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: 89QYY

Calculation Name: 3F56-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F56

Chain ID: A

ChEMBL ID:

UniProt ID: Q7V2D3

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptAll
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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2292313.818854
FMO2-HF: Nuclear repulsion 2213034.349654
FMO2-HF: Total energy -79279.4692
FMO2-MP2: Total energy -79508.109105


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:50:GLN)


Summations of interaction energy for fragment #1(A:50:GLN)
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.
-66.112-63.17320.144-11.363-11.719-0.04
Interaction energy analysis for fragmet #1(A:50:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.042
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].
3A52GLU-1-0.807-0.8981.823-41.365-37.67211.527-7.517-7.702-0.086
4A53GLN0-0.068-0.0263.8101.9132.3230.000-0.051-0.3590.000
5A54ILE0-0.041-0.0185.5231.3501.3500.0000.0000.0000.000
6A55GLU-1-0.770-0.8478.097-0.714-0.7140.0000.0000.0000.000
7A56LEU00.002-0.00811.5600.2570.2570.0000.0000.0000.000
8A57ARG10.8250.90513.6240.3380.3380.0000.0000.0000.000
9A58THR00.008-0.01716.6640.0150.0150.0000.0000.0000.000
10A59TYR00.0290.01117.1380.0190.0190.0000.0000.0000.000
11A60VAL0-0.0040.00119.499-0.019-0.0190.0000.0000.0000.000
12A61PHE00.0450.02223.1440.0260.0260.0000.0000.0000.000
13A62LEU0-0.002-0.00725.117-0.005-0.0050.0000.0000.0000.000
14A63ASP-1-0.820-0.90528.472-0.141-0.1410.0000.0000.0000.000
15A64SER0-0.018-0.02030.3170.0110.0110.0000.0000.0000.000
16A65LEU0-0.0160.00329.348-0.006-0.0060.0000.0000.0000.000
17A66GLN0-0.0060.00332.8840.0100.0100.0000.0000.0000.000
18A67PRO00.0280.00335.7700.0080.0080.0000.0000.0000.000
19A68GLN0-0.024-0.02937.5290.0140.0140.0000.0000.0000.000
20A69LEU00.0010.00830.5800.0090.0090.0000.0000.0000.000
21A70ALA0-0.0050.00332.6910.0090.0090.0000.0000.0000.000
22A71ALA00.0270.01333.3920.0130.0130.0000.0000.0000.000
23A72TYR0-0.046-0.03230.3570.0120.0120.0000.0000.0000.000
24A73MET0-0.013-0.00325.9930.0060.0060.0000.0000.0000.000
25A74GLY0-0.009-0.00229.8150.0180.0180.0000.0000.0000.000
26A75THR0-0.070-0.02532.1460.0130.0130.0000.0000.0000.000
27A76VAL0-0.022-0.01828.3170.0120.0120.0000.0000.0000.000
28A77SER0-0.094-0.04826.2410.0130.0130.0000.0000.0000.000
29A78ARG10.8630.90824.212-0.166-0.1660.0000.0000.0000.000
30A79GLY00.0150.02625.0980.0280.0280.0000.0000.0000.000
31A80PHE0-0.064-0.04225.083-0.013-0.0130.0000.0000.0000.000
32A81LEU00.0370.02128.273-0.010-0.0100.0000.0000.0000.000
33A82PRO0-0.0020.01529.8600.0020.0020.0000.0000.0000.000
34A83ILE0-0.021-0.01931.3920.0040.0040.0000.0000.0000.000
35A84PRO0-0.026-0.03234.103-0.010-0.0100.0000.0000.0000.000
36A85GLY00.0280.03035.2300.0020.0020.0000.0000.0000.000
37A86ASP-1-0.842-0.91030.291-0.020-0.0200.0000.0000.0000.000
38A87SER0-0.035-0.01428.161-0.010-0.0100.0000.0000.0000.000
39A88CYS0-0.041-0.03025.8070.0230.0230.0000.0000.0000.000
40A89LEU0-0.0150.02118.728-0.030-0.0300.0000.0000.0000.000
41A90TRP00.0410.01921.0430.0600.0600.0000.0000.0000.000
42A91MET0-0.014-0.01516.168-0.097-0.0970.0000.0000.0000.000
43A92GLU-1-0.785-0.87216.660-0.105-0.1050.0000.0000.0000.000
44A93VAL0-0.003-0.00511.166-0.112-0.1120.0000.0000.0000.000
45A94SER00.0320.02511.8140.2150.2150.0000.0000.0000.000
46A95PRO00.0660.0377.656-0.270-0.2700.0000.0000.0000.000
47A96GLY00.0470.01210.0510.1370.1370.0000.0000.0000.000
48A97MET0-0.016-0.0249.9970.0120.0120.0000.0000.0000.000
49A98ALA00.0110.0107.5820.3200.3200.0000.0000.0000.000
50A99VAL00.0150.0068.7120.0460.0460.0000.0000.0000.000
51A100HIS00.0130.02010.942-0.091-0.0910.0000.0000.0000.000
52A101ARG10.9020.9462.025-25.410-26.5748.617-3.795-3.6580.046
53A102VAL00.0270.0139.535-0.191-0.1910.0000.0000.0000.000
54A103THR00.010-0.01811.839-0.160-0.1600.0000.0000.0000.000
55A104ASP-1-0.859-0.90312.4020.6920.6920.0000.0000.0000.000
56A105ILE00.0160.0068.866-0.089-0.0890.0000.0000.0000.000
57A106ALA00.0360.01413.533-0.108-0.1080.0000.0000.0000.000
58A107LEU0-0.038-0.01616.561-0.054-0.0540.0000.0000.0000.000
59A108LYS10.7720.86815.234-0.643-0.6430.0000.0000.0000.000
60A109ALA0-0.0050.02716.908-0.039-0.0390.0000.0000.0000.000
61A110SER0-0.016-0.03618.753-0.041-0.0410.0000.0000.0000.000
62A111ASN0-0.014-0.00922.3730.0450.0450.0000.0000.0000.000
63A112VAL0-0.0230.01320.7890.0030.0030.0000.0000.0000.000
64A113ARG10.8830.94823.947-0.082-0.0820.0000.0000.0000.000
65A114LEU00.0390.01618.934-0.022-0.0220.0000.0000.0000.000
66A115GLY00.0420.01322.4960.0140.0140.0000.0000.0000.000
67A116GLN00.0320.00422.0520.0270.0270.0000.0000.0000.000
68A117MET0-0.007-0.00316.8780.0180.0180.0000.0000.0000.000
69A118ILE0-0.044-0.00718.5880.0120.0120.0000.0000.0000.000
70A119VAL00.001-0.00414.7970.0090.0090.0000.0000.0000.000
71A120GLU-1-0.825-0.91417.3350.0780.0780.0000.0000.0000.000
72A121ARG10.9230.95317.766-0.122-0.1220.0000.0000.0000.000
73A122ALA0-0.031-0.00916.0230.0370.0370.0000.0000.0000.000
74A123PHE00.0340.01614.442-0.003-0.0030.0000.0000.0000.000
75A124GLY00.0210.01414.6690.0970.0970.0000.0000.0000.000
76A125SER0-0.058-0.03015.552-0.102-0.1020.0000.0000.0000.000
77A126LEU0-0.011-0.00315.6730.0720.0720.0000.0000.0000.000
78A127ALA00.0030.00818.976-0.063-0.0630.0000.0000.0000.000
79A128LEU0-0.012-0.00118.0150.0450.0450.0000.0000.0000.000
80A129TYR00.0560.02722.582-0.040-0.0400.0000.0000.0000.000
81A130HIS00.025-0.00226.1350.0050.0050.0000.0000.0000.000
82A131LYS10.8870.93828.1840.0330.0330.0000.0000.0000.000
83A132ASP-1-0.835-0.89629.831-0.064-0.0640.0000.0000.0000.000
84A133GLN00.023-0.00228.168-0.016-0.0160.0000.0000.0000.000
85A134SER00.0310.01426.360-0.013-0.0130.0000.0000.0000.000
86A135THR0-0.041-0.02224.846-0.021-0.0210.0000.0000.0000.000
87A136VAL0-0.022-0.01023.1740.0000.0000.0000.0000.0000.000
88A137LEU0-0.0130.00021.695-0.009-0.0090.0000.0000.0000.000
89A138HIS00.0370.03520.598-0.067-0.0670.0000.0000.0000.000
90A139SER0-0.011-0.01918.527-0.031-0.0310.0000.0000.0000.000
91A140GLY0-0.011-0.01416.9130.0120.0120.0000.0000.0000.000
92A141ASP-1-0.913-0.96116.140-0.530-0.5300.0000.0000.0000.000
93A142VAL00.0100.00314.706-0.108-0.1080.0000.0000.0000.000
94A143VAL0-0.046-0.02712.119-0.027-0.0270.0000.0000.0000.000
95A144LEU0-0.067-0.02911.365-0.151-0.1510.0000.0000.0000.000
96A145ASP-1-0.848-0.92211.626-1.292-1.2920.0000.0000.0000.000
97A146ALA0-0.081-0.0319.528-0.370-0.3700.0000.0000.0000.000
98A147ILE0-0.087-0.0557.006-0.058-0.0580.0000.0000.0000.000
99A148GLY00.0160.0248.059-0.699-0.6990.0000.0000.0000.000
100A149SER0-0.035-0.0329.830-0.008-0.0080.0000.0000.0000.000
101A150GLU-1-0.796-0.90912.442-1.138-1.1380.0000.0000.0000.000
102A151VAL00.0250.00316.1580.0040.0040.0000.0000.0000.000
103A152ARG10.8710.92219.1060.6130.6130.0000.0000.0000.000
104A153LYS10.8050.91012.5921.9351.9350.0000.0000.0000.000
105A154ARG10.8060.93015.6050.4180.4180.0000.0000.0000.000
106A155THR0-0.039-0.04016.430-0.022-0.0220.0000.0000.0000.000
107A156LYS10.8800.93618.3650.5840.5840.0000.0000.0000.000
108A157PRO0-0.0150.00422.1620.0050.0050.0000.0000.0000.000
109A158SER00.0200.02224.5170.0080.0080.0000.0000.0000.000
110A159THR00.009-0.01826.4520.0170.0170.0000.0000.0000.000
111A160SER0-0.048-0.04329.353-0.002-0.0020.0000.0000.0000.000
112A161TRP0-0.065-0.04730.9980.0060.0060.0000.0000.0000.000
113A162THR0-0.006-0.01633.828-0.008-0.0080.0000.0000.0000.000
114A163GLU-1-0.874-0.91536.486-0.066-0.0660.0000.0000.0000.000
115A164VAL00.019-0.00740.1560.0020.0020.0000.0000.0000.000
116A165ILE0-0.0220.01242.2810.0020.0020.0000.0000.0000.000
117A166CYS0-0.031-0.03345.3490.0020.0020.0000.0000.0000.000
118A167ALA0-0.0030.00448.6070.0020.0020.0000.0000.0000.000
119A168ILE0-0.0160.00944.9300.0030.0030.0000.0000.0000.000
120A169THR00.024-0.01648.6050.0020.0020.0000.0000.0000.000
121A170PRO00.039-0.00949.3270.0010.0010.0000.0000.0000.000
122A171ASP-1-0.827-0.90249.350-0.001-0.0010.0000.0000.0000.000
123A172HIS00.0320.01842.0930.0080.0080.0000.0000.0000.000
124A173ALA00.0560.03544.7190.0010.0010.0000.0000.0000.000
125A174VAL0-0.045-0.02745.2290.0040.0040.0000.0000.0000.000
126A175LEU0-0.012-0.01542.2140.0060.0060.0000.0000.0000.000
127A176ILE00.0380.02339.9730.0050.0050.0000.0000.0000.000
128A177ASN0-0.049-0.04540.3720.0040.0040.0000.0000.0000.000
129A178ARG10.9180.96441.586-0.032-0.0320.0000.0000.0000.000
130A179GLN0-0.0110.00537.3160.0120.0120.0000.0000.0000.000
131A180ASN0-0.042-0.02431.7400.0000.0000.0000.0000.0000.000
132A181ARG10.8440.95134.484-0.019-0.0190.0000.0000.0000.000
133A182SER0-0.037-0.02633.3300.0080.0080.0000.0000.0000.000
134A183GLY00.0370.03035.4200.0020.0020.0000.0000.0000.000
135A184SER0-0.022-0.00237.4040.0080.0080.0000.0000.0000.000
136A185MET0-0.031-0.01841.0280.0010.0010.0000.0000.0000.000
137A186ILE00.0290.02142.923-0.004-0.0040.0000.0000.0000.000
138A187GLN0-0.028-0.03344.9320.0030.0030.0000.0000.0000.000
139A188SER00.0110.00848.709-0.002-0.0020.0000.0000.0000.000
140A189GLY0-0.042-0.01550.3960.0010.0010.0000.0000.0000.000
141A190MET0-0.0360.01046.861-0.003-0.0030.0000.0000.0000.000
142A191SER00.0250.00546.6440.0020.0020.0000.0000.0000.000
143A192MET0-0.038-0.02240.9060.0050.0050.0000.0000.0000.000
144A193PHE00.0510.02335.813-0.004-0.0040.0000.0000.0000.000
145A194ILE0-0.054-0.02136.2220.0070.0070.0000.0000.0000.000
146A195LEU00.0310.00831.015-0.009-0.0090.0000.0000.0000.000
147A196GLU-1-0.825-0.86029.257-0.065-0.0650.0000.0000.0000.000
148A197THR0-0.022-0.02625.523-0.010-0.0100.0000.0000.0000.000
149A198GLU-1-0.925-0.95122.778-0.184-0.1840.0000.0000.0000.000
150A199PRO0-0.025-0.02419.305-0.024-0.0240.0000.0000.0000.000
151A200ALA00.0200.02921.3620.0070.0070.0000.0000.0000.000
152A201GLY00.040-0.00921.6980.0180.0180.0000.0000.0000.000
153A202TYR00.011-0.02020.2020.0150.0150.0000.0000.0000.000
154A203VAL0-0.0110.01125.3620.0030.0030.0000.0000.0000.000
155A204LEU00.0140.00425.3340.0110.0110.0000.0000.0000.000
156A205LYS10.8000.89827.1740.1920.1920.0000.0000.0000.000
157A206ALA00.0240.01528.9780.0060.0060.0000.0000.0000.000
158A207ALA00.0250.01231.4730.0080.0080.0000.0000.0000.000
159A208ASN0-0.019-0.02231.2380.0200.0200.0000.0000.0000.000
160A209GLU-1-0.750-0.87031.994-0.149-0.1490.0000.0000.0000.000
161A210ALA00.0330.03734.8000.0020.0020.0000.0000.0000.000
162A211GLU-1-0.787-0.89736.672-0.040-0.0400.0000.0000.0000.000
163A212LYS10.7270.83533.3880.1420.1420.0000.0000.0000.000
164A213SER0-0.053-0.03038.592-0.003-0.0030.0000.0000.0000.000
165A214ALA0-0.0150.00541.1750.0010.0010.0000.0000.0000.000
166A215ASN0-0.088-0.02742.9300.0060.0060.0000.0000.0000.000
167A216ILE0-0.031-0.00739.2830.0030.0030.0000.0000.0000.000
168A217THR0-0.021-0.00742.1150.0050.0050.0000.0000.0000.000
169A218ILE0-0.005-0.01035.295-0.002-0.0020.0000.0000.0000.000
170A219ILE0-0.031-0.00938.2620.0080.0080.0000.0000.0000.000
171A220ASP-1-0.716-0.85733.6970.0260.0260.0000.0000.0000.000
172A221VAL00.0090.00629.349-0.014-0.0140.0000.0000.0000.000
173A222LYS10.8160.90228.617-0.020-0.0200.0000.0000.0000.000
174A223ALA00.0080.00425.039-0.009-0.0090.0000.0000.0000.000
175A224VAL0-0.013-0.01821.098-0.005-0.0050.0000.0000.0000.000
176A225GLY00.0030.00221.7820.0150.0150.0000.0000.0000.000
177A226ALA0-0.021-0.01621.539-0.025-0.0250.0000.0000.0000.000
178A227PHE0-0.0030.00822.552-0.025-0.0250.0000.0000.0000.000
179A228GLY0-0.0160.01325.5600.0250.0250.0000.0000.0000.000
180A229ARG10.8020.87426.5230.0340.0340.0000.0000.0000.000
181A230LEU00.0040.00630.2980.0100.0100.0000.0000.0000.000
182A231THR0-0.041-0.03032.9630.0020.0020.0000.0000.0000.000
183A232LEU00.0390.02036.1710.0070.0070.0000.0000.0000.000
184A233ALA00.0120.01239.261-0.001-0.0010.0000.0000.0000.000
185A234GLY00.0580.02143.075-0.001-0.0010.0000.0000.0000.000
186A235LYS10.9410.97046.3010.0410.0410.0000.0000.0000.000
187A236GLU-1-0.835-0.90747.565-0.055-0.0550.0000.0000.0000.000
188A237GLY00.0870.04147.332-0.003-0.0030.0000.0000.0000.000
189A238ASP-1-0.870-0.94545.774-0.060-0.0600.0000.0000.0000.000
190A239VAL0-0.029-0.02742.702-0.005-0.0050.0000.0000.0000.000
191A240GLU-1-0.913-0.95142.585-0.082-0.0820.0000.0000.0000.000
192A241GLU-1-0.762-0.84742.696-0.122-0.1220.0000.0000.0000.000
193A242ALA0-0.0140.00239.812-0.008-0.0080.0000.0000.0000.000
194A243ALA0-0.002-0.00438.382-0.008-0.0080.0000.0000.0000.000
195A244ALA0-0.003-0.00138.022-0.012-0.0120.0000.0000.0000.000
196A245ALA0-0.034-0.02437.459-0.013-0.0130.0000.0000.0000.000
197A246ALA0-0.013-0.00534.182-0.014-0.0140.0000.0000.0000.000
198A247ILE00.0050.00633.236-0.015-0.0150.0000.0000.0000.000
199A248ARG10.8220.87133.5140.1180.1180.0000.0000.0000.000
200A249ALA0-0.0160.00131.012-0.020-0.0200.0000.0000.0000.000
201A250ILE00.0310.01028.604-0.027-0.0270.0000.0000.0000.000
202A251ASP-1-0.853-0.91128.953-0.259-0.2590.0000.0000.0000.000
203A252GLN0-0.047-0.02830.039-0.019-0.0190.0000.0000.0000.000
204A253ILE0-0.062-0.03324.545-0.033-0.0330.0000.0000.0000.000
205A254SER00.002-0.00425.447-0.058-0.0580.0000.0000.0000.000
206A255ASN0-0.061-0.02826.328-0.053-0.0530.0000.0000.0000.000
207A256TYR0-0.0250.00222.988-0.062-0.0620.0000.0000.0000.000