# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:50:55 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: cis-4-(carbamimidamidomethyl)cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NC[C@@H]1CC[C@@H](CC1)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
 029  029  'cis-4-(carbamimidamidomethyl)cyclohexanecarboxylic acid'  peptide  31  14  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_029
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
 029  C1    C  CH2   0  -0.431   0.8283  -0.6342  -1.3635
 029  C6    C  CH1   0  -0.272  -0.2455   0.2697  -0.7605
 029  C7    C  CH2   0  -0.242  -1.5450  -0.5052  -0.5820
 029  N8    N  NH1   0  -0.630  -2.6232   0.3825  -0.1868
 029  C9    C  C     0   0.517  -3.8974  -0.0614   0.0723
 029  N11   N  N     0  -0.716  -4.8912   0.7111  -0.1798
 029  N10   N  NH2   0  -0.826  -3.9787  -1.3408   0.5688
 029  C5    C  CH2   0  -0.419   0.2506   0.8833   0.5471
 029  C4    C  CH2   0  -0.427   1.5777   1.6150   0.3657
 029  C3    C  CH1   0  -0.397   2.6553   0.7268  -0.2536
 029  C12   C  C     0   0.560   3.1720  -0.2992   0.7328
 029  O13   O  O     0  -0.445   2.9882  -0.2700   1.9255
 029  C2    C  CH2   0  -0.434   2.1425   0.1116  -1.5608
 029  H11A  H  HCH2  0   0.217   0.9812  -1.5052  -0.7146
 029  H12   H  HCH2  0   0.238   0.4858  -1.0279  -2.3243
 029  H6    H  HCH1  0   0.221  -0.4299   1.0821  -1.4785
 029  H71   H  HCH2  0   0.225  -1.7803  -1.0381  -1.5130
 029  H72   H  HCH2  0   0.220  -1.3864  -1.2666   0.1862
 029  HN8   H  HNH1  0   0.370  -2.6396   1.2499  -0.7035
 029  H11   H  H     0   0.313  -5.7594   0.2987   0.1417
 029  H101  H  HNH2  0   0.387  -3.2085  -1.6652   1.1322
 029  H102  H  HNH2  0   0.388  -4.8685  -1.5892   0.9699
 029  H51   H  HCH2  0   0.236  -0.4926   1.5743   0.9501
 029  H52A  H  HCH2  0   0.215   0.3652   0.0878   1.2912
 029  H41   H  HCH2  0   0.232   1.4278   2.4708  -0.2990
 029  H42   H  HCH2  0   0.239   1.9169   2.0250   1.3182
 029  H3    H  HCH1  0   0.295   3.5285   1.3481  -0.4914
 029  H21   H  HCH2  0   0.246   2.8903  -0.5390  -2.0145
 029  H22   H  HCH2  0   0.234   1.9833   0.9291  -2.2698
 029  OXT   O  OH1   0  -0.594   3.9128  -1.2389   0.1530
 029  HXT   H  HOH1  0   0.477   4.2522  -1.8478   0.8259

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
 029  C1   C6    single  1.528  0.020  1.528
 029  C1   C2    single  1.524  0.020  1.524
 029  C1   H11A  single  0.970  0.020  1.090
 029  C1   H12   single  0.970  0.020  1.090
 029  C6   C7    single  1.524  0.020  1.524
 029  C6   C5    single  1.527  0.020  1.527
 029  C6   H6    single  0.970  0.020  1.090
 029  C7   N8    single  1.451  0.020  1.451
 029  C7   H71   single  0.970  0.020  1.090
 029  C7   H72   single  0.970  0.020  1.090
 029  N8   C9    single  1.374  0.020  1.374
 029  N8   HN8   single  0.890  0.020  1.040
 029  C9   N11   double  1.284  0.020  1.284
 029  C9   N10   single  1.375  0.020  1.375
 029  N11  H11   single  0.890  0.020  1.040
 029  N10  H101  single  0.890  0.020  1.040
 029  N10  H102  single  0.890  0.020  1.040
 029  C5   C4    single  1.526  0.020  1.526
 029  C5   H51   single  0.970  0.020  1.090
 029  C5   H52A  single  0.970  0.020  1.090
 029  C4   C3    single  1.528  0.020  1.528
 029  C4   H41   single  0.970  0.020  1.090
 029  C4   H42   single  0.970  0.020  1.090
 029  C3   C12   single  1.514  0.020  1.514
 029  C3   C2    single  1.533  0.020  1.533
 029  C3   H3    single  0.970  0.020  1.090
 029  C12  O13   double  1.207  0.020  1.207
 029  C2   H21   single  0.970  0.020  1.090
 029  C2   H22   single  0.970  0.020  1.090
 029  C12  OXT   single  1.330  0.020  1.330
 029  OXT  HXT   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
 029  H12   C1   H11A  106.12  3.000
 029  H12   C1   C2    109.43  3.000
 029  H11A  C1   C2    110.18  3.000
 029  H12   C1   C6    109.86  3.000
 029  H11A  C1   C6    109.53  3.000
 029  C2    C1   C6    111.57  3.000
 029  H6    C6   C5    108.46  3.000
 029  H6    C6   C7    108.01  3.000
 029  C5    C6   C7    112.40  3.000
 029  H6    C6   C1    107.30  3.000
 029  C5    C6   C1    110.33  3.000
 029  C7    C6   C1    110.17  3.000
 029  H72   C7   H71   106.79  3.000
 029  H72   C7   N8    110.02  3.000
 029  H71   C7   N8    111.62  3.000
 029  H72   C7   C6    108.23  3.000
 029  H71   C7   C6    109.28  3.000
 029  N8    C7   C6    110.76  3.000
 029  HN8   N8   C9    111.03  3.000
 029  HN8   N8   C7    113.46  3.000
 029  C9    N8   C7    122.87  3.000
 029  N10   C9   N11   125.81  3.000
 029  N10   C9   N8    115.06  3.000
 029  N11   C9   N8    119.12  3.000
 029  H11   N11  C9    110.86  3.000
 029  H102  N10  H101  111.91  3.000
 029  H102  N10  C9    115.18  3.000
 029  H101  N10  C9    117.14  3.000
 029  H52A  C5   H51   106.27  3.000
 029  H52A  C5   C4    109.75  3.000
 029  H51   C5   C4    109.41  3.000
 029  H52A  C5   C6    108.90  3.000
 029  H51   C5   C6    110.44  3.000
 029  C4    C5   C6    111.92  3.000
 029  H42   C4   H41   106.21  3.000
 029  H42   C4   C3    110.68  3.000
 029  H41   C4   C3    107.77  3.000
 029  H42   C4   C5    110.29  3.000
 029  H41   C4   C5    109.15  3.000
 029  C3    C4   C5    112.50  3.000
 029  H3    C3   C2    107.97  3.000
 029  H3    C3   C12   104.67  3.000
 029  C2    C3   C12   113.44  3.000
 029  H3    C3   C4    108.65  3.000
 029  C2    C3   C4    110.06  3.000
 029  C12   C3   C4    111.75  3.000
 029  OXT   C12  O13   122.19  3.000
 029  OXT   C12  C3    112.64  3.000
 029  O13   C12  C3    125.13  3.000
 029  H22   C2   H21   106.03  3.000
 029  H22   C2   C3    107.55  3.000
 029  H21   C2   C3    111.40  3.000
 029  H22   C2   C1    108.92  3.000
 029  H21   C2   C1    110.70  3.000
 029  C3    C2   C1    111.99  3.000
 029  HXT   OXT  C12   109.66  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
 029  CONST_01  HXT   OXT  C12  C3    180.00   0.0  0
 029  CONST_04  H11   N11  C9   N8    180.00   0.0  0
 029  CONST_06  H102  N10  C9   N8    180.00   0.0  0
 029  CONST_07  HN8   N8   C9   N11     0.00   0.0  0
 029  Var_01    C3    C2   C1   C6     56.45  30.0  1
 029  Var_02    C3    C4   C5   C6    -54.76  30.0  1
 029  Var_03    C9    N8   C7   C6   -178.42  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
 029  chir_01  C6  C1  C7   C5  negativ
 029  chir_02  C3  C4  C12  C2  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
 029  plan-1  C7    0.020
 029  plan-1  N8    0.020
 029  plan-1  C9    0.020
 029  plan-1  N11   0.020
 029  plan-1  N10   0.020
 029  plan-1  HN8   0.020
 029  plan-1  H11   0.020
 029  plan-1  H101  0.020
 029  plan-1  H102  0.020
 029  plan-2  C3    0.020
 029  plan-2  C12   0.020
 029  plan-2  O13   0.020
 029  plan-2  OXT   0.020
 029  plan-2  HXT   0.020

