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: R8V78

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2526998.084427
FMO2-HF: Nuclear repulsion 2438761.062967
FMO2-HF: Total energy -88237.02146
FMO2-MP2: Total energy -88491.940654


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.
-2.0610.38811.171-5.83-7.787-0.009
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 : 0.014 / q_NPA : -0.017
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].
3A58SER0-0.035-0.0052.908-2.5401.6390.035-1.983-2.2300.004
4A59LYS10.8980.9484.5330.0390.069-0.001-0.023-0.0060.000
5A60ILE00.0200.0107.506-0.014-0.0140.0000.0000.0000.000
6A61ALA0-0.009-0.0029.9360.0780.0780.0000.0000.0000.000
7A62VAL0-0.002-0.00413.290-0.005-0.0050.0000.0000.0000.000
8A63LEU0-0.034-0.01615.8730.0130.0130.0000.0000.0000.000
9A64GLU-1-0.833-0.91119.472-0.006-0.0060.0000.0000.0000.000
10A65VAL00.0040.01222.7010.0000.0000.0000.0000.0000.000
11A66SER00.009-0.00326.1250.0020.0020.0000.0000.0000.000
12A67GLY00.0080.00228.4150.0010.0010.0000.0000.0000.000
13A68THR0-0.051-0.06331.937-0.004-0.0040.0000.0000.0000.000
14A69ILE0-0.046-0.02330.4960.0000.0000.0000.0000.0000.000
15A70GLN00.0110.00133.2670.0010.0010.0000.0000.0000.000
16A71ASP-1-0.813-0.89434.577-0.023-0.0230.0000.0000.0000.000
17A72ASN0-0.071-0.02235.6890.0030.0030.0000.0000.0000.000
18A82ASP-1-0.809-0.88034.074-0.010-0.0100.0000.0000.0000.000
19A83GLY0-0.017-0.00831.2120.0030.0030.0000.0000.0000.000
20A84TYR0-0.049-0.02627.756-0.003-0.0030.0000.0000.0000.000
21A85ASN00.0200.01229.329-0.002-0.0020.0000.0000.0000.000
22A86HIS00.0370.02429.015-0.003-0.0030.0000.0000.0000.000
23A87ARG10.8760.90529.2410.0180.0180.0000.0000.0000.000
24A88THR00.000-0.00325.385-0.004-0.0040.0000.0000.0000.000
25A89PHE00.0340.02223.085-0.007-0.0070.0000.0000.0000.000
26A90LEU00.0170.00724.226-0.009-0.0090.0000.0000.0000.000
27A91LYS10.8060.88924.4380.0450.0450.0000.0000.0000.000
28A92ASN00.009-0.01020.787-0.011-0.0110.0000.0000.0000.000
29A93LEU0-0.0020.01120.020-0.014-0.0140.0000.0000.0000.000
30A94GLU-1-0.827-0.89320.280-0.077-0.0770.0000.0000.0000.000
31A95ARG10.9150.95018.7200.0400.0400.0000.0000.0000.000
32A96ALA00.0090.01015.909-0.018-0.0180.0000.0000.0000.000
33A97LYS10.8000.90315.6240.0670.0670.0000.0000.0000.000
34A98ASP-1-0.844-0.92516.935-0.124-0.1240.0000.0000.0000.000
35A99ASP-1-0.788-0.84612.576-0.228-0.2280.0000.0000.0000.000
36A100LYS10.8850.91112.3570.1130.1130.0000.0000.0000.000
37A101THR0-0.052-0.0508.316-0.040-0.0400.0000.0000.0000.000
38A102VAL0-0.0350.0028.106-0.195-0.1950.0000.0000.0000.000
39A103LYS10.8430.9064.9810.8000.8000.0000.0000.0000.000
40A104GLY00.0550.0229.9960.0140.0140.0000.0000.0000.000
41A105ILE0-0.034-0.00512.263-0.005-0.0050.0000.0000.0000.000
42A106VAL00.0160.00513.9710.0060.0060.0000.0000.0000.000
43A107LEU0-0.011-0.00116.3760.0110.0110.0000.0000.0000.000
44A108LYS10.8600.91719.0830.0060.0060.0000.0000.0000.000
45A109VAL0-0.0060.00221.7620.0020.0020.0000.0000.0000.000
46A110ASN00.0150.01925.4800.0020.0020.0000.0000.0000.000
47A111SER00.023-0.00828.3290.0020.0020.0000.0000.0000.000
48A112PRO00.0640.01531.310-0.001-0.0010.0000.0000.0000.000
49A113GLY0-0.0230.00033.833-0.001-0.0010.0000.0000.0000.000
50A114GLY00.0220.00834.6990.0010.0010.0000.0000.0000.000
51A115GLY00.0060.03236.5010.0000.0000.0000.0000.0000.000
52A116VAL00.029-0.00636.097-0.002-0.0020.0000.0000.0000.000
53A117TYR0-0.060-0.03835.231-0.002-0.0020.0000.0000.0000.000
54A118GLU-1-0.765-0.89233.202-0.028-0.0280.0000.0000.0000.000
55A119SER0-0.021-0.02131.739-0.004-0.0040.0000.0000.0000.000
56A120ALA00.020-0.00131.378-0.004-0.0040.0000.0000.0000.000
57A121GLU-1-0.858-0.89831.005-0.041-0.0410.0000.0000.0000.000
58A122ILE0-0.012-0.01226.344-0.005-0.0050.0000.0000.0000.000
59A123HIS0-0.018-0.00127.049-0.007-0.0070.0000.0000.0000.000
60A124LYS10.9400.96627.4940.0550.0550.0000.0000.0000.000
61A125LYS10.8300.90625.1600.0600.0600.0000.0000.0000.000
62A126LEU00.0190.00922.172-0.010-0.0100.0000.0000.0000.000
63A127GLU-1-0.817-0.91022.888-0.095-0.0950.0000.0000.0000.000
64A128GLU-1-0.878-0.91624.232-0.076-0.0760.0000.0000.0000.000
65A129ILE00.0440.01918.341-0.007-0.0070.0000.0000.0000.000
66A130LYS10.8400.92619.6160.0850.0850.0000.0000.0000.000
67A131LYS10.9210.95720.6420.0740.0740.0000.0000.0000.000
68A132GLU-1-0.926-0.95321.199-0.098-0.0980.0000.0000.0000.000
69A133THR0-0.072-0.05716.193-0.013-0.0130.0000.0000.0000.000
70A134LYS10.8550.92816.0670.1520.1520.0000.0000.0000.000
71A135LYS10.8020.92213.0850.2290.2290.0000.0000.0000.000
72A136PRO00.0010.01613.2380.0280.0280.0000.0000.0000.000
73A137ILE00.009-0.01015.613-0.018-0.0180.0000.0000.0000.000
74A138TYR0-0.057-0.05216.2070.0020.0020.0000.0000.0000.000
75A139VAL00.0430.02518.5860.0010.0010.0000.0000.0000.000
76A140SER0-0.050-0.01919.5870.0050.0050.0000.0000.0000.000
77A141MET0-0.020-0.00621.6130.0050.0050.0000.0000.0000.000
78A142GLY00.0140.01225.3300.0040.0040.0000.0000.0000.000
79A143SER0-0.050-0.04726.6020.0000.0000.0000.0000.0000.000
80A144MET0-0.0030.01029.8630.0000.0000.0000.0000.0000.000
81A145ALA00.0420.01428.442-0.002-0.0020.0000.0000.0000.000
82A146ALA00.0110.03130.557-0.002-0.0020.0000.0000.0000.000
83A147SER00.0520.03133.998-0.001-0.0010.0000.0000.0000.000
84A148GLY00.0390.01233.833-0.003-0.0030.0000.0000.0000.000
85A149GLY00.0470.01230.100-0.003-0.0030.0000.0000.0000.000
86A150TYR0-0.033-0.04229.134-0.004-0.0040.0000.0000.0000.000
87A151TYR0-0.004-0.00230.115-0.005-0.0050.0000.0000.0000.000
88A152ILE0-0.020-0.01126.641-0.004-0.0040.0000.0000.0000.000
89A153SER0-0.003-0.01725.690-0.007-0.0070.0000.0000.0000.000
90A154THR0-0.075-0.03325.805-0.007-0.0070.0000.0000.0000.000
91A155ALA00.0320.02625.478-0.002-0.0020.0000.0000.0000.000
92A156ALA0-0.068-0.02521.816-0.010-0.0100.0000.0000.0000.000
93A157ASP-1-0.853-0.92919.396-0.141-0.1410.0000.0000.0000.000
94A158LYS10.8390.90918.8830.1220.1220.0000.0000.0000.000
95A159ILE0-0.010-0.01121.328-0.003-0.0030.0000.0000.0000.000
96A160PHE00.0110.00219.0740.0000.0000.0000.0000.0000.000
97A161ALA00.0300.01523.2590.0020.0020.0000.0000.0000.000
98A162THR00.0260.01925.5590.0010.0010.0000.0000.0000.000
99A163PRO0-0.066-0.05027.714-0.002-0.0020.0000.0000.0000.000
100A164GLU-1-0.855-0.94630.296-0.003-0.0030.0000.0000.0000.000
101A165THR0-0.066-0.00428.3520.0000.0000.0000.0000.0000.000
102A166LEU0-0.0090.00630.886-0.001-0.0010.0000.0000.0000.000
103A167THR00.008-0.03831.302-0.002-0.0020.0000.0000.0000.000
104A168GLY00.0230.01933.3840.0020.0020.0000.0000.0000.000
105A169SER00.007-0.00535.6340.0000.0000.0000.0000.0000.000
106A170LEU0-0.072-0.01934.780-0.001-0.0010.0000.0000.0000.000
107A171GLY00.0410.00138.4840.0010.0010.0000.0000.0000.000
108A172VAL0-0.023-0.01540.161-0.001-0.0010.0000.0000.0000.000
109A173ILE00.0100.01442.5800.0010.0010.0000.0000.0000.000
110A174MET0-0.003-0.01544.6730.0000.0000.0000.0000.0000.000
111A175GLU-1-0.944-0.95646.146-0.010-0.0100.0000.0000.0000.000
112A176SER0-0.014-0.00749.2900.0000.0000.0000.0000.0000.000
113A177VAL00.0160.00152.6580.0000.0000.0000.0000.0000.000
114A178ASN00.0260.04055.1150.0000.0000.0000.0000.0000.000
115A179TYR0-0.024-0.00657.2010.0000.0000.0000.0000.0000.000
116A180SER0-0.012-0.04560.5720.0010.0010.0000.0000.0000.000
117A181LYS10.8830.93163.2530.0060.0060.0000.0000.0000.000
118A182LEU0-0.0040.00461.1610.0000.0000.0000.0000.0000.000
119A183ALA00.0230.00864.0620.0000.0000.0000.0000.0000.000
120A184ASP-1-0.866-0.94465.758-0.004-0.0040.0000.0000.0000.000
121A185LYS10.8400.91967.3920.0040.0040.0000.0000.0000.000
122A186LEU0-0.057-0.02264.5280.0000.0000.0000.0000.0000.000
123A187GLY0-0.0020.02168.9400.0000.0000.0000.0000.0000.000
124A188ILE0-0.050-0.02265.1480.0000.0000.0000.0000.0000.000
125A189SER0-0.016-0.01367.8310.0000.0000.0000.0000.0000.000
126A190PHE00.008-0.01061.7600.0000.0000.0000.0000.0000.000
127A191GLU-1-0.912-0.95566.590-0.006-0.0060.0000.0000.0000.000
128A192THR0-0.029-0.01363.0050.0000.0000.0000.0000.0000.000
129A193ILE00.0190.01865.8370.0000.0000.0000.0000.0000.000
130A194LYS10.7990.87763.2050.0090.0090.0000.0000.0000.000
131A195SER0-0.0010.00062.5610.0000.0000.0000.0000.0000.000
132A196GLY00.0610.02163.6200.0000.0000.0000.0000.0000.000
133A197ALA00.0050.00363.3840.0000.0000.0000.0000.0000.000
134A198HIS0-0.009-0.02158.6670.0000.0000.0000.0000.0000.000
135A199ALA0-0.017-0.00158.3950.0000.0000.0000.0000.0000.000
136A200ASP-1-0.736-0.82958.346-0.009-0.0090.0000.0000.0000.000
137A201ILE0-0.002-0.00454.8330.0000.0000.0000.0000.0000.000
138A202MET0-0.027-0.02450.9950.0000.0000.0000.0000.0000.000
139A203SER00.0020.02355.3210.0000.0000.0000.0000.0000.000
140A204PRO00.0420.02055.6990.0000.0000.0000.0000.0000.000
141A205SER0-0.060-0.02257.6730.0010.0010.0000.0000.0000.000
142A206ARG10.7350.80160.7520.0090.0090.0000.0000.0000.000
143A207GLU-1-0.816-0.89360.944-0.008-0.0080.0000.0000.0000.000
144A208MET00.0100.03054.3120.0000.0000.0000.0000.0000.000
145A209THR00.031-0.01060.1650.0000.0000.0000.0000.0000.000
146A210LYS10.9300.95058.5800.0110.0110.0000.0000.0000.000
147A211GLU-1-0.836-0.91359.773-0.010-0.0100.0000.0000.0000.000
148A212GLU-1-0.725-0.83057.840-0.011-0.0110.0000.0000.0000.000
149A213LYS10.8840.92455.7460.0090.0090.0000.0000.0000.000
150A214ASN00.0250.03054.714-0.001-0.0010.0000.0000.0000.000
151A215ILE00.0330.02754.019-0.001-0.0010.0000.0000.0000.000
152A216MET00.0150.00751.610-0.001-0.0010.0000.0000.0000.000
153A217GLN0-0.072-0.04449.9540.0000.0000.0000.0000.0000.000
154A218SER00.0000.00449.971-0.001-0.0010.0000.0000.0000.000
155A219MET00.0030.00447.525-0.001-0.0010.0000.0000.0000.000
156A220VAL00.0080.00645.831-0.001-0.0010.0000.0000.0000.000
157A221ASP-1-0.821-0.90845.184-0.019-0.0190.0000.0000.0000.000
158A222ASN0-0.070-0.05545.004-0.002-0.0020.0000.0000.0000.000
159A223SER0-0.036-0.01341.382-0.002-0.0020.0000.0000.0000.000
160A224TYR0-0.049-0.03140.496-0.002-0.0020.0000.0000.0000.000
161A225GLU-1-0.787-0.88240.853-0.028-0.0280.0000.0000.0000.000
162A226GLY0-0.0050.00638.988-0.002-0.0020.0000.0000.0000.000
163A227PHE0-0.026-0.01834.244-0.003-0.0030.0000.0000.0000.000
164A228VAL00.017-0.00336.247-0.002-0.0020.0000.0000.0000.000
165A229ASP-1-0.854-0.90036.216-0.043-0.0430.0000.0000.0000.000
166A230VAL00.0180.01631.974-0.002-0.0020.0000.0000.0000.000
167A231ILE00.0130.00932.077-0.004-0.0040.0000.0000.0000.000
168A232SER0-0.089-0.05232.949-0.002-0.0020.0000.0000.0000.000
169A233LYS10.8320.88131.4690.0440.0440.0000.0000.0000.000
170A234GLY00.0000.01428.722-0.003-0.0030.0000.0000.0000.000
171A235ARG10.7710.84526.1400.0560.0560.0000.0000.0000.000
172A236GLY0-0.0160.01330.5740.0000.0000.0000.0000.0000.000
173A237MET0-0.029-0.00232.3510.0030.0030.0000.0000.0000.000
174A238PRO00.0310.02035.5580.0000.0000.0000.0000.0000.000
175A239LYS10.9570.95038.9350.0360.0360.0000.0000.0000.000
176A240ALA00.0000.00840.6980.0010.0010.0000.0000.0000.000
177A241GLU-1-0.823-0.90739.652-0.024-0.0240.0000.0000.0000.000
178A242VAL00.0280.01136.6720.0010.0010.0000.0000.0000.000
179A243LYS10.8020.87139.3650.0260.0260.0000.0000.0000.000
180A244LYS10.7700.88542.7710.0250.0250.0000.0000.0000.000
181A245ILE00.0120.02036.8670.0010.0010.0000.0000.0000.000
182A246ALA0-0.0140.01239.4060.0000.0000.0000.0000.0000.000
183A247ASP-1-0.760-0.84441.047-0.017-0.0170.0000.0000.0000.000
184A248GLY00.0090.00441.7160.0010.0010.0000.0000.0000.000
185A249ARG10.8290.90940.9060.0170.0170.0000.0000.0000.000
186A250VAL00.0010.00238.006-0.002-0.0020.0000.0000.0000.000
187A251TYR0-0.046-0.05535.6390.0010.0010.0000.0000.0000.000
188A252ASP-1-0.778-0.85534.659-0.014-0.0140.0000.0000.0000.000
189A253GLY00.0940.03430.786-0.003-0.0030.0000.0000.0000.000
190A254ARG10.9180.95931.4710.0070.0070.0000.0000.0000.000
191A255GLN0-0.074-0.06733.230-0.003-0.0030.0000.0000.0000.000
192A256ALA00.0490.02631.800-0.002-0.0020.0000.0000.0000.000
193A257LYS10.8520.92026.6900.0410.0410.0000.0000.0000.000
194A258LYS10.8720.93831.1740.0180.0180.0000.0000.0000.000
195A259LEU0-0.018-0.00534.4960.0000.0000.0000.0000.0000.000
196A260ASN00.0020.01830.229-0.003-0.0030.0000.0000.0000.000
197A261LEU0-0.0040.01331.430-0.003-0.0030.0000.0000.0000.000
198A262VAL00.0100.02026.842-0.002-0.0020.0000.0000.0000.000
199A263ASP-1-0.758-0.83823.935-0.070-0.0700.0000.0000.0000.000
200A264GLU-1-0.919-0.95621.976-0.053-0.0530.0000.0000.0000.000
201A265LEU0-0.063-0.03524.7740.0020.0020.0000.0000.0000.000
202A266GLY0-0.009-0.00722.2630.0000.0000.0000.0000.0000.000
203A267PHE00.017-0.00121.669-0.002-0.0020.0000.0000.0000.000
204A268TYR00.0540.01315.102-0.022-0.0220.0000.0000.0000.000
205A269ASP-1-0.854-0.93216.2830.0340.0340.0000.0000.0000.000
206A270ASP-1-0.829-0.90515.828-0.012-0.0120.0000.0000.0000.000
207A271THR0-0.040-0.01816.828-0.019-0.0190.0000.0000.0000.000
208A272ILE0-0.008-0.00611.177-0.038-0.0380.0000.0000.0000.000
209A273THR0-0.036-0.02312.018-0.045-0.0450.0000.0000.0000.000
210A274ALA0-0.009-0.00413.000-0.036-0.0360.0000.0000.0000.000
211A275MET0-0.0020.02011.096-0.042-0.0420.0000.0000.0000.000
212A276LYS10.8930.9526.843-0.131-0.1310.0000.0000.0000.000
213A277LYS10.8480.9119.9430.0700.0700.0000.0000.0000.000
214A278ASP-1-0.797-0.86312.579-0.151-0.1510.0000.0000.0000.000
215A279HIS00.0460.04010.966-0.004-0.0040.0000.0000.0000.000
216A280LYS10.9600.9767.6570.2470.2470.0000.0000.0000.000
217A281ASP-1-0.855-0.9385.776-0.786-0.7860.0000.0000.0000.000
218A282LEU00.0460.0145.002-0.642-0.584-0.001-0.003-0.0540.000
219A283LYS10.8150.9265.9700.2640.2640.0000.0000.0000.000
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