# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:26:25 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (3R,4S)-3-(2-aminoethyl)-4-(aminomethyl)heptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](CC(O)=O)[C@@H](CN)CCC(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
 PB1  PB1  '(3R,4S)-3-(2-aminoethyl)-4-(aminomethyl)heptanedioic acid'  ligand  34  16  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PB1
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
 PB1  O3    O  OC    -1  -0.642  -0.1339  -0.3842  -5.1469
 PB1  C8    C  C      0   0.438   0.1586   0.1730  -4.0655
 PB1  O4    O  O      0  -0.656   0.7870   1.2467  -3.9529
 PB1  C7    C  CH2    0  -0.557  -0.2186  -0.5778  -2.7774
 PB1  C6    C  CH2    0  -0.370  -0.2675   0.2730  -1.5157
 PB1  C3    C  CH1    0  -0.195  -0.6082  -0.5188  -0.2455
 PB1  C2    C  CH2    0  -0.323  -2.0954  -0.8898  -0.2274
 PB1  N1    N  NH2    0  -0.762  -2.9569   0.2741  -0.0652
 PB1  C4    C  CH1    0  -0.282  -0.1632   0.2238   1.0349
 PB1  C9    C  CH2    0  -0.558  -0.6221  -0.4729   2.3183
 PB1  C10   C  C      0   0.378  -0.4079   0.3205   3.6214
 PB1  O1    O  O      0  -0.547  -0.4927   1.5648   3.5589
 PB1  O2    O  OC    -1  -0.683  -0.1590  -0.3455   4.6476
 PB1  C5    C  CH2    0  -0.462   1.3558   0.4692   1.0701
 PB1  C11   C  CH2    0  -0.275   2.2305  -0.7543   0.8309
 PB1  N12   N  NH2    0  -0.767   3.6290  -0.4373   1.1001
 PB1  H71   H  HCH2   0   0.181   0.5217  -1.3773  -2.6344
 PB1  H72   H  HCH2   0   0.204  -1.1671  -1.0975  -2.9411
 PB1  H61   H  HCH2   0   0.179  -1.0063   1.0717  -1.6251
 PB1  H62   H  HCH2   0   0.228   0.6970   0.7710  -1.4120
 PB1  H3    H  HCH1   0   0.217  -0.0699  -1.4747  -0.2841
 PB1  H21   H  HCH2   0   0.190  -2.2634  -1.6644   0.5329
 PB1  H22   H  HCH2   0   0.224  -2.3500  -1.3594  -1.1805
 PB1  HN11  H  HNH2   0   0.279  -3.9242  -0.0137  -0.1353
 PB1  HN12  H  HNH2   0   0.360  -2.8538   0.6495   0.8695
 PB1  H4    H  HCH1   0   0.242  -0.6311   1.2139   1.0239
 PB1  H91   H  HCH2   0   0.240  -0.1575  -1.4588   2.4100
 PB1  H92   H  HCH2   0   0.222  -1.7002  -0.6682   2.2739
 PB1  H51   H  HCH2   0   0.292   1.6195   0.8954   2.0408
 PB1  H52   H  HCH2   0   0.175   1.6288   1.2332   0.3351
 PB1  H111  H  HCH2   0   0.196   1.9328  -1.5648   1.5026
 PB1  H112  H  HCH2   0   0.208   2.0690  -1.1282  -0.1897
 PB1  H121  H  HNH2   0   0.316   4.2011  -1.2427   0.8805
 PB1  H122  H  HNH2   0   0.314   3.9303   0.2856   0.4575

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
 PB1  O3   C8    deloc   1.251  0.020  1.251
 PB1  C8   O4    deloc   1.249  0.020  1.249
 PB1  C8   C7    single  1.538  0.020  1.538
 PB1  C7   C6    single  1.523  0.020  1.523
 PB1  C7   H71   single  0.970  0.020  1.090
 PB1  C7   H72   single  0.970  0.020  1.090
 PB1  C6   C3    single  1.535  0.020  1.535
 PB1  C6   H61   single  0.970  0.020  1.090
 PB1  C6   H62   single  0.970  0.020  1.090
 PB1  C3   C2    single  1.533  0.020  1.533
 PB1  C3   C4    single  1.546  0.020  1.546
 PB1  C3   H3    single  0.970  0.020  1.090
 PB1  C2   N1    single  1.457  0.020  1.457
 PB1  C2   H21   single  0.970  0.020  1.090
 PB1  C2   H22   single  0.970  0.020  1.090
 PB1  N1   HN11  single  0.890  0.020  1.040
 PB1  N1   HN12  single  0.890  0.020  1.040
 PB1  C4   C9    single  1.531  0.020  1.531
 PB1  C4   C5    single  1.539  0.020  1.539
 PB1  C4   H4    single  0.970  0.020  1.090
 PB1  C9   C10   single  1.541  0.020  1.541
 PB1  C9   H91   single  0.970  0.020  1.090
 PB1  C9   H92   single  0.970  0.020  1.090
 PB1  C10  O1    deloc   1.249  0.020  1.249
 PB1  C10  O2    deloc   1.249  0.020  1.249
 PB1  C5   C11   single  1.523  0.020  1.523
 PB1  C5   H51   single  0.970  0.020  1.090
 PB1  C5   H52   single  0.970  0.020  1.090
 PB1  C11  N12   single  1.459  0.020  1.459
 PB1  C11  H111  single  0.970  0.020  1.090
 PB1  C11  H112  single  0.970  0.020  1.090
 PB1  N12  H121  single  0.890  0.020  1.040
 PB1  N12  H122  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
 PB1  C7    C8   O4    117.88  3.000
 PB1  C7    C8   O3    116.69  3.000
 PB1  O4    C8   O3    125.33  3.000
 PB1  H72   C7   H71   104.95  3.000
 PB1  H72   C7   C6    111.20  3.000
 PB1  H71   C7   C6    108.68  3.000
 PB1  H72   C7   C8    108.62  3.000
 PB1  H71   C7   C8    107.40  3.000
 PB1  C6    C7   C8    115.41  3.000
 PB1  H62   C6   H61   105.88  3.000
 PB1  H62   C6   C3    110.69  3.000
 PB1  H61   C6   C3    108.04  3.000
 PB1  H62   C6   C7    107.79  3.000
 PB1  H61   C6   C7    110.30  3.000
 PB1  C3    C6   C7    113.86  3.000
 PB1  H3    C3   C4    107.84  3.000
 PB1  H3    C3   C2    105.39  3.000
 PB1  C4    C3   C2    112.69  3.000
 PB1  H3    C3   C6    108.14  3.000
 PB1  C4    C3   C6    111.95  3.000
 PB1  C2    C3   C6    110.49  3.000
 PB1  H22   C2   H21   105.37  3.000
 PB1  H22   C2   N1    107.61  3.000
 PB1  H21   C2   N1    113.32  3.000
 PB1  H22   C2   C3    108.65  3.000
 PB1  H21   C2   C3    109.10  3.000
 PB1  N1    C2   C3    112.43  3.000
 PB1  HN12  N1   HN11  105.47  3.000
 PB1  HN12  N1   C2    109.80  3.000
 PB1  HN11  N1   C2    109.29  3.000
 PB1  H4    C4   C5    106.12  3.000
 PB1  H4    C4   C9    106.97  3.000
 PB1  C5    C4   C9    110.44  3.000
 PB1  H4    C4   C3    107.64  3.000
 PB1  C5    C4   C3    112.31  3.000
 PB1  C9    C4   C3    112.93  3.000
 PB1  H92   C9   H91   105.09  3.000
 PB1  H92   C9   C10   105.23  3.000
 PB1  H91   C9   C10   109.53  3.000
 PB1  H92   C9   C4    109.99  3.000
 PB1  H91   C9   C4    110.69  3.000
 PB1  C10   C9   C4    115.66  3.000
 PB1  O2    C10  O1    125.89  3.000
 PB1  O2    C10  C9    116.63  3.000
 PB1  O1    C10  C9    117.48  3.000
 PB1  H52   C5   H51   105.31  3.000
 PB1  H52   C5   C11   108.18  3.000
 PB1  H51   C5   C11   108.32  3.000
 PB1  H52   C5   C4    110.00  3.000
 PB1  H51   C5   C4    108.70  3.000
 PB1  C11   C5   C4    115.80  3.000
 PB1  H112  C11  H111  106.15  3.000
 PB1  H112  C11  N12   112.72  3.000
 PB1  H111  C11  N12   107.97  3.000
 PB1  H112  C11  C5    109.56  3.000
 PB1  H111  C11  C5    110.03  3.000
 PB1  N12   C11  C5    110.30  3.000
 PB1  H122  N12  H121  105.19  3.000
 PB1  H122  N12  C11   108.85  3.000
 PB1  H121  N12  C11   109.20  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
 PB1  Var_01  C6    C7   C8   O3  -161.40  30.0  3
 PB1  Var_02  C3    C6   C7   C8  -178.36  30.0  3
 PB1  Var_03  O1    C10  C9   C4    32.43  30.0  3
 PB1  Var_04  N12   C11  C5   C4  -170.93  30.0  3
 PB1  Var_05  HN11  N1   C2   C3   175.42  30.0  3
 PB1  Var_06  H121  N12  C11  C5  -176.47  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
 PB1  chir_01  C3  C6  C2  C4  positiv
 PB1  chir_02  C4  C5  C9  C3  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
 PB1  plan-1  O3   0.020
 PB1  plan-1  C8   0.020
 PB1  plan-1  O4   0.020
 PB1  plan-1  C7   0.020
 PB1  plan-2  C9   0.020
 PB1  plan-2  C10  0.020
 PB1  plan-2  O1   0.020
 PB1  plan-2  O2   0.020

