# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 19:28:01 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2S)-1-[4-(aminomethyl)phenyl]-4-(methylsulfonyl)butan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)CC[C@@H](N)Cc1ccc(CN)cc1
#
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
 1G3  1G3  (2S)-1-[4-(aminomethyl)phenyl]-4-(methylsulfonyl)butan-2-amine  L-peptide  37  17  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1G3
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
 1G3  O50  O  OS    0  -0.683   4.8622  -0.3909  -1.0649
 1G3  S48  S  S     0   1.195   4.4581   0.0175   0.2784
 1G3  O49  O  OS    0  -0.630   4.5257  -0.9580   1.3556
 1G3  C51  C  CH3   0  -0.766   5.4387   1.4373   0.7365
 1G3  C47  C  CH2   0  -0.601   2.7828   0.6562   0.1871
 1G3  C46  C  CH2   0  -0.434   1.8100  -0.4686  -0.1344
 1G3  C36  C  CH1   0  -0.083   0.3622   0.0349  -0.2505
 1G3  C37  C  CH2   0  -0.506  -0.5805  -1.1569  -0.4668
 1G3  C38  C  CR6   0   0.177  -2.0270  -0.7825  -0.3273
 1G3  C43  C  CR16  0  -0.277  -2.6316  -0.7580   0.9266
 1G3  C42  C  CR16  0  -0.244  -3.9551  -0.3785   1.0809
 1G3  C41  C  CR6   0   0.083  -4.7213  -0.0192  -0.0237
 1G3  C44  C  CH2   0  -0.331  -6.1754   0.3472   0.1269
 1G3  N45  N  NH2   0  -0.754  -6.4144   1.1099   1.3369
 1G3  C40  C  CR16  0  -0.268  -4.1184  -0.0392  -1.2757
 1G3  C39  C  CR16  0  -0.254  -2.7919  -0.4137  -1.4260
 1G3  N35  N  NH2   0  -0.734   0.1426   1.0236  -1.2832
 1G3  H1   H  HCH3  0   0.264   5.3577   2.2088  -0.0256
 1G3  H2   H  HCH3  0   0.274   5.1187   1.8144   1.7050
 1G3  H3   H  HCH3  0   0.299   6.4711   1.0969   0.8034
 1G3  H4   H  HCH2  0   0.273   2.5551   1.1109   1.1538
 1G3  H5   H  HCH2  0   0.251   2.7780   1.4345  -0.5788
 1G3  H6   H  HCH2  0   0.236   2.1010  -0.9504  -1.0726
 1G3  H7   H  HCH2  0   0.256   1.8728  -1.2289   0.6467
 1G3  H8   H  HCH1  0   0.231   0.0841   0.4990   0.7021
 1G3  H9   H  HCH2  0   0.224  -0.3917  -1.5832  -1.4575
 1G3  H10  H  HCH2  0   0.233  -0.3309  -1.9394   0.2550
 1G3  H11  H  HCR6  0   0.203  -2.0592  -1.0449   1.8023
 1G3  H12  H  HCR6  0   0.238  -4.4036  -0.3570   2.0656
 1G3  H13  H  HCH2  0   0.193  -6.5110   0.8442  -0.7952
 1G3  H14  H  HCH2  0   0.231  -6.7631  -0.5732   0.1970
 1G3  H15  H  HNH2  0   0.324  -6.0100   2.0327   1.2537
 1G3  H16  H  HNH2  0   0.330  -7.4061   1.2326   1.4843
 1G3  H18  H  HCR6  0   0.208  -4.6908   0.2459  -2.1510
 1G3  H19  H  HCR6  0   0.201  -2.3458  -0.4140  -2.4126
 1G3  H20  H  HNH2  0   0.326   0.5323   1.9245  -1.0502
 1G3  H21  H  HNH2  0   0.316   0.5319   0.7298  -2.1694

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
 1G3  O50  S48  double    1.461  0.020  1.461
 1G3  C47  C46  single    1.521  0.020  1.521
 1G3  C47  S48  single    1.795  0.020  1.795
 1G3  C46  C36  single    1.537  0.020  1.537
 1G3  S48  C51  single    1.785  0.020  1.785
 1G3  S48  O49  double    1.455  0.020  1.455
 1G3  C37  C36  single    1.535  0.020  1.535
 1G3  C37  C38  single    1.501  0.020  1.501
 1G3  C43  C38  aromatic  1.392  0.020  1.392
 1G3  C43  C42  aromatic  1.385  0.020  1.385
 1G3  C36  N35  single    1.447  0.020  1.447
 1G3  C38  C39  aromatic  1.389  0.020  1.389
 1G3  C42  C41  aromatic  1.392  0.020  1.392
 1G3  C39  C40  aromatic  1.387  0.020  1.387
 1G3  C41  C40  aromatic  1.390  0.020  1.390
 1G3  C41  C44  single    1.507  0.020  1.507
 1G3  C44  N45  single    1.450  0.020  1.450
 1G3  C51  H1   single    0.970  0.020  1.090
 1G3  C51  H2   single    0.970  0.020  1.090
 1G3  C51  H3   single    0.970  0.020  1.090
 1G3  C47  H4   single    0.970  0.020  1.090
 1G3  C47  H5   single    0.970  0.020  1.090
 1G3  C46  H6   single    0.970  0.020  1.090
 1G3  C46  H7   single    0.970  0.020  1.090
 1G3  C36  H8   single    0.970  0.020  1.090
 1G3  C37  H9   single    0.970  0.020  1.090
 1G3  C37  H10  single    0.970  0.020  1.090
 1G3  C43  H11  single    0.930  0.020  1.080
 1G3  C42  H12  single    0.930  0.020  1.080
 1G3  C44  H13  single    0.970  0.020  1.090
 1G3  C44  H14  single    0.970  0.020  1.090
 1G3  N45  H15  single    0.890  0.020  1.040
 1G3  N45  H16  single    0.890  0.020  1.040
 1G3  C40  H18  single    0.930  0.020  1.080
 1G3  C39  H19  single    0.930  0.020  1.080
 1G3  N35  H20  single    0.890  0.020  1.040
 1G3  N35  H21  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
 1G3  C47  S48  C51  104.05  3.000
 1G3  C51  S48  O49  108.53  3.000
 1G3  C47  S48  O49  108.64  3.000
 1G3  O49  S48  O50  118.72  3.000
 1G3  C51  S48  O50  107.84  3.000
 1G3  C47  S48  O50  108.11  3.000
 1G3  H3   C51  H2   109.43  3.000
 1G3  H3   C51  H1   109.60  3.000
 1G3  H2   C51  H1   110.86  3.000
 1G3  H3   C51  S48  106.73  3.000
 1G3  H2   C51  S48  110.04  3.000
 1G3  H1   C51  S48  110.09  3.000
 1G3  H5   C47  H4   108.85  3.000
 1G3  H5   C47  C46  112.08  3.000
 1G3  H4   C47  C46  111.19  3.000
 1G3  H5   C47  S48  107.06  3.000
 1G3  H4   C47  S48  107.31  3.000
 1G3  C46  C47  S48  110.15  3.000
 1G3  H7   C46  H6   106.95  3.000
 1G3  H7   C46  C36  109.65  3.000
 1G3  H6   C46  C36  109.27  3.000
 1G3  H7   C46  C47  109.08  3.000
 1G3  H6   C46  C47  109.68  3.000
 1G3  C36  C46  C47  112.09  3.000
 1G3  H8   C36  N35  107.02  3.000
 1G3  H8   C36  C37  107.19  3.000
 1G3  N35  C36  C37  109.68  3.000
 1G3  H8   C36  C46  108.19  3.000
 1G3  N35  C36  C46  114.88  3.000
 1G3  C37  C36  C46  109.56  3.000
 1G3  H10  C37  H9   106.22  3.000
 1G3  H10  C37  C38  109.70  3.000
 1G3  H9   C37  C38  110.33  3.000
 1G3  H10  C37  C36  108.81  3.000
 1G3  H9   C37  C36  108.90  3.000
 1G3  C38  C37  C36  112.66  3.000
 1G3  C39  C38  C43  117.95  3.000
 1G3  C39  C38  C37  121.58  3.000
 1G3  C43  C38  C37  120.45  3.000
 1G3  H11  C43  C42  119.12  3.000
 1G3  H11  C43  C38  119.55  3.000
 1G3  C42  C43  C38  121.33  3.000
 1G3  H12  C42  C41  119.27  3.000
 1G3  H12  C42  C43  120.18  3.000
 1G3  C41  C42  C43  120.55  3.000
 1G3  C40  C41  C44  120.80  3.000
 1G3  C44  C41  C42  120.98  3.000
 1G3  C40  C41  C42  118.20  3.000
 1G3  H14  C44  H13  105.66  3.000
 1G3  H14  C44  N45  107.48  3.000
 1G3  H13  C44  N45  114.30  3.000
 1G3  H14  C44  C41  108.66  3.000
 1G3  H13  C44  C41  108.69  3.000
 1G3  N45  C44  C41  111.73  3.000
 1G3  H16  N45  H15  107.09  3.000
 1G3  H16  N45  C44  110.33  3.000
 1G3  H15  N45  C44  110.21  3.000
 1G3  H18  C40  C39  119.26  3.000
 1G3  H18  C40  C41  119.64  3.000
 1G3  C39  C40  C41  121.10  3.000
 1G3  H19  C39  C40  119.53  3.000
 1G3  H19  C39  C38  119.60  3.000
 1G3  C40  C39  C38  120.86  3.000
 1G3  H21  N35  H20  108.24  3.000
 1G3  H21  N35  C36  111.63  3.000
 1G3  H20  N35  C36  112.75  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
 1G3  CONST_01  C41  C42  C43  C38     0.00   0.0  0
 1G3  CONST_02  C41  C40  C39  C38     0.00   0.0  0
 1G3  CONST_03  C40  C39  C38  C43     0.00   0.0  0
 1G3  CONST_04  C40  C41  C42  C43     0.00   0.0  0
 1G3  CONST_05  C39  C38  C43  C42     0.00   0.0  0
 1G3  CONST_06  C39  C40  C41  C42     0.00   0.0  0
 1G3  CONST_07  C42  C43  C38  C37   180.00   0.0  0
 1G3  CONST_08  C40  C39  C38  C37   180.00   0.0  0
 1G3  CONST_09  C44  C41  C42  C43   180.00   0.0  0
 1G3  CONST_10  C39  C40  C41  C44   180.00   0.0  0
 1G3  CONST_11  H12  C42  C43  C38   180.00   0.0  0
 1G3  CONST_12  H18  C40  C39  C38   180.00   0.0  0
 1G3  CONST_13  H19  C39  C38  C43   180.00   0.0  0
 1G3  CONST_14  H11  C43  C42  C41   180.00   0.0  0
 1G3  Var_01    C43  C38  C37  C36   -85.02  30.0  2
 1G3  Var_02    N45  C44  C41  C42    38.14  30.0  2
 1G3  Var_03    H15  N45  C44  C41    69.86  30.0  3
 1G3  Var_04    C46  C47  S48  O50    68.21  30.0  1
 1G3  Var_05    C36  C46  C47  S48  -178.88  30.0  3
 1G3  Var_06    H1   C51  S48  O50    53.59  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
 1G3  chir_01  C36  C46  C37  N35  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
 1G3  plan-1  C37  0.020
 1G3  plan-1  C38  0.020
 1G3  plan-1  C43  0.020
 1G3  plan-1  C42  0.020
 1G3  plan-1  C41  0.020
 1G3  plan-1  C44  0.020
 1G3  plan-1  C40  0.020
 1G3  plan-1  C39  0.020
 1G3  plan-1  H11  0.020
 1G3  plan-1  H12  0.020
 1G3  plan-1  H18  0.020
 1G3  plan-1  H19  0.020

