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: 2NV1R

Calculation Name: 1SGV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SGV

Chain ID: A

ChEMBL ID:

UniProt ID: P9WHP7

Base Structure: X-ray

Registration Date: 2023-09-24

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 262
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3012138.478888
FMO2-HF: Nuclear repulsion 2913912.513741
FMO2-HF: Total energy -98225.965147
FMO2-MP2: Total energy -98512.157792


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:3:ALA)


Summations of interaction energy for fragment #1(A:3:ALA)
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.
-1.5730.650.017-0.998-1.2410.002
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.006
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].
3A5GLY0-0.0090.0142.864-2.647-0.5930.019-0.983-1.0900.002
4A6PRO0-0.037-0.0354.7620.8100.844-0.001-0.005-0.0280.000
5A7GLY00.0580.0157.669-0.129-0.1290.0000.0000.0000.000
6A8ILE0-0.016-0.00710.2620.0840.0840.0000.0000.0000.000
7A9VAL00.017-0.00411.6210.0120.0120.0000.0000.0000.000
8A10VAL0-0.0090.00713.600-0.022-0.0220.0000.0000.0000.000
9A11ILE0-0.012-0.00514.1590.0120.0120.0000.0000.0000.000
10A12ASP-1-0.752-0.84118.0130.1280.1280.0000.0000.0000.000
11A13LYS10.7280.86521.102-0.145-0.1450.0000.0000.0000.000
12A14PRO00.0480.01521.129-0.018-0.0180.0000.0000.0000.000
13A15ALA00.0690.02124.1940.0030.0030.0000.0000.0000.000
14A16GLY00.0280.02127.3220.0020.0020.0000.0000.0000.000
15A17MET0-0.071-0.01520.8330.0120.0120.0000.0000.0000.000
16A18THR00.054-0.00123.6430.0030.0030.0000.0000.0000.000
17A19SER00.0760.01421.4660.0200.0200.0000.0000.0000.000
18A20HIS0-0.064-0.03219.7080.0320.0320.0000.0000.0000.000
19A21ASP-1-0.787-0.87718.9310.2080.2080.0000.0000.0000.000
20A22VAL00.0240.02516.6090.0300.0300.0000.0000.0000.000
21A23VAL00.0170.01214.6960.0650.0650.0000.0000.0000.000
22A24GLY0-0.010-0.00514.0170.0680.0680.0000.0000.0000.000
23A25ARG10.9290.95614.149-0.233-0.2330.0000.0000.0000.000
24A26CYS00.0100.00811.3410.0520.0520.0000.0000.0000.000
25A27ARG10.8450.9299.593-0.121-0.1210.0000.0000.0000.000
26A28ARG10.9310.9649.062-0.196-0.1960.0000.0000.0000.000
27A29ILE00.0030.0138.3580.0110.0110.0000.0000.0000.000
28A30PHE0-0.005-0.0055.621-0.080-0.0800.0000.0000.0000.000
29A31ALA0-0.0240.0024.4110.8470.982-0.001-0.010-0.1230.000
30A32THR00.009-0.0245.447-0.520-0.5200.0000.0000.0000.000
31A33ARG10.9780.9797.287-0.129-0.1290.0000.0000.0000.000
32A34ARG10.8430.9499.120-0.216-0.2160.0000.0000.0000.000
33A35VAL00.0330.0259.5790.1070.1070.0000.0000.0000.000
34A36GLY00.001-0.00311.906-0.090-0.0900.0000.0000.0000.000
35A37HIS00.0460.01915.0810.0410.0410.0000.0000.0000.000
36A38ALA00.0150.01417.841-0.021-0.0210.0000.0000.0000.000
37A39GLY00.0550.03320.242-0.024-0.0240.0000.0000.0000.000
38A40THR0-0.037-0.02123.2000.0140.0140.0000.0000.0000.000
39A41LEU0-0.0230.00424.224-0.010-0.0100.0000.0000.0000.000
40A42ASP-1-0.775-0.87826.0360.1040.1040.0000.0000.0000.000
41A43PRO00.0260.00327.2780.0060.0060.0000.0000.0000.000
42A44MET00.0120.01928.3520.0070.0070.0000.0000.0000.000
43A45ALA0-0.0020.01328.748-0.003-0.0030.0000.0000.0000.000
44A46THR0-0.054-0.01926.2450.0090.0090.0000.0000.0000.000
45A47GLY00.0310.01924.848-0.010-0.0100.0000.0000.0000.000
46A48VAL0-0.0050.00221.8640.0210.0210.0000.0000.0000.000
47A49LEU0-0.0070.00519.275-0.013-0.0130.0000.0000.0000.000
48A50VAL00.0220.01917.1480.0290.0290.0000.0000.0000.000
49A51ILE0-0.002-0.01012.456-0.015-0.0150.0000.0000.0000.000
50A52GLY00.0150.01212.6320.0080.0080.0000.0000.0000.000
51A53ILE00.0230.0026.300-0.048-0.0480.0000.0000.0000.000
52A54GLU-1-0.738-0.8815.3070.1540.1540.0000.0000.0000.000
53A55ARG10.9110.9568.5560.0000.0000.0000.0000.0000.000
54A56ALA00.0580.04710.649-0.053-0.0530.0000.0000.0000.000
55A57THR0-0.042-0.05212.243-0.046-0.0460.0000.0000.0000.000
56A58LYS10.7920.88614.311-0.065-0.0650.0000.0000.0000.000
57A59ILE00.0480.02615.569-0.022-0.0220.0000.0000.0000.000
58A60LEU0-0.0220.01115.327-0.004-0.0040.0000.0000.0000.000
59A61GLY00.0140.00418.754-0.006-0.0060.0000.0000.0000.000
60A62LEU0-0.047-0.02721.270-0.010-0.0100.0000.0000.0000.000
61A63LEU0-0.008-0.00618.192-0.004-0.0040.0000.0000.0000.000
62A64THR0-0.036-0.02122.509-0.005-0.0050.0000.0000.0000.000
63A65ALA0-0.027-0.01324.541-0.003-0.0030.0000.0000.0000.000
64A66ALA0-0.0090.01625.615-0.007-0.0070.0000.0000.0000.000
65A67PRO00.0510.03527.5900.0040.0040.0000.0000.0000.000
66A68LYS10.7750.86826.816-0.090-0.0900.0000.0000.0000.000
67A69SER00.0430.01129.790-0.006-0.0060.0000.0000.0000.000
68A70TYR0-0.032-0.03529.5810.0130.0130.0000.0000.0000.000
69A71ALA00.0580.04932.541-0.006-0.0060.0000.0000.0000.000
70A72ALA0-0.027-0.03033.9570.0060.0060.0000.0000.0000.000
71A73THR0-0.017-0.00836.598-0.002-0.0020.0000.0000.0000.000
72A74ILE00.000-0.00439.3220.0020.0020.0000.0000.0000.000
73A75ARG10.8450.92342.246-0.050-0.0500.0000.0000.0000.000
74A76LEU00.012-0.00944.9140.0000.0000.0000.0000.0000.000
75A77GLY00.032-0.00548.328-0.001-0.0010.0000.0000.0000.000
76A78GLN0-0.002-0.00947.5530.0010.0010.0000.0000.0000.000
77A79THR00.0540.04946.7000.0020.0020.0000.0000.0000.000
78A80THR00.003-0.02042.207-0.002-0.0020.0000.0000.0000.000
79A81SER00.009-0.00742.6830.0000.0000.0000.0000.0000.000
80A82THR0-0.036-0.03838.700-0.002-0.0020.0000.0000.0000.000
81A83GLU-1-0.847-0.90739.5870.0560.0560.0000.0000.0000.000
82A84ASP-1-0.783-0.87036.3500.0750.0750.0000.0000.0000.000
83A85ALA00.0250.00938.197-0.003-0.0030.0000.0000.0000.000
84A86GLU-1-0.963-0.95834.6050.0800.0800.0000.0000.0000.000
85A87GLY0-0.057-0.00938.531-0.001-0.0010.0000.0000.0000.000
86A88GLN0-0.013-0.01241.672-0.002-0.0020.0000.0000.0000.000
87A89VAL00.016-0.00845.2750.0000.0000.0000.0000.0000.000
88A90LEU0-0.056-0.02047.287-0.001-0.0010.0000.0000.0000.000
89A91GLN0-0.054-0.02449.994-0.003-0.0030.0000.0000.0000.000
90A92SER00.026-0.00451.0640.0020.0020.0000.0000.0000.000
91A93VAL0-0.0230.01053.247-0.002-0.0020.0000.0000.0000.000
92A94PRO0-0.037-0.02854.1620.0010.0010.0000.0000.0000.000
93A95ALA00.0790.03252.3110.0000.0000.0000.0000.0000.000
94A96LYS10.8310.91254.306-0.026-0.0260.0000.0000.0000.000
95A97HIS00.0540.02556.135-0.001-0.0010.0000.0000.0000.000
96A98LEU0-0.0110.01352.497-0.001-0.0010.0000.0000.0000.000
97A99THR00.0140.00355.1710.0000.0000.0000.0000.0000.000
98A100ILE00.0440.00149.9330.0010.0010.0000.0000.0000.000
99A101GLU-1-0.907-0.94651.9590.0250.0250.0000.0000.0000.000
100A102ALA0-0.028-0.01153.7690.0000.0000.0000.0000.0000.000
101A103ILE0-0.015-0.01548.2790.0010.0010.0000.0000.0000.000
102A104ASP-1-0.877-0.94548.0080.0360.0360.0000.0000.0000.000
103A105ALA00.0030.01049.2580.0010.0010.0000.0000.0000.000
104A106ALA0-0.037-0.01950.3570.0000.0000.0000.0000.0000.000
105A107MET0-0.033-0.01743.6420.0010.0010.0000.0000.0000.000
106A108GLU-1-0.834-0.90246.1660.0360.0360.0000.0000.0000.000
107A109ARG10.8690.93447.689-0.029-0.0290.0000.0000.0000.000
108A110LEU0-0.012-0.00444.9350.0000.0000.0000.0000.0000.000
109A111ARG10.8240.92842.863-0.036-0.0360.0000.0000.0000.000
110A112GLY0-0.021-0.00842.893-0.002-0.0020.0000.0000.0000.000
111A113GLU-1-1.021-1.02141.8370.0390.0390.0000.0000.0000.000
112A114ILE00.0250.01041.015-0.001-0.0010.0000.0000.0000.000
113A143DLE0-0.003-0.00334.9190.0010.0010.0000.0000.0000.000
114A144GLU-1-0.961-0.98837.8250.0380.0380.0000.0000.0000.000
115A145ALA0-0.034-0.01338.2830.0030.0030.0000.0000.0000.000
116A146ARG10.9030.95331.801-0.072-0.0720.0000.0000.0000.000
117A147PRO00.0620.02437.8680.0010.0010.0000.0000.0000.000
118A148ILE0-0.082-0.03035.0780.0040.0040.0000.0000.0000.000
119A149ARG10.8930.93737.137-0.044-0.0440.0000.0000.0000.000
120A150ILE0-0.0010.00937.3920.0050.0050.0000.0000.0000.000
121A151ASP-1-0.850-0.92537.0840.0470.0470.0000.0000.0000.000
122A152ARG10.6990.79136.909-0.056-0.0560.0000.0000.0000.000
123A153PHE00.027-0.00239.4480.0040.0040.0000.0000.0000.000
124A154GLU-1-0.808-0.86640.9490.0410.0410.0000.0000.0000.000
125A155LEU00.0300.00441.8320.0030.0030.0000.0000.0000.000
126A156LEU0-0.037-0.01138.128-0.001-0.0010.0000.0000.0000.000
127A157ALA0-0.016-0.01342.738-0.002-0.0020.0000.0000.0000.000
128A158ALA00.0410.01644.5830.0010.0010.0000.0000.0000.000
129A159ARG10.7580.86441.610-0.051-0.0510.0000.0000.0000.000
130A160ARG10.9400.97047.870-0.029-0.0290.0000.0000.0000.000
131A161ARG10.8530.92045.755-0.039-0.0390.0000.0000.0000.000
132A162ASP-1-0.805-0.89649.9940.0310.0310.0000.0000.0000.000
133A163GLN0-0.014-0.00853.553-0.001-0.0010.0000.0000.0000.000
134A164LEU00.0050.02048.7110.0000.0000.0000.0000.0000.000
135A165ILE0-0.017-0.00648.384-0.001-0.0010.0000.0000.0000.000
136A166ASP-1-0.802-0.85943.7600.0490.0490.0000.0000.0000.000
137A167ILE00.004-0.01343.616-0.002-0.0020.0000.0000.0000.000
138A168ASP-1-0.811-0.87039.5410.0560.0560.0000.0000.0000.000
139A169VAL00.0340.00339.032-0.003-0.0030.0000.0000.0000.000
140A170GLU-1-0.831-0.90635.6720.0640.0640.0000.0000.0000.000
141A171ILE0-0.043-0.01836.075-0.003-0.0030.0000.0000.0000.000
142A172ASP-1-0.796-0.85034.5090.0680.0680.0000.0000.0000.000
143A173CYS0-0.021-0.00933.790-0.002-0.0020.0000.0000.0000.000
144A174SER00.0700.03732.7800.0050.0050.0000.0000.0000.000
145A175SER0-0.026-0.02930.6750.0070.0070.0000.0000.0000.000
146A176GLY00.1220.04731.034-0.004-0.0040.0000.0000.0000.000
147A177THR0-0.111-0.06031.9430.0020.0020.0000.0000.0000.000
148A178TYR00.0390.01333.1840.0000.0000.0000.0000.0000.000
149A179ILE00.0470.04133.525-0.003-0.0030.0000.0000.0000.000
150A180ARG10.7630.84933.337-0.082-0.0820.0000.0000.0000.000
151A181ALA00.0280.01538.888-0.003-0.0030.0000.0000.0000.000
152A182LEU00.0320.03239.609-0.002-0.0020.0000.0000.0000.000
153A183ALA0-0.007-0.01140.951-0.003-0.0030.0000.0000.0000.000
154A184ARG10.7890.87142.740-0.049-0.0490.0000.0000.0000.000
155A185ASP-1-0.824-0.90044.7400.0410.0410.0000.0000.0000.000
156A186LEU0-0.018-0.00545.206-0.002-0.0020.0000.0000.0000.000
157A187GLY0-0.005-0.01346.980-0.002-0.0020.0000.0000.0000.000
158A188ASP-1-0.916-0.96848.8690.0360.0360.0000.0000.0000.000
159A189ALA0-0.065-0.02450.229-0.002-0.0020.0000.0000.0000.000
160A190LEU0-0.057-0.02949.708-0.002-0.0020.0000.0000.0000.000
161A191GLY0-0.0120.00653.262-0.001-0.0010.0000.0000.0000.000
162A192VAL0-0.097-0.05550.991-0.001-0.0010.0000.0000.0000.000
163A193GLY00.0420.03349.7630.0010.0010.0000.0000.0000.000
164A194GLY00.035-0.00846.2780.0000.0000.0000.0000.0000.000
165A195HIS0-0.094-0.03941.6330.0020.0020.0000.0000.0000.000
166A196VAL00.0130.01036.500-0.001-0.0010.0000.0000.0000.000
167A197THR0-0.013-0.02538.7620.0020.0020.0000.0000.0000.000
168A198ALA00.0120.01334.7910.0030.0030.0000.0000.0000.000
169A199LEU00.0050.00731.849-0.003-0.0030.0000.0000.0000.000
170A200ARG10.8480.88325.411-0.117-0.1170.0000.0000.0000.000
171A201ARG10.7870.89723.670-0.149-0.1490.0000.0000.0000.000
172A202THR00.049-0.00126.9950.0120.0120.0000.0000.0000.000
173A203ARG10.8870.93926.548-0.076-0.0760.0000.0000.0000.000
174A204VAL0-0.041-0.01823.332-0.001-0.0010.0000.0000.0000.000
175A205GLY00.0180.00424.1600.0070.0070.0000.0000.0000.000
176A206ARG10.8780.94623.241-0.065-0.0650.0000.0000.0000.000
177A207PHE0-0.032-0.00619.2600.0030.0030.0000.0000.0000.000
178A208GLU-1-0.787-0.89523.0440.0810.0810.0000.0000.0000.000
179A209LEU0-0.006-0.02222.9630.0140.0140.0000.0000.0000.000
180A210ASP-1-0.865-0.90422.9140.1120.1120.0000.0000.0000.000
181A211GLN0-0.049-0.03319.4440.0090.0090.0000.0000.0000.000
182A212ALA0-0.082-0.04118.2740.0330.0330.0000.0000.0000.000
183A213ARG10.8830.93911.647-0.385-0.3850.0000.0000.0000.000
184A214SER00.022-0.01117.7160.0190.0190.0000.0000.0000.000
185A215LEU0-0.013-0.03914.8630.0320.0320.0000.0000.0000.000
186A216ASP-1-0.859-0.90814.8930.2540.2540.0000.0000.0000.000
187A217ASP-1-0.790-0.87815.4140.2450.2450.0000.0000.0000.000
188A218LEU0-0.043-0.02810.7000.0250.0250.0000.0000.0000.000
189A219ALA0-0.060-0.04310.5660.1050.1050.0000.0000.0000.000
190A220GLU-1-0.969-0.96211.1710.1760.1760.0000.0000.0000.000
191A221ARG10.8270.9039.792-0.224-0.2240.0000.0000.0000.000
192A222PRO0-0.0110.0065.7180.0490.0490.0000.0000.0000.000
193A223ALA00.0370.0126.5350.0030.0030.0000.0000.0000.000
194A224LEU0-0.038-0.0047.0700.0440.0440.0000.0000.0000.000
195A225SER0-0.0200.00310.014-0.092-0.0920.0000.0000.0000.000
196A226LEU00.0300.01913.149-0.063-0.0630.0000.0000.0000.000
197A227SER00.016-0.02110.5670.0880.0880.0000.0000.0000.000
198A228LEU0-0.036-0.03510.8910.0080.0080.0000.0000.0000.000
199A229ASP-1-0.811-0.90812.793-0.112-0.1120.0000.0000.0000.000
200A230GLU-1-0.789-0.86213.7490.0220.0220.0000.0000.0000.000
201A231ALA0-0.019-0.00615.4100.0030.0030.0000.0000.0000.000
202A232CYS0-0.064-0.04316.374-0.002-0.0020.0000.0000.0000.000
203A233LEU00.012-0.00418.902-0.004-0.0040.0000.0000.0000.000
204A234LEU0-0.0140.02120.129-0.002-0.0020.0000.0000.0000.000
205A235MET0-0.089-0.04720.3550.0060.0060.0000.0000.0000.000
206A236PHE0-0.037-0.02020.2100.0010.0010.0000.0000.0000.000
207A237ALA00.0860.05824.789-0.004-0.0040.0000.0000.0000.000
208A238ARG10.8680.89122.1190.0370.0370.0000.0000.0000.000
209A239ARG10.8210.90125.7720.0130.0130.0000.0000.0000.000
210A240ASP-1-0.826-0.87825.537-0.038-0.0380.0000.0000.0000.000
211A241LEU0-0.061-0.02324.6290.0040.0040.0000.0000.0000.000
212A242THR00.019-0.01826.912-0.006-0.0060.0000.0000.0000.000
213A243ALA00.0490.00526.3640.0000.0000.0000.0000.0000.000
214A244ALA00.0140.00926.957-0.002-0.0020.0000.0000.0000.000
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