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: ZV2NN

Calculation Name: 3HIM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HIM

Chain ID: A

ChEMBL ID:

UniProt ID: Q0SD48

Base Structure: X-ray

Registration Date: 2023-09-20

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889105.423933
FMO2-HF: Nuclear repulsion 1817738.648656
FMO2-HF: Total energy -71366.775277
FMO2-MP2: Total energy -71577.51831


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:14:THR)


Summations of interaction energy for fragment #1(A:14: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.
-2.806-1.018-0.026-0.868-0.8940.004
Interaction energy analysis for fragmet #1(A:14:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.002
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].
3A16LYS11.0320.9983.827-1.3500.438-0.026-0.868-0.8940.004
4A17ALA00.0170.0076.5610.0850.0850.0000.0000.0000.000
5A18ALA00.0190.0095.244-0.040-0.0400.0000.0000.0000.000
6A19ALA00.0120.0044.914-0.078-0.0780.0000.0000.0000.000
7A20ARG10.9720.9786.701-0.113-0.1130.0000.0000.0000.000
8A21ILE00.0150.0189.906-0.025-0.0250.0000.0000.0000.000
9A22ARG10.7790.8554.841-0.711-0.7110.0000.0000.0000.000
10A23ALA00.0090.00910.701-0.050-0.0500.0000.0000.0000.000
11A24ALA00.0440.01912.565-0.021-0.0210.0000.0000.0000.000
12A25ALA0-0.021-0.02414.137-0.014-0.0140.0000.0000.0000.000
13A26ILE0-0.0230.00012.795-0.018-0.0180.0000.0000.0000.000
14A27GLU-1-0.847-0.92716.4100.0040.0040.0000.0000.0000.000
15A28VAL0-0.008-0.00418.860-0.006-0.0060.0000.0000.0000.000
16A29PHE0-0.060-0.04416.3470.0020.0020.0000.0000.0000.000
17A30ALA0-0.011-0.00220.383-0.009-0.0090.0000.0000.0000.000
18A31ALA0-0.051-0.01322.220-0.006-0.0060.0000.0000.0000.000
19A32LYS10.8200.90224.069-0.088-0.0880.0000.0000.0000.000
20A33GLY00.0530.04224.468-0.002-0.0020.0000.0000.0000.000
21A34TYR00.0470.01219.1020.0190.0190.0000.0000.0000.000
22A35GLY0-0.018-0.00922.7930.0130.0130.0000.0000.0000.000
23A36ALA00.0090.01425.5670.0050.0050.0000.0000.0000.000
24A37THR0-0.0080.01821.1540.0030.0030.0000.0000.0000.000
25A38THR00.0140.00322.4150.0140.0140.0000.0000.0000.000
26A39THR00.0570.00217.612-0.005-0.0050.0000.0000.0000.000
27A40ARG10.9090.95718.199-0.205-0.2050.0000.0000.0000.000
28A41GLU-1-0.714-0.85221.4950.1010.1010.0000.0000.0000.000
29A42ILE00.0200.02415.548-0.002-0.0020.0000.0000.0000.000
30A43ALA0-0.051-0.02817.3000.0060.0060.0000.0000.0000.000
31A44ALA00.0270.01118.297-0.008-0.0080.0000.0000.0000.000
32A45SER0-0.058-0.02618.454-0.010-0.0100.0000.0000.0000.000
33A46LEU0-0.067-0.04113.653-0.007-0.0070.0000.0000.0000.000
34A47ASP-1-0.925-0.95317.8290.1020.1020.0000.0000.0000.000
35A48MET0-0.086-0.03012.3300.0180.0180.0000.0000.0000.000
36A49SER00.0480.02318.1390.0000.0000.0000.0000.0000.000
37A50PRO00.019-0.01619.1690.0260.0260.0000.0000.0000.000
38A51GLY00.0020.00019.2310.0010.0010.0000.0000.0000.000
39A52ALA00.0120.01715.1630.0390.0390.0000.0000.0000.000
40A53VAL00.010-0.00913.6210.0650.0650.0000.0000.0000.000
41A54TYR00.0360.03513.3810.1120.1120.0000.0000.0000.000
42A55PRO00.006-0.01112.1800.0240.0240.0000.0000.0000.000
43A56HIS0-0.029-0.0097.8000.2080.2080.0000.0000.0000.000
44A57TYR00.021-0.0037.7800.1030.1030.0000.0000.0000.000
45A58LYS10.9080.96813.140-0.617-0.6170.0000.0000.0000.000
46A59THR00.0270.01616.284-0.045-0.0450.0000.0000.0000.000
47A60LYS10.8510.91416.501-0.093-0.0930.0000.0000.0000.000
48A61GLU-1-0.757-0.84517.1610.2100.2100.0000.0000.0000.000
49A62SER00.009-0.00613.9540.0270.0270.0000.0000.0000.000
50A63LEU0-0.023-0.00511.8430.0640.0640.0000.0000.0000.000
51A64LEU00.0220.01513.339-0.005-0.0050.0000.0000.0000.000
52A65TYR00.008-0.00412.966-0.040-0.0400.0000.0000.0000.000
53A66ALA0-0.004-0.0119.229-0.025-0.0250.0000.0000.0000.000
54A67ILE00.0080.00210.728-0.047-0.0470.0000.0000.0000.000
55A68SER0-0.002-0.01212.605-0.073-0.0730.0000.0000.0000.000
56A69LEU0-0.0270.00410.174-0.045-0.0450.0000.0000.0000.000
57A70GLU-1-0.791-0.8486.833-0.080-0.0800.0000.0000.0000.000
58A71GLY00.0200.00810.438-0.073-0.0730.0000.0000.0000.000
59A72HIS10.7740.84813.6480.0090.0090.0000.0000.0000.000
60A73HIS00.0530.02410.385-0.019-0.0190.0000.0000.0000.000
61A74SER0-0.0130.01211.561-0.028-0.0280.0000.0000.0000.000
62A75VAL00.0330.02513.031-0.003-0.0030.0000.0000.0000.000
63A76LEU00.0200.01716.0000.0060.0060.0000.0000.0000.000
64A77ALA00.000-0.00113.4630.0040.0040.0000.0000.0000.000
65A78ALA0-0.022-0.00715.5180.0080.0080.0000.0000.0000.000
66A79ILE0-0.014-0.01417.6030.0110.0110.0000.0000.0000.000
67A80THR0-0.053-0.04118.3160.0130.0130.0000.0000.0000.000
68A81ALA0-0.037-0.01217.6380.0060.0060.0000.0000.0000.000
69A82ALA0-0.0280.00519.7200.0100.0100.0000.0000.0000.000
70A83ASP-1-0.722-0.81422.955-0.092-0.0920.0000.0000.0000.000
71A84PHE0-0.010-0.00923.934-0.009-0.0090.0000.0000.0000.000
72A85PRO0-0.030-0.04025.7850.0080.0080.0000.0000.0000.000
73A86ASP-1-0.893-0.93028.871-0.091-0.0910.0000.0000.0000.000
74A87ILE0-0.069-0.02430.1680.0050.0050.0000.0000.0000.000
75A88ALA00.0430.02132.8110.0000.0000.0000.0000.0000.000
76A89ALA00.0250.01533.309-0.004-0.0040.0000.0000.0000.000
77A90PRO00.0530.01233.203-0.003-0.0030.0000.0000.0000.000
78A91ASP-1-0.856-0.92632.798-0.064-0.0640.0000.0000.0000.000
79A92ARG10.8100.89327.9010.0870.0870.0000.0000.0000.000
80A93LEU0-0.0070.02028.777-0.005-0.0050.0000.0000.0000.000
81A94MET0-0.0010.00629.878-0.001-0.0010.0000.0000.0000.000
82A95SER0-0.033-0.02126.112-0.001-0.0010.0000.0000.0000.000
83A96THR0-0.015-0.03024.618-0.003-0.0030.0000.0000.0000.000
84A97VAL00.003-0.00325.059-0.003-0.0030.0000.0000.0000.000
85A98THR0-0.003-0.01226.4020.0030.0030.0000.0000.0000.000
86A99ALA0-0.0240.00821.6400.0000.0000.0000.0000.0000.000
87A100TYR0-0.062-0.03421.767-0.004-0.0040.0000.0000.0000.000
88A101VAL0-0.014-0.00922.9370.0040.0040.0000.0000.0000.000
89A102THR0-0.042-0.03222.3420.0070.0070.0000.0000.0000.000
90A103TRP00.0050.01214.7550.0170.0170.0000.0000.0000.000
91A104HIS00.0250.00419.7580.0070.0070.0000.0000.0000.000
92A105ALA0-0.0020.00821.8240.0090.0090.0000.0000.0000.000
93A106ASP-1-0.911-0.95519.319-0.083-0.0830.0000.0000.0000.000
94A107ASN0-0.123-0.05715.486-0.013-0.0130.0000.0000.0000.000
95A108ARG10.9260.96818.3590.0470.0470.0000.0000.0000.000
96A109ALA00.0250.02218.7630.0080.0080.0000.0000.0000.000
97A110SER00.0370.00013.7750.0240.0240.0000.0000.0000.000
98A111ALA00.0230.01816.8460.0140.0140.0000.0000.0000.000
99A112ARG10.8910.93019.1190.0060.0060.0000.0000.0000.000
100A113VAL0-0.0130.00117.1940.0080.0080.0000.0000.0000.000
101A114GLY0-0.023-0.01317.4710.0120.0120.0000.0000.0000.000
102A115GLN00.0520.02718.232-0.002-0.0020.0000.0000.0000.000
103A116TYR0-0.017-0.00721.652-0.003-0.0030.0000.0000.0000.000
104A117GLU-1-0.827-0.92221.3020.0710.0710.0000.0000.0000.000
105A118LEU0-0.019-0.00420.6170.0110.0110.0000.0000.0000.000
106A119ARG10.9470.96622.985-0.021-0.0210.0000.0000.0000.000
107A120SER0-0.025-0.00722.4070.0010.0010.0000.0000.0000.000
108A121LEU0-0.072-0.02117.9540.0180.0180.0000.0000.0000.000
109A122SER00.0050.00619.907-0.019-0.0190.0000.0000.0000.000
110A123PRO00.0540.01121.684-0.005-0.0050.0000.0000.0000.000
111A124GLU-1-0.876-0.92417.7710.1180.1180.0000.0000.0000.000
112A125HIS10.7960.86616.712-0.186-0.1860.0000.0000.0000.000
113A126PHE00.005-0.00218.571-0.019-0.0190.0000.0000.0000.000
114A127ALA00.0200.00221.387-0.013-0.0130.0000.0000.0000.000
115A128ILE00.0510.04315.069-0.014-0.0140.0000.0000.0000.000
116A129ILE0-0.025-0.02215.589-0.024-0.0240.0000.0000.0000.000
117A130ALA0-0.059-0.03918.637-0.018-0.0180.0000.0000.0000.000
118A131ASP-1-0.836-0.90519.431-0.065-0.0650.0000.0000.0000.000
119A132ILE0-0.044-0.01214.541-0.012-0.0120.0000.0000.0000.000
120A133ARG10.9180.96918.6510.0090.0090.0000.0000.0000.000
121A134ARG10.8410.91121.5970.0430.0430.0000.0000.0000.000
122A135SER0-0.005-0.01119.709-0.004-0.0040.0000.0000.0000.000
123A136THR0-0.052-0.04419.983-0.008-0.0080.0000.0000.0000.000
124A137THR00.007-0.00921.9490.0000.0000.0000.0000.0000.000
125A138LYS10.8190.91424.5010.0760.0760.0000.0000.0000.000
126A139VAL0-0.0200.00922.0180.0020.0020.0000.0000.0000.000
127A140PHE00.0580.01624.6180.0030.0030.0000.0000.0000.000
128A141THR0-0.030-0.03628.2470.0020.0020.0000.0000.0000.000
129A142ARG10.8310.90723.3630.1240.1240.0000.0000.0000.000
130A143ILE0-0.014-0.00227.1370.0030.0030.0000.0000.0000.000
131A144ILE00.006-0.01031.0450.0040.0040.0000.0000.0000.000
132A145GLU-1-0.770-0.87532.033-0.063-0.0630.0000.0000.0000.000
133A146ALA0-0.0150.00533.1050.0030.0030.0000.0000.0000.000
134A147GLY00.0700.02035.0390.0020.0020.0000.0000.0000.000
135A148ALA0-0.030-0.01137.0850.0030.0030.0000.0000.0000.000
136A149THR0-0.127-0.08237.3360.0010.0010.0000.0000.0000.000
137A150ALA0-0.0030.01338.8480.0010.0010.0000.0000.0000.000
138A151GLY0-0.017-0.00340.6820.0010.0010.0000.0000.0000.000
139A152ASP-1-0.876-0.93938.675-0.049-0.0490.0000.0000.0000.000
140A153PHE0-0.109-0.05234.4730.0000.0000.0000.0000.0000.000
141A154HIS0-0.015-0.01140.3940.0010.0010.0000.0000.0000.000
142A155PRO0-0.0110.00238.2970.0010.0010.0000.0000.0000.000
143A156PHE00.0020.00240.5140.0010.0010.0000.0000.0000.000
144A157ASP-1-0.851-0.93537.516-0.031-0.0310.0000.0000.0000.000
145A158ILE00.0200.00833.614-0.001-0.0010.0000.0000.0000.000
146A159GLU-1-0.811-0.87532.056-0.040-0.0400.0000.0000.0000.000
147A160ALA0-0.008-0.00632.975-0.001-0.0010.0000.0000.0000.000
148A161ALA00.0290.01434.3620.0010.0010.0000.0000.0000.000
149A162ALA00.0370.01829.514-0.002-0.0020.0000.0000.0000.000
150A163LEU0-0.0210.00429.391-0.003-0.0030.0000.0000.0000.000
151A164ALA00.0050.00430.1280.0010.0010.0000.0000.0000.000
152A165ILE00.0220.01328.0530.0000.0000.0000.0000.0000.000
153A166THR0-0.022-0.03625.1150.0000.0000.0000.0000.0000.000
154A167SER00.0030.00526.3450.0020.0020.0000.0000.0000.000
155A168LEU0-0.017-0.00528.5870.0030.0030.0000.0000.0000.000
156A169GLY00.0220.00225.8220.0010.0010.0000.0000.0000.000
157A170ILE0-0.046-0.02222.9280.0010.0010.0000.0000.0000.000
158A171ASP-1-0.752-0.85424.921-0.009-0.0090.0000.0000.0000.000
159A172VAL00.0230.02325.9340.0040.0040.0000.0000.0000.000
160A173SER0-0.018-0.00822.6230.0010.0010.0000.0000.0000.000
161A174ARG10.7410.83424.6710.0140.0140.0000.0000.0000.000
162A175TRP0-0.044-0.02127.5300.0030.0030.0000.0000.0000.000
163A176PHE00.0200.04426.3570.0000.0000.0000.0000.0000.000
164A177PRO0-0.072-0.03827.5410.0010.0010.0000.0000.0000.000
165A178SER00.031-0.00730.3210.0040.0040.0000.0000.0000.000
166A179HIS0-0.004-0.00933.865-0.001-0.0010.0000.0000.0000.000
167A180THR0-0.022-0.00636.069-0.001-0.0010.0000.0000.0000.000
168A181TYR00.005-0.00532.677-0.003-0.0030.0000.0000.0000.000
169A182SER00.0490.01531.1060.0000.0000.0000.0000.0000.000
170A183ASP-1-0.798-0.89729.995-0.051-0.0510.0000.0000.0000.000
171A184PRO00.017-0.00825.5290.0020.0020.0000.0000.0000.000
172A185ARG10.9660.97827.2970.0680.0680.0000.0000.0000.000
173A186ILE0-0.0190.00629.7310.0010.0010.0000.0000.0000.000
174A187ILE0-0.0060.00629.0930.0010.0010.0000.0000.0000.000
175A188ALA00.0080.00728.0510.0000.0000.0000.0000.0000.000
176A189ALA00.0110.00830.0170.0000.0000.0000.0000.0000.000
177A190ARG10.7990.85933.3010.0380.0380.0000.0000.0000.000
178A191TYR0-0.004-0.02329.8020.0030.0030.0000.0000.0000.000
179A192VAL00.0040.01130.8480.0000.0000.0000.0000.0000.000
180A193GLU-1-0.792-0.85433.208-0.036-0.0360.0000.0000.0000.000
181A194LEU0-0.027-0.01435.3960.0010.0010.0000.0000.0000.000
182A195ALA0-0.009-0.00132.7330.0010.0010.0000.0000.0000.000
183A196LEU00.0410.00734.7960.0000.0000.0000.0000.0000.000
184A197ARG10.8870.93037.0750.0310.0310.0000.0000.0000.000
185A198MET0-0.076-0.03034.2120.0020.0020.0000.0000.0000.000
186A199VAL0-0.041-0.01635.1960.0020.0020.0000.0000.0000.000
187A200GLY00.0280.02338.5510.0000.0000.0000.0000.0000.000
188A201CYS0-0.046-0.02039.211-0.001-0.0010.0000.0000.0000.000
189A202ALA00.0030.00741.3730.0020.0020.0000.0000.0000.000
190A203ASP-1-0.920-0.94642.038-0.035-0.0350.0000.0000.0000.000