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: ZVZ5N

Calculation Name: 3D8H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D8H

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CXZ9

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2957903.386002
FMO2-HF: Nuclear repulsion 2866310.107976
FMO2-HF: Total energy -91593.278025
FMO2-MP2: Total energy -91860.167335


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:20:THR)


Summations of interaction energy for fragment #1(A:20:THR)
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.
-21.645-14.1187.399-6.729-8.197-0.06
Interaction energy analysis for fragmet #1(A:20:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / 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].
3A22LYS10.9380.9623.831-2.144-0.153-0.017-1.093-0.8790.005
4A23LEU0-0.0080.0136.630-0.197-0.1970.0000.0000.0000.000
5A24THR00.0070.0119.7170.0210.0210.0000.0000.0000.000
6A25LEU0-0.0010.00012.952-0.049-0.0490.0000.0000.0000.000
7A26ILE00.0310.01615.8060.0130.0130.0000.0000.0000.000
8A27ARG10.9100.96619.399-0.076-0.0760.0000.0000.0000.000
9A28HIS00.0230.00322.6340.0020.0020.0000.0000.0000.000
10A29GLY00.0850.03425.986-0.002-0.0020.0000.0000.0000.000
11A30GLU-1-0.820-0.82428.5570.0470.0470.0000.0000.0000.000
12A31SER00.024-0.00331.8940.0010.0010.0000.0000.0000.000
13A32GLU-1-0.782-0.90033.9760.0390.0390.0000.0000.0000.000
14A33TRP00.0290.00636.573-0.003-0.0030.0000.0000.0000.000
15A34ASN0-0.053-0.00932.3610.0010.0010.0000.0000.0000.000
16A35LYS10.8930.92835.755-0.049-0.0490.0000.0000.0000.000
17A36GLU-1-0.868-0.92738.6750.0280.0280.0000.0000.0000.000
18A37ASN0-0.063-0.02838.414-0.003-0.0030.0000.0000.0000.000
19A38ARG10.8650.93038.672-0.026-0.0260.0000.0000.0000.000
20A39PHE0-0.041-0.01435.5200.0020.0020.0000.0000.0000.000
21A40THR00.0080.00333.4890.0010.0010.0000.0000.0000.000
22A41GLY00.0040.01032.069-0.002-0.0020.0000.0000.0000.000
23A42TRP00.007-0.01629.7420.0040.0040.0000.0000.0000.000
24A43THR00.0080.01533.5000.0000.0000.0000.0000.0000.000
25A44ASP-1-0.739-0.84633.8020.0470.0470.0000.0000.0000.000
26A45VAL0-0.070-0.02634.5250.0000.0000.0000.0000.0000.000
27A46SER0-0.020-0.03534.4310.0040.0040.0000.0000.0000.000
28A47LEU0-0.050-0.02829.614-0.002-0.0020.0000.0000.0000.000
29A48SER0-0.059-0.06333.771-0.002-0.0020.0000.0000.0000.000
30A49GLU-1-0.878-0.95734.8280.0530.0530.0000.0000.0000.000
31A50GLN0-0.035-0.02232.1710.0020.0020.0000.0000.0000.000
32A51GLY00.0240.01931.1120.0060.0060.0000.0000.0000.000
33A52VAL0-0.019-0.01830.1660.0080.0080.0000.0000.0000.000
34A53SER0-0.039-0.02630.7910.0070.0070.0000.0000.0000.000
35A54GLU-1-0.783-0.89328.0020.0860.0860.0000.0000.0000.000
36A55ALA0-0.011-0.00526.2030.0120.0120.0000.0000.0000.000
37A56ILE0-0.045-0.01826.2120.0110.0110.0000.0000.0000.000
38A57GLU-1-0.821-0.90727.2750.1260.1260.0000.0000.0000.000
39A58ALA0-0.0180.00022.4790.0140.0140.0000.0000.0000.000
40A59GLY00.003-0.01322.3180.0210.0210.0000.0000.0000.000
41A60ARG10.8150.89223.155-0.097-0.0970.0000.0000.0000.000
42A61MET00.0010.01920.3410.0210.0210.0000.0000.0000.000
43A62LEU0-0.023-0.02617.1410.0290.0290.0000.0000.0000.000
44A63LEU0-0.017-0.00719.2660.0280.0280.0000.0000.0000.000
45A64GLU-1-0.885-0.92121.2870.2250.2250.0000.0000.0000.000
46A65LYS10.7710.87216.707-0.257-0.2570.0000.0000.0000.000
47A66GLY0-0.0030.01016.4790.0600.0600.0000.0000.0000.000
48A67PHE0-0.048-0.02312.4950.0530.0530.0000.0000.0000.000
49A68LYS10.9050.93915.514-0.236-0.2360.0000.0000.0000.000
50A69PHE0-0.0130.00613.9170.0260.0260.0000.0000.0000.000
51A70ASP-1-0.786-0.89314.3660.2080.2080.0000.0000.0000.000
52A71VAL0-0.050-0.03315.812-0.027-0.0270.0000.0000.0000.000
53A72VAL0-0.0020.00017.2240.0240.0240.0000.0000.0000.000
54A73TYR0-0.0060.00815.403-0.016-0.0160.0000.0000.0000.000
55A74THR00.003-0.02220.0080.0040.0040.0000.0000.0000.000
56A75SER0-0.038-0.02922.892-0.006-0.0060.0000.0000.0000.000
57A76VAL0-0.018-0.02325.7920.0030.0030.0000.0000.0000.000
58A77LEU0-0.029-0.00228.804-0.003-0.0030.0000.0000.0000.000
59A78LYS10.9060.91829.522-0.036-0.0360.0000.0000.0000.000
60A79ARG10.8240.92529.543-0.042-0.0420.0000.0000.0000.000
61A80ALA00.0010.00625.2640.0060.0060.0000.0000.0000.000
62A81ILE00.0410.03126.1360.0090.0090.0000.0000.0000.000
63A82MET00.0220.01427.9080.0070.0070.0000.0000.0000.000
64A83THR00.0150.00024.4710.0040.0040.0000.0000.0000.000
65A84THR00.0090.00022.9130.0130.0130.0000.0000.0000.000
66A85TRP0-0.010-0.01124.9140.0060.0060.0000.0000.0000.000
67A86THR0-0.058-0.03027.7550.0000.0000.0000.0000.0000.000
68A87VAL00.0200.00421.4770.0030.0030.0000.0000.0000.000
69A88LEU0-0.003-0.00721.4400.0100.0100.0000.0000.0000.000
70A89LYS10.8870.93424.699-0.096-0.0960.0000.0000.0000.000
71A90GLU-1-0.839-0.89726.1660.1110.1110.0000.0000.0000.000
72A91LEU00.0000.00720.2200.0060.0060.0000.0000.0000.000
73A92GLY0-0.0170.00823.6710.0060.0060.0000.0000.0000.000
74A93ASN0-0.045-0.03819.8860.0000.0000.0000.0000.0000.000
75A94ILE00.0340.01523.9090.0010.0010.0000.0000.0000.000
76A95ASN0-0.041-0.01724.982-0.001-0.0010.0000.0000.0000.000
77A96CYS0-0.062-0.00519.717-0.001-0.0010.0000.0000.0000.000
78A97PRO00.0210.01321.006-0.008-0.0080.0000.0000.0000.000
79A98ILE00.0040.00321.7040.0120.0120.0000.0000.0000.000
80A99ILE0-0.018-0.00120.384-0.011-0.0110.0000.0000.0000.000
81A100ASN00.0180.00622.9840.0100.0100.0000.0000.0000.000
82A101HIS00.022-0.00123.662-0.006-0.0060.0000.0000.0000.000
83A102TRP00.1000.03625.4090.0030.0030.0000.0000.0000.000
84A103ARG10.8750.95523.090-0.013-0.0130.0000.0000.0000.000
85A104LEU00.0270.02119.255-0.004-0.0040.0000.0000.0000.000
86A105ASN00.0430.01223.3600.0100.0100.0000.0000.0000.000
87A106GLU-1-0.793-0.88826.1390.0350.0350.0000.0000.0000.000
88A107ARG10.8490.93727.684-0.009-0.0090.0000.0000.0000.000
89A108HIS00.0100.00428.9910.0020.0020.0000.0000.0000.000
90A109TYR00.003-0.03230.677-0.003-0.0030.0000.0000.0000.000
91A110GLY00.0500.02835.259-0.001-0.0010.0000.0000.0000.000
92A111ALA0-0.046-0.02738.1320.0020.0020.0000.0000.0000.000
93A112LEU0-0.005-0.00537.3760.0010.0010.0000.0000.0000.000
94A113GLN00.0290.02235.4370.0030.0030.0000.0000.0000.000
95A114GLY00.0490.01839.254-0.001-0.0010.0000.0000.0000.000
96A115LEU0-0.054-0.00141.2050.0000.0000.0000.0000.0000.000
97A116ASN00.0360.00441.2580.0020.0020.0000.0000.0000.000
98A117LYS10.9130.96140.252-0.016-0.0160.0000.0000.0000.000
99A118SER00.004-0.00942.135-0.002-0.0020.0000.0000.0000.000
100A119GLU-1-0.776-0.88145.4240.0160.0160.0000.0000.0000.000
101A120THR0-0.036-0.03941.261-0.001-0.0010.0000.0000.0000.000
102A121ALA0-0.028-0.01244.558-0.001-0.0010.0000.0000.0000.000
103A122SER0-0.0460.00446.240-0.001-0.0010.0000.0000.0000.000
104A123LYS10.8680.92547.096-0.013-0.0130.0000.0000.0000.000
105A124PHE00.0000.00143.920-0.001-0.0010.0000.0000.0000.000
106A125GLY00.0560.03546.1740.0000.0000.0000.0000.0000.000
107A126GLU-1-0.830-0.93544.2300.0100.0100.0000.0000.0000.000
108A127ASP-1-0.860-0.92942.7110.0030.0030.0000.0000.0000.000
109A128GLN0-0.002-0.01341.1880.0000.0000.0000.0000.0000.000
110A129VAL00.0280.01939.6840.0000.0000.0000.0000.0000.000
111A130LYS10.8400.91337.776-0.002-0.0020.0000.0000.0000.000
112A131ILE00.0390.01836.4720.0000.0000.0000.0000.0000.000
113A132TRP00.0320.04535.4320.0000.0000.0000.0000.0000.000
114A133ARG10.9170.96733.034-0.020-0.0200.0000.0000.0000.000
115A134ARG10.9170.95531.688-0.006-0.0060.0000.0000.0000.000
116A135SER00.0060.00831.769-0.003-0.0030.0000.0000.0000.000
117A136PHE00.0420.00624.0180.0030.0030.0000.0000.0000.000
118A137ASP-1-0.884-0.96429.388-0.023-0.0230.0000.0000.0000.000
119A138VAL00.0120.01731.7500.0010.0010.0000.0000.0000.000
120A139PRO0-0.0140.00134.4280.0020.0020.0000.0000.0000.000
121A140PRO0-0.010-0.00735.1870.0000.0000.0000.0000.0000.000
122A141PRO00.0070.02238.360-0.001-0.0010.0000.0000.0000.000
123A142VAL00.0150.00839.8170.0020.0020.0000.0000.0000.000
124A143LEU0-0.036-0.00139.4820.0000.0000.0000.0000.0000.000
125A144GLU-1-0.889-0.95442.6300.0040.0040.0000.0000.0000.000
126A145LYS10.9160.93741.802-0.002-0.0020.0000.0000.0000.000
127A146SER0-0.0020.01444.8390.0010.0010.0000.0000.0000.000
128A147ASP-1-0.775-0.86744.9030.0130.0130.0000.0000.0000.000
129A148PRO00.039-0.00344.4200.0000.0000.0000.0000.0000.000
130A149ARG10.7600.86240.985-0.012-0.0120.0000.0000.0000.000
131A150TRP0-0.0270.00238.3800.0010.0010.0000.0000.0000.000
132A151PRO00.0690.01835.6910.0000.0000.0000.0000.0000.000
133A152GLY0-0.044-0.02137.9080.0010.0010.0000.0000.0000.000
134A153ASN0-0.052-0.00839.930-0.001-0.0010.0000.0000.0000.000
135A154GLU-1-0.916-0.95237.0660.0280.0280.0000.0000.0000.000
136A155LEU0-0.008-0.02439.1200.0000.0000.0000.0000.0000.000
137A156ILE0-0.001-0.00133.5160.0000.0000.0000.0000.0000.000
138A157TYR00.001-0.00731.4560.0020.0020.0000.0000.0000.000
139A158LYS10.9590.98235.480-0.025-0.0250.0000.0000.0000.000
140A159GLY0-0.0030.00136.202-0.002-0.0020.0000.0000.0000.000
141A160ILE0-0.028-0.00231.2340.0000.0000.0000.0000.0000.000
142A161CYS0-0.001-0.01032.783-0.002-0.0020.0000.0000.0000.000
143A162PRO00.0660.02034.3620.0000.0000.0000.0000.0000.000
144A163SER0-0.014-0.00434.2200.0010.0010.0000.0000.0000.000
145A164CYS0-0.062-0.02230.882-0.001-0.0010.0000.0000.0000.000
146A165LEU0-0.0200.00332.1650.0010.0010.0000.0000.0000.000
147A166PRO00.0350.03031.917-0.002-0.0020.0000.0000.0000.000
148A167THR0-0.023-0.01034.8440.0010.0010.0000.0000.0000.000
149A168THR0-0.007-0.05436.0470.0020.0020.0000.0000.0000.000
150A169GLU-1-0.733-0.82929.3190.0110.0110.0000.0000.0000.000
151A170CYS0-0.095-0.02331.1680.0010.0010.0000.0000.0000.000
152A171LEU0-0.019-0.02724.0920.0020.0020.0000.0000.0000.000
153A172LYS10.8790.92525.9310.0240.0240.0000.0000.0000.000
154A173ASP-1-0.745-0.87526.236-0.014-0.0140.0000.0000.0000.000
155A174THR0-0.044-0.01624.1670.0020.0020.0000.0000.0000.000
156A175VAL00.018-0.00420.5580.0050.0050.0000.0000.0000.000
157A176GLU-1-0.855-0.91221.697-0.031-0.0310.0000.0000.0000.000
158A177ARG10.6700.80824.004-0.018-0.0180.0000.0000.0000.000
159A178VAL0-0.0070.00018.7710.0070.0070.0000.0000.0000.000
160A179LYS10.9190.96617.9960.0760.0760.0000.0000.0000.000
161A180PRO00.0510.02817.9480.0040.0040.0000.0000.0000.000
162A181TYR0-0.007-0.00419.3120.0070.0070.0000.0000.0000.000
163A182PHE00.020-0.00610.0190.0100.0100.0000.0000.0000.000
164A183GLU-1-0.862-0.94814.665-0.026-0.0260.0000.0000.0000.000
165A184ASP-1-0.868-0.93115.2400.0220.0220.0000.0000.0000.000
166A185VAL0-0.075-0.03717.1490.0060.0060.0000.0000.0000.000
167A186ILE0-0.054-0.02612.9360.0140.0140.0000.0000.0000.000
168A187ALA00.0230.01410.9520.0400.0400.0000.0000.0000.000
169A188PRO00.0370.01810.7230.0660.0660.0000.0000.0000.000
170A189SER0-0.029-0.02112.4380.0030.0030.0000.0000.0000.000
171A190ILE0-0.0020.0076.982-0.010-0.0100.0000.0000.0000.000
172A191MET00.0110.0117.586-0.007-0.0070.0000.0000.0000.000
173A192SER0-0.100-0.0528.547-0.094-0.0940.0000.0000.0000.000
174A193GLY00.0190.0098.359-0.051-0.0510.0000.0000.0000.000
175A194LYS10.8530.9439.391-0.107-0.1070.0000.0000.0000.000
176A195SER0-0.030-0.02310.6680.0750.0750.0000.0000.0000.000
177A196VAL00.005-0.00811.752-0.055-0.0550.0000.0000.0000.000
178A197LEU0-0.0200.00313.1360.0390.0390.0000.0000.0000.000
179A198VAL0-0.009-0.01314.875-0.030-0.0300.0000.0000.0000.000
180A199SER0-0.019-0.01017.3950.0030.0030.0000.0000.0000.000
181A200ALA00.0220.00520.824-0.014-0.0140.0000.0000.0000.000
182A201HIS0-0.0160.00222.6620.0020.0020.0000.0000.0000.000
183A202GLY00.0090.01022.8150.0010.0010.0000.0000.0000.000
184A203ASN0-0.058-0.05822.902-0.008-0.0080.0000.0000.0000.000
185A204SER00.0320.00921.901-0.006-0.0060.0000.0000.0000.000
186A205LEU00.0120.00717.604-0.005-0.0050.0000.0000.0000.000
187A206ARG10.8670.93018.092-0.017-0.0170.0000.0000.0000.000
188A207ALA00.0130.01119.423-0.016-0.0160.0000.0000.0000.000
189A208LEU00.0130.00115.121-0.015-0.0150.0000.0000.0000.000
190A209LEU00.0110.01814.209-0.023-0.0230.0000.0000.0000.000
191A210TYR00.0380.00115.353-0.037-0.0370.0000.0000.0000.000
192A211LEU0-0.034-0.00215.346-0.025-0.0250.0000.0000.0000.000
193A212LEU00.000-0.0059.923-0.034-0.0340.0000.0000.0000.000
194A213GLU-1-0.767-0.87610.965-0.179-0.1790.0000.0000.0000.000
195A214GLY0-0.080-0.02313.227-0.029-0.0290.0000.0000.0000.000
196A215MET0-0.0620.00215.5650.0110.0110.0000.0000.0000.000
197A216THR00.0520.00818.7270.0090.0090.0000.0000.0000.000
198A217PRO0-0.006-0.03422.3970.0060.0060.0000.0000.0000.000
199A218GLU-1-0.930-0.97125.004-0.046-0.0460.0000.0000.0000.000
200A219GLN00.0960.06619.5710.0010.0010.0000.0000.0000.000
201A220ILE0-0.0010.00219.5670.0100.0100.0000.0000.0000.000
202A221LEU0-0.092-0.04122.5340.0140.0140.0000.0000.0000.000
203A222GLU-1-0.936-0.94824.163-0.018-0.0180.0000.0000.0000.000
204A223VAL0-0.056-0.00719.6140.0090.0090.0000.0000.0000.000
205A224ASN0-0.037-0.03422.7170.0030.0030.0000.0000.0000.000
206A225ILE0-0.0010.00918.9670.0050.0050.0000.0000.0000.000
207A226PRO00.0100.01321.034-0.008-0.0080.0000.0000.0000.000
208A227THR0-0.014-0.01922.9190.0070.0070.0000.0000.0000.000
209A228ALA0-0.0070.00023.6720.0040.0040.0000.0000.0000.000
210A229CYS0-0.0210.00221.2470.0110.0110.0000.0000.0000.000
211A230PRO00.001-0.00117.282-0.005-0.0050.0000.0000.0000.000
212A231LEU0-0.0040.00313.8380.0100.0100.0000.0000.0000.000
213A232VAL0-0.004-0.0059.308-0.004-0.0040.0000.0000.0000.000
214A233LEU0-0.003-0.0098.906-0.041-0.0410.0000.0000.0000.000
215A234GLU-1-0.784-0.8634.3681.8601.999-0.001-0.009-0.1280.000
216A235LEU0-0.036-0.0243.613-0.754-0.2340.001-0.171-0.3500.000
217A236ASP-1-0.860-0.9432.108-16.795-15.7076.166-3.618-3.636-0.051
218A237ASP-1-0.860-0.9332.774-2.3801.0131.247-1.790-2.851-0.014
219A238TYR0-0.068-0.0454.084-0.314-0.1190.005-0.037-0.1640.000
220A239LEU0-0.059-0.0235.175-0.170-0.080-0.001-0.006-0.0840.000
221A240LYS10.8900.9476.1610.4430.4430.0000.0000.0000.000
222A241VAL0-0.005-0.0116.307-0.598-0.5980.0000.0000.0000.000
223A242THR00.0120.0204.2750.3630.474-0.001-0.005-0.1050.000
224A243LYS10.8320.8987.074-0.843-0.8430.0000.0000.0000.000
225A244LYS10.8100.8828.5400.1000.1000.0000.0000.0000.000
226A245TYR0-0.068-0.0508.995-0.146-0.1460.0000.0000.0000.000
227A246TYR00.0360.00913.9610.0180.0180.0000.0000.0000.000
228A247LEU0-0.040-0.00614.8020.0190.0190.0000.0000.0000.000
229A248ILE00.0140.00418.165-0.020-0.0200.0000.0000.0000.000