Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 727VK

Calculation Name: 1A58-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A58

Chain ID: A

ChEMBL ID:

UniProt ID: Q27450

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1881752.74708
FMO2-HF: Nuclear repulsion 1811945.796159
FMO2-HF: Total energy -69806.95092
FMO2-MP2: Total energy -70005.375348


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-10.354-4.1421.278-3.266-4.223-0.003
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.010
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3LYS11.0471.0083.820-0.2621.918-0.022-1.247-0.9120.007
4A4LYS10.9030.9386.3010.1990.1990.0000.0000.0000.000
5A5ASP-1-0.901-0.9562.731-7.327-5.0690.879-1.459-1.677-0.015
6A6ARG10.7470.8944.824-0.991-0.900-0.001-0.004-0.0860.000
7A7ARG10.9490.9947.7020.0800.0800.0000.0000.0000.000
8A8ARG10.9340.96810.358-0.028-0.0280.0000.0000.0000.000
9A9VAL00.0240.01814.091-0.044-0.0440.0000.0000.0000.000
10A10PHE0-0.026-0.02316.8340.0180.0180.0000.0000.0000.000
11A11LEU00.0280.00520.629-0.010-0.0100.0000.0000.0000.000
12A12ASP-1-0.777-0.85423.782-0.023-0.0230.0000.0000.0000.000
13A13VAL0-0.009-0.01827.241-0.003-0.0030.0000.0000.0000.000
14A14THR0-0.018-0.00729.7320.0010.0010.0000.0000.0000.000
15A15ILE00.010-0.01333.5070.0010.0010.0000.0000.0000.000
16A16ASP-1-0.838-0.92536.077-0.011-0.0110.0000.0000.0000.000
17A17GLY0-0.024-0.00837.3940.0000.0000.0000.0000.0000.000
18A18ASN0-0.019-0.00637.715-0.002-0.0020.0000.0000.0000.000
19A19LEU0-0.032-0.01930.7520.0010.0010.0000.0000.0000.000
20A20ALA0-0.026-0.01031.9050.0020.0020.0000.0000.0000.000
21A21GLY00.0240.00930.1030.0030.0030.0000.0000.0000.000
22A22ARG10.8370.89923.0680.0260.0260.0000.0000.0000.000
23A23ILE0-0.0030.01021.9650.0050.0050.0000.0000.0000.000
24A24VAL0-0.021-0.01118.160-0.008-0.0080.0000.0000.0000.000
25A25MET0-0.033-0.01316.8480.0110.0110.0000.0000.0000.000
26A26GLU-1-0.925-0.96311.7680.2620.2620.0000.0000.0000.000
27A27LEU0-0.004-0.02410.580-0.002-0.0020.0000.0000.0000.000
28A28TYR00.019-0.0048.4620.1330.1330.0000.0000.0000.000
29A29ASN00.038-0.0115.421-0.048-0.0480.0000.0000.0000.000
30A30ASP-1-0.789-0.8773.1110.2281.6220.412-0.560-1.2450.004
31A31ILE0-0.053-0.0214.013-2.389-2.1000.0100.004-0.3030.001
32A32ALA00.0250.0236.833-0.254-0.2540.0000.0000.0000.000
33A33PRO00.0450.0305.3840.0040.0040.0000.0000.0000.000
34A34ARG10.9460.9797.2810.1850.1850.0000.0000.0000.000
35A35THR00.009-0.02210.849-0.005-0.0050.0000.0000.0000.000
36A36CYS0-0.046-0.0058.9660.0290.0290.0000.0000.0000.000
37A37ASN0-0.027-0.0049.750-0.044-0.0440.0000.0000.0000.000
38A38ASN00.0330.01211.354-0.014-0.0140.0000.0000.0000.000
39A39PHE00.0340.00614.4060.0040.0040.0000.0000.0000.000
40A40LEU00.0100.00312.2590.0030.0030.0000.0000.0000.000
41A41MET0-0.007-0.00814.253-0.015-0.0150.0000.0000.0000.000
42A42LEU0-0.0190.01116.6190.0110.0110.0000.0000.0000.000
43A43CYS0-0.0410.00218.0650.0160.0160.0000.0000.0000.000
44A44THR00.012-0.00217.2020.0070.0070.0000.0000.0000.000
45A45GLY0-0.001-0.00220.0930.0030.0030.0000.0000.0000.000
46A46MET0-0.052-0.02918.332-0.001-0.0010.0000.0000.0000.000
47A47ALA00.0190.00218.218-0.026-0.0260.0000.0000.0000.000
48A48GLY0-0.0090.01420.1300.0030.0030.0000.0000.0000.000
49A49THR0-0.015-0.01923.9170.0050.0050.0000.0000.0000.000
50A50GLY0-0.008-0.00224.824-0.009-0.0090.0000.0000.0000.000
51A51LYS10.9350.97222.3610.1540.1540.0000.0000.0000.000
52A52ILE0-0.008-0.01526.4770.0060.0060.0000.0000.0000.000
53A53SER0-0.073-0.04927.6210.0060.0060.0000.0000.0000.000
54A54GLY00.0170.01129.0710.0050.0050.0000.0000.0000.000
55A55LYS10.9090.95229.1090.0560.0560.0000.0000.0000.000
56A56PRO00.0150.00226.902-0.007-0.0070.0000.0000.0000.000
57A57LEU0-0.0060.01321.1300.0080.0080.0000.0000.0000.000
58A58HIS0-0.037-0.03722.238-0.005-0.0050.0000.0000.0000.000
59A59TYR0-0.024-0.02919.4630.0060.0060.0000.0000.0000.000
60A60LYS10.9310.98624.5500.0650.0650.0000.0000.0000.000
61A61GLY00.0050.00827.027-0.002-0.0020.0000.0000.0000.000
62A62SER0-0.081-0.03726.8330.0040.0040.0000.0000.0000.000
63A63THR00.023-0.00829.3690.0020.0020.0000.0000.0000.000
64A64PHE00.0090.00925.1590.0000.0000.0000.0000.0000.000
65A65HIS0-0.017-0.01228.6140.0000.0000.0000.0000.0000.000
66A66ARG10.9140.95430.5750.0010.0010.0000.0000.0000.000
67A67VAL00.0220.02230.8580.0020.0020.0000.0000.0000.000
68A68ILE0-0.050-0.02231.946-0.002-0.0020.0000.0000.0000.000
69A69LYS10.9540.97632.733-0.006-0.0060.0000.0000.0000.000
70A70ASN00.0090.01633.5390.0000.0000.0000.0000.0000.000
71A71PHE0-0.0190.00727.3000.0030.0030.0000.0000.0000.000
72A72MET00.0120.01926.8760.0030.0030.0000.0000.0000.000
73A73ILE00.0060.02326.465-0.005-0.0050.0000.0000.0000.000
74A74GLN00.013-0.02026.2350.0060.0060.0000.0000.0000.000
75A75GLY00.0450.02025.654-0.002-0.0020.0000.0000.0000.000
76A76GLY00.0360.02224.0960.0010.0010.0000.0000.0000.000
77A77ASP-1-0.751-0.86224.919-0.041-0.0410.0000.0000.0000.000
78A78PHE00.0710.01423.2130.0040.0040.0000.0000.0000.000
79A79THR0-0.038-0.00528.185-0.002-0.0020.0000.0000.0000.000
80A80LYS10.8640.93730.7160.0340.0340.0000.0000.0000.000
81A81GLY00.0420.06131.4530.0020.0020.0000.0000.0000.000
82A82ASP-1-0.917-0.96932.528-0.020-0.0200.0000.0000.0000.000
83A83GLY0-0.024-0.00930.1760.0030.0030.0000.0000.0000.000
84A84THR0-0.088-0.04930.395-0.001-0.0010.0000.0000.0000.000
85A85GLY0-0.016-0.01229.981-0.002-0.0020.0000.0000.0000.000
86A86GLY00.0080.00326.0700.0030.0030.0000.0000.0000.000
87A87GLU-1-0.774-0.86423.745-0.087-0.0870.0000.0000.0000.000
88A88SER0-0.0120.00218.781-0.007-0.0070.0000.0000.0000.000
89A89ILE00.020-0.01114.6600.0010.0010.0000.0000.0000.000
90A90TYR0-0.097-0.06712.917-0.053-0.0530.0000.0000.0000.000
91A91GLY0-0.046-0.01319.1390.0030.0030.0000.0000.0000.000
92A92GLY00.0100.00422.7140.0030.0030.0000.0000.0000.000
93A93MET0-0.061-0.01222.187-0.001-0.0010.0000.0000.0000.000
94A94PHE0-0.049-0.03115.018-0.015-0.0150.0000.0000.0000.000
95A95ASP-1-0.838-0.93817.774-0.054-0.0540.0000.0000.0000.000
96A96ASP-1-0.874-0.91816.933-0.018-0.0180.0000.0000.0000.000
97A97GLU-1-0.791-0.88010.404-0.112-0.1120.0000.0000.0000.000
98A98GLU-1-0.905-0.95611.6740.0780.0780.0000.0000.0000.000
99A99PHE0-0.011-0.00613.1480.0210.0210.0000.0000.0000.000
100A100VAL0-0.023-0.00610.0780.0080.0080.0000.0000.0000.000
101A101MET0-0.037-0.00811.6330.0250.0250.0000.0000.0000.000
102A102LYS10.9480.97214.199-0.116-0.1160.0000.0000.0000.000
103A103HIS0-0.003-0.01917.9880.0060.0060.0000.0000.0000.000
104A104ASP-1-0.922-0.97218.7290.1050.1050.0000.0000.0000.000
105A105GLU-1-0.886-0.94118.9670.1100.1100.0000.0000.0000.000
106A106PRO0-0.054-0.01722.4960.0000.0000.0000.0000.0000.000
107A107PHE0-0.020-0.03122.4730.0070.0070.0000.0000.0000.000
108A108VAL00.0390.04617.7630.0110.0110.0000.0000.0000.000
109A109VAL0-0.033-0.02917.046-0.019-0.0190.0000.0000.0000.000
110A110SER00.0270.00117.2480.0170.0170.0000.0000.0000.000
111A111MET00.0320.03017.135-0.011-0.0110.0000.0000.0000.000
112A112ALA0-0.030-0.00819.9180.0030.0030.0000.0000.0000.000
113A113ASN0-0.042-0.02522.113-0.005-0.0050.0000.0000.0000.000
114A114LYS10.8450.90724.8360.0190.0190.0000.0000.0000.000
115A115GLY00.0500.03926.591-0.001-0.0010.0000.0000.0000.000
116A116PRO0-0.0230.00323.924-0.002-0.0020.0000.0000.0000.000
117A117ASN00.0220.01620.791-0.005-0.0050.0000.0000.0000.000
118A118THR00.030-0.01822.308-0.006-0.0060.0000.0000.0000.000
119A119ASN0-0.064-0.04118.8320.0150.0150.0000.0000.0000.000
120A120GLY00.0590.02520.950-0.013-0.0130.0000.0000.0000.000
121A121SER0-0.009-0.02520.199-0.007-0.0070.0000.0000.0000.000
122A122GLN0-0.071-0.03421.8470.0110.0110.0000.0000.0000.000
123A123PHE00.0280.02820.3770.0030.0030.0000.0000.0000.000
124A124PHE0-0.041-0.03121.947-0.004-0.0040.0000.0000.0000.000
125A125ILE00.0260.01921.7910.0090.0090.0000.0000.0000.000
126A126THR0-0.008-0.01223.208-0.005-0.0050.0000.0000.0000.000
127A127THR0-0.016-0.02725.0770.0040.0040.0000.0000.0000.000
128A128THR0-0.017-0.01227.0800.0000.0000.0000.0000.0000.000
129A129PRO0-0.0090.00424.7480.0020.0020.0000.0000.0000.000
130A130ALA0-0.004-0.00824.459-0.006-0.0060.0000.0000.0000.000
131A131PRO00.0390.00523.5840.0010.0010.0000.0000.0000.000
132A132HIS00.0150.01024.5210.0030.0030.0000.0000.0000.000
133A133LEU0-0.0010.00023.834-0.005-0.0050.0000.0000.0000.000
134A134ASN00.0470.02820.7640.0040.0040.0000.0000.0000.000
135A135ASN0-0.032-0.02419.8530.0000.0000.0000.0000.0000.000
136A136ILE0-0.0120.02820.981-0.007-0.0070.0000.0000.0000.000
137A137HIS10.8250.89720.911-0.028-0.0280.0000.0000.0000.000
138A138VAL00.0780.04414.4120.0120.0120.0000.0000.0000.000
139A139VAL00.0030.00915.391-0.006-0.0060.0000.0000.0000.000
140A140PHE00.015-0.01212.2510.0150.0150.0000.0000.0000.000
141A141GLY00.0450.01112.2600.0700.0700.0000.0000.0000.000
142A142LYS10.8910.97514.447-0.124-0.1240.0000.0000.0000.000
143A143VAL0-0.0080.00216.9740.0010.0010.0000.0000.0000.000
144A144VAL0-0.074-0.04716.4910.0040.0040.0000.0000.0000.000
145A145SER00.012-0.00619.737-0.006-0.0060.0000.0000.0000.000
146A146GLY00.0670.04222.966-0.001-0.0010.0000.0000.0000.000
147A147GLN00.014-0.00122.980-0.008-0.0080.0000.0000.0000.000
148A148GLU-1-0.844-0.94226.1490.0170.0170.0000.0000.0000.000
149A149VAL0-0.0150.00327.360-0.003-0.0030.0000.0000.0000.000
150A150VAL0-0.014-0.00624.899-0.003-0.0030.0000.0000.0000.000
151A151THR00.0260.01228.299-0.002-0.0020.0000.0000.0000.000
152A152LYS10.9360.97731.267-0.003-0.0030.0000.0000.0000.000
153A153ILE0-0.010-0.01129.023-0.002-0.0020.0000.0000.0000.000
154A154GLU-1-0.808-0.91130.9380.0200.0200.0000.0000.0000.000
155A155TYR0-0.091-0.06432.812-0.001-0.0010.0000.0000.0000.000
156A156LEU0-0.0210.01334.960-0.001-0.0010.0000.0000.0000.000
157A157LYS10.9310.96837.8840.0010.0010.0000.0000.0000.000
158A158THR00.0230.02336.975-0.001-0.0010.0000.0000.0000.000
159A159ASN00.0220.01040.1490.0010.0010.0000.0000.0000.000
160A160SER00.036-0.00140.9140.0010.0010.0000.0000.0000.000
161A161LYS10.9310.98536.9570.0130.0130.0000.0000.0000.000
162A162ASN0-0.030-0.02635.6220.0000.0000.0000.0000.0000.000
163A163ARG10.9020.95535.1350.0170.0170.0000.0000.0000.000
164A164PRO0-0.001-0.00634.2220.0010.0010.0000.0000.0000.000
165A165LEU0-0.050-0.04237.479-0.001-0.0010.0000.0000.0000.000
166A166ALA00.0120.03138.312-0.001-0.0010.0000.0000.0000.000
167A167ASP-1-0.895-0.94836.836-0.018-0.0180.0000.0000.0000.000
168A168VAL0-0.064-0.02431.1410.0000.0000.0000.0000.0000.000
169A169VAL00.0250.00231.526-0.001-0.0010.0000.0000.0000.000
170A170ILE00.0090.01224.7210.0030.0030.0000.0000.0000.000
171A171LEU0-0.0090.00628.570-0.005-0.0050.0000.0000.0000.000
172A172ASN0-0.048-0.03926.525-0.009-0.0090.0000.0000.0000.000
173A173CYS0-0.035-0.01722.1800.0080.0080.0000.0000.0000.000
174A174GLY00.0260.02820.189-0.011-0.0110.0000.0000.0000.000
175A175GLU-1-0.884-0.94812.965-0.206-0.2060.0000.0000.0000.000
176A176LEU0-0.059-0.03416.1580.0030.0030.0000.0000.0000.000
177A177VAL00.0160.01814.723-0.013-0.0130.0000.0000.0000.000