FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZV14N

Calculation Name: 3RST-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RST

Chain ID: A

ChEMBL ID:

UniProt ID: O34525

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2524578.643742
FMO2-HF: Nuclear repulsion 2436342.775515
FMO2-HF: Total energy -88235.868227
FMO2-MP2: Total energy -88490.699158


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:56:PRO)


Summations of interaction energy for fragment #1(A:56:PRO)
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.
-4.65-0.45511.483-6.978-8.698-0.011
Interaction energy analysis for fragmet #1(A:56:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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].
3A58SER0-0.0310.0253.007-3.3311.3040.013-2.312-2.3360.009
4A59LYS10.9550.9814.624-0.181-0.149-0.001-0.023-0.0070.000
5A60ILE00.0310.0177.568-0.075-0.0750.0000.0000.0000.000
6A61ALA0-0.009-0.0019.9910.0800.0800.0000.0000.0000.000
7A62VAL0-0.013-0.00713.354-0.021-0.0210.0000.0000.0000.000
8A63LEU0-0.035-0.01915.9390.0130.0130.0000.0000.0000.000
9A64GLU-1-0.914-0.96419.5370.0420.0420.0000.0000.0000.000
10A65VAL0-0.0110.00522.7670.0000.0000.0000.0000.0000.000
11A66SER00.0170.00026.281-0.003-0.0030.0000.0000.0000.000
12A67GLY00.0100.00228.4820.0020.0020.0000.0000.0000.000
13A68THR0-0.042-0.05031.999-0.003-0.0030.0000.0000.0000.000
14A69ILE0-0.042-0.01930.4790.0010.0010.0000.0000.0000.000
15A70GLN0-0.006-0.02033.327-0.001-0.0010.0000.0000.0000.000
16A71ASP-1-0.890-0.94934.6430.0110.0110.0000.0000.0000.000
17A72ASN0-0.063-0.01235.7670.0010.0010.0000.0000.0000.000
18A82ASP-1-0.834-0.91034.0230.0130.0130.0000.0000.0000.000
19A83GLY0-0.018-0.01031.2870.0020.0020.0000.0000.0000.000
20A84TYR0-0.051-0.03527.7830.0020.0020.0000.0000.0000.000
21A85ASN00.0310.01729.328-0.003-0.0030.0000.0000.0000.000
22A86HIS00.0350.02629.0850.0020.0020.0000.0000.0000.000
23A87ARG10.9730.97929.306-0.012-0.0120.0000.0000.0000.000
24A88THR0-0.010-0.00425.4510.0000.0000.0000.0000.0000.000
25A89PHE00.0470.02522.8390.0000.0000.0000.0000.0000.000
26A90LEU00.0260.01024.289-0.003-0.0030.0000.0000.0000.000
27A91LYS10.8560.93524.028-0.021-0.0210.0000.0000.0000.000
28A92ASN0-0.026-0.03720.8150.0020.0020.0000.0000.0000.000
29A93LEU0-0.023-0.00320.082-0.003-0.0030.0000.0000.0000.000
30A94GLU-1-0.874-0.93120.3720.0000.0000.0000.0000.0000.000
31A95ARG10.9280.95818.245-0.056-0.0560.0000.0000.0000.000
32A96ALA00.0140.01216.008-0.002-0.0020.0000.0000.0000.000
33A97LYS10.8080.90815.7300.0050.0050.0000.0000.0000.000
34A98ASP-1-0.836-0.91117.061-0.024-0.0240.0000.0000.0000.000
35A99ASP-1-0.861-0.89512.7390.0300.0300.0000.0000.0000.000
36A100LYS10.9140.94212.351-0.002-0.0020.0000.0000.0000.000
37A101THR0-0.063-0.0608.475-0.012-0.0120.0000.0000.0000.000
38A102VAL0-0.0150.0148.219-0.093-0.0930.0000.0000.0000.000
39A103LYS10.8930.9325.2040.1880.1880.0000.0000.0000.000
40A104GLY00.0650.03310.082-0.024-0.0240.0000.0000.0000.000
41A105ILE0-0.026-0.00212.2880.0230.0230.0000.0000.0000.000
42A106VAL00.0100.00114.071-0.009-0.0090.0000.0000.0000.000
43A107LEU0-0.0020.00416.4210.0160.0160.0000.0000.0000.000
44A108LYS10.9390.97419.175-0.051-0.0510.0000.0000.0000.000
45A109VAL00.0060.00721.8170.0030.0030.0000.0000.0000.000
46A110ASN00.0130.00725.533-0.003-0.0030.0000.0000.0000.000
47A111SER00.0310.01428.3860.0020.0020.0000.0000.0000.000
48A112PRO00.0600.01931.367-0.002-0.0020.0000.0000.0000.000
49A113GLY0-0.0100.00633.883-0.002-0.0020.0000.0000.0000.000
50A114GLY00.0190.00834.7550.0020.0020.0000.0000.0000.000
51A115GLY00.0000.02836.556-0.001-0.0010.0000.0000.0000.000
52A116VAL00.034-0.00536.146-0.001-0.0010.0000.0000.0000.000
53A117TYR0-0.0090.00536.012-0.002-0.0020.0000.0000.0000.000
54A118GLU-1-0.803-0.91233.2150.0000.0000.0000.0000.0000.000
55A119SER0-0.017-0.01531.777-0.001-0.0010.0000.0000.0000.000
56A120ALA00.0190.00031.419-0.003-0.0030.0000.0000.0000.000
57A121GLU-1-0.900-0.93530.914-0.004-0.0040.0000.0000.0000.000
58A122ILE0-0.018-0.01526.358-0.002-0.0020.0000.0000.0000.000
59A123HIS0-0.0090.00427.089-0.002-0.0020.0000.0000.0000.000
60A124LYS11.0111.00427.5610.0130.0130.0000.0000.0000.000
61A125LYS10.9220.96725.1840.0090.0090.0000.0000.0000.000
62A126LEU00.0040.00222.181-0.004-0.0040.0000.0000.0000.000
63A127GLU-1-0.889-0.95922.962-0.052-0.0520.0000.0000.0000.000
64A128GLU-1-0.977-0.98524.271-0.026-0.0260.0000.0000.0000.000
65A129ILE00.0310.01718.498-0.004-0.0040.0000.0000.0000.000
66A130LYS10.8740.96019.7150.0510.0510.0000.0000.0000.000
67A131LYS10.9240.95920.7330.0340.0340.0000.0000.0000.000
68A132GLU-1-0.910-0.96621.050-0.033-0.0330.0000.0000.0000.000
69A133THR0-0.098-0.06116.311-0.006-0.0060.0000.0000.0000.000
70A134LYS10.8670.93416.1770.0860.0860.0000.0000.0000.000
71A135LYS10.7990.91713.1110.0590.0590.0000.0000.0000.000
72A136PRO00.0100.02313.2760.0210.0210.0000.0000.0000.000
73A137ILE00.007-0.00615.632-0.001-0.0010.0000.0000.0000.000
74A138TYR0-0.060-0.06416.364-0.005-0.0050.0000.0000.0000.000
75A139VAL00.0350.02018.6100.0090.0090.0000.0000.0000.000
76A140SER0-0.056-0.01619.7620.0000.0000.0000.0000.0000.000
77A141MET0-0.003-0.00521.6530.0070.0070.0000.0000.0000.000
78A142GLY00.0010.00325.3730.0020.0020.0000.0000.0000.000
79A143SER0-0.049-0.04626.653-0.003-0.0030.0000.0000.0000.000
80A144MET00.0160.01929.939-0.002-0.0020.0000.0000.0000.000
81A145ALA00.0410.01028.4880.0010.0010.0000.0000.0000.000
82A146ALA00.0130.03930.602-0.003-0.0030.0000.0000.0000.000
83A147SER00.0580.03034.0400.0010.0010.0000.0000.0000.000
84A148GLY00.0320.00833.872-0.002-0.0020.0000.0000.0000.000
85A149GLY00.0500.01530.148-0.001-0.0010.0000.0000.0000.000
86A150TYR0-0.040-0.05429.176-0.003-0.0030.0000.0000.0000.000
87A151TYR00.002-0.00230.147-0.004-0.0040.0000.0000.0000.000
88A152ILE0-0.018-0.00626.570-0.003-0.0030.0000.0000.0000.000
89A153SER00.001-0.01125.725-0.004-0.0040.0000.0000.0000.000
90A154THR0-0.075-0.03425.830-0.006-0.0060.0000.0000.0000.000
91A155ALA00.0330.02725.515-0.003-0.0030.0000.0000.0000.000
92A156ALA0-0.066-0.03021.801-0.006-0.0060.0000.0000.0000.000
93A157ASP-1-0.877-0.94419.493-0.097-0.0970.0000.0000.0000.000
94A158LYS10.8490.91318.6470.1150.1150.0000.0000.0000.000
95A159ILE0-0.016-0.01121.3460.0030.0030.0000.0000.0000.000
96A160PHE00.0220.00819.097-0.004-0.0040.0000.0000.0000.000
97A161ALA00.0240.00823.2820.0060.0060.0000.0000.0000.000
98A162THR00.0200.01825.439-0.002-0.0020.0000.0000.0000.000
99A163PRO0-0.060-0.04927.745-0.002-0.0020.0000.0000.0000.000
100A164GLU-1-0.858-0.94530.3600.0020.0020.0000.0000.0000.000
101A165THR0-0.075-0.00728.3360.0010.0010.0000.0000.0000.000
102A166LEU00.0050.01230.925-0.002-0.0020.0000.0000.0000.000
103A167THR00.000-0.04131.282-0.001-0.0010.0000.0000.0000.000
104A168GLY00.0160.01233.4210.0010.0010.0000.0000.0000.000
105A169SER00.001-0.00635.6700.0010.0010.0000.0000.0000.000
106A170LEU0-0.070-0.02034.9380.0000.0000.0000.0000.0000.000
107A171GLY00.0400.00138.5150.0000.0000.0000.0000.0000.000
108A172VAL0-0.021-0.00940.1990.0000.0000.0000.0000.0000.000
109A173ILE00.0040.00942.6190.0000.0000.0000.0000.0000.000
110A174MET0-0.006-0.02044.7200.0000.0000.0000.0000.0000.000
111A175GLU-1-0.949-0.95646.5370.0020.0020.0000.0000.0000.000
112A176SER0-0.018-0.00449.3420.0000.0000.0000.0000.0000.000
113A177VAL00.0160.00352.7110.0000.0000.0000.0000.0000.000
114A178ASN00.0100.00455.1720.0000.0000.0000.0000.0000.000
115A179TYR0-0.034-0.01557.2770.0000.0000.0000.0000.0000.000
116A180SER00.002-0.00560.6340.0000.0000.0000.0000.0000.000
117A181LYS10.9750.98363.326-0.001-0.0010.0000.0000.0000.000
118A182LEU0-0.041-0.01261.2260.0000.0000.0000.0000.0000.000
119A183ALA00.0310.00964.1770.0000.0000.0000.0000.0000.000
120A184ASP-1-0.916-0.95665.8220.0020.0020.0000.0000.0000.000
121A185LYS10.9080.94666.802-0.003-0.0030.0000.0000.0000.000
122A186LEU0-0.064-0.02964.5420.0000.0000.0000.0000.0000.000
123A187GLY00.0080.02869.0070.0000.0000.0000.0000.0000.000
124A188ILE0-0.054-0.02465.2790.0000.0000.0000.0000.0000.000
125A189SER0-0.003-0.00667.8960.0000.0000.0000.0000.0000.000
126A190PHE00.006-0.00962.1590.0000.0000.0000.0000.0000.000
127A191GLU-1-0.912-0.95466.6530.0020.0020.0000.0000.0000.000
128A192THR0-0.044-0.02362.9470.0000.0000.0000.0000.0000.000
129A193ILE00.0240.02165.8960.0000.0000.0000.0000.0000.000
130A194LYS10.8390.91363.2570.0000.0000.0000.0000.0000.000
131A195SER0-0.008-0.00462.6890.0000.0000.0000.0000.0000.000
132A196GLY00.0700.02563.6660.0000.0000.0000.0000.0000.000
133A197ALA00.005-0.00263.4330.0000.0000.0000.0000.0000.000
134A198HIS0-0.016-0.01958.7010.0000.0000.0000.0000.0000.000
135A199ALA0-0.019-0.00258.4430.0000.0000.0000.0000.0000.000
136A200ASP-1-0.762-0.85358.4020.0010.0010.0000.0000.0000.000
137A201ILE00.008-0.00154.9130.0000.0000.0000.0000.0000.000
138A202MET0-0.033-0.03050.8370.0000.0000.0000.0000.0000.000
139A203SER00.0060.01955.3760.0010.0010.0000.0000.0000.000
140A204PRO00.0420.02255.8270.0000.0000.0000.0000.0000.000
141A205SER0-0.081-0.02657.7320.0000.0000.0000.0000.0000.000
142A206ARG10.7540.82460.9960.0000.0000.0000.0000.0000.000
143A207GLU-1-0.876-0.92860.9980.0010.0010.0000.0000.0000.000
144A208MET0-0.0070.01054.4920.0000.0000.0000.0000.0000.000
145A209THR00.0410.01260.2140.0000.0000.0000.0000.0000.000
146A210LYS10.9390.94959.1230.0030.0030.0000.0000.0000.000
147A211GLU-1-0.870-0.94459.812-0.003-0.0030.0000.0000.0000.000
148A212GLU-1-0.753-0.86257.830-0.001-0.0010.0000.0000.0000.000
149A213LYS10.9740.98455.8140.0020.0020.0000.0000.0000.000
150A214ASN0-0.0040.00954.7530.0000.0000.0000.0000.0000.000
151A215ILE00.0170.01954.0880.0000.0000.0000.0000.0000.000
152A216MET00.012-0.00151.5820.0000.0000.0000.0000.0000.000
153A217GLN0-0.061-0.02650.0880.0000.0000.0000.0000.0000.000
154A218SER0-0.013-0.00450.005-0.001-0.0010.0000.0000.0000.000
155A219MET0-0.004-0.00647.541-0.001-0.0010.0000.0000.0000.000
156A220VAL0-0.006-0.00145.891-0.001-0.0010.0000.0000.0000.000
157A221ASP-1-0.837-0.92845.217-0.008-0.0080.0000.0000.0000.000
158A222ASN0-0.016-0.01645.013-0.002-0.0020.0000.0000.0000.000
159A223SER0-0.037-0.01341.271-0.001-0.0010.0000.0000.0000.000
160A224TYR0-0.057-0.04740.527-0.001-0.0010.0000.0000.0000.000
161A225GLU-1-0.831-0.90740.879-0.016-0.0160.0000.0000.0000.000
162A226GLY0-0.0060.00639.031-0.002-0.0020.0000.0000.0000.000
163A227PHE0-0.023-0.01534.253-0.002-0.0020.0000.0000.0000.000
164A228VAL00.008-0.00436.269-0.002-0.0020.0000.0000.0000.000
165A229ASP-1-0.855-0.90236.360-0.026-0.0260.0000.0000.0000.000
166A230VAL00.0130.01032.005-0.003-0.0030.0000.0000.0000.000
167A231ILE00.0090.01032.092-0.003-0.0030.0000.0000.0000.000
168A232SER0-0.107-0.09532.959-0.003-0.0030.0000.0000.0000.000
169A233LYS10.8340.88331.5380.0250.0250.0000.0000.0000.000
170A234GLY00.0050.01828.729-0.003-0.0030.0000.0000.0000.000
171A235ARG10.7680.84326.1660.0410.0410.0000.0000.0000.000
172A236GLY0-0.0130.01530.578-0.001-0.0010.0000.0000.0000.000
173A237MET0-0.0160.00532.3460.0010.0010.0000.0000.0000.000
174A238PRO00.0340.05135.5560.0010.0010.0000.0000.0000.000
175A239LYS10.9740.95839.0850.0220.0220.0000.0000.0000.000
176A240ALA00.0010.00840.7030.0010.0010.0000.0000.0000.000
177A241GLU-1-0.880-0.95639.647-0.020-0.0200.0000.0000.0000.000
178A242VAL00.0140.01036.7180.0010.0010.0000.0000.0000.000
179A243LYS10.8550.89739.3760.0150.0150.0000.0000.0000.000
180A244LYS10.8340.93742.7850.0190.0190.0000.0000.0000.000
181A245ILE00.0020.01636.8510.0010.0010.0000.0000.0000.000
182A246ALA0-0.0160.00839.5040.0010.0010.0000.0000.0000.000
183A247ASP-1-0.761-0.84441.069-0.009-0.0090.0000.0000.0000.000
184A248GLY00.0110.00341.7480.0010.0010.0000.0000.0000.000
185A249ARG10.8310.91640.8690.0100.0100.0000.0000.0000.000
186A250VAL00.0030.00537.981-0.001-0.0010.0000.0000.0000.000
187A251TYR0-0.047-0.05235.648-0.001-0.0010.0000.0000.0000.000
188A252ASP-1-0.825-0.89134.685-0.008-0.0080.0000.0000.0000.000
189A253GLY00.0890.03030.812-0.002-0.0020.0000.0000.0000.000
190A254ARG10.9200.95931.4910.0080.0080.0000.0000.0000.000
191A255GLN00.003-0.01633.248-0.003-0.0030.0000.0000.0000.000
192A256ALA00.0490.02931.798-0.002-0.0020.0000.0000.0000.000
193A257LYS10.9400.98327.5900.0370.0370.0000.0000.0000.000
194A258LYS10.8570.92331.1850.0180.0180.0000.0000.0000.000
195A259LEU0-0.019-0.00334.501-0.001-0.0010.0000.0000.0000.000
196A260ASN00.0010.01330.212-0.002-0.0020.0000.0000.0000.000
197A261LEU0-0.0020.01331.436-0.002-0.0020.0000.0000.0000.000
198A262VAL00.0030.02526.8540.0000.0000.0000.0000.0000.000
199A263ASP-1-0.770-0.85123.961-0.056-0.0560.0000.0000.0000.000
200A264GLU-1-0.982-0.99121.742-0.067-0.0670.0000.0000.0000.000
201A265LEU0-0.078-0.04924.7810.0050.0050.0000.0000.0000.000
202A266GLY00.0120.00322.284-0.004-0.0040.0000.0000.0000.000
203A267PHE00.005-0.00621.7970.0020.0020.0000.0000.0000.000
204A268TYR00.014-0.00314.759-0.003-0.0030.0000.0000.0000.000
205A269ASP-1-0.850-0.93016.3180.0680.0680.0000.0000.0000.000
206A270ASP-1-0.834-0.90815.859-0.016-0.0160.0000.0000.0000.000
207A271THR0-0.033-0.01416.847-0.022-0.0220.0000.0000.0000.000
208A272ILE0-0.012-0.00811.168-0.031-0.0310.0000.0000.0000.000
209A273THR0-0.047-0.02912.038-0.046-0.0460.0000.0000.0000.000
210A274ALA0-0.003-0.00312.998-0.052-0.0520.0000.0000.0000.000
211A275MET0-0.0060.02611.436-0.038-0.0380.0000.0000.0000.000
212A276LYS10.9300.9727.296-0.215-0.2150.0000.0000.0000.000
213A277LYS10.9090.9539.9350.0650.0650.0000.0000.0000.000
214A278ASP-1-0.828-0.88612.660-0.183-0.1830.0000.0000.0000.000
215A279HIS00.0350.03511.0750.0010.0010.0000.0000.0000.000
216A280LYS10.9540.9717.6230.4590.4590.0000.0000.0000.000
217A281ASP-1-0.913-0.9696.006-0.710-0.7100.0000.0000.0000.000
218A282LEU00.0350.0065.004-0.512-0.458-0.001-0.002-0.0500.000
219A283LYS10.8340.9335.9890.4320.4320.0000.0000.0000.000
220A284ASN0-0.075-0.0472.060-1.388-3.2059.065-3.138-4.110-0.005
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