# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:38:48 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (6R)-1-aminoundecan-6-yl hydrogen carbonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](CCCCCN)OC(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
 7C2  7C2  '(6R)-1-aminoundecan-6-yl hydrogen carbonate'  ligand  40  16  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7C2
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
 7C2  C01  C  CH3    0  -0.662   6.5584   1.8072  -0.1903
 7C2  C02  C  CH2    0  -0.419   5.4220   0.8027  -0.3249
 7C2  C03  C  CH2    0  -0.405   4.0868   1.3510   0.1627
 7C2  C04  C  CH2    0  -0.416   2.9272   0.3787  -0.0202
 7C2  C05  C  CH2    0  -0.424   1.5977   0.9613   0.4438
 7C2  C06  C  CH1    0   0.065   0.3783   0.1216   0.0800
 7C2  C24  C  CH2    0  -0.424  -0.9220   0.8176   0.4651
 7C2  C25  C  CH2    0  -0.417  -2.1672   0.1579  -0.1130
 7C2  C26  C  CH2    0  -0.418  -3.4553   0.8562   0.3055
 7C2  C27  C  CH2    0  -0.426  -4.6975   0.2711  -0.3530
 7C2  C28  C  CH2    0  -0.271  -5.9814   0.9438   0.1064
 7C2  N29  N  NH2    0  -0.801  -7.1409   0.3867  -0.5767
 7C2  O07  O  O2     0  -0.532   0.4339  -1.1291   0.7463
 7C2  O23  O  O      0  -0.627   0.8334  -2.2408  -1.1804
 7C2  H1   H  HCH3   0   0.215   6.7166   2.0904   0.8519
 7C2  H2   H  HCH3   0   0.225   7.4989   1.4042  -0.5678
 7C2  H3   H  HCH3   0   0.215   6.3417   2.7200  -0.7490
 7C2  H4   H  HCH2   0   0.209   5.3264   0.4996  -1.3722
 7C2  H5   H  HCH2   0   0.210   5.6683  -0.1075   0.2309
 7C2  H6   H  HCH2   0   0.205   4.1725   1.6263   1.2198
 7C2  H7   H  HCH2   0   0.203   3.8621   2.2808  -0.3727
 7C2  H8   H  HCH2   0   0.206   2.8513   0.1028  -1.0767
 7C2  H9   H  HCH2   0   0.210   3.1454  -0.5472   0.5206
 7C2  H10  H  HCH2   0   0.207   1.6213   1.1303   1.5266
 7C2  H11  H  HCH2   0   0.207   1.4668   1.9491  -0.0114
 7C2  H12  H  HCH1   0   0.199   0.3828  -0.0359  -1.0026
 7C2  H30  H  HCH2   0   0.208  -0.9982   0.8728   1.5572
 7C2  H31  H  HCH2   0   0.211  -0.8749   1.8536   0.1146
 7C2  H32  H  HCH2   0   0.206  -2.0949   0.1569  -1.2063
 7C2  H33  H  HCH2   0   0.214  -2.2124  -0.8927   0.1892
 7C2  H34  H  HCH2   0   0.208  -3.5572   0.8020   1.3951
 7C2  H35  H  HCH2   0   0.207  -3.3858   1.9226   0.0629
 7C2  H36  H  HCH2   0   0.211  -4.6164   0.3616  -1.4409
 7C2  H37  H  HCH2   0   0.209  -4.7541  -0.8022  -0.1366
 7C2  H38  H  HCH2   0   0.185  -6.0439   0.8748   1.2028
 7C2  H39  H  HCH2   0   0.209  -5.9281   2.0110  -0.1271
 7C2  H42  H  HNH2   0   0.336  -7.2599  -0.5792  -0.2960
 7C2  H13  H  HNH2   0   0.344  -7.9774   0.8632  -0.2642
 7C2  OXT  O  OC    -1  -0.634   0.7489  -3.2858   0.7938
 7C2  C08  C  C      0   0.550   0.6948  -2.2994   0.0473

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
 7C2  C28  N29  single  1.456  0.020  1.456
 7C2  C28  C27  single  1.521  0.020  1.521
 7C2  C27  C26  single  1.523  0.020  1.523
 7C2  C26  C25  single  1.524  0.020  1.524
 7C2  C25  C24  single  1.523  0.020  1.523
 7C2  O23  C08  deloc   1.237  0.020  1.237
 7C2  C08  O07  deloc   1.388  0.020  1.388
 7C2  C24  C06  single  1.524  0.020  1.524
 7C2  O07  C06  single  1.418  0.020  1.418
 7C2  C06  C05  single  1.525  0.020  1.525
 7C2  C05  C04  single  1.524  0.020  1.524
 7C2  C04  C03  single  1.524  0.020  1.524
 7C2  C01  C02  single  1.523  0.020  1.523
 7C2  C03  C02  single  1.523  0.020  1.523
 7C2  C01  H1   single  0.970  0.020  1.090
 7C2  C01  H2   single  0.970  0.020  1.090
 7C2  C01  H3   single  0.970  0.020  1.090
 7C2  C02  H4   single  0.970  0.020  1.090
 7C2  C02  H5   single  0.970  0.020  1.090
 7C2  C03  H6   single  0.970  0.020  1.090
 7C2  C03  H7   single  0.970  0.020  1.090
 7C2  C04  H8   single  0.970  0.020  1.090
 7C2  C04  H9   single  0.970  0.020  1.090
 7C2  C05  H10  single  0.970  0.020  1.090
 7C2  C05  H11  single  0.970  0.020  1.090
 7C2  C06  H12  single  0.970  0.020  1.090
 7C2  C24  H30  single  0.970  0.020  1.090
 7C2  C24  H31  single  0.970  0.020  1.090
 7C2  C25  H32  single  0.970  0.020  1.090
 7C2  C25  H33  single  0.970  0.020  1.090
 7C2  C26  H34  single  0.970  0.020  1.090
 7C2  C26  H35  single  0.970  0.020  1.090
 7C2  C27  H36  single  0.970  0.020  1.090
 7C2  C27  H37  single  0.970  0.020  1.090
 7C2  C28  H38  single  0.970  0.020  1.090
 7C2  C28  H39  single  0.970  0.020  1.090
 7C2  N29  H42  single  0.890  0.020  1.040
 7C2  N29  H13  single  0.890  0.020  1.040
 7C2  C08  OXT  deloc   1.238  0.020  1.238

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
 7C2  H3   C01  H2   107.64  3.000
 7C2  H3   C01  H1   107.48  3.000
 7C2  H2   C01  H1   107.54  3.000
 7C2  H3   C01  C02  110.98  3.000
 7C2  H2   C01  C02  111.67  3.000
 7C2  H1   C01  C02  111.33  3.000
 7C2  H5   C02  H4   105.98  3.000
 7C2  H5   C02  C03  109.51  3.000
 7C2  H4   C02  C03  109.23  3.000
 7C2  H5   C02  C01  109.62  3.000
 7C2  H4   C02  C01  109.42  3.000
 7C2  C03  C02  C01  112.85  3.000
 7C2  H7   C03  H6   105.91  3.000
 7C2  H7   C03  C04  109.06  3.000
 7C2  H6   C03  C04  109.60  3.000
 7C2  H7   C03  C02  109.19  3.000
 7C2  H6   C03  C02  109.30  3.000
 7C2  C04  C03  C02  113.50  3.000
 7C2  H9   C04  H8   106.12  3.000
 7C2  H9   C04  C05  110.30  3.000
 7C2  H8   C04  C05  109.25  3.000
 7C2  H9   C04  C03  109.20  3.000
 7C2  H8   C04  C03  109.22  3.000
 7C2  C05  C04  C03  112.54  3.000
 7C2  H11  C05  H10  105.90  3.000
 7C2  H11  C05  C06  107.57  3.000
 7C2  H10  C05  C06  109.74  3.000
 7C2  H11  C05  C04  108.81  3.000
 7C2  H10  C05  C04  109.94  3.000
 7C2  C06  C05  C04  114.49  3.000
 7C2  H12  C06  O07  109.74  3.000
 7C2  H12  C06  C24  108.61  3.000
 7C2  O07  C06  C24  108.51  3.000
 7C2  H12  C06  C05  108.19  3.000
 7C2  O07  C06  C05  110.01  3.000
 7C2  C24  C06  C05  111.75  3.000
 7C2  H31  C24  H30  105.93  3.000
 7C2  H31  C24  C25  108.88  3.000
 7C2  H30  C24  C25  110.06  3.000
 7C2  H31  C24  C06  108.33  3.000
 7C2  H30  C24  C06  109.51  3.000
 7C2  C25  C24  C06  113.81  3.000
 7C2  H33  C25  H32  106.11  3.000
 7C2  H33  C25  C26  109.23  3.000
 7C2  H32  C25  C26  109.28  3.000
 7C2  H33  C25  C24  110.17  3.000
 7C2  H32  C25  C24  108.98  3.000
 7C2  C26  C25  C24  112.85  3.000
 7C2  H35  C26  H34  105.91  3.000
 7C2  H35  C26  C27  109.26  3.000
 7C2  H34  C26  C27  109.58  3.000
 7C2  H35  C26  C25  109.37  3.000
 7C2  H34  C26  C25  109.21  3.000
 7C2  C27  C26  C25  113.24  3.000
 7C2  H37  C27  H36  106.32  3.000
 7C2  H37  C27  C28  109.26  3.000
 7C2  H36  C27  C28  109.04  3.000
 7C2  H37  C27  C26  109.45  3.000
 7C2  H36  C27  C26  109.72  3.000
 7C2  C28  C27  C26  112.84  3.000
 7C2  H39  C28  H38  106.06  3.000
 7C2  H39  C28  N29  108.17  3.000
 7C2  H38  C28  N29  113.46  3.000
 7C2  H39  C28  C27  109.03  3.000
 7C2  H38  C28  C27  108.74  3.000
 7C2  N29  C28  C27  111.18  3.000
 7C2  H13  N29  H42  105.45  3.000
 7C2  H13  N29  C28  109.46  3.000
 7C2  H42  N29  C28  109.16  3.000
 7C2  C08  O07  C06  120.96  3.000
 7C2  OXT  C08  O23  129.14  3.000
 7C2  OXT  C08  O07  112.11  3.000
 7C2  O23  C08  O07  118.75  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
 7C2  CONST_01  O23  C08  O07  C06     0.00   0.0  0
 7C2  CONST_02  OXT  C08  O07  C06   180.00   0.0  0
 7C2  Var_01    C04  C03  C02  C01   177.54  30.0  1
 7C2  Var_02    C05  C04  C03  C02  -178.64  30.0  1
 7C2  Var_03    C06  C05  C04  C03   170.71  30.0  1
 7C2  Var_04    C26  C25  C24  C06   178.98  30.0  1
 7C2  Var_05    C27  C26  C25  C24   175.53  30.0  1
 7C2  Var_06    C28  C27  C26  C25   178.07  30.0  1
 7C2  Var_07    N29  C28  C27  C26   178.16  30.0  1
 7C2  Var_08    H1   C01  C02  C03    61.23  30.0  3
 7C2  Var_09    H42  N29  C28  C27    66.04  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
 7C2  chir_01  C06  C24  O07  C05  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
 7C2  plan-1  C06  0.020
 7C2  plan-1  O07  0.020
 7C2  plan-1  O23  0.020
 7C2  plan-1  OXT  0.020
 7C2  plan-1  C08  0.020

