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: 98QM2

Calculation Name: 4H86-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H86

Chain ID: A

ChEMBL ID:

UniProt ID: P38013

Base Structure: X-ray

Registration Date: 2023-09-23

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1953169.949839
FMO2-HF: Nuclear repulsion 1881868.540222
FMO2-HF: Total energy -71301.409617
FMO2-MP2: Total energy -71508.331426


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:-10:GLY)


Summations of interaction energy for fragment #1(A:-10:GLY)
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.
0.0952.14-0.008-0.99-1.0470.003
Interaction energy analysis for fragmet #1(A:-10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.016
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].
3A-8VAL00.0210.0043.708-0.7681.007-0.006-0.967-0.8020.003
4A-7PRO0-0.0060.0154.2580.4670.685-0.001-0.021-0.1960.000
5A-6ARG11.0000.9715.1771.1691.221-0.001-0.002-0.0490.000
6A-5GLY0-0.004-0.0048.520-0.067-0.0670.0000.0000.0000.000
7A-4SER0-0.0370.0088.6410.0030.0030.0000.0000.0000.000
8A-3HIS00.007-0.00710.4570.0750.0750.0000.0000.0000.000
9A-2MET00.0020.0029.670-0.162-0.1620.0000.0000.0000.000
10A-1ALA00.0180.02112.8230.0950.0950.0000.0000.0000.000
11A0SER0-0.0010.00015.681-0.031-0.0310.0000.0000.0000.000
12A1MET0-0.033-0.00617.3150.0240.0240.0000.0000.0000.000
13A2SER00.003-0.00520.5670.0120.0120.0000.0000.0000.000
14A3ASP-1-0.811-0.91823.001-0.108-0.1080.0000.0000.0000.000
15A4LEU0-0.0220.00024.5580.0150.0150.0000.0000.0000.000
16A5VAL0-0.006-0.00225.4010.0090.0090.0000.0000.0000.000
17A6ASN0-0.049-0.02927.1340.0080.0080.0000.0000.0000.000
18A7LYS10.7890.90127.2220.1200.1200.0000.0000.0000.000
19A8LYS10.9620.97032.3100.0590.0590.0000.0000.0000.000
20A9PHE00.0400.02134.062-0.002-0.0020.0000.0000.0000.000
21A10PRO0-0.0160.00432.6870.0080.0080.0000.0000.0000.000
22A11ALA00.005-0.00535.961-0.001-0.0010.0000.0000.0000.000
23A12GLY0-0.002-0.00138.7720.0010.0010.0000.0000.0000.000
24A13ASP-1-0.919-0.95740.632-0.053-0.0530.0000.0000.0000.000
25A14TYR0-0.034-0.01237.2490.0010.0010.0000.0000.0000.000
26A15LYS10.8180.87741.3300.0570.0570.0000.0000.0000.000
27A16PHE0-0.0040.02140.441-0.003-0.0030.0000.0000.0000.000
28A17GLN0-0.006-0.01742.4490.0020.0020.0000.0000.0000.000
29A18TYR00.003-0.01143.336-0.007-0.0070.0000.0000.0000.000
30A19ILE00.0010.00945.2370.0040.0040.0000.0000.0000.000
31A20ALA00.0110.02147.164-0.004-0.0040.0000.0000.0000.000
32A21ILE0-0.010-0.02645.5470.0020.0020.0000.0000.0000.000
33A22SER00.0460.00449.540-0.002-0.0020.0000.0000.0000.000
34A23GLN0-0.031-0.02950.7690.0010.0010.0000.0000.0000.000
35A24SER0-0.0170.00653.7560.0020.0020.0000.0000.0000.000
36A25ASP-1-0.868-0.93856.332-0.055-0.0550.0000.0000.0000.000
37A26ALA00.0100.01254.646-0.001-0.0010.0000.0000.0000.000
38A27ASP-1-0.854-0.92455.512-0.058-0.0580.0000.0000.0000.000
39A28SER00.0220.02756.5740.0020.0020.0000.0000.0000.000
40A29GLU-1-0.850-0.94956.580-0.054-0.0540.0000.0000.0000.000
41A30SER0-0.053-0.02153.858-0.002-0.0020.0000.0000.0000.000
42A31CYS0-0.034-0.00751.975-0.004-0.0040.0000.0000.0000.000
43A32LYS10.7560.87952.4080.0550.0550.0000.0000.0000.000
44A33MET00.010-0.00152.429-0.002-0.0020.0000.0000.0000.000
45A34PRO0-0.046-0.01348.102-0.001-0.0010.0000.0000.0000.000
46A35GLN00.0200.02748.7030.0030.0030.0000.0000.0000.000
47A36THR0-0.007-0.01446.561-0.004-0.0040.0000.0000.0000.000
48A37VAL0-0.0030.00344.3490.0030.0030.0000.0000.0000.000
49A38GLU-1-0.828-0.89544.281-0.060-0.0600.0000.0000.0000.000
50A39TRP00.0720.01136.862-0.002-0.0020.0000.0000.0000.000
51A40SER00.010-0.00541.388-0.003-0.0030.0000.0000.0000.000
52A41LYS10.8870.94142.8380.0590.0590.0000.0000.0000.000
53A42LEU00.0330.02139.8700.0000.0000.0000.0000.0000.000
54A43ILE0-0.010-0.00537.629-0.001-0.0010.0000.0000.0000.000
55A44SER0-0.047-0.02141.2950.0010.0010.0000.0000.0000.000
56A45GLU-1-0.930-0.95144.290-0.063-0.0630.0000.0000.0000.000
57A46ASN0-0.058-0.02942.271-0.001-0.0010.0000.0000.0000.000
58A47LYS10.9340.97441.5810.0800.0800.0000.0000.0000.000
59A48LYS10.8350.92236.4090.1140.1140.0000.0000.0000.000
60A49VAL0-0.0040.00336.9180.0010.0010.0000.0000.0000.000
61A50ILE00.0120.01932.335-0.007-0.0070.0000.0000.0000.000
62A51ILE0-0.028-0.01232.8610.0080.0080.0000.0000.0000.000
63A52THR0-0.035-0.03229.424-0.016-0.0160.0000.0000.0000.000
64A53GLY00.0480.03929.9030.0130.0130.0000.0000.0000.000
65A54ALA00.017-0.02529.512-0.019-0.0190.0000.0000.0000.000
66A55PRO0-0.052-0.02828.0130.0110.0110.0000.0000.0000.000
67A56ALA00.0530.01330.9720.0100.0100.0000.0000.0000.000
68A57ALA00.0610.05034.064-0.008-0.0080.0000.0000.0000.000
69A58PHE0-0.024-0.02436.8800.0040.0040.0000.0000.0000.000
70A59SER0-0.032-0.00932.104-0.006-0.0060.0000.0000.0000.000
71A60PRO00.0460.01030.384-0.003-0.0030.0000.0000.0000.000
72A61THR00.010-0.01025.7500.0060.0060.0000.0000.0000.000
73A62CYS0-0.0350.01629.080-0.010-0.0100.0000.0000.0000.000
74A63THR0-0.005-0.00631.2900.0050.0050.0000.0000.0000.000
75A64VAL0-0.015-0.00831.4550.0050.0050.0000.0000.0000.000
76A65SER0-0.014-0.01227.544-0.001-0.0010.0000.0000.0000.000
77A66HIS0-0.0170.01928.537-0.008-0.0080.0000.0000.0000.000
78A67ILE00.010-0.00129.8630.0020.0020.0000.0000.0000.000
79A68PRO00.0240.01532.7950.0060.0060.0000.0000.0000.000
80A69GLY00.0470.02832.0810.0060.0060.0000.0000.0000.000
81A70TYR0-0.016-0.04928.8410.0090.0090.0000.0000.0000.000
82A71ILE0-0.024-0.00834.6360.0080.0080.0000.0000.0000.000
83A72ASN0-0.065-0.02235.5050.0120.0120.0000.0000.0000.000
84A73TYR00.001-0.00431.5650.0070.0070.0000.0000.0000.000
85A74LEU0-0.0060.01436.8060.0030.0030.0000.0000.0000.000
86A75ASP-1-0.801-0.89339.234-0.098-0.0980.0000.0000.0000.000
87A76GLU-1-0.839-0.90636.322-0.151-0.1510.0000.0000.0000.000
88A77LEU0-0.010-0.01834.0060.0010.0010.0000.0000.0000.000
89A78VAL0-0.029-0.01138.1260.0030.0030.0000.0000.0000.000
90A79LYS10.7900.87241.6280.1000.1000.0000.0000.0000.000
91A80GLU-1-0.937-0.96739.219-0.106-0.1060.0000.0000.0000.000
92A81LYS10.7760.89434.9350.1440.1440.0000.0000.0000.000
93A82GLU-1-0.881-0.92738.242-0.102-0.1020.0000.0000.0000.000
94A83VAL0-0.032-0.01536.4430.0010.0010.0000.0000.0000.000
95A84ASP-1-0.796-0.89239.474-0.090-0.0900.0000.0000.0000.000
96A85GLN0-0.058-0.02540.2550.0040.0040.0000.0000.0000.000
97A86VAL00.0250.01835.602-0.006-0.0060.0000.0000.0000.000
98A87ILE0-0.032-0.02636.6670.0060.0060.0000.0000.0000.000
99A88VAL00.0260.01834.532-0.010-0.0100.0000.0000.0000.000
100A89VAL0-0.009-0.01033.8350.0100.0100.0000.0000.0000.000
101A90THR00.019-0.00433.858-0.008-0.0080.0000.0000.0000.000
102A91VAL00.0240.01134.4910.0060.0060.0000.0000.0000.000
103A92ASP-1-0.845-0.87737.149-0.113-0.1130.0000.0000.0000.000
104A93ASN00.0180.01739.5580.0030.0030.0000.0000.0000.000
105A94PRO00.0920.03143.038-0.003-0.0030.0000.0000.0000.000
106A95PHE00.0230.00544.662-0.001-0.0010.0000.0000.0000.000
107A96ALA0-0.025-0.00842.360-0.001-0.0010.0000.0000.0000.000
108A97ASN00.0500.00638.965-0.008-0.0080.0000.0000.0000.000
109A98GLN0-0.041-0.00141.948-0.003-0.0030.0000.0000.0000.000
110A99ALA00.008-0.00244.924-0.001-0.0010.0000.0000.0000.000
111A100TRP00.0010.00534.232-0.002-0.0020.0000.0000.0000.000
112A101ALA00.0560.03641.168-0.004-0.0040.0000.0000.0000.000
113A102LYS10.8780.92942.1270.0770.0770.0000.0000.0000.000
114A103SER0-0.120-0.06641.545-0.001-0.0010.0000.0000.0000.000
115A104LEU0-0.010-0.00536.984-0.003-0.0030.0000.0000.0000.000
116A105GLY0-0.029-0.00840.830-0.003-0.0030.0000.0000.0000.000
117A106VAL0-0.0050.00141.6250.0020.0020.0000.0000.0000.000
118A107LYS10.9010.94544.1520.0960.0960.0000.0000.0000.000
119A108ASP-1-0.799-0.88346.519-0.076-0.0760.0000.0000.0000.000
120A109THR00.0210.02144.829-0.003-0.0030.0000.0000.0000.000
121A110THR0-0.063-0.03945.9560.0000.0000.0000.0000.0000.000
122A111HIS0-0.004-0.01942.7050.0030.0030.0000.0000.0000.000
123A112ILE0-0.0020.01638.228-0.006-0.0060.0000.0000.0000.000
124A113LYS10.8200.89940.6540.0940.0940.0000.0000.0000.000
125A114PHE00.020-0.00138.088-0.006-0.0060.0000.0000.0000.000
126A115ALA0-0.014-0.00238.5700.0060.0060.0000.0000.0000.000
127A116SER0-0.010-0.03238.791-0.005-0.0050.0000.0000.0000.000
128A117ASP-1-0.754-0.86935.587-0.100-0.1000.0000.0000.0000.000
129A118PRO00.0290.00538.055-0.002-0.0020.0000.0000.0000.000
130A119GLY0-0.004-0.00838.6920.0020.0020.0000.0000.0000.000
131A120CYS0-0.093-0.02932.320-0.003-0.0030.0000.0000.0000.000
132A121ALA00.0030.01534.606-0.003-0.0030.0000.0000.0000.000
133A122PHE00.0250.00233.9680.0000.0000.0000.0000.0000.000
134A123THR0-0.026-0.03430.282-0.005-0.0050.0000.0000.0000.000
135A124LYS10.8710.93530.6120.0800.0800.0000.0000.0000.000
136A125SER0-0.110-0.04431.0020.0010.0010.0000.0000.0000.000
137A126ILE0-0.029-0.01029.6410.0030.0030.0000.0000.0000.000
138A127GLY00.0270.03226.932-0.010-0.0100.0000.0000.0000.000
139A128PHE0-0.022-0.02724.469-0.024-0.0240.0000.0000.0000.000
140A129GLU-1-0.882-0.94526.605-0.152-0.1520.0000.0000.0000.000
141A130LEU0-0.008-0.01724.955-0.018-0.0180.0000.0000.0000.000
142A131ALA0-0.029-0.01227.0050.0120.0120.0000.0000.0000.000
143A132VAL0-0.011-0.01427.952-0.011-0.0110.0000.0000.0000.000
144A133GLY00.0150.01630.4420.0030.0030.0000.0000.0000.000
145A134ASP-1-0.904-0.95732.121-0.067-0.0670.0000.0000.0000.000
146A135GLY0-0.037-0.01733.7350.0030.0030.0000.0000.0000.000
147A136VAL0-0.0200.00134.5760.0000.0000.0000.0000.0000.000
148A137TYR00.015-0.01129.642-0.003-0.0030.0000.0000.0000.000
149A138TRP00.0280.01630.9760.0010.0010.0000.0000.0000.000
150A139SER00.0500.00729.9650.0000.0000.0000.0000.0000.000
151A140GLY00.0280.01726.355-0.005-0.0050.0000.0000.0000.000
152A141ARG10.7820.86224.9840.2630.2630.0000.0000.0000.000
153A142TRP00.0020.00224.656-0.028-0.0280.0000.0000.0000.000
154A143ALA00.0090.02826.2030.0130.0130.0000.0000.0000.000
155A144MET0-0.035-0.02127.196-0.004-0.0040.0000.0000.0000.000
156A145VAL00.0360.02829.6730.0040.0040.0000.0000.0000.000
157A146VAL0-0.024-0.01531.8670.0020.0020.0000.0000.0000.000
158A147GLU-1-0.785-0.88533.593-0.130-0.1300.0000.0000.0000.000
159A148ASN0-0.046-0.03636.7300.0070.0070.0000.0000.0000.000
160A149GLY00.0310.01538.6910.0050.0050.0000.0000.0000.000
161A150ILE0-0.063-0.03333.1420.0030.0030.0000.0000.0000.000
162A151VAL00.0170.01529.236-0.005-0.0050.0000.0000.0000.000
163A152THR0-0.019-0.02530.166-0.002-0.0020.0000.0000.0000.000
164A153TYR0-0.023-0.03123.473-0.021-0.0210.0000.0000.0000.000
165A154ALA00.0170.00125.4840.0140.0140.0000.0000.0000.000
166A155ALA00.0240.02221.433-0.012-0.0120.0000.0000.0000.000
167A156LYS10.8790.94421.8240.2270.2270.0000.0000.0000.000
168A157GLU-1-0.753-0.82520.215-0.435-0.4350.0000.0000.0000.000
169A158THR00.005-0.00615.3410.0180.0180.0000.0000.0000.000
170A159ASN0-0.050-0.03415.7900.0560.0560.0000.0000.0000.000
171A160PRO00.0270.02520.0280.0020.0020.0000.0000.0000.000
172A161GLY00.0000.00623.5900.0140.0140.0000.0000.0000.000
173A162THR0-0.033-0.02620.2500.0280.0280.0000.0000.0000.000
174A163ASP-1-0.836-0.88818.150-0.529-0.5290.0000.0000.0000.000
175A164VAL0-0.023-0.02521.5670.0340.0340.0000.0000.0000.000
176A165THR00.013-0.01518.659-0.023-0.0230.0000.0000.0000.000
177A166VAL00.0010.03619.2770.0320.0320.0000.0000.0000.000
178A167SER0-0.041-0.04922.0540.0390.0390.0000.0000.0000.000
179A168SER0-0.0040.00024.2300.0330.0330.0000.0000.0000.000
180A169VAL00.0390.02326.5120.0030.0030.0000.0000.0000.000
181A170GLU-1-0.844-0.93226.099-0.245-0.2450.0000.0000.0000.000
182A171SER0-0.036-0.03122.961-0.008-0.0080.0000.0000.0000.000
183A172VAL00.0020.00825.2490.0080.0080.0000.0000.0000.000
184A173LEU00.0210.01428.3650.0110.0110.0000.0000.0000.000
185A174ALA0-0.064-0.02025.5020.0100.0100.0000.0000.0000.000
186A175HIS10.7550.85822.8820.2780.2780.0000.0000.0000.000
187A176LEU00.0330.04228.1180.0150.0150.0000.0000.0000.000