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: 6YQ3Z

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1730462.703225
FMO2-HF: Nuclear repulsion 1658997.651955
FMO2-HF: Total energy -71465.051269
FMO2-MP2: Total energy -71673.563828


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.
1.3014.2590.451-1.47-1.9390
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 : -0.013 / q_NPA : -0.017
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].
3A72ALA00.0610.0353.813-0.3701.307-0.023-0.772-0.882-0.001
4A73THR00.0360.0115.9260.2920.2920.0000.0000.0000.000
5A74SER00.0130.0089.066-0.038-0.0380.0000.0000.0000.000
6A75THR0-0.067-0.07712.5810.0540.0540.0000.0000.0000.000
7A76THR0-0.017-0.00415.285-0.022-0.0220.0000.0000.0000.000
8A77SER00.013-0.00119.0320.0240.0240.0000.0000.0000.000
9A78SER0-0.021-0.01421.826-0.006-0.0060.0000.0000.0000.000
10A79THR0-0.010-0.00724.9640.0000.0000.0000.0000.0000.000
11A80THR00.010-0.00224.992-0.001-0.0010.0000.0000.0000.000
12A81ALA00.0180.01926.429-0.002-0.0020.0000.0000.0000.000
13A82PHE00.0400.02921.3090.0060.0060.0000.0000.0000.000
14A83SER0-0.0070.00019.609-0.005-0.0050.0000.0000.0000.000
15A84ALA00.0380.00515.6180.0170.0170.0000.0000.0000.000
16A85THR0-0.0290.02912.537-0.016-0.0160.0000.0000.0000.000
17A86THR00.004-0.0058.7370.0140.0140.0000.0000.0000.000
18A87ALA0-0.0120.0106.685-0.182-0.1820.0000.0000.0000.000
19A88GLY0-0.020-0.0302.584-0.750-0.3920.266-0.298-0.3270.000
20A89ASN0-0.038-0.0323.5422.8923.7430.209-0.397-0.6630.001
21A90ALA00.0600.0485.310-0.572-0.500-0.001-0.003-0.0670.000
22A91ILE0-0.013-0.0038.517-0.036-0.0360.0000.0000.0000.000
23A92ALA00.0150.00711.460-0.106-0.1060.0000.0000.0000.000
24A93GLY0-0.008-0.01412.9830.0130.0130.0000.0000.0000.000
25A94LYS10.8820.94816.718-0.103-0.1030.0000.0000.0000.000
26A95TYR0-0.054-0.04114.0070.0110.0110.0000.0000.0000.000
27A96THR0-0.018-0.01320.346-0.014-0.0140.0000.0000.0000.000
28A97ILE00.0040.00519.7910.0110.0110.0000.0000.0000.000
29A98SER0-0.0390.00224.314-0.011-0.0110.0000.0000.0000.000
30A99VAL00.0550.01925.6660.0070.0070.0000.0000.0000.000
31A100THR0-0.048-0.04628.237-0.005-0.0050.0000.0000.0000.000
32A101HIS00.0030.00530.405-0.006-0.0060.0000.0000.0000.000
33A102LEU00.0340.03928.0530.0040.0040.0000.0000.0000.000
34A103ALA00.019-0.00128.0000.0010.0010.0000.0000.0000.000
35A104GLN0-0.083-0.05929.869-0.006-0.0060.0000.0000.0000.000
36A105ALA00.0570.03332.4190.0030.0030.0000.0000.0000.000
37A106GLN00.0380.01833.842-0.001-0.0010.0000.0000.0000.000
38A107THR0-0.002-0.03637.409-0.002-0.0020.0000.0000.0000.000
39A108LEU0-0.040-0.01340.0860.0010.0010.0000.0000.0000.000
40A109THR00.008-0.01743.517-0.002-0.0020.0000.0000.0000.000
41A110THR00.0510.03346.4490.0010.0010.0000.0000.0000.000
42A111ARG10.9871.00250.000-0.007-0.0070.0000.0000.0000.000
43A112THR0-0.060-0.01152.2970.0000.0000.0000.0000.0000.000
44A113THR0-0.048-0.03453.4850.0000.0000.0000.0000.0000.000
45A114ARG10.9380.97654.6430.0020.0020.0000.0000.0000.000
46A115ASP-1-0.860-0.93356.624-0.004-0.0040.0000.0000.0000.000
47A116ASP-1-0.803-0.87456.984-0.006-0.0060.0000.0000.0000.000
48A117THR0-0.007-0.02952.1280.0000.0000.0000.0000.0000.000
49A118LYS10.8900.95453.9100.0080.0080.0000.0000.0000.000
50A119THR0-0.027-0.01456.6970.0000.0000.0000.0000.0000.000
51A120ALA0-0.047-0.02557.2410.0000.0000.0000.0000.0000.000
52A121ILE0-0.050-0.03054.1120.0000.0000.0000.0000.0000.000
53A122ALA0-0.028-0.00456.5320.0010.0010.0000.0000.0000.000
54A123THR0-0.087-0.04858.5330.0000.0000.0000.0000.0000.000
55A124SER0-0.030-0.00659.7790.0000.0000.0000.0000.0000.000
56A125ASP-1-0.874-0.93756.2330.0000.0000.0000.0000.0000.000
57A126SER0-0.069-0.03354.0000.0010.0010.0000.0000.0000.000
58A127LYS10.9330.96550.248-0.005-0.0050.0000.0000.0000.000
59A128LEU0-0.0010.00545.4410.0010.0010.0000.0000.0000.000
60A129THR0-0.022-0.01244.6270.0000.0000.0000.0000.0000.000
61A130ILE00.0030.00339.8960.0000.0000.0000.0000.0000.000
62A131GLN0-0.030-0.04238.7500.0000.0000.0000.0000.0000.000
63A132GLN00.0090.00934.212-0.001-0.0010.0000.0000.0000.000
64A133GLY00.0690.05336.3210.0010.0010.0000.0000.0000.000
65A134GLY00.000-0.01932.567-0.001-0.0010.0000.0000.0000.000
66A135ASP-1-0.980-0.98832.6870.0410.0410.0000.0000.0000.000
67A136LYS10.8960.96730.873-0.027-0.0270.0000.0000.0000.000
68A137ASP-1-0.923-0.94835.1290.0160.0160.0000.0000.0000.000
69A138PRO0-0.053-0.01437.906-0.002-0.0020.0000.0000.0000.000
70A139ILE00.0250.01237.518-0.001-0.0010.0000.0000.0000.000
71A140THR0-0.048-0.03241.6980.0000.0000.0000.0000.0000.000
72A141ILE0-0.026-0.02142.599-0.001-0.0010.0000.0000.0000.000
73A142ASP-1-0.893-0.94146.5580.0030.0030.0000.0000.0000.000
74A143ILE0-0.040-0.02348.523-0.001-0.0010.0000.0000.0000.000
75A144SER00.0180.00751.9400.0010.0010.0000.0000.0000.000
76A145ALA00.0850.02855.2530.0000.0000.0000.0000.0000.000
77A146ALA0-0.042-0.00857.4760.0000.0000.0000.0000.0000.000
78A147ASN0-0.020-0.01152.182-0.001-0.0010.0000.0000.0000.000
79A148SER00.0220.01252.6180.0000.0000.0000.0000.0000.000
80A149SER00.0390.03254.0180.0000.0000.0000.0000.0000.000
81A150LEU00.0330.02150.9810.0000.0000.0000.0000.0000.000
82A151SER0-0.069-0.07849.676-0.001-0.0010.0000.0000.0000.000
83A152GLY0-0.0110.00749.077-0.001-0.0010.0000.0000.0000.000
84A153ILE00.0590.02147.5460.0000.0000.0000.0000.0000.000
85A154ARG10.8700.94844.4230.0100.0100.0000.0000.0000.000
86A155ASP-1-0.898-0.95644.324-0.010-0.0100.0000.0000.0000.000
87A156ALA0-0.020-0.00344.5720.0000.0000.0000.0000.0000.000
88A157ILE00.0250.00241.4320.0000.0000.0000.0000.0000.000
89A158ASN0-0.026-0.01440.1050.0010.0010.0000.0000.0000.000
90A159ASN0-0.081-0.05639.524-0.002-0.0020.0000.0000.0000.000
91A160ALA00.0110.01840.7400.0000.0000.0000.0000.0000.000
92A161LYS10.8490.93735.2710.0140.0140.0000.0000.0000.000
93A162ALA00.0750.03736.5940.0010.0010.0000.0000.0000.000
94A163GLY0-0.0120.00033.7320.0020.0020.0000.0000.0000.000
95A164VAL00.0220.01234.6200.0010.0010.0000.0000.0000.000
96A165SER0-0.044-0.00536.651-0.002-0.0020.0000.0000.0000.000
97A166ALA00.0240.01038.4400.0010.0010.0000.0000.0000.000
98A167SER0-0.047-0.02941.691-0.002-0.0020.0000.0000.0000.000
99A168ILE00.004-0.00943.6010.0010.0010.0000.0000.0000.000
100A169ILE00.0060.01044.464-0.001-0.0010.0000.0000.0000.000
101A170ASN0-0.013-0.01247.9490.0010.0010.0000.0000.0000.000
102A171VAL0-0.017-0.00650.098-0.001-0.0010.0000.0000.0000.000
103A172GLY00.0210.02252.1400.0000.0000.0000.0000.0000.000
104A173ASN0-0.084-0.06055.2280.0000.0000.0000.0000.0000.000
105A174GLY00.0030.01657.7920.0000.0000.0000.0000.0000.000
106A175GLU-1-0.838-0.90656.002-0.002-0.0020.0000.0000.0000.000
107A176TYR0-0.070-0.04251.884-0.001-0.0010.0000.0000.0000.000
108A177ARG10.8780.92449.3640.0020.0020.0000.0000.0000.000
109A178LEU0-0.003-0.00446.305-0.001-0.0010.0000.0000.0000.000
110A179SER00.0260.02042.8040.0020.0020.0000.0000.0000.000
111A180VAL0-0.018-0.01840.585-0.002-0.0020.0000.0000.0000.000
112A181THR00.0130.03735.7670.0020.0020.0000.0000.0000.000
113A182SER0-0.0030.02433.515-0.002-0.0020.0000.0000.0000.000
114A183ASN0-0.026-0.03331.469-0.002-0.0020.0000.0000.0000.000
115A184ASP-1-0.921-0.93228.5910.0040.0040.0000.0000.0000.000
116A185THR0-0.073-0.09228.1670.0000.0000.0000.0000.0000.000
117A186GLY00.0930.04829.7270.0030.0030.0000.0000.0000.000
118A187LEU0-0.065-0.04230.969-0.003-0.0030.0000.0000.0000.000
119A188ASP-1-0.885-0.94029.8790.0350.0350.0000.0000.0000.000
120A189ASN0-0.074-0.06429.555-0.001-0.0010.0000.0000.0000.000
121A190ALA00.0060.02233.790-0.003-0.0030.0000.0000.0000.000
122A191MET0-0.056-0.03637.3280.0000.0000.0000.0000.0000.000
123A192THR0-0.023-0.01239.9510.0000.0000.0000.0000.0000.000
124A193LEU0-0.043-0.02142.667-0.001-0.0010.0000.0000.0000.000
125A194SER00.002-0.00345.6970.0000.0000.0000.0000.0000.000
126A195VAL00.0310.01748.8710.0000.0000.0000.0000.0000.000
127A196SER0-0.030-0.01351.5190.0000.0000.0000.0000.0000.000
128A197GLY00.042-0.00154.064-0.001-0.0010.0000.0000.0000.000
129A198ASP-1-0.756-0.91356.6400.0020.0020.0000.0000.0000.000
130A199ASP-1-0.861-0.91956.7670.0050.0050.0000.0000.0000.000
131A200ALA0-0.0270.00057.8420.0000.0000.0000.0000.0000.000
132A201LEU0-0.005-0.00852.0890.0000.0000.0000.0000.0000.000
133A202GLN00.0820.04151.6290.0000.0000.0000.0000.0000.000
134A203SER0-0.068-0.03853.2950.0000.0000.0000.0000.0000.000
135A204PHE0-0.032-0.01551.6230.0000.0000.0000.0000.0000.000
136A205MET0-0.010-0.01847.2170.0000.0000.0000.0000.0000.000
137A206GLY00.0070.03048.6730.0000.0000.0000.0000.0000.000
138A207TYR0-0.056-0.05143.4850.0000.0000.0000.0000.0000.000
139A208ASP-1-0.734-0.86046.4120.0160.0160.0000.0000.0000.000
140A209ALA0-0.0090.00644.0370.0000.0000.0000.0000.0000.000
141A210SER0-0.089-0.04146.2110.0000.0000.0000.0000.0000.000
142A211ALA0-0.0170.00248.7590.0000.0000.0000.0000.0000.000
143A212SER0-0.030-0.02851.3390.0000.0000.0000.0000.0000.000
144A213SER0-0.076-0.03453.881-0.001-0.0010.0000.0000.0000.000
145A214ASN00.0130.00249.5570.0000.0000.0000.0000.0000.000
146A215GLY00.0930.05151.6040.0000.0000.0000.0000.0000.000
147A216MET0-0.083-0.03045.526-0.001-0.0010.0000.0000.0000.000
148A217GLU-1-0.981-1.00147.5470.0040.0040.0000.0000.0000.000
149A218VAL0-0.004-0.01041.776-0.001-0.0010.0000.0000.0000.000
150A219SER0-0.030-0.01343.4770.0000.0000.0000.0000.0000.000
151A220VAL00.0040.01137.0380.0000.0000.0000.0000.0000.000
152A221ALA00.0110.00138.7530.0010.0010.0000.0000.0000.000
153A222ALA00.0330.02735.386-0.001-0.0010.0000.0000.0000.000
154A223GLN0-0.064-0.04432.9490.0010.0010.0000.0000.0000.000
155A224ASN00.0320.02729.460-0.005-0.0050.0000.0000.0000.000
156A225ALA00.0120.01326.244-0.002-0.0020.0000.0000.0000.000
157A226GLN0-0.015-0.01328.2200.0030.0030.0000.0000.0000.000
158A227LEU0-0.0080.00422.227-0.006-0.0060.0000.0000.0000.000
159A228THR0-0.045-0.02425.8770.0050.0050.0000.0000.0000.000
160A229VAL00.0550.02519.439-0.007-0.0070.0000.0000.0000.000
161A230ASN0-0.016-0.02220.062-0.007-0.0070.0000.0000.0000.000
162A231ASN0-0.047-0.03023.654-0.001-0.0010.0000.0000.0000.000
163A232VAL00.0290.03123.197-0.004-0.0040.0000.0000.0000.000
164A233ALA0-0.029-0.01925.001-0.002-0.0020.0000.0000.0000.000
165A234ILE00.003-0.00121.1700.0080.0080.0000.0000.0000.000
166A235GLU-1-0.864-0.91725.4650.0460.0460.0000.0000.0000.000
167A236ASN0-0.006-0.02621.719-0.003-0.0030.0000.0000.0000.000
168A237SER00.0610.03625.671-0.004-0.0040.0000.0000.0000.000
169A238SER00.0330.05323.004-0.011-0.0110.0000.0000.0000.000
170A239ASN00.0240.01324.5310.0110.0110.0000.0000.0000.000
171A240THR0-0.044-0.01919.135-0.005-0.0050.0000.0000.0000.000
172A241ILE00.001-0.00318.8180.0050.0050.0000.0000.0000.000
173A242SER00.003-0.00614.4160.0040.0040.0000.0000.0000.000
174A243ASP-1-0.874-0.92215.0280.1190.1190.0000.0000.0000.000
175A244ALA0-0.0180.00517.4190.0150.0150.0000.0000.0000.000
176A245LEU0-0.035-0.02615.4250.0170.0170.0000.0000.0000.000
177A246GLU-1-0.890-0.94911.3850.5620.5620.0000.0000.0000.000
178A247ASN0-0.065-0.0337.736-0.100-0.1000.0000.0000.0000.000
179A248ILE00.0090.0139.506-0.073-0.0730.0000.0000.0000.000
180A249THR0-0.015-0.00512.334-0.006-0.0060.0000.0000.0000.000
181A250LEU0-0.025-0.01614.860-0.020-0.0200.0000.0000.0000.000
182A251ASN0-0.035-0.01417.622-0.001-0.0010.0000.0000.0000.000
183A252LEU0-0.016-0.02120.871-0.001-0.0010.0000.0000.0000.000
184A253ASN0-0.051-0.04424.064-0.003-0.0030.0000.0000.0000.000
185A254ASP-1-0.894-0.95626.996-0.003-0.0030.0000.0000.0000.000
186A255VAL0-0.0050.01428.5810.0040.0040.0000.0000.0000.000
187A256THR0-0.0130.00327.343-0.002-0.0020.0000.0000.0000.000
188A257THR0-0.003-0.01630.7350.0010.0010.0000.0000.0000.000
189A258GLY0-0.029-0.01532.107-0.002-0.0020.0000.0000.0000.000
190A259ASN0-0.034-0.02128.2430.0060.0060.0000.0000.0000.000
191A260GLN00.0690.07126.376-0.009-0.0090.0000.0000.0000.000
192A261THR0-0.045-0.03522.9680.0100.0100.0000.0000.0000.000
193A262LEU00.0240.02516.412-0.013-0.0130.0000.0000.0000.000
194A263THR0-0.062-0.05118.0430.0200.0200.0000.0000.0000.000
195A264ILE00.0600.04711.827-0.033-0.0330.0000.0000.0000.000
196A265THR00.0090.00513.7620.0520.0520.0000.0000.0000.000
197A266GLN00.006-0.0037.9790.0830.0830.0000.0000.0000.000
198A267ASP-1-0.912-0.9319.198-0.526-0.5260.0000.0000.0000.000