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: MVN8Z

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1719681.200033
FMO2-HF: Nuclear repulsion 1648032.638443
FMO2-HF: Total energy -71648.56159
FMO2-MP2: Total energy -71857.660357


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.
-9.058-8.71118.67-6.62-12.3930.011
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 : 0.075 / q_NPA : 0.025
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-1-0.888-0.9393.2500.2642.2030.017-0.619-1.3360.003
4A5ILE00.0150.0041.648-2.014-5.18411.349-3.882-4.2950.009
5A6ARG10.9350.9603.196-2.031-0.7610.013-0.525-0.7580.001
6A7LYS10.9951.0014.918-0.619-0.481-0.001-0.013-0.1240.000
7A8ASP-1-0.830-0.9116.7240.7470.7470.0000.0000.0000.000
8A9ALA00.0250.0076.906-0.139-0.1390.0000.0000.0000.000
9A10GLU-1-0.927-0.9658.6250.0020.0020.0000.0000.0000.000
10A11VAL0-0.042-0.02610.919-0.015-0.0150.0000.0000.0000.000
11A12ARG10.6970.7908.946-0.523-0.5230.0000.0000.0000.000
12A13MET0-0.0110.01610.696-0.035-0.0350.0000.0000.0000.000
13A14ASP-1-0.855-0.92414.4760.0650.0650.0000.0000.0000.000
14A15LYS10.9150.95015.995-0.228-0.2280.0000.0000.0000.000
15A16CYS0-0.042-0.01216.558-0.009-0.0090.0000.0000.0000.000
16A17VAL00.0060.00118.431-0.013-0.0130.0000.0000.0000.000
17A18GLU-1-0.792-0.88320.6960.0510.0510.0000.0000.0000.000
18A19ALA0-0.0300.00721.949-0.003-0.0030.0000.0000.0000.000
19A20PHE00.0180.00823.301-0.006-0.0060.0000.0000.0000.000
20A21LYS10.8310.88024.438-0.053-0.0530.0000.0000.0000.000
21A22THR0-0.034-0.01726.227-0.002-0.0020.0000.0000.0000.000
22A23GLN0-0.118-0.08126.5760.0020.0020.0000.0000.0000.000
23A24ILE00.0490.02829.042-0.004-0.0040.0000.0000.0000.000
24A25SER0-0.032-0.01831.195-0.003-0.0030.0000.0000.0000.000
25A26LYS10.9400.98031.299-0.052-0.0520.0000.0000.0000.000
26A27ILE0-0.0200.00733.595-0.002-0.0020.0000.0000.0000.000
27A28ARG10.8600.90236.780-0.023-0.0230.0000.0000.0000.000
28A29THR0-0.063-0.06638.370-0.001-0.0010.0000.0000.0000.000
29A30GLY00.027-0.00341.2710.0000.0000.0000.0000.0000.000
30A31ARG10.8310.91437.353-0.019-0.0190.0000.0000.0000.000
31A32ALA0-0.027-0.01942.2500.0020.0020.0000.0000.0000.000
32A33SER00.009-0.00238.2270.0000.0000.0000.0000.0000.000
33A34PRO00.019-0.00439.1560.0010.0010.0000.0000.0000.000
34A35SER0-0.054-0.03234.2160.0020.0020.0000.0000.0000.000
35A36LEU00.0090.01735.7240.0020.0020.0000.0000.0000.000
36A37LEU0-0.021-0.02137.8570.0010.0010.0000.0000.0000.000
37A38ASP-1-0.781-0.86434.3440.0530.0530.0000.0000.0000.000
38A39GLY0-0.044-0.02635.6830.0040.0040.0000.0000.0000.000
39A40ILE0-0.0220.01236.3490.0010.0010.0000.0000.0000.000
40A41VAL0-0.017-0.01238.0590.0020.0020.0000.0000.0000.000
41A42VAL0-0.025-0.02641.026-0.003-0.0030.0000.0000.0000.000
42A43GLU-1-0.934-0.95644.1880.0420.0420.0000.0000.0000.000
43A44TYR0-0.023-0.02945.544-0.002-0.0020.0000.0000.0000.000
44A45TYR0-0.012-0.01346.7930.0010.0010.0000.0000.0000.000
45A46GLY00.0310.02547.9600.0010.0010.0000.0000.0000.000
46A47THR0-0.014-0.00241.9280.0030.0030.0000.0000.0000.000
47A48PRO0-0.033-0.01039.991-0.002-0.0020.0000.0000.0000.000
48A49THR00.0110.00140.3420.0040.0040.0000.0000.0000.000
49A50PRO00.0050.00336.969-0.003-0.0030.0000.0000.0000.000
50A51LEU00.0810.03839.420-0.002-0.0020.0000.0000.0000.000
51A52ARG10.8100.88734.987-0.059-0.0590.0000.0000.0000.000
52A53GLN0-0.036-0.02338.5750.0020.0020.0000.0000.0000.000
53A54LEU00.0020.01541.984-0.001-0.0010.0000.0000.0000.000
54A55ALA00.0050.01444.273-0.003-0.0030.0000.0000.0000.000
55A56SER0-0.0280.00043.6430.0010.0010.0000.0000.0000.000
56A57VAL00.0130.00841.592-0.002-0.0020.0000.0000.0000.000
57A58THR0-0.032-0.01742.5380.0000.0000.0000.0000.0000.000
58A59VAL00.002-0.01042.7870.0000.0000.0000.0000.0000.000
59A60GLU-1-0.834-0.87145.7190.0180.0180.0000.0000.0000.000
60A61ASP-1-0.765-0.88648.4220.0130.0130.0000.0000.0000.000
61A62SER0-0.030-0.02246.1690.0010.0010.0000.0000.0000.000
62A63ARG10.9180.96646.127-0.010-0.0100.0000.0000.0000.000
63A64THR0-0.024-0.00747.9910.0000.0000.0000.0000.0000.000
64A65LEU0-0.0040.00242.7510.0000.0000.0000.0000.0000.000
65A66LYS10.9160.96146.643-0.024-0.0240.0000.0000.0000.000
66A67ILE0-0.010-0.00645.3340.0020.0020.0000.0000.0000.000
67A68ASN0-0.034-0.01447.777-0.002-0.0020.0000.0000.0000.000
68A69VAL00.011-0.01248.2210.0020.0020.0000.0000.0000.000
69A70PHE0-0.052-0.03844.337-0.002-0.0020.0000.0000.0000.000
70A71ASP-1-0.773-0.86050.0900.0310.0310.0000.0000.0000.000
71A72ARG10.9530.95752.232-0.023-0.0230.0000.0000.0000.000
72A73SER0-0.055-0.04654.491-0.001-0.0010.0000.0000.0000.000
73A74MET0-0.001-0.00448.2120.0000.0000.0000.0000.0000.000
74A75SER0-0.024-0.01050.6140.0010.0010.0000.0000.0000.000
75A76PRO00.0480.01451.7960.0000.0000.0000.0000.0000.000
76A77ALA0-0.015-0.00549.5070.0000.0000.0000.0000.0000.000
77A78VAL00.0280.01846.5340.0010.0010.0000.0000.0000.000
78A79GLU-1-0.797-0.89547.6060.0240.0240.0000.0000.0000.000
79A80LYS10.9350.96449.830-0.032-0.0320.0000.0000.0000.000
80A81ALA0-0.027-0.01544.6820.0000.0000.0000.0000.0000.000
81A82ILE00.0090.00544.4970.0010.0010.0000.0000.0000.000
82A83MET0-0.0090.01145.698-0.001-0.0010.0000.0000.0000.000
83A84ALA0-0.057-0.02246.149-0.001-0.0010.0000.0000.0000.000
84A85SER0-0.072-0.03241.5230.0010.0010.0000.0000.0000.000
85A86ASP-1-0.763-0.86442.4940.0250.0250.0000.0000.0000.000
86A87LEU00.0170.01744.854-0.001-0.0010.0000.0000.0000.000
87A88GLY0-0.053-0.02846.866-0.001-0.0010.0000.0000.0000.000
88A89LEU0-0.060-0.02944.134-0.001-0.0010.0000.0000.0000.000
89A90ASN0-0.029-0.01848.5630.0000.0000.0000.0000.0000.000
90A91PRO0-0.037-0.01450.220-0.001-0.0010.0000.0000.0000.000
91A92ASN0-0.0010.00052.124-0.001-0.0010.0000.0000.0000.000
92A93SER0-0.004-0.00754.2880.0000.0000.0000.0000.0000.000
93A94ALA0-0.023-0.00155.851-0.001-0.0010.0000.0000.0000.000
94A95GLY00.009-0.01357.0110.0000.0000.0000.0000.0000.000
95A96SER0-0.0030.01053.4480.0000.0000.0000.0000.0000.000
96A97ASP-1-0.883-0.92352.2560.0240.0240.0000.0000.0000.000
97A98ILE00.0160.00249.535-0.001-0.0010.0000.0000.0000.000
98A99ARG10.8350.88450.208-0.016-0.0160.0000.0000.0000.000
99A100VAL00.002-0.01446.8080.0000.0000.0000.0000.0000.000
100A101PRO00.0370.02948.1720.0000.0000.0000.0000.0000.000
101A102LEU0-0.005-0.01143.4470.0010.0010.0000.0000.0000.000
102A103PRO0-0.032-0.01846.951-0.001-0.0010.0000.0000.0000.000
103A104PRO0-0.019-0.00147.4140.0000.0000.0000.0000.0000.000
104A105LEU00.0110.01742.2900.0000.0000.0000.0000.0000.000
105A106THR00.0360.01546.940-0.001-0.0010.0000.0000.0000.000
106A107GLU-1-0.775-0.90446.5990.0040.0040.0000.0000.0000.000
107A108GLU-1-0.843-0.92345.7680.0050.0050.0000.0000.0000.000
108A109ARG10.9490.97941.751-0.017-0.0170.0000.0000.0000.000
109A110ARG10.8970.94942.191-0.005-0.0050.0000.0000.0000.000
110A111LYS10.8280.93240.709-0.004-0.0040.0000.0000.0000.000
111A112ASP-1-0.855-0.92939.9200.0120.0120.0000.0000.0000.000
112A113LEU0-0.030-0.02438.5680.0010.0010.0000.0000.0000.000
113A114THR00.018-0.00236.2440.0010.0010.0000.0000.0000.000
114A115LYS10.8360.90635.116-0.008-0.0080.0000.0000.0000.000
115A116ILE0-0.002-0.00234.1000.0000.0000.0000.0000.0000.000
116A117VAL00.0420.03731.3560.0020.0020.0000.0000.0000.000
117A118ARG10.7950.84530.3510.0030.0030.0000.0000.0000.000
118A119GLY0-0.026-0.00529.664-0.002-0.0020.0000.0000.0000.000
119A120GLU-1-0.855-0.92828.1930.0370.0370.0000.0000.0000.000
120A121ALA00.0380.02525.9820.0040.0040.0000.0000.0000.000
121A122GLU-1-0.759-0.85024.182-0.015-0.0150.0000.0000.0000.000
122A123GLN0-0.032-0.01123.7610.0040.0040.0000.0000.0000.000
123A124ALA00.0280.01222.0170.0070.0070.0000.0000.0000.000
124A125ARG10.7880.85820.1940.0130.0130.0000.0000.0000.000
125A126VAL0-0.044-0.02819.136-0.008-0.0080.0000.0000.0000.000
126A127ALA0-0.0080.00318.2990.0020.0020.0000.0000.0000.000
127A128VAL00.0300.01115.2200.0140.0140.0000.0000.0000.000
128A129ARG10.8760.93014.1030.0180.0180.0000.0000.0000.000
129A130ASN0-0.034-0.01613.769-0.031-0.0310.0000.0000.0000.000
130A131VAL00.0000.01410.8840.0210.0210.0000.0000.0000.000
131A132GLY00.0460.0179.6860.0170.0170.0000.0000.0000.000
132A133ARG10.9060.9449.362-0.023-0.0230.0000.0000.0000.000
133A134ASP-1-0.695-0.8289.3310.3490.3490.0000.0000.0000.000
134A135ALA00.006-0.0015.5890.1180.1180.0000.0000.0000.000
135A136ASN00.027-0.0035.266-0.386-0.3860.0000.0000.0000.000
136A137ASP-1-0.939-0.9637.597-0.112-0.1120.0000.0000.0000.000
137A138LYS10.7630.8975.601-0.848-0.8480.0000.0000.0000.000
138A139VAL0-0.0090.0022.426-1.230-0.1350.784-0.473-1.4060.002
139A140LYS10.8740.9364.8590.3560.434-0.001-0.004-0.0730.000
140A141ALA0-0.041-0.0258.0950.0110.0110.0000.0000.0000.000
141A142LEU00.0290.0112.394-0.615-0.2371.456-0.316-1.518-0.001
142A143LEU0-0.0270.0016.457-0.020-0.0200.0000.0000.0000.000
143A144LYS10.8630.9308.1680.1700.1700.0000.0000.0000.000
144A145ASP-1-0.852-0.8948.808-0.091-0.0910.0000.0000.0000.000
145A146LYS10.8040.8668.9230.1900.1900.0000.0000.0000.000
146A147GLU-1-0.963-0.9654.772-0.688-0.605-0.001-0.001-0.0800.000
147A148ILE0-0.058-0.0042.1380.282-1.6465.050-0.659-2.463-0.003
148A149SER00.0420.0125.7890.3070.3070.0000.0000.0000.000
149A150GLU-1-0.848-0.9337.782-0.407-0.4070.0000.0000.0000.000
150A151ASP-1-0.847-0.9129.502-0.449-0.4490.0000.0000.0000.000
151A152ASP-1-0.808-0.9044.016-1.144-1.0740.000-0.017-0.0530.000
152A153ASP-1-0.849-0.9395.124-0.782-0.728-0.001-0.004-0.0490.000
153A154ARG10.7920.8716.2930.4240.4240.0000.0000.0000.000
154A155ARG10.9200.9576.7490.5260.5260.0000.0000.0000.000
155A156SER0-0.009-0.0053.777-0.499-0.1590.005-0.107-0.2380.000
156A157GLN0-0.0070.0035.6200.1060.1060.0000.0000.0000.000
157A158ASP-1-0.892-0.9308.849-0.311-0.3110.0000.0000.0000.000
158A159ASP-1-0.857-0.9506.807-0.469-0.4690.0000.0000.0000.000
159A160VAL0-0.027-0.0066.2430.0980.0980.0000.0000.0000.000
160A161GLN0-0.039-0.0268.8920.1070.1070.0000.0000.0000.000
161A162LYS10.8800.94010.9700.3940.3940.0000.0000.0000.000
162A163LEU0-0.021-0.0038.6260.0500.0500.0000.0000.0000.000
163A164THR0-0.015-0.01112.4230.0650.0650.0000.0000.0000.000
164A165ASP-1-0.865-0.92214.531-0.102-0.1020.0000.0000.0000.000
165A166ALA0-0.045-0.02415.7060.0200.0200.0000.0000.0000.000
166A167ALA0-0.003-0.00716.0420.0190.0190.0000.0000.0000.000
167A168ILE00.022-0.01017.8860.0140.0140.0000.0000.0000.000
168A169LYS10.9490.97720.1230.0590.0590.0000.0000.0000.000
169A170LYS10.8990.95518.736-0.029-0.0290.0000.0000.0000.000
170A171ILE0-0.023-0.00320.4740.0060.0060.0000.0000.0000.000
171A172GLU-1-0.825-0.91024.008-0.015-0.0150.0000.0000.0000.000
172A173ALA0-0.037-0.00725.8930.0010.0010.0000.0000.0000.000
173A174ALA00.0220.01826.7550.0020.0020.0000.0000.0000.000
174A175LEU0-0.021-0.00828.0400.0020.0020.0000.0000.0000.000
175A176ALA0-0.016-0.00929.8620.0010.0010.0000.0000.0000.000
176A177ASP-1-0.899-0.94331.3840.0060.0060.0000.0000.0000.000
177A178LYS10.8090.90832.520-0.022-0.0220.0000.0000.0000.000
178A179GLU-1-0.789-0.87133.355-0.001-0.0010.0000.0000.0000.000
179A180ALA00.0010.00235.9330.0000.0000.0000.0000.0000.000
180A181GLU-1-0.784-0.86037.3670.0190.0190.0000.0000.0000.000
181A182LEU0-0.038-0.02236.9360.0010.0010.0000.0000.0000.000
182A183MET0-0.031-0.02540.1390.0000.0000.0000.0000.0000.000
183A184GLN0-0.0180.00841.8690.0000.0000.0000.0000.0000.000
184A185PHE0-0.050-0.00141.8690.0010.0010.0000.0000.0000.000