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: 436MN

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 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 403
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7322587.222134
FMO2-HF: Nuclear repulsion 7164015.793599
FMO2-HF: Total energy -158571.428535
FMO2-MP2: Total energy -159041.76507


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.
-7.137-4.6760.042-0.797-1.7020.001
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 : -0.004 / q_NPA : -0.004
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].
3A42ILE0-0.0260.0043.667-0.0321.4390.010-0.597-0.8830.001
4A43ALA00.1210.0584.648-0.262-0.102-0.001-0.008-0.1500.000
5A44LYS11.0100.9886.333-1.871-1.8710.0000.0000.0000.000
6A45TRP00.0340.0069.214-0.273-0.2730.0000.0000.0000.000
7A46LEU00.0490.0266.777-0.249-0.2490.0000.0000.0000.000
8A47GLU-1-0.881-0.94110.3351.1171.1170.0000.0000.0000.000
9A48ALA0-0.087-0.04112.620-0.152-0.1520.0000.0000.0000.000
10A49HIS0-0.056-0.04014.126-0.183-0.1830.0000.0000.0000.000
11A50ALA0-0.0010.02014.616-0.077-0.0770.0000.0000.0000.000
12A51LYN0-0.0090.00416.315-0.015-0.0150.0000.0000.0000.000
13A52PRO0-0.005-0.01519.481-0.020-0.0200.0000.0000.0000.000
14A53LEU0-0.0130.01120.454-0.039-0.0390.0000.0000.0000.000
15A54LYS10.9290.98022.625-0.209-0.2090.0000.0000.0000.000
16A55THR00.009-0.01525.155-0.007-0.0070.0000.0000.0000.000
17A56THR00.0920.04324.5370.0060.0060.0000.0000.0000.000
18A57ASN00.0350.03226.503-0.021-0.0210.0000.0000.0000.000
19A58PRO00.0760.02730.3170.0090.0090.0000.0000.0000.000
20A59THR0-0.032-0.00232.663-0.001-0.0010.0000.0000.0000.000
21A60ALA00.0150.02131.1940.0050.0050.0000.0000.0000.000
22A61SER0-0.007-0.01830.8790.0030.0030.0000.0000.0000.000
23A62LEU00.0420.01530.700-0.005-0.0050.0000.0000.0000.000
24A63ASN00.0410.00730.791-0.006-0.0060.0000.0000.0000.000
25A64ASP-1-0.887-0.94825.3900.2260.2260.0000.0000.0000.000
26A65LEU00.0460.02025.4370.0200.0200.0000.0000.0000.000
27A66LYS10.9760.99827.274-0.178-0.1780.0000.0000.0000.000
28A67PRO0-0.046-0.02323.886-0.014-0.0140.0000.0000.0000.000
29A68LEU00.0770.03724.263-0.002-0.0020.0000.0000.0000.000
30A69LYS10.9510.97826.511-0.146-0.1460.0000.0000.0000.000
31A70ASN00.016-0.02227.846-0.021-0.0210.0000.0000.0000.000
32A71MET0-0.0330.02221.295-0.005-0.0050.0000.0000.0000.000
33A72VAL00.0170.00625.461-0.010-0.0100.0000.0000.0000.000
34A73GLY0-0.0010.00627.577-0.015-0.0150.0000.0000.0000.000
35A74SER0-0.054-0.04429.8550.0020.0020.0000.0000.0000.000
36A75ALA00.0000.01429.822-0.008-0.0080.0000.0000.0000.000
37A76SER0-0.012-0.00831.9350.0020.0020.0000.0000.0000.000
38A77ILE00.0230.01931.814-0.001-0.0010.0000.0000.0000.000
39A78VAL0-0.020-0.02327.5520.0030.0030.0000.0000.0000.000
40A79GLY00.0010.02627.154-0.004-0.0040.0000.0000.0000.000
41A80LEU0-0.036-0.02524.9610.0160.0160.0000.0000.0000.000
42A81GLY00.0610.01323.997-0.010-0.0100.0000.0000.0000.000
43A82GLU-1-0.822-0.89223.2630.0100.0100.0000.0000.0000.000
44A83ALA0-0.015-0.01519.124-0.022-0.0220.0000.0000.0000.000
45A84THR00.0490.02820.893-0.029-0.0290.0000.0000.0000.000
46A85HIS10.8010.87823.5760.0820.0820.0000.0000.0000.000
47A86GLY00.0760.03726.1780.0050.0050.0000.0000.0000.000
48A87ALA00.0250.02823.937-0.001-0.0010.0000.0000.0000.000
49A88HIS00.005-0.00925.9440.0170.0170.0000.0000.0000.000
50A89GLU-1-0.800-0.85923.6560.0770.0770.0000.0000.0000.000
51A90VAL0-0.026-0.01122.1040.0160.0160.0000.0000.0000.000
52A91PHE00.0320.01924.5640.0070.0070.0000.0000.0000.000
53A92THR00.023-0.01128.1150.0030.0030.0000.0000.0000.000
54A93MET0-0.0120.01122.5490.0100.0100.0000.0000.0000.000
55A94LYS10.7990.90025.329-0.008-0.0080.0000.0000.0000.000
56A95HIS00.0260.00227.353-0.001-0.0010.0000.0000.0000.000
57A96ARG10.8160.92927.231-0.167-0.1670.0000.0000.0000.000
58A97ILE00.0220.01024.4450.0040.0040.0000.0000.0000.000
59A98VAL00.0330.03229.014-0.002-0.0020.0000.0000.0000.000
60A99LYS10.8590.92532.173-0.094-0.0940.0000.0000.0000.000
61A100TYR00.014-0.01229.9750.0010.0010.0000.0000.0000.000
62A101LEU0-0.036-0.02429.0100.0000.0000.0000.0000.0000.000
63A102VAL0-0.0180.00432.884-0.005-0.0050.0000.0000.0000.000
64A103SER0-0.090-0.04735.767-0.001-0.0010.0000.0000.0000.000
65A104GLU-1-0.917-0.95233.7440.1150.1150.0000.0000.0000.000
66A105LYS10.7410.90531.275-0.112-0.1120.0000.0000.0000.000
67A106GLY00.0450.02735.166-0.006-0.0060.0000.0000.0000.000
68A107PHE0-0.020-0.01032.298-0.004-0.0040.0000.0000.0000.000
69A108THR00.001-0.01036.9900.0020.0020.0000.0000.0000.000
70A109ASN00.0320.02438.027-0.007-0.0070.0000.0000.0000.000
71A110LEU00.0120.00333.2860.0050.0050.0000.0000.0000.000
72A111VAL00.0250.01434.830-0.003-0.0030.0000.0000.0000.000
73A112LEU00.0420.01133.3870.0010.0010.0000.0000.0000.000
74A113GLU-1-0.846-0.91829.604-0.071-0.0710.0000.0000.0000.000
75A114GLU-1-0.747-0.84033.605-0.034-0.0340.0000.0000.0000.000
76A115GLY00.0090.00537.0360.0000.0000.0000.0000.0000.000
77A116TRP00.002-0.01340.1820.0050.0050.0000.0000.0000.000
78A117ASP-1-0.743-0.86742.090-0.029-0.0290.0000.0000.0000.000
79A118ARG10.8900.94440.9000.0380.0380.0000.0000.0000.000
80A119ALA00.014-0.01040.6480.0040.0040.0000.0000.0000.000
81A120LEU00.0010.01742.5670.0050.0050.0000.0000.0000.000
82A121GLU-1-0.935-0.97545.874-0.002-0.0020.0000.0000.0000.000
83A122LEU0-0.062-0.02839.7080.0030.0030.0000.0000.0000.000
84A123ASP-1-0.830-0.91743.7470.0150.0150.0000.0000.0000.000
85A124ARG10.9720.98244.8590.0020.0020.0000.0000.0000.000
86A125TYR00.0020.02343.0070.0020.0020.0000.0000.0000.000
87A126VAL00.0050.00541.2920.0030.0030.0000.0000.0000.000
88A127LEU0-0.028-0.00244.6460.0050.0050.0000.0000.0000.000
89A128THR0-0.076-0.06547.8040.0010.0010.0000.0000.0000.000
90A129GLY0-0.005-0.00848.3610.0000.0000.0000.0000.0000.000
91A130LYS10.9190.96749.415-0.011-0.0110.0000.0000.0000.000
92A131GLY0-0.005-0.01049.439-0.001-0.0010.0000.0000.0000.000
93A132ASN00.0420.01646.6580.0040.0040.0000.0000.0000.000
94A133PRO00.0870.03542.451-0.004-0.0040.0000.0000.0000.000
95A134SER0-0.0110.00541.742-0.004-0.0040.0000.0000.0000.000
96A135GLN0-0.021-0.01242.807-0.006-0.0060.0000.0000.0000.000
97A136HIS00.0220.00643.883-0.006-0.0060.0000.0000.0000.000
98A137LEU0-0.0140.01937.404-0.002-0.0020.0000.0000.0000.000
99A138THR0-0.033-0.06936.138-0.004-0.0040.0000.0000.0000.000
100A139PRO0-0.038-0.03437.4650.0030.0030.0000.0000.0000.000
101A140VAL00.0290.01131.4540.0030.0030.0000.0000.0000.000
102A141PHE0-0.028-0.01430.5700.0030.0030.0000.0000.0000.000
103A142LYS10.8140.93934.8690.0330.0330.0000.0000.0000.000
104A143THR00.003-0.00432.529-0.002-0.0020.0000.0000.0000.000
105A144LYS10.9720.96435.696-0.022-0.0220.0000.0000.0000.000
106A145GLU-1-0.736-0.87330.8720.0290.0290.0000.0000.0000.000
107A146MET0-0.031-0.00733.2090.0070.0070.0000.0000.0000.000
108A147LEU0-0.035-0.02135.4940.0000.0000.0000.0000.0000.000
109A148ASP-1-0.912-0.95035.8150.0530.0530.0000.0000.0000.000
110A149LEU0-0.050-0.02033.1590.0040.0040.0000.0000.0000.000
111A150LEU00.004-0.00836.1990.0020.0020.0000.0000.0000.000
112A151ASP-1-0.832-0.90439.5060.0390.0390.0000.0000.0000.000
113A152TRP00.0270.00236.9180.0040.0040.0000.0000.0000.000
114A153ILE00.000-0.00637.0760.0030.0030.0000.0000.0000.000
115A154ARG10.8890.95840.688-0.033-0.0330.0000.0000.0000.000
116A155GLN0-0.069-0.02642.6870.0040.0040.0000.0000.0000.000
117A156TYR0-0.029-0.00640.9620.0030.0030.0000.0000.0000.000
118A157ASN00.006-0.02343.4140.0040.0040.0000.0000.0000.000
119A158ALA0-0.0080.01245.766-0.003-0.0030.0000.0000.0000.000
120A159ASN0-0.0050.00846.885-0.003-0.0030.0000.0000.0000.000
121A160PRO00.0450.00848.6610.0000.0000.0000.0000.0000.000
122A161LYN0-0.023-0.00248.007-0.003-0.0030.0000.0000.0000.000
123A162HIS00.0150.00443.0300.0010.0010.0000.0000.0000.000
124A163LYS10.9100.93946.891-0.047-0.0470.0000.0000.0000.000
125A164SER0-0.036-0.00544.367-0.005-0.0050.0000.0000.0000.000
126A165LYS10.8420.93144.269-0.035-0.0350.0000.0000.0000.000
127A166VAL00.000-0.00438.853-0.001-0.0010.0000.0000.0000.000
128A167ARG10.8590.94341.781-0.012-0.0120.0000.0000.0000.000
129A168VAL0-0.006-0.01038.8780.0030.0030.0000.0000.0000.000
130A169ILE00.0030.01439.217-0.002-0.0020.0000.0000.0000.000
131A170GLY00.0140.02538.0480.0010.0010.0000.0000.0000.000
132A171MET0-0.023-0.02731.2080.0000.0000.0000.0000.0000.000
133A172ASP-1-0.759-0.88235.195-0.071-0.0710.0000.0000.0000.000
134A173ILE0-0.008-0.00437.6200.0050.0050.0000.0000.0000.000
135A174GLN0-0.065-0.05635.353-0.005-0.0050.0000.0000.0000.000
136A175SER0-0.021-0.01640.795-0.002-0.0020.0000.0000.0000.000
137A176VAL0-0.046-0.00444.4230.0020.0020.0000.0000.0000.000
138A177ASN00.0320.00847.1390.0010.0010.0000.0000.0000.000
139A178GLU-1-0.863-0.96449.401-0.023-0.0230.0000.0000.0000.000
140A179ASN0-0.036-0.00148.8630.0010.0010.0000.0000.0000.000
141A180VAL00.0050.00147.4460.0020.0020.0000.0000.0000.000
142A181TYR00.031-0.00450.5460.0010.0010.0000.0000.0000.000
143A182ASN00.0330.00353.9320.0010.0010.0000.0000.0000.000
144A183ASN0-0.043-0.01750.9850.0030.0030.0000.0000.0000.000
145A184ILE00.0120.00752.2150.0010.0010.0000.0000.0000.000
146A185ILE0-0.026-0.01555.6810.0010.0010.0000.0000.0000.000
147A186GLU-1-0.881-0.95258.061-0.007-0.0070.0000.0000.0000.000
148A187TYR00.0280.00857.0220.0010.0010.0000.0000.0000.000
149A188ILE0-0.040-0.00958.5740.0010.0010.0000.0000.0000.000
150A189LYS10.8450.90861.5160.0100.0100.0000.0000.0000.000
151A190ALA00.0180.00961.8340.0010.0010.0000.0000.0000.000
152A191ASN0-0.055-0.02860.6590.0020.0020.0000.0000.0000.000
153A192ASN00.027-0.00463.761-0.001-0.0010.0000.0000.0000.000
154A193SER00.0620.05665.460-0.002-0.0020.0000.0000.0000.000
155A194LYS10.8950.95166.6210.0140.0140.0000.0000.0000.000
156A195LEU00.0180.00662.623-0.001-0.0010.0000.0000.0000.000
157A196LEU00.0260.02762.695-0.001-0.0010.0000.0000.0000.000
158A197PRO00.005-0.00964.203-0.001-0.0010.0000.0000.0000.000
159A198ARG10.8930.96861.1390.0250.0250.0000.0000.0000.000
160A199VAL0-0.004-0.01458.442-0.002-0.0020.0000.0000.0000.000
161A200GLU-1-0.916-0.99060.155-0.019-0.0190.0000.0000.0000.000
162A201GLU-1-0.915-0.94661.843-0.027-0.0270.0000.0000.0000.000
163A202LYS10.8300.89758.2880.0310.0310.0000.0000.0000.000
164A203ILE00.0030.02655.986-0.002-0.0020.0000.0000.0000.000
165A204LYS10.9570.99257.1790.0240.0240.0000.0000.0000.000
166A205GLY0-0.039-0.02358.823-0.001-0.0010.0000.0000.0000.000
167A206LEU00.001-0.00152.559-0.002-0.0020.0000.0000.0000.000
168A207ILE00.0220.01653.627-0.002-0.0020.0000.0000.0000.000
169A208PRO0-0.059-0.03352.875-0.001-0.0010.0000.0000.0000.000
170A209VAL00.0350.01852.286-0.002-0.0020.0000.0000.0000.000
171A210THR00.0490.03048.491-0.003-0.0030.0000.0000.0000.000
172A211LYS10.8530.94447.8270.0430.0430.0000.0000.0000.000
173A212ASP-1-0.838-0.91445.156-0.055-0.0550.0000.0000.0000.000
174A213MET00.0210.00538.381-0.001-0.0010.0000.0000.0000.000
175A214ASN00.0330.03243.418-0.005-0.0050.0000.0000.0000.000
176A215THR0-0.077-0.06545.9970.0000.0000.0000.0000.0000.000
177A216PHE0-0.030-0.01747.0760.0030.0030.0000.0000.0000.000
178A217GLU-1-0.875-0.96543.278-0.087-0.0870.0000.0000.0000.000
179A218SER0-0.092-0.02046.767-0.002-0.0020.0000.0000.0000.000
180A219LEU00.0030.01849.7110.0040.0040.0000.0000.0000.000
181A220THR00.025-0.01352.330-0.002-0.0020.0000.0000.0000.000
182A221LYS10.8350.91852.8880.0580.0580.0000.0000.0000.000
183A222GLU-1-0.853-0.92954.954-0.053-0.0530.0000.0000.0000.000
184A223GLU-1-0.811-0.91349.101-0.070-0.0700.0000.0000.0000.000
185A224LYS10.8940.94750.2200.0700.0700.0000.0000.0000.000
186A225GLU-1-0.962-0.98851.989-0.047-0.0470.0000.0000.0000.000
187A226LYS10.9510.99154.5450.0410.0410.0000.0000.0000.000
188A227TYR00.0480.02252.6620.0020.0020.0000.0000.0000.000
189A228VAL00.0520.03249.3300.0020.0020.0000.0000.0000.000
190A229LEU00.007-0.02351.7530.0020.0020.0000.0000.0000.000
191A230ASP-1-0.807-0.91254.589-0.034-0.0340.0000.0000.0000.000
192A231ALA00.0100.01151.0110.0030.0030.0000.0000.0000.000
193A232LYS10.9730.99450.1990.0530.0530.0000.0000.0000.000
194A233THR0-0.042-0.00853.4460.0030.0030.0000.0000.0000.000
195A234ILE0-0.039-0.01754.6910.0030.0030.0000.0000.0000.000
196A235SER0-0.022-0.01950.6290.0040.0040.0000.0000.0000.000
197A236ALA0-0.045-0.01953.8060.0020.0020.0000.0000.0000.000
198A237LEU00.0120.01456.3090.0020.0020.0000.0000.0000.000
199A238LEU0-0.029-0.03254.6140.0020.0020.0000.0000.0000.000
200A239GLU-1-0.996-0.98554.322-0.018-0.0180.0000.0000.0000.000
201A240GLU-1-0.852-0.92757.227-0.022-0.0220.0000.0000.0000.000
202A241ASN0-0.069-0.04760.8930.0010.0010.0000.0000.0000.000
203A242LYS11.0001.03354.1950.0130.0130.0000.0000.0000.000
204A243SER0-0.071-0.05459.4260.0020.0020.0000.0000.0000.000
205A244TYR0-0.045-0.01162.2380.0010.0010.0000.0000.0000.000
206A245LEU00.0070.01759.0730.0010.0010.0000.0000.0000.000
207A246ASN00.0470.03858.9050.0010.0010.0000.0000.0000.000
208A247GLY00.1080.06457.1670.0010.0010.0000.0000.0000.000
209A248LYS10.8640.91855.1460.0000.0000.0000.0000.0000.000
210A249SER0-0.082-0.03954.6940.0020.0020.0000.0000.0000.000
211A250LYS11.0040.97051.451-0.014-0.0140.0000.0000.0000.000
212A251GLU-1-0.882-0.94251.537-0.001-0.0010.0000.0000.0000.000
213A252PHE00.0540.03453.467-0.002-0.0020.0000.0000.0000.000
214A253ALA0-0.019-0.00349.352-0.002-0.0020.0000.0000.0000.000
215A254TRP0-0.001-0.01345.102-0.002-0.0020.0000.0000.0000.000
216A255ILE0-0.0100.01049.591-0.002-0.0020.0000.0000.0000.000
217A256LYS10.9590.98549.8470.0220.0220.0000.0000.0000.000
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