# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:09:38 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2S)-(carboxyamino)[(2Z,4R)-2-iminohexahydropyrimidin-4-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)N[C@@H]([C@H]1CCNC(=N)N1)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
 CSI  CSI  '(2S)-(carboxyamino)[(2Z,4R)-2-iminohexahydropyrimidin-4-yl]acetic acid'  ligand  27  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CSI
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
 CSI  NE    N  NH1   0  -0.634  -3.5402  -0.1062  -0.2960
 CSI  CD2   C  C     0   0.571  -2.7498  -1.2171  -0.2218
 CSI  CD1   C  CH2   0  -0.278  -3.1069   1.1808   0.1954
 CSI  NH    N  N     0  -0.732  -3.2858  -2.3809  -0.3176
 CSI  CB    C  CH1   0  -0.071  -0.8117   0.2717   0.2944
 CSI  CG1   C  CH2   0  -0.476  -1.6675   1.4205  -0.2128
 CSI  NG2   N  NH1   0  -0.675  -1.3980  -0.9839  -0.1327
 CSI  N     N  NH1   0  -0.658   1.3737  -0.7723   0.3567
 CSI  CA    C  CH1   0  -0.164   0.6329   0.3131  -0.2318
 CSI  C     C  C     0   0.529   1.2991   1.6435   0.0976
 CSI  O     O  O     0  -0.427   1.8534   1.8641   1.1426
 CSI  OXT   O  OH1   0  -0.581   1.1857   2.5193  -0.8868
 CSI  HE    H  HNH1  0   0.384  -4.5241  -0.3089  -0.2265
 CSI  HD13  H  HCH2  0   0.258  -3.7489   1.9488  -0.2350
 CSI  HD12  H  HCH2  0   0.225  -3.1978   1.2595   1.2861
 CSI  HH    H  H     0   0.312  -2.5799  -3.1076  -0.3063
 CSI  HB    H  HCH1  0   0.254  -0.7729   0.3347   1.3924
 CSI  HG13  H  HCH2  0   0.251  -1.5922   1.5006  -1.2999
 CSI  HG12  H  HCH2  0   0.263  -1.3325   2.3629   0.2190
 CSI  HG2   H  HNH1  0   0.390  -0.8517  -1.8060   0.0735
 CSI  H     H  HNH1  0   0.412   1.1566  -1.0355   1.3073
 CSI  HCA   H  HCH1  0   0.298   0.5979   0.1832  -1.3154
 CSI  HXT   H  HOH1  0   0.487   1.5800   3.3676  -0.6305
 CSI  O3    O  O     0  -0.503   3.0842  -0.5952  -1.1220
 CSI  O4    O  OH1   0  -0.612   3.1946  -2.0129   0.6227
 CSI  H12   H  HOH1  0   0.488   4.0647  -2.2141   0.2528
 CSI  C7    C  C     0   0.689   2.5991  -1.0860  -0.1244

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
 CSI  NE   CD2   single  1.365  0.020  1.365
 CSI  NE   CD1   single  1.444  0.020  1.444
 CSI  NE   HE    single  0.890  0.020  1.040
 CSI  CD2  NH    double  1.285  0.020  1.285
 CSI  CD2  NG2   single  1.375  0.020  1.375
 CSI  CD1  CG1   single  1.515  0.020  1.515
 CSI  CD1  HD13  single  0.970  0.020  1.090
 CSI  CD1  HD12  single  0.970  0.020  1.090
 CSI  NH   HH    single  0.890  0.020  1.040
 CSI  CB   CG1   single  1.520  0.020  1.520
 CSI  CB   NG2   single  1.450  0.020  1.450
 CSI  CB   CA    single  1.538  0.020  1.538
 CSI  CB   HB    single  0.970  0.020  1.090
 CSI  CG1  HG13  single  0.970  0.020  1.090
 CSI  CG1  HG12  single  0.970  0.020  1.090
 CSI  NG2  HG2   single  0.890  0.020  1.040
 CSI  N    CA    single  1.440  0.020  1.440
 CSI  N    H     single  0.860  0.020  1.020
 CSI  CA   C     single  1.524  0.020  1.524
 CSI  CA   HCA   single  0.970  0.020  1.090
 CSI  C    O     double  1.203  0.020  1.203
 CSI  C    OXT   single  1.322  0.020  1.322
 CSI  OXT  HXT   single  0.850  0.020  0.980
 CSI  C7   O3    double  1.213  0.020  1.213
 CSI  C7   O4    single  1.331  0.020  1.331
 CSI  O4   H12   single  0.850  0.020  0.980
 CSI  N    C7    single  1.353  0.020  1.353

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
 CSI  HE    NE   CD1   116.69  3.000
 CSI  HE    NE   CD2   113.46  3.000
 CSI  CD1   NE   CD2   122.20  3.000
 CSI  NG2   CD2  NH    124.66  3.000
 CSI  NG2   CD2  NE    115.77  3.000
 CSI  NH    CD2  NE    119.43  3.000
 CSI  HD12  CD1  HD13  107.05  3.000
 CSI  HD12  CD1  CG1   109.58  3.000
 CSI  HD13  CD1  CG1   109.98  3.000
 CSI  HD12  CD1  NE    112.17  3.000
 CSI  HD13  CD1  NE    108.48  3.000
 CSI  CG1   CD1  NE    109.53  3.000
 CSI  HH    NH   CD2   110.99  3.000
 CSI  HB    CB   CA    107.86  3.000
 CSI  HB    CB   NG2   110.96  3.000
 CSI  CA    CB   NG2   107.60  3.000
 CSI  HB    CB   CG1   108.03  3.000
 CSI  CA    CB   CG1   113.23  3.000
 CSI  NG2   CB   CG1   109.18  3.000
 CSI  HG12  CG1  HG13  108.04  3.000
 CSI  HG12  CG1  CB    110.40  3.000
 CSI  HG13  CG1  CB    110.40  3.000
 CSI  HG12  CG1  CD1   108.80  3.000
 CSI  HG13  CG1  CD1   110.19  3.000
 CSI  CB    CG1  CD1   108.99  3.000
 CSI  HG2   NG2  CB    115.25  3.000
 CSI  HG2   NG2  CD2   114.06  3.000
 CSI  CB    NG2  CD2   124.31  3.000
 CSI  C7    N    H     117.96  3.000
 CSI  C7    N    CA    119.69  3.000
 CSI  H     N    CA    118.07  3.000
 CSI  HCA   CA   C     109.41  3.000
 CSI  HCA   CA   N     109.42  3.000
 CSI  C     CA   N     110.17  3.000
 CSI  HCA   CA   CB    107.83  3.000
 CSI  C     CA   CB    111.11  3.000
 CSI  N     CA   CB    108.85  3.000
 CSI  OXT   C    O     124.37  3.000
 CSI  OXT   C    CA    112.32  3.000
 CSI  O     C    CA    123.31  3.000
 CSI  HXT   OXT  C     110.35  3.000
 CSI  C7    O4   H12   109.44  3.000
 CSI  O4    C7   O3    124.36  3.000
 CSI  O4    C7   N     111.53  3.000
 CSI  O3    C7   N     124.10  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
 CSI  CONST_05  HG2  NG2  CD2  NE   180.00   0.0  0
 CSI  CONST_06  HE   NE   CD2  NG2  180.00   0.0  0
 CSI  CONST_07  HH   NH   CD2  NE   180.00   0.0  0
 CSI  CONST_08  H12  O4   C7   N    180.00   0.0  0
 CSI  CONST_09  HXT  OXT  C    CA   180.00   0.0  0
 CSI  Var_01    CB   CG1  CD1  NE   -55.88  30.0  1
 CSI  Var_02    CG1  CD1  NE   CD2   42.86  30.0  1
 CSI  Var_03    O3   C7   N    CA    -7.54  30.0  2

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
 CSI  chir_01  CB  CG1  NG2  CA  negativ
 CSI  chir_02  CA  N    CB   C   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
 CSI  plan-1  NE   0.020
 CSI  plan-1  CD2  0.020
 CSI  plan-1  CD1  0.020
 CSI  plan-1  NH   0.020
 CSI  plan-1  CB   0.020
 CSI  plan-1  NG2  0.020
 CSI  plan-1  HE   0.020
 CSI  plan-1  HH   0.020
 CSI  plan-1  HG2  0.020
 CSI  plan-2  CA   0.020
 CSI  plan-2  C    0.020
 CSI  plan-2  O    0.020
 CSI  plan-2  OXT  0.020
 CSI  plan-2  HXT  0.020
 CSI  plan-3  N    0.020
 CSI  plan-3  O3   0.020
 CSI  plan-3  O4   0.020
 CSI  plan-3  H12  0.020
 CSI  plan-3  C7   0.020

