCW  NCY   single  1.340  0.020  1.340
 UM1  NCY  CCZ   single  1.442  0.020  1.442
 UM1  CCZ  CDA   single  1.531  0.020  1.531
 UM1  CCZ  CDB   single  1.516  0.020  1.516
 UM1  CDB  ODC   double  1.204  0.020  1.204
 UM1  CDB  ODB   single  1.323  0.020  1.323
 UM1  NCF  HNCF  single  0.890  0.020  1.040
 UM1  NCF  HNCA  single  0.890  0.020  1.040
 UM1  CCG  HCG   single  0.970  0.020  1.090
 UM1  CCG  HCGA  single  0.970  0.020  1.090
 UM1  NCT  HNCT  single  0.860  0.020  1.020
 UM1  CCU  HCU   single  0.970  0.020  1.090
 UM1  CCV  HCV   single  0.970  0.020  1.090
 UM1  CCV  HCVA  single  0.970  0.020  1.090
 UM1  CCV  HCVB  single  0.970  0.020  1.090
 UM1  NCY  HNCY  single  0.860  0.020  1.020
 UM1  CCZ  HCZ   single  0.970  0.020  1.090
 UM1  CDA  HDA   single  0.970  0.020  1.090
 UM1  CDA  HDAA  single  0.970  0.020  1.090
 UM1  CDA  HDAB  single  0.970  0.020  1.090
 UM1  ODB  HODB  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
 UM1  HNCA  NCF  HNCF  105.93  3.000
 UM1  HNCA  NCF  CCG   108.80  3.000
 UM1  HNCF  NCF  CCG   109.56  3.000
 UM1  HCGA  CCG  HCG   105.89  3.000
 UM1  HCGA  CCG  CCR   106.47  3.000
 UM1  HCG   CCG  CCR   109.48  3.000
 UM1  HCGA  CCG  NCF   114.63  3.000
 UM1  HCG   CCG  NCF   109.26  3.000
 UM1  CCR   CCG  NCF   110.90  3.000
 UM1  NCT   CCR  OCS   123.20  3.000
 UM1  NCT   CCR  CCG   114.52  3.000
 UM1  OCS   CCR  CCG   122.25  3.000
 UM1  HNCT  NCT  CCU   116.91  3.000
 UM1  HNCT  NCT  CCR   119.54  3.000
 UM1  CCU   NCT  CCR   123.34  3.000
 UM1  HCU   CCU  CCW   109.25  3.000
 UM1  HCU   CCU  CCV   108.96  3.000
 UM1  CCW   CCU  CCV   109.52  3.000
 UM1  HCU   CCU  NCT   108.46  3.000
 UM1  CCW   CCU  NCT   108.24  3.000
 UM1  CCV   CCU  NCT   112.36  3.000
 UM1  HCVB  CCV  HCVA  107.86  3.000
 UM1  HCVB  CCV  HCV   108.43  3.000
 UM1  HCVA  CCV  HCV   108.40  3.000
 UM1  HCVB  CCV  CCU   111.26  3.000
 UM1  HCVA  CCV  CCU   109.97  3.000
 UM1  HCV   CCV  CCU   110.83  3.000
 UM1  NCY   CCW  OCX   123.60  3.000
 UM1  NCY   CCW  CCU   114.60  3.000
 UM1  OCX   CCW  CCU   121.75  3.000
 UM1  HNCY  NCY  CCZ   117.86  3.000
 UM1  HNCY  NCY  CCW   119.22  3.000
 UM1  CCZ   NCY  CCW   122.80  3.000
 UM1  HCZ   CCZ  CDB   107.76  3.000
 UM1  HCZ   CCZ  CDA   108.75  3.000
 UM1  CDB   CCZ  CDA   111.03  3.000
 UM1  HCZ   CCZ  NCY   108.19  3.000
 UM1  CDB   CCZ  NCY   108.94  3.000
 UM1  CDA   CCZ  NCY   112.04  3.000
 UM1  HDAB  CDA  HDAA  108.69  3.000
 UM1  HDAB  CDA  HDA   108.32  3.000
 UM1  HDAA  CDA  HDA   107.95  3.000
 UM1  HDAB  CDA  CCZ   111.00  3.000
 UM1  HDAA  CDA  CCZ   111.54  3.000
 UM1  HDA   CDA  CCZ   109.24  3.000
 UM1  ODB   CDB  ODC   124.10  3.000
 UM1  ODB   CDB  CCZ   111.21  3.000
 UM1  ODC   CDB  CCZ   124.67  3.000
 UM1  HODB  ODB  CDB   110.35  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
 UM1  CONST_01  CCU   NCT  CCR  CCG  180.00   0.0  0
 UM1  CONST_02  CCU   NCT  CCR  OCS    0.00   0.0  0
 UM1  CONST_03  CCZ   NCY  CCW  CCU  180.00   0.0  0
 UM1  CONST_04  CCZ   NCY  CCW  OCX    0.00   0.0  0
 UM1  CONST_05  HNCT  NCT  CCR  CCG    0.00   0.0  0
 UM1  CONST_06  HNCY  NCY  CCW  CCU    0.00   0.0  0
 UM1  CONST_07  HODB  ODB  CDB  CCZ  180.00   0.0  0
 UM1  Var_01    OCS   CCR  CCG  NCF  -23.33  30.0  3
 UM1  Var_02    HNCF  NCF  CCG  CCR   64.62  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
 UM1  chir_01  CCU  NCT  CCV  CCW  positiv
 UM1  chir_02  CCZ  NCY  CDA  CDB  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
 UM1  plan-1  CCG   0.020
 UM1  plan-1  CCR   0.020
 UM1  plan-1  OCS   0.020
 UM1  plan-1  NCT   0.020
 UM1  plan-1  CCU   0.020
 UM1  plan-1  HNCT  0.020
 UM1  plan-2  CCU   0.020
 UM1  plan-2  CCW   0.020
 UM1  plan-2  OCX   0.020
 UM1  plan-2  NCY   0.020
 UM1  plan-2  CCZ   0.020
 UM1  plan-2  HNCY  0.020
 UM1  plan-3  CCZ   0.020
 UM1  plan-3  CDB   0.020
 UM1  plan-3  ODC   0.020
 UM1  plan-3  ODB   0.020
 UM1  plan-3  HODB  0.020

