# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 18:15:51 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (1S)-2-[(2S,5R)-2-(aminomethyl)-5-ethynylpyrrolidin-1-yl]-1-cyclopentyl-2-oxoethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CC[C@H](C#C)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
 AIA  AIA  (1S)-2-[(2S,5R)-2-(aminomethyl)-5-ethynylpyrrolidin-1-yl]-1-cyclopentyl-2-oxoethanamine  ligand  41  18  .  2022-07-24  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_AIA
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
 AIA  C2    C  CR15  0  -0.284   1.1822  -1.3703   0.8596
 AIA  C3    C  CR15  0  -0.051   2.4250   0.5687   0.1472
 AIA  C4    C  C     0   0.540   0.0841   0.8882   0.8210
 AIA  C5    C  CH2   0  -0.444   2.6161  -1.5110   1.3778
 AIA  C6    C  CSP   0   0.344   0.9593  -2.2017  -0.3294
 AIA  C7    C  CH2   0  -0.476   3.3942  -0.5827   0.4533
 AIA  C8    C  CH2   0  -0.287   2.4392   0.9817  -1.3206
 AIA  C9    C  CH1   0  -0.247  -1.2658   0.2926   1.2432
 AIA  N1    N  NR5   0  -0.466   1.1115   0.0522   0.5537
 AIA  O10   O  O     0  -0.494   0.2106   2.0991   0.6920
 AIA  C11   C  CSP1  0  -0.544   0.7972  -2.8967  -1.2965
 AIA  N12   N  NH2   0  -0.798   3.7641   1.4563  -1.6843
 AIA  C13   C  CH1   0  -0.228  -1.9742  -0.2820   0.0048
 AIA  N14   N  NH2   0  -0.772  -2.1053   1.2444   1.9350
 AIA  C16   C  CH2   0  -0.430  -3.3436  -0.9206   0.3436
 AIA  C17   C  CH2   0  -0.448  -2.2634   0.7582  -1.0984
 AIA  C18   C  CH2   0  -0.438  -4.3811  -0.1184  -0.4438
 AIA  C19   C  CH2   0  -0.441  -3.6123   0.3394  -1.6793
 AIA  H2    H  HCR5  0   0.304   0.4549  -1.6456   1.6231
 AIA  H3    H  HCR5  0   0.248   2.6615   1.4392   0.7668
 AIA  H51   H  HCH2  0   0.260   2.9693  -2.5410   1.3629
 AIA  H52   H  HCH2  0   0.256   2.6455  -1.1560   2.4094
 AIA  H71   H  HCH2  0   0.240   3.6646  -1.1023  -0.4684
 AIA  H72   H  HCH2  0   0.257   4.3182  -0.2270   0.9054
 AIA  H81   H  HCH2  0   0.215   1.6432   1.7142  -1.5004
 AIA  H82   H  HCH2  0   0.218   2.2052   0.1028  -1.9272
 AIA  H9    H  HCH1  0   0.257  -1.1026  -0.5365   1.9379
 AIA  H11   H  H     0   0.284   0.6490  -3.5025  -2.1613
 AIA  H121  H  HNH2  0   0.351   3.7985   1.6242  -2.6809
 AIA  H122  H  HNH2  0   0.340   3.9320   2.3560  -1.2504
 AIA  H13   H  HCH1  0   0.260  -1.3274  -1.0529  -0.4182
 AIA  H141  H  HNH2  0   0.350  -1.6754   1.4988   2.8153
 AIA  H142  H  HNH2  0   0.342  -2.1684   2.1048   1.4060
 AIA  H161  H  HCH2  0   0.220  -3.3520  -1.9632   0.0177
 AIA  H162  H  HCH2  0   0.230  -3.5446  -0.9177   1.4151
 AIA  H171  H  HCH2  0   0.218  -2.3542   1.7663  -0.6857
 AIA  H172  H  HCH2  0   0.233  -1.4679   0.7983  -1.8441
 AIA  H181  H  HCH2  0   0.225  -5.2788  -0.6934  -0.6779
 AIA  H182  H  HCH2  0   0.214  -4.6934   0.7561   0.1339
 AIA  H191  H  HCH2  0   0.215  -3.4849  -0.4975  -2.3726
 AIA  H192  H  HCH2  0   0.228  -4.1079   1.1424  -2.2275

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
 AIA  C2   C5    single  1.531  0.020  1.531
 AIA  C2   C6    single  1.468  0.020  1.468
 AIA  C2   N1    single  1.457  0.020  1.457
 AIA  C2   H2    single  0.939  0.020  1.096
 AIA  C3   C7    single  1.536  0.020  1.536
 AIA  C3   C8    single  1.525  0.020  1.525
 AIA  C3   N1    single  1.469  0.020  1.469
 AIA  C3   H3    single  0.939  0.020  1.096
 AIA  C4   C9    single  1.535  0.020  1.535
 AIA  C4   N1    single  1.351  0.020  1.351
 AIA  C4   O10   double  1.224  0.020  1.224
 AIA  C5   C7    single  1.524  0.020  1.524
 AIA  C5   H51   single  0.939  0.020  1.096
 AIA  C5   H52   single  0.939  0.020  1.096
 AIA  C6   C11   triple  1.202  0.020  1.202
 AIA  C7   H71   single  0.939  0.020  1.096
 AIA  C7   H72   single  0.939  0.020  1.096
 AIA  C8   N12   single  1.454  0.020  1.454
 AIA  C8   H81   single  0.939  0.020  1.096
 AIA  C8   H82   single  0.939  0.020  1.096
 AIA  C9   C13   single  1.538  0.020  1.538
 AIA  C9   N14   single  1.445  0.020  1.445
 AIA  C9   H9    single  0.939  0.020  1.096
 AIA  C11  H11   single  0.913  0.020  1.066
 AIA  N12  H121  single  0.868  0.020  1.013
 AIA  N12  H122  single  0.868  0.020  1.013
 AIA  C13  C16   single  1.549  0.020  1.549
 AIA  C13  C17   single  1.544  0.020  1.544
 AIA  C13  H13   single  0.939  0.020  1.096
 AIA  N14  H141  single  0.868  0.020  1.013
 AIA  N14  H142  single  0.868  0.020  1.013
 AIA  C16  C18   single  1.530  0.020  1.530
 AIA  C16  H161  single  0.939  0.020  1.096
 AIA  C16  H162  single  0.939  0.020  1.096
 AIA  C17  C19   single  1.527  0.020  1.527
 AIA  C17  H171  single  0.939  0.020  1.096
 AIA  C17  H172  single  0.939  0.020  1.096
 AIA  C18  C19   single  1.525  0.020  1.525
 AIA  C18  H181  single  0.939  0.020  1.096
 AIA  C18  H182  single  0.939  0.020  1.096
 AIA  C19  H191  single  0.939  0.020  1.096
 AIA  C19  H192  single  0.939  0.020  1.096

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
 AIA  H2    C2   N1    111.19  3.000
 AIA  H2    C2   C6    108.85  3.000
 AIA  N1    C2   C6    112.06  3.000
 AIA  H2    C2   C5    111.38  3.000
 AIA  N1    C2   C5    101.90  3.000
 AIA  C6    C2   C5    111.37  3.000
 AIA  H3    C3   N1    108.44  3.000
 AIA  H3    C3   C8    109.12  3.000
 AIA  N1    C3   C8    111.71  3.000
 AIA  H3    C3   C7    110.32  3.000
 AIA  N1    C3   C7    104.22  3.000
 AIA  C8    C3   C7    112.89  3.000
 AIA  O10   C4   N1    120.83  3.000
 AIA  O10   C4   C9    120.25  3.000
 AIA  N1    C4   C9    118.89  3.000
 AIA  H52   C5   H51   108.18  3.000
 AIA  H52   C5   C7    111.20  3.000
 AIA  H51   C5   C7    113.72  3.000
 AIA  H52   C5   C2    108.37  3.000
 AIA  H51   C5   C2    112.71  3.000
 AIA  C7    C5   C2    102.52  3.000
 AIA  C11   C6   C2    180.00  3.000
 AIA  H72   C7   H71   107.21  3.000
 AIA  H72   C7   C5    112.37  3.000
 AIA  H71   C7   C5    110.41  3.000
 AIA  H72   C7   C3    111.93  3.000
 AIA  H71   C7   C3    110.17  3.000
 AIA  C5    C7   C3    104.80  3.000
 AIA  H82   C8   H81   106.90  3.000
 AIA  H82   C8   N12   108.59  3.000
 AIA  H81   C8   N12   113.74  3.000
 AIA  H82   C8   C3    108.32  3.000
 AIA  H81   C8   C3    109.39  3.000
 AIA  N12   C8   C3    109.74  3.000
 AIA  H9    C9   N14   106.37  3.000
 AIA  H9    C9   C13   107.27  3.000
 AIA  N14   C9   C13   111.33  3.000
 AIA  H9    C9   C4    109.74  3.000
 AIA  N14   C9   C4    112.77  3.000
 AIA  C13   C9   C4    109.18  3.000
 AIA  C4    N1   C3    121.14  3.000
 AIA  C4    N1   C2    126.83  3.000
 AIA  C3    N1   C2    110.98  3.000
 AIA  H11   C11  C6    180.00  3.000
 AIA  H122  N12  H121  105.61  3.000
 AIA  H122  N12  C8    109.51  3.000
 AIA  H121  N12  C8    109.37  3.000
 AIA  H13   C13  C17   108.06  3.000
 AIA  H13   C13  C16   108.51  3.000
 AIA  C17   C13  C16   105.58  3.000
 AIA  H13   C13  C9    107.64  3.000
 AIA  C17   C13  C9    114.21  3.000
 AIA  C16   C13  C9    112.66  3.000
 AIA  H142  N14  H141  105.51  3.000
 AIA  H142  N14  C9    110.24  3.000
 AIA  H141  N14  C9    109.57  3.000
 AIA  H162  C16  H161  107.12  3.000
 AIA  H162  C16  C18   112.30  3.000
 AIA  H161  C16  C18   109.98  3.000
 AIA  H162  C16  C13   112.15  3.000
 AIA  H161  C16  C13   109.59  3.000
 AIA  C18   C16  C13   105.71  3.000
 AIA  H172  C17  H171  106.54  3.000
 AIA  H172  C17  C19   113.21  3.000
 AIA  H171  C17  C19   108.86  3.000
 AIA  H172  C17  C13   112.12  3.000
 AIA  H171  C17  C13   111.54  3.000
 AIA  C19   C17  C13   104.63  3.000
 AIA  H182  C18  H181  107.44  3.000
 AIA  H182  C18  C19   109.38  3.000
 AIA  H181  C18  C19   113.51  3.000
 AIA  H182  C18  C16   109.94  3.000
 AIA  H181  C18  C16   113.07  3.000
 AIA  C19   C18  C16   103.45  3.000
 AIA  H192  C19  H191  107.30  3.000
 AIA  H192  C19  C18   113.50  3.000
 AIA  H191  C19  C18   110.02  3.000
 AIA  H192  C19  C17   112.98  3.000
 AIA  H191  C19  C17   110.36  3.000
 AIA  C18   C19  C17   102.67  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
 AIA  CONST_01  C9    C4   N1   C2     0.00   0.0  0
 AIA  CONST_02  O10   C4   N1   C2   180.00   0.0  0
 AIA  CONST_03  C9    C4   N1   C3   180.00   0.0  0
 AIA  CONST_04  O10   C4   N1   C3     0.00   0.0  0
 AIA  Var_01    C3    C7   C5   C2    33.98  30.0  1
 AIA  Var_02    C19   C18  C16  C13   30.15  30.0  1
 AIA  Var_03    C17   C19  C18  C16  -42.28  30.0  1
 AIA  Var_04    H121  N12  C8   C3   173.31  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
 AIA  chir_01  C2   C5   C6   N1   positiv
 AIA  chir_02  C3   N1   C8   C7   positiv
 AIA  chir_03  C9   N14  C4   C13  positiv
 AIA  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
 AIA  plan-1  C2   0.020
 AIA  plan-1  C3   0.020
 AIA  plan-1  C4   0.020
 AIA  plan-1  C9   0.020
 AIA  plan-1  N1   0.020
 AIA  plan-1  O10  0.020

