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: JQY59

Calculation Name: 1VF7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VF7

Chain ID: A

ChEMBL ID:

UniProt ID: P52477

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2354805.013402
FMO2-HF: Nuclear repulsion 2265440.198675
FMO2-HF: Total energy -89364.814727
FMO2-MP2: Total energy -89630.448265


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:26:THR)


Summations of interaction energy for fragment #1(A:26: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.
-2.9931.5210.149-2.019-2.644-0.005
Interaction energy analysis for fragmet #1(A:26:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.012
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].
3A28ASN0-0.0020.0003.051-0.3711.9060.028-0.964-1.342-0.001
4A29THR0-0.0010.0005.3590.1550.225-0.001-0.004-0.0650.000
5A30GLU-1-0.878-0.9458.953-0.583-0.5830.0000.0000.0000.000
6A31LEU0-0.063-0.03311.9750.0400.0400.0000.0000.0000.000
7A32PRO00.0260.03115.2130.0180.0180.0000.0000.0000.000
8A33GLY00.0220.01118.5580.0200.0200.0000.0000.0000.000
9A34ARG10.8600.93921.0190.1020.1020.0000.0000.0000.000
10A35THR00.0660.04023.3250.0040.0040.0000.0000.0000.000
11A36ASN0-0.096-0.06925.2180.0100.0100.0000.0000.0000.000
12A37ALA00.0170.01727.9980.0010.0010.0000.0000.0000.000
13A38PHE0-0.0040.02427.9210.0020.0020.0000.0000.0000.000
14A39ARG10.9340.95630.5720.0240.0240.0000.0000.0000.000
15A40ILE00.0130.00734.364-0.001-0.0010.0000.0000.0000.000
16A41ALA0-0.0190.00337.1580.0010.0010.0000.0000.0000.000
17A42GLU-1-0.855-0.92940.856-0.029-0.0290.0000.0000.0000.000
18A43VAL0-0.009-0.00243.9290.0020.0020.0000.0000.0000.000
19A44ARG10.8100.89046.7330.0230.0230.0000.0000.0000.000
20A45PRO00.0080.02250.1180.0010.0010.0000.0000.0000.000
21A46GLN00.003-0.01351.3980.0000.0000.0000.0000.0000.000
22A47VAL0-0.046-0.01555.1590.0010.0010.0000.0000.0000.000
23A48ASN00.0730.03558.205-0.001-0.0010.0000.0000.0000.000
24A49GLY00.0360.03260.7570.0010.0010.0000.0000.0000.000
25A50ILE00.0660.05960.573-0.001-0.0010.0000.0000.0000.000
26A51ILE0-0.037-0.00455.0400.0010.0010.0000.0000.0000.000
27A52LEU00.0300.03258.1690.0000.0000.0000.0000.0000.000
28A53LYS10.9160.93455.3760.0100.0100.0000.0000.0000.000
29A54ARG10.9230.96148.5590.0190.0190.0000.0000.0000.000
30A55LEU0-0.026-0.01050.5700.0000.0000.0000.0000.0000.000
31A56PHE00.0550.04545.1030.0000.0000.0000.0000.0000.000
32A57LYS10.9500.98043.6840.0210.0210.0000.0000.0000.000
33A58GLU-1-0.838-0.90844.010-0.026-0.0260.0000.0000.0000.000
34A59GLY0-0.029-0.00339.844-0.001-0.0010.0000.0000.0000.000
35A60SER0-0.134-0.09139.3500.0010.0010.0000.0000.0000.000
36A61ASP-1-0.815-0.91735.952-0.029-0.0290.0000.0000.0000.000
37A62VAL0-0.0220.00438.8830.0020.0020.0000.0000.0000.000
38A63LYS10.9620.97039.4840.0060.0060.0000.0000.0000.000
39A64ALA0-0.001-0.00540.3870.0000.0000.0000.0000.0000.000
40A65GLY0-0.008-0.01142.2100.0020.0020.0000.0000.0000.000
41A66GLN0-0.027-0.01544.3170.0000.0000.0000.0000.0000.000
42A67GLN0-0.075-0.07046.7720.0000.0000.0000.0000.0000.000
43A68LEU0-0.045-0.02944.8660.0000.0000.0000.0000.0000.000
44A69TYR00.0890.01848.772-0.001-0.0010.0000.0000.0000.000
45A70GLN0-0.068-0.02152.5510.0010.0010.0000.0000.0000.000
46A71ILE0-0.0070.00155.897-0.001-0.0010.0000.0000.0000.000
47A72ASP-1-0.860-0.95158.452-0.008-0.0080.0000.0000.0000.000
48A73PRO00.0020.00861.3320.0000.0000.0000.0000.0000.000
49A74ALA0-0.008-0.00162.9900.0010.0010.0000.0000.0000.000
50A75THR00.0440.00266.7860.0000.0000.0000.0000.0000.000
51A76TYR0-0.039-0.02362.5070.0000.0000.0000.0000.0000.000
52A77GLU-1-0.922-0.97065.315-0.004-0.0040.0000.0000.0000.000
53A78ALA00.0210.00466.5310.0000.0000.0000.0000.0000.000
54A79ASP-1-0.897-0.97368.000-0.006-0.0060.0000.0000.0000.000
55A80TYR0-0.038-0.02464.9440.0000.0000.0000.0000.0000.000
56A81GLN0-0.0160.00467.9860.0010.0010.0000.0000.0000.000
57A82SER0-0.008-0.00770.7150.0000.0000.0000.0000.0000.000
58A83ALA00.0110.01269.5830.0000.0000.0000.0000.0000.000
59A84GLN00.003-0.01168.2520.0010.0010.0000.0000.0000.000
60A85ALA0-0.0320.00671.3990.0000.0000.0000.0000.0000.000
61A86ASN0-0.007-0.02374.5090.0000.0000.0000.0000.0000.000
62A87LEU00.0350.02270.0340.0000.0000.0000.0000.0000.000
63A88ALA0-0.010-0.00974.1100.0000.0000.0000.0000.0000.000
64A89SER0-0.032-0.00175.8740.0000.0000.0000.0000.0000.000
65A90THR00.030-0.00776.0680.0000.0000.0000.0000.0000.000
66A91GLN00.0020.00173.2790.0000.0000.0000.0000.0000.000
67A92GLU-1-0.861-0.91676.976-0.001-0.0010.0000.0000.0000.000
68A93GLN00.0360.01680.0900.0000.0000.0000.0000.0000.000
69A94ALA0-0.013-0.00478.3610.0000.0000.0000.0000.0000.000
70A95GLN00.002-0.01976.7490.0000.0000.0000.0000.0000.000
71A96ARG10.8940.94680.7030.0010.0010.0000.0000.0000.000
72A97TYR0-0.017-0.02983.7100.0000.0000.0000.0000.0000.000
73A98LYS10.9290.98178.3250.0000.0000.0000.0000.0000.000
74A99LEU00.002-0.00383.3260.0000.0000.0000.0000.0000.000
75A100LEU00.0290.01685.8510.0000.0000.0000.0000.0000.000
76A101VAL0-0.073-0.02084.7730.0000.0000.0000.0000.0000.000
77A102ALA0-0.066-0.02786.2290.0000.0000.0000.0000.0000.000
78A103ASP-1-0.893-0.92688.0030.0010.0010.0000.0000.0000.000
79A104GLN0-0.121-0.07690.7150.0000.0000.0000.0000.0000.000
80A105ALA00.0360.02591.6180.0000.0000.0000.0000.0000.000
81A106VAL0-0.068-0.02687.4670.0000.0000.0000.0000.0000.000
82A107SER00.019-0.00889.9100.0000.0000.0000.0000.0000.000
83A108LYS11.0000.96886.0370.0010.0010.0000.0000.0000.000
84A109GLN0-0.0260.00283.7070.0000.0000.0000.0000.0000.000
85A110GLN00.1230.06885.0390.0000.0000.0000.0000.0000.000
86A111TYR00.0190.01679.0370.0000.0000.0000.0000.0000.000
87A112ALA0-0.013-0.00681.0190.0000.0000.0000.0000.0000.000
88A113ASP-1-0.851-0.92280.247-0.003-0.0030.0000.0000.0000.000
89A114ALA0-0.025-0.01680.4860.0000.0000.0000.0000.0000.000
90A115ASN0-0.034-0.02975.5540.0000.0000.0000.0000.0000.000
91A116ALA0-0.003-0.00376.1240.0000.0000.0000.0000.0000.000
92A117ALA0-0.0040.00075.5570.0000.0000.0000.0000.0000.000
93A118TYR00.0190.01272.2590.0000.0000.0000.0000.0000.000
94A119LEU0-0.024-0.01370.9250.0000.0000.0000.0000.0000.000
95A120GLN0-0.002-0.00470.8070.0000.0000.0000.0000.0000.000
96A121SER0-0.0210.01670.8930.0000.0000.0000.0000.0000.000
97A122LYS10.9750.98067.2920.0020.0020.0000.0000.0000.000
98A123ALA0-0.031-0.01066.7090.0000.0000.0000.0000.0000.000
99A124ALA00.012-0.00766.3970.0000.0000.0000.0000.0000.000
100A125VAL00.0180.01666.3650.0000.0000.0000.0000.0000.000
101A126GLU-1-0.820-0.88660.436-0.004-0.0040.0000.0000.0000.000
102A127GLN0-0.013-0.01360.9110.0000.0000.0000.0000.0000.000
103A128ALA00.0080.00362.743-0.001-0.0010.0000.0000.0000.000
104A129ARG10.8400.91257.7810.0040.0040.0000.0000.0000.000
105A130ILE0-0.075-0.02957.5750.0000.0000.0000.0000.0000.000
106A131ASN00.021-0.00558.561-0.001-0.0010.0000.0000.0000.000
107A132LEU00.0550.04259.897-0.001-0.0010.0000.0000.0000.000
108A133ARG10.8700.95354.5020.0070.0070.0000.0000.0000.000
109A134TYR00.012-0.01853.4290.0000.0000.0000.0000.0000.000
110A135THR0-0.033-0.01155.735-0.001-0.0010.0000.0000.0000.000
111A136LYS10.9030.97353.6270.0060.0060.0000.0000.0000.000
112A137VAL00.0340.02549.8460.0000.0000.0000.0000.0000.000
113A138LEU0-0.016-0.00248.0440.0000.0000.0000.0000.0000.000
114A139SER00.0140.00342.063-0.002-0.0020.0000.0000.0000.000
115A140PRO00.0440.04442.9180.0020.0020.0000.0000.0000.000
116A141ILE0-0.007-0.01737.0550.0020.0020.0000.0000.0000.000
117A142SER00.002-0.01136.9190.0010.0010.0000.0000.0000.000
118A143GLY0-0.009-0.01035.628-0.002-0.0020.0000.0000.0000.000
119A144ARG10.9641.01734.2010.0360.0360.0000.0000.0000.000
120A145ILE0-0.0310.00137.322-0.002-0.0020.0000.0000.0000.000
121A146GLY00.0360.01440.672-0.001-0.0010.0000.0000.0000.000
122A147ARG10.9690.96441.4500.0370.0370.0000.0000.0000.000
123A148SER0-0.060-0.01844.8100.0000.0000.0000.0000.0000.000
124A149ALA0-0.053-0.02747.8710.0000.0000.0000.0000.0000.000
125A150VAL0-0.0290.00149.3840.0000.0000.0000.0000.0000.000
126A151THR00.0270.01052.4510.0000.0000.0000.0000.0000.000
127A152GLU-1-0.833-0.94754.824-0.014-0.0140.0000.0000.0000.000
128A153GLY0-0.031-0.02456.7900.0000.0000.0000.0000.0000.000
129A154ALA0-0.0290.00556.8360.0000.0000.0000.0000.0000.000
130A155LEU0-0.005-0.00858.9130.0010.0010.0000.0000.0000.000
131A156VAL0-0.021-0.01355.329-0.001-0.0010.0000.0000.0000.000
132A157THR0-0.026-0.01657.4480.0010.0010.0000.0000.0000.000
133A158ASN00.017-0.00856.100-0.001-0.0010.0000.0000.0000.000
134A159GLY00.0150.01354.1940.0000.0000.0000.0000.0000.000
135A160GLN00.0110.02153.1390.0000.0000.0000.0000.0000.000
136A161ALA00.0460.01052.461-0.001-0.0010.0000.0000.0000.000
137A162ASN00.0020.00849.887-0.002-0.0020.0000.0000.0000.000
138A163ALA00.0250.02046.5130.0010.0010.0000.0000.0000.000
139A164MET0-0.031-0.01548.5930.0000.0000.0000.0000.0000.000
140A165ALA00.0580.03244.8870.0000.0000.0000.0000.0000.000
141A166THR0-0.015-0.00639.5750.0000.0000.0000.0000.0000.000
142A167VAL00.0110.01038.362-0.001-0.0010.0000.0000.0000.000
143A168GLN00.0250.00034.368-0.002-0.0020.0000.0000.0000.000
144A169GLN0-0.012-0.01232.1720.0000.0000.0000.0000.0000.000
145A170LEU0-0.032-0.03630.120-0.004-0.0040.0000.0000.0000.000
146A171ASP-1-0.839-0.89428.687-0.029-0.0290.0000.0000.0000.000
147A172PRO00.0220.01026.481-0.002-0.0020.0000.0000.0000.000
148A173ILE0-0.049-0.02424.2390.0010.0010.0000.0000.0000.000
149A174TYR0-0.016-0.02324.5420.0000.0000.0000.0000.0000.000
150A175VAL00.006-0.00819.205-0.003-0.0030.0000.0000.0000.000
151A176ASP-1-0.893-0.94421.999-0.093-0.0930.0000.0000.0000.000
152A177VAL00.0270.01317.600-0.011-0.0110.0000.0000.0000.000
153A178THR00.0040.00020.8930.0160.0160.0000.0000.0000.000
154A179GLN0-0.012-0.01316.358-0.047-0.0470.0000.0000.0000.000
155A180PRO00.0720.02719.1510.0180.0180.0000.0000.0000.000
156A181SER00.1020.04420.537-0.005-0.0050.0000.0000.0000.000
157A182THR0-0.007-0.00219.1450.0120.0120.0000.0000.0000.000
158A183ALA0-0.034-0.01516.6370.0080.0080.0000.0000.0000.000
159A184LEU00.0480.05117.2260.0150.0150.0000.0000.0000.000
160A185LEU0-0.007-0.01918.8720.0200.0200.0000.0000.0000.000
161A186ARG10.8220.92312.1320.2050.2050.0000.0000.0000.000
162A187LEU00.0400.02012.8850.0430.0430.0000.0000.0000.000
163A188ARG10.9850.98915.6660.0460.0460.0000.0000.0000.000
164A189ARG10.9260.96514.699-0.038-0.0380.0000.0000.0000.000
165A190GLH0-0.049-0.05810.727-0.003-0.0030.0000.0000.0000.000
166A191LEU00.0130.03814.0430.0600.0600.0000.0000.0000.000
167A192ALA0-0.098-0.06015.9100.0170.0170.0000.0000.0000.000
168A193SER0-0.068-0.05015.0780.0070.0070.0000.0000.0000.000
169A194GLY00.0230.02015.0960.0110.0110.0000.0000.0000.000
170A195GLN0-0.0360.00010.543-0.051-0.0510.0000.0000.0000.000
171A196LEU0-0.014-0.0069.8180.1090.1090.0000.0000.0000.000
172A197GLU-1-0.869-0.93710.6730.1240.1240.0000.0000.0000.000
173A198ARG10.9090.94812.987-0.167-0.1670.0000.0000.0000.000
174A199ALA0-0.008-0.01016.590-0.001-0.0010.0000.0000.0000.000
175A200GLY0-0.014-0.01918.549-0.001-0.0010.0000.0000.0000.000
176A201ASP-1-0.911-0.96621.2070.0590.0590.0000.0000.0000.000
177A202ASN0-0.093-0.06022.1900.0010.0010.0000.0000.0000.000
178A203ALA00.0410.03219.683-0.012-0.0120.0000.0000.0000.000
179A204ALA00.0120.02414.0580.0260.0260.0000.0000.0000.000
180A205LYS10.9160.97213.432-0.145-0.1450.0000.0000.0000.000
181A206VAL0-0.040-0.00812.890-0.014-0.0140.0000.0000.0000.000
182A207SER00.0630.02811.7070.0300.0300.0000.0000.0000.000
183A208LEU00.004-0.00413.819-0.029-0.0290.0000.0000.0000.000
184A209LYS10.9370.99513.0080.4480.4480.0000.0000.0000.000
185A210LEU00.015-0.00115.9500.0060.0060.0000.0000.0000.000
186A211GLU-1-0.890-0.94019.266-0.156-0.1560.0000.0000.0000.000
187A212ASP-1-0.862-0.91021.464-0.149-0.1490.0000.0000.0000.000
188A213GLY0-0.086-0.05117.428-0.004-0.0040.0000.0000.0000.000
189A214SER0-0.049-0.04716.612-0.021-0.0210.0000.0000.0000.000
190A215GLN0-0.057-0.05312.6310.0110.0110.0000.0000.0000.000
191A216TYR00.005-0.03316.2350.0300.0300.0000.0000.0000.000
192A217PRO0-0.0010.00916.803-0.014-0.0140.0000.0000.0000.000
193A218LEU0-0.061-0.04818.0370.0220.0220.0000.0000.0000.000
194A219GLU-1-0.930-0.94514.0710.0160.0160.0000.0000.0000.000
195A220GLY00.0080.01016.8960.0180.0180.0000.0000.0000.000
196A221ARG10.8420.90917.5160.0090.0090.0000.0000.0000.000
197A222LEU0-0.0090.00015.914-0.010-0.0100.0000.0000.0000.000
198A223GLU-1-0.831-0.92118.6140.0090.0090.0000.0000.0000.000
199A224PHE0-0.001-0.01416.105-0.011-0.0110.0000.0000.0000.000
200A225SER0-0.102-0.04022.2550.0010.0010.0000.0000.0000.000
201A226GLU-1-0.789-0.89423.802-0.045-0.0450.0000.0000.0000.000
202A227VAL0-0.013-0.01126.805-0.003-0.0030.0000.0000.0000.000
203A228SER0-0.0400.00427.7580.0020.0020.0000.0000.0000.000
204A229VAL00.011-0.01427.958-0.001-0.0010.0000.0000.0000.000
205A230ASP-1-0.921-0.96628.812-0.075-0.0750.0000.0000.0000.000
206A231GLU-1-0.945-0.95530.674-0.046-0.0460.0000.0000.0000.000
207A232GLY0-0.0070.01033.1770.0000.0000.0000.0000.0000.000
208A233THR0-0.059-0.03228.146-0.005-0.0050.0000.0000.0000.000
209A234GLY00.0370.01427.3070.0030.0030.0000.0000.0000.000
210A235SER0-0.063-0.04424.060-0.003-0.0030.0000.0000.0000.000
211A236VAL00.0250.01723.7850.0110.0110.0000.0000.0000.000
212A237THR0-0.022-0.01623.784-0.015-0.0150.0000.0000.0000.000
213A238ILE0-0.029-0.01518.6190.0120.0120.0000.0000.0000.000
214A239ARG10.8640.92622.5880.0500.0500.0000.0000.0000.000
215A240ALA00.0450.01718.8300.0070.0070.0000.0000.0000.000
216A241VAL0-0.036-0.01920.852-0.002-0.0020.0000.0000.0000.000
217A242PHE00.0200.00416.5470.0040.0040.0000.0000.0000.000
218A243PRO00.0230.01721.3410.0020.0020.0000.0000.0000.000
219A244ASN0-0.0010.02123.646-0.013-0.0130.0000.0000.0000.000
220A245PRO00.0640.04725.8380.0020.0020.0000.0000.0000.000
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222A247ASN0-0.040-0.00728.394-0.001-0.0010.0000.0000.0000.000
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