# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 14:37:00 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3R,5R)-5-amino-3-methyl-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](N)N[C@H]1C(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
 X7O  X7O  (3R,5R)-5-amino-3-methyl-D-proline  ligand  22  10  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X7O
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
 X7O  C1    C  C     0   0.533  -0.2370   0.7731   0.8182
 X7O  C2    C  CH1   0  -0.207  -1.5408   0.4725   1.5369
 X7O  C3    C  CH1   0  -0.253  -1.4929   0.9869   2.9906
 X7O  C4    C  CH2   0  -0.499  -1.8778   2.4589   2.8022
 X7O  C5    C  CH1   0   0.085  -2.7618   2.5119   1.5319
 X7O  C6    C  CH3   0  -0.657  -2.4641   0.2203   3.8800
 X7O  O1    O  O     0  -0.438  -0.0853   1.6436  -0.0023
 X7O  N1    N  NH1   0  -0.605  -2.6779   1.1621   0.9966
 X7O  N2    N  NH2   0  -0.793  -4.1576   2.8627   1.7085
 X7O  O2    O  OH1   0  -0.595   0.7371  -0.0443   1.2041
 X7O  HC2   H  HCH1  0   0.276  -1.6878  -0.6134   1.5119
 X7O  HC3   H  HCH1  0   0.254  -0.4904   0.8906   3.4105
 X7O  HC41  H  HCH2  0   0.244  -2.4008   2.8623   3.6712
 X7O  HC42  H  HCH2  0   0.245  -0.9842   3.0702   2.6631
 X7O  HC5   H  HCH1  0   0.218  -2.3478   3.2542   0.8406
 X7O  HC61  H  HCH3  0   0.232  -2.4964   0.6598   4.8778
 X7O  HC62  H  HCH3  0   0.223  -3.4777   0.2334   3.4769
 X7O  HC63  H  HCH3  0   0.231  -2.1613  -0.8225   3.9866
 X7O  HN1   H  HNH1  0   0.353  -2.7437   1.1260  -0.0108
 X7O  HN21  H  HNH2  0   0.340  -4.2305   3.8305   1.9979
 X7O  HN22  H  HNH2  0   0.332  -4.5556   2.3098   2.4594
 X7O  HO2   H  HOH1  0   0.480   1.5615   0.1806   0.7477

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
 X7O  C1  C2    single  1.519  0.020  1.519
 X7O  C1  O1    double  1.206  0.020  1.206
 X7O  C1  O2    single  1.329  0.020  1.329
 X7O  C2  C3    single  1.543  0.020  1.543
 X7O  C2  N1    single  1.435  0.020  1.435
 X7O  C2  HC2   single  0.970  0.020  1.090
 X7O  C3  C4    single  1.533  0.020  1.533
 X7O  C3  C6    single  1.524  0.020  1.524
 X7O  C3  HC3   single  0.970  0.020  1.090
 X7O  C4  C5    single  1.548  0.020  1.548
 X7O  C4  HC41  single  0.970  0.020  1.090
 X7O  C4  HC42  single  0.970  0.020  1.090
 X7O  C5  N1    single  1.454  0.020  1.454
 X7O  C5  N2    single  1.450  0.020  1.450
 X7O  C5  HC5   single  0.970  0.020  1.090
 X7O  C6  HC61  single  0.970  0.020  1.090
 X7O  C6  HC62  single  0.970  0.020  1.090
 X7O  C6  HC63  single  0.970  0.020  1.090
 X7O  N1  HN1   single  0.890  0.020  1.040
 X7O  N2  HN21  single  0.890  0.020  1.040
 X7O  N2  HN22  single  0.890  0.020  1.040
 X7O  O2  HO2   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
 X7O  O2    C1  O1    123.33  3.000
 X7O  O2    C1  C2    111.72  3.000
 X7O  O1    C1  C2    124.95  3.000
 X7O  HC2   C2  N1    111.17  3.000
 X7O  HC2   C2  C3    110.86  3.000
 X7O  N1    C2  C3    102.65  3.000
 X7O  HC2   C2  C1    107.48  3.000
 X7O  N1    C2  C1    114.00  3.000
 X7O  C3    C2  C1    110.68  3.000
 X7O  HC3   C3  C6    108.46  3.000
 X7O  HC3   C3  C4    111.27  3.000
 X7O  C6    C3  C4    113.25  3.000
 X7O  HC3   C3  C2    111.20  3.000
 X7O  C6    C3  C2    111.25  3.000
 X7O  C4    C3  C2    101.33  3.000
 X7O  HC42  C4  HC41  106.66  3.000
 X7O  HC42  C4  C5    110.10  3.000
 X7O  HC41  C4  C5    111.53  3.000
 X7O  HC42  C4  C3    110.36  3.000
 X7O  HC41  C4  C3    112.16  3.000
 X7O  C5    C4  C3    106.08  3.000
 X7O  HC5   C5  N2    106.06  3.000
 X7O  HC5   C5  N1    112.01  3.000
 X7O  N2    C5  N1    108.96  3.000
 X7O  HC5   C5  C4    108.97  3.000
 X7O  N2    C5  C4    117.25  3.000
 X7O  N1    C5  C4    103.72  3.000
 X7O  HC63  C6  HC62  107.78  3.000
 X7O  HC63  C6  HC61  107.69  3.000
 X7O  HC62  C6  HC61  107.80  3.000
 X7O  HC63  C6  C3    111.16  3.000
 X7O  HC62  C6  C3    111.75  3.000
 X7O  HC61  C6  C3    110.50  3.000
 X7O  HN1   N1  C5    113.35  3.000
 X7O  HN1   N1  C2    114.19  3.000
 X7O  C5    N1  C2    110.68  3.000
 X7O  HN22  N2  HN21  106.34  3.000
 X7O  HN22  N2  C5    109.64  3.000
 X7O  HN21  N2  C5    109.60  3.000
 X7O  HO2   O2  C1    110.13  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
 X7O  CONST_01  HO2  O2  C1  C2  180.00  0.0  0

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
 X7O  chir_01  C2  C1  C3  N1  negativ
 X7O  chir_02  C3  C2  C4  C6  negativ
 X7O  chir_03  C5  N2  N1  C4  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
 X7O  plan-1  C1   0.020
 X7O  plan-1  C2   0.020
 X7O  plan-1  O1   0.020
 X7O  plan-1  O2   0.020
 X7O  plan-1  HO2  0.020

