# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:35:22 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@@](N)(CC[C@](N)(CCCCN)C(O)=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
 3VN  3VN  '(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid (non-preferred name)'  ligand  50  22  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3VN
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
 3VN  N01  N  NH2    0  -0.802   1.8275   0.9135  -1.7456
 3VN  C02  C  CT     0  -0.038   1.8901   0.3974  -0.3817
 3VN  C03  C  C      0   0.425   1.9751   1.5710   0.6278
 3VN  O04  O  O      0  -0.616   1.8649   1.2658   1.8327
 3VN  O05  O  OC    -1  -0.609   2.1784   2.7169   0.1775
 3VN  C06  C  CH2    0  -0.400   3.1247  -0.5021  -0.1617
 3VN  C07  C  CH2    0  -0.427   4.4716   0.1873  -0.3478
 3VN  C08  C  CH2    0  -0.423   5.6422  -0.7868  -0.2891
 3VN  C09  C  CH2    0  -0.272   6.9894  -0.0953  -0.4289
 3VN  N10  N  NH2    0  -0.801   8.0819  -1.0579  -0.3847
 3VN  C11  C  CH2    0  -0.368   0.6285  -0.4409  -0.1263
 3VN  C12  C  CH2    0  -0.411  -0.6675   0.3572  -0.1719
 3VN  C13  C  CT     0  -0.037  -1.9521  -0.4854  -0.3235
 3VN  N14  N  NH2    0  -0.814  -1.9685  -1.2346  -1.5770
 3VN  C15  C  CH2    0  -0.359  -3.1534   0.4713  -0.3095
 3VN  C16  C  CH2    0  -0.421  -4.5132  -0.2085  -0.3786
 3VN  C17  C  CH2    0  -0.425  -5.6705   0.7822  -0.4120
 3VN  C18  C  CH2    0  -0.271  -7.0265   0.0986  -0.4930
 3VN  N19  N  NH2    0  -0.801  -8.1094   1.0735  -0.5147
 3VN  C20  C  C      0   0.428  -2.0230  -1.4609   0.8796
 3VN  O21  O  O      0  -0.616  -2.2500  -0.9464   1.9935
 3VN  O22  O  OC    -1  -0.610  -1.8140  -2.6725   0.6623
 3VN  H1   H  HNH2   0   0.331   2.4703   1.6877  -1.8410
 3VN  H2   H  HNH2   0   0.321   2.1259   0.1945  -2.3946
 3VN  H5   H  HCH2   0   0.204   3.0851  -0.9383   0.8405
 3VN  H6   H  HCH2   0   0.197   4.4916   0.7124  -1.3082
 3VN  H7   H  HCH2   0   0.208   5.6209  -1.3410   0.6551
 3VN  H8   H  HCH2   0   0.207   5.5325  -1.5314  -1.0862
 3VN  H9   H  HCH2   0   0.184   6.9814   0.5156  -1.3441
 3VN  H10  H  HCH2   0   0.209   7.1171   0.6053   0.4015
 3VN  H11  H  HNH2   0   0.336   8.0388  -1.6433  -1.2101
 3VN  H12  H  HNH2   0   0.344   8.9659  -0.5691  -0.4467
 3VN  H14  H  HCH2   0   0.183   0.6004  -1.2357  -0.8817
 3VN  H15  H  HCH2   0   0.203  -0.7436   0.9675   0.7313
 3VN  H16  H  HNH2   0   0.322  -1.4781  -0.7109  -2.2929
 3VN  H17  H  HNH2   0   0.332  -1.4601  -2.0990  -1.4445
 3VN  H19  H  HCH2   0   0.198  -3.1047   1.0952   0.5871
 3VN  H20  H  HCH2   0   0.190  -3.0531   1.1566  -1.1611
 3VN  H21  H  HCH2   0   0.203  -4.5516  -0.8485  -1.2642
 3VN  H22  H  HCH2   0   0.204  -5.6364   1.4130   0.4844
 3VN  H23  H  HCH2   0   0.208  -7.0742  -0.4870  -1.4161
 3VN  H24  H  HCH2   0   0.184  -7.1077  -0.6256   0.3315
 3VN  H25  H  HNH2   0   0.343  -8.9963   0.5896  -0.5756
 3VN  H26  H  HNH2   0   0.335  -8.1305   1.5604   0.3735
 3VN  H3   H  HCH2   0   0.197   3.0602  -1.3462  -0.8615
 3VN  H29  H  HCH2   0   0.212   4.6060   0.9532   0.4225
 3VN  H13  H  HCH2   0   0.204   0.7174  -0.9406   0.8407
 3VN  H30  H  HCH2   0   0.200  -0.6209   1.0527  -1.0172
 3VN  H18  H  HCH2   0   0.204  -4.6365  -0.8710   0.4844
 3VN  H31  H  HCH2   0   0.206  -5.5592   1.4576  -1.2666

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
 3VN  N10  C09  single  1.457  0.020  1.457
 3VN  C09  C08  single  1.521  0.020  1.521
 3VN  C08  C07  single  1.524  0.020  1.524
 3VN  C07  C06  single  1.525  0.020  1.525
 3VN  O04  C03  deloc   1.248  0.020  1.248
 3VN  C06  C02  single  1.543  0.020  1.543
 3VN  O05  C03  deloc   1.248  0.020  1.248
 3VN  C03  C02  single  1.550  0.020  1.550
 3VN  N01  C02  single  1.460  0.020  1.460
 3VN  C02  C11  single  1.536  0.020  1.536
 3VN  C11  C12  single  1.523  0.020  1.523
 3VN  C12  C13  single  1.544  0.020  1.544
 3VN  C13  N14  single  1.460  0.020  1.460
 3VN  C13  C15  single  1.536  0.020  1.536
 3VN  C13  C20  single  1.551  0.020  1.551
 3VN  C15  C16  single  1.522  0.020  1.522
 3VN  C20  O21  deloc   1.248  0.020  1.248
 3VN  C20  O22  deloc   1.249  0.020  1.249
 3VN  C16  C17  single  1.524  0.020  1.524
 3VN  C17  C18  single  1.521  0.020  1.521
 3VN  C18  N19  single  1.457  0.020  1.457
 3VN  N01  H1   single  0.890  0.020  1.040
 3VN  N01  H2   single  0.890  0.020  1.040
 3VN  C06  H5   single  0.970  0.020  1.090
 3VN  C07  H6   single  0.970  0.020  1.090
 3VN  C08  H7   single  0.970  0.020  1.090
 3VN  C08  H8   single  0.970  0.020  1.090
 3VN  C09  H9   single  0.970  0.020  1.090
 3VN  C09  H10  single  0.970  0.020  1.090
 3VN  N10  H11  single  0.890  0.020  1.040
 3VN  N10  H12  single  0.890  0.020  1.040
 3VN  C11  H14  single  0.970  0.020  1.090
 3VN  C12  H15  single  0.970  0.020  1.090
 3VN  N14  H16  single  0.890  0.020  1.040
 3VN  N14  H17  single  0.890  0.020  1.040
 3VN  C15  H19  single  0.970  0.020  1.090
 3VN  C15  H20  single  0.970  0.020  1.090
 3VN  C16  H21  single  0.970  0.020  1.090
 3VN  C17  H22  single  0.970  0.020  1.090
 3VN  C18  H23  single  0.970  0.020  1.090
 3VN  C18  H24  single  0.970  0.020  1.090
 3VN  N19  H25  single  0.890  0.020  1.040
 3VN  N19  H26  single  0.890  0.020  1.040
 3VN  C06  H3   single  0.970  0.020  1.090
 3VN  C07  H29  single  0.970  0.020  1.090
 3VN  C11  H13  single  0.970  0.020  1.090
 3VN  C12  H30  single  0.970  0.020  1.090
 3VN  C16  H18  single  0.970  0.020  1.090
 3VN  C17  H31  single  0.970  0.020  1.090

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
 3VN  H2   N01  H1   107.20  3.000
 3VN  H2   N01  C02  109.57  3.000
 3VN  H1   N01  C02  109.37  3.000
 3VN  C11  C02  C06  108.38  3.000
 3VN  C11  C02  C03  110.48  3.000
 3VN  C06  C02  C03  107.73  3.000
 3VN  C11  C02  N01  108.25  3.000
 3VN  C03  C02  N01  110.07  3.000
 3VN  C06  C02  N01  111.94  3.000
 3VN  O05  C03  O04  125.97  3.000
 3VN  O05  C03  C02  117.98  3.000
 3VN  O04  C03  C02  116.02  3.000
 3VN  H3   C06  H5   105.97  3.000
 3VN  H3   C06  C07  108.77  3.000
 3VN  H5   C06  C07  108.92  3.000
 3VN  H3   C06  C02  108.07  3.000
 3VN  H5   C06  C02  109.52  3.000
 3VN  C07  C06  C02  115.20  3.000
 3VN  H29  C07  H6   106.23  3.000
 3VN  H29  C07  C08  109.02  3.000
 3VN  H6   C07  C08  109.04  3.000
 3VN  H29  C07  C06  109.82  3.000
 3VN  H6   C07  C06  109.88  3.000
 3VN  C08  C07  C06  112.63  3.000
 3VN  H8   C08  H7   106.33  3.000
 3VN  H8   C08  C09  109.31  3.000
 3VN  H7   C08  C09  109.06  3.000
 3VN  H8   C08  C07  109.22  3.000
 3VN  H7   C08  C07  109.99  3.000
 3VN  C09  C08  C07  112.72  3.000
 3VN  H10  C09  H9   106.06  3.000
 3VN  H10  C09  N10  108.22  3.000
 3VN  H9   C09  N10  113.43  3.000
 3VN  H10  C09  C08  108.95  3.000
 3VN  H9   C09  C08  108.81  3.000
 3VN  N10  C09  C08  111.17  3.000
 3VN  H12  N10  H11  105.45  3.000
 3VN  H12  N10  C09  109.51  3.000
 3VN  H11  N10  C09  108.99  3.000
 3VN  H13  C11  H14  106.28  3.000
 3VN  H13  C11  C12  109.61  3.000
 3VN  H14  C11  C12  109.71  3.000
 3VN  H13  C11  C02  109.28  3.000
 3VN  H14  C11  C02  107.57  3.000
 3VN  C12  C11  C02  114.08  3.000
 3VN  H30  C12  H15  106.63  3.000
 3VN  H30  C12  C13  107.82  3.000
 3VN  H15  C12  C13  109.16  3.000
 3VN  H30  C12  C11  108.64  3.000
 3VN  H15  C12  C11  109.10  3.000
 3VN  C13  C12  C11  115.15  3.000
 3VN  C20  C13  C15  110.43  3.000
 3VN  C20  C13  N14  110.04  3.000
 3VN  C15  C13  N14  108.58  3.000
 3VN  C20  C13  C12  107.77  3.000
 3VN  C15  C13  C12  108.06  3.000
 3VN  N14  C13  C12  111.94  3.000
 3VN  H17  N14  H16  106.91  3.000
 3VN  H17  N14  C13  108.69  3.000
 3VN  H16  N14  C13  109.62  3.000
 3VN  H20  C15  H19  106.02  3.000
 3VN  H20  C15  C16  108.99  3.000
 3VN  H19  C15  C16  109.39  3.000
 3VN  H20  C15  C13  108.08  3.000
 3VN  H19  C15  C13  109.15  3.000
 3VN  C16  C15  C13  114.85  3.000
 3VN  H18  C16  H21  106.28  3.000
 3VN  H18  C16  C17  108.97  3.000
 3VN  H21  C16  C17  109.64  3.000
 3VN  H18  C16  C15  109.58  3.000
 3VN  H21  C16  C15  109.25  3.000
 3VN  C17  C16  C15  112.90  3.000
 3VN  H31  C17  H22  106.26  3.000
 3VN  H31  C17  C18  109.05  3.000
 3VN  H22  C17  C18  109.26  3.000
 3VN  H31  C17  C16  109.94  3.000
 3VN  H22  C17  C16  109.42  3.000
 3VN  C18  C17  C16  112.72  3.000
 3VN  H24  C18  H23  106.06  3.000
 3VN  H24  C18  N19  113.37  3.000
 3VN  H23  C18  N19  108.25  3.000
 3VN  H24  C18  C17  108.76  3.000
 3VN  H23  C18  C17  108.93  3.000
 3VN  N19  C18  C17  111.26  3.000
 3VN  H26  N19  H25  105.32  3.000
 3VN  H26  N19  C18  108.91  3.000
 3VN  H25  N19  C18  109.40  3.000
 3VN  O22  C20  O21  125.87  3.000
 3VN  O22  C20  C13  117.89  3.000
 3VN  O21  C20  C13  116.21  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
 3VN  Var_01  C08  C07  C06  C02  -172.85  30.0  1
 3VN  Var_02  C13  C12  C11  C02   163.30  30.0  3
 3VN  Var_03  C09  C08  C07  C06  -178.12  30.0  1
 3VN  Var_04  N10  C09  C08  C07  -179.30  30.0  1
 3VN  Var_05  C17  C16  C15  C13  -177.95  30.0  3
 3VN  Var_06  C18  C17  C16  C15   179.51  30.0  3
 3VN  Var_07  N19  C18  C17  C16   179.64  30.0  3
 3VN  Var_08  H11  N10  C09  C08    67.11  30.0  3
 3VN  Var_09  H25  N19  C18  C17   179.58  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
 3VN  chir_01  C02  C03  N01  C11  positiv
 3VN  chir_02  C13  C12  C15  C20  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
 3VN  plan-1  C02  0.020
 3VN  plan-1  C03  0.020
 3VN  plan-1  O04  0.020
 3VN  plan-1  O05  0.020
 3VN  plan-2  C13  0.020
 3VN  plan-2  C20  0.020
 3VN  plan-2  O21  0.020
 3VN  plan-2  O22  0.020

