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: R8NN8

Calculation Name: 1SGM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SGM

Chain ID: A

ChEMBL ID:

UniProt ID: P42105

Base Structure: X-ray

Registration Date: 2023-09-20

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1885790.91477
FMO2-HF: Nuclear repulsion 1814832.788845
FMO2-HF: Total energy -70958.125925
FMO2-MP2: Total energy -71165.145357


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:5:GLY)


Summations of interaction energy for fragment #1(A:5:GLY)
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.
-1.5210.5840.018-0.89-1.2340.002
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.002
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].
3A7SER00.007-0.0103.3560.2841.7450.003-0.663-0.8010.001
4A8ARG10.7890.8944.285-0.399-0.149-0.001-0.053-0.1960.000
5A9GLU-1-0.792-0.8685.852-0.445-0.4450.0000.0000.0000.000
6A10LYS10.8620.9127.6901.1591.1590.0000.0000.0000.000
7A11ILE0-0.054-0.0297.9820.0910.0910.0000.0000.0000.000
8A12LEU00.0200.02010.0420.0040.0040.0000.0000.0000.000
9A13HIS00.0330.04211.6740.0470.0470.0000.0000.0000.000
10A14THR00.0330.02213.5760.0310.0310.0000.0000.0000.000
11A15ALA00.000-0.00514.6520.0110.0110.0000.0000.0000.000
12A16SER0-0.003-0.00215.2300.0080.0080.0000.0000.0000.000
13A17ARG10.8260.89617.5160.0350.0350.0000.0000.0000.000
14A18LEU0-0.042-0.01918.9770.0050.0050.0000.0000.0000.000
15A19SER0-0.015-0.02219.7220.0070.0070.0000.0000.0000.000
16A20GLN00.0200.02021.529-0.001-0.0010.0000.0000.0000.000
17A21LEU0-0.046-0.01323.739-0.002-0.0020.0000.0000.0000.000
18A22GLN0-0.049-0.03823.701-0.001-0.0010.0000.0000.0000.000
19A23GLY00.0720.05125.5170.0030.0030.0000.0000.0000.000
20A24TYR0-0.053-0.03621.8280.0130.0130.0000.0000.0000.000
21A25HIS0-0.019-0.01624.5800.0140.0140.0000.0000.0000.000
22A26ALA00.0040.00026.7100.0080.0080.0000.0000.0000.000
23A27THR00.0220.01920.4840.0030.0030.0000.0000.0000.000
24A28GLY00.0210.01422.5020.0110.0110.0000.0000.0000.000
25A29LEU00.028-0.00817.6560.0000.0000.0000.0000.0000.000
26A30ASN00.004-0.00917.6810.0300.0300.0000.0000.0000.000
27A31GLN00.0030.01019.0300.0100.0100.0000.0000.0000.000
28A32ILE00.0600.03114.366-0.007-0.0070.0000.0000.0000.000
29A33VAL0-0.045-0.01213.6800.0040.0040.0000.0000.0000.000
30A34LYS10.8510.93014.759-0.058-0.0580.0000.0000.0000.000
31A35GLU-1-0.802-0.89516.9630.0010.0010.0000.0000.0000.000
32A36SER0-0.025-0.01211.611-0.007-0.0070.0000.0000.0000.000
33A37GLY00.0020.01011.939-0.066-0.0660.0000.0000.0000.000
34A38ALA0-0.0050.0078.4580.0210.0210.0000.0000.0000.000
35A39PRO00.0300.0107.716-0.001-0.0010.0000.0000.0000.000
36A40LYS10.9620.9749.752-0.199-0.1990.0000.0000.0000.000
37A41GLY00.0290.0018.223-0.055-0.0550.0000.0000.0000.000
38A42SER0-0.0050.0039.2850.1050.1050.0000.0000.0000.000
39A43LEU00.014-0.00711.6950.0140.0140.0000.0000.0000.000
40A44TYR0-0.055-0.0185.998-0.185-0.1850.0000.0000.0000.000
41A45HIS00.017-0.0033.636-1.862-1.4680.016-0.174-0.2370.001
42A46PHE00.0220.0138.418-0.190-0.1900.0000.0000.0000.000
43A47PHE00.0300.02611.0310.0280.0280.0000.0000.0000.000
44A48PRO00.001-0.03314.206-0.052-0.0520.0000.0000.0000.000
45A49ASN0-0.042-0.00317.435-0.037-0.0370.0000.0000.0000.000
46A50GLY0-0.0090.00616.922-0.024-0.0240.0000.0000.0000.000
47A51LYS10.8150.89117.385-0.093-0.0930.0000.0000.0000.000
48A52GLU-1-0.798-0.87019.3730.0770.0770.0000.0000.0000.000
49A53GLU-1-0.814-0.90614.0990.2950.2950.0000.0000.0000.000
50A54LEU0-0.012-0.01212.851-0.015-0.0150.0000.0000.0000.000
51A55ALA00.0250.01615.520-0.034-0.0340.0000.0000.0000.000
52A56ILE00.0070.00617.527-0.025-0.0250.0000.0000.0000.000
53A57GLU-1-0.817-0.88311.6690.0280.0280.0000.0000.0000.000
54A58ALA00.0230.00415.273-0.041-0.0410.0000.0000.0000.000
55A59VAL00.0100.01516.450-0.027-0.0270.0000.0000.0000.000
56A60THR0-0.002-0.01416.521-0.016-0.0160.0000.0000.0000.000
57A61TYR0-0.145-0.11311.8060.0200.0200.0000.0000.0000.000
58A62THR00.015-0.01115.962-0.023-0.0230.0000.0000.0000.000
59A63GLY00.016-0.00319.193-0.004-0.0040.0000.0000.0000.000
60A64LYS10.9460.98413.6240.1530.1530.0000.0000.0000.000
61A65ILE0-0.0040.00915.913-0.005-0.0050.0000.0000.0000.000
62A66VAL00.001-0.00419.7820.0000.0000.0000.0000.0000.000
63A67GLU-1-0.821-0.89622.705-0.068-0.0680.0000.0000.0000.000
64A68HIS0-0.001-0.00317.9670.0110.0110.0000.0000.0000.000
65A69LEU00.0050.00022.7680.0020.0020.0000.0000.0000.000
66A70ILE0-0.0120.02125.4660.0060.0060.0000.0000.0000.000
67A71GLN00.021-0.00226.0140.0060.0060.0000.0000.0000.000
68A72GLN00.013-0.00525.9620.0030.0030.0000.0000.0000.000
69A73SER0-0.040-0.03927.9880.0030.0030.0000.0000.0000.000
70A74MET0-0.065-0.01930.8680.0070.0070.0000.0000.0000.000
71A75ASP-1-0.846-0.91528.716-0.078-0.0780.0000.0000.0000.000
72A76GLU-1-0.881-0.90631.610-0.072-0.0720.0000.0000.0000.000
73A77SER0-0.018-0.04233.9060.0030.0030.0000.0000.0000.000
74A78SER0-0.001-0.00237.132-0.001-0.0010.0000.0000.0000.000
75A79ASP-1-0.803-0.88939.731-0.033-0.0330.0000.0000.0000.000
76A80PRO00.0220.00638.174-0.002-0.0020.0000.0000.0000.000
77A81VAL0-0.0130.00638.642-0.001-0.0010.0000.0000.0000.000
78A82GLU-1-0.876-0.91439.350-0.043-0.0430.0000.0000.0000.000
79A83ALA00.0300.01935.180-0.002-0.0020.0000.0000.0000.000
80A84ILE0-0.012-0.01335.036-0.003-0.0030.0000.0000.0000.000
81A85GLN0-0.009-0.00936.072-0.002-0.0020.0000.0000.0000.000
82A86LEU0-0.041-0.00534.6920.0000.0000.0000.0000.0000.000
83A87PHE00.0140.00828.089-0.002-0.0020.0000.0000.0000.000
84A88ILE00.0070.01132.606-0.001-0.0010.0000.0000.0000.000
85A89LYS10.9050.94734.8220.0400.0400.0000.0000.0000.000
86A90LYS10.8210.89729.8570.0750.0750.0000.0000.0000.000
87A91THR0-0.052-0.02029.7050.0000.0000.0000.0000.0000.000
88A92ALA00.0270.00231.5970.0020.0020.0000.0000.0000.000
89A93SER0-0.092-0.06231.5480.0010.0010.0000.0000.0000.000
90A94GLN00.0180.00928.795-0.002-0.0020.0000.0000.0000.000
91A95PHE00.019-0.00130.9220.0010.0010.0000.0000.0000.000
92A96ASP-1-0.848-0.88534.112-0.044-0.0440.0000.0000.0000.000
93A97ASN0-0.003-0.00932.9670.0030.0030.0000.0000.0000.000
94A98THR00.004-0.02332.5080.0000.0000.0000.0000.0000.000
95A99GLU-1-0.981-0.97728.447-0.050-0.0500.0000.0000.0000.000
96A100SER0-0.027-0.01527.936-0.004-0.0040.0000.0000.0000.000
97A101ILE0-0.051-0.00828.230-0.003-0.0030.0000.0000.0000.000
98A102LYS10.8450.94224.3240.0590.0590.0000.0000.0000.000
99A103GLY00.0400.00526.2860.0030.0030.0000.0000.0000.000
100A104ILE0-0.032-0.01227.522-0.006-0.0060.0000.0000.0000.000
101A105PRO0-0.047-0.02424.3230.0040.0040.0000.0000.0000.000
102A106VAL00.0080.00123.2030.0020.0020.0000.0000.0000.000
103A107GLY00.0260.01125.5630.0080.0080.0000.0000.0000.000
104A108LEU0-0.0270.02027.2040.0040.0040.0000.0000.0000.000
105A109LEU00.0920.04122.3450.0050.0050.0000.0000.0000.000
106A110ALA00.0080.00926.5470.0060.0060.0000.0000.0000.000
107A111SER0-0.037-0.03228.5020.0030.0030.0000.0000.0000.000
108A112GLU-1-0.817-0.89627.6640.0330.0330.0000.0000.0000.000
109A113THR0-0.077-0.07425.9520.0060.0060.0000.0000.0000.000
110A114ALA00.0150.00629.3360.0030.0030.0000.0000.0000.000
111A115LEU0-0.019-0.00431.662-0.001-0.0010.0000.0000.0000.000
112A116ILE0-0.053-0.02329.1920.0030.0030.0000.0000.0000.000
113A117SER0-0.011-0.03625.358-0.005-0.0050.0000.0000.0000.000
114A118GLU-1-0.728-0.82427.7830.0290.0290.0000.0000.0000.000
115A119PRO0-0.029-0.00123.348-0.007-0.0070.0000.0000.0000.000
116A120LEU00.0300.01821.706-0.006-0.0060.0000.0000.0000.000
117A121ARG10.8510.91224.747-0.033-0.0330.0000.0000.0000.000
118A122THR00.002-0.01926.164-0.009-0.0090.0000.0000.0000.000
119A123VAL0-0.062-0.03620.476-0.008-0.0080.0000.0000.0000.000
120A124CYS0-0.008-0.00123.767-0.010-0.0100.0000.0000.0000.000
121A125MET0-0.0300.00125.663-0.007-0.0070.0000.0000.0000.000
122A126LYS10.9190.94821.519-0.006-0.0060.0000.0000.0000.000
123A127VAL00.0040.04021.803-0.006-0.0060.0000.0000.0000.000
124A128PHE00.0250.02424.715-0.005-0.0050.0000.0000.0000.000
125A129LYS10.8520.90428.3040.0090.0090.0000.0000.0000.000
126A130SER0-0.056-0.03524.727-0.004-0.0040.0000.0000.0000.000
127A131TRP00.003-0.02623.639-0.001-0.0010.0000.0000.0000.000
128A132GLU-1-0.755-0.83828.187-0.018-0.0180.0000.0000.0000.000
129A133ALA00.0380.01729.0480.0000.0000.0000.0000.0000.000
130A134VAL0-0.044-0.00527.345-0.001-0.0010.0000.0000.0000.000
131A135PHE00.013-0.00430.3130.0000.0000.0000.0000.0000.000
132A136ALA00.0070.00833.7250.0010.0010.0000.0000.0000.000
133A137ARG10.7740.87226.2930.0630.0630.0000.0000.0000.000
134A138LYS10.8900.95533.8110.0520.0520.0000.0000.0000.000
135A139LEU0-0.034-0.01735.5160.0020.0020.0000.0000.0000.000
136A140MET0-0.017-0.00535.7790.0020.0020.0000.0000.0000.000
137A141GLU-1-0.962-0.98433.521-0.049-0.0490.0000.0000.0000.000
138A142ASN0-0.068-0.04838.312-0.002-0.0020.0000.0000.0000.000
139A143GLY0-0.021-0.00141.2970.0010.0010.0000.0000.0000.000
140A144PHE0-0.050-0.02241.3840.0020.0020.0000.0000.0000.000
141A145ALA00.0250.00542.069-0.001-0.0010.0000.0000.0000.000
142A146GLU-1-0.891-0.96937.324-0.019-0.0190.0000.0000.0000.000
143A147GLU-1-0.966-0.97839.545-0.011-0.0110.0000.0000.0000.000
144A148GLU-1-0.883-0.94041.276-0.018-0.0180.0000.0000.0000.000
145A149ALA00.0170.01638.0120.0000.0000.0000.0000.0000.000
146A150ASN0-0.021-0.02535.160-0.003-0.0030.0000.0000.0000.000
147A151GLN0-0.052-0.02137.3090.0010.0010.0000.0000.0000.000
148A152LEU0-0.003-0.00639.6460.0000.0000.0000.0000.0000.000
149A153GLY00.0520.02835.539-0.001-0.0010.0000.0000.0000.000
150A154THR0-0.084-0.06434.9530.0000.0000.0000.0000.0000.000
151A155LEU00.0030.02036.1130.0010.0010.0000.0000.0000.000
152A156ILE00.0040.00134.6010.0000.0000.0000.0000.0000.000
153A157ASN0-0.040-0.03531.032-0.004-0.0040.0000.0000.0000.000
154A158SER0-0.053-0.03433.6770.0000.0000.0000.0000.0000.000
155A159MET0-0.014-0.00935.8150.0010.0010.0000.0000.0000.000
156A160ILE00.0200.01832.1960.0000.0000.0000.0000.0000.000
157A161GLU-1-0.748-0.89928.975-0.025-0.0250.0000.0000.0000.000
158A162GLY00.0260.00433.0340.0020.0020.0000.0000.0000.000
159A163GLY00.0400.00136.4920.0010.0010.0000.0000.0000.000
160A164ILE0-0.0160.00529.8760.0000.0000.0000.0000.0000.000
161A165MET0-0.035-0.00633.2110.0020.0020.0000.0000.0000.000
162A166LEU00.0180.01635.0470.0020.0020.0000.0000.0000.000
163A167SER0-0.010-0.01435.2810.0000.0000.0000.0000.0000.000
164A168LEU00.0020.00631.000-0.001-0.0010.0000.0000.0000.000
165A169THR0-0.078-0.04434.6150.0030.0030.0000.0000.0000.000
166A170ASN0-0.073-0.05337.7300.0030.0030.0000.0000.0000.000
167A171LYS10.8180.91535.4480.0120.0120.0000.0000.0000.000
168A172ASP-1-0.758-0.85437.314-0.022-0.0220.0000.0000.0000.000
169A173LYS10.8600.91336.5570.0420.0420.0000.0000.0000.000
170A174THR0-0.027-0.04138.313-0.001-0.0010.0000.0000.0000.000
171A175PRO0-0.038-0.01439.1450.0000.0000.0000.0000.0000.000
172A176LEU00.0160.01534.0940.0000.0000.0000.0000.0000.000
173A177LEU0-0.026-0.01538.373-0.001-0.0010.0000.0000.0000.000
174A178LEU00.0410.03140.7480.0000.0000.0000.0000.0000.000
175A179ILE0-0.003-0.00238.4270.0010.0010.0000.0000.0000.000
176A180ALA0-0.025-0.01339.3230.0000.0000.0000.0000.0000.000
177A181GLU-1-0.928-0.97440.932-0.023-0.0230.0000.0000.0000.000
178A182GLN0-0.053-0.02543.5090.0020.0020.0000.0000.0000.000
179A183ILE00.0140.01039.8610.0010.0010.0000.0000.0000.000
180A184PRO00.016-0.00342.7120.0000.0000.0000.0000.0000.000
181A185VAL0-0.0170.01045.6030.0010.0010.0000.0000.0000.000
182A186LEU0-0.063-0.01542.9140.0020.0020.0000.0000.0000.000
183A187VAL00.0250.01140.4970.0010.0010.0000.0000.0000.000
184A188ARG10.8650.93343.9360.0170.0170.0000.0000.0000.000