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: 726NK

Calculation Name: 1ISE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ISE

Chain ID: A

ChEMBL ID:

UniProt ID: P0A805

Base Structure: X-ray

Registration Date: 2023-06-22

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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1724044.287977
FMO2-HF: Nuclear repulsion 1652395.112371
FMO2-HF: Total energy -71649.175606
FMO2-MP2: Total energy -71858.246829


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:2:ILE)


Summations of interaction energy for fragment #1(A:2:ILE)
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.
-9.939-2.865.831-3.534-9.3750.005
Interaction energy analysis for fragmet #1(A:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.085 / q_NPA : 0.029
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].
3A4ASP-1-0.884-0.9393.149-0.7261.0290.018-0.555-1.2170.001
4A5ILE00.0030.0052.363-3.549-1.4861.788-1.159-2.6930.009
5A6ARG10.8260.9043.637-0.1540.4590.000-0.234-0.3790.000
6A7LYS10.9971.0015.2300.1050.217-0.001-0.008-0.1020.000
7A8ASP-1-0.831-0.8997.4120.5040.5040.0000.0000.0000.000
8A9ALA00.0390.0157.530-0.013-0.0130.0000.0000.0000.000
9A10GLU-1-0.836-0.9119.150-0.325-0.3250.0000.0000.0000.000
10A11VAL0-0.036-0.02111.1330.0400.0400.0000.0000.0000.000
11A12ARG10.7130.7889.792-0.233-0.2330.0000.0000.0000.000
12A13MET0-0.0010.02310.9500.0000.0000.0000.0000.0000.000
13A14ASP-1-0.773-0.86314.912-0.058-0.0580.0000.0000.0000.000
14A15LYS10.8960.94316.766-0.057-0.0570.0000.0000.0000.000
15A16CYS0-0.034-0.01117.1100.0100.0100.0000.0000.0000.000
16A17VAL00.0150.01318.8540.0000.0000.0000.0000.0000.000
17A18GLU-1-0.805-0.88821.266-0.020-0.0200.0000.0000.0000.000
18A19ALA0-0.0260.01222.5290.0040.0040.0000.0000.0000.000
19A20PHE00.0370.02023.6900.0010.0010.0000.0000.0000.000
20A21LYS10.8130.87324.8140.0250.0250.0000.0000.0000.000
21A22THR0-0.034-0.02226.7620.0020.0020.0000.0000.0000.000
22A23GLN0-0.100-0.06526.5360.0010.0010.0000.0000.0000.000
23A24ILE00.0680.03429.5380.0010.0010.0000.0000.0000.000
24A25SER0-0.032-0.01431.6070.0000.0000.0000.0000.0000.000
25A26LYS10.8070.90031.559-0.007-0.0070.0000.0000.0000.000
26A27ILE0-0.037-0.00134.0400.0000.0000.0000.0000.0000.000
27A28ARG10.8680.90537.159-0.003-0.0030.0000.0000.0000.000
28A29THR0-0.035-0.04538.9710.0000.0000.0000.0000.0000.000
29A30GLY00.0120.00141.8810.0010.0010.0000.0000.0000.000
30A31ARG10.8580.91637.6520.0110.0110.0000.0000.0000.000
31A32ALA0-0.012-0.00442.9720.0010.0010.0000.0000.0000.000
32A33SER00.012-0.00538.767-0.002-0.0020.0000.0000.0000.000
33A34PRO00.0230.00139.3710.0010.0010.0000.0000.0000.000
34A35SER0-0.030-0.03434.6300.0010.0010.0000.0000.0000.000
35A36LEU0-0.0030.01036.6040.0010.0010.0000.0000.0000.000
36A37LEU0-0.008-0.01438.6220.0010.0010.0000.0000.0000.000
37A38ASP-1-0.798-0.85934.8440.0100.0100.0000.0000.0000.000
38A39GLY0-0.019-0.01236.3300.0020.0020.0000.0000.0000.000
39A40ILE0-0.0240.00537.0290.0010.0010.0000.0000.0000.000
40A41VAL0-0.014-0.00838.5560.0010.0010.0000.0000.0000.000
41A42VAL0-0.016-0.01841.622-0.001-0.0010.0000.0000.0000.000
42A43GLU-1-0.940-0.95445.0590.0200.0200.0000.0000.0000.000
43A44TYR0-0.019-0.04746.681-0.001-0.0010.0000.0000.0000.000
44A45TYR00.001-0.00147.8260.0010.0010.0000.0000.0000.000
45A46GLY00.0320.02348.6880.0010.0010.0000.0000.0000.000
46A47THR0-0.024-0.01742.9410.0020.0020.0000.0000.0000.000
47A48PRO0-0.043-0.02041.093-0.002-0.0020.0000.0000.0000.000
48A49THR00.0110.00341.2580.0020.0020.0000.0000.0000.000
49A50PRO0-0.004-0.00937.629-0.002-0.0020.0000.0000.0000.000
50A51LEU00.0600.02740.173-0.001-0.0010.0000.0000.0000.000
51A52ARG10.8230.89135.819-0.016-0.0160.0000.0000.0000.000
52A53GLN0-0.034-0.02039.1140.0000.0000.0000.0000.0000.000
53A54LEU0-0.0120.00742.8790.0000.0000.0000.0000.0000.000
54A55ALA0-0.005-0.00245.027-0.001-0.0010.0000.0000.0000.000
55A56SER00.0090.02444.1360.0010.0010.0000.0000.0000.000
56A57VAL0-0.019-0.00341.962-0.001-0.0010.0000.0000.0000.000
57A58THR0-0.049-0.03243.220-0.001-0.0010.0000.0000.0000.000
58A59VAL00.001-0.00843.4700.0000.0000.0000.0000.0000.000
59A60GLU-1-0.825-0.87146.4300.0000.0000.0000.0000.0000.000
60A61ASP-1-0.776-0.88149.235-0.005-0.0050.0000.0000.0000.000
61A62SER0-0.017-0.00946.5950.0000.0000.0000.0000.0000.000
62A63ARG10.8790.95546.4190.0070.0070.0000.0000.0000.000
63A64THR0-0.025-0.02248.3180.0010.0010.0000.0000.0000.000
64A65LEU00.0140.00943.057-0.001-0.0010.0000.0000.0000.000
65A66LYS10.9150.95847.270-0.002-0.0020.0000.0000.0000.000
66A67ILE0-0.010-0.00145.9360.0000.0000.0000.0000.0000.000
67A68ASN0-0.024-0.02248.016-0.001-0.0010.0000.0000.0000.000
68A69VAL00.010-0.00949.0440.0000.0000.0000.0000.0000.000
69A70PHE0-0.028-0.02145.055-0.001-0.0010.0000.0000.0000.000
70A71ASP-1-0.760-0.83050.8310.0120.0120.0000.0000.0000.000
71A72ARG10.9450.94452.732-0.007-0.0070.0000.0000.0000.000
72A73SER0-0.060-0.04854.8850.0000.0000.0000.0000.0000.000
73A74MET00.0360.02448.8830.0000.0000.0000.0000.0000.000
74A75SER00.0030.01051.5950.0000.0000.0000.0000.0000.000
75A76PRO00.0260.00052.6450.0000.0000.0000.0000.0000.000
76A77ALA0-0.022-0.00350.5280.0000.0000.0000.0000.0000.000
77A78VAL00.0270.00647.0960.0000.0000.0000.0000.0000.000
78A79GLU-1-0.782-0.87148.4560.0060.0060.0000.0000.0000.000
79A80LYS10.9440.96450.356-0.014-0.0140.0000.0000.0000.000
80A81ALA0-0.013-0.00345.5780.0000.0000.0000.0000.0000.000
81A82ILE00.0130.00745.2760.0000.0000.0000.0000.0000.000
82A83MET0-0.0120.01046.4160.0000.0000.0000.0000.0000.000
83A84ALA0-0.056-0.02146.8670.0000.0000.0000.0000.0000.000
84A85SER0-0.079-0.04042.1800.0010.0010.0000.0000.0000.000
85A86ASP-1-0.767-0.86443.0750.0030.0030.0000.0000.0000.000
86A87LEU00.0270.01945.328-0.001-0.0010.0000.0000.0000.000
87A88GLY0-0.036-0.01447.578-0.001-0.0010.0000.0000.0000.000
88A89LEU0-0.055-0.02944.339-0.001-0.0010.0000.0000.0000.000
89A90ASN0-0.041-0.02548.7970.0010.0010.0000.0000.0000.000
90A91PRO0-0.038-0.01350.992-0.001-0.0010.0000.0000.0000.000
91A92ASN0-0.028-0.01952.749-0.001-0.0010.0000.0000.0000.000
92A93SER0-0.058-0.04654.7960.0000.0000.0000.0000.0000.000
93A94ALA0-0.017-0.00556.0700.0000.0000.0000.0000.0000.000
94A95GLY0-0.015-0.01257.2520.0000.0000.0000.0000.0000.000
95A96SER0-0.0260.00053.8700.0010.0010.0000.0000.0000.000
96A97ASP-1-0.865-0.91552.7160.0040.0040.0000.0000.0000.000
97A98ILE00.010-0.00350.2140.0000.0000.0000.0000.0000.000
98A99ARG10.8340.89750.7070.0000.0000.0000.0000.0000.000
99A100VAL00.012-0.01146.9440.0010.0010.0000.0000.0000.000
100A101PRO00.0280.02348.682-0.001-0.0010.0000.0000.0000.000
101A102LEU0-0.015-0.01143.9790.0010.0010.0000.0000.0000.000
102A103PRO0-0.048-0.02547.642-0.001-0.0010.0000.0000.0000.000
103A104PRO0-0.0020.00547.5840.0000.0000.0000.0000.0000.000
104A105LEU00.0010.01542.2650.0010.0010.0000.0000.0000.000
105A106THR00.0430.01346.900-0.001-0.0010.0000.0000.0000.000
106A107GLU-1-0.786-0.90046.835-0.011-0.0110.0000.0000.0000.000
107A108GLU-1-0.850-0.90745.988-0.007-0.0070.0000.0000.0000.000
108A109ARG10.9230.95042.2240.0000.0000.0000.0000.0000.000
109A110ARG10.8510.92942.3680.0100.0100.0000.0000.0000.000
110A111LYS10.8600.92540.9110.0080.0080.0000.0000.0000.000
111A112ASP-1-0.862-0.91940.226-0.003-0.0030.0000.0000.0000.000
112A113LEU00.0230.00338.7610.0010.0010.0000.0000.0000.000
113A114THR00.013-0.00436.195-0.001-0.0010.0000.0000.0000.000
114A115LYS10.8320.91035.2370.0040.0040.0000.0000.0000.000
115A116ILE0-0.0070.00534.1690.0000.0000.0000.0000.0000.000
116A117VAL00.0300.02131.8770.0000.0000.0000.0000.0000.000
117A118ARG10.8040.85630.6210.0210.0210.0000.0000.0000.000
118A119GLY0-0.0010.01229.613-0.002-0.0020.0000.0000.0000.000
119A120GLU-1-0.795-0.90428.5400.0040.0040.0000.0000.0000.000
120A121ALA00.0320.02226.3380.0000.0000.0000.0000.0000.000
121A122GLU-1-0.771-0.85424.657-0.042-0.0420.0000.0000.0000.000
122A123GLN0-0.030-0.01324.0900.0010.0010.0000.0000.0000.000
123A124ALA00.0400.02122.2490.0030.0030.0000.0000.0000.000
124A125ARG10.8020.86720.4320.0390.0390.0000.0000.0000.000
125A126VAL0-0.042-0.02119.398-0.009-0.0090.0000.0000.0000.000
126A127ALA0-0.011-0.00218.6670.0030.0030.0000.0000.0000.000
127A128VAL00.0180.00415.5250.0050.0050.0000.0000.0000.000
128A129ARG10.8600.90214.5300.0340.0340.0000.0000.0000.000
129A130ASN0-0.034-0.01714.283-0.016-0.0160.0000.0000.0000.000
130A131VAL0-0.0210.00611.2100.0290.0290.0000.0000.0000.000
131A132GLY00.0430.01410.089-0.004-0.0040.0000.0000.0000.000
132A133ARG10.9040.9589.716-0.039-0.0390.0000.0000.0000.000
133A134ASP-1-0.720-0.83810.2500.2860.2860.0000.0000.0000.000
134A135ALA00.0110.0086.0980.1890.1890.0000.0000.0000.000
135A136ASN00.0660.0145.754-0.072-0.0720.0000.0000.0000.000
136A137ASP-1-0.914-0.9597.4930.0940.0940.0000.0000.0000.000
137A138LYS10.7660.8856.348-0.654-0.6540.0000.0000.0000.000
138A139VAL0-0.025-0.0022.466-0.4930.1311.098-0.527-1.1940.000
139A140LYS10.8160.8824.8830.0910.148-0.001-0.002-0.0540.000
140A141ALA0-0.051-0.0318.417-0.061-0.0610.0000.0000.0000.000
141A142LEU00.0390.0192.664-0.5150.0850.324-0.146-0.7790.000
142A143LEU0-0.0220.0056.719-0.171-0.1710.0000.0000.0000.000
143A144LYS10.8600.9348.296-0.154-0.1540.0000.0000.0000.000
144A145ASP-1-0.840-0.8899.0440.2030.2030.0000.0000.0000.000
145A146LYS10.8010.8629.150-0.138-0.1380.0000.0000.0000.000
146A147GLU-1-0.948-0.9584.791-0.0420.025-0.001-0.001-0.0640.000
147A148ILE0-0.058-0.0142.216-1.460-1.2232.562-0.541-2.258-0.003
148A149SER00.014-0.0075.5920.2190.2190.0000.0000.0000.000
149A150GLU-1-0.837-0.9217.435-0.302-0.3020.0000.0000.0000.000
150A151ASP-1-0.784-0.8749.263-0.369-0.3690.0000.0000.0000.000
151A152ASP-1-0.791-0.8823.621-0.881-0.7540.003-0.032-0.0990.000
152A153ASP-1-0.824-0.9074.778-0.744-0.657-0.001-0.007-0.0790.000
153A154ARG10.7580.8526.3980.2350.2350.0000.0000.0000.000
154A155ARG10.8830.9336.6290.4080.4080.0000.0000.0000.000
155A156SER00.0110.0083.381-1.231-0.5050.043-0.321-0.448-0.002
156A157GLN0-0.037-0.0125.2520.0760.087-0.001-0.001-0.0090.000
157A158ASP-1-0.881-0.9428.395-0.334-0.3340.0000.0000.0000.000
158A159ASP-1-0.879-0.9506.690-0.623-0.6230.0000.0000.0000.000
159A160VAL0-0.0160.0015.9640.0960.0960.0000.0000.0000.000
160A161GLN0-0.043-0.0118.7030.1280.1280.0000.0000.0000.000
161A162LYS10.8930.94010.3100.4900.4900.0000.0000.0000.000
162A163LEU0-0.028-0.0048.8570.0550.0550.0000.0000.0000.000
163A164THR0-0.009-0.02312.1480.0720.0720.0000.0000.0000.000
164A165ASP-1-0.873-0.92714.370-0.144-0.1440.0000.0000.0000.000
165A166ALA0-0.030-0.01515.9450.0280.0280.0000.0000.0000.000
166A167ALA00.010-0.00216.1370.0240.0240.0000.0000.0000.000
167A168ILE00.0180.00117.9260.0220.0220.0000.0000.0000.000
168A169LYS10.9330.96220.2490.1060.1060.0000.0000.0000.000
169A170LYS10.8420.90319.1830.0840.0840.0000.0000.0000.000
170A171ILE0-0.033-0.00620.8250.0090.0090.0000.0000.0000.000
171A172GLU-1-0.849-0.92824.148-0.049-0.0490.0000.0000.0000.000
172A173ALA0-0.0250.00326.0070.0050.0050.0000.0000.0000.000
173A174ALA00.0400.01926.9870.0050.0050.0000.0000.0000.000
174A175LEU0-0.024-0.01028.3130.0050.0050.0000.0000.0000.000
175A176ALA0-0.010-0.00530.1290.0030.0030.0000.0000.0000.000
176A177ASP-1-0.894-0.94331.220-0.030-0.0300.0000.0000.0000.000
177A178LYS10.8010.89432.8300.0110.0110.0000.0000.0000.000
178A179GLU-1-0.765-0.86233.434-0.023-0.0230.0000.0000.0000.000
179A180ALA00.0080.01136.1110.0020.0020.0000.0000.0000.000
180A181GLU-1-0.779-0.84337.445-0.009-0.0090.0000.0000.0000.000
181A182LEU0-0.045-0.01237.0270.0020.0020.0000.0000.0000.000
182A183MET0-0.026-0.02439.8580.0020.0020.0000.0000.0000.000
183A184GLN0-0.0180.00141.5680.0010.0010.0000.0000.0000.000
184A185PHE0-0.059-0.04141.9250.0030.0030.0000.0000.0000.000