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: YY1K2

Calculation Name: 2RAD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RAD

Chain ID: A

ChEMBL ID:

UniProt ID: Q81BN2

Base Structure: X-ray

Registration Date: 2023-03-14

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 403
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7336966.168004
FMO2-HF: Nuclear repulsion 7178389.630876
FMO2-HF: Total energy -158576.537128
FMO2-MP2: Total energy -159046.471471


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:40:ASN)


Summations of interaction energy for fragment #1(A:40:ASN)
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.
-3.7770.1720.33-1.54-2.7380.004
Interaction energy analysis for fragmet #1(A:40:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.037
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].
3A42ILE0-0.006-0.0093.875-0.6021.531-0.006-1.040-1.0870.003
4A43ALA00.1060.0603.901-0.826-0.5130.000-0.070-0.2440.000
5A44LYS10.9620.9745.282-0.837-0.745-0.001-0.002-0.0880.000
6A45TRP00.0280.0107.754-0.100-0.1000.0000.0000.0000.000
7A46LEU00.0490.0225.676-0.026-0.0260.0000.0000.0000.000
8A47GLU-1-0.800-0.8839.3641.0441.0440.0000.0000.0000.000
9A48ALA0-0.034-0.00711.538-0.039-0.0390.0000.0000.0000.000
10A49HIS00.0250.01912.748-0.060-0.0600.0000.0000.0000.000
11A50ALA00.0030.02212.895-0.040-0.0400.0000.0000.0000.000
12A51LYN00.0090.01314.6820.0050.0050.0000.0000.0000.000
13A52PRO00.0080.00418.5050.0020.0020.0000.0000.0000.000
14A53LEU0-0.043-0.01819.342-0.032-0.0320.0000.0000.0000.000
15A54LYS10.9360.96421.976-0.181-0.1810.0000.0000.0000.000
16A55THR0-0.002-0.01424.5330.0000.0000.0000.0000.0000.000
17A56THR00.0830.04123.634-0.015-0.0150.0000.0000.0000.000
18A57ASN00.0320.01925.419-0.021-0.0210.0000.0000.0000.000
19A58PRO00.0620.01829.277-0.001-0.0010.0000.0000.0000.000
20A59THR0-0.042-0.00131.420-0.009-0.0090.0000.0000.0000.000
21A60ALA00.0680.03630.327-0.001-0.0010.0000.0000.0000.000
22A61SER0-0.0020.00229.8040.0080.0080.0000.0000.0000.000
23A62LEU00.0240.02029.514-0.005-0.0050.0000.0000.0000.000
24A63ASN00.012-0.01028.971-0.004-0.0040.0000.0000.0000.000
25A64ASP-1-0.777-0.85024.3830.1950.1950.0000.0000.0000.000
26A65LEU00.0390.01723.9740.0090.0090.0000.0000.0000.000
27A66LYS10.8300.90525.822-0.120-0.1200.0000.0000.0000.000
28A67PRO0-0.014-0.00422.607-0.013-0.0130.0000.0000.0000.000
29A68LEU00.0300.01322.725-0.013-0.0130.0000.0000.0000.000
30A69LYS10.9510.98725.282-0.088-0.0880.0000.0000.0000.000
31A70ASN00.008-0.01126.129-0.008-0.0080.0000.0000.0000.000
32A71MET0-0.0320.01419.813-0.008-0.0080.0000.0000.0000.000
33A72VAL00.0560.02323.747-0.009-0.0090.0000.0000.0000.000
34A73GLY00.0070.00926.244-0.008-0.0080.0000.0000.0000.000
35A74SER0-0.022-0.01128.7540.0030.0030.0000.0000.0000.000
36A75ALA0-0.0110.01228.388-0.005-0.0050.0000.0000.0000.000
37A76SER0-0.017-0.00730.5220.0020.0020.0000.0000.0000.000
38A77ILE00.0070.00731.1650.0030.0030.0000.0000.0000.000
39A78VAL0-0.026-0.01626.334-0.002-0.0020.0000.0000.0000.000
40A79GLY00.0250.02826.1590.0020.0020.0000.0000.0000.000
41A80LEU0-0.023-0.02023.9450.0070.0070.0000.0000.0000.000
42A81GLY00.0460.02022.592-0.003-0.0030.0000.0000.0000.000
43A82GLU-1-0.792-0.86522.3060.1220.1220.0000.0000.0000.000
44A83ALA00.004-0.00518.865-0.013-0.0130.0000.0000.0000.000
45A84THR00.0270.01320.557-0.013-0.0130.0000.0000.0000.000
46A85HIS10.7830.88723.580-0.074-0.0740.0000.0000.0000.000
47A86GLY00.0610.03426.171-0.009-0.0090.0000.0000.0000.000
48A87ALA00.0340.02823.5770.0050.0050.0000.0000.0000.000
49A88HIS0-0.030-0.03025.552-0.002-0.0020.0000.0000.0000.000
50A89GLU-1-0.771-0.86323.0890.2130.2130.0000.0000.0000.000
51A90VAL0-0.023-0.00721.3210.0060.0060.0000.0000.0000.000
52A91PHE00.0180.01123.902-0.008-0.0080.0000.0000.0000.000
53A92THR0-0.004-0.01226.746-0.007-0.0070.0000.0000.0000.000
54A93MET0-0.0020.01521.412-0.012-0.0120.0000.0000.0000.000
55A94LYS10.7780.89024.448-0.117-0.1170.0000.0000.0000.000
56A95HIS00.0700.04326.485-0.012-0.0120.0000.0000.0000.000
57A96ARG10.7540.85125.328-0.191-0.1910.0000.0000.0000.000
58A97ILE00.0090.00022.904-0.006-0.0060.0000.0000.0000.000
59A98VAL00.0110.00327.465-0.009-0.0090.0000.0000.0000.000
60A99LYS10.7860.89530.802-0.116-0.1160.0000.0000.0000.000
61A100TYR0-0.013-0.02628.893-0.005-0.0050.0000.0000.0000.000
62A101LEU0-0.019-0.01627.707-0.006-0.0060.0000.0000.0000.000
63A102VAL00.0060.00931.515-0.006-0.0060.0000.0000.0000.000
64A103SER0-0.002-0.01334.426-0.003-0.0030.0000.0000.0000.000
65A104GLU-1-0.840-0.88832.4620.1010.1010.0000.0000.0000.000
66A105LYS10.7860.89629.915-0.068-0.0680.0000.0000.0000.000
67A106GLY00.0540.05933.941-0.005-0.0050.0000.0000.0000.000
68A107PHE0-0.060-0.03231.319-0.004-0.0040.0000.0000.0000.000
69A108THR00.0170.00035.6910.0030.0030.0000.0000.0000.000
70A109ASN0-0.026-0.01936.921-0.002-0.0020.0000.0000.0000.000
71A110LEU0-0.012-0.00432.1590.0030.0030.0000.0000.0000.000
72A111VAL00.0390.02433.884-0.002-0.0020.0000.0000.0000.000
73A112LEU00.002-0.00832.5440.0060.0060.0000.0000.0000.000
74A113GLU-1-0.819-0.90228.9250.0530.0530.0000.0000.0000.000
75A114GLU-1-0.745-0.83832.8130.0500.0500.0000.0000.0000.000
76A115GLY00.0070.00536.351-0.003-0.0030.0000.0000.0000.000
77A116TRP00.020-0.01239.8300.0030.0030.0000.0000.0000.000
78A117ASP-1-0.755-0.86941.6780.0280.0280.0000.0000.0000.000
79A118ARG10.8480.93340.673-0.034-0.0340.0000.0000.0000.000
80A119ALA00.006-0.00940.1160.0020.0020.0000.0000.0000.000
81A120LEU0-0.0260.00341.9970.0020.0020.0000.0000.0000.000
82A121GLU-1-0.771-0.86645.4410.0370.0370.0000.0000.0000.000
83A122LEU0-0.050-0.01639.1670.0020.0020.0000.0000.0000.000
84A123ASP-1-0.757-0.85242.9520.0420.0420.0000.0000.0000.000
85A124ARG10.9000.93343.964-0.034-0.0340.0000.0000.0000.000
86A125TYR0-0.017-0.01242.8300.0000.0000.0000.0000.0000.000
87A126VAL0-0.009-0.01240.3730.0010.0010.0000.0000.0000.000
88A127LEU0-0.0200.00643.7730.0010.0010.0000.0000.0000.000
89A128THR0-0.104-0.07446.720-0.001-0.0010.0000.0000.0000.000
90A129GLY0-0.003-0.00947.532-0.001-0.0010.0000.0000.0000.000
91A130LYS10.8920.96748.561-0.035-0.0350.0000.0000.0000.000
92A131GLY00.0580.02448.7760.0000.0000.0000.0000.0000.000
93A132ASN00.0440.02845.7620.0040.0040.0000.0000.0000.000
94A133PRO00.0650.03041.482-0.002-0.0020.0000.0000.0000.000
95A134SER0-0.017-0.01341.611-0.001-0.0010.0000.0000.0000.000
96A135GLN0-0.030-0.00842.693-0.002-0.0020.0000.0000.0000.000
97A136HIS0-0.022-0.02543.520-0.001-0.0010.0000.0000.0000.000
98A137LEU0-0.0170.00636.858-0.002-0.0020.0000.0000.0000.000
99A138THR00.024-0.03336.736-0.003-0.0030.0000.0000.0000.000
100A139PRO0-0.018-0.02837.2590.0050.0050.0000.0000.0000.000
101A140VAL0-0.0010.01631.4560.0030.0030.0000.0000.0000.000
102A141PHE0-0.021-0.01030.4600.0080.0080.0000.0000.0000.000
103A142LYS10.7790.89834.753-0.050-0.0500.0000.0000.0000.000
104A143THR0-0.022-0.04232.8030.0010.0010.0000.0000.0000.000
105A144LYS10.9360.96035.493-0.105-0.1050.0000.0000.0000.000
106A145GLU-1-0.703-0.81530.6570.1200.1200.0000.0000.0000.000
107A146MET0-0.028-0.00432.3450.0020.0020.0000.0000.0000.000
108A147LEU0-0.018-0.00834.919-0.006-0.0060.0000.0000.0000.000
109A148ASP-1-0.891-0.95435.1020.0990.0990.0000.0000.0000.000
110A149LEU0-0.051-0.01532.401-0.001-0.0010.0000.0000.0000.000
111A150LEU00.0190.00135.431-0.004-0.0040.0000.0000.0000.000
112A151ASP-1-0.755-0.82438.7420.0650.0650.0000.0000.0000.000
113A152TRP00.0440.01035.8250.0000.0000.0000.0000.0000.000
114A153ILE0-0.003-0.00635.877-0.002-0.0020.0000.0000.0000.000
115A154ARG10.8690.92039.688-0.065-0.0650.0000.0000.0000.000
116A155GLN0-0.090-0.05440.7810.0000.0000.0000.0000.0000.000
117A156TYR0-0.079-0.04440.083-0.001-0.0010.0000.0000.0000.000
118A157ASN00.023-0.02642.222-0.003-0.0030.0000.0000.0000.000
119A158ALA00.0100.02444.802-0.003-0.0030.0000.0000.0000.000
120A159ASN00.0130.02144.456-0.005-0.0050.0000.0000.0000.000
121A160PRO00.0420.00647.379-0.001-0.0010.0000.0000.0000.000
122A161LYN00.0200.04046.998-0.003-0.0030.0000.0000.0000.000
123A162HIS0-0.0120.00442.2440.0020.0020.0000.0000.0000.000
124A163LYS10.8580.89345.358-0.044-0.0440.0000.0000.0000.000
125A164SER0-0.0010.01242.579-0.003-0.0030.0000.0000.0000.000
126A165LYS10.8250.91542.862-0.045-0.0450.0000.0000.0000.000
127A166VAL0-0.025-0.00837.856-0.001-0.0010.0000.0000.0000.000
128A167ARG10.8260.90540.732-0.035-0.0350.0000.0000.0000.000
129A168VAL0-0.016-0.02038.0280.0040.0040.0000.0000.0000.000
130A169ILE0-0.0020.00238.191-0.003-0.0030.0000.0000.0000.000
131A170GLY00.0140.01937.2350.0040.0040.0000.0000.0000.000
132A171MET0-0.024-0.02630.271-0.005-0.0050.0000.0000.0000.000
133A172ASP-1-0.767-0.85535.3180.0220.0220.0000.0000.0000.000
134A173ILE0-0.009-0.02637.2000.0010.0010.0000.0000.0000.000
135A174GLN0-0.045-0.04335.583-0.003-0.0030.0000.0000.0000.000
136A175SER0-0.038-0.02140.7100.0000.0000.0000.0000.0000.000
137A176VAL0-0.039-0.01044.1400.0010.0010.0000.0000.0000.000
138A177ASN00.0190.00046.309-0.002-0.0020.0000.0000.0000.000
139A178GLU-1-0.846-0.94549.1150.0170.0170.0000.0000.0000.000
140A179ASN0-0.0340.00447.802-0.001-0.0010.0000.0000.0000.000
141A180VAL0-0.0040.00946.8210.0000.0000.0000.0000.0000.000
142A181TYR00.019-0.02849.875-0.001-0.0010.0000.0000.0000.000
143A182ASN0-0.011-0.01953.384-0.001-0.0010.0000.0000.0000.000
144A183ASN0-0.046-0.02050.5680.0000.0000.0000.0000.0000.000
145A184ILE0-0.012-0.00351.274-0.001-0.0010.0000.0000.0000.000
146A185ILE0-0.023-0.01054.840-0.001-0.0010.0000.0000.0000.000
147A186GLU-1-0.787-0.89757.7210.0150.0150.0000.0000.0000.000
148A187TYR0-0.008-0.00256.1400.0000.0000.0000.0000.0000.000
149A188ILE0-0.080-0.04457.382-0.001-0.0010.0000.0000.0000.000
150A189LYS10.8250.90960.634-0.014-0.0140.0000.0000.0000.000
151A190ALA00.003-0.00460.8140.0000.0000.0000.0000.0000.000
152A191ASN0-0.065-0.02659.1430.0000.0000.0000.0000.0000.000
153A192ASN00.002-0.02762.734-0.001-0.0010.0000.0000.0000.000
154A193SER00.0820.06664.5110.0000.0000.0000.0000.0000.000
155A194LYS10.8410.92266.326-0.005-0.0050.0000.0000.0000.000
156A195LEU00.002-0.00461.622-0.001-0.0010.0000.0000.0000.000
157A196LEU00.0300.03362.229-0.001-0.0010.0000.0000.0000.000
158A197PRO00.0340.01063.6640.0000.0000.0000.0000.0000.000
159A198ARG10.8680.94260.867-0.002-0.0020.0000.0000.0000.000
160A199VAL0-0.017-0.00758.309-0.001-0.0010.0000.0000.0000.000
161A200GLU-1-0.804-0.93459.6920.0110.0110.0000.0000.0000.000
162A201GLU-1-0.853-0.90661.2250.0050.0050.0000.0000.0000.000
163A202LYS10.8340.88758.144-0.001-0.0010.0000.0000.0000.000
164A203ILE00.0090.01155.4100.0000.0000.0000.0000.0000.000
165A204LYS10.8230.91256.697-0.006-0.0060.0000.0000.0000.000
166A205GLY0-0.0010.00958.6100.0000.0000.0000.0000.0000.000
167A206LEU0-0.0080.00152.153-0.001-0.0010.0000.0000.0000.000
168A207ILE00.0480.02953.1930.0000.0000.0000.0000.0000.000
169A208PRO0-0.034-0.02052.8930.0010.0010.0000.0000.0000.000
170A209VAL0-0.001-0.00952.1950.0000.0000.0000.0000.0000.000
171A210THR00.0160.02348.532-0.001-0.0010.0000.0000.0000.000
172A211LYS10.8110.90547.663-0.012-0.0120.0000.0000.0000.000
173A212ASP-1-0.809-0.87445.3020.0160.0160.0000.0000.0000.000
174A213MET00.0410.01538.673-0.002-0.0020.0000.0000.0000.000
175A214ASN00.0240.02343.745-0.002-0.0020.0000.0000.0000.000
176A215THR0-0.072-0.04246.208-0.002-0.0020.0000.0000.0000.000
177A216PHE0-0.021-0.01347.187-0.001-0.0010.0000.0000.0000.000
178A217GLU-1-0.860-0.93743.429-0.006-0.0060.0000.0000.0000.000
179A218SER0-0.070-0.05147.046-0.001-0.0010.0000.0000.0000.000
180A219LEU0-0.0360.00250.2770.0010.0010.0000.0000.0000.000
181A220THR0-0.006-0.00852.508-0.002-0.0020.0000.0000.0000.000
182A221LYS10.8130.87954.1490.0080.0080.0000.0000.0000.000
183A222GLU-1-0.771-0.87955.392-0.005-0.0050.0000.0000.0000.000
184A223GLU-1-0.823-0.91049.775-0.006-0.0060.0000.0000.0000.000
185A224LYS10.9230.96249.5760.0150.0150.0000.0000.0000.000
186A225GLU-1-0.907-0.98551.790-0.008-0.0080.0000.0000.0000.000
187A226LYS10.9371.00854.4170.0000.0000.0000.0000.0000.000
188A227TYR0-0.002-0.02552.5430.0010.0010.0000.0000.0000.000
189A228VAL00.0400.02849.1540.0010.0010.0000.0000.0000.000
190A229LEU00.006-0.00751.6340.0000.0000.0000.0000.0000.000
191A230ASP-1-0.815-0.88254.7130.0010.0010.0000.0000.0000.000
192A231ALA00.0060.00650.5040.0010.0010.0000.0000.0000.000
193A232LYS10.9230.96847.7290.0060.0060.0000.0000.0000.000
194A233THR0-0.036-0.02652.8720.0000.0000.0000.0000.0000.000
195A234ILE0-0.045-0.01854.1220.0000.0000.0000.0000.0000.000
196A235SER0-0.034-0.04350.0860.0010.0010.0000.0000.0000.000
197A236ALA00.002-0.00353.1280.0000.0000.0000.0000.0000.000
198A237LEU00.0060.01255.6970.0000.0000.0000.0000.0000.000
199A238LEU0-0.009-0.01653.3770.0000.0000.0000.0000.0000.000
200A239GLU-1-0.812-0.88353.5690.0040.0040.0000.0000.0000.000
201A240GLU-1-0.911-0.94656.577-0.001-0.0010.0000.0000.0000.000
202A241ASN0-0.019-0.01960.0560.0000.0000.0000.0000.0000.000
203A242LYS10.8580.93852.941-0.004-0.0040.0000.0000.0000.000
204A243SER0-0.040-0.03358.7620.0010.0010.0000.0000.0000.000
205A244TYR0-0.053-0.02361.7340.0000.0000.0000.0000.0000.000
206A245LEU00.0420.03458.3460.0010.0010.0000.0000.0000.000
207A246ASN00.0480.03558.4090.0000.0000.0000.0000.0000.000
208A247GLY00.0810.04156.1650.0010.0010.0000.0000.0000.000
209A248LYS10.9020.94054.357-0.009-0.0090.0000.0000.0000.000
210A249SER0-0.043-0.00853.9870.0010.0010.0000.0000.0000.000
211A250LYS10.9810.96150.000-0.022-0.0220.0000.0000.0000.000
212A251GLU-1-0.885-0.93550.1990.0200.0200.0000.0000.0000.000
213A252PHE00.0490.03052.0410.0000.0000.0000.0000.0000.000
214A253ALA0-0.0080.00248.159-0.001-0.0010.0000.0000.0000.000
215A254TRP00.0200.00244.2070.0000.0000.0000.0000.0000.000
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