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: QV1RY

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2731650.983486
FMO2-HF: Nuclear repulsion 2640070.552707
FMO2-HF: Total energy -91580.430779
FMO2-MP2: Total energy -91848.193419


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.
-4.772-1.7820.185-1.487-1.688-0.005
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 : -0.038 / q_NPA : -0.034
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].
3A248ALA0-0.025-0.0162.940-3.464-0.7050.184-1.426-1.517-0.005
4A249GLN00.0020.0075.4150.7040.7040.0000.0000.0000.000
5A250ALA0-0.0040.0049.073-0.064-0.0640.0000.0000.0000.000
6A251ASN00.010-0.00511.8540.0850.0850.0000.0000.0000.000
7A252GLU-1-0.766-0.8816.993-2.363-2.3630.0000.0000.0000.000
8A253ASP-1-0.776-0.90210.181-0.343-0.3430.0000.0000.0000.000
9A254ILE0-0.025-0.0113.725-0.1860.0450.001-0.061-0.1710.000
10A255VAL0-0.015-0.0147.1340.4020.4020.0000.0000.0000.000
11A256VAL0-0.040-0.0176.646-0.250-0.2500.0000.0000.0000.000
12A257SER00.0350.0108.203-0.001-0.0010.0000.0000.0000.000
13A258LYS10.8900.94911.6280.3170.3170.0000.0000.0000.000
14A259THR00.0220.02514.5030.0300.0300.0000.0000.0000.000
15A260SER00.008-0.01518.232-0.018-0.0180.0000.0000.0000.000
16A261LEU00.0270.00721.350-0.007-0.0070.0000.0000.0000.000
17A262TRP00.0270.02818.668-0.003-0.0030.0000.0000.0000.000
18A263LYS10.9670.97513.9400.3390.3390.0000.0000.0000.000
19A264GLU-1-0.798-0.86911.8110.0100.0100.0000.0000.0000.000
20A265MET0-0.0200.00510.254-0.110-0.1100.0000.0000.0000.000
21A266GLN00.0480.0375.8000.5450.5450.0000.0000.0000.000
22A267TYR0-0.030-0.0068.749-0.256-0.2560.0000.0000.0000.000
23A268ASN0-0.045-0.0327.4990.3720.3720.0000.0000.0000.000
24A269ARG10.8450.91111.3390.2730.2730.0000.0000.0000.000
25A270ASP-1-0.807-0.89514.878-0.073-0.0730.0000.0000.0000.000
26A271ILE0-0.074-0.04417.066-0.013-0.0130.0000.0000.0000.000
27A272THR00.0150.01920.5920.0180.0180.0000.0000.0000.000
28A273ILE0-0.0160.02623.336-0.005-0.0050.0000.0000.0000.000
29A274ARG10.8950.95226.3240.0510.0510.0000.0000.0000.000
30A275PHE00.0210.01929.987-0.002-0.0020.0000.0000.0000.000
31A276LYS10.9390.97632.5820.0230.0230.0000.0000.0000.000
32A277PHE00.0190.00036.2310.0000.0000.0000.0000.0000.000
33A278ALA0-0.0040.00138.691-0.002-0.0020.0000.0000.0000.000
34A279SER0-0.006-0.03741.6860.0010.0010.0000.0000.0000.000
35A280SER0-0.064-0.01545.111-0.002-0.0020.0000.0000.0000.000
36A281ILE00.001-0.00647.9750.0010.0010.0000.0000.0000.000
37A282VAL00.0100.01851.236-0.001-0.0010.0000.0000.0000.000
38A283LYS10.8650.92254.3530.0050.0050.0000.0000.0000.000
39A284SER0-0.019-0.02057.9320.0000.0000.0000.0000.0000.000
40A285GLY00.0350.02060.7470.0000.0000.0000.0000.0000.000
41A286GLY0-0.011-0.01563.8980.0000.0000.0000.0000.0000.000
42A287LEU00.019-0.00466.6620.0000.0000.0000.0000.0000.000
43A288GLY00.0300.03363.6570.0000.0000.0000.0000.0000.000
44A289TYR00.0790.03163.3260.0000.0000.0000.0000.0000.000
45A290LYS10.8100.89961.4180.0000.0000.0000.0000.0000.000
46A291TRP00.0370.02055.268-0.001-0.0010.0000.0000.0000.000
47A292SER0-0.009-0.01656.3570.0010.0010.0000.0000.0000.000
48A293GLU-1-0.854-0.88449.500-0.002-0.0020.0000.0000.0000.000
49A294ILE0-0.0190.00348.603-0.001-0.0010.0000.0000.0000.000
50A295SER0-0.033-0.05746.3810.0010.0010.0000.0000.0000.000
51A296PHE00.0380.01241.087-0.001-0.0010.0000.0000.0000.000
52A297LYS10.9170.97041.7840.0120.0120.0000.0000.0000.000
53A298PRO00.001-0.01837.0530.0000.0000.0000.0000.0000.000
54A299ALA0-0.0230.00236.854-0.001-0.0010.0000.0000.0000.000
55A300ASN0-0.0340.00134.470-0.001-0.0010.0000.0000.0000.000
56A301TYR00.005-0.01232.0580.0020.0020.0000.0000.0000.000
57A302GLN00.0460.03531.6210.0000.0000.0000.0000.0000.000
58A303TYR0-0.077-0.08426.5090.0040.0040.0000.0000.0000.000
59A304THR00.0710.03428.501-0.003-0.0030.0000.0000.0000.000
60A305TYR0-0.050-0.04922.4090.0070.0070.0000.0000.0000.000
61A306THR00.0180.01323.369-0.004-0.0040.0000.0000.0000.000
62A307ARG10.8250.91818.0610.1850.1850.0000.0000.0000.000
63A308ASP-1-0.845-0.91515.846-0.325-0.3250.0000.0000.0000.000
64A309GLY0-0.045-0.02418.968-0.005-0.0050.0000.0000.0000.000
65A310GLU-1-0.947-0.96520.217-0.221-0.2210.0000.0000.0000.000
66A311GLU-1-0.969-0.99323.161-0.080-0.0800.0000.0000.0000.000
67A312VAL0-0.0310.00121.868-0.009-0.0090.0000.0000.0000.000
68A313THR00.0380.01324.7480.0190.0190.0000.0000.0000.000
69A314ALA0-0.046-0.03025.361-0.007-0.0070.0000.0000.0000.000
70A315HIS0-0.030-0.02226.9780.0070.0070.0000.0000.0000.000
71A316THR0-0.051-0.04027.6510.0010.0010.0000.0000.0000.000
72A317THR00.008-0.02929.8840.0000.0000.0000.0000.0000.000
73A318CYS0-0.084-0.01531.6030.0050.0050.0000.0000.0000.000
74A319SER00.0220.00833.4410.0000.0000.0000.0000.0000.000
75A320VAL00.0380.01034.9030.0020.0020.0000.0000.0000.000
76A321ASN0-0.034-0.03237.0170.0000.0000.0000.0000.0000.000
77A322GLY00.0840.04138.6630.0020.0020.0000.0000.0000.000
78A323MET0-0.0390.02740.8410.0020.0020.0000.0000.0000.000
79A324ASN0-0.044-0.02443.1900.0010.0010.0000.0000.0000.000
80A325ASP-1-0.794-0.88646.3720.0040.0040.0000.0000.0000.000
81A326PHE0-0.055-0.02347.9350.0010.0010.0000.0000.0000.000
82A327ASN0-0.013-0.01652.191-0.001-0.0010.0000.0000.0000.000
83A328PHE0-0.027-0.01655.5070.0010.0010.0000.0000.0000.000
84A329ASN00.0840.02758.341-0.001-0.0010.0000.0000.0000.000
85A330GLY0-0.015-0.02261.9230.0000.0000.0000.0000.0000.000
86A331GLY00.0140.02164.3970.0000.0000.0000.0000.0000.000
87A332SER0-0.028-0.03266.5240.0000.0000.0000.0000.0000.000
88A333LEU00.0320.02868.6400.0000.0000.0000.0000.0000.000
89A334PRO00.004-0.00868.6620.0000.0000.0000.0000.0000.000
90A335THR00.024-0.00868.0380.0000.0000.0000.0000.0000.000
91A336ASP-1-0.855-0.89666.6460.0010.0010.0000.0000.0000.000
92A337PHE0-0.012-0.00457.7300.0000.0000.0000.0000.0000.000
93A338VAL0-0.041-0.01660.4170.0010.0010.0000.0000.0000.000
94A339ILE00.0000.03154.247-0.001-0.0010.0000.0000.0000.000
95A340SER0-0.030-0.02757.1150.0010.0010.0000.0000.0000.000
96A341ARG10.8410.89748.125-0.001-0.0010.0000.0000.0000.000
97A342TYR0-0.026-0.01149.555-0.001-0.0010.0000.0000.0000.000
98A343GLU-1-0.745-0.86944.9320.0030.0030.0000.0000.0000.000
99A344VAL0-0.042-0.01744.645-0.001-0.0010.0000.0000.0000.000
100A345ILE0-0.0220.01138.1620.0010.0010.0000.0000.0000.000
101A346LYS10.9530.94541.127-0.015-0.0150.0000.0000.0000.000
102A347GLU-1-0.789-0.89238.1940.0290.0290.0000.0000.0000.000
103A348ASN0-0.048-0.00638.0110.0020.0020.0000.0000.0000.000
104A349SER0-0.043-0.03438.621-0.001-0.0010.0000.0000.0000.000
105A350TYR0-0.036-0.02332.1520.0050.0050.0000.0000.0000.000
106A351VAL00.0170.01532.747-0.004-0.0040.0000.0000.0000.000
107A352TYR0-0.039-0.03930.0380.0070.0070.0000.0000.0000.000
108A353VAL00.0170.00728.329-0.004-0.0040.0000.0000.0000.000
109A354ASP-1-0.776-0.85927.155-0.007-0.0070.0000.0000.0000.000
110A355TYR0-0.017-0.04821.3460.0020.0020.0000.0000.0000.000
111A356TRP00.0170.01723.4640.0020.0020.0000.0000.0000.000
112A357ASP-1-0.697-0.80820.813-0.141-0.1410.0000.0000.0000.000
113A358ASP-1-0.836-0.93022.631-0.139-0.1390.0000.0000.0000.000
114A359SER0-0.088-0.05418.139-0.028-0.0280.0000.0000.0000.000
115A360GLN0-0.011-0.04215.9320.0420.0420.0000.0000.0000.000
116A361ALA00.0300.00815.1710.0100.0100.0000.0000.0000.000
117A362PHE0-0.0150.00616.4670.0300.0300.0000.0000.0000.000
118A363ARG10.9170.97319.1000.1790.1790.0000.0000.0000.000
119A364ASN0-0.049-0.03019.4880.0050.0050.0000.0000.0000.000
120A365MET00.0030.01617.3300.0090.0090.0000.0000.0000.000
121A366VAL00.0220.01220.1840.0120.0120.0000.0000.0000.000
122A367TYR0-0.006-0.00519.2180.0170.0170.0000.0000.0000.000
123A368VAL00.0130.00515.582-0.011-0.0110.0000.0000.0000.000
124A369ARG10.8520.91811.301-0.140-0.1400.0000.0000.0000.000
125A370SER0-0.015-0.03311.645-0.031-0.0310.0000.0000.0000.000
126A371LEU0-0.0020.01413.1170.0430.0430.0000.0000.0000.000
127A372ALA0-0.0070.01113.5700.0100.0100.0000.0000.0000.000
128A373ALA00.022-0.00715.533-0.032-0.0320.0000.0000.0000.000
129A374ASN0-0.084-0.03417.074-0.002-0.0020.0000.0000.0000.000
130A375LEU0-0.005-0.00518.696-0.019-0.0190.0000.0000.0000.000
131A376ASN00.0130.02222.0740.0170.0170.0000.0000.0000.000
132A377SER0-0.050-0.04124.700-0.001-0.0010.0000.0000.0000.000
133A378VAL00.005-0.00328.272-0.004-0.0040.0000.0000.0000.000
134A379ILE00.0140.01231.2770.0020.0020.0000.0000.0000.000
135A380CYS0-0.063-0.01835.017-0.003-0.0030.0000.0000.0000.000
136A381THR00.028-0.00137.4070.0020.0020.0000.0000.0000.000
137A382GLY0-0.023-0.00941.061-0.002-0.0020.0000.0000.0000.000
138A383GLY0-0.021-0.01344.1930.0000.0000.0000.0000.0000.000
139A384ASP-1-0.885-0.92646.3590.0020.0020.0000.0000.0000.000
140A385TYR0-0.007-0.00849.978-0.001-0.0010.0000.0000.0000.000
141A386SER0-0.017-0.00851.9260.0010.0010.0000.0000.0000.000
142A387PHE0-0.019-0.01553.532-0.001-0.0010.0000.0000.0000.000
143A388ALA00.019-0.01157.9560.0000.0000.0000.0000.0000.000
144A389LEU0-0.046-0.01060.6920.0000.0000.0000.0000.0000.000
145A390PRO0-0.033-0.00863.8250.0000.0000.0000.0000.0000.000
146A391VAL00.0270.01066.8320.0000.0000.0000.0000.0000.000
147A392GLY0-0.0030.00867.7230.0000.0000.0000.0000.0000.000
148A393GLN0-0.039-0.03164.4080.0000.0000.0000.0000.0000.000
149A394TRP00.0650.02959.0130.0000.0000.0000.0000.0000.000
150A395PRO0-0.0070.00758.9830.0000.0000.0000.0000.0000.000
151A396VAL0-0.0010.00253.985-0.001-0.0010.0000.0000.0000.000
152A397MET0-0.034-0.00150.2960.0010.0010.0000.0000.0000.000
153A398THR0-0.011-0.03050.2440.0000.0000.0000.0000.0000.000
154A399GLY00.0780.04247.2490.0010.0010.0000.0000.0000.000
155A400GLY0-0.011-0.00945.099-0.001-0.0010.0000.0000.0000.000
156A401ALA00.001-0.01540.379-0.001-0.0010.0000.0000.0000.000
157A402VAL0-0.0190.01036.8250.0010.0010.0000.0000.0000.000
158A403SER0-0.005-0.01333.492-0.002-0.0020.0000.0000.0000.000
159A404LEU0-0.023-0.01530.8100.0020.0020.0000.0000.0000.000
160A405HIS0-0.0040.00228.5980.0050.0050.0000.0000.0000.000
161A406SER00.0170.01122.958-0.002-0.0020.0000.0000.0000.000
162A407ALA0-0.001-0.00326.0580.0080.0080.0000.0000.0000.000
163A408GLY00.0090.00423.952-0.003-0.0030.0000.0000.0000.000
164A409VAL00.005-0.00720.705-0.009-0.0090.0000.0000.0000.000
165A410THR0-0.026-0.00122.6280.0120.0120.0000.0000.0000.000
166A411LEU00.0220.02219.871-0.006-0.0060.0000.0000.0000.000
167A412SER0-0.063-0.03723.7610.0020.0020.0000.0000.0000.000
168A413THR00.0230.01126.188-0.005-0.0050.0000.0000.0000.000
169A414GLN0-0.0140.02827.2560.0080.0080.0000.0000.0000.000
170A415PHE0-0.002-0.02330.718-0.005-0.0050.0000.0000.0000.000
171A416THR0-0.031-0.03132.2350.0020.0020.0000.0000.0000.000
172A417ASP-1-0.890-0.94935.026-0.032-0.0320.0000.0000.0000.000
173A418PHE0-0.062-0.02135.140-0.001-0.0010.0000.0000.0000.000
174A419VAL00.0110.01229.552-0.001-0.0010.0000.0000.0000.000
175A420SER00.0040.02531.0780.0050.0050.0000.0000.0000.000
176A421LEU0-0.011-0.00626.935-0.005-0.0050.0000.0000.0000.000
177A422ASN0-0.0110.00922.9630.0150.0150.0000.0000.0000.000
178A423SER0-0.008-0.02323.491-0.011-0.0110.0000.0000.0000.000
179A424LEU00.0100.02218.3680.0090.0090.0000.0000.0000.000
180A425ARG10.8280.88122.866-0.003-0.0030.0000.0000.0000.000
181A426PHE00.008-0.00320.6730.0130.0130.0000.0000.0000.000
182A427ARG10.9060.96425.808-0.052-0.0520.0000.0000.0000.000
183A428PHE0-0.0040.00126.7160.0070.0070.0000.0000.0000.000
184A429ARG10.9810.99029.636-0.053-0.0530.0000.0000.0000.000
185A430LEU0-0.024-0.03132.365-0.001-0.0010.0000.0000.0000.000
186A431THR0-0.0140.01535.1490.0030.0030.0000.0000.0000.000
187A432VAL0-0.073-0.04436.853-0.003-0.0030.0000.0000.0000.000
188A433GLU-1-0.822-0.89936.6750.0270.0270.0000.0000.0000.000
189A434GLU-1-0.868-0.87340.7210.0140.0140.0000.0000.0000.000
190A435PRO0-0.029-0.01542.2570.0000.0000.0000.0000.0000.000
191A436SER00.0190.00245.4190.0000.0000.0000.0000.0000.000
192A437PHE0-0.011-0.03246.967-0.001-0.0010.0000.0000.0000.000
193A438SER0-0.087-0.05049.4230.0010.0010.0000.0000.0000.000
194A439ILE00.0100.01452.977-0.001-0.0010.0000.0000.0000.000
195A440THR00.0340.04255.6940.0000.0000.0000.0000.0000.000
196A441ARG10.9290.94658.266-0.002-0.0020.0000.0000.0000.000
197A442THR0-0.006-0.01358.6230.0000.0000.0000.0000.0000.000
198A443ARG10.9480.97660.451-0.005-0.0050.0000.0000.0000.000
199A444VAL0-0.0100.00054.3560.0010.0010.0000.0000.0000.000
200A445SER00.012-0.02054.0280.0000.0000.0000.0000.0000.000
201A446ARG10.9520.98249.714-0.013-0.0130.0000.0000.0000.000
202A447LEU00.0140.03849.6740.0010.0010.0000.0000.0000.000
203A448TYR0-0.033-0.05844.400-0.001-0.0010.0000.0000.0000.000
204A449GLY00.0310.00442.6690.0000.0000.0000.0000.0000.000
205A450LEU0-0.0100.01439.533-0.001-0.0010.0000.0000.0000.000
206A451PRO00.007-0.00743.0400.0000.0000.0000.0000.0000.000
207A452ALA00.0270.02544.505-0.001-0.0010.0000.0000.0000.000
208A453ALA0-0.0130.00345.543-0.001-0.0010.0000.0000.0000.000
209A454ASN0-0.008-0.02045.791-0.002-0.0020.0000.0000.0000.000
210A455PRO00.0610.04440.7900.0000.0000.0000.0000.0000.000
211A456ASN00.0480.04439.3020.0010.0010.0000.0000.0000.000
212A457ASN0-0.015-0.01540.898-0.001-0.0010.0000.0000.0000.000
213A458GLY0-0.0010.00843.0240.0000.0000.0000.0000.0000.000
214A459LYS10.9180.97837.0280.0010.0010.0000.0000.0000.000
215A460GLU-1-0.896-0.94637.674-0.022-0.0220.0000.0000.0000.000
216A461TYR0-0.042-0.03532.213-0.003-0.0030.0000.0000.0000.000
217A462TYR0-0.050-0.04633.1010.0020.0020.0000.0000.0000.000
218A463GLU-1-0.844-0.93127.919-0.035-0.0350.0000.0000.0000.000
219A464VAL0-0.0210.00024.7880.0060.0060.0000.0000.0000.000
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