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: ZVQ2N

Calculation Name: 5H5W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H5W

Chain ID: A

ChEMBL ID:

UniProt ID: P24216

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1731052.479809
FMO2-HF: Nuclear repulsion 1659586.714267
FMO2-HF: Total energy -71465.765542
FMO2-MP2: Total energy -71674.226078


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:70:LEU)


Summations of interaction energy for fragment #1(A:70:LEU)
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.
-0.213.2171.173-1.933-2.6670.003
Interaction energy analysis for fragmet #1(A:70:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / 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].
3A72ALA00.0280.0233.813-0.3381.365-0.024-0.772-0.907-0.001
4A73THR00.0400.0125.8750.3510.3510.0000.0000.0000.000
5A74SER00.002-0.0019.010-0.030-0.0300.0000.0000.0000.000
6A75THR0-0.041-0.05712.5330.0560.0560.0000.0000.0000.000
7A76THR0-0.023-0.01515.238-0.018-0.0180.0000.0000.0000.000
8A77SER00.0070.00018.9840.0250.0250.0000.0000.0000.000
9A78SER0-0.018-0.01721.780-0.006-0.0060.0000.0000.0000.000
10A79THR0-0.021-0.02724.9290.0000.0000.0000.0000.0000.000
11A80THR00.0070.00324.955-0.002-0.0020.0000.0000.0000.000
12A81ALA00.0280.02326.402-0.002-0.0020.0000.0000.0000.000
13A82PHE00.0340.02521.3630.0060.0060.0000.0000.0000.000
14A83SER0-0.0130.00119.683-0.006-0.0060.0000.0000.0000.000
15A84ALA00.0500.01115.5450.0190.0190.0000.0000.0000.000
16A85THR0-0.0350.02112.495-0.019-0.0190.0000.0000.0000.000
17A86THR00.014-0.0048.5520.0370.0370.0000.0000.0000.000
18A87ALA0-0.0280.0056.759-0.188-0.1880.0000.0000.0000.000
19A88GLY0-0.016-0.0272.568-0.785-0.4360.287-0.305-0.3310.000
20A89ASN0-0.044-0.0392.8961.2302.5240.911-0.852-1.3540.004
21A90ALA00.0710.0605.252-0.485-0.404-0.001-0.004-0.0750.000
22A91ILE0-0.011-0.0038.463-0.047-0.0470.0000.0000.0000.000
23A92ALA00.0160.01511.396-0.107-0.1070.0000.0000.0000.000
24A93GLY0-0.006-0.01412.9140.0190.0190.0000.0000.0000.000
25A94LYS10.8730.94216.650-0.097-0.0970.0000.0000.0000.000
26A95TYR0-0.048-0.04313.9980.0160.0160.0000.0000.0000.000
27A96THR0-0.020-0.01820.289-0.015-0.0150.0000.0000.0000.000
28A97ILE00.0040.00719.6660.0120.0120.0000.0000.0000.000
29A98SER0-0.0260.00424.268-0.012-0.0120.0000.0000.0000.000
30A99VAL00.0410.00925.5320.0080.0080.0000.0000.0000.000
31A100THR0-0.057-0.04628.204-0.005-0.0050.0000.0000.0000.000
32A101HIS0-0.012-0.01130.380-0.007-0.0070.0000.0000.0000.000
33A102LEU00.0400.04028.0390.0040.0040.0000.0000.0000.000
34A103ALA00.003-0.00227.9770.0010.0010.0000.0000.0000.000
35A104GLN0-0.082-0.05629.861-0.006-0.0060.0000.0000.0000.000
36A105ALA00.0500.03032.3960.0040.0040.0000.0000.0000.000
37A106GLN00.0470.03033.847-0.001-0.0010.0000.0000.0000.000
38A107THR0-0.034-0.02737.415-0.002-0.0020.0000.0000.0000.000
39A108LEU0-0.021-0.00540.0940.0010.0010.0000.0000.0000.000
40A109THR00.009-0.00743.527-0.002-0.0020.0000.0000.0000.000
41A110THR00.0400.02446.4590.0010.0010.0000.0000.0000.000
42A111ARG10.8560.94150.012-0.007-0.0070.0000.0000.0000.000
43A112THR0-0.041-0.02052.3040.0000.0000.0000.0000.0000.000
44A113THR0-0.056-0.05953.4970.0000.0000.0000.0000.0000.000
45A114ARG10.8690.93854.9190.0020.0020.0000.0000.0000.000
46A115ASP-1-0.849-0.92856.640-0.004-0.0040.0000.0000.0000.000
47A116ASP-1-0.818-0.86957.009-0.006-0.0060.0000.0000.0000.000
48A117THR00.006-0.02052.1130.0010.0010.0000.0000.0000.000
49A118LYS10.8840.93753.7240.0090.0090.0000.0000.0000.000
50A119THR0-0.015-0.01656.7250.0000.0000.0000.0000.0000.000
51A120ALA0-0.022-0.01457.2760.0000.0000.0000.0000.0000.000
52A121ILE0-0.031-0.01854.0400.0000.0000.0000.0000.0000.000
53A122ALA0-0.037-0.00756.5380.0010.0010.0000.0000.0000.000
54A123THR0-0.081-0.04458.561-0.001-0.0010.0000.0000.0000.000
55A124SER0-0.027-0.00659.9570.0000.0000.0000.0000.0000.000
56A125ASP-1-0.879-0.93856.2830.0000.0000.0000.0000.0000.000
57A126SER0-0.061-0.02853.9690.0010.0010.0000.0000.0000.000
58A127LYS10.8350.88850.321-0.006-0.0060.0000.0000.0000.000
59A128LEU00.0060.00545.6260.0010.0010.0000.0000.0000.000
60A129THR0-0.017-0.00844.7660.0000.0000.0000.0000.0000.000
61A130ILE00.0090.00540.1020.0000.0000.0000.0000.0000.000
62A131GLN0-0.027-0.03138.9160.0000.0000.0000.0000.0000.000
63A132GLN00.0140.01434.3360.0000.0000.0000.0000.0000.000
64A133GLY00.0760.05436.3340.0010.0010.0000.0000.0000.000
65A134GLY00.002-0.01332.582-0.001-0.0010.0000.0000.0000.000
66A135ASP-1-0.985-0.99532.7060.0460.0460.0000.0000.0000.000
67A136LYS10.8180.92130.986-0.032-0.0320.0000.0000.0000.000
68A137ASP-1-0.920-0.95635.1390.0200.0200.0000.0000.0000.000
69A138PRO0-0.046-0.01037.886-0.002-0.0020.0000.0000.0000.000
70A139ILE00.0080.00437.790-0.001-0.0010.0000.0000.0000.000
71A140THR0-0.041-0.03141.7310.0000.0000.0000.0000.0000.000
72A141ILE0-0.027-0.01842.700-0.001-0.0010.0000.0000.0000.000
73A142ASP-1-0.822-0.88746.5940.0040.0040.0000.0000.0000.000
74A143ILE0-0.032-0.01548.448-0.001-0.0010.0000.0000.0000.000
75A144SER00.0360.01351.9750.0010.0010.0000.0000.0000.000
76A145ALA00.0750.02355.2870.0000.0000.0000.0000.0000.000
77A146ALA0-0.042-0.00557.4560.0000.0000.0000.0000.0000.000
78A147ASN0-0.026-0.01351.849-0.001-0.0010.0000.0000.0000.000
79A148SER00.0240.01152.6500.0000.0000.0000.0000.0000.000
80A149SER00.0420.02954.2390.0000.0000.0000.0000.0000.000
81A150LEU00.0270.01951.0930.0000.0000.0000.0000.0000.000
82A151SER0-0.070-0.07149.709-0.001-0.0010.0000.0000.0000.000
83A152GLY0-0.0040.01249.1080.0000.0000.0000.0000.0000.000
84A153ILE00.0500.01947.6730.0000.0000.0000.0000.0000.000
85A154ARG10.8260.89344.6620.0110.0110.0000.0000.0000.000
86A155ASP-1-0.854-0.90744.355-0.011-0.0110.0000.0000.0000.000
87A156ALA00.0080.01644.6080.0000.0000.0000.0000.0000.000
88A157ILE00.0260.00341.3330.0010.0010.0000.0000.0000.000
89A158ASN0-0.027-0.01140.1370.0010.0010.0000.0000.0000.000
90A159ASN0-0.090-0.07339.560-0.002-0.0020.0000.0000.0000.000
91A160ALA00.0100.01840.7810.0000.0000.0000.0000.0000.000
92A161LYS10.8290.93235.3960.0120.0120.0000.0000.0000.000
93A162ALA00.0780.03836.6310.0010.0010.0000.0000.0000.000
94A163GLY00.0040.01133.7690.0020.0020.0000.0000.0000.000
95A164VAL00.0050.00534.6490.0010.0010.0000.0000.0000.000
96A165SER0-0.0360.00036.550-0.002-0.0020.0000.0000.0000.000
97A166ALA00.0150.00838.4640.0010.0010.0000.0000.0000.000
98A167SER0-0.032-0.01941.785-0.002-0.0020.0000.0000.0000.000
99A168ILE0-0.016-0.01343.6220.0010.0010.0000.0000.0000.000
100A169ILE00.0100.00844.285-0.001-0.0010.0000.0000.0000.000
101A170ASN0-0.014-0.00947.9630.0010.0010.0000.0000.0000.000
102A171VAL0-0.006-0.00450.165-0.001-0.0010.0000.0000.0000.000
103A172GLY00.0230.02452.1480.0000.0000.0000.0000.0000.000
104A173ASN0-0.087-0.07555.2370.0000.0000.0000.0000.0000.000
105A174GLY0-0.0050.01157.8110.0000.0000.0000.0000.0000.000
106A175GLU-1-0.820-0.86255.990-0.003-0.0030.0000.0000.0000.000
107A176TYR0-0.063-0.04351.786-0.001-0.0010.0000.0000.0000.000
108A177ARG10.9030.96549.4780.0020.0020.0000.0000.0000.000
109A178LEU0-0.006-0.00246.617-0.001-0.0010.0000.0000.0000.000
110A179SER00.0170.00642.6900.0010.0010.0000.0000.0000.000
111A180VAL0-0.008-0.01340.696-0.002-0.0020.0000.0000.0000.000
112A181THR00.0090.00935.8190.0020.0020.0000.0000.0000.000
113A182SER00.0350.03533.791-0.002-0.0020.0000.0000.0000.000
114A183ASN0-0.041-0.04631.525-0.002-0.0020.0000.0000.0000.000
115A184ASP-1-0.911-0.92828.0300.0050.0050.0000.0000.0000.000
116A185THR0-0.077-0.07728.137-0.001-0.0010.0000.0000.0000.000
117A186GLY00.1070.05029.7350.0030.0030.0000.0000.0000.000
118A187LEU0-0.065-0.03930.972-0.003-0.0030.0000.0000.0000.000
119A188ASP-1-0.858-0.91830.2390.0370.0370.0000.0000.0000.000
120A189ASN0-0.031-0.03129.581-0.001-0.0010.0000.0000.0000.000
121A190ALA0-0.0080.01433.803-0.004-0.0040.0000.0000.0000.000
122A191MET0-0.053-0.02737.3380.0010.0010.0000.0000.0000.000
123A192THR0-0.023-0.01139.9650.0000.0000.0000.0000.0000.000
124A193LEU0-0.033-0.01842.686-0.001-0.0010.0000.0000.0000.000
125A194SER00.003-0.00545.7170.0000.0000.0000.0000.0000.000
126A195VAL00.0290.01548.8960.0000.0000.0000.0000.0000.000
127A196SER0-0.036-0.01251.5440.0000.0000.0000.0000.0000.000
128A197GLY00.036-0.00654.091-0.001-0.0010.0000.0000.0000.000
129A198ASP-1-0.747-0.90056.6660.0020.0020.0000.0000.0000.000
130A199ASP-1-0.874-0.92856.7910.0060.0060.0000.0000.0000.000
131A200ALA0-0.0040.02457.8610.0000.0000.0000.0000.0000.000
132A201LEU0-0.006-0.01252.0650.0000.0000.0000.0000.0000.000
133A202GLN00.0780.04151.5410.0000.0000.0000.0000.0000.000
134A203SER0-0.065-0.05053.3120.0000.0000.0000.0000.0000.000
135A204PHE0-0.054-0.02351.9560.0000.0000.0000.0000.0000.000
136A205MET0-0.024-0.02246.791-0.001-0.0010.0000.0000.0000.000
137A206GLY00.0230.03448.6900.0000.0000.0000.0000.0000.000
138A207TYR0-0.052-0.04843.3790.0000.0000.0000.0000.0000.000
139A208ASP-1-0.737-0.85446.4000.0180.0180.0000.0000.0000.000
140A209ALA0-0.0030.00544.086-0.001-0.0010.0000.0000.0000.000
141A210SER0-0.090-0.05246.2160.0000.0000.0000.0000.0000.000
142A211ALA0-0.025-0.00348.7630.0000.0000.0000.0000.0000.000
143A212SER0-0.020-0.02451.3430.0000.0000.0000.0000.0000.000
144A213SER0-0.059-0.02353.883-0.001-0.0010.0000.0000.0000.000
145A214ASN0-0.008-0.00749.8250.0000.0000.0000.0000.0000.000
146A215GLY00.0930.05451.620-0.001-0.0010.0000.0000.0000.000
147A216MET0-0.091-0.02945.543-0.001-0.0010.0000.0000.0000.000
148A217GLU-1-0.880-0.95947.9310.0040.0040.0000.0000.0000.000
149A218VAL0-0.009-0.01341.789-0.001-0.0010.0000.0000.0000.000
150A219SER0-0.045-0.02443.3740.0000.0000.0000.0000.0000.000
151A220VAL00.0170.01436.999-0.001-0.0010.0000.0000.0000.000
152A221ALA00.007-0.00238.8210.0010.0010.0000.0000.0000.000
153A222ALA00.0380.02535.346-0.001-0.0010.0000.0000.0000.000
154A223GLN0-0.067-0.04533.2300.0010.0010.0000.0000.0000.000
155A224ASN00.0290.01329.558-0.005-0.0050.0000.0000.0000.000
156A225ALA00.0210.01826.242-0.003-0.0030.0000.0000.0000.000
157A226GLN0-0.030-0.02528.2040.0030.0030.0000.0000.0000.000
158A227LEU00.0040.01322.209-0.007-0.0070.0000.0000.0000.000
159A228THR0-0.030-0.01825.8830.0050.0050.0000.0000.0000.000
160A229VAL00.0430.01819.412-0.008-0.0080.0000.0000.0000.000
161A230ASN0-0.025-0.02219.963-0.007-0.0070.0000.0000.0000.000
162A231ASN0-0.036-0.02423.6020.0010.0010.0000.0000.0000.000
163A232VAL00.0310.03522.923-0.004-0.0040.0000.0000.0000.000
164A233ALA0-0.025-0.01824.964-0.003-0.0030.0000.0000.0000.000
165A234ILE0-0.002-0.00321.1130.0090.0090.0000.0000.0000.000
166A235GLU-1-0.831-0.88325.4390.0450.0450.0000.0000.0000.000
167A236ASN00.005-0.02221.824-0.002-0.0020.0000.0000.0000.000
168A237SER00.0410.01525.662-0.005-0.0050.0000.0000.0000.000
169A238SER00.0150.03022.483-0.013-0.0130.0000.0000.0000.000
170A239ASN00.0330.00924.5240.0110.0110.0000.0000.0000.000
171A240THR0-0.049-0.01419.142-0.006-0.0060.0000.0000.0000.000
172A241ILE0-0.004-0.00318.9850.0070.0070.0000.0000.0000.000
173A242SER00.0150.00014.449-0.007-0.0070.0000.0000.0000.000
174A243ASP-1-0.888-0.92615.0290.1290.1290.0000.0000.0000.000
175A244ALA0-0.0180.00217.4180.0170.0170.0000.0000.0000.000
176A245LEU0-0.032-0.02015.3160.0180.0180.0000.0000.0000.000
177A246GLU-1-0.887-0.94911.4030.6010.6010.0000.0000.0000.000
178A247ASN0-0.075-0.0407.625-0.087-0.0870.0000.0000.0000.000
179A248ILE00.0200.0159.481-0.088-0.0880.0000.0000.0000.000
180A249THR0-0.022-0.00412.308-0.002-0.0020.0000.0000.0000.000
181A250LEU0-0.027-0.02214.847-0.024-0.0240.0000.0000.0000.000
182A251ASN0-0.020-0.00717.7560.0050.0050.0000.0000.0000.000
183A252LEU0-0.005-0.01720.856-0.002-0.0020.0000.0000.0000.000
184A253ASN0-0.062-0.04923.901-0.003-0.0030.0000.0000.0000.000
185A254ASP-1-0.878-0.94526.977-0.006-0.0060.0000.0000.0000.000
186A255VAL0-0.0190.00628.5530.0040.0040.0000.0000.0000.000
187A256THR0-0.0180.00627.414-0.002-0.0020.0000.0000.0000.000
188A257THR0-0.005-0.01730.6970.0010.0010.0000.0000.0000.000
189A258GLY0-0.018-0.00932.061-0.002-0.0020.0000.0000.0000.000
190A259ASN0-0.030-0.02028.1970.0070.0070.0000.0000.0000.000
191A260GLN00.0600.07226.387-0.010-0.0100.0000.0000.0000.000
192A261THR0-0.026-0.02422.7530.0100.0100.0000.0000.0000.000
193A262LEU00.0040.01616.435-0.014-0.0140.0000.0000.0000.000
194A263THR0-0.075-0.05117.8530.0230.0230.0000.0000.0000.000
195A264ILE00.0620.04011.716-0.033-0.0330.0000.0000.0000.000
196A265THR00.0190.01513.6840.0560.0560.0000.0000.0000.000
197A266GLN00.002-0.0058.2010.1170.1170.0000.0000.0000.000
198A267ASP-1-0.894-0.9208.897-0.635-0.6350.0000.0000.0000.000