# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 23:32:20 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (1S)-2-[(2S,5R)-2-(aminomethyl)-5-prop-1-yn-1-ylpyrrolidin-1-yl]-1-cyclopentyl-2-oxoethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#C[C@H]1CC[C@@H](CN)N1C(=O)[C@@H](N)C2CCCC2
#
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
 1AD  1AD  (1S)-2-[(2S,5R)-2-(aminomethyl)-5-prop-1-yn-1-ylpyrrolidin-1-yl]-1-cyclopentyl-2-oxoethanamine  ligand  44  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1AD
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
 1AD  C2    C  CR15  0  -0.327  -1.4853  -0.8155  -1.2320
 1AD  C3    C  CR15  0  -0.079  -2.4227   0.8414   0.2371
 1AD  C4    C  C     0   0.580  -0.1793   1.2503  -0.6851
 1AD  C5    C  CH2   0  -0.439  -2.9598  -0.6430  -1.6120
 1AD  C6    C  CSP   0   0.224  -1.2457  -2.0164  -0.4260
 1AD  C7    C  CH2   0  -0.482  -3.5620   0.0022  -0.3698
 1AD  C8    C  CH2   0  -0.258  -2.3189   0.6054   1.7407
 1AD  C9    C  CH1   0  -0.244   1.0978   0.6642  -1.2756
 1AD  N1    N  NR5   0  -0.453  -1.2258   0.4155  -0.4921
 1AD  O10   O  O     0  -0.495  -0.2099   2.4204  -0.3315
 1AD  C11   C  CSP   0  -0.050  -1.0463  -3.0121   0.2202
 1AD  N12   N  NH2   0  -0.771  -1.1886   1.2741   2.3534
 1AD  C13   C  CR15  0  -0.227   1.8430  -0.0813  -0.1435
 1AD  N14   N  NH2   0  -0.793   1.8372   1.7190  -1.9382
 1AD  C15   C  CH3   0  -0.821  -0.8037  -4.2060   1.0148
 1AD  C16   C  CH2   0  -0.462   3.1286  -0.7880  -0.6458
 1AD  C17   C  CH2   0  -0.451   2.2977   0.8245   1.0151
 1AD  C18   C  CH2   0  -0.436   4.2838  -0.1498   0.1307
 1AD  C19   C  CH2   0  -0.441   3.6410   0.2483   1.4567
 1AD  H2    H  HCR5  0   0.293  -0.8652  -0.8638  -2.1269
 1AD  H3    H  HCR5  0   0.250  -2.5845   1.9052   0.0487
 1AD  H51   H  HCH2  0   0.252  -3.0139   0.0319  -2.4681
 1AD  H52   H  HCH2  0   0.256  -3.4355  -1.5825  -1.8893
 1AD  H71   H  HCH2  0   0.258  -4.4350   0.6115  -0.5998
 1AD  H72   H  HCH2  0   0.239  -3.8859  -0.7691   0.3330
 1AD  H81   H  HCH2  0   0.195  -3.2931   0.8934   2.1657
 1AD  H82   H  HCH2  0   0.213  -2.2156  -0.4696   1.9140
 1AD  H9    H  HCH1  0   0.252   0.8662  -0.0843  -2.0369
 1AD  H121  H  HNH2  0   0.337  -1.2403   2.2701   2.1856
 1AD  H122  H  HNH2  0   0.344  -1.2345   1.1507   3.3565
 1AD  H13   H  HCR5  0   0.251   1.1617  -0.8398   0.2506
 1AD  H141  H  HNH2  0   0.345   1.9911   2.4902  -1.3025
 1AD  H142  H  HNH2  0   0.351   2.7507   1.3770  -2.2097
 1AD  H151  H  HCH3  0   0.266  -1.5619  -4.3234   1.7894
 1AD  H152  H  HCH3  0   0.266  -0.8211  -5.1018   0.3937
 1AD  H153  H  HCH3  0   0.266   0.1693  -4.1596   1.5044
 1AD  H161  H  HCH2  0   0.232   3.0706  -1.8553  -0.4215
 1AD  H162  H  HCH2  0   0.228   3.2620  -0.7093  -1.7281
 1AD  H171  H  HCH2  0   0.206   2.4602   1.8478   0.6635
 1AD  H172  H  HCH2  0   0.246   1.5453   0.8782   1.8021
 1AD  H181  H  HCH2  0   0.228   5.1426  -0.8141   0.2397
 1AD  H182  H  HCH2  0   0.213   4.6291   0.7495  -0.3880
 1AD  H191  H  HCH2  0   0.213   3.4959  -0.6357   2.0848
 1AD  H192  H  HCH2  0   0.225   4.2408   0.9576   2.0301

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
 1AD  C2   C5    single  1.533  0.020  1.533
 1AD  C2   C6    single  1.466  0.020  1.466
 1AD  C2   N1    single  1.459  0.020  1.459
 1AD  C2   H2    single  0.970  0.020  1.090
 1AD  C3   C7    single  1.540  0.020  1.540
 1AD  C3   C8    single  1.525  0.020  1.525
 1AD  C3   N1    single  1.465  0.020  1.465
 1AD  C3   H3    single  0.970  0.020  1.090
 1AD  C4   C9    single  1.524  0.020  1.524
 1AD  C4   N1    single  1.352  0.020  1.352
 1AD  C4   O10   double  1.223  0.020  1.223
 1AD  C5   C7    single  1.524  0.020  1.524
 1AD  C5   H51   single  0.970  0.020  1.090
 1AD  C5   H52   single  0.970  0.020  1.090
 1AD  C6   C11   triple  1.204  0.020  1.204
 1AD  C7   H71   single  0.970  0.020  1.090
 1AD  C7   H72   single  0.970  0.020  1.090
 1AD  C8   N12   single  1.449  0.020  1.449
 1AD  C8   H81   single  0.970  0.020  1.090
 1AD  C8   H82   single  0.970  0.020  1.090
 1AD  C9   C13   single  1.547  0.020  1.547
 1AD  C9   N14   single  1.449  0.020  1.449
 1AD  C9   H9    single  0.970  0.020  1.090
 1AD  C11  C15   single  1.455  0.020  1.455
 1AD  N12  H121  single  0.890  0.020  1.040
 1AD  N12  H122  single  0.890  0.020  1.040
 1AD  C13  C16   single  1.551  0.020  1.551
 1AD  C13  C17   single  1.539  0.020  1.539
 1AD  C13  H13   single  0.970  0.020  1.090
 1AD  N14  H141  single  0.890  0.020  1.040
 1AD  N14  H142  single  0.890  0.020  1.040
 1AD  C15  H151  single  0.970  0.020  1.090
 1AD  C15  H152  single  0.970  0.020  1.090
 1AD  C15  H153  single  0.970  0.020  1.090
 1AD  C16  C18   single  1.531  0.020  1.531
 1AD  C16  H161  single  0.970  0.020  1.090
 1AD  C16  H162  single  0.970  0.020  1.090
 1AD  C17  C19   single  1.527  0.020  1.527
 1AD  C17  H171  single  0.970  0.020  1.090
 1AD  C17  H172  single  0.970  0.020  1.090
 1AD  C18  C19   single  1.526  0.020  1.526
 1AD  C18  H181  single  0.970  0.020  1.090
 1AD  C18  H182  single  0.970  0.020  1.090
 1AD  C19  H191  single  0.970  0.020  1.090
 1AD  C19  H192  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
 1AD  H2    C2   N1    110.64  3.000
 1AD  H2    C2   C6    108.80  3.000
 1AD  N1    C2   C6    112.53  3.000
 1AD  H2    C2   C5    110.41  3.000
 1AD  N1    C2   C5    101.64  3.000
 1AD  C6    C2   C5    112.69  3.000
 1AD  H3    C3   N1    108.56  3.000
 1AD  H3    C3   C8    109.31  3.000
 1AD  N1    C3   C8    112.96  3.000
 1AD  H3    C3   C7    110.68  3.000
 1AD  N1    C3   C7    104.47  3.000
 1AD  C8    C3   C7    110.76  3.000
 1AD  O10   C4   N1    122.01  3.000
 1AD  O10   C4   C9    120.06  3.000
 1AD  N1    C4   C9    117.80  3.000
 1AD  H52   C5   H51   108.19  3.000
 1AD  H52   C5   C7    113.60  3.000
 1AD  H51   C5   C7    110.98  3.000
 1AD  H52   C5   C2    112.73  3.000
 1AD  H51   C5   C2    108.17  3.000
 1AD  C7    C5   C2    103.05  3.000
 1AD  C11   C6   C2    180.00  3.000
 1AD  H72   C7   H71   107.04  3.000
 1AD  H72   C7   C5    110.03  3.000
 1AD  H71   C7   C5    112.42  3.000
 1AD  H72   C7   C3    110.53  3.000
 1AD  H71   C7   C3    111.81  3.000
 1AD  C5    C7   C3    105.05  3.000
 1AD  H82   C8   H81   106.22  3.000
 1AD  H82   C8   N12   108.23  3.000
 1AD  H81   C8   N12   113.96  3.000
 1AD  H82   C8   C3    108.34  3.000
 1AD  H81   C8   C3    106.25  3.000
 1AD  N12   C8   C3    113.48  3.000
 1AD  H9    C9   N14   106.76  3.000
 1AD  H9    C9   C13   106.37  3.000
 1AD  N14   C9   C13   116.09  3.000
 1AD  H9    C9   C4    110.84  3.000
 1AD  N14   C9   C4    108.96  3.000
 1AD  C13   C9   C4    107.78  3.000
 1AD  C4    N1   C3    121.59  3.000
 1AD  C4    N1   C2    125.86  3.000
 1AD  C3    N1   C2    110.64  3.000
 1AD  C15   C11  C6    180.00  3.000
 1AD  H122  N12  H121  106.40  3.000
 1AD  H122  N12  C8    109.12  3.000
 1AD  H121  N12  C8    110.14  3.000
 1AD  H13   C13  C17   108.73  3.000
 1AD  H13   C13  C16   108.50  3.000
 1AD  C17   C13  C16   105.49  3.000
 1AD  H13   C13  C9    107.34  3.000
 1AD  C17   C13  C9    114.18  3.000
 1AD  C16   C13  C9    112.45  3.000
 1AD  H142  N14  H141  106.79  3.000
 1AD  H142  N14  C9    109.71  3.000
 1AD  H141  N14  C9    110.21  3.000
 1AD  H153  C15  H152  107.76  3.000
 1AD  H153  C15  H151  107.83  3.000
 1AD  H152  C15  H151  107.77  3.000
 1AD  H153  C15  C11   111.05  3.000
 1AD  H152  C15  C11   111.14  3.000
 1AD  H151  C15  C11   111.13  3.000
 1AD  H162  C16  H161  106.26  3.000
 1AD  H162  C16  C18   112.33  3.000
 1AD  H161  C16  C18   110.08  3.000
 1AD  H162  C16  C13   112.90  3.000
 1AD  H161  C16  C13   109.56  3.000
 1AD  C18   C16  C13   105.74  3.000
 1AD  H172  C17  H171  106.76  3.000
 1AD  H172  C17  C19   114.65  3.000
 1AD  H171  C17  C19   108.37  3.000
 1AD  H172  C17  C13   111.62  3.000
 1AD  H171  C17  C13   110.63  3.000
 1AD  C19   C17  C13   104.80  3.000
 1AD  H182  C18  H181  107.42  3.000
 1AD  H182  C18  C19   109.29  3.000
 1AD  H181  C18  C19   113.79  3.000
 1AD  H182  C18  C16   109.89  3.000
 1AD  H181  C18  C16   113.00  3.000
 1AD  C19   C18  C16   103.38  3.000
 1AD  H192  C19  H191  107.23  3.000
 1AD  H192  C19  C18   113.23  3.000
 1AD  H191  C19  C18   110.11  3.000
 1AD  H192  C19  C17   112.96  3.000
 1AD  H191  C19  C17   110.75  3.000
 1AD  C18   C19  C17   102.57  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
 1AD  CONST_03  C9    C4   N1   C3   180.00   0.0  0
 1AD  CONST_04  O10   C4   N1   C3     0.00   0.0  0
 1AD  Var_01    C3    C7   C5   C2    30.93  30.0  1
 1AD  Var_02    C19   C18  C16  C13   29.84  30.0  1
 1AD  Var_03    C17   C19  C18  C16  -42.19  30.0  1
 1AD  Var_04    H121  N12  C8   C3    57.98  30.0  3
 1AD  Var_05    H151  C15  C11  C6    61.15  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
 1AD  chir_01  C2   C5   C6   N1   positiv
 1AD  chir_02  C3   N1   C8   C7   positiv
 1AD  chir_03  C9   N14  C4   C13  positiv
 1AD  chir_04  C13  C17  C16  C9   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
 1AD  plan-1  C2   0.020
 1AD  plan-1  C3   0.020
 1AD  plan-1  C4   0.020
 1AD  plan-1  C9   0.020
 1AD  plan-1  N1   0.020
 1AD  plan-1  O10  0.020

