# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 21:49:20 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: (1R,2S,3R,4R)-3-amino-4-(3-methylphenyl)cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)[C@H]2C[C@@H](O)[C@@H](O)[C@@H]2N
#
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
 D74  D74  (1R,2S,3R,4R)-3-amino-4-(3-methylphenyl)cyclopentane-1,2-diol  ligand  32  15  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D74
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
 D74  C4   C  CR16  0  -0.356  -11.6824   1.1730  -0.6437
 D74  C5   C  CR6   0   0.200  -10.9055   1.9285   0.2281
 D74  C6   C  CR16  0  -0.362  -11.4163   3.1396   0.6953
 D74  C7   C  CH1   0  -0.357   -9.5529   1.4461   0.6733
 D74  C8   C  CH2   0  -0.456   -8.3821   2.4322   0.4105
 D74  C9   C  CH1   0   0.008   -7.5707   2.5074   1.7040
 D74  C10  C  CH1   0   0.028   -7.9773   1.2313   2.4398
 D74  C11  C  CH1   0  -0.071   -9.4753   1.1374   2.1746
 D74  O1   O  OH1   0  -0.675   -7.9604   3.6634   2.4183
 D74  O    O  OH1   0  -0.680   -7.6176   1.2935   3.7988
 D74  N    N  NH2   0  -0.806  -10.0255  -0.1653   2.4970
 D74  C3   C  CR16  0  -0.226  -12.9359   1.6237  -1.0400
 D74  C2   C  CR16  0  -0.320  -13.4274   2.8295  -0.5651
 D74  C1   C  CR6   0   0.116  -12.6714   3.6035   0.3160
 D74  C    C  CH3   0  -0.722  -13.2107   4.8929   0.8655
 D74  H1   H  HCR6  0   0.244  -11.3044   0.2293  -1.0192
 D74  H2   H  HCR6  0   0.234  -10.8170   3.7409   1.3719
 D74  H3   H  HCH1  0   0.247   -9.3391   0.5069   0.1535
 D74  H4   H  HCH2  0   0.254   -7.7644   2.0672  -0.4099
 D74  H5   H  HCH2  0   0.246   -8.7282   3.4255   0.1223
 D74  H6   H  HCH1  0   0.220   -6.4908   2.5247   1.5093
 D74  H7   H  HCH1  0   0.212   -7.4909   0.3817   1.9390
 D74  H8   H  HCH1  0   0.208   -9.9632   1.9546   2.7274
 D74  H9   H  HOH1  0   0.445   -7.5541   3.6255   3.2908
 D74  H10  H  HOH1  0   0.458   -7.4632   0.4041   4.1264
 D74  H11  H  HNH2  0   0.342   -9.9950  -0.3026   3.5004
 D74  H12  H  HNH2  0   0.344  -11.0115  -0.1809   2.2630
 D74  H14  H  HCR6  0   0.250  -13.5290   1.0325  -1.7262
 D74  H15  H  HCR6  0   0.244  -14.4047   3.1746  -0.8820
 D74  H16  H  HCH3  0   0.247  -13.7762   4.7191   1.7835
 D74  H17  H  HCH3  0   0.242  -12.4103   5.5919   1.1073
 D74  H18  H  HCH3  0   0.242  -13.8841   5.3799   0.1606

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
 D74  C3   C4   aromatic  1.390  0.020  1.390
 D74  C3   C2   aromatic  1.386  0.020  1.386
 D74  C4   C5   aromatic  1.391  0.020  1.391
 D74  C2   C1   aromatic  1.395  0.020  1.395
 D74  C5   C7   single    1.503  0.020  1.503
 D74  C5   C6   aromatic  1.395  0.020  1.395
 D74  C1   C6   aromatic  1.391  0.020  1.391
 D74  C1   C    single    1.502  0.020  1.502
 D74  C8   C7   single    1.553  0.020  1.553
 D74  C8   C9   single    1.529  0.020  1.529
 D74  C7   C11  single    1.535  0.020  1.535
 D74  C9   C10  single    1.528  0.020  1.528
 D74  C9   O1   single    1.414  0.020  1.414
 D74  C11  C10  single    1.524  0.020  1.524
 D74  C11  N    single    1.450  0.020  1.450
 D74  C10  O    single    1.407  0.020  1.407
 D74  C4   H1   single    0.930  0.020  1.080
 D74  C6   H2   single    0.930  0.020  1.080
 D74  C7   H3   single    0.970  0.020  1.090
 D74  C8   H4   single    0.970  0.020  1.090
 D74  C8   H5   single    0.970  0.020  1.090
 D74  C9   H6   single    0.970  0.020  1.090
 D74  C10  H7   single    0.970  0.020  1.090
 D74  C11  H8   single    0.970  0.020  1.090
 D74  O1   H9   single    0.850  0.020  0.980
 D74  O    H10  single    0.850  0.020  0.980
 D74  N    H11  single    0.890  0.020  1.040
 D74  N    H12  single    0.890  0.020  1.040
 D74  C3   H14  single    0.930  0.020  1.080
 D74  C2   H15  single    0.930  0.020  1.080
 D74  C    H16  single    0.970  0.020  1.090
 D74  C    H17  single    0.970  0.020  1.090
 D74  C    H18  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
 D74  H1   C4   C3   119.88  3.000
 D74  H1   C4   C5   119.69  3.000
 D74  C3   C4   C5   120.43  3.000
 D74  C7   C5   C6   120.59  3.000
 D74  C6   C5   C4   118.48  3.000
 D74  C7   C5   C4   120.92  3.000
 D74  H2   C6   C1   118.91  3.000
 D74  H2   C6   C5   119.17  3.000
 D74  C1   C6   C5   121.92  3.000
 D74  H3   C7   C11  106.39  3.000
 D74  H3   C7   C8   108.49  3.000
 D74  C11  C7   C8   104.78  3.000
 D74  H3   C7   C5   108.09  3.000
 D74  C11  C7   C5   113.56  3.000
 D74  C8   C7   C5   115.11  3.000
 D74  H5   C8   H4   106.62  3.000
 D74  H5   C8   C9   110.31  3.000
 D74  H4   C8   C9   110.65  3.000
 D74  H5   C8   C7   112.56  3.000
 D74  H4   C8   C7   110.00  3.000
 D74  C9   C8   C7   106.75  3.000
 D74  H6   C9   O1   110.37  3.000
 D74  H6   C9   C10  111.13  3.000
 D74  O1   C9   C10  111.48  3.000
 D74  H6   C9   C8   111.89  3.000
 D74  O1   C9   C8   108.75  3.000
 D74  C10  C9   C8   103.01  3.000
 D74  H7   C10  O    111.16  3.000
 D74  H7   C10  C11  107.93  3.000
 D74  O    C10  C11  114.96  3.000
 D74  H7   C10  C9   107.95  3.000
 D74  O    C10  C9   111.10  3.000
 D74  C11  C10  C9   103.25  3.000
 D74  H8   C11  N    112.77  3.000
 D74  H8   C11  C10  107.61  3.000
 D74  N    C11  C10  112.92  3.000
 D74  H8   C11  C7   108.64  3.000
 D74  N    C11  C7   112.26  3.000
 D74  C10  C11  C7   101.98  3.000
 D74  H9   O1   C9   108.01  3.000
 D74  H10  O    C10  109.24  3.000
 D74  H12  N    H11  104.82  3.000
 D74  H12  N    C11  109.36  3.000
 D74  H11  N    C11  109.29  3.000
 D74  H14  C3   C2   119.87  3.000
 D74  H14  C3   C4   119.85  3.000
 D74  C2   C3   C4   120.28  3.000
 D74  H15  C2   C1   119.78  3.000
 D74  H15  C2   C3   119.77  3.000
 D74  C1   C2   C3   120.46  3.000
 D74  C    C1   C2   120.84  3.000
 D74  C    C1   C6   120.71  3.000
 D74  C2   C1   C6   118.43  3.000
 D74  H18  C    H17  108.10  3.000
 D74  H18  C    H16  107.15  3.000
 D74  H17  C    H16  107.21  3.000
 D74  H18  C    C1   111.66  3.000
 D74  H17  C    C1   111.60  3.000
 D74  H16  C    C1   110.91  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
 D74  CONST_01  C1   C2  C3  C4    0.00   0.0  0
 D74  CONST_02  C1   C6  C5  C4    0.00   0.0  0
 D74  CONST_03  C2   C3  C4  C5    0.00   0.0  0
 D74  CONST_04  C2   C1  C6  C5    0.00   0.0  0
 D74  CONST_05  C3   C4  C5  C6    0.00   0.0  0
 D74  CONST_06  C3   C2  C1  C6    0.00   0.0  0
 D74  CONST_07  C3   C4  C5  C7  180.00   0.0  0
 D74  CONST_08  C1   C6  C5  C7  180.00   0.0  0
 D74  CONST_09  C    C1  C6  C5  180.00   0.0  0
 D74  CONST_10  C    C1  C2  C3  180.00   0.0  0
 D74  CONST_11  H15  C2  C3  C4  180.00   0.0  0
 D74  CONST_12  H2   C6  C5  C4  180.00   0.0  0
 D74  CONST_13  H14  C3  C4  C5  180.00   0.0  0
 D74  CONST_14  H1   C4  C5  C6  180.00   0.0  0
 D74  Var_01    H16  C   C1  C6  -90.19  30.0  2

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
 D74  chir_01  C7   C5  C8   C11  negativ
 D74  chir_02  C9   O1  C10  C8   negativ
 D74  chir_03  C10  O   C11  C9   negativ
 D74  chir_04  C11  N   C7   C10  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
 D74  plan-1  C4   0.020
 D74  plan-1  C5   0.020
 D74  plan-1  C6   0.020
 D74  plan-1  C7   0.020
 D74  plan-1  C3   0.020
 D74  plan-1  C2   0.020
 D74  plan-1  C1   0.020
 D74  plan-1  C    0.020
 D74  plan-1  H1   0.020
 D74  plan-1  H2   0.020
 D74  plan-1  H14  0.020
 D74  plan-1  H15  0.020

