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: YVVL2

Calculation Name: 2J5U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J5U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y6Y4

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2197543.217558
FMO2-HF: Nuclear repulsion 2117696.394337
FMO2-HF: Total energy -79846.823221
FMO2-MP2: Total energy -80081.073324


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:74:THR)


Summations of interaction energy for fragment #1(A:74:THR)
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.
-14.826-12.00813.456-6.806-9.468-0.023
Interaction energy analysis for fragmet #1(A:74:THR)
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 : -0.026
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].
3A76ASN0-0.029-0.0343.223-2.5170.3320.008-1.261-1.5960.002
4A77GLN0-0.0210.0142.070-12.541-12.98311.879-5.095-6.342-0.026
5A78HIS00.0500.0122.247-0.723-0.3121.569-0.450-1.5300.001
6A79LEU00.0110.0165.4940.3070.3070.0000.0000.0000.000
7A80LYS10.8830.9327.2160.4970.4970.0000.0000.0000.000
8A81GLU-1-0.768-0.8678.710-0.718-0.7180.0000.0000.0000.000
9A82ARG10.8320.9136.7380.9740.9740.0000.0000.0000.000
10A83LEU00.001-0.00410.8240.0470.0470.0000.0000.0000.000
11A84GLU-1-0.931-0.96012.7130.0110.0110.0000.0000.0000.000
12A85GLU-1-0.945-0.98213.963-0.278-0.2780.0000.0000.0000.000
13A86LEU0-0.087-0.02714.260-0.002-0.0020.0000.0000.0000.000
14A87ALA00.0620.02516.1750.0190.0190.0000.0000.0000.000
15A88GLN0-0.033-0.00618.3660.0280.0280.0000.0000.0000.000
16A89LEU0-0.009-0.00618.1780.0120.0120.0000.0000.0000.000
17A90GLU-1-0.962-0.98219.687-0.148-0.1480.0000.0000.0000.000
18A91SER0-0.038-0.02522.2710.0140.0140.0000.0000.0000.000
19A92GLU-1-0.868-0.92523.881-0.115-0.1150.0000.0000.0000.000
20A93VAL0-0.035-0.03324.3580.0080.0080.0000.0000.0000.000
21A94ALA0-0.054-0.02326.5430.0080.0080.0000.0000.0000.000
22A95ASP-1-0.852-0.91128.555-0.055-0.0550.0000.0000.0000.000
23A96LEU00.0120.00928.2310.0040.0040.0000.0000.0000.000
24A97LYS10.8470.91527.3400.1000.1000.0000.0000.0000.000
25A98LYS10.8360.91431.9270.0470.0470.0000.0000.0000.000
26A99GLU-1-0.903-0.94734.366-0.055-0.0550.0000.0000.0000.000
27A100ASN0-0.052-0.04634.6700.0020.0020.0000.0000.0000.000
28A101LYS10.8080.89436.2950.0460.0460.0000.0000.0000.000
29A102ASP-1-0.769-0.87838.029-0.041-0.0410.0000.0000.0000.000
30A103LEU0-0.0120.00138.4570.0030.0030.0000.0000.0000.000
31A104LYS10.8110.90536.8520.0630.0630.0000.0000.0000.000
32A105GLU-1-0.805-0.88742.177-0.038-0.0380.0000.0000.0000.000
33A106SER0-0.103-0.04244.2130.0030.0030.0000.0000.0000.000
34A107LEU0-0.087-0.03544.0970.0020.0020.0000.0000.0000.000
35A108ASP-1-0.898-0.94946.536-0.034-0.0340.0000.0000.0000.000
36A109ILE0-0.100-0.04842.296-0.001-0.0010.0000.0000.0000.000
37A110THR00.0430.01943.439-0.001-0.0010.0000.0000.0000.000
38A111ASP-1-0.945-0.97140.973-0.048-0.0480.0000.0000.0000.000
39A112SER0-0.031-0.03738.181-0.002-0.0020.0000.0000.0000.000
40A113ILE0-0.011-0.02736.816-0.002-0.0020.0000.0000.0000.000
41A114ARG10.9150.94629.4490.0900.0900.0000.0000.0000.000
42A115ASP-1-0.801-0.86133.830-0.068-0.0680.0000.0000.0000.000
43A116TYR00.027-0.00928.464-0.002-0.0020.0000.0000.0000.000
44A117ASP-1-0.830-0.88134.457-0.057-0.0570.0000.0000.0000.000
45A118PRO0-0.038-0.02030.333-0.001-0.0010.0000.0000.0000.000
46A119LEU00.0070.00832.0420.0050.0050.0000.0000.0000.000
47A120ASN0-0.012-0.00627.475-0.010-0.0100.0000.0000.0000.000
48A121ALA0-0.031-0.02028.9090.0080.0080.0000.0000.0000.000
49A122SER00.0360.01127.368-0.007-0.0070.0000.0000.0000.000
50A123VAL0-0.035-0.01327.2100.0080.0080.0000.0000.0000.000
51A124ILE0-0.029-0.02829.4490.0000.0000.0000.0000.0000.000
52A125SER0-0.039-0.01831.9700.0040.0040.0000.0000.0000.000
53A126ARG10.8380.90625.1190.1140.1140.0000.0000.0000.000
54A127ASN00.0390.04231.8240.0010.0010.0000.0000.0000.000
55A128PRO00.0520.01231.061-0.003-0.0030.0000.0000.0000.000
56A129THR0-0.062-0.04432.2920.0000.0000.0000.0000.0000.000
57A130ASN00.0100.00034.4690.0010.0010.0000.0000.0000.000
58A131TRP00.0060.02825.3840.0030.0030.0000.0000.0000.000
59A132ASN00.0250.00627.604-0.011-0.0110.0000.0000.0000.000
60A133ASP-1-0.784-0.86630.068-0.076-0.0760.0000.0000.0000.000
61A134GLN0-0.033-0.02632.7600.0010.0010.0000.0000.0000.000
62A135VAL00.0130.01528.546-0.002-0.0020.0000.0000.0000.000
63A136GLU-1-0.901-0.93632.033-0.053-0.0530.0000.0000.0000.000
64A137ILE0-0.0090.00030.676-0.004-0.0040.0000.0000.0000.000
65A138ASP-1-0.786-0.89532.615-0.065-0.0650.0000.0000.0000.000
66A139LYS10.8260.91933.3590.0680.0680.0000.0000.0000.000
67A140GLY00.008-0.01436.302-0.002-0.0020.0000.0000.0000.000
68A141SER00.0100.01239.5080.0010.0010.0000.0000.0000.000
69A142SER0-0.105-0.04142.1920.0010.0010.0000.0000.0000.000
70A143ASP-1-0.856-0.93438.108-0.048-0.0480.0000.0000.0000.000
71A144GLY0-0.009-0.00739.124-0.002-0.0020.0000.0000.0000.000
72A145VAL0-0.031-0.00936.421-0.001-0.0010.0000.0000.0000.000
73A146LYS10.9460.94439.0210.0490.0490.0000.0000.0000.000
74A147PRO00.004-0.01139.240-0.003-0.0030.0000.0000.0000.000
75A148ASP-1-0.858-0.95738.459-0.060-0.0600.0000.0000.0000.000
76A149MET0-0.0510.02235.696-0.002-0.0020.0000.0000.0000.000
77A150ALA00.0210.01331.641-0.002-0.0020.0000.0000.0000.000
78A151VAL00.0110.00128.8230.0020.0020.0000.0000.0000.000
79A152THR0-0.036-0.03025.805-0.002-0.0020.0000.0000.0000.000
80A153THR00.0610.04021.578-0.003-0.0030.0000.0000.0000.000
81A154PRO00.0420.00218.8540.0020.0020.0000.0000.0000.000
82A155SER0-0.0080.00217.2190.0050.0050.0000.0000.0000.000
83A156GLY00.005-0.00619.309-0.003-0.0030.0000.0000.0000.000
84A157LEU0-0.032-0.01522.8140.0060.0060.0000.0000.0000.000
85A158ILE00.016-0.00624.287-0.005-0.0050.0000.0000.0000.000
86A159GLY00.0360.00926.9420.0040.0040.0000.0000.0000.000
87A160LYS10.8390.93830.7290.0720.0720.0000.0000.0000.000
88A161VAL00.0110.01534.0780.0010.0010.0000.0000.0000.000
89A162THR0-0.0020.00336.4140.0020.0020.0000.0000.0000.000
90A163THR00.0230.00839.2170.0030.0030.0000.0000.0000.000
91A164THR0-0.056-0.02739.787-0.002-0.0020.0000.0000.0000.000
92A165GLY00.0690.04741.4280.0030.0030.0000.0000.0000.000
93A166ALA0-0.030-0.04042.780-0.001-0.0010.0000.0000.0000.000
94A167LYS10.9260.92840.4140.0400.0400.0000.0000.0000.000
95A168SER0-0.0080.04037.5520.0000.0000.0000.0000.0000.000
96A169ALA00.028-0.00336.7540.0030.0030.0000.0000.0000.000
97A170THR00.0240.03135.984-0.003-0.0030.0000.0000.0000.000
98A171VAL0-0.005-0.00531.0140.0010.0010.0000.0000.0000.000
99A172GLU-1-0.842-0.89833.315-0.072-0.0720.0000.0000.0000.000
100A173LEU00.000-0.00428.000-0.004-0.0040.0000.0000.0000.000
101A174LEU0-0.015-0.02726.9130.0050.0050.0000.0000.0000.000
102A175THR0-0.094-0.06426.2350.0010.0010.0000.0000.0000.000
103A176SER0-0.070-0.04029.4130.0040.0040.0000.0000.0000.000
104A177SER0-0.048-0.03833.0020.0010.0010.0000.0000.0000.000
105A178ASP-1-0.840-0.90435.545-0.053-0.0530.0000.0000.0000.000
106A179VAL00.0410.00637.625-0.002-0.0020.0000.0000.0000.000
107A180LYS10.8410.91739.3550.0530.0530.0000.0000.0000.000
108A181ASN0-0.0210.00533.5820.0020.0020.0000.0000.0000.000
109A182ARG10.8560.90935.8040.0580.0580.0000.0000.0000.000
110A183VAL00.0180.01031.8590.0000.0000.0000.0000.0000.000
111A184SER0-0.0190.00734.939-0.001-0.0010.0000.0000.0000.000
112A185ALA00.000-0.00331.535-0.004-0.0040.0000.0000.0000.000
113A186LYS10.8850.93332.0530.0960.0960.0000.0000.0000.000
114A187VAL00.0190.02429.299-0.009-0.0090.0000.0000.0000.000
115A188GLN0-0.023-0.02126.5190.0000.0000.0000.0000.0000.000
116A189GLY00.0660.01929.187-0.006-0.0060.0000.0000.0000.000
117A190LYS10.9110.96131.0660.0830.0830.0000.0000.0000.000
118A191GLU-1-0.902-0.94133.330-0.061-0.0610.0000.0000.0000.000
119A192ASN0-0.031-0.01233.202-0.008-0.0080.0000.0000.0000.000
120A193ALA00.0710.04734.2920.0050.0050.0000.0000.0000.000
121A194PHE0-0.039-0.04134.799-0.005-0.0050.0000.0000.0000.000
122A195GLY00.0730.04136.1070.0020.0020.0000.0000.0000.000
123A196ILE0-0.058-0.02436.332-0.001-0.0010.0000.0000.0000.000
124A197ILE00.0000.00829.815-0.001-0.0010.0000.0000.0000.000
125A198ASN0-0.063-0.07233.6330.0050.0050.0000.0000.0000.000
126A199GLY00.0930.06934.0150.0030.0030.0000.0000.0000.000
127A200TYR00.0000.00324.889-0.006-0.0060.0000.0000.0000.000
128A201ASP-1-0.800-0.85229.462-0.084-0.0840.0000.0000.0000.000
129A202SER00.007-0.01728.016-0.009-0.0090.0000.0000.0000.000
130A203ASP-1-0.906-0.94526.744-0.087-0.0870.0000.0000.0000.000
131A204THR0-0.114-0.10025.529-0.010-0.0100.0000.0000.0000.000
132A205LYS10.8650.94521.9500.1250.1250.0000.0000.0000.000
133A206LEU0-0.048-0.02423.684-0.013-0.0130.0000.0000.0000.000
134A207LEU00.011-0.00226.6150.0080.0080.0000.0000.0000.000
135A208GLU-1-0.835-0.89928.954-0.078-0.0780.0000.0000.0000.000
136A209LEU0-0.046-0.02330.9920.0020.0020.0000.0000.0000.000
137A210LYS10.8720.91233.0440.0730.0730.0000.0000.0000.000
138A211GLN0-0.025-0.02836.764-0.001-0.0010.0000.0000.0000.000
139A212LEU00.0050.03332.9950.0000.0000.0000.0000.0000.000
140A213PRO00.036-0.00137.6410.0020.0020.0000.0000.0000.000
141A214TYR00.0370.00439.020-0.003-0.0030.0000.0000.0000.000
142A215ASP-1-0.926-0.94240.759-0.056-0.0560.0000.0000.0000.000
143A216MET0-0.0030.02235.983-0.002-0.0020.0000.0000.0000.000
144A217LYS10.9490.97534.3300.0690.0690.0000.0000.0000.000
145A218PHE00.0270.00730.733-0.004-0.0040.0000.0000.0000.000
146A219LYS10.9240.95626.1480.1140.1140.0000.0000.0000.000
147A220LYS10.8480.91020.2890.1690.1690.0000.0000.0000.000
148A221GLY00.013-0.00722.047-0.006-0.0060.0000.0000.0000.000
149A222GLN0-0.033-0.01422.899-0.004-0.0040.0000.0000.0000.000
150A223LYS10.9890.99619.8970.2060.2060.0000.0000.0000.000
151A224VAL00.0200.01525.0920.0130.0130.0000.0000.0000.000
152A225VAL0-0.020-0.01226.608-0.009-0.0090.0000.0000.0000.000
153A226THR00.0590.03328.8610.0050.0050.0000.0000.0000.000
154A227SER0-0.002-0.00931.8370.0010.0010.0000.0000.0000.000
155A228GLY00.0320.02435.1040.0030.0030.0000.0000.0000.000
156A229LEU0-0.005-0.02437.0510.0040.0040.0000.0000.0000.000
157A230GLY00.0330.03938.8730.0030.0030.0000.0000.0000.000
158A231GLY0-0.043-0.02740.4670.0020.0020.0000.0000.0000.000
159A232LYS10.8980.95838.1360.0600.0600.0000.0000.0000.000
160A233PHE0-0.015-0.00133.211-0.003-0.0030.0000.0000.0000.000
161A234PRO00.0680.05532.5010.0030.0030.0000.0000.0000.000
162A235ALA0-0.019-0.01633.415-0.005-0.0050.0000.0000.0000.000
163A236GLY0-0.091-0.05930.0410.0000.0000.0000.0000.0000.000
164A237ILE00.0180.02026.883-0.009-0.0090.0000.0000.0000.000
165A238PHE0-0.011-0.00819.9630.0050.0050.0000.0000.0000.000
166A239ILE00.0230.00725.092-0.001-0.0010.0000.0000.0000.000
167A240GLY00.0670.02322.508-0.008-0.0080.0000.0000.0000.000
168A241THR0-0.077-0.01820.781-0.002-0.0020.0000.0000.0000.000
169A242ILE00.0070.01923.2140.0030.0030.0000.0000.0000.000
170A243GLU-1-0.838-0.90921.566-0.185-0.1850.0000.0000.0000.000
171A244LYS10.8430.91724.7840.0900.0900.0000.0000.0000.000
172A245VAL0-0.015-0.01728.086-0.001-0.0010.0000.0000.0000.000
173A246GLU-1-0.852-0.90631.607-0.074-0.0740.0000.0000.0000.000
174A247THR00.0200.00735.045-0.001-0.0010.0000.0000.0000.000
175A248ASP-1-0.816-0.89938.753-0.054-0.0540.0000.0000.0000.000
176A249LYS10.9710.96040.8360.0480.0480.0000.0000.0000.000
177A250MET0-0.048-0.01943.9640.0020.0020.0000.0000.0000.000
178A251GLY00.0290.02943.9000.0020.0020.0000.0000.0000.000
179A252LEU0-0.051-0.02644.7530.0010.0010.0000.0000.0000.000
180A253SER0-0.095-0.03640.641-0.001-0.0010.0000.0000.0000.000
181A254GLN0-0.056-0.05636.115-0.002-0.0020.0000.0000.0000.000
182A255THR0-0.017-0.01134.0210.0010.0010.0000.0000.0000.000
183A256ALA0-0.031-0.00930.002-0.001-0.0010.0000.0000.0000.000
184A257PHE00.0350.01528.4130.0000.0000.0000.0000.0000.000
185A258ILE00.001-0.02825.174-0.007-0.0070.0000.0000.0000.000
186A259LYS11.0071.01316.0400.2790.2790.0000.0000.0000.000
187A260PRO0-0.0050.00322.079-0.009-0.0090.0000.0000.0000.000
188A261GLY0-0.015-0.01619.382-0.016-0.0160.0000.0000.0000.000
189A262ALA0-0.0280.00618.530-0.027-0.0270.0000.0000.0000.000
190A263ASP-1-0.850-0.93517.824-0.211-0.2110.0000.0000.0000.000
191A264MET0-0.047-0.01919.8220.0070.0070.0000.0000.0000.000
192A265TYR0-0.0230.00320.8150.0220.0220.0000.0000.0000.000
193A266ASP-1-0.923-0.96419.950-0.157-0.1570.0000.0000.0000.000
194A267LEU0-0.041-0.00321.251-0.012-0.0120.0000.0000.0000.000
195A268ASN00.0290.00722.5330.0190.0190.0000.0000.0000.000
196A269HIS00.0220.01522.3010.0140.0140.0000.0000.0000.000
197A270VAL0-0.010-0.01423.924-0.013-0.0130.0000.0000.0000.000
198A271THR0-0.013-0.01226.4000.0050.0050.0000.0000.0000.000
199A272VAL0-0.0080.00328.514-0.002-0.0020.0000.0000.0000.000
200A273LEU0-0.042-0.02429.2630.0030.0030.0000.0000.0000.000
201A274LYS10.8900.93833.2260.0540.0540.0000.0000.0000.000
202A275ARG10.7620.85836.4840.0580.0580.0000.0000.0000.000
203A276SER0-0.010-0.00737.8870.0020.0020.0000.0000.0000.000
204A277ALA0-0.0080.01039.6370.0030.0030.0000.0000.0000.000
205A278GLU-1-0.799-0.89341.609-0.043-0.0430.0000.0000.0000.000
206A279ALA0-0.050-0.01443.658-0.003-0.0030.0000.0000.0000.000
207A280GLY0-0.019-0.00644.0420.0020.0020.0000.0000.0000.000
208A281THR00.041-0.00345.635-0.001-0.0010.0000.0000.0000.000
209A282THR0-0.073-0.03246.4320.0010.0010.0000.0000.0000.000
210A283ASP-1-0.832-0.88042.975-0.056-0.0560.0000.0000.0000.000