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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: 2J7RR

Calculation Name: 3T5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5X

Chain ID: A

ChEMBL ID:

UniProt ID: Q5JVF3

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2255468.543395
FMO2-HF: Nuclear repulsion 2175355.023594
FMO2-HF: Total energy -80113.519802
FMO2-MP2: Total energy -80344.898763


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:205:SER)


Summations of interaction energy for fragment #1(A:205:SER)
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.
-21.198-14.9815.868-4.91-7.1720.023
Interaction energy analysis for fragmet #1(A:205:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.085 / q_NPA : 0.033
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].
3A207ALA00.0200.0052.240-9.473-6.1112.724-2.806-3.2790.028
4A208GLN00.0430.0172.136-8.124-5.7853.132-2.106-3.364-0.005
5A209ARG10.9840.9953.556-1.427-0.9640.0130.004-0.4790.000
6A210VAL00.0070.0115.6520.0790.0790.0000.0000.0000.000
7A211THR0-0.006-0.0106.526-0.164-0.1640.0000.0000.0000.000
8A212TYR00.008-0.0017.5460.0350.0350.0000.0000.0000.000
9A213LYS10.9350.9749.463-0.072-0.0720.0000.0000.0000.000
10A214TYR00.0260.02411.1270.0320.0320.0000.0000.0000.000
11A215TYR00.013-0.00511.4830.0340.0340.0000.0000.0000.000
12A216VAL0-0.033-0.00712.9440.0080.0080.0000.0000.0000.000
13A217GLY00.0440.02115.2680.0270.0270.0000.0000.0000.000
14A218ARG10.9170.96116.4760.1110.1110.0000.0000.0000.000
15A219LYS10.9450.96916.3870.2480.2480.0000.0000.0000.000
16A220ALA00.0810.04719.5600.0050.0050.0000.0000.0000.000
17A221MET0-0.042-0.00821.2210.0140.0140.0000.0000.0000.000
18A222PHE0-0.112-0.06922.4870.0040.0040.0000.0000.0000.000
19A223ASP-1-0.918-0.93524.280-0.056-0.0560.0000.0000.0000.000
20A224SER0-0.070-0.03525.9580.0080.0080.0000.0000.0000.000
21A225ASP-1-0.837-0.90823.5920.0290.0290.0000.0000.0000.000
22A226PHE00.014-0.03123.5500.0060.0060.0000.0000.0000.000
23A227LYS10.9570.97923.826-0.082-0.0820.0000.0000.0000.000
24A228GLN00.0720.05018.4850.0300.0300.0000.0000.0000.000
25A229ALA0-0.009-0.01319.2390.0090.0090.0000.0000.0000.000
26A230GLU-1-0.846-0.93619.2510.1630.1630.0000.0000.0000.000
27A231GLU-1-0.922-0.93317.8680.1880.1880.0000.0000.0000.000
28A232TYR0-0.026-0.01714.3440.0400.0400.0000.0000.0000.000
29A233LEU00.008-0.01014.5750.0530.0530.0000.0000.0000.000
30A234SER0-0.009-0.01615.9740.0510.0510.0000.0000.0000.000
31A235PHE00.0030.0119.2070.0890.0890.0000.0000.0000.000
32A236ALA0-0.013-0.02211.3030.1410.1410.0000.0000.0000.000
33A237PHE0-0.024-0.01512.1030.1360.1360.0000.0000.0000.000
34A238GLU-1-0.971-0.99314.3250.5100.5100.0000.0000.0000.000
35A239HIS10.8540.9349.548-0.912-0.9120.0000.0000.0000.000
36A240CYS0-0.0430.0029.2060.3770.3770.0000.0000.0000.000
37A241HIS00.0320.0124.967-0.910-0.857-0.001-0.002-0.0500.000
38A242ARG10.9680.96410.391-0.767-0.7670.0000.0000.0000.000
39A243SER00.0230.02911.861-0.052-0.0520.0000.0000.0000.000
40A244SER00.0260.02311.451-0.054-0.0540.0000.0000.0000.000
41A245GLN00.0670.01813.5170.0160.0160.0000.0000.0000.000
42A246LYS10.9690.97015.765-0.048-0.0480.0000.0000.0000.000
43A247ASN00.0600.02710.115-0.146-0.1460.0000.0000.0000.000
44A248LYS10.9500.97613.926-0.538-0.5380.0000.0000.0000.000
45A249ARG10.8890.95515.541-0.104-0.1040.0000.0000.0000.000
46A250MET0-0.009-0.00915.688-0.018-0.0180.0000.0000.0000.000
47A251ILE00.0190.01112.230-0.021-0.0210.0000.0000.0000.000
48A252LEU0-0.0070.00116.770-0.018-0.0180.0000.0000.0000.000
49A253ILE0-0.013-0.00720.056-0.013-0.0130.0000.0000.0000.000
50A254TYR0-0.034-0.03918.444-0.022-0.0220.0000.0000.0000.000
51A255LEU0-0.005-0.00818.859-0.004-0.0040.0000.0000.0000.000
52A256LEU0-0.016-0.00621.2060.0010.0010.0000.0000.0000.000
53A257PRO00.0230.01323.9400.0000.0000.0000.0000.0000.000
54A258VAL00.0260.01622.385-0.004-0.0040.0000.0000.0000.000
55A259LYS10.8380.91822.626-0.179-0.1790.0000.0000.0000.000
56A260MET0-0.010-0.00426.158-0.004-0.0040.0000.0000.0000.000
57A261LEU0-0.027-0.00427.834-0.004-0.0040.0000.0000.0000.000
58A262LEU0-0.066-0.01825.700-0.004-0.0040.0000.0000.0000.000
59A263GLY0-0.032-0.02729.8590.0040.0040.0000.0000.0000.000
60A264HIS0-0.054-0.02027.3210.0050.0050.0000.0000.0000.000
61A265MET00.0150.01429.082-0.001-0.0010.0000.0000.0000.000
62A266PRO0-0.0180.00027.1100.0110.0110.0000.0000.0000.000
63A267THR00.0630.03428.679-0.007-0.0070.0000.0000.0000.000
64A268VAL00.0570.00829.4240.0020.0020.0000.0000.0000.000
65A269GLU-1-0.861-0.94629.2340.1240.1240.0000.0000.0000.000
66A270LEU0-0.025-0.00122.6530.0100.0100.0000.0000.0000.000
67A271LEU00.0220.00125.3880.0060.0060.0000.0000.0000.000
68A272LYS10.9650.98327.187-0.102-0.1020.0000.0000.0000.000
69A273LYS10.9100.97621.285-0.273-0.2730.0000.0000.0000.000
70A274TYR0-0.026-0.01018.6080.0280.0280.0000.0000.0000.000
71A275HIS00.0010.00023.408-0.020-0.0200.0000.0000.0000.000
72A276LEU0-0.025-0.02222.562-0.013-0.0130.0000.0000.0000.000
73A277MET00.0450.01526.9980.0030.0030.0000.0000.0000.000
74A278GLN00.0290.02528.7150.0060.0060.0000.0000.0000.000
75A279PHE00.0460.01325.926-0.004-0.0040.0000.0000.0000.000
76A280ALA0-0.024-0.00430.8070.0020.0020.0000.0000.0000.000
77A281GLU-1-0.878-0.95233.3510.0360.0360.0000.0000.0000.000
78A282VAL00.0360.03132.440-0.001-0.0010.0000.0000.0000.000
79A283THR00.016-0.01031.7130.0020.0020.0000.0000.0000.000
80A284ARG10.9020.96033.973-0.044-0.0440.0000.0000.0000.000
81A285ALA00.0440.02337.5130.0000.0000.0000.0000.0000.000
82A286VAL00.0490.02134.123-0.001-0.0010.0000.0000.0000.000
83A287SER0-0.053-0.02235.6840.0020.0020.0000.0000.0000.000
84A288GLU-1-0.989-0.99037.9020.0450.0450.0000.0000.0000.000
85A289GLY0-0.016-0.02040.548-0.002-0.0020.0000.0000.0000.000
86A290ASN0-0.0030.00641.585-0.006-0.0060.0000.0000.0000.000
87A291LEU00.0610.00441.1670.0010.0010.0000.0000.0000.000
88A292LEU00.0620.04342.204-0.001-0.0010.0000.0000.0000.000
89A293LEU0-0.013-0.01240.246-0.001-0.0010.0000.0000.0000.000
90A294LEU0-0.034-0.02435.5510.0010.0010.0000.0000.0000.000
91A295HIS0-0.0050.00538.269-0.003-0.0030.0000.0000.0000.000
92A296GLU-1-0.861-0.93239.9120.0090.0090.0000.0000.0000.000
93A297ALA0-0.073-0.04136.503-0.001-0.0010.0000.0000.0000.000
94A298LEU0-0.051-0.04533.5300.0010.0010.0000.0000.0000.000
95A299ALA00.0650.04235.685-0.004-0.0040.0000.0000.0000.000
96A300LYS10.9010.96237.379-0.023-0.0230.0000.0000.0000.000
97A301HIS0-0.040-0.02632.482-0.002-0.0020.0000.0000.0000.000
98A302GLU-1-0.866-0.92132.600-0.017-0.0170.0000.0000.0000.000
99A303ALA00.0420.01232.392-0.004-0.0040.0000.0000.0000.000
100A304PHE0-0.060-0.03125.980-0.006-0.0060.0000.0000.0000.000
101A305PHE00.0510.01627.858-0.001-0.0010.0000.0000.0000.000
102A306ILE00.0420.02127.783-0.004-0.0040.0000.0000.0000.000
103A307ARG10.9090.95626.6030.0170.0170.0000.0000.0000.000
104A308CYS0-0.095-0.04123.741-0.004-0.0040.0000.0000.0000.000
105A309GLY00.0030.02723.113-0.003-0.0030.0000.0000.0000.000
106A310ILE0-0.022-0.02423.841-0.001-0.0010.0000.0000.0000.000
107A311PHE00.0500.02726.3910.0060.0060.0000.0000.0000.000
108A312LEU00.1020.03529.8290.0050.0050.0000.0000.0000.000
109A313ILE0-0.035-0.01625.6680.0040.0040.0000.0000.0000.000
110A314LEU0-0.018-0.01528.7290.0080.0080.0000.0000.0000.000
111A315GLU-1-0.807-0.90231.0200.0030.0030.0000.0000.0000.000
112A316LYS10.8960.95230.1790.0080.0080.0000.0000.0000.000
113A317LEU0-0.007-0.00830.8710.0050.0050.0000.0000.0000.000
114A318LYS10.9541.00134.3240.0020.0020.0000.0000.0000.000
115A319ILE00.0370.03835.3160.0010.0010.0000.0000.0000.000
116A320ILE00.0080.00133.3090.0010.0010.0000.0000.0000.000
117A321THR0-0.004-0.01137.3480.0040.0040.0000.0000.0000.000
118A322TYR00.0620.02839.3850.0010.0010.0000.0000.0000.000
119A323ARG10.8600.93539.206-0.050-0.0500.0000.0000.0000.000
120A324ASN0-0.074-0.06637.3510.0020.0020.0000.0000.0000.000
121A325LEU00.0090.02141.6870.0010.0010.0000.0000.0000.000
122A326PHE00.0390.00544.7970.0000.0000.0000.0000.0000.000
123A327LYS10.9490.98641.493-0.055-0.0550.0000.0000.0000.000
124A328LYS10.9240.95943.722-0.046-0.0460.0000.0000.0000.000
125A329VAL00.0430.03447.2870.0000.0000.0000.0000.0000.000
126A330TYR0-0.008-0.00747.9420.0010.0010.0000.0000.0000.000
127A331LEU0-0.082-0.05045.7000.0010.0010.0000.0000.0000.000
128A332LEU0-0.030-0.01750.1670.0010.0010.0000.0000.0000.000
129A333LEU00.0030.01152.820-0.001-0.0010.0000.0000.0000.000
130A334LYS10.8750.95652.622-0.040-0.0400.0000.0000.0000.000
131A335THR00.0650.03354.515-0.001-0.0010.0000.0000.0000.000
132A336HIS0-0.012-0.02351.8530.0020.0020.0000.0000.0000.000
133A337GLN0-0.022-0.00554.391-0.002-0.0020.0000.0000.0000.000
134A338LEU00.0050.01151.5130.0000.0000.0000.0000.0000.000
135A339SER00.0070.01155.587-0.001-0.0010.0000.0000.0000.000
136A340LEU00.0750.01653.3700.0010.0010.0000.0000.0000.000
137A341ASP-1-0.875-0.94654.8160.0130.0130.0000.0000.0000.000
138A342ALA0-0.0130.00655.0420.0000.0000.0000.0000.0000.000
139A343PHE0-0.040-0.03049.5340.0010.0010.0000.0000.0000.000
140A344LEU00.0210.02751.5610.0000.0000.0000.0000.0000.000
141A345VAL00.0030.00853.5900.0000.0000.0000.0000.0000.000
142A346ALA0-0.034-0.02249.6800.0000.0000.0000.0000.0000.000
143A347LEU00.007-0.01047.2150.0010.0010.0000.0000.0000.000
144A348LYS11.0081.01450.146-0.010-0.0100.0000.0000.0000.000
145A349PHE0-0.044-0.00849.8660.0000.0000.0000.0000.0000.000
146A350MET0-0.112-0.04046.3470.0020.0020.0000.0000.0000.000
147A351GLN0-0.030-0.02147.837-0.002-0.0020.0000.0000.0000.000
148A352VAL0-0.015-0.00446.737-0.001-0.0010.0000.0000.0000.000
149A353GLU-1-0.945-0.97749.1840.0000.0000.0000.0000.0000.000
150A354ASP-1-0.924-0.96151.373-0.003-0.0030.0000.0000.0000.000
151A355VAL0-0.068-0.00851.0510.0010.0010.0000.0000.0000.000
152A356ASP-1-0.818-0.93652.9330.0030.0030.0000.0000.0000.000
153A357ILE0-0.048-0.05353.9280.0010.0010.0000.0000.0000.000
154A358ASP-1-0.855-0.92754.3140.0040.0040.0000.0000.0000.000
155A359GLU-1-0.886-0.93048.6110.0030.0030.0000.0000.0000.000
156A360VAL0-0.044-0.02849.5620.0010.0010.0000.0000.0000.000
157A361GLN0-0.021-0.01949.8390.0010.0010.0000.0000.0000.000
158A362CYS00.0250.02447.5600.0010.0010.0000.0000.0000.000
159A363ILE00.0150.02444.4810.0010.0010.0000.0000.0000.000
160A364LEU0-0.029-0.03345.1620.0020.0020.0000.0000.0000.000
161A365ALA00.0030.00946.2950.0020.0020.0000.0000.0000.000
162A366ASN0-0.031-0.03142.126-0.001-0.0010.0000.0000.0000.000
163A367LEU0-0.028-0.01640.8650.0020.0020.0000.0000.0000.000
164A368ILE0-0.063-0.03242.0320.0030.0030.0000.0000.0000.000
165A369TYR0-0.039-0.00740.0390.0020.0020.0000.0000.0000.000
166A370MET0-0.040-0.02037.7230.0000.0000.0000.0000.0000.000
167A371GLY00.0410.03537.8640.0030.0030.0000.0000.0000.000
168A372HIS0-0.044-0.03435.7440.0030.0030.0000.0000.0000.000
169A373VAL0-0.023-0.01640.2660.0030.0030.0000.0000.0000.000
170A374LYS10.9000.95942.786-0.044-0.0440.0000.0000.0000.000
171A375GLY00.008-0.02145.7060.0010.0010.0000.0000.0000.000
172A376TYR00.0120.01948.779-0.001-0.0010.0000.0000.0000.000
173A377ILE00.0700.03451.1590.0010.0010.0000.0000.0000.000
174A378SER0-0.045-0.01253.907-0.001-0.0010.0000.0000.0000.000
175A379HIS00.1060.02055.2370.0010.0010.0000.0000.0000.000
176A380GLN0-0.0200.01159.4080.0000.0000.0000.0000.0000.000
177A381HIS00.0070.00161.2630.0000.0000.0000.0000.0000.000
178A382GLN00.0320.02758.7800.0010.0010.0000.0000.0000.000
179A383LYS10.8970.95557.196-0.016-0.0160.0000.0000.0000.000
180A384LEU00.0150.01649.197-0.001-0.0010.0000.0000.0000.000
181A385VAL0-0.039-0.01553.6650.0020.0020.0000.0000.0000.000
182A386VAL0-0.0010.00149.1840.0000.0000.0000.0000.0000.000
183A387SER0-0.034-0.03347.7670.0000.0000.0000.0000.0000.000
184A388LYS10.9580.96449.969-0.028-0.0280.0000.0000.0000.000
185A389GLN00.0300.02246.8620.0030.0030.0000.0000.0000.000
186A390ASN0-0.029-0.02443.563-0.001-0.0010.0000.0000.0000.000
187A391PRO00.0510.02344.3230.0010.0010.0000.0000.0000.000
188A392PHE00.0520.03742.179-0.002-0.0020.0000.0000.0000.000
189A393PRO00.0080.01838.3710.0050.0050.0000.0000.0000.000
190A394PRO00.0140.00435.241-0.001-0.0010.0000.0000.0000.000
191A395LEU00.0860.04833.567-0.001-0.0010.0000.0000.0000.000
192A396SER0-0.036-0.00529.960-0.005-0.0050.0000.0000.0000.000
193A397THR0-0.046-0.05531.0150.0020.0020.0000.0000.0000.000
194A398VAL0-0.0020.01933.694-0.002-0.0020.0000.0000.0000.000
195A399CYS0-0.0030.01629.5110.0010.0010.0000.0000.0000.000