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: KG3Y3

Calculation Name: 2B4I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B4I

Chain ID: A

ChEMBL ID:

UniProt ID: P12473

Base Structure: X-ray

Registration Date: 2023-09-21

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2733830.2586
FMO2-HF: Nuclear repulsion 2642249.131108
FMO2-HF: Total energy -91581.127491
FMO2-MP2: Total energy -91848.869974


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:246:MET)


Summations of interaction energy for fragment #1(A:246: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.
-6.808-2.7560.21-2.096-2.165-0.001
Interaction energy analysis for fragmet #1(A:246:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / 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].
3A248ALA0-0.039-0.0272.922-3.5100.2150.211-2.029-1.906-0.001
4A249GLN0-0.032-0.0155.3420.7250.829-0.001-0.002-0.1010.000
5A250ALA00.0100.0108.994-0.283-0.2830.0000.0000.0000.000
6A251ASN00.023-0.00811.784-0.049-0.0490.0000.0000.0000.000
7A252GLU-1-0.732-0.8516.911-3.564-3.5640.0000.0000.0000.000
8A253ASP-1-0.814-0.89310.389-0.899-0.8990.0000.0000.0000.000
9A254ILE0-0.018-0.0103.844-0.1120.1110.000-0.065-0.1580.000
10A255VAL0-0.009-0.0097.3050.2930.2930.0000.0000.0000.000
11A256VAL0-0.032-0.0166.860-0.178-0.1780.0000.0000.0000.000
12A257SER00.011-0.0078.2670.2640.2640.0000.0000.0000.000
13A258LYS10.9020.95111.6410.1620.1620.0000.0000.0000.000
14A259THR00.0010.01314.5060.0640.0640.0000.0000.0000.000
15A260SER00.009-0.00818.234-0.024-0.0240.0000.0000.0000.000
16A261LEU00.0270.00421.355-0.014-0.0140.0000.0000.0000.000
17A262TRP00.0360.02318.835-0.020-0.0200.0000.0000.0000.000
18A263LYS10.8870.95114.0570.4270.4270.0000.0000.0000.000
19A264GLU-1-0.801-0.85211.904-0.242-0.2420.0000.0000.0000.000
20A265MET0-0.0140.00510.434-0.037-0.0370.0000.0000.0000.000
21A266GLN00.0090.0115.365-0.165-0.1650.0000.0000.0000.000
22A267TYR0-0.0040.0068.709-0.193-0.1930.0000.0000.0000.000
23A268ASN0-0.024-0.0056.6990.3640.3640.0000.0000.0000.000
24A269ARG10.8200.88510.9120.8740.8740.0000.0000.0000.000
25A270ASP-1-0.748-0.85714.468-0.569-0.5690.0000.0000.0000.000
26A271ILE0-0.057-0.02916.8470.0160.0160.0000.0000.0000.000
27A272THR00.0150.01820.1740.0240.0240.0000.0000.0000.000
28A273ILE0-0.0120.00822.5700.0070.0070.0000.0000.0000.000
29A274ARG10.8630.93225.7750.2090.2090.0000.0000.0000.000
30A275PHE00.0140.01129.469-0.001-0.0010.0000.0000.0000.000
31A276LYS10.8490.93331.9520.1250.1250.0000.0000.0000.000
32A277PHE00.0320.00635.367-0.003-0.0030.0000.0000.0000.000
33A278ALA00.0060.00837.9740.0010.0010.0000.0000.0000.000
34A279SER00.025-0.01241.028-0.001-0.0010.0000.0000.0000.000
35A280SER0-0.050-0.01244.4120.0000.0000.0000.0000.0000.000
36A281ILE0-0.006-0.00347.3020.0020.0020.0000.0000.0000.000
37A282VAL00.0050.01250.5340.0010.0010.0000.0000.0000.000
38A283LYS10.8490.92253.6690.0470.0470.0000.0000.0000.000
39A284SER0-0.008-0.01357.2310.0000.0000.0000.0000.0000.000
40A285GLY00.0350.01760.0290.0000.0000.0000.0000.0000.000
41A286GLY0-0.014-0.01663.2230.0000.0000.0000.0000.0000.000
42A287LEU00.017-0.00465.989-0.001-0.0010.0000.0000.0000.000
43A288GLY00.0540.04462.9450.0000.0000.0000.0000.0000.000
44A289TYR00.0500.02262.582-0.001-0.0010.0000.0000.0000.000
45A290LYS10.8010.89660.5910.0360.0360.0000.0000.0000.000
46A291TRP00.0390.02254.2900.0000.0000.0000.0000.0000.000
47A292SER00.0220.00155.2820.0010.0010.0000.0000.0000.000
48A293GLU-1-0.852-0.89048.854-0.062-0.0620.0000.0000.0000.000
49A294ILE0-0.026-0.00447.969-0.001-0.0010.0000.0000.0000.000
50A295SER0-0.006-0.01745.6030.0000.0000.0000.0000.0000.000
51A296PHE00.0380.00240.335-0.002-0.0020.0000.0000.0000.000
52A297LYS10.8600.93441.0770.0850.0850.0000.0000.0000.000
53A298PRO00.007-0.01636.340-0.003-0.0030.0000.0000.0000.000
54A299ALA0-0.0250.00036.2330.0050.0050.0000.0000.0000.000
55A300ASN0-0.0290.00234.001-0.007-0.0070.0000.0000.0000.000
56A301TYR0-0.022-0.02231.8770.0050.0050.0000.0000.0000.000
57A302GLN00.0240.02031.199-0.011-0.0110.0000.0000.0000.000
58A303TYR0-0.063-0.05126.0640.0100.0100.0000.0000.0000.000
59A304THR00.023-0.00528.339-0.010-0.0100.0000.0000.0000.000
60A305TYR0-0.047-0.04221.9820.0010.0010.0000.0000.0000.000
61A306THR00.0150.01223.390-0.005-0.0050.0000.0000.0000.000
62A307ARG10.7900.88718.0400.4630.4630.0000.0000.0000.000
63A308ASP-1-0.835-0.90815.589-0.602-0.6020.0000.0000.0000.000
64A309GLY0-0.037-0.01918.8570.0100.0100.0000.0000.0000.000
65A310GLU-1-0.946-0.95920.136-0.356-0.3560.0000.0000.0000.000
66A311GLU-1-0.924-0.95923.008-0.196-0.1960.0000.0000.0000.000
67A312VAL0-0.046-0.01121.826-0.016-0.0160.0000.0000.0000.000
68A313THR00.025-0.00624.7460.0320.0320.0000.0000.0000.000
69A314ALA0-0.060-0.04025.090-0.021-0.0210.0000.0000.0000.000
70A315HIS0-0.026-0.02026.7590.0300.0300.0000.0000.0000.000
71A316THR0-0.046-0.04127.030-0.010-0.0100.0000.0000.0000.000
72A317THR00.011-0.01629.4100.0170.0170.0000.0000.0000.000
73A318CYS0-0.089-0.01230.970-0.004-0.0040.0000.0000.0000.000
74A319SER00.0290.00932.8050.0100.0100.0000.0000.0000.000
75A320VAL00.0160.00234.076-0.005-0.0050.0000.0000.0000.000
76A321ASN0-0.024-0.02636.1160.0050.0050.0000.0000.0000.000
77A322GLY00.0910.04537.741-0.001-0.0010.0000.0000.0000.000
78A323MET0-0.0350.02739.8360.0000.0000.0000.0000.0000.000
79A324ASN0-0.046-0.02142.2100.0060.0060.0000.0000.0000.000
80A325ASP-1-0.785-0.88245.406-0.059-0.0590.0000.0000.0000.000
81A326PHE0-0.056-0.02246.9500.0030.0030.0000.0000.0000.000
82A327ASN0-0.013-0.00951.3180.0010.0010.0000.0000.0000.000
83A328PHE0-0.017-0.01554.6370.0010.0010.0000.0000.0000.000
84A329ASN00.0810.02857.5600.0000.0000.0000.0000.0000.000
85A330GLY0-0.001-0.01261.0960.0010.0010.0000.0000.0000.000
86A331GLY00.0180.02363.6540.0010.0010.0000.0000.0000.000
87A332SER0-0.016-0.02865.643-0.001-0.0010.0000.0000.0000.000
88A333LEU00.0260.02367.7300.0000.0000.0000.0000.0000.000
89A334PRO00.004-0.00867.804-0.001-0.0010.0000.0000.0000.000
90A335THR00.027-0.00767.232-0.001-0.0010.0000.0000.0000.000
91A336ASP-1-0.861-0.89865.967-0.032-0.0320.0000.0000.0000.000
92A337PHE0-0.002-0.00257.015-0.001-0.0010.0000.0000.0000.000
93A338VAL0-0.046-0.02259.5330.0010.0010.0000.0000.0000.000
94A339ILE0-0.0030.03753.396-0.001-0.0010.0000.0000.0000.000
95A340SER0-0.031-0.03556.2740.0010.0010.0000.0000.0000.000
96A341ARG10.7690.84946.9380.0630.0630.0000.0000.0000.000
97A342TYR0-0.017-0.01448.895-0.001-0.0010.0000.0000.0000.000
98A343GLU-1-0.735-0.85444.081-0.073-0.0730.0000.0000.0000.000
99A344VAL0-0.048-0.02343.961-0.001-0.0010.0000.0000.0000.000
100A345ILE0-0.0300.01137.3680.0010.0010.0000.0000.0000.000
101A346LYS10.9710.95440.3340.0590.0590.0000.0000.0000.000
102A347GLU-1-0.789-0.89137.548-0.073-0.0730.0000.0000.0000.000
103A348ASN0-0.058-0.01737.248-0.003-0.0030.0000.0000.0000.000
104A349SER0-0.047-0.04037.6820.0010.0010.0000.0000.0000.000
105A350TYR0-0.034-0.01531.084-0.004-0.0040.0000.0000.0000.000
106A351VAL00.0170.01132.0850.0040.0040.0000.0000.0000.000
107A352TYR0-0.029-0.03329.018-0.007-0.0070.0000.0000.0000.000
108A353VAL00.0170.00327.6460.0080.0080.0000.0000.0000.000
109A354ASP-1-0.761-0.81326.527-0.194-0.1940.0000.0000.0000.000
110A355TYR0-0.018-0.05021.0000.0150.0150.0000.0000.0000.000
111A356TRP00.0380.02123.157-0.012-0.0120.0000.0000.0000.000
112A357ASP-1-0.688-0.80320.633-0.433-0.4330.0000.0000.0000.000
113A358ASP-1-0.807-0.89822.584-0.310-0.3100.0000.0000.0000.000
114A359SER0-0.053-0.02618.391-0.037-0.0370.0000.0000.0000.000
115A360GLN0-0.009-0.03515.9950.0570.0570.0000.0000.0000.000
116A361ALA00.0260.00315.1420.0150.0150.0000.0000.0000.000
117A362PHE0-0.0040.01216.4880.0150.0150.0000.0000.0000.000
118A363ARG10.9370.97619.3530.3590.3590.0000.0000.0000.000
119A364ASN0-0.043-0.03219.640-0.007-0.0070.0000.0000.0000.000
120A365MET00.0070.02317.0130.0090.0090.0000.0000.0000.000
121A366VAL00.0130.00120.0770.0240.0240.0000.0000.0000.000
122A367TYR0-0.013-0.00419.1320.0260.0260.0000.0000.0000.000
123A368VAL00.0140.00415.111-0.038-0.0380.0000.0000.0000.000
124A369ARG10.8690.92211.2520.2670.2670.0000.0000.0000.000
125A370SER0-0.010-0.03010.849-0.049-0.0490.0000.0000.0000.000
126A371LEU0-0.0050.01112.151-0.088-0.0880.0000.0000.0000.000
127A372ALA0-0.0040.01212.5370.0710.0710.0000.0000.0000.000
128A373ALA00.024-0.00614.547-0.072-0.0720.0000.0000.0000.000
129A374ASN0-0.062-0.02216.6720.0280.0280.0000.0000.0000.000
130A375LEU0-0.003-0.00218.350-0.022-0.0220.0000.0000.0000.000
131A376ASN0-0.0090.01121.7650.0150.0150.0000.0000.0000.000
132A377SER0-0.036-0.02924.6560.0040.0040.0000.0000.0000.000
133A378VAL00.005-0.00328.144-0.002-0.0020.0000.0000.0000.000
134A379ILE00.0190.01331.1230.0040.0040.0000.0000.0000.000
135A380CYS0-0.055-0.01234.866-0.005-0.0050.0000.0000.0000.000
136A381THR00.0310.00537.0920.0040.0040.0000.0000.0000.000
137A382GLY00.003-0.00840.803-0.003-0.0030.0000.0000.0000.000
138A383GLY0-0.020-0.01443.8210.0020.0020.0000.0000.0000.000
139A384ASP-1-0.860-0.90946.041-0.056-0.0560.0000.0000.0000.000
140A385TYR0-0.013-0.01049.485-0.001-0.0010.0000.0000.0000.000
141A386SER0-0.010-0.00251.4410.0030.0030.0000.0000.0000.000
142A387PHE0-0.012-0.01252.885-0.001-0.0010.0000.0000.0000.000
143A388ALA00.020-0.01257.3470.0020.0020.0000.0000.0000.000
144A389LEU0-0.037-0.00560.1040.0000.0000.0000.0000.0000.000
145A390PRO0-0.024-0.00263.1850.0000.0000.0000.0000.0000.000
146A391VAL00.0190.00366.1650.0010.0010.0000.0000.0000.000
147A392GLY0-0.0040.00767.1510.0000.0000.0000.0000.0000.000
148A393GLN0-0.025-0.02664.064-0.002-0.0020.0000.0000.0000.000
149A394TRP00.0590.03159.086-0.001-0.0010.0000.0000.0000.000
150A395PRO00.0010.02258.3270.0000.0000.0000.0000.0000.000
151A396VAL0-0.011-0.00553.518-0.001-0.0010.0000.0000.0000.000
152A397MET0-0.0230.00149.8440.0000.0000.0000.0000.0000.000
153A398THR0-0.020-0.04049.900-0.002-0.0020.0000.0000.0000.000
154A399GLY00.0760.04247.0400.0020.0020.0000.0000.0000.000
155A400GLY0-0.010-0.00844.758-0.002-0.0020.0000.0000.0000.000
156A401ALA00.003-0.01340.151-0.003-0.0030.0000.0000.0000.000
157A402VAL0-0.0320.00036.5600.0040.0040.0000.0000.0000.000
158A403SER00.003-0.01933.371-0.005-0.0050.0000.0000.0000.000
159A404LEU0-0.021-0.01430.2220.0030.0030.0000.0000.0000.000
160A405HIS0-0.017-0.01728.227-0.013-0.0130.0000.0000.0000.000
161A406SER00.0130.01222.2670.0060.0060.0000.0000.0000.000
162A407ALA00.0140.00225.3500.0090.0090.0000.0000.0000.000
163A408GLY00.0150.01322.9440.0140.0140.0000.0000.0000.000
164A409VAL00.002-0.00919.895-0.005-0.0050.0000.0000.0000.000
165A410THR0-0.025-0.00121.7010.0030.0030.0000.0000.0000.000
166A411LEU00.0310.02519.275-0.016-0.0160.0000.0000.0000.000
167A412SER0-0.069-0.05923.1710.0170.0170.0000.0000.0000.000
168A413THR00.0150.00525.786-0.012-0.0120.0000.0000.0000.000
169A414GLN0-0.0100.02026.7680.0250.0250.0000.0000.0000.000
170A415PHE0-0.003-0.02330.368-0.005-0.0050.0000.0000.0000.000
171A416THR0-0.025-0.01832.0380.0080.0080.0000.0000.0000.000
172A417ASP-1-0.901-0.95334.825-0.110-0.1100.0000.0000.0000.000
173A418PHE0-0.048-0.01835.0300.0040.0040.0000.0000.0000.000
174A419VAL0-0.0050.00729.6840.0000.0000.0000.0000.0000.000
175A420SER00.0130.02030.9310.0030.0030.0000.0000.0000.000
176A421LEU0-0.009-0.00226.773-0.009-0.0090.0000.0000.0000.000
177A422ASN0-0.032-0.00422.9000.0230.0230.0000.0000.0000.000
178A423SER0-0.019-0.01523.156-0.020-0.0200.0000.0000.0000.000
179A424LEU00.0080.02217.7720.0020.0020.0000.0000.0000.000
180A425ARG10.8190.86222.2660.1710.1710.0000.0000.0000.000
181A426PHE00.012-0.00519.785-0.001-0.0010.0000.0000.0000.000
182A427ARG10.8840.94524.9260.1410.1410.0000.0000.0000.000
183A428PHE0-0.008-0.00326.049-0.006-0.0060.0000.0000.0000.000
184A429ARG10.9470.98029.2740.1120.1120.0000.0000.0000.000
185A430LEU0-0.003-0.02531.625-0.006-0.0060.0000.0000.0000.000
186A431THR0-0.0080.01234.5650.0030.0030.0000.0000.0000.000
187A432VAL0-0.050-0.03236.472-0.003-0.0030.0000.0000.0000.000
188A433GLU-1-0.831-0.88036.418-0.082-0.0820.0000.0000.0000.000
189A434GLU-1-0.834-0.86040.579-0.052-0.0520.0000.0000.0000.000
190A435PRO0-0.032-0.01642.225-0.004-0.0040.0000.0000.0000.000
191A436SER00.0120.00545.214-0.001-0.0010.0000.0000.0000.000
192A437PHE0-0.004-0.03046.5790.0000.0000.0000.0000.0000.000
193A438SER0-0.082-0.04549.0800.0030.0030.0000.0000.0000.000
194A439ILE0-0.0020.00352.566-0.002-0.0020.0000.0000.0000.000
195A440THR00.0310.03055.2560.0030.0030.0000.0000.0000.000
196A441ARG10.9110.93357.9300.0390.0390.0000.0000.0000.000
197A442THR0-0.011-0.00358.1030.0010.0010.0000.0000.0000.000
198A443ARG10.9260.96160.0620.0350.0350.0000.0000.0000.000
199A444VAL0-0.014-0.00453.8380.0000.0000.0000.0000.0000.000
200A445SER00.009-0.02053.675-0.001-0.0010.0000.0000.0000.000
201A446ARG10.9000.94348.8260.0470.0470.0000.0000.0000.000
202A447LEU00.0140.04049.2270.0000.0000.0000.0000.0000.000
203A448TYR0-0.014-0.04444.1050.0000.0000.0000.0000.0000.000
204A449GLY00.0380.00642.1550.0010.0010.0000.0000.0000.000
205A450LEU0-0.0220.01038.9100.0020.0020.0000.0000.0000.000
206A451PRO00.016-0.00442.478-0.001-0.0010.0000.0000.0000.000
207A452ALA00.0200.02543.718-0.003-0.0030.0000.0000.0000.000
208A453ALA0-0.012-0.00244.756-0.001-0.0010.0000.0000.0000.000
209A454ASN0-0.010-0.02545.017-0.004-0.0040.0000.0000.0000.000
210A455PRO00.0620.04540.0970.0000.0000.0000.0000.0000.000
211A456ASN00.0450.02238.732-0.008-0.0080.0000.0000.0000.000
212A457ASN0-0.049-0.02240.4920.0000.0000.0000.0000.0000.000
213A458GLY00.0020.00542.8130.0000.0000.0000.0000.0000.000
214A459LYS10.8820.96037.0800.0990.0990.0000.0000.0000.000
215A460GLU-1-0.795-0.90137.137-0.115-0.1150.0000.0000.0000.000
216A461TYR0-0.049-0.03331.631-0.003-0.0030.0000.0000.0000.000
217A462TYR0-0.0070.00132.6950.0060.0060.0000.0000.0000.000
218A463GLU-1-0.807-0.90927.705-0.205-0.2050.0000.0000.0000.000
219A464VAL0-0.021-0.00224.4340.0090.0090.0000.0000.0000.000
220A465ALA00.0260.02322.705-0.014-0.0140.0000.0000.0000.000
221A466GLY00.030-0.00920.0220.0230.0230.0000.0000.0000.000
222A467ARG10.8380.91213.9050.4640.4640.0000.0000.0000.000
223A468PHE0-0.023-0.00814.3010.0550.0550.0000.0000.0000.000
224A469SER00.001-0.0118.622-0.082-0.0820.0000.0000.0000.000
225A470LEU0-0.0110.00110.9400.1660.1660.0000.0000.0000.000
226A471ILE00.0140.0138.297-0.185-0.1850.0000.0000.0000.000
227A472SER00.0370.01011.5260.1400.1400.0000.0000.0000.000
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230A475PRO00.0390.01118.2180.0040.0040.0000.0000.0000.000
231A476SER0-0.035-0.02818.397-0.052-0.0520.0000.0000.0000.000
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