# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 00:42:50 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  36  16  .  2021-08-20  2021-08-20  
;
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  OH1   0  -0.599  -0.3441  -0.4843  -5.1285
 PB1  C8    C  C     0   0.555   0.1228   0.0604  -4.0069
 PB1  O4    O  O     0  -0.446   0.9936   0.8952  -4.0012
 PB1  C7    C  CH2   0  -0.600  -0.5722  -0.4908  -2.7930
 PB1  C6    C  CH2   0  -0.408  -0.0674   0.0974  -1.4862
 PB1  C3    C  CH1   0  -0.228  -0.6275  -0.6027  -0.2426
 PB1  C2    C  CH2   0  -0.314  -2.1485  -0.7768  -0.3345
 PB1  N1    N  NH2   0  -0.796  -2.8355   0.4813  -0.5821
 PB1  C4    C  CH1   0  -0.228  -0.2083   0.1326   1.0539
 PB1  C9    C  CH2   0  -0.588  -0.5368  -0.7144   2.2865
 PB1  C10   C  C     0   0.547  -0.4255   0.0256   3.5911
 PB1  O1    O  O     0  -0.447  -0.6217   1.2075   3.7385
 PB1  O2    O  OH1   0  -0.594  -0.1275  -0.7847   4.6026
 PB1  C5    C  CH2   0  -0.460   1.2632   0.5702   1.0791
 PB1  C11   C  CH2   0  -0.285   2.2900  -0.5536   1.0364
 PB1  N12   N  NH2   0  -0.799   3.6366   0.0027   1.0094
 PB1  HO3   H  HOH1  0   0.477   0.1194  -0.1129  -5.8937
 PB1  H71   H  HCH2  0   0.273  -0.4560  -1.5798  -2.8062
 PB1  H72   H  HCH2  0   0.282  -1.6425  -0.3036  -2.9139
 PB1  H61   H  HCH2  0   0.225  -0.3148   1.1610  -1.4509
 PB1  H62   H  HCH2  0   0.234   1.0219   0.0337  -1.4714
 PB1  H3    H  HCH1  0   0.221  -0.2094  -1.6168  -0.2104
 PB1  H21   H  HCH2  0   0.216  -2.5168  -1.3057   0.5545
 PB1  H22   H  HCH2  0   0.235  -2.3715  -1.4482  -1.1659
 PB1  HN11  H  HNH2  0   0.349  -3.8189   0.2998  -0.7346
 PB1  HN12  H  HNH2  0   0.342  -2.7952   1.0685   0.2410
 PB1  H4    H  HCH1  0   0.229  -0.7977   1.0540   1.1109
 PB1  H91   H  HCH2  0   0.266   0.0784  -1.6155   2.3163
 PB1  H92   H  HCH2  0   0.296  -1.5704  -1.0734   2.2481
 PB1  HO2   H  HOH1  0   0.478  -0.1182  -0.2852   5.4330
 PB1  H51   H  HCH2  0   0.236   1.4419   1.1651   1.9784
 PB1  H52   H  HCH2  0   0.235   1.4479   1.2555   0.2474
 PB1  H111  H  HCH2  0   0.218   2.2055  -1.1686   1.9356
 PB1  H112  H  HCH2  0   0.196   2.0850  -1.2256   0.1902
 PB1  H121  H  HNH2  0   0.346   4.3124  -0.7479   1.0717
 PB1  H122  H  HNH2  0   0.337   3.7997   0.4398   0.1104

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    single  1.331  0.020  1.331
 PB1  O3   HO3   single  0.850  0.020  0.980
 PB1  C8   O4    double  1.206  0.020  1.206
 PB1  C8   C7    single  1.503  0.020  1.503
 PB1  C7   C6    single  1.519  0.020  1.519
 PB1  C7   H71   single  0.970  0.020  1.090
 PB1  C7   H72   single  0.970  0.020  1.090
 PB1  C6   C3    single  1.533  0.020  1.533
 PB1  C6   H61   single  0.970  0.020  1.090
 PB1  C6   H62   single  0.970  0.020  1.090
 PB1  C3   C2    single  1.534  0.020  1.534
 PB1  C3   C4    single  1.548  0.020  1.548
 PB1  C3   H3    single  0.970  0.020  1.090
 PB1  C2   N1    single  1.455  0.020  1.455
 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  1.535  0.020  1.535
 PB1  C4   H4    single  0.970  0.020  1.090
 PB1  C9   C10   single  1.504  0.020  1.504
 PB1  C9   H91   single  0.970  0.020  1.090
 PB1  C9   H92   single  0.970  0.020  1.090
 PB1  C10  O1    double  1.207  0.020  1.207
 PB1  C10  O2    single  1.330  0.020  1.330
 PB1  O2   HO2   single  0.850  0.020  0.980
 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  1.457  0.020  1.457
 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  HO3   O3   C8    109.93  3.000
 PB1  C7    C8   O4    125.70  3.000
 PB1  C7    C8   O3    111.60  3.000
 PB1  O4    C8   O3    122.70  3.000
 PB1  H72   C7   H71   105.83  3.000
 PB1  H72   C7   C6    110.74  3.000
 PB1  H71   C7   C6    111.10  3.000
 PB1  H72   C7   C8    107.49  3.000
 PB1  H71   C7   C8    107.81  3.000
 PB1  C6    C7   C8    113.51  3.000
 PB1  H62   C6   H61   106.40  3.000
 PB1  H62   C6   C3    109.09  3.000
 PB1  H61   C6   C3    109.61  3.000
 PB1  H62   C6   C7    108.71  3.000
 PB1  H61   C6   C7    109.23  3.000
 PB1  C3    C6   C7    113.55  3.000
 PB1  H3    C3   C4    108.13  3.000
 PB1  H3    C3   C2    105.94  3.000
 PB1  C4    C3   C2    111.88  3.000
 PB1  H3    C3   C6    107.85  3.000
 PB1  C4    C3   C6    111.32  3.000
 PB1  C2    C3   C6    111.44  3.000
 PB1  H22   C2   H21   104.59  3.000
 PB1  H22   C2   N1    107.81  3.000
 PB1  H21   C2   N1    113.33  3.000
 PB1  H22   C2   C3    108.54  3.000
 PB1  H21   C2   C3    109.81  3.000
 PB1  N1    C2   C3    112.36  3.000
 PB1  HN12  N1   HN11  105.39  3.000
 PB1  HN12  N1   C2    110.16  3.000
 PB1  HN11  N1   C2    109.25  3.000
 PB1  H4    C4   C5    105.97  3.000
 PB1  H4    C4   C9    107.94  3.000
 PB1  C5    C4   C9    110.49  3.000
 PB1  H4    C4   C3    107.30  3.000
 PB1  C5    C4   C3    114.12  3.000
 PB1  C9    C4   C3    110.69  3.000
 PB1  H92   C9   H91   105.21  3.000
 PB1  H92   C9   C10   105.17  3.000
 PB1  H91   C9   C10   109.92  3.000
 PB1  H92   C9   C4    110.84  3.000
 PB1  H91   C9   C4    110.96  3.000
 PB1  C10   C9   C4    114.22  3.000
 PB1  O2    C10  O1    122.70  3.000
 PB1  O2    C10  C9    112.12  3.000
 PB1  O1    C10  C9    125.14  3.000
 PB1  HO2   O2   C10   109.86  3.000
 PB1  H52   C5   H51   104.90  3.000
 PB1  H52   C5   C11   109.11  3.000
 PB1  H51   C5   C11   108.33  3.000
 PB1  H52   C5   C4    109.15  3.000
 PB1  H51   C5   C4    108.99  3.000
 PB1  C11   C5   C4    115.81  3.000
 PB1  H112  C11  H111  105.96  3.000
 PB1  H112  C11  N12   113.04  3.000
 PB1  H111  C11  N12   107.55  3.000
 PB1  H112  C11  C5    110.29  3.000
 PB1  H111  C11  C5    109.88  3.000
 PB1  N12   C11  C5    109.99  3.000
 PB1  H122  N12  H121  105.50  3.000
 PB1  H122  N12  C11   109.27  3.000
 PB1  H121  N12  C11   109.44  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  CONST_01  HO3   O3   C8   O4     0.00   0.0  0
 PB1  CONST_02  HO2   O2   C10  C9   180.00   0.0  0
 PB1  Var_01    C6    C7   C8   O3   179.72  30.0  3
 PB1  Var_02    C3    C6   C7   C8  -171.72  30.0  3
 PB1  Var_03    O1    C10  C9   C4    30.20  30.0  3
 PB1  Var_04    N12   C11  C5   C4   177.63  30.0  3
 PB1  Var_05    HN11  N1   C2   C3   173.86  30.0  3
 PB1  Var_06    H121  N12  C11  C5   174.56  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-1  HO3  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
 PB1  plan-2  HO2  0.020

