# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:43:57 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: N~5~-carbamoyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=O)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
 CIR  CIR  N~5~-carbamoyl-L-ornithine  L-peptide  25  12  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CIR
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
 CIR  C1    C  C     0   0.524   3.4575   0.1117   0.1204
 CIR  O1    O  O     0  -0.420   4.0972  -0.1395   1.1102
 CIR  O2    O  OH1   0  -0.608   3.8012   1.0525  -0.7524
 CIR  C2    C  CH1   0  -0.190   2.1591  -0.5667  -0.2615
 CIR  N2    N  NH2   0  -0.768   2.1165  -1.8807   0.3429
 CIR  C3    C  CH2   0  -0.470   0.9818   0.3671   0.0860
 CIR  C4    C  CH2   0  -0.523  -0.3600  -0.2470  -0.3009
 CIR  C5    C  CH2   0  -0.229  -1.4667   0.8020  -0.3581
 CIR  N6    N  NH1   0  -0.642  -2.7655   0.2527  -0.6641
 CIR  C7    C  C     0   0.684  -3.5857  -0.2725   0.2810
 CIR  O7    O  O     0  -0.538  -3.3221  -0.2522   1.4792
 CIR  N8    N  NH2   0  -0.878  -4.7584  -0.7802  -0.1984
 CIR  HO2   H  HOH1  0   0.481   4.6138   1.4939  -0.4610
 CIR  H2    H  HCH1  0   0.264   2.1466  -0.6594  -1.3474
 CIR  HN21  H  HNH2  0   0.338   1.9846  -1.7929   1.3440
 CIR  HN22  H  HNH2  0   0.367   1.3057  -2.3793   0.0008
 CIR  H31   H  HCH2  0   0.222   0.9918   0.5974   1.1565
 CIR  H32   H  HCH2  0   0.245   1.1124   1.3194  -0.4373
 CIR  H41   H  HCH2  0   0.260  -0.2817  -0.7329  -1.2794
 CIR  H42   H  HCH2  0   0.244  -0.6419  -1.0239   0.4125
 CIR  H51   H  HCH2  0   0.223  -1.5171   1.3497   0.5843
 CIR  H52   H  HCH2  0   0.249  -1.2313   1.5343  -1.1328
 CIR  HN6   H  HNH1  0   0.388  -2.9971   0.1317  -1.6357
 CIR  HN81  H  HNH2  0   0.388  -4.8552  -0.9793  -1.1809
 CIR  HN82  H  HNH2  0   0.389  -5.2672  -1.3970   0.4120

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
 CIR  C1  O1    double  1.205  0.020  1.205
 CIR  C1  O2    single  1.329  0.020  1.329
 CIR  C1  C2    single  1.514  0.020  1.514
 CIR  O2  HO2   single  0.850  0.020  0.980
 CIR  C2  N2    single  1.447  0.020  1.447
 CIR  C2  C3    single  1.542  0.020  1.542
 CIR  C2  H2    single  0.970  0.020  1.090
 CIR  N2  HN21  single  0.890  0.020  1.040
 CIR  N2  HN22  single  0.890  0.020  1.040
 CIR  C3  C4    single  1.526  0.020  1.526
 CIR  C3  H31   single  0.970  0.020  1.090
 CIR  C3  H32   single  0.970  0.020  1.090
 CIR  C4  C5    single  1.526  0.020  1.526
 CIR  C4  H41   single  0.970  0.020  1.090
 CIR  C4  H42   single  0.970  0.020  1.090
 CIR  C5  N6    single  1.443  0.020  1.443
 CIR  C5  H51   single  0.970  0.020  1.090
 CIR  C5  H52   single  0.970  0.020  1.090
 CIR  N6  C7    single  1.357  0.020  1.357
 CIR  N6  HN6   single  0.860  0.020  1.020
 CIR  C7  O7    double  1.227  0.020  1.227
 CIR  C7  N8    single  1.365  0.020  1.365
 CIR  N8  HN81  single  0.890  0.020  1.040
 CIR  N8  HN82  single  0.890  0.020  1.040

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
 CIR  C2    C1  O2    111.93  3.000
 CIR  C2    C1  O1    124.69  3.000
 CIR  O2    C1  O1    123.36  3.000
 CIR  HO2   O2  C1    109.99  3.000
 CIR  H2    C2  C3    105.50  3.000
 CIR  H2    C2  N2    109.79  3.000
 CIR  C3    C2  N2    115.68  3.000
 CIR  H2    C2  C1    107.41  3.000
 CIR  C3    C2  C1    109.05  3.000
 CIR  N2    C2  C1    109.07  3.000
 CIR  HN22  N2  HN21  105.81  3.000
 CIR  HN22  N2  C2    109.26  3.000
 CIR  HN21  N2  C2    109.74  3.000
 CIR  H32   C3  H31   106.46  3.000
 CIR  H32   C3  C4    109.51  3.000
 CIR  H31   C3  C4    109.91  3.000
 CIR  H32   C3  C2    109.15  3.000
 CIR  H31   C3  C2    109.92  3.000
 CIR  C4    C3  C2    111.74  3.000
 CIR  H42   C4  H41   106.65  3.000
 CIR  H42   C4  C5    109.05  3.000
 CIR  H41   C4  C5    108.87  3.000
 CIR  H42   C4  C3    110.35  3.000
 CIR  H41   C4  C3    110.01  3.000
 CIR  C5    C4  C3    111.76  3.000
 CIR  H52   C5  H51   106.63  3.000
 CIR  H52   C5  N6    107.39  3.000
 CIR  H51   C5  N6    109.43  3.000
 CIR  H52   C5  C4    109.35  3.000
 CIR  H51   C5  C4    110.26  3.000
 CIR  N6    C5  C4    113.52  3.000
 CIR  HN6   N6  C7    119.14  3.000
 CIR  HN6   N6  C5    117.24  3.000
 CIR  C7    N6  C5    122.93  3.000
 CIR  N8    C7  O7    122.26  3.000
 CIR  N8    C7  N6    114.74  3.000
 CIR  O7    C7  N6    122.95  3.000
 CIR  HN82  N8  HN81  114.97  3.000
 CIR  HN82  N8  C7    116.71  3.000
 CIR  HN81  N8  C7    119.92  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
 CIR  CONST_01  O7    C7  N6  C5     0.00   0.0  0
 CIR  CONST_02  N8    C7  N6  C5   180.00   0.0  0
 CIR  CONST_03  HN6   N6  C7  O7   180.00   0.0  0
 CIR  CONST_04  HN81  N8  C7  O7   180.00   0.0  0
 CIR  CONST_06  HO2   O2  C1  O1     0.00   0.0  0
 CIR  Var_01    C5    C4  C3  C2  -162.79  30.0  3
 CIR  Var_02    N6    C5  C4  C3  -177.46  30.0  3
 CIR  Var_03    C7    N6  C5  C4    84.72  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
 CIR  chir_01  C2  C1  N2  C3  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
 CIR  plan-1  C5    0.020
 CIR  plan-1  N6    0.020
 CIR  plan-1  C7    0.020
 CIR  plan-1  O7    0.020
 CIR  plan-1  N8    0.020
 CIR  plan-1  HN6   0.020
 CIR  plan-1  HN81  0.020
 CIR  plan-1  HN82  0.020
 CIR  plan-2  C1    0.020
 CIR  plan-2  O1    0.020
 CIR  plan-2  O2    0.020
 CIR  plan-2  C2    0.020
 CIR  plan-2  HO2   0.020

