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: 761RK

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 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 262
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3009468.627057
FMO2-HF: Nuclear repulsion 2911243.863489
FMO2-HF: Total energy -98224.763569
FMO2-MP2: Total energy -98510.921667


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.
-2.1670.070.01-1.027-1.2210.003
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 : 0.025 / q_NPA : -0.001
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].
3A5GLY0-0.0060.0152.984-3.079-1.0140.012-1.009-1.0680.003
4A6PRO0-0.033-0.0364.8550.7970.831-0.001-0.005-0.0280.000
5A7GLY00.0560.0147.764-0.137-0.1370.0000.0000.0000.000
6A8ILE0-0.023-0.00510.3740.0800.0800.0000.0000.0000.000
7A9VAL00.0320.00311.5520.0100.0100.0000.0000.0000.000
8A10VAL0-0.0140.00413.606-0.025-0.0250.0000.0000.0000.000
9A11ILE0-0.010-0.00814.3310.0100.0100.0000.0000.0000.000
10A12ASP-1-0.770-0.86918.0770.1300.1300.0000.0000.0000.000
11A13LYS10.7330.86121.166-0.147-0.1470.0000.0000.0000.000
12A14PRO00.0500.01721.187-0.018-0.0180.0000.0000.0000.000
13A15ALA00.0680.02124.2630.0030.0030.0000.0000.0000.000
14A16GLY00.0260.02127.3950.0010.0010.0000.0000.0000.000
15A17MET0-0.055-0.00720.7570.0100.0100.0000.0000.0000.000
16A18THR00.0810.04123.6240.0060.0060.0000.0000.0000.000
17A19SER00.0740.01521.4740.0190.0190.0000.0000.0000.000
18A20HIS0-0.041-0.01919.7620.0340.0340.0000.0000.0000.000
19A21ASP-1-0.826-0.92218.8680.2030.2030.0000.0000.0000.000
20A22VAL0-0.0050.01116.7010.0270.0270.0000.0000.0000.000
21A23VAL00.0060.00214.7240.0620.0620.0000.0000.0000.000
22A24GLY0-0.012-0.00613.9500.0650.0650.0000.0000.0000.000
23A25ARG10.9520.96314.074-0.220-0.2200.0000.0000.0000.000
24A26CYS00.0150.01511.2690.0480.0480.0000.0000.0000.000
25A27ARG10.8660.9379.507-0.116-0.1160.0000.0000.0000.000
26A28ARG10.9290.9629.000-0.175-0.1750.0000.0000.0000.000
27A29ILE00.0130.0188.389-0.012-0.0120.0000.0000.0000.000
28A30PHE0-0.014-0.0095.462-0.117-0.1170.0000.0000.0000.000
29A31ALA0-0.0230.0054.2910.7230.861-0.001-0.013-0.1250.000
30A32THR00.006-0.0065.441-0.532-0.5320.0000.0000.0000.000
31A33ARG10.9990.9797.281-0.126-0.1260.0000.0000.0000.000
32A34ARG10.8530.9619.185-0.241-0.2410.0000.0000.0000.000
33A35VAL00.0430.0299.6480.1260.1260.0000.0000.0000.000
34A36GLY0-0.017-0.01011.955-0.093-0.0930.0000.0000.0000.000
35A37HIS00.0480.02215.1570.0460.0460.0000.0000.0000.000
36A38ALA00.0050.01017.918-0.022-0.0220.0000.0000.0000.000
37A39GLY00.0310.00720.329-0.024-0.0240.0000.0000.0000.000
38A40THR0-0.047-0.02923.2850.0140.0140.0000.0000.0000.000
39A41LEU0-0.0140.00224.347-0.009-0.0090.0000.0000.0000.000
40A42ASP-1-0.783-0.88026.1170.1030.1030.0000.0000.0000.000
41A43PRO00.0250.00527.2690.0060.0060.0000.0000.0000.000
42A44MET00.0190.02128.3430.0060.0060.0000.0000.0000.000
43A45ALA0-0.0090.01128.732-0.003-0.0030.0000.0000.0000.000
44A46THR0-0.054-0.02026.3140.0080.0080.0000.0000.0000.000
45A47GLY00.0260.01924.922-0.009-0.0090.0000.0000.0000.000
46A48VAL0-0.0030.00321.7760.0210.0210.0000.0000.0000.000
47A49LEU0-0.0030.00519.351-0.013-0.0130.0000.0000.0000.000
48A50VAL00.0200.01917.3150.0290.0290.0000.0000.0000.000
49A51ILE0-0.001-0.00912.439-0.018-0.0180.0000.0000.0000.000
50A52GLY00.0050.00712.7330.0140.0140.0000.0000.0000.000
51A53ILE00.0350.0086.273-0.064-0.0640.0000.0000.0000.000
52A54GLU-1-0.781-0.9165.2280.3870.3870.0000.0000.0000.000
53A55ARG10.8950.9408.609-0.082-0.0820.0000.0000.0000.000
54A56ALA00.0610.05010.731-0.065-0.0650.0000.0000.0000.000
55A57THR0-0.050-0.05112.141-0.058-0.0580.0000.0000.0000.000
56A58LYS10.8100.89914.380-0.098-0.0980.0000.0000.0000.000
57A59ILE00.0540.03015.704-0.025-0.0250.0000.0000.0000.000
58A60LEU0-0.0250.00915.494-0.006-0.0060.0000.0000.0000.000
59A61GLY00.0120.00418.839-0.009-0.0090.0000.0000.0000.000
60A62LEU0-0.047-0.02521.113-0.012-0.0120.0000.0000.0000.000
61A63LEU0-0.007-0.00718.352-0.004-0.0040.0000.0000.0000.000
62A64THR0-0.0270.00422.608-0.007-0.0070.0000.0000.0000.000
63A65ALA0-0.012-0.00724.633-0.004-0.0040.0000.0000.0000.000
64A66ALA0-0.0080.01625.754-0.008-0.0080.0000.0000.0000.000
65A67PRO00.0520.04227.6940.0030.0030.0000.0000.0000.000
66A68LYS10.7810.87126.766-0.099-0.0990.0000.0000.0000.000
67A69SER00.0280.00829.900-0.007-0.0070.0000.0000.0000.000
68A70TYR0-0.029-0.03329.3640.0130.0130.0000.0000.0000.000
69A71ALA00.0610.05132.593-0.006-0.0060.0000.0000.0000.000
70A72ALA0-0.028-0.03034.0210.0050.0050.0000.0000.0000.000
71A73THR0-0.017-0.00436.663-0.002-0.0020.0000.0000.0000.000
72A74ILE0-0.011-0.00839.3870.0020.0020.0000.0000.0000.000
73A75ARG10.8760.95042.289-0.049-0.0490.0000.0000.0000.000
74A76LEU00.004-0.01344.9830.0000.0000.0000.0000.0000.000
75A77GLY00.026-0.00548.357-0.001-0.0010.0000.0000.0000.000
76A78GLN0-0.001-0.00947.4340.0010.0010.0000.0000.0000.000
77A79THR00.0440.04146.7100.0020.0020.0000.0000.0000.000
78A80THR00.005-0.01942.178-0.001-0.0010.0000.0000.0000.000
79A81SER00.014-0.00542.5690.0000.0000.0000.0000.0000.000
80A82THR0-0.049-0.04638.632-0.002-0.0020.0000.0000.0000.000
81A83GLU-1-0.865-0.92939.5870.0560.0560.0000.0000.0000.000
82A84ASP-1-0.783-0.86736.5410.0740.0740.0000.0000.0000.000
83A85ALA00.0210.00438.340-0.003-0.0030.0000.0000.0000.000
84A86GLU-1-0.961-0.95734.6870.0760.0760.0000.0000.0000.000
85A87GLY0-0.058-0.00938.441-0.001-0.0010.0000.0000.0000.000
86A88GLN0-0.022-0.01941.582-0.003-0.0030.0000.0000.0000.000
87A89VAL00.016-0.00545.1830.0000.0000.0000.0000.0000.000
88A90LEU0-0.073-0.03247.232-0.001-0.0010.0000.0000.0000.000
89A91GLN0-0.024-0.00449.949-0.003-0.0030.0000.0000.0000.000
90A92SER00.024-0.00451.0640.0020.0020.0000.0000.0000.000
91A93VAL0-0.0350.00553.247-0.002-0.0020.0000.0000.0000.000
92A94PRO0-0.037-0.03054.2070.0010.0010.0000.0000.0000.000
93A95ALA00.0820.03452.3850.0000.0000.0000.0000.0000.000
94A96LYS10.8200.90054.374-0.026-0.0260.0000.0000.0000.000
95A97HIS00.0390.01556.199-0.001-0.0010.0000.0000.0000.000
96A98LEU0-0.0130.01152.387-0.001-0.0010.0000.0000.0000.000
97A99THR00.0140.00355.2330.0000.0000.0000.0000.0000.000
98A100ILE00.0450.00549.7670.0010.0010.0000.0000.0000.000
99A101GLU-1-0.903-0.95252.0150.0260.0260.0000.0000.0000.000
100A102ALA0-0.026-0.00553.7740.0000.0000.0000.0000.0000.000
101A103ILE0-0.018-0.01548.2790.0010.0010.0000.0000.0000.000
102A104ASP-1-0.873-0.94848.0920.0380.0380.0000.0000.0000.000
103A105ALA0-0.0060.01049.3120.0010.0010.0000.0000.0000.000
104A106ALA0-0.036-0.01850.3810.0000.0000.0000.0000.0000.000
105A107MET0-0.047-0.02443.6220.0010.0010.0000.0000.0000.000
106A108GLU-1-0.923-0.96546.2690.0370.0370.0000.0000.0000.000
107A109ARG10.8990.94847.793-0.030-0.0300.0000.0000.0000.000
108A110LEU0-0.015-0.00344.9790.0000.0000.0000.0000.0000.000
109A111ARG10.8860.98343.201-0.040-0.0400.0000.0000.0000.000
110A112GLY0-0.020-0.00842.992-0.002-0.0020.0000.0000.0000.000
111A113GLU-1-1.016-1.01941.9300.0430.0430.0000.0000.0000.000
112A114ILE00.0340.01441.039-0.001-0.0010.0000.0000.0000.000
113A143DLE0-0.006-0.00535.0350.0010.0010.0000.0000.0000.000
114A144GLU-1-0.961-0.98937.8990.0420.0420.0000.0000.0000.000
115A145ALA0-0.025-0.00738.3500.0030.0030.0000.0000.0000.000
116A146ARG10.9320.96731.584-0.077-0.0770.0000.0000.0000.000
117A147PRO00.0680.03137.7060.0000.0000.0000.0000.0000.000
118A148ILE0-0.092-0.03635.0960.0050.0050.0000.0000.0000.000
119A149ARG10.9680.99237.223-0.049-0.0490.0000.0000.0000.000
120A150ILE0-0.0060.00837.4910.0050.0050.0000.0000.0000.000
121A151ASP-1-0.920-0.98137.2960.0510.0510.0000.0000.0000.000
122A152ARG10.7460.84836.288-0.060-0.0600.0000.0000.0000.000
123A153PHE00.032-0.00739.5540.0040.0040.0000.0000.0000.000
124A154GLU-1-0.862-0.92640.9820.0440.0440.0000.0000.0000.000
125A155LEU00.0280.00341.8500.0030.0030.0000.0000.0000.000
126A156LEU0-0.040-0.00638.062-0.001-0.0010.0000.0000.0000.000
127A157ALA0-0.010-0.01042.791-0.002-0.0020.0000.0000.0000.000
128A158ALA00.0430.01744.6370.0010.0010.0000.0000.0000.000
129A159ARG10.8280.91341.358-0.051-0.0510.0000.0000.0000.000
130A160ARG10.9540.98547.927-0.029-0.0290.0000.0000.0000.000
131A161ARG10.8850.93145.922-0.039-0.0390.0000.0000.0000.000
132A162ASP-1-0.839-0.90750.0550.0300.0300.0000.0000.0000.000
133A163GLN00.0050.00153.615-0.001-0.0010.0000.0000.0000.000
134A164LEU00.0190.02448.3510.0000.0000.0000.0000.0000.000
135A165ILE0-0.016-0.00548.354-0.001-0.0010.0000.0000.0000.000
136A166ASP-1-0.848-0.90643.7940.0480.0480.0000.0000.0000.000
137A167ILE0-0.004-0.01543.605-0.002-0.0020.0000.0000.0000.000
138A168ASP-1-0.822-0.88439.6360.0580.0580.0000.0000.0000.000
139A169VAL00.015-0.00538.956-0.003-0.0030.0000.0000.0000.000
140A170GLU-1-0.847-0.92236.1350.0660.0660.0000.0000.0000.000
141A171ILE0-0.033-0.02136.061-0.003-0.0030.0000.0000.0000.000
142A172ASP-1-0.782-0.84534.6680.0710.0710.0000.0000.0000.000
143A173CYS0-0.007-0.00833.981-0.002-0.0020.0000.0000.0000.000
144A174SER00.0560.03532.8880.0050.0050.0000.0000.0000.000
145A175SER0-0.043-0.04331.2080.0100.0100.0000.0000.0000.000
146A176GLY00.1060.03731.125-0.005-0.0050.0000.0000.0000.000
147A177THR0-0.107-0.05531.8350.0020.0020.0000.0000.0000.000
148A178TYR00.0170.00533.2650.0000.0000.0000.0000.0000.000
149A179ILE00.0400.03433.798-0.004-0.0040.0000.0000.0000.000
150A180ARG10.7700.84633.292-0.083-0.0830.0000.0000.0000.000
151A181ALA00.0260.01638.949-0.003-0.0030.0000.0000.0000.000
152A182LEU00.0370.03739.761-0.002-0.0020.0000.0000.0000.000
153A183ALA0-0.007-0.01340.997-0.003-0.0030.0000.0000.0000.000
154A184ARG10.8690.94242.773-0.050-0.0500.0000.0000.0000.000
155A185ASP-1-0.859-0.93544.8310.0430.0430.0000.0000.0000.000
156A186LEU0-0.029-0.01345.206-0.002-0.0020.0000.0000.0000.000
157A187GLY0-0.007-0.01547.011-0.002-0.0020.0000.0000.0000.000
158A188ASP-1-0.927-0.96748.8780.0370.0370.0000.0000.0000.000
159A189ALA0-0.066-0.02750.315-0.002-0.0020.0000.0000.0000.000
160A190LEU0-0.061-0.03349.757-0.002-0.0020.0000.0000.0000.000
161A191GLY0-0.0120.00753.284-0.001-0.0010.0000.0000.0000.000
162A192VAL0-0.094-0.05050.859-0.001-0.0010.0000.0000.0000.000
163A193GLY00.0370.02649.7630.0000.0000.0000.0000.0000.000
164A194GLY00.040-0.00546.2790.0000.0000.0000.0000.0000.000
165A195HIS0-0.097-0.03441.5360.0020.0020.0000.0000.0000.000
166A196VAL00.0130.01436.431-0.001-0.0010.0000.0000.0000.000
167A197THR0-0.018-0.02738.8210.0020.0020.0000.0000.0000.000
168A198ALA00.0140.01334.8140.0030.0030.0000.0000.0000.000
169A199LEU00.0100.01031.886-0.002-0.0020.0000.0000.0000.000
170A200ARG10.8600.90725.454-0.117-0.1170.0000.0000.0000.000
171A201ARG10.8130.91123.869-0.154-0.1540.0000.0000.0000.000
172A202THR00.038-0.00427.0370.0120.0120.0000.0000.0000.000
173A203ARG10.9600.98126.578-0.084-0.0840.0000.0000.0000.000
174A204VAL0-0.034-0.01623.398-0.002-0.0020.0000.0000.0000.000
175A205GLY00.0100.00224.2730.0080.0080.0000.0000.0000.000
176A206ARG10.8950.95423.329-0.082-0.0820.0000.0000.0000.000
177A207PHE0-0.043-0.01219.1950.0040.0040.0000.0000.0000.000
178A208GLU-1-0.859-0.94523.1430.0880.0880.0000.0000.0000.000
179A209LEU0-0.010-0.02323.0090.0150.0150.0000.0000.0000.000
180A210ASP-1-0.857-0.90222.9560.1190.1190.0000.0000.0000.000
181A211GLN0-0.034-0.02019.3990.0120.0120.0000.0000.0000.000
182A212ALA0-0.079-0.04218.3150.0350.0350.0000.0000.0000.000
183A213ARG10.9110.94111.642-0.413-0.4130.0000.0000.0000.000
184A214SER00.0410.01817.7630.0260.0260.0000.0000.0000.000
185A215LEU0-0.010-0.04015.2250.0310.0310.0000.0000.0000.000
186A216ASP-1-0.894-0.94514.9520.2270.2270.0000.0000.0000.000
187A217ASP-1-0.876-0.92315.4550.2100.2100.0000.0000.0000.000
188A218LEU0-0.077-0.04210.8280.0300.0300.0000.0000.0000.000
189A219ALA0-0.066-0.04610.6120.0980.0980.0000.0000.0000.000
190A220GLU-1-0.955-0.95111.2070.1540.1540.0000.0000.0000.000
191A221ARG10.9220.9599.818-0.182-0.1820.0000.0000.0000.000
192A222PRO0-0.0040.0125.7190.0590.0590.0000.0000.0000.000
193A223ALA00.0290.0056.5550.0030.0030.0000.0000.0000.000
194A224LEU0-0.046-0.0077.1550.0340.0340.0000.0000.0000.000
195A225SER0-0.0300.00410.053-0.100-0.1000.0000.0000.0000.000
196A226LEU00.0460.02613.238-0.064-0.0640.0000.0000.0000.000
197A227SER00.0380.03010.6660.1020.1020.0000.0000.0000.000
198A228LEU0-0.022-0.03110.998-0.003-0.0030.0000.0000.0000.000
199A229ASP-1-0.821-0.91412.897-0.057-0.0570.0000.0000.0000.000
200A230GLU-1-0.857-0.93514.1890.0650.0650.0000.0000.0000.000
201A231ALA0-0.015-0.00515.522-0.003-0.0030.0000.0000.0000.000
202A232CYS0-0.065-0.03816.554-0.007-0.0070.0000.0000.0000.000
203A233LEU00.013-0.00419.040-0.007-0.0070.0000.0000.0000.000
204A234LEU0-0.0100.02120.241-0.004-0.0040.0000.0000.0000.000
205A235MET0-0.091-0.05120.6510.0040.0040.0000.0000.0000.000
206A236PHE0-0.035-0.01520.459-0.001-0.0010.0000.0000.0000.000
207A237ALA00.0850.05824.893-0.004-0.0040.0000.0000.0000.000
208A238ARG10.8920.92022.8370.0180.0180.0000.0000.0000.000
209A239ARG10.8480.93025.859-0.001-0.0010.0000.0000.0000.000
210A240ASP-1-0.826-0.89525.839-0.019-0.0190.0000.0000.0000.000
211A241LEU0-0.050-0.02724.4380.0030.0030.0000.0000.0000.000
212A242THR00.0350.01626.968-0.005-0.0050.0000.0000.0000.000
213A243ALA00.0350.00126.3460.0000.0000.0000.0000.0000.000
214A244ALA00.0230.01526.988-0.001-0.0010.0000.0000.0000.000
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