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: R81Y8

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1891970.868696
FMO2-HF: Nuclear repulsion 1820603.753281
FMO2-HF: Total energy -71367.115415
FMO2-MP2: Total energy -71577.758834


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.
-3.928-2.649-0.008-0.532-0.7380.003
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 : 0.045 / q_NPA : 0.011
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].
3A16LYS11.0280.9993.868-0.7940.422-0.007-0.532-0.6770.003
4A17ALA00.0060.0096.3250.0160.0160.0000.0000.0000.000
5A18ALA00.0100.0005.216-0.150-0.1500.0000.0000.0000.000
6A19ALA00.0240.0134.955-0.189-0.1890.0000.0000.0000.000
7A20ARG10.9730.9886.708-0.077-0.0770.0000.0000.0000.000
8A21ILE00.0150.0109.994-0.036-0.0360.0000.0000.0000.000
9A22ARG10.7910.8534.756-1.552-1.489-0.0010.000-0.0610.000
10A23ALA00.0130.01110.663-0.093-0.0930.0000.0000.0000.000
11A24ALA00.0340.01612.496-0.040-0.0400.0000.0000.0000.000
12A25ALA0-0.019-0.02013.927-0.026-0.0260.0000.0000.0000.000
13A26ILE0-0.0220.00512.557-0.022-0.0220.0000.0000.0000.000
14A27GLU-1-0.819-0.92216.2360.0330.0330.0000.0000.0000.000
15A28VAL0-0.030-0.01318.628-0.009-0.0090.0000.0000.0000.000
16A29PHE0-0.048-0.04416.2400.0060.0060.0000.0000.0000.000
17A30ALA0-0.022-0.00920.331-0.017-0.0170.0000.0000.0000.000
18A31ALA0-0.040-0.00622.121-0.017-0.0170.0000.0000.0000.000
19A32LYS10.7830.88723.948-0.210-0.2100.0000.0000.0000.000
20A33GLY00.0550.04624.464-0.004-0.0040.0000.0000.0000.000
21A34TYR00.005-0.01619.0430.0300.0300.0000.0000.0000.000
22A35GLY0-0.0080.00522.3600.0220.0220.0000.0000.0000.000
23A36ALA0-0.0020.00725.4270.0120.0120.0000.0000.0000.000
24A37THR0-0.0150.00320.8430.0040.0040.0000.0000.0000.000
25A38THR00.0430.02022.0360.0310.0310.0000.0000.0000.000
26A39THR00.0440.00017.404-0.018-0.0180.0000.0000.0000.000
27A40ARG10.8970.95617.945-0.458-0.4580.0000.0000.0000.000
28A41GLU-1-0.724-0.85721.4950.2210.2210.0000.0000.0000.000
29A42ILE00.0030.01415.396-0.008-0.0080.0000.0000.0000.000
30A43ALA0-0.028-0.00817.028-0.004-0.0040.0000.0000.0000.000
31A44ALA00.0500.02718.032-0.026-0.0260.0000.0000.0000.000
32A45SER0-0.067-0.04318.326-0.031-0.0310.0000.0000.0000.000
33A46LEU0-0.068-0.04213.600-0.023-0.0230.0000.0000.0000.000
34A47ASP-1-0.920-0.95017.7090.1520.1520.0000.0000.0000.000
35A48MET0-0.085-0.02812.4990.0350.0350.0000.0000.0000.000
36A49SER00.0540.02118.0780.0060.0060.0000.0000.0000.000
37A50PRO00.016-0.01719.2140.0590.0590.0000.0000.0000.000
38A51GLY00.0200.01918.9990.0040.0040.0000.0000.0000.000
39A52ALA00.0110.00415.2140.1020.1020.0000.0000.0000.000
40A53VAL00.004-0.00513.4260.1300.1300.0000.0000.0000.000
41A54TYR00.0350.03512.9890.2310.2310.0000.0000.0000.000
42A55PRO0-0.011-0.01111.5600.0830.0830.0000.0000.0000.000
43A56HIS00.0050.0167.1090.4350.4350.0000.0000.0000.000
44A57TYR00.0280.0107.7550.2300.2300.0000.0000.0000.000
45A58LYS10.8950.94712.528-1.487-1.4870.0000.0000.0000.000
46A59THR00.0350.02015.823-0.095-0.0950.0000.0000.0000.000
47A60LYS10.8380.91516.420-0.253-0.2530.0000.0000.0000.000
48A61GLU-1-0.740-0.83217.2320.6250.6250.0000.0000.0000.000
49A62SER0-0.009-0.02213.4990.0740.0740.0000.0000.0000.000
50A63LEU0-0.027-0.00911.8790.1460.1460.0000.0000.0000.000
51A64LEU00.0300.01813.0540.0130.0130.0000.0000.0000.000
52A65TYR00.0160.00413.051-0.063-0.0630.0000.0000.0000.000
53A66ALA00.001-0.0049.117-0.020-0.0200.0000.0000.0000.000
54A67ILE00.002-0.00110.608-0.063-0.0630.0000.0000.0000.000
55A68SER00.011-0.01012.375-0.121-0.1210.0000.0000.0000.000
56A69LEU0-0.028-0.0039.869-0.086-0.0860.0000.0000.0000.000
57A70GLU-1-0.808-0.8607.0400.1910.1910.0000.0000.0000.000
58A71GLY00.0300.01210.498-0.157-0.1570.0000.0000.0000.000
59A72HIS10.7700.86313.847-0.238-0.2380.0000.0000.0000.000
60A73HIS00.0500.01610.402-0.100-0.1000.0000.0000.0000.000
61A74SER0-0.0060.01511.806-0.085-0.0850.0000.0000.0000.000
62A75VAL00.0200.01513.190-0.034-0.0340.0000.0000.0000.000
63A76LEU00.0180.01216.032-0.012-0.0120.0000.0000.0000.000
64A77ALA00.0050.00613.629-0.014-0.0140.0000.0000.0000.000
65A78ALA0-0.025-0.01115.695-0.015-0.0150.0000.0000.0000.000
66A79ILE0-0.010-0.00817.8230.0030.0030.0000.0000.0000.000
67A80THR0-0.050-0.04218.1600.0140.0140.0000.0000.0000.000
68A81ALA0-0.050-0.02217.844-0.005-0.0050.0000.0000.0000.000
69A82ALA0-0.0170.00519.912-0.003-0.0030.0000.0000.0000.000
70A83ASP-1-0.743-0.82623.276-0.094-0.0940.0000.0000.0000.000
71A84PHE0-0.001-0.00324.066-0.016-0.0160.0000.0000.0000.000
72A85PRO0-0.017-0.03126.2020.0110.0110.0000.0000.0000.000
73A86ASP-1-0.912-0.94629.291-0.126-0.1260.0000.0000.0000.000
74A87ILE0-0.050-0.01230.7190.0020.0020.0000.0000.0000.000
75A88ALA00.0460.02633.4930.0050.0050.0000.0000.0000.000
76A89ALA00.0130.01933.454-0.006-0.0060.0000.0000.0000.000
77A90PRO00.0380.00133.366-0.002-0.0020.0000.0000.0000.000
78A91ASP-1-0.847-0.92132.902-0.099-0.0990.0000.0000.0000.000
79A92ARG10.8360.91428.3960.0930.0930.0000.0000.0000.000
80A93LEU00.0090.02928.770-0.005-0.0050.0000.0000.0000.000
81A94MET0-0.007-0.01129.9150.0000.0000.0000.0000.0000.000
82A95SER0-0.039-0.01526.270-0.007-0.0070.0000.0000.0000.000
83A96THR0-0.015-0.02724.501-0.002-0.0020.0000.0000.0000.000
84A97VAL00.000-0.00625.1390.0010.0010.0000.0000.0000.000
85A98THR0-0.006-0.01526.6540.0050.0050.0000.0000.0000.000
86A99ALA0-0.0160.00721.849-0.003-0.0030.0000.0000.0000.000
87A100TYR0-0.056-0.03022.009-0.001-0.0010.0000.0000.0000.000
88A101VAL0-0.001-0.00223.0010.0100.0100.0000.0000.0000.000
89A102THR0-0.046-0.02822.3410.0080.0080.0000.0000.0000.000
90A103TRP0-0.013-0.00215.1380.0280.0280.0000.0000.0000.000
91A104HIS00.0310.00220.0460.0140.0140.0000.0000.0000.000
92A105ALA00.0010.00922.1080.0150.0150.0000.0000.0000.000
93A106ASP-1-0.903-0.94919.846-0.151-0.1510.0000.0000.0000.000
94A107ASN0-0.100-0.05715.677-0.016-0.0160.0000.0000.0000.000
95A108ARG10.8660.94118.5940.0940.0940.0000.0000.0000.000
96A109ALA00.0170.02218.9670.0240.0240.0000.0000.0000.000
97A110SER00.033-0.00514.0610.0600.0600.0000.0000.0000.000
98A111ALA00.0180.01617.0250.0430.0430.0000.0000.0000.000
99A112ARG10.9000.94119.376-0.033-0.0330.0000.0000.0000.000
100A113VAL0-0.021-0.00217.2180.0200.0200.0000.0000.0000.000
101A114GLY00.0100.00417.4440.0380.0380.0000.0000.0000.000
102A115GLN00.0550.02918.0790.0250.0250.0000.0000.0000.000
103A116TYR0-0.015-0.01921.643-0.003-0.0030.0000.0000.0000.000
104A117GLU-1-0.814-0.90521.2560.2350.2350.0000.0000.0000.000
105A118LEU0-0.0190.00020.2060.0310.0310.0000.0000.0000.000
106A119ARG10.9380.95822.687-0.130-0.1300.0000.0000.0000.000
107A120SER0-0.033-0.01522.388-0.006-0.0060.0000.0000.0000.000
108A121LEU0-0.045-0.01117.7760.0440.0440.0000.0000.0000.000
109A122SER0-0.008-0.00419.343-0.044-0.0440.0000.0000.0000.000
110A123PRO00.0500.00421.3600.0010.0010.0000.0000.0000.000
111A124GLU-1-0.867-0.91717.1840.5590.5590.0000.0000.0000.000
112A125HIS10.7770.85316.317-0.631-0.6310.0000.0000.0000.000
113A126PHE00.0360.00818.183-0.022-0.0220.0000.0000.0000.000
114A127ALA00.0140.01121.108-0.029-0.0290.0000.0000.0000.000
115A128ILE00.0630.03514.896-0.023-0.0230.0000.0000.0000.000
116A129ILE0-0.036-0.01915.061-0.034-0.0340.0000.0000.0000.000
117A130ALA0-0.048-0.02518.435-0.043-0.0430.0000.0000.0000.000
118A131ASP-1-0.845-0.91019.6560.1370.1370.0000.0000.0000.000
119A132ILE0-0.0130.00814.839-0.033-0.0330.0000.0000.0000.000
120A133ARG10.8770.96018.989-0.190-0.1900.0000.0000.0000.000
121A134ARG10.8120.87521.869-0.069-0.0690.0000.0000.0000.000
122A135SER0-0.008-0.02320.103-0.020-0.0200.0000.0000.0000.000
123A136THR0-0.036-0.03620.150-0.026-0.0260.0000.0000.0000.000
124A137THR0-0.003-0.01122.134-0.009-0.0090.0000.0000.0000.000
125A138LYS10.8060.89024.8380.0160.0160.0000.0000.0000.000
126A139VAL0-0.031-0.00321.890-0.009-0.0090.0000.0000.0000.000
127A140PHE00.0480.01224.492-0.005-0.0050.0000.0000.0000.000
128A141THR0-0.043-0.05028.140-0.001-0.0010.0000.0000.0000.000
129A142ARG10.8340.91323.1820.1060.1060.0000.0000.0000.000
130A143ILE0-0.0250.00127.134-0.003-0.0030.0000.0000.0000.000
131A144ILE00.008-0.00531.0010.0010.0010.0000.0000.0000.000
132A145GLU-1-0.746-0.84832.025-0.024-0.0240.0000.0000.0000.000
133A146ALA00.0050.02333.2460.0010.0010.0000.0000.0000.000
134A147GLY00.0670.01435.1430.0000.0000.0000.0000.0000.000
135A148ALA0-0.040-0.02337.1750.0020.0020.0000.0000.0000.000
136A149THR0-0.110-0.07137.5610.0010.0010.0000.0000.0000.000
137A150ALA0-0.0220.00238.7860.0000.0000.0000.0000.0000.000
138A151GLY00.0070.00740.6730.0000.0000.0000.0000.0000.000
139A152ASP-1-0.879-0.93738.195-0.061-0.0610.0000.0000.0000.000
140A153PHE0-0.087-0.05234.3820.0000.0000.0000.0000.0000.000
141A154HIS0-0.014-0.00240.3190.0040.0040.0000.0000.0000.000
142A155PRO0-0.020-0.00138.2530.0020.0020.0000.0000.0000.000
143A156PHE00.006-0.00740.6360.0020.0020.0000.0000.0000.000
144A157ASP-1-0.848-0.92837.3540.0150.0150.0000.0000.0000.000
145A158ILE00.0310.01233.752-0.002-0.0020.0000.0000.0000.000
146A159GLU-1-0.798-0.85631.8980.0340.0340.0000.0000.0000.000
147A160ALA0-0.007-0.01032.9690.0020.0020.0000.0000.0000.000
148A161ALA00.0290.02234.5830.0000.0000.0000.0000.0000.000
149A162ALA00.0400.01729.542-0.003-0.0030.0000.0000.0000.000
150A163LEU0-0.0320.00429.5590.0010.0010.0000.0000.0000.000
151A164ALA00.0110.00930.5220.0030.0030.0000.0000.0000.000
152A165ILE00.0230.01328.483-0.001-0.0010.0000.0000.0000.000
153A166THR0-0.033-0.04425.4050.0020.0020.0000.0000.0000.000
154A167SER00.0020.00026.5430.0060.0060.0000.0000.0000.000
155A168LEU0-0.019-0.00628.8590.0040.0040.0000.0000.0000.000
156A169GLY00.017-0.00226.474-0.002-0.0020.0000.0000.0000.000
157A170ILE0-0.037-0.01223.3280.0000.0000.0000.0000.0000.000
158A171ASP-1-0.738-0.83925.3260.0400.0400.0000.0000.0000.000
159A172VAL00.0150.01926.1940.0020.0020.0000.0000.0000.000
160A173SER0-0.011-0.01223.099-0.006-0.0060.0000.0000.0000.000
161A174ARG10.7480.84124.929-0.027-0.0270.0000.0000.0000.000
162A175TRP0-0.038-0.01327.8020.0000.0000.0000.0000.0000.000
163A176PHE00.0280.05226.509-0.004-0.0040.0000.0000.0000.000
164A177PRO0-0.066-0.03627.7330.0030.0030.0000.0000.0000.000
165A178SER00.022-0.01330.5060.0070.0070.0000.0000.0000.000
166A179HIS00.005-0.00934.128-0.005-0.0050.0000.0000.0000.000
167A180THR0-0.016-0.00236.096-0.002-0.0020.0000.0000.0000.000
168A181TYR0-0.001-0.00532.887-0.006-0.0060.0000.0000.0000.000
169A182SER00.0350.00831.4660.0030.0030.0000.0000.0000.000
170A183ASP-1-0.799-0.89829.926-0.109-0.1090.0000.0000.0000.000
171A184PRO00.029-0.00225.5590.0090.0090.0000.0000.0000.000
172A185ARG10.9400.96927.3540.1460.1460.0000.0000.0000.000
173A186ILE0-0.0150.00430.1160.0050.0050.0000.0000.0000.000
174A187ILE0-0.0090.00329.3460.0050.0050.0000.0000.0000.000
175A188ALA00.0070.00528.3350.0050.0050.0000.0000.0000.000
176A189ALA00.0150.01330.2840.0030.0030.0000.0000.0000.000
177A190ARG10.8120.87033.6540.0590.0590.0000.0000.0000.000
178A191TYR00.009-0.02429.8480.0070.0070.0000.0000.0000.000
179A192VAL00.0050.02030.9650.0040.0040.0000.0000.0000.000
180A193GLU-1-0.776-0.84533.311-0.050-0.0500.0000.0000.0000.000
181A194LEU0-0.022-0.01535.4360.0040.0040.0000.0000.0000.000
182A195ALA0-0.016-0.00632.6850.0050.0050.0000.0000.0000.000
183A196LEU00.0350.00434.7540.0030.0030.0000.0000.0000.000
184A197ARG10.8700.92537.2790.0350.0350.0000.0000.0000.000
185A198MET0-0.054-0.02334.2330.0060.0060.0000.0000.0000.000
186A199VAL0-0.051-0.01635.0430.0040.0040.0000.0000.0000.000
187A200GLY00.0360.02138.360-0.001-0.0010.0000.0000.0000.000
188A201CYS0-0.066-0.02539.205-0.003-0.0030.0000.0000.0000.000
189A202ALA00.0310.02041.3620.0030.0030.0000.0000.0000.000
190A203ASP-1-0.969-0.97342.401-0.047-0.0470.0000.0000.0000.000