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: V5271

Calculation Name: 2A6T-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A6T

Chain ID: B

ChEMBL ID:

UniProt ID: O13828

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2128681.127695
FMO2-HF: Nuclear repulsion 2049594.881034
FMO2-HF: Total energy -79086.246661
FMO2-MP2: Total energy -79313.024634


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(B:35:CYS)


Summations of interaction energy for fragment #1(B:35:CYS)
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.
-12.581-7.3414.107-7.037-12.311-0.038
Interaction energy analysis for fragmet #1(B:35:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.002
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].
3B37GLN00.0440.0062.928-4.796-2.1220.151-1.278-1.5460.006
4B38ILE00.0070.0142.041-1.287-1.3944.124-1.530-2.487-0.004
5B39GLU-1-0.785-0.8874.120-2.829-2.420-0.001-0.095-0.3140.000
6B40GLN0-0.0290.0036.1180.5090.5090.0000.0000.0000.000
7B41ALA00.0210.0077.5400.1780.1780.0000.0000.0000.000
8B42HIS0-0.036-0.0168.376-0.027-0.0270.0000.0000.0000.000
9B43TRP00.0170.0009.6900.2820.2820.0000.0000.0000.000
10B44PHE00.0060.01211.8300.1380.1380.0000.0000.0000.000
11B45TYR0-0.013-0.01512.9220.0830.0830.0000.0000.0000.000
12B46GLU-1-0.783-0.87813.855-0.502-0.5020.0000.0000.0000.000
13B47ASP-1-0.879-0.94115.739-0.458-0.4580.0000.0000.0000.000
14B48PHE0-0.0230.00717.0700.0570.0570.0000.0000.0000.000
15B49ILE00.001-0.00315.8910.0340.0340.0000.0000.0000.000
16B50ARG10.8230.89718.4250.4040.4040.0000.0000.0000.000
17B51ALA0-0.0320.00420.7460.0210.0210.0000.0000.0000.000
18B52GLN0-0.111-0.05821.8670.0400.0400.0000.0000.0000.000
19B53ASN00.025-0.00423.2180.0190.0190.0000.0000.0000.000
20B54ASP-1-0.846-0.88623.450-0.251-0.2510.0000.0000.0000.000
21B55GLN0-0.053-0.02524.595-0.015-0.0150.0000.0000.0000.000
22B56LEU0-0.023-0.00622.851-0.019-0.0190.0000.0000.0000.000
23B57PRO0-0.037-0.02219.107-0.014-0.0140.0000.0000.0000.000
24B58SER0-0.070-0.05117.6800.0060.0060.0000.0000.0000.000
25B59LEU0-0.028-0.04614.4680.0360.0360.0000.0000.0000.000
26B60GLY00.0340.02213.910-0.066-0.0660.0000.0000.0000.000
27B61LEU00.0310.0156.4060.0480.0480.0000.0000.0000.000
28B62ARG10.8770.9229.1940.8380.8380.0000.0000.0000.000
29B63VAL0-0.005-0.00210.5990.0710.0710.0000.0000.0000.000
30B64PHE00.0060.0138.5600.0870.0870.0000.0000.0000.000
31B65SER00.013-0.0217.0090.0770.0770.0000.0000.0000.000
32B66ALA00.0020.0168.9130.1290.1290.0000.0000.0000.000
33B67LYS10.8630.93811.9890.5240.5240.0000.0000.0000.000
34B68LEU0-0.0030.0218.1500.0840.0840.0000.0000.0000.000
35B83GLU-1-0.949-0.9857.9180.3880.3880.0000.0000.0000.000
36B84GLU-1-0.900-0.9449.132-0.071-0.0710.0000.0000.0000.000
37B85ALA0-0.005-0.0176.022-0.158-0.1580.0000.0000.0000.000
38B86PHE0-0.001-0.0162.922-2.067-0.9681.213-0.673-1.6390.000
39B87ASP-1-0.699-0.8264.383-2.081-2.069-0.0010.000-0.0110.000
40B88ASP-1-0.814-0.9237.030-0.577-0.5770.0000.0000.0000.000
41B89PHE0-0.071-0.0352.413-6.841-5.7688.622-3.450-6.244-0.040
42B90LEU0-0.0140.0094.639-0.126-0.045-0.001-0.011-0.0700.000
43B91ARG10.8000.8926.1680.8130.8130.0000.0000.0000.000
44B92TYR0-0.0120.0008.3460.0780.0780.0000.0000.0000.000
45B93LYS10.8340.9035.5372.4882.4880.0000.0000.0000.000
46B94THR0-0.109-0.0558.7230.1270.1270.0000.0000.0000.000
47B95ARG10.8890.92510.7220.7020.7020.0000.0000.0000.000
48B96ILE0-0.0250.01314.1290.0760.0760.0000.0000.0000.000
49B97PRO00.0100.00916.5580.0160.0160.0000.0000.0000.000
50B98VAL0-0.0040.00519.3650.0190.0190.0000.0000.0000.000
51B99ARG10.8420.91622.0190.3170.3170.0000.0000.0000.000
52B100GLY00.1080.03326.1390.0040.0040.0000.0000.0000.000
53B101ALA0-0.0350.00029.6310.0010.0010.0000.0000.0000.000
54B102ILE0-0.053-0.02132.4590.0030.0030.0000.0000.0000.000
55B103MET00.0100.01735.3350.0060.0060.0000.0000.0000.000
56B104LEU0-0.017-0.03538.6960.0020.0020.0000.0000.0000.000
57B105ASP-1-0.787-0.88341.649-0.083-0.0830.0000.0000.0000.000
58B106MET00.0500.03245.398-0.001-0.0010.0000.0000.0000.000
59B107SER00.0080.00447.2360.0000.0000.0000.0000.0000.000
60B108MET0-0.115-0.06443.245-0.004-0.0040.0000.0000.0000.000
61B109GLN00.0290.01644.315-0.001-0.0010.0000.0000.0000.000
62B110GLN0-0.041-0.02044.004-0.002-0.0020.0000.0000.0000.000
63B111CYS0-0.043-0.02238.843-0.004-0.0040.0000.0000.0000.000
64B112VAL00.0450.03638.9000.0030.0030.0000.0000.0000.000
65B113LEU0-0.099-0.04835.840-0.009-0.0090.0000.0000.0000.000
66B114VAL00.0750.02734.6510.0090.0090.0000.0000.0000.000
67B115LYS10.9721.00434.9250.1050.1050.0000.0000.0000.000
68B123TRP0-0.092-0.05434.735-0.002-0.0020.0000.0000.0000.000
69B124GLY0-0.013-0.02132.207-0.008-0.0080.0000.0000.0000.000
70B125PHE00.0260.01031.5670.0080.0080.0000.0000.0000.000
71B126PRO00.0260.03231.425-0.011-0.0110.0000.0000.0000.000
72B127LYS10.8380.90527.0090.2200.2200.0000.0000.0000.000
73B128GLY00.0440.03325.6810.0030.0030.0000.0000.0000.000
74B129LYS10.9010.94418.6300.4080.4080.0000.0000.0000.000
75B130ILE0-0.003-0.01920.1250.0130.0130.0000.0000.0000.000
76B131ASP-1-0.881-0.93621.105-0.259-0.2590.0000.0000.0000.000
77B132LYS10.7690.85218.9200.1970.1970.0000.0000.0000.000
78B133ASP-1-0.876-0.92421.261-0.185-0.1850.0000.0000.0000.000
79B134GLU-1-0.719-0.84023.284-0.200-0.2000.0000.0000.0000.000
80B135SER0-0.034-0.04223.881-0.021-0.0210.0000.0000.0000.000
81B136ASP-1-0.850-0.92923.915-0.278-0.2780.0000.0000.0000.000
82B137VAL00.002-0.02125.9910.0000.0000.0000.0000.0000.000
83B138ASP-1-0.806-0.88228.620-0.153-0.1530.0000.0000.0000.000
84B139CYS0-0.0230.04225.587-0.001-0.0010.0000.0000.0000.000
85B140ALA0-0.030-0.02527.6260.0030.0030.0000.0000.0000.000
86B141ILE0-0.036-0.02529.9510.0080.0080.0000.0000.0000.000
87B142ARG10.7950.86726.4310.2080.2080.0000.0000.0000.000
88B143GLU-1-0.834-0.90026.781-0.217-0.2170.0000.0000.0000.000
89B144VAL0-0.013-0.01830.8580.0070.0070.0000.0000.0000.000
90B145TYR0-0.0190.01934.1100.0100.0100.0000.0000.0000.000
91B146GLU-1-0.839-0.91230.699-0.158-0.1580.0000.0000.0000.000
92B147GLU-1-0.859-0.91731.610-0.174-0.1740.0000.0000.0000.000
93B148THR0-0.124-0.11335.1960.0080.0080.0000.0000.0000.000
94B149GLY00.0280.01938.2170.0070.0070.0000.0000.0000.000
95B150PHE0-0.073-0.04039.3730.0070.0070.0000.0000.0000.000
96B151ASP-1-0.787-0.86938.494-0.116-0.1160.0000.0000.0000.000
97B152CYS0-0.060-0.02936.0260.0020.0020.0000.0000.0000.000
98B153SER00.057-0.01036.874-0.004-0.0040.0000.0000.0000.000
99B154SER0-0.046-0.02037.902-0.002-0.0020.0000.0000.0000.000
100B155ARG10.8640.91939.7610.0980.0980.0000.0000.0000.000
101B156ILE0-0.0320.01632.487-0.002-0.0020.0000.0000.0000.000
102B157ASN00.0630.02835.936-0.001-0.0010.0000.0000.0000.000
103B158PRO00.0430.01531.700-0.007-0.0070.0000.0000.0000.000
104B159ASN0-0.024-0.02931.325-0.014-0.0140.0000.0000.0000.000
105B160GLU-1-0.837-0.88833.555-0.126-0.1260.0000.0000.0000.000
106B161PHE00.006-0.01227.910-0.005-0.0050.0000.0000.0000.000
107B162ILE0-0.062-0.02029.0000.0050.0050.0000.0000.0000.000
108B163ASP-1-0.821-0.88423.649-0.326-0.3260.0000.0000.0000.000
109B164MET0-0.021-0.00924.1160.0100.0100.0000.0000.0000.000
110B165THR00.0050.01417.466-0.023-0.0230.0000.0000.0000.000
111B166ILE0-0.008-0.01020.4970.0180.0180.0000.0000.0000.000
112B167ARG10.9120.95216.9900.3980.3980.0000.0000.0000.000
113B168GLY00.0800.04614.538-0.062-0.0620.0000.0000.0000.000
114B169GLN0-0.042-0.02815.372-0.038-0.0380.0000.0000.0000.000
115B170ASN0-0.026-0.01417.8100.0620.0620.0000.0000.0000.000
116B171VAL00.0180.00619.8290.0050.0050.0000.0000.0000.000
117B172ARG10.8220.90123.4040.2800.2800.0000.0000.0000.000
118B173LEU0-0.047-0.01526.2350.0070.0070.0000.0000.0000.000
119B174TYR00.0630.02528.3880.0030.0030.0000.0000.0000.000
120B175ILE0-0.057-0.02632.3630.0040.0040.0000.0000.0000.000
121B176ILE00.0120.00635.4070.0050.0050.0000.0000.0000.000
122B177PRO0-0.025-0.01038.6430.0020.0020.0000.0000.0000.000
123B178GLY00.036-0.00242.0870.0010.0010.0000.0000.0000.000
124B179ILE0-0.063-0.01041.1240.0030.0030.0000.0000.0000.000
125B180SER00.0570.03044.5800.0010.0010.0000.0000.0000.000
126B181LEU00.0510.01646.816-0.003-0.0030.0000.0000.0000.000
127B182ASP-1-0.918-0.94448.463-0.069-0.0690.0000.0000.0000.000
128B183THR0-0.120-0.07843.8820.0010.0010.0000.0000.0000.000
129B184ARG10.9050.92245.2370.0780.0780.0000.0000.0000.000
130B185PHE00.0760.04641.183-0.001-0.0010.0000.0000.0000.000
131B186GLU-1-0.807-0.87543.105-0.080-0.0800.0000.0000.0000.000
132B187SER00.0000.01741.6480.0000.0000.0000.0000.0000.000
133B188ARG10.8570.90643.7810.0830.0830.0000.0000.0000.000
134B189THR0-0.057-0.02341.835-0.003-0.0030.0000.0000.0000.000
135B190ARG10.8900.94138.0590.1130.1130.0000.0000.0000.000
136B191LYS10.9160.96035.5730.0960.0960.0000.0000.0000.000
137B192GLU-1-0.829-0.92033.603-0.119-0.1190.0000.0000.0000.000
138B193ILE00.0310.03732.851-0.006-0.0060.0000.0000.0000.000
139B194SER0-0.047-0.01936.0960.0090.0090.0000.0000.0000.000
140B195LYS10.8810.91138.6750.0960.0960.0000.0000.0000.000
141B196ILE00.0440.02038.816-0.006-0.0060.0000.0000.0000.000
142B197GLU-1-0.915-0.94740.858-0.093-0.0930.0000.0000.0000.000
143B198TRP00.0310.02541.684-0.009-0.0090.0000.0000.0000.000
144B199HIS10.8870.93240.9420.1110.1110.0000.0000.0000.000
145B200ASN00.0560.03043.162-0.003-0.0030.0000.0000.0000.000
146B201LEU00.024-0.00339.638-0.003-0.0030.0000.0000.0000.000
147B202MET0-0.037-0.03241.838-0.004-0.0040.0000.0000.0000.000
148B203ASP-1-0.831-0.91544.378-0.086-0.0860.0000.0000.0000.000
149B204LEU0-0.042-0.00638.222-0.003-0.0030.0000.0000.0000.000
150B205PRO00.004-0.00237.2130.0020.0020.0000.0000.0000.000
151B206THR00.022-0.01435.0540.0060.0060.0000.0000.0000.000
152B207PHE00.0250.05638.3630.0020.0020.0000.0000.0000.000
153B208LYS11.0050.97140.1150.0890.0890.0000.0000.0000.000
154B209LYS10.7990.95142.6230.0950.0950.0000.0000.0000.000
155B210ASN00.0820.02743.910-0.002-0.0020.0000.0000.0000.000
156B211LYS10.9450.98237.6430.1190.1190.0000.0000.0000.000
157B212PRO00.0840.04839.733-0.006-0.0060.0000.0000.0000.000
158B213GLN00.0990.05033.797-0.003-0.0030.0000.0000.0000.000
159B214THR00.0210.02437.2110.0080.0080.0000.0000.0000.000
160B215MET00.0460.01238.335-0.004-0.0040.0000.0000.0000.000
161B216LYS10.7870.88035.5510.1270.1270.0000.0000.0000.000
162B217ASN00.0550.01233.188-0.008-0.0080.0000.0000.0000.000
163B218LYS10.9660.99933.4680.1010.1010.0000.0000.0000.000
164B219PHE00.0270.00934.884-0.001-0.0010.0000.0000.0000.000
165B220TYR0-0.006-0.01526.523-0.005-0.0050.0000.0000.0000.000
166B221MET00.0370.02828.021-0.015-0.0150.0000.0000.0000.000
167B222VAL0-0.0110.00029.873-0.006-0.0060.0000.0000.0000.000
168B223ILE0-0.015-0.02331.9560.0000.0000.0000.0000.0000.000
169B224PRO00.0260.01827.6460.0110.0110.0000.0000.0000.000
170B225PHE00.0830.04026.7370.0050.0050.0000.0000.0000.000
171B226LEU0-0.030-0.00231.7050.0110.0110.0000.0000.0000.000
172B227ALA0-0.013-0.00433.8600.0080.0080.0000.0000.0000.000
173B228PRO00.0530.00930.9290.0100.0100.0000.0000.0000.000
174B229LEU00.0590.03434.0830.0060.0060.0000.0000.0000.000
175B230LYS10.8460.92036.4020.1150.1150.0000.0000.0000.000
176B231LYS10.9540.97635.3240.1420.1420.0000.0000.0000.000
177B232TRP0-0.048-0.04035.8810.0090.0090.0000.0000.0000.000
178B233ILE00.0350.00138.5390.0050.0050.0000.0000.0000.000
179B234LYS10.9410.97741.7010.0940.0940.0000.0000.0000.000
180B235LYS10.9480.98537.5350.1270.1270.0000.0000.0000.000
181B236ARG10.8810.94640.4210.1070.1070.0000.0000.0000.000
182B237ASN0-0.006-0.01743.9000.0060.0060.0000.0000.0000.000
183B238ILE0-0.0170.00945.2970.0040.0040.0000.0000.0000.000
184B239ALA0-0.0020.00144.9560.0030.0030.0000.0000.0000.000
185B240ASN0-0.027-0.02446.9220.0010.0010.0000.0000.0000.000
186B241ASN0-0.064-0.03349.2280.0050.0050.0000.0000.0000.000
187B242THR0-0.0130.00349.6980.0010.0010.0000.0000.0000.000
188B243THR00.0180.02352.2980.0000.0000.0000.0000.0000.000