FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LZJV9

Calculation Name: 3F84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F84

Chain ID: A

ChEMBL ID:

UniProt ID: E3PPC4

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 302
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3254883.764113
FMO2-HF: Nuclear repulsion 3145603.356559
FMO2-HF: Total energy -109280.407554
FMO2-MP2: Total energy -109599.615278


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-8.906-4.7896.643-3.354-7.404-0.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.028
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].
3A3ASP-1-0.846-0.9143.880-2.491-0.319-0.021-1.094-1.057-0.002
4A4LEU0-0.059-0.0266.3960.2820.2820.0000.0000.0000.000
5A5LEU0-0.016-0.0019.715-0.006-0.0060.0000.0000.0000.000
6A6GLN0-0.012-0.04012.3200.0400.0400.0000.0000.0000.000
7A7ALA0-0.031-0.03715.1960.0060.0060.0000.0000.0000.000
8A8ASP-1-0.966-0.95117.260-0.025-0.0250.0000.0000.0000.000
9A9GLY0-0.0050.00514.0810.0250.0250.0000.0000.0000.000
10A10ASN00.004-0.00914.109-0.016-0.0160.0000.0000.0000.000
11A11ALA00.0320.01513.501-0.016-0.0160.0000.0000.0000.000
12A12LEU00.0130.00613.5750.0310.0310.0000.0000.0000.000
13A13PRO0-0.039-0.00915.909-0.017-0.0170.0000.0000.0000.000
14A14SER00.0400.02618.157-0.004-0.0040.0000.0000.0000.000
15A15ALA0-0.0010.00519.1800.0090.0090.0000.0000.0000.000
16A16VAL0-0.0120.00622.4610.0010.0010.0000.0000.0000.000
17A17LYS10.9160.96224.8350.0480.0480.0000.0000.0000.000
18A18LEU00.0040.01226.8160.0010.0010.0000.0000.0000.000
19A19ALA00.0160.00930.3280.0010.0010.0000.0000.0000.000
20A20TYR00.0680.03633.5940.0020.0020.0000.0000.0000.000
21A21SER0-0.007-0.00736.6200.0010.0010.0000.0000.0000.000
22A22PRO00.020-0.00139.8730.0010.0010.0000.0000.0000.000
23A23ALA0-0.022-0.00242.9840.0010.0010.0000.0000.0000.000
24A24SER00.0040.00239.6450.0010.0010.0000.0000.0000.000
25A25LYS10.9520.98641.0410.0110.0110.0000.0000.0000.000
26A26THR0-0.023-0.01136.3070.0000.0000.0000.0000.0000.000
27A27PHE0-0.024-0.02832.332-0.001-0.0010.0000.0000.0000.000
28A28GLU-1-0.942-0.96531.593-0.024-0.0240.0000.0000.0000.000
29A29SER0-0.086-0.05627.900-0.002-0.0020.0000.0000.0000.000
30A30TYR00.0700.02820.667-0.004-0.0040.0000.0000.0000.000
31A31ARG10.9020.94524.1100.0170.0170.0000.0000.0000.000
32A32VAL00.0220.02018.887-0.001-0.0010.0000.0000.0000.000
33A33MET00.0140.03219.9540.0010.0010.0000.0000.0000.000
34A34THR00.0040.00314.575-0.015-0.0150.0000.0000.0000.000
35A35GLN00.006-0.00513.2490.0300.0300.0000.0000.0000.000
36A36VAL00.0300.0068.480-0.060-0.0600.0000.0000.0000.000
37A37HIS00.0170.0097.0680.2270.2270.0000.0000.0000.000
38A38THR0-0.011-0.0184.528-0.485-0.371-0.001-0.044-0.0690.000
39A39ASN00.004-0.0102.813-1.690-0.1340.529-0.847-1.238-0.008
40A40ASP-1-0.898-0.9564.8700.3180.429-0.001-0.003-0.1070.000
41A41ALA00.0370.0356.666-0.186-0.1860.0000.0000.0000.000
42A42THR0-0.062-0.0519.946-0.007-0.0070.0000.0000.0000.000
43A43LYS10.9180.9719.089-0.640-0.6400.0000.0000.0000.000
44A44LYS10.9710.99711.140-0.307-0.3070.0000.0000.0000.000
45A45VAL00.0210.0099.2540.0480.0480.0000.0000.0000.000
46A46ILE0-0.033-0.01410.4700.0070.0070.0000.0000.0000.000
47A47VAL00.0130.00211.352-0.019-0.0190.0000.0000.0000.000
48A48LYS10.9510.97013.694-0.151-0.1510.0000.0000.0000.000
49A49LEU0-0.025-0.00615.440-0.026-0.0260.0000.0000.0000.000
50A50ALA00.002-0.00715.7360.0220.0220.0000.0000.0000.000
51A51ASP-1-0.906-0.95917.430-0.008-0.0080.0000.0000.0000.000
52A52THR0-0.064-0.03921.200-0.003-0.0030.0000.0000.0000.000
53A53PRO00.0120.03622.383-0.002-0.0020.0000.0000.0000.000
54A54GLN00.001-0.02124.4210.0040.0040.0000.0000.0000.000
55A55LEU0-0.0130.00027.478-0.006-0.0060.0000.0000.0000.000
56A56THR00.0050.01029.7490.0060.0060.0000.0000.0000.000
57A57ASP-1-0.853-0.93532.001-0.030-0.0300.0000.0000.0000.000
58A58VAL0-0.039-0.03831.8850.0000.0000.0000.0000.0000.000
59A59LEU0-0.046-0.01834.467-0.001-0.0010.0000.0000.0000.000
60A60ASN0-0.016-0.00437.0000.0020.0020.0000.0000.0000.000
61A61SER00.0730.02434.3550.0000.0000.0000.0000.0000.000
62A62THR0-0.055-0.03135.2520.0010.0010.0000.0000.0000.000
63A63VAL0-0.0490.00237.0890.0020.0020.0000.0000.0000.000
64A64GLN0-0.021-0.02930.5360.0000.0000.0000.0000.0000.000
65A65MET0-0.066-0.02532.2650.0030.0030.0000.0000.0000.000
66A66PRO00.0060.01929.503-0.003-0.0030.0000.0000.0000.000
67A67ILE0-0.0010.00024.365-0.002-0.0020.0000.0000.0000.000
68A68SER0-0.077-0.03925.9610.0070.0070.0000.0000.0000.000
69A69VAL00.0500.01319.495-0.006-0.0060.0000.0000.0000.000
70A70SER0-0.061-0.01921.8930.0080.0080.0000.0000.0000.000
71A71TRP00.0700.00713.927-0.009-0.0090.0000.0000.0000.000
72A72GLY00.0690.04519.2670.0110.0110.0000.0000.0000.000
73A73GLY0-0.027-0.00820.0640.0110.0110.0000.0000.0000.000
74A74GLN0-0.044-0.01620.3370.0090.0090.0000.0000.0000.000
75A75VAL00.0220.00221.557-0.008-0.0080.0000.0000.0000.000
76A76LEU00.0140.01617.2800.0090.0090.0000.0000.0000.000
77A77SER00.0200.00120.329-0.001-0.0010.0000.0000.0000.000
78A78THR00.0530.02319.4640.0010.0010.0000.0000.0000.000
79A79THR0-0.054-0.01419.2820.0180.0180.0000.0000.0000.000
80A80ALA0-0.026-0.01115.379-0.009-0.0090.0000.0000.0000.000
81A81LYS10.8440.92116.922-0.034-0.0340.0000.0000.0000.000
82A82GLU-1-0.920-0.97215.1300.1820.1820.0000.0000.0000.000
83A83PHE0-0.035-0.00514.523-0.010-0.0100.0000.0000.0000.000
84A84GLU-1-0.877-0.95514.5660.1690.1690.0000.0000.0000.000
85A85ALA00.005-0.00412.752-0.020-0.0200.0000.0000.0000.000
86A86ALA00.001-0.01614.162-0.010-0.0100.0000.0000.0000.000
87A87ALA0-0.0140.00217.356-0.007-0.0070.0000.0000.0000.000
88A88LEU0-0.0110.00412.631-0.011-0.0110.0000.0000.0000.000
89A89GLY00.0060.02115.916-0.003-0.0030.0000.0000.0000.000
90A90TYR0-0.004-0.0179.834-0.023-0.0230.0000.0000.0000.000
91A91SER0-0.0360.00114.4210.0000.0000.0000.0000.0000.000
92A92ALA00.056-0.01313.7320.0590.0590.0000.0000.0000.000
93A93SER0-0.068-0.02815.531-0.010-0.0100.0000.0000.0000.000
94A94GLY00.0530.01717.989-0.013-0.0130.0000.0000.0000.000
95A95VAL0-0.027-0.00414.1750.0050.0050.0000.0000.0000.000
96A96ASN0-0.043-0.01612.6290.0120.0120.0000.0000.0000.000
97A97GLY00.0350.0369.0860.1600.1600.0000.0000.0000.000
98A98VAL00.0200.0159.168-0.007-0.0070.0000.0000.0000.000
99A99SER0-0.0260.00111.819-0.013-0.0130.0000.0000.0000.000
100A100SER00.010-0.00113.780-0.012-0.0120.0000.0000.0000.000
101A101SER00.005-0.01116.495-0.015-0.0150.0000.0000.0000.000
102A102GLN0-0.0080.00316.7920.0060.0060.0000.0000.0000.000
103A103GLU-1-0.824-0.92518.515-0.032-0.0320.0000.0000.0000.000
104A104LEU0-0.063-0.03317.4410.0000.0000.0000.0000.0000.000
105A105VAL0-0.0140.00020.3140.0020.0020.0000.0000.0000.000
106A106ILE0-0.010-0.00620.2800.0010.0010.0000.0000.0000.000
107A107SER00.0180.00624.4110.0000.0000.0000.0000.0000.000
108A108ALA00.0470.01727.594-0.001-0.0010.0000.0000.0000.000
109A109ALA00.0160.01330.2940.0010.0010.0000.0000.0000.000
110A110PRO00.0380.01133.5820.0000.0000.0000.0000.0000.000
111A111LYS10.9760.99034.5270.0030.0030.0000.0000.0000.000
112A112THR0-0.0370.00035.9010.0020.0020.0000.0000.0000.000
113A113ALA00.0380.01037.279-0.002-0.0020.0000.0000.0000.000
114A114GLY00.0250.00939.0400.0010.0010.0000.0000.0000.000
115A115THR0-0.070-0.02840.8940.0000.0000.0000.0000.0000.000
116A116ALA00.0260.00540.7730.0000.0000.0000.0000.0000.000
117A117PRO0-0.008-0.00637.5710.0000.0000.0000.0000.0000.000
118A118THR00.0050.01139.6220.0010.0010.0000.0000.0000.000
119A119ALA0-0.003-0.00239.496-0.002-0.0020.0000.0000.0000.000
120A120GLY00.0720.05138.6310.0000.0000.0000.0000.0000.000
121A121ASN0-0.037-0.00534.756-0.002-0.0020.0000.0000.0000.000
122A122TYR00.0070.00031.9490.0010.0010.0000.0000.0000.000
123A123SER0-0.018-0.02728.051-0.005-0.0050.0000.0000.0000.000
124A124GLY00.0460.02426.1150.0060.0060.0000.0000.0000.000
125A125VAL00.0300.01520.059-0.008-0.0080.0000.0000.0000.000
126A126VAL0-0.042-0.01418.3400.0130.0130.0000.0000.0000.000
127A127SER00.0630.04016.113-0.018-0.0180.0000.0000.0000.000
128A128LEU0-0.028-0.01713.6610.0320.0320.0000.0000.0000.000
129A129VAL00.0080.00310.781-0.033-0.0330.0000.0000.0000.000
130A130MET0-0.024-0.0038.924-0.008-0.0080.0000.0000.0000.000
131A131THR0-0.011-0.0096.7560.0240.0240.0000.0000.0000.000
132A132LEU0-0.0190.0024.328-0.308-0.173-0.001-0.019-0.1150.000
133A133GLY0-0.046-0.0317.4470.2870.2870.0000.0000.0000.000
134A134SER0-0.040-0.00910.097-0.009-0.0090.0000.0000.0000.000
135A135ASP-1-0.868-0.9307.5841.2181.2180.0000.0000.0000.000
136A136ASN0-0.066-0.0566.648-0.383-0.3830.0000.0000.0000.000
137A137LYS10.9460.9902.354-3.436-3.1406.144-1.976-4.4630.008
138A138GLN00.007-0.0113.851-1.832-2.223-0.0050.636-0.2400.000
139A139VAL00.0010.0165.013-0.188-0.064-0.001-0.007-0.1150.000
140A140GLU-1-0.889-0.9456.9850.0300.0300.0000.0000.0000.000
141A141LYS10.9030.97010.1650.3600.3600.0000.0000.0000.000
142A142ASN0-0.007-0.01212.8780.0640.0640.0000.0000.0000.000
143A143ILE0-0.020-0.00516.331-0.016-0.0160.0000.0000.0000.000
144A144THR0-0.005-0.02019.2700.0170.0170.0000.0000.0000.000
145A145VAL0-0.001-0.00122.662-0.001-0.0010.0000.0000.0000.000
146A146THR0-0.004-0.00525.3510.0040.0040.0000.0000.0000.000
147A147ALA00.016-0.00228.9560.0010.0010.0000.0000.0000.000
148A148SER0-0.026-0.04132.253-0.002-0.0020.0000.0000.0000.000
149A149VAL0-0.0380.01035.9530.0010.0010.0000.0000.0000.000
150A150ASP-1-0.866-0.93539.078-0.026-0.0260.0000.0000.0000.000
151A151PRO00.0240.01142.1200.0020.0020.0000.0000.0000.000
152A152VAL0-0.033-0.02645.0290.0000.0000.0000.0000.0000.000
153A153ILE00.0070.00347.8330.0010.0010.0000.0000.0000.000
154A154GLU-1-0.935-0.95851.406-0.010-0.0100.0000.0000.0000.000
155A155LEU0-0.028-0.02654.1130.0000.0000.0000.0000.0000.000
156A156LEU0-0.0060.00755.2900.0000.0000.0000.0000.0000.000
157A157GLN00.0370.00259.0230.0000.0000.0000.0000.0000.000
158A158ALA0-0.028-0.01860.1590.0000.0000.0000.0000.0000.000
159A159ASP-1-0.897-0.94860.091-0.004-0.0040.0000.0000.0000.000
160A160GLY0-0.020-0.00757.9200.0000.0000.0000.0000.0000.000
161A161ASN0-0.021-0.00258.2430.0000.0000.0000.0000.0000.000
162A162ALA0-0.012-0.01160.2360.0000.0000.0000.0000.0000.000
163A163LEU00.014-0.00161.1600.0000.0000.0000.0000.0000.000
164A164PRO0-0.038-0.00963.7220.0000.0000.0000.0000.0000.000
165A165SER00.0350.01965.8260.0000.0000.0000.0000.0000.000
166A166ALA0-0.029-0.01367.3850.0000.0000.0000.0000.0000.000
167A167VAL00.0050.00670.7480.0000.0000.0000.0000.0000.000
168A168LYS10.9030.95473.3380.0040.0040.0000.0000.0000.000
169A169LEU0-0.0050.00375.7320.0000.0000.0000.0000.0000.000
170A170ALA00.0000.00379.0060.0000.0000.0000.0000.0000.000
171A171TYR00.0370.01982.2880.0000.0000.0000.0000.0000.000
172A172SER00.0130.00485.3640.0000.0000.0000.0000.0000.000
173A173PRO00.0460.00487.6770.0000.0000.0000.0000.0000.000
174A174ALA0-0.040-0.01391.1880.0000.0000.0000.0000.0000.000
175A175SER0-0.039-0.05887.3040.0000.0000.0000.0000.0000.000
176A176LYS10.9380.98289.7580.0030.0030.0000.0000.0000.000
177A177THR00.0250.05084.5710.0000.0000.0000.0000.0000.000
178A178PHE0-0.023-0.02081.0350.0000.0000.0000.0000.0000.000
179A179GLU-1-0.957-0.96579.300-0.003-0.0030.0000.0000.0000.000
180A180SER0-0.063-0.05275.6310.0000.0000.0000.0000.0000.000
181A181TYR00.0640.03568.4590.0000.0000.0000.0000.0000.000
182A182ARG10.9500.96771.1800.0040.0040.0000.0000.0000.000
183A183VAL0-0.0090.01666.0960.0000.0000.0000.0000.0000.000
184A184MET00.0210.02164.6250.0000.0000.0000.0000.0000.000
185A185THR0-0.018-0.05961.4000.0000.0000.0000.0000.0000.000
186A186GLN00.0100.00656.8910.0000.0000.0000.0000.0000.000
187A187VAL00.0260.01953.5890.0000.0000.0000.0000.0000.000
188A188HIS0-0.0020.01151.4350.0000.0000.0000.0000.0000.000
189A189THR0-0.064-0.05749.251-0.001-0.0010.0000.0000.0000.000
190A190ASN00.023-0.01243.5500.0020.0020.0000.0000.0000.000
191A191ASP-1-0.859-0.92544.400-0.019-0.0190.0000.0000.0000.000
192A192ALA0-0.008-0.00246.1990.0000.0000.0000.0000.0000.000
193A193THR0-0.033-0.02145.4680.0000.0000.0000.0000.0000.000
194A194LYS10.8660.95744.2430.0190.0190.0000.0000.0000.000
195A195LYS10.9580.97749.8330.0140.0140.0000.0000.0000.000
196A196VAL00.0050.00953.095-0.001-0.0010.0000.0000.0000.000
197A197ILE0-0.0050.00554.7360.0010.0010.0000.0000.0000.000
198A198VAL0-0.017-0.00657.9110.0000.0000.0000.0000.0000.000
199A199LYS10.9490.97660.7320.0130.0130.0000.0000.0000.000
200A200LEU0-0.040-0.02063.6530.0000.0000.0000.0000.0000.000
201A201ALA0-0.011-0.01163.9240.0000.0000.0000.0000.0000.000
202A202ASP-1-0.872-0.93465.475-0.011-0.0110.0000.0000.0000.000
203A203THR0-0.059-0.03969.2910.0000.0000.0000.0000.0000.000
204A204PRO00.0010.01671.3020.0000.0000.0000.0000.0000.000
205A205GLN00.020-0.01073.5660.0000.0000.0000.0000.0000.000
206A206LEU0-0.042-0.01276.9510.0000.0000.0000.0000.0000.000
207A207THR0-0.023-0.02279.2800.0000.0000.0000.0000.0000.000
208A208ASP-1-0.821-0.92081.389-0.005-0.0050.0000.0000.0000.000
209A209VAL0-0.064-0.04581.2680.0000.0000.0000.0000.0000.000
210A210LEU0-0.040-0.01183.6100.0000.0000.0000.0000.0000.000
211A211ASN0-0.0060.00286.4730.0000.0000.0000.0000.0000.000
212A212SER00.0290.01083.6630.0000.0000.0000.0000.0000.000
213A213THR0-0.028-0.00983.9530.0000.0000.0000.0000.0000.000
214A214VAL0-0.021-0.00786.4870.0000.0000.0000.0000.0000.000
215A215GLN00.0120.00880.6450.0000.0000.0000.0000.0000.000
216A216MET0-0.101-0.04881.6900.0000.0000.0000.0000.0000.000
217A217PRO00.0220.02378.4510.0000.0000.0000.0000.0000.000
218A218ILE00.0010.00573.6440.0000.0000.0000.0000.0000.000
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