Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 94442

Calculation Name: 4F2H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F2H

Chain ID: A

ChEMBL ID:

UniProt ID: P32917

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2235542.185413
FMO2-HF: Nuclear repulsion 2159878.978127
FMO2-HF: Total energy -75663.207286
FMO2-MP2: Total energy -75886.924631


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:584:SER)


Summations of interaction energy for fragment #1(A:584:SER)
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.
-15.44-12.44411.431-7.418-7.009-0.002
Interaction energy analysis for fragmet #1(A:584:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.015
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].
3A586VAL00.0240.0022.350-4.859-2.3941.634-1.734-2.3650.012
4A587ASP-1-0.834-0.9031.828-8.907-9.3079.783-5.382-4.001-0.015
5A588SER0-0.0290.0253.588-0.3500.4350.015-0.277-0.5230.001
6A589ILE0-0.005-0.0085.501-0.336-0.3360.0000.0000.0000.000
7A590GLN00.0510.0196.358-0.078-0.0780.0000.0000.0000.000
8A591SER00.0250.0316.510-0.141-0.1410.0000.0000.0000.000
9A592VAL00.0150.0239.162-0.057-0.0570.0000.0000.0000.000
10A593LEU0-0.014-0.00311.346-0.066-0.0660.0000.0000.0000.000
11A594THR0-0.022-0.05511.133-0.058-0.0580.0000.0000.0000.000
12A595THR00.0080.00312.193-0.046-0.0460.0000.0000.0000.000
13A596ILE0-0.027-0.01914.663-0.016-0.0160.0000.0000.0000.000
14A597SER0-0.0340.00016.578-0.022-0.0220.0000.0000.0000.000
15A598SER00.051-0.01016.542-0.018-0.0180.0000.0000.0000.000
16A599ILE00.009-0.00417.955-0.011-0.0110.0000.0000.0000.000
17A600LEU0-0.027-0.01320.579-0.005-0.0050.0000.0000.0000.000
18A601SER0-0.027-0.02221.721-0.002-0.0020.0000.0000.0000.000
19A602LEU00.0280.02923.232-0.003-0.0030.0000.0000.0000.000
20A603LYS10.8810.93024.197-0.073-0.0730.0000.0000.0000.000
21A604ARG10.9230.98025.552-0.054-0.0540.0000.0000.0000.000
22A605GLU-1-0.938-0.96628.1130.0150.0150.0000.0000.0000.000
23A606LYS10.8290.91530.336-0.035-0.0350.0000.0000.0000.000
24A607PRO0-0.0120.00328.613-0.003-0.0030.0000.0000.0000.000
25A608ASP-1-0.811-0.91331.8260.0090.0090.0000.0000.0000.000
26A609ASN0-0.049-0.05332.9610.0020.0020.0000.0000.0000.000
27A610LEU00.0100.00425.9630.0010.0010.0000.0000.0000.000
28A611ALA0-0.0050.00428.748-0.001-0.0010.0000.0000.0000.000
29A612ILE0-0.011-0.01523.690-0.002-0.0020.0000.0000.0000.000
30A613ILE0-0.010-0.00624.976-0.001-0.0010.0000.0000.0000.000
31A614LEU0-0.007-0.00921.768-0.007-0.0070.0000.0000.0000.000
32A615GLN0-0.010-0.01621.501-0.009-0.0090.0000.0000.0000.000
33A616ILE00.0260.00020.517-0.022-0.0220.0000.0000.0000.000
34A617ASP-1-0.913-0.96219.283-0.264-0.2640.0000.0000.0000.000
35A618PHE00.1060.00020.105-0.019-0.0190.0000.0000.0000.000
36A619THR0-0.088-0.02221.3770.0010.0010.0000.0000.0000.000
37A620LYS10.9130.95115.2530.4240.4240.0000.0000.0000.000
38A621LEU0-0.084-0.00315.870-0.035-0.0350.0000.0000.0000.000
39A622LYS10.9140.96211.4740.3570.3570.0000.0000.0000.000
40A623GLU-1-0.886-0.91315.541-0.130-0.1300.0000.0000.0000.000
41A624GLU-1-0.768-0.91518.146-0.147-0.1470.0000.0000.0000.000
42A625ASP-1-0.906-0.93319.702-0.084-0.0840.0000.0000.0000.000
43A626SER00.037-0.00917.1850.0090.0090.0000.0000.0000.000
44A627LEU0-0.094-0.05819.5150.0070.0070.0000.0000.0000.000
45A628ILE00.016-0.00722.9440.0090.0090.0000.0000.0000.000
46A629VAL00.0460.03519.5690.0090.0090.0000.0000.0000.000
47A630VAL00.0110.01021.2080.0090.0090.0000.0000.0000.000
48A631TYR0-0.047-0.02123.2710.0080.0080.0000.0000.0000.000
49A632ASN00.0380.00524.8220.0030.0030.0000.0000.0000.000
50A633SER0-0.015-0.01922.5060.0110.0110.0000.0000.0000.000
51A634LEU0-0.016-0.01124.8550.0050.0050.0000.0000.0000.000
52A635LYS10.9230.95327.2340.0270.0270.0000.0000.0000.000
53A636ALA00.0340.08026.9340.0040.0040.0000.0000.0000.000
54A637LEU00.020-0.00424.5370.0050.0050.0000.0000.0000.000
55A638THR0-0.132-0.11628.6500.0010.0010.0000.0000.0000.000
56A639ILE0-0.020-0.00131.2500.0010.0010.0000.0000.0000.000
57A640LYS10.8940.96829.921-0.023-0.0230.0000.0000.0000.000
58A641PHE0-0.039-0.03128.3800.0000.0000.0000.0000.0000.000
59A642ALA00.0850.04233.187-0.004-0.0040.0000.0000.0000.000
60A643ARG10.8120.88535.8350.0050.0050.0000.0000.0000.000
61A644LEU00.0360.04128.383-0.003-0.0030.0000.0000.0000.000
62A645GLN0-0.045-0.01431.587-0.005-0.0050.0000.0000.0000.000
63A646PHE00.0180.01728.585-0.001-0.0010.0000.0000.0000.000
64A647CYS0-0.035-0.02528.0930.0000.0000.0000.0000.0000.000
65A648PHE00.0440.04525.790-0.006-0.0060.0000.0000.0000.000
66A649VAL00.0160.02425.5060.0040.0040.0000.0000.0000.000
67A650ASP-1-0.700-0.84125.573-0.149-0.1490.0000.0000.0000.000
68A651ARG10.9660.95422.8870.2110.2110.0000.0000.0000.000
69A652ASN0-0.139-0.08424.125-0.022-0.0220.0000.0000.0000.000
70A653ASN00.000-0.00426.5560.0020.0020.0000.0000.0000.000
71A654TYR0-0.009-0.00627.6870.0130.0130.0000.0000.0000.000
72A655VAL0-0.012-0.00729.698-0.004-0.0040.0000.0000.0000.000
73A656LEU0-0.050-0.02228.0570.0020.0020.0000.0000.0000.000
74A657ASP-1-0.844-0.93931.444-0.055-0.0550.0000.0000.0000.000
75A658TYR0-0.020-0.02831.609-0.004-0.0040.0000.0000.0000.000
76A659GLY00.0130.01533.1880.0030.0030.0000.0000.0000.000
77A660SER00.0320.01833.6790.0000.0000.0000.0000.0000.000
78A661VAL00.0440.01329.627-0.001-0.0010.0000.0000.0000.000
79A662LEU0-0.018-0.00532.7210.0000.0000.0000.0000.0000.000
80A663HIS0-0.017-0.02735.497-0.001-0.0010.0000.0000.0000.000
81A664LYS10.8700.94935.3670.0430.0430.0000.0000.0000.000
82A665ILE00.0000.02230.070-0.004-0.0040.0000.0000.0000.000
83A666ASP-1-0.772-0.87134.107-0.034-0.0340.0000.0000.0000.000
84A667SER0-0.067-0.00934.6050.0020.0020.0000.0000.0000.000
85A668LEU00.0330.01027.2650.0000.0000.0000.0000.0000.000
86A669ASP-1-0.826-0.93630.345-0.063-0.0630.0000.0000.0000.000
87A670SER0-0.050-0.02132.349-0.005-0.0050.0000.0000.0000.000
88A671ILE0-0.0090.00726.200-0.003-0.0030.0000.0000.0000.000
89A672SER0-0.066-0.02628.305-0.012-0.0120.0000.0000.0000.000
90A673ASN00.0810.00829.359-0.011-0.0110.0000.0000.0000.000
91A674LEU0-0.078-0.02329.572-0.004-0.0040.0000.0000.0000.000
92A675LYS10.8820.94825.4890.1220.1220.0000.0000.0000.000
93A676SER0-0.084-0.04229.311-0.007-0.0070.0000.0000.0000.000
94A677LYS10.9330.98932.2690.0800.0800.0000.0000.0000.000
95A678SER00.0010.00032.973-0.005-0.0050.0000.0000.0000.000
96A679SER0-0.024-0.04733.6270.0060.0060.0000.0000.0000.000
97A680SER00.0080.00435.240-0.003-0.0030.0000.0000.0000.000
98A681THR00.0070.01234.7870.0020.0020.0000.0000.0000.000
99A682GLN0-0.025-0.00630.472-0.007-0.0070.0000.0000.0000.000
100A683PHE00.0070.00527.4520.0080.0080.0000.0000.0000.000
101A684SER00.0170.00830.214-0.002-0.0020.0000.0000.0000.000
102A685PRO00.0400.01628.7500.0060.0060.0000.0000.0000.000
103A686ILE00.0740.01831.1940.0050.0050.0000.0000.0000.000
104A687TRP0-0.0040.02432.2760.0020.0020.0000.0000.0000.000
105A688LEU00.0480.02229.6550.0040.0040.0000.0000.0000.000
106A689LYS10.8490.93333.6920.0380.0380.0000.0000.0000.000
107A690ASN0-0.003-0.00535.5140.0060.0060.0000.0000.0000.000
108A691THR0-0.067-0.01736.2240.0030.0030.0000.0000.0000.000
109A692LEU0-0.081-0.05333.4480.0020.0020.0000.0000.0000.000
110A693TYR0-0.070-0.04033.9120.0050.0050.0000.0000.0000.000
111A694PRO00.0250.01539.1260.0000.0000.0000.0000.0000.000
112A695GLU-1-0.919-0.95942.391-0.020-0.0200.0000.0000.0000.000
113A696ASN0-0.063-0.03040.3350.0000.0000.0000.0000.0000.000
114A697ILE00.0280.00835.651-0.001-0.0010.0000.0000.0000.000
115A698HIS0-0.010-0.00138.9870.0020.0020.0000.0000.0000.000
116A699GLU-1-0.849-0.89236.244-0.009-0.0090.0000.0000.0000.000
117A700HIS10.8530.93133.564-0.008-0.0080.0000.0000.0000.000
118A701LEU00.0180.01831.1280.0010.0010.0000.0000.0000.000
119A702GLY0-0.020-0.00828.1730.0010.0010.0000.0000.0000.000
120A703ILE0-0.032-0.02425.910-0.002-0.0020.0000.0000.0000.000
121A704VAL00.0420.02321.1730.0010.0010.0000.0000.0000.000
122A705ALA0-0.0110.00221.739-0.002-0.0020.0000.0000.0000.000
123A706VAL00.0310.02017.067-0.009-0.0090.0000.0000.0000.000
124A707SER00.004-0.01017.588-0.002-0.0020.0000.0000.0000.000
125A708ASN00.0800.04315.456-0.013-0.0130.0000.0000.0000.000
126A709SER0-0.035-0.00716.248-0.046-0.0460.0000.0000.0000.000
127A710ASN00.008-0.02117.205-0.027-0.0270.0000.0000.0000.000
128A711MET00.0130.01815.4210.0390.0390.0000.0000.0000.000
129A712GLU-1-0.925-0.94618.618-0.213-0.2130.0000.0000.0000.000
130A713ALA00.0390.00022.2050.0150.0150.0000.0000.0000.000
131A714LYS10.9260.95323.6510.1400.1400.0000.0000.0000.000
132A715LYS10.9110.97424.1080.1960.1960.0000.0000.0000.000
133A716SER00.0350.05419.7160.0110.0110.0000.0000.0000.000
134A717ILE00.0920.03421.7400.0110.0110.0000.0000.0000.000
135A718LEU00.0100.04816.8110.0180.0180.0000.0000.0000.000
136A719PHE00.0220.01219.3710.0110.0110.0000.0000.0000.000
137A720GLN0-0.0120.00722.6930.0250.0250.0000.0000.0000.000
138A721ASP-1-0.778-0.84525.538-0.067-0.0670.0000.0000.0000.000
139A722TYR0-0.022-0.07624.2940.0080.0080.0000.0000.0000.000
140A723ARG10.9070.89228.8610.0670.0670.0000.0000.0000.000
141A724CYS0-0.0630.02231.1000.0050.0050.0000.0000.0000.000
142A725PHE00.036-0.01031.0070.0030.0030.0000.0000.0000.000
143A726THR0-0.123-0.06432.6350.0040.0040.0000.0000.0000.000
144A727SER00.0110.01133.6150.0000.0000.0000.0000.0000.000
145A728PHE00.0470.00736.3080.0000.0000.0000.0000.0000.000
146A729GLY00.004-0.00538.0050.0020.0020.0000.0000.0000.000
147A730ARG10.8970.97631.616-0.006-0.0060.0000.0000.0000.000
148A731ARG10.9940.98730.0660.0120.0120.0000.0000.0000.000
149A732ARG10.9630.97225.0410.0440.0440.0000.0000.0000.000
150A733PRO0-0.0020.01427.7370.0070.0070.0000.0000.0000.000
151A734ASN00.0020.00926.9710.0010.0010.0000.0000.0000.000
152A735GLU-1-0.885-0.96423.702-0.071-0.0710.0000.0000.0000.000
153A736LEU00.0130.00718.4490.0030.0030.0000.0000.0000.000
154A737LYS10.8580.94119.2060.1130.1130.0000.0000.0000.000
155A738ILE00.0120.00013.969-0.010-0.0100.0000.0000.0000.000
156A739LYS10.8830.95412.1860.4980.4980.0000.0000.0000.000
157A740VAL0-0.035-0.02111.953-0.033-0.0330.0000.0000.0000.000
158A741GLY0-0.045-0.0359.5590.0000.0000.0000.0000.0000.000
159A742TYR0-0.019-0.0264.6510.0610.207-0.001-0.025-0.1200.000
160A743LEU0-0.048-0.0167.7730.1000.1000.0000.0000.0000.000
161A744ASN00.0050.0087.541-0.438-0.4380.0000.0000.0000.000
162A745VAL0-0.050-0.0359.6240.1370.1370.0000.0000.0000.000
163A746ASP-1-0.783-0.83212.465-0.277-0.2770.0000.0000.0000.000
164A747TYR0-0.042-0.05514.0350.0270.0270.0000.0000.0000.000
165A748SER0-0.010-0.05415.3060.0300.0300.0000.0000.0000.000
166A749ASP-1-0.910-0.93617.620-0.142-0.1420.0000.0000.0000.000
167A750LYS10.8130.90519.8190.2270.2270.0000.0000.0000.000
168A751ILE0-0.064-0.02217.5750.0090.0090.0000.0000.0000.000
169A752ASP-1-0.917-0.97519.442-0.107-0.1070.0000.0000.0000.000
170A753GLU-1-0.945-0.95717.007-0.005-0.0050.0000.0000.0000.000
171A754LEU0-0.046-0.01614.1280.0090.0090.0000.0000.0000.000
172A755VAL0-0.018-0.00812.721-0.005-0.0050.0000.0000.0000.000
173A756GLU-1-0.835-0.9218.641-0.991-0.9910.0000.0000.0000.000
174A757ALA00.0080.0119.0990.0540.0540.0000.0000.0000.000
175A758SER00.0270.0137.406-0.170-0.1700.0000.0000.0000.000
176A759SER0-0.035-0.0069.423-0.015-0.0150.0000.0000.0000.000
177A760TRP00.000-0.00513.0650.0150.0150.0000.0000.0000.000
178A761THR00.0690.00315.4090.0060.0060.0000.0000.0000.000
179A762PHE00.0660.03112.4760.0190.0190.0000.0000.0000.000
180A763VAL00.0080.02113.8530.0150.0150.0000.0000.0000.000
181A764LEU00.0040.01116.0020.0120.0120.0000.0000.0000.000
182A765GLU-1-0.848-0.91918.0600.0690.0690.0000.0000.0000.000
183A766THR0-0.012-0.02415.9430.0210.0210.0000.0000.0000.000
184A767LEU0-0.045-0.01918.5100.0040.0040.0000.0000.0000.000
185A768CYS0-0.038-0.02020.961-0.003-0.0030.0000.0000.0000.000
186A769TYR00.0620.03518.9340.0000.0000.0000.0000.0000.000
187A770SER0-0.069-0.02020.7940.0060.0060.0000.0000.0000.000
188A771PHE0-0.077-0.06023.3350.0000.0000.0000.0000.0000.000
189A772GLY0-0.024-0.00826.163-0.005-0.0050.0000.0000.0000.000
190A773LEU0-0.0190.00326.471-0.002-0.0020.0000.0000.0000.000
191A774SER0-0.0120.00324.6820.0080.0080.0000.0000.0000.000