# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 00:02:30 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1R,2Z)-2-[(2R)-2-amino-3-(phosphonooxy)propylidene]cyclopentanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO[P](O)(O)=O)\C=C/1CCC[C@H]/1C(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
 4CG  4CG  '(1R,2Z)-2-[(2R)-2-amino-3-(phosphonooxy)propylidene]cyclopentanecarboxylic acid'  peptide  30  17  .  2022-09-22  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_4CG
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
 4CG  C10  C  CR5    0   0.151  -2.3687   0.6563  -0.5855
 4CG  C13  C  CH2    0  -0.440  -3.6636   0.8178   1.4506
 4CG  O    O  O      0  -0.607  -4.0515  -1.6759  -0.1176
 4CG  C    C  C      0   0.424  -3.0156  -1.4996   0.5552
 4CG  C14  C  CR15   0  -0.416  -2.5738  -0.0320   0.7505
 4CG  C12  C  CH2    0  -0.450  -3.8119   2.0917   0.6110
 4CG  C11  C  CH2    0  -0.485  -3.5074   1.6112  -0.8054
 4CG  C09  C  C1     0  -0.319  -1.3135   0.5238  -1.3852
 4CG  CA   C  CH1    0  -0.196  -0.1293  -0.3668  -1.1330
 4CG  N    N  NH2    0  -0.797   0.3373  -0.9304  -2.3983
 4CG  C03  C  CH2    0  -0.101   0.9509   0.4070  -0.3733
 4CG  O04  O  O2     0  -0.656   2.0403  -0.4332  -0.1286
 4CG  P05  P  P      0   1.221   3.4521   0.2616   0.5273
 4CG  O06  O  O      0  -0.907   3.9205   1.2760  -0.5105
 4CG  O07  O  OP    -1  -0.909   3.0063   0.8841   1.8473
 4CG  O08  O  OP    -1  -0.902   4.3340  -0.9735   0.6640
 4CG  H1   H  HCH2   0   0.221  -4.6116   0.2770   1.4559
 4CG  H2   H  HCH2   0   0.227  -3.4085   1.0330   2.4890
 4CG  H4   H  HCR5   0   0.224  -1.6461  -0.0077   1.3283
 4CG  H5   H  HCH2   0   0.225  -4.7972   2.5506   0.7098
 4CG  H6   H  HCH2   0   0.219  -3.0720   2.8381   0.9135
 4CG  H7   H  HCH2   0   0.232  -3.2762   2.4100  -1.5116
 4CG  H8   H  HCH2   0   0.228  -4.3709   1.0607  -1.1942
 4CG  H9   H  H      0   0.215  -1.2644   1.1374  -2.2839
 4CG  H10  H  HCH1   0   0.225  -0.4425  -1.2036  -0.4999
 4CG  H11  H  HNH2   0   0.327   0.6136  -0.1673  -3.0085
 4CG  H12  H  HNH2   0   0.337   1.1952  -1.4385  -2.2169
 4CG  H14  H  HCH2   0   0.156   1.2419   1.2858  -0.9700
 4CG  H15  H  HCH2   0   0.167   0.5182   0.7931   0.5618
 4CG  O1   O  OC    -1  -0.613  -2.3140  -2.3882   1.0796

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
 4CG  C12  C11  single  1.526  0.020  1.526
 4CG  C12  C13  single  1.533  0.020  1.533
 4CG  C11  C10  single  1.502  0.020  1.502
 4CG  C13  C14  single  1.549  0.020  1.549
 4CG  C10  C14  single  1.517  0.020  1.517
 4CG  C10  C09  double  1.331  0.020  1.331
 4CG  C14  C    single  1.545  0.020  1.545
 4CG  C    O    deloc   1.231  0.020  1.231
 4CG  C09  CA   single  1.503  0.020  1.503
 4CG  CA   C03  single  1.531  0.020  1.531
 4CG  CA   N    single  1.458  0.019  1.458
 4CG  C03  O04  single  1.397  0.020  1.397
 4CG  O06  P05  deloc   1.525  0.020  1.525
 4CG  O04  P05  single  1.705  0.020  1.705
 4CG  P05  O07  deloc   1.526  0.020  1.526
 4CG  P05  O08  deloc   1.524  0.020  1.524
 4CG  C13  H1   single  0.970  0.020  1.090
 4CG  C13  H2   single  0.970  0.020  1.090
 4CG  C14  H4   single  0.970  0.020  1.090
 4CG  C12  H5   single  0.970  0.020  1.090
 4CG  C12  H6   single  0.970  0.020  1.090
 4CG  C11  H7   single  0.970  0.020  1.090
 4CG  C11  H8   single  0.970  0.020  1.090
 4CG  C09  H9   single  0.930  0.020  1.080
 4CG  CA   H10  single  0.970  0.020  1.090
 4CG  N    H11  single  0.890  0.020  1.040
 4CG  N    H12  single  0.890  0.020  1.040
 4CG  C03  H14  single  0.970  0.020  1.090
 4CG  C03  H15  single  0.970  0.020  1.090
 4CG  C    O1   deloc   1.248  0.020  1.248

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
 4CG  C09  C10  C11  125.20  3.000
 4CG  C09  C10  C14  126.26  3.000
 4CG  C11  C10  C14  108.35  3.000
 4CG  H2   C13  H1   107.23  3.000
 4CG  H2   C13  C12  112.34  3.000
 4CG  H1   C13  C12  109.30  3.000
 4CG  H2   C13  C14  111.96  3.000
 4CG  H1   C13  C14  109.96  3.000
 4CG  C12  C13  C14  106.05  3.000
 4CG  O1   C    C14  117.56  3.000
 4CG  O1   C    O    126.35  3.000
 4CG  C14  C    O    116.09  3.000
 4CG  H4   C14  C    109.30  3.000
 4CG  H4   C14  C13  110.24  3.000
 4CG  C    C14  C13  112.15  3.000
 4CG  H4   C14  C10  109.91  3.000
 4CG  C    C14  C10  111.00  3.000
 4CG  C13  C14  C10  104.14  3.000
 4CG  H6   C12  H5   107.38  3.000
 4CG  H6   C12  C11  109.67  3.000
 4CG  H5   C12  C11  113.36  3.000
 4CG  H6   C12  C13  110.50  3.000
 4CG  H5   C12  C13  112.78  3.000
 4CG  C11  C12  C13  103.14  3.000
 4CG  H8   C11  H7   107.77  3.000
 4CG  H8   C11  C12  109.29  3.000
 4CG  H7   C11  C12  114.36  3.000
 4CG  H8   C11  C10  109.27  3.000
 4CG  H7   C11  C10  113.55  3.000
 4CG  C12  C11  C10  102.45  3.000
 4CG  H9   C09  CA   115.89  3.000
 4CG  H9   C09  C10  118.39  3.000
 4CG  CA   C09  C10  125.66  3.000
 4CG  H10  CA   C03  107.53  3.000
 4CG  H10  CA   N    107.28  3.000
 4CG  C03  CA   N    113.54  3.000
 4CG  H10  CA   C09  108.93  3.000
 4CG  N    CA   C09  109.56  3.000
 4CG  C03  CA   C09  109.86  3.000
 4CG  H12  N    H11  104.72  3.000
 4CG  H12  N    CA   107.97  3.000
 4CG  H11  N    CA   108.50  3.000
 4CG  H15  C03  H14  106.52  3.000
 4CG  H15  C03  O04  111.64  3.000
 4CG  H14  C03  O04  111.64  3.000
 4CG  H15  C03  CA   108.76  3.000
 4CG  H14  C03  CA   108.72  3.000
 4CG  O04  C03  CA   109.46  3.000
 4CG  P05  O04  C03  117.90  3.000
 4CG  O08  P05  O07  114.97  3.000
 4CG  O08  P05  O06  114.99  3.000
 4CG  O07  P05  O06  114.02  3.000
 4CG  O08  P05  O04  100.57  3.000
 4CG  O07  P05  O04  104.90  3.000
 4CG  O06  P05  O04  105.29  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
 4CG  Var_01  C13  C12  C11  C10  -39.79  30.0  1
 4CG  Var_02  C11  C12  C13  C14   31.82  30.0  1
 4CG  Var_03  C12  C11  C10  C14   33.90  30.0  1
 4CG  Var_04  CA   C09  C10  C14    1.67  30.0  2
 4CG  Var_05  O06  P05  O04  C03  -61.79  30.0  3
 4CG  Var_06  H14  C03  O04  P05   51.80  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
 4CG  chir_01  C14  C13  C10  C    positiv
 4CG  chir_02  CA   N    C09  C03  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
 4CG  plan-1  O    0.020
 4CG  plan-1  C    0.020
 4CG  plan-1  C14  0.020
 4CG  plan-1  O1   0.020

