Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: R8KV8

Calculation Name: 2A1F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A1F

Chain ID: A

ChEMBL ID:

UniProt ID: P43890

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptAll
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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2785144.642399
FMO2-HF: Nuclear repulsion 2694525.60905
FMO2-HF: Total energy -90619.03335
FMO2-MP2: Total energy -90874.642037


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-2.6260.0170.09-1.114-1.62-0.001
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.001
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].
3A3GLN00.017-0.0062.985-1.923-0.0700.033-0.788-1.0990.002
4A4PRO00.0340.0096.5080.4160.4160.0000.0000.0000.000
5A5ILE0-0.060-0.0229.714-0.020-0.0200.0000.0000.0000.000
6A6TYR0-0.026-0.00412.5800.0620.0620.0000.0000.0000.000
7A7LYS10.9420.97113.9530.0970.0970.0000.0000.0000.000
8A8ARG10.7510.84516.4860.0740.0740.0000.0000.0000.000
9A9ILE0-0.0010.01414.6560.0230.0230.0000.0000.0000.000
10A10LEU0-0.0050.01918.611-0.008-0.0080.0000.0000.0000.000
11A11LEU0-0.0030.00316.9410.0180.0180.0000.0000.0000.000
12A12LYS10.8510.91620.163-0.053-0.0530.0000.0000.0000.000
13A13LEU00.0550.02220.0480.0170.0170.0000.0000.0000.000
14A14SER0-0.066-0.06823.648-0.005-0.0050.0000.0000.0000.000
15A15GLY00.0400.01926.147-0.002-0.0020.0000.0000.0000.000
16A16GLU-1-0.738-0.85928.0120.0420.0420.0000.0000.0000.000
17A17ALA0-0.115-0.04722.8020.0090.0090.0000.0000.0000.000
18A18LEU00.0540.02623.4170.0030.0030.0000.0000.0000.000
19A19GLN0-0.033-0.00125.773-0.007-0.0070.0000.0000.0000.000
20A20GLY00.0850.06226.9330.0050.0050.0000.0000.0000.000
21A21GLU-1-0.987-1.00028.7710.0530.0530.0000.0000.0000.000
22A22ASP-1-0.904-0.95130.0740.0330.0330.0000.0000.0000.000
23A23GLY0-0.058-0.02431.635-0.002-0.0020.0000.0000.0000.000
24A24LEU0-0.082-0.05532.535-0.001-0.0010.0000.0000.0000.000
25A25GLY00.0240.01531.6500.0000.0000.0000.0000.0000.000
26A26ILE0-0.012-0.02027.2600.0020.0020.0000.0000.0000.000
27A27ASP-1-0.789-0.88425.6790.0280.0280.0000.0000.0000.000
28A28PRO00.011-0.01525.440-0.001-0.0010.0000.0000.0000.000
29A29ALA00.0330.02822.903-0.007-0.0070.0000.0000.0000.000
30A30ILE0-0.048-0.02221.1080.0030.0030.0000.0000.0000.000
31A31LEU0-0.039-0.02320.6020.0020.0020.0000.0000.0000.000
32A32ASP-1-0.713-0.81320.621-0.043-0.0430.0000.0000.0000.000
33A33ARG10.7550.87515.490-0.127-0.1270.0000.0000.0000.000
34A34MET0-0.038-0.02415.938-0.005-0.0050.0000.0000.0000.000
35A35ALA00.0170.01816.552-0.016-0.0160.0000.0000.0000.000
36A36VAL00.0140.00512.721-0.031-0.0310.0000.0000.0000.000
37A37GLU-1-0.800-0.89811.8100.1000.1000.0000.0000.0000.000
38A38ILE0-0.033-0.02512.193-0.021-0.0210.0000.0000.0000.000
39A39LYS10.8140.90413.5700.1970.1970.0000.0000.0000.000
40A40GLU-1-0.838-0.9306.957-0.343-0.3430.0000.0000.0000.000
41A41LEU0-0.015-0.0149.228-0.116-0.1160.0000.0000.0000.000
42A42VAL00.0300.03111.056-0.041-0.0410.0000.0000.0000.000
43A43GLU-1-0.961-0.98110.326-0.502-0.5020.0000.0000.0000.000
44A44MET0-0.061-0.0254.988-0.137-0.1370.0000.0000.0000.000
45A45GLY0-0.055-0.0349.863-0.023-0.0230.0000.0000.0000.000
46A46VAL0-0.034-0.01111.6300.0580.0580.0000.0000.0000.000
47A47GLU-1-0.767-0.87714.402-0.135-0.1350.0000.0000.0000.000
48A48VAL0-0.006-0.01015.2120.0270.0270.0000.0000.0000.000
49A49SER00.0250.00018.1800.0060.0060.0000.0000.0000.000
50A50VAL0-0.001-0.00620.0900.0100.0100.0000.0000.0000.000
51A51VAL0-0.0030.00322.589-0.001-0.0010.0000.0000.0000.000
52A52LEU00.0430.03124.6440.0080.0080.0000.0000.0000.000
53A53GLY00.001-0.00327.119-0.001-0.0010.0000.0000.0000.000
54A54GLY00.0590.01129.904-0.004-0.0040.0000.0000.0000.000
55A55GLY0-0.061-0.03032.124-0.001-0.0010.0000.0000.0000.000
56A56ASN00.0180.00130.0940.0010.0010.0000.0000.0000.000
57A57LEU0-0.0160.00532.395-0.001-0.0010.0000.0000.0000.000
58A58PHE0-0.016-0.01635.249-0.001-0.0010.0000.0000.0000.000
59A59ARG10.8690.92932.734-0.035-0.0350.0000.0000.0000.000
60A60GLY00.0390.01538.5930.0000.0000.0000.0000.0000.000
61A61ALA0-0.0010.00541.429-0.001-0.0010.0000.0000.0000.000
62A62LYS10.9760.97343.055-0.022-0.0220.0000.0000.0000.000
63A63LEU00.0450.02944.913-0.001-0.0010.0000.0000.0000.000
64A64ALA00.0100.01045.441-0.001-0.0010.0000.0000.0000.000
65A65LYS10.9260.96247.265-0.023-0.0230.0000.0000.0000.000
66A66ALA0-0.024-0.00949.1880.0000.0000.0000.0000.0000.000
67A67GLY00.0370.02750.823-0.001-0.0010.0000.0000.0000.000
68A68MET0-0.071-0.02946.127-0.001-0.0010.0000.0000.0000.000
69A69ASN00.0350.01148.5190.0020.0020.0000.0000.0000.000
70A70ARG10.8770.91539.770-0.018-0.0180.0000.0000.0000.000
71A71VAL00.0570.02644.0830.0000.0000.0000.0000.0000.000
72A72VAL00.0000.00444.236-0.001-0.0010.0000.0000.0000.000
73A73GLY00.0480.01442.986-0.001-0.0010.0000.0000.0000.000
74A74ASP-1-0.771-0.86139.8310.0140.0140.0000.0000.0000.000
75A75HIS00.0360.01639.330-0.001-0.0010.0000.0000.0000.000
76A76MET0-0.025-0.00840.017-0.001-0.0010.0000.0000.0000.000
77A77GLY00.0080.00737.0010.0000.0000.0000.0000.0000.000
78A78MET0-0.035-0.00535.465-0.001-0.0010.0000.0000.0000.000
79A79LEU00.0450.03135.331-0.002-0.0020.0000.0000.0000.000
80A80ALA00.0080.01034.626-0.002-0.0020.0000.0000.0000.000
81A81THR0-0.068-0.04530.968-0.001-0.0010.0000.0000.0000.000
82A82VAL00.0260.00830.720-0.003-0.0030.0000.0000.0000.000
83A83MET0-0.045-0.01231.953-0.003-0.0030.0000.0000.0000.000
84A84ASN00.026-0.00528.068-0.002-0.0020.0000.0000.0000.000
85A85GLY00.0280.01227.428-0.003-0.0030.0000.0000.0000.000
86A86LEU0-0.033-0.02227.736-0.007-0.0070.0000.0000.0000.000
87A87ALA00.0130.01728.015-0.005-0.0050.0000.0000.0000.000
88A88MET00.0170.00921.686-0.006-0.0060.0000.0000.0000.000
89A89ARG10.8850.92723.7490.0370.0370.0000.0000.0000.000
90A90ASP-1-0.865-0.91725.360-0.050-0.0500.0000.0000.0000.000
91A91SER00.002-0.03122.291-0.008-0.0080.0000.0000.0000.000
92A92LEU0-0.020-0.01818.916-0.009-0.0090.0000.0000.0000.000
93A93PHE0-0.0210.00121.278-0.014-0.0140.0000.0000.0000.000
94A94ARG10.7220.80723.7170.0360.0360.0000.0000.0000.000
95A95ALA0-0.0260.01118.162-0.001-0.0010.0000.0000.0000.000
96A96ASP-1-0.879-0.93118.703-0.215-0.2150.0000.0000.0000.000
97A97VAL0-0.0070.00317.258-0.020-0.0200.0000.0000.0000.000
98A98ASN0-0.027-0.02119.8800.0290.0290.0000.0000.0000.000
99A99ALA00.0480.02321.831-0.006-0.0060.0000.0000.0000.000
100A100LYN0-0.0070.00923.7920.0040.0040.0000.0000.0000.000
101A101LEU0-0.043-0.01326.3240.0020.0020.0000.0000.0000.000
102A102MET0-0.0040.03328.9610.0020.0020.0000.0000.0000.000
103A103SER0-0.015-0.00631.2170.0050.0050.0000.0000.0000.000
104A104ALA00.008-0.00434.059-0.002-0.0020.0000.0000.0000.000
105A105PHE0-0.050-0.01536.3540.0010.0010.0000.0000.0000.000
106A106GLN00.0710.05137.926-0.001-0.0010.0000.0000.0000.000
107A107LEU0-0.010-0.00936.4000.0020.0020.0000.0000.0000.000
108A108ASN00.015-0.01538.380-0.004-0.0040.0000.0000.0000.000
109A109GLY00.0130.01439.0370.0020.0020.0000.0000.0000.000
110A110ILE0-0.0230.00835.332-0.001-0.0010.0000.0000.0000.000
111A111CYS0-0.061-0.04932.477-0.001-0.0010.0000.0000.0000.000
112A112ASP-1-0.833-0.89231.190-0.053-0.0530.0000.0000.0000.000
113A113THR0-0.005-0.02133.9910.0050.0050.0000.0000.0000.000
114A114TYR0-0.056-0.08529.815-0.005-0.0050.0000.0000.0000.000
115A115ASN00.0380.01932.8410.0020.0020.0000.0000.0000.000
116A116TRP00.0830.04530.880-0.005-0.0050.0000.0000.0000.000
117A117SER00.0150.00530.168-0.006-0.0060.0000.0000.0000.000
118A118GLU-1-0.811-0.90330.780-0.065-0.0650.0000.0000.0000.000
119A119ALA00.0090.00727.498-0.007-0.0070.0000.0000.0000.000
120A120ILE00.0040.01026.206-0.009-0.0090.0000.0000.0000.000
121A121LYS10.7640.86425.9800.0520.0520.0000.0000.0000.000
122A122MET00.0160.00425.925-0.010-0.0100.0000.0000.0000.000
123A123LEU0-0.0140.00021.187-0.010-0.0100.0000.0000.0000.000
124A124ARG10.9420.97921.3800.0950.0950.0000.0000.0000.000
125A125GLU-1-0.935-0.95822.618-0.120-0.1200.0000.0000.0000.000
126A126LYS10.8250.92114.8140.3320.3320.0000.0000.0000.000
127A127ARG10.8040.90619.7080.0940.0940.0000.0000.0000.000
128A128VAL00.0140.00818.5160.0030.0030.0000.0000.0000.000
129A129VAL0-0.030-0.01421.1830.0090.0090.0000.0000.0000.000
130A130ILE0-0.0180.00023.8540.0070.0070.0000.0000.0000.000
131A131PHE00.012-0.00525.4310.0000.0000.0000.0000.0000.000
132A132SER0-0.037-0.03428.5330.0060.0060.0000.0000.0000.000
133A133ALA00.0070.00231.279-0.002-0.0020.0000.0000.0000.000
134A134GLY00.0270.01632.9270.0010.0010.0000.0000.0000.000
135A135THR00.0380.00633.849-0.003-0.0030.0000.0000.0000.000
136A136GLY00.0270.02336.300-0.001-0.0010.0000.0000.0000.000
137A137ASN0-0.074-0.04739.0160.0010.0010.0000.0000.0000.000
138A138PRO00.0040.00739.6070.0010.0010.0000.0000.0000.000
139A139PHE0-0.022-0.03641.1180.0000.0000.0000.0000.0000.000
140A140PHE0-0.0160.00536.3990.0030.0030.0000.0000.0000.000
141A141THR0-0.008-0.02633.334-0.001-0.0010.0000.0000.0000.000
142A142THR00.0270.00328.419-0.002-0.0020.0000.0000.0000.000
143A143ASP-1-0.791-0.86727.9180.0460.0460.0000.0000.0000.000
144A144SER00.0430.00329.596-0.002-0.0020.0000.0000.0000.000
145A145THR0-0.052-0.02330.034-0.004-0.0040.0000.0000.0000.000
146A146ALA0-0.005-0.00725.782-0.005-0.0050.0000.0000.0000.000
147A147CYS0-0.023-0.00227.006-0.002-0.0020.0000.0000.0000.000
148A148LEU00.0180.01728.749-0.003-0.0030.0000.0000.0000.000
149A149ARG10.8050.87927.9350.0130.0130.0000.0000.0000.000
150A150GLY00.0420.01725.298-0.007-0.0070.0000.0000.0000.000
151A151ILE00.0030.00626.071-0.006-0.0060.0000.0000.0000.000
152A152GLU-1-0.822-0.87328.726-0.026-0.0260.0000.0000.0000.000
153A153ILE0-0.055-0.02623.946-0.005-0.0050.0000.0000.0000.000
154A154GLU-1-0.877-0.92425.232-0.079-0.0790.0000.0000.0000.000
155A155ALA0-0.026-0.00921.534-0.009-0.0090.0000.0000.0000.000
156A156ASP-1-0.809-0.90418.627-0.085-0.0850.0000.0000.0000.000
157A157VAL0-0.050-0.03217.2640.0180.0180.0000.0000.0000.000
158A158VAL0-0.0060.00220.551-0.011-0.0110.0000.0000.0000.000
159A159LEU0-0.002-0.00115.4060.0210.0210.0000.0000.0000.000
160A160LYS10.8140.89119.487-0.082-0.0820.0000.0000.0000.000
161A161ALA00.0330.02519.9240.0180.0180.0000.0000.0000.000
162A162THR0-0.091-0.05721.141-0.015-0.0150.0000.0000.0000.000
163A163LYS10.8870.92821.858-0.080-0.0800.0000.0000.0000.000
164A164VAL00.0080.00423.0520.0050.0050.0000.0000.0000.000
165A165ASP-1-0.801-0.89718.7220.2910.2910.0000.0000.0000.000
166A166GLY00.0290.01720.0630.0190.0190.0000.0000.0000.000
167A167VAL0-0.058-0.03722.492-0.015-0.0150.0000.0000.0000.000
168A168TYR00.0200.00323.8000.0090.0090.0000.0000.0000.000
169A169ASP-1-0.814-0.89127.8530.1040.1040.0000.0000.0000.000
170A170CYS0-0.080-0.03630.348-0.006-0.0060.0000.0000.0000.000
171A178ALA0-0.014-0.01730.089-0.002-0.0020.0000.0000.0000.000
172A179LYS10.9670.98927.793-0.124-0.1240.0000.0000.0000.000
173A180LEU00.0000.01121.040-0.009-0.0090.0000.0000.0000.000
174A181TYR0-0.035-0.03225.0160.0070.0070.0000.0000.0000.000
175A182LYS10.8690.95016.673-0.317-0.3170.0000.0000.0000.000
176A183ASN0-0.023-0.02520.5020.0190.0190.0000.0000.0000.000
177A184LEU0-0.0220.00023.619-0.003-0.0030.0000.0000.0000.000
178A185SER00.025-0.01226.595-0.005-0.0050.0000.0000.0000.000
179A186TYR00.002-0.04627.1560.0020.0020.0000.0000.0000.000
180A187ALA0-0.0060.01131.009-0.002-0.0020.0000.0000.0000.000
181A188GLU-1-0.746-0.85030.1550.0910.0910.0000.0000.0000.000
182A189VAL0-0.042-0.01729.1370.0030.0030.0000.0000.0000.000
183A190ILE0-0.027-0.00932.089-0.001-0.0010.0000.0000.0000.000
184A191ASP-1-0.893-0.95135.7700.0480.0480.0000.0000.0000.000
185A192LYS10.7800.89430.528-0.093-0.0930.0000.0000.0000.000
186A193GLU-1-0.945-0.96635.6600.0520.0520.0000.0000.0000.000
187A194LEU0-0.041-0.00329.8550.0030.0030.0000.0000.0000.000
188A195LYS10.9370.96229.174-0.095-0.0950.0000.0000.0000.000
189A196VAL0-0.0040.00727.0190.0080.0080.0000.0000.0000.000
190A197MET0-0.059-0.03927.2080.0000.0000.0000.0000.0000.000
191A198ASP-1-0.745-0.83831.2240.0300.0300.0000.0000.0000.000
192A199LEU00.0840.02933.8670.0000.0000.0000.0000.0000.000
193A200SER00.0070.01735.890-0.001-0.0010.0000.0000.0000.000
194A201ALA0-0.0100.00131.019-0.002-0.0020.0000.0000.0000.000
195A202PHE00.015-0.00728.598-0.001-0.0010.0000.0000.0000.000
196A203THR0-0.046-0.02931.9770.0010.0010.0000.0000.0000.000
197A204LEU0-0.0100.00832.334-0.002-0.0020.0000.0000.0000.000
198A205ALA00.007-0.00328.108-0.004-0.0040.0000.0000.0000.000
199A206ARG10.9530.97729.933-0.033-0.0330.0000.0000.0000.000
200A207ASP-1-0.917-0.96431.5230.0180.0180.0000.0000.0000.000
201A208HIS0-0.096-0.05530.975-0.007-0.0070.0000.0000.0000.000
202A209GLY00.0110.01629.074-0.005-0.0050.0000.0000.0000.000
203A210MET0-0.0210.01824.6540.0020.0020.0000.0000.0000.000
204A211PRO0-0.0080.02021.6730.0100.0100.0000.0000.0000.000
205A212ILE0-0.020-0.02822.479-0.006-0.0060.0000.0000.0000.000
206A213ARG10.8600.92313.783-0.233-0.2330.0000.0000.0000.000
207A214VAL0-0.032-0.00719.915-0.009-0.0090.0000.0000.0000.000
208A215PHE00.0570.01815.8140.0230.0230.0000.0000.0000.000
209A216ASN00.0100.00318.116-0.047-0.0470.0000.0000.0000.000
210A217MET00.0330.01715.8790.0350.0350.0000.0000.0000.000
211A218GLY0-0.0020.00318.306-0.013-0.0130.0000.0000.0000.000
212A219LYS10.7640.86515.049-0.426-0.4260.0000.0000.0000.000
213A220PRO00.0220.01013.9290.0050.0050.0000.0000.0000.000
214A221GLY00.0130.01510.1110.0700.0700.0000.0000.0000.000
215A222ALA00.0060.00310.0590.0980.0980.0000.0000.0000.000
216A223LEU00.0260.00712.3020.0180.0180.0000.0000.0000.000
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