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

tag_button

FMODB ID: V5831

Calculation Name: 4P4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P4H

Chain ID: A

ChEMBL ID:

UniProt ID: O95786

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2222404.046253
FMO2-HF: Nuclear repulsion 2144030.024024
FMO2-HF: Total energy -78374.022229
FMO2-MP2: Total energy -78600.755422


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-7.491-12.54918.634-4.71-8.8660.004
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.055
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].
3A3THR00.058-0.0082.229-3.959-10.89018.144-5.140-6.0730.008
4A4GLU-1-0.913-0.9422.752-3.766-3.0200.4850.716-1.946-0.003
5A5GLN00.0410.0233.7000.4841.4870.006-0.281-0.728-0.001
6A6ARG10.8890.9505.365-0.556-0.432-0.001-0.005-0.1190.000
7A7ARG10.8580.9316.359-1.284-1.2840.0000.0000.0000.000
8A8SER00.001-0.0117.3550.1820.1820.0000.0000.0000.000
9A9LEU00.0000.0029.1750.0960.0960.0000.0000.0000.000
10A10GLN0-0.022-0.02811.0900.1710.1710.0000.0000.0000.000
11A11ALA0-0.037-0.00812.6910.0180.0180.0000.0000.0000.000
12A12PHE00.0100.00712.6240.0200.0200.0000.0000.0000.000
13A13GLN00.0140.01315.7670.0280.0280.0000.0000.0000.000
14A14ASP-1-0.859-0.93517.2220.0150.0150.0000.0000.0000.000
15A15TYR0-0.057-0.04518.4320.0020.0020.0000.0000.0000.000
16A16ILE00.0390.04314.8940.0050.0050.0000.0000.0000.000
17A17ARG10.8560.91519.535-0.017-0.0170.0000.0000.0000.000
18A18LYS10.7250.86422.4670.0310.0310.0000.0000.0000.000
19A19THR0-0.016-0.01622.1100.0000.0000.0000.0000.0000.000
20A20LEU00.0080.00119.3640.0020.0020.0000.0000.0000.000
21A21ASP-1-0.754-0.83423.0960.0340.0340.0000.0000.0000.000
22A22PRO0-0.022-0.01622.121-0.002-0.0020.0000.0000.0000.000
23A23THR0-0.064-0.07023.7190.0040.0040.0000.0000.0000.000
24A24TYR0-0.041-0.03925.9070.0010.0010.0000.0000.0000.000
25A25ILE0-0.0020.00118.9620.0010.0010.0000.0000.0000.000
26A26LEU00.003-0.01621.1610.0030.0030.0000.0000.0000.000
27A27SER0-0.038-0.00422.8550.0070.0070.0000.0000.0000.000
28A28TYR00.0220.00921.0460.0040.0040.0000.0000.0000.000
29A29MET0-0.0300.00615.107-0.003-0.0030.0000.0000.0000.000
30A30ALA00.0050.00819.4080.0150.0150.0000.0000.0000.000
31A31PRO0-0.060-0.03517.6970.0030.0030.0000.0000.0000.000
32A32TRP0-0.0040.02813.088-0.020-0.0200.0000.0000.0000.000
33A33PHE0-0.026-0.02217.3900.0210.0210.0000.0000.0000.000
34A34ARG10.7780.86420.421-0.141-0.1410.0000.0000.0000.000
35A35GLU-1-0.884-0.95323.6610.0640.0640.0000.0000.0000.000
36A36GLU-1-0.871-0.92525.8410.0950.0950.0000.0000.0000.000
37A37GLU-1-0.778-0.87521.0270.1470.1470.0000.0000.0000.000
38A38VAL00.0220.01424.058-0.007-0.0070.0000.0000.0000.000
39A39GLN00.0350.01525.731-0.008-0.0080.0000.0000.0000.000
40A40TYR0-0.047-0.02926.278-0.008-0.0080.0000.0000.0000.000
41A41ILE0-0.030-0.00922.124-0.005-0.0050.0000.0000.0000.000
42A42GLN00.016-0.00126.617-0.010-0.0100.0000.0000.0000.000
43A43ALA0-0.032-0.00529.639-0.005-0.0050.0000.0000.0000.000
44A44GLU-1-0.755-0.86128.0990.0500.0500.0000.0000.0000.000
45A45LYS10.7720.89129.380-0.031-0.0310.0000.0000.0000.000
46A46ASN0-0.025-0.02430.842-0.005-0.0050.0000.0000.0000.000
47A47ASN0-0.101-0.05033.467-0.004-0.0040.0000.0000.0000.000
48A48LYS10.7550.85131.062-0.052-0.0520.0000.0000.0000.000
49A49GLY00.0400.04531.835-0.002-0.0020.0000.0000.0000.000
50A50PRO00.031-0.00228.1960.0040.0040.0000.0000.0000.000
51A51MET00.0380.02325.7550.0030.0030.0000.0000.0000.000
52A52ALA0-0.0130.01525.4790.0040.0040.0000.0000.0000.000
53A53ALA00.0380.02325.7940.0080.0080.0000.0000.0000.000
54A54ALA00.0460.01222.2480.0090.0090.0000.0000.0000.000
55A55THR0-0.047-0.04021.1020.0030.0030.0000.0000.0000.000
56A56LEU0-0.029-0.00721.2760.0160.0160.0000.0000.0000.000
57A57PHE00.0310.00417.5360.0200.0200.0000.0000.0000.000
58A58LEU00.0150.00515.2990.0160.0160.0000.0000.0000.000
59A59LYS10.7690.88116.604-0.144-0.1440.0000.0000.0000.000
60A60PHE00.041-0.00916.7980.0370.0370.0000.0000.0000.000
61A61LEU00.0010.01513.4810.0320.0320.0000.0000.0000.000
62A62LEU0-0.046-0.02111.6780.0620.0620.0000.0000.0000.000
63A63GLU-1-0.859-0.90312.1210.3770.3770.0000.0000.0000.000
64A64LEU0-0.0010.01113.6270.0200.0200.0000.0000.0000.000
65A65GLN0-0.078-0.0348.2960.0670.0670.0000.0000.0000.000
66A66GLU-1-0.918-0.95611.0340.2940.2940.0000.0000.0000.000
67A67GLU-1-0.896-0.9667.9520.8400.8400.0000.0000.0000.000
68A68GLY0-0.028-0.0158.434-0.082-0.0820.0000.0000.0000.000
69A69TRP00.0380.0137.154-0.314-0.3140.0000.0000.0000.000
70A70PHE0-0.014-0.0076.860-0.168-0.1680.0000.0000.0000.000
71A71ARG10.7340.8179.0070.0060.0060.0000.0000.0000.000
72A72GLY00.0900.03010.4550.0020.0020.0000.0000.0000.000
73A73PHE0-0.020-0.03412.0740.0040.0040.0000.0000.0000.000
74A74LEU0-0.027-0.0139.7480.0000.0000.0000.0000.0000.000
75A75ASP-1-0.785-0.88413.6530.0160.0160.0000.0000.0000.000
76A76ALA00.0000.00616.1050.0080.0080.0000.0000.0000.000
77A77LEU0-0.043-0.02515.6680.0030.0030.0000.0000.0000.000
78A78ASP-1-0.919-0.94718.181-0.004-0.0040.0000.0000.0000.000
79A79HIS0-0.051-0.03319.5500.0090.0090.0000.0000.0000.000
80A80ALA0-0.044-0.01421.7440.0030.0030.0000.0000.0000.000
81A81GLY00.0210.02123.2640.0010.0010.0000.0000.0000.000
82A82TYR0-0.040-0.03420.6360.0000.0000.0000.0000.0000.000
83A83SER00.0570.03220.425-0.010-0.0100.0000.0000.0000.000
84A84GLY00.0220.02120.5590.0060.0060.0000.0000.0000.000
85A85LEU0-0.021-0.03517.835-0.012-0.0120.0000.0000.0000.000
86A86TYR0-0.055-0.04413.878-0.016-0.0160.0000.0000.0000.000
87A87GLU-1-0.859-0.93515.043-0.067-0.0670.0000.0000.0000.000
88A88ALA0-0.0320.01415.685-0.018-0.0180.0000.0000.0000.000
89A89ILE0-0.022-0.01411.060-0.030-0.0300.0000.0000.0000.000
90A90GLU-1-0.776-0.83710.567-0.193-0.1930.0000.0000.0000.000
91A91SER0-0.087-0.06911.023-0.014-0.0140.0000.0000.0000.000
92A92TRP0-0.032-0.0226.927-0.002-0.0020.0000.0000.0000.000
93A93ASP-1-0.811-0.87712.804-0.068-0.0680.0000.0000.0000.000
94A94PHE00.0650.01314.5190.0250.0250.0000.0000.0000.000
95A95LYS10.7830.87419.0030.1010.1010.0000.0000.0000.000
96A96LYS10.8050.88621.4960.0460.0460.0000.0000.0000.000
97A97ILE00.0540.03320.0440.0070.0070.0000.0000.0000.000
98A98GLU-1-0.837-0.89823.078-0.033-0.0330.0000.0000.0000.000
99A99LYS10.9310.96424.8050.0280.0280.0000.0000.0000.000
100A100LEU00.0290.03126.4390.0040.0040.0000.0000.0000.000
101A101GLU-1-0.782-0.87727.354-0.009-0.0090.0000.0000.0000.000
102A102GLU-1-0.903-0.92329.198-0.013-0.0130.0000.0000.0000.000
103A103TYR0-0.013-0.03131.7180.0030.0030.0000.0000.0000.000
104A104ARG10.8860.91927.8670.0120.0120.0000.0000.0000.000
105A105LEU0-0.043-0.02431.7150.0030.0030.0000.0000.0000.000
106A106LEU00.0190.03034.3640.0020.0020.0000.0000.0000.000
107A107LEU00.0540.02234.8870.0010.0010.0000.0000.0000.000
108A108LYS10.8650.92031.6580.0050.0050.0000.0000.0000.000
109A109ARG10.7990.89736.7730.0040.0040.0000.0000.0000.000
110A110LEU00.0190.01640.4090.0000.0000.0000.0000.0000.000
111A111GLN00.0120.01738.3860.0010.0010.0000.0000.0000.000
112A112PRO0-0.003-0.01141.4900.0010.0010.0000.0000.0000.000
113A113GLU-1-0.801-0.87945.2220.0030.0030.0000.0000.0000.000
114A114PHE00.017-0.00139.6540.0000.0000.0000.0000.0000.000
115A115LYS10.7930.87943.697-0.009-0.0090.0000.0000.0000.000
116A116THR0-0.053-0.03544.9860.0000.0000.0000.0000.0000.000
117A117ARG10.7310.86647.294-0.003-0.0030.0000.0000.0000.000
118A118ILE0-0.0190.00242.4630.0000.0000.0000.0000.0000.000
119A119ILE00.0120.01245.8440.0010.0010.0000.0000.0000.000
120A120PRO0-0.034-0.01542.3730.0000.0000.0000.0000.0000.000
121A121THR0-0.006-0.03042.8480.0000.0000.0000.0000.0000.000
122A122ASP-1-0.893-0.94244.3550.0060.0060.0000.0000.0000.000
123A123ILE00.0100.00841.2780.0000.0000.0000.0000.0000.000
124A124ILE0-0.007-0.00138.3030.0000.0000.0000.0000.0000.000
125A125SER0-0.011-0.02738.3500.0000.0000.0000.0000.0000.000
126A126ASP-1-0.872-0.90038.8410.0040.0040.0000.0000.0000.000
127A127LEU00.010-0.00735.916-0.001-0.0010.0000.0000.0000.000
128A128SER0-0.021-0.02334.524-0.001-0.0010.0000.0000.0000.000
129A129GLU-1-0.837-0.89731.778-0.004-0.0040.0000.0000.0000.000
130A130CYS0-0.090-0.03430.161-0.002-0.0020.0000.0000.0000.000
131A131LEU0-0.0330.00629.849-0.002-0.0020.0000.0000.0000.000
132A132ILE00.0370.03425.2120.0000.0000.0000.0000.0000.000
133A133ASN00.0270.00028.9830.0020.0020.0000.0000.0000.000
134A134GLN00.0550.02630.3340.0000.0000.0000.0000.0000.000
135A135GLU-1-0.717-0.86330.0750.0090.0090.0000.0000.0000.000
136A136CYS0-0.013-0.00533.292-0.001-0.0010.0000.0000.0000.000
137A137GLU-1-0.924-0.95735.6570.0190.0190.0000.0000.0000.000
138A138GLU-1-0.801-0.87133.2020.0210.0210.0000.0000.0000.000
139A139ILE00.007-0.00235.4680.0000.0000.0000.0000.0000.000
140A140LEU00.0420.02739.0050.0000.0000.0000.0000.0000.000
141A141GLN00.0320.01640.906-0.001-0.0010.0000.0000.0000.000
142A142ILE0-0.0030.00940.1720.0000.0000.0000.0000.0000.000
143A143CYS0-0.081-0.04042.607-0.001-0.0010.0000.0000.0000.000
144A144SER0-0.068-0.02045.217-0.001-0.0010.0000.0000.0000.000
145A145THR0-0.045-0.03545.0520.0000.0000.0000.0000.0000.000
146A146LYS10.8840.93944.424-0.015-0.0150.0000.0000.0000.000
147A147GLY00.0380.04147.789-0.001-0.0010.0000.0000.0000.000
148A148MET00.008-0.01446.6340.0000.0000.0000.0000.0000.000
149A149MET00.0160.02245.6210.0000.0000.0000.0000.0000.000
150A150ALA00.0280.00744.2050.0000.0000.0000.0000.0000.000
151A151GLY00.0450.01242.1470.0000.0000.0000.0000.0000.000
152A152ALA00.0170.00140.8790.0000.0000.0000.0000.0000.000
153A153GLU-1-0.822-0.89840.3260.0090.0090.0000.0000.0000.000
154A154LYS10.8020.89733.759-0.016-0.0160.0000.0000.0000.000
155A155LEU00.0130.00536.3040.0000.0000.0000.0000.0000.000
156A156VAL0-0.006-0.00435.701-0.001-0.0010.0000.0000.0000.000
157A157GLU-1-0.851-0.91132.8590.0140.0140.0000.0000.0000.000
158A158CYS0-0.012-0.00131.5820.0000.0000.0000.0000.0000.000
159A159LEU00.0350.01730.753-0.002-0.0020.0000.0000.0000.000
160A160LEU0-0.064-0.03131.039-0.003-0.0030.0000.0000.0000.000
161A161ARG10.7240.86127.336-0.012-0.0120.0000.0000.0000.000
162A162SER00.006-0.00826.427-0.004-0.0040.0000.0000.0000.000
163A163ASP-1-0.798-0.90422.690-0.024-0.0240.0000.0000.0000.000
164A164LYS10.8100.89424.1700.0090.0090.0000.0000.0000.000
165A165GLU-1-0.795-0.89424.305-0.030-0.0300.0000.0000.0000.000
166A166ASN0-0.006-0.01027.2190.0000.0000.0000.0000.0000.000
167A167TRP00.0780.02829.0920.0030.0030.0000.0000.0000.000
168A168PRO0-0.013-0.00331.4430.0020.0020.0000.0000.0000.000
169A169LYS10.9610.99234.2250.0090.0090.0000.0000.0000.000
170A170THR0-0.019-0.03733.6270.0010.0010.0000.0000.0000.000
171A171LEU00.0270.02436.0640.0010.0010.0000.0000.0000.000
172A172LYS10.7730.88337.9130.0030.0030.0000.0000.0000.000
173A173LEU0-0.026-0.01638.2090.0010.0010.0000.0000.0000.000
174A174ALA00.0340.01540.0160.0010.0010.0000.0000.0000.000
175A175LEU0-0.073-0.04741.1820.0010.0010.0000.0000.0000.000
176A176GLU-1-0.837-0.89643.9340.0000.0000.0000.0000.0000.000
177A177LYS10.7180.86843.978-0.004-0.0040.0000.0000.0000.000
178A178GLU-1-0.786-0.87646.2800.0040.0040.0000.0000.0000.000
179A179ARG10.9480.96947.968-0.002-0.0020.0000.0000.0000.000
180A180ASN00.0420.01645.9300.0000.0000.0000.0000.0000.000
181A181LYS10.8940.94849.300-0.002-0.0020.0000.0000.0000.000
182A182PHE00.0420.01341.7830.0000.0000.0000.0000.0000.000
183A183SER00.035-0.01744.714-0.001-0.0010.0000.0000.0000.000
184A184GLU-1-0.900-0.93844.723-0.003-0.0030.0000.0000.0000.000
185A185LEU0-0.050-0.01644.5630.0000.0000.0000.0000.0000.000
186A186TRP0-0.100-0.04535.578-0.001-0.0010.0000.0000.0000.000
187A187ILE0-0.003-0.00641.0050.0000.0000.0000.0000.0000.000
188A188VAL0-0.029-0.00836.136-0.001-0.0010.0000.0000.0000.000