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: R8K28

Calculation Name: 2D1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1L

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R1S4

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 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 249
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2487835.385239
FMO2-HF: Nuclear repulsion 2387800.17266
FMO2-HF: Total energy -100035.212579
FMO2-MP2: Total energy -100321.570116


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:-2:ALA)


Summations of interaction energy for fragment #1(A:-2:ALA)
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.
-2.6871.3233.17-3.091-4.088-0.004
Interaction energy analysis for fragmet #1(A:-2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.025
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].
3A0HIS00.014-0.0023.876-1.1390.127-0.015-0.673-0.5790.002
4A1MET00.0290.0196.427-0.012-0.0120.0000.0000.0000.000
5A2GLU-1-0.798-0.9052.3650.7781.1852.248-1.338-1.316-0.004
6A3ALA00.0100.0094.344-0.169-0.050-0.001-0.022-0.0950.000
7A4VAL0-0.040-0.0145.4600.1180.1180.0000.0000.0000.000
8A5ILE00.0620.0357.162-0.003-0.0030.0000.0000.0000.000
9A6GLU-1-0.740-0.8234.802-0.542-0.5420.0000.0000.0000.000
10A7LYS10.8310.9217.9920.4810.4810.0000.0000.0000.000
11A8GLU-1-0.834-0.90210.991-0.014-0.0140.0000.0000.0000.000
12A9CYS0-0.059-0.02810.7190.0230.0230.0000.0000.0000.000
13A10SER0-0.059-0.04511.007-0.007-0.0070.0000.0000.0000.000
14A11ALA0-0.0080.00613.5580.0090.0090.0000.0000.0000.000
15A12LEU0-0.013-0.00115.3130.0100.0100.0000.0000.0000.000
16A13GLY00.0510.02216.2590.0070.0070.0000.0000.0000.000
17A14GLY0-0.020-0.01017.4870.0020.0020.0000.0000.0000.000
18A15LEU00.0120.01919.3490.0060.0060.0000.0000.0000.000
19A16PHE0-0.008-0.01620.6810.0080.0080.0000.0000.0000.000
20A17GLN0-0.035-0.03821.4800.0070.0070.0000.0000.0000.000
21A18THR0-0.022-0.01223.215-0.001-0.0010.0000.0000.0000.000
22A19ILE00.0460.02625.1070.0030.0030.0000.0000.0000.000
23A20ILE0-0.040-0.02025.0860.0040.0040.0000.0000.0000.000
24A21SER0-0.014-0.00227.0250.0010.0010.0000.0000.0000.000
25A22ASP-1-0.887-0.94328.747-0.039-0.0390.0000.0000.0000.000
26A23MET0-0.076-0.03429.4970.0040.0040.0000.0000.0000.000
27A24LYS10.7850.88327.7520.0420.0420.0000.0000.0000.000
28A25GLY00.0130.01332.8880.0000.0000.0000.0000.0000.000
29A26SER0-0.060-0.04034.7620.0020.0020.0000.0000.0000.000
30A27TYR00.0150.01434.2970.0030.0030.0000.0000.0000.000
31A28PRO00.0900.03539.3330.0020.0020.0000.0000.0000.000
32A29VAL0-0.0060.00940.6280.0010.0010.0000.0000.0000.000
33A30TRP00.0270.00738.5980.0020.0020.0000.0000.0000.000
34A31GLU-1-0.812-0.90842.637-0.018-0.0180.0000.0000.0000.000
35A32ASP-1-0.856-0.90545.656-0.016-0.0160.0000.0000.0000.000
36A33PHE00.0110.00546.7050.0010.0010.0000.0000.0000.000
37A34ILE00.0430.01946.0400.0010.0010.0000.0000.0000.000
38A35ASN0-0.0050.00949.6710.0010.0010.0000.0000.0000.000
39A36LYS10.8070.87150.3570.0170.0170.0000.0000.0000.000
40A37ALA00.0430.02952.2100.0010.0010.0000.0000.0000.000
41A38GLY00.0600.02853.7790.0010.0010.0000.0000.0000.000
42A39LYS10.8560.92654.5030.0140.0140.0000.0000.0000.000
43A40LEU00.0200.01356.3380.0000.0000.0000.0000.0000.000
44A41GLN00.000-0.01257.6950.0000.0000.0000.0000.0000.000
45A42SER0-0.026-0.01959.5720.0000.0000.0000.0000.0000.000
46A43GLN00.013-0.00561.7430.0010.0010.0000.0000.0000.000
47A44LEU00.0220.03860.1230.0000.0000.0000.0000.0000.000
48A45ARG10.9480.97663.5090.0070.0070.0000.0000.0000.000
49A46THR0-0.021-0.02165.4280.0000.0000.0000.0000.0000.000
50A47THR0-0.016-0.01866.5340.0000.0000.0000.0000.0000.000
51A48VAL00.0070.00766.8870.0000.0000.0000.0000.0000.000
52A49VAL0-0.024-0.00269.4970.0000.0000.0000.0000.0000.000
53A50ALA0-0.004-0.00271.7440.0000.0000.0000.0000.0000.000
54A51ALA00.0130.00571.8710.0000.0000.0000.0000.0000.000
55A52ALA00.0050.00573.5670.0000.0000.0000.0000.0000.000
56A53ALA00.0100.00575.3780.0000.0000.0000.0000.0000.000
57A54PHE0-0.013-0.00576.5840.0000.0000.0000.0000.0000.000
58A55LEU00.014-0.00175.2850.0000.0000.0000.0000.0000.000
59A56ASP-1-0.833-0.89979.201-0.002-0.0020.0000.0000.0000.000
60A57ALA0-0.053-0.01481.5270.0000.0000.0000.0000.0000.000
61A58PHE0-0.029-0.01681.3380.0000.0000.0000.0000.0000.000
62A59GLN00.035-0.01683.1560.0000.0000.0000.0000.0000.000
63A60LYS10.8700.93184.5150.0020.0020.0000.0000.0000.000
64A61VAL0-0.021-0.00486.6690.0000.0000.0000.0000.0000.000
65A62ALA00.0350.02586.3930.0000.0000.0000.0000.0000.000
66A63ASP-1-0.838-0.89988.473-0.001-0.0010.0000.0000.0000.000
67A64MET0-0.033-0.01490.7860.0000.0000.0000.0000.0000.000
68A65ALA00.0090.01391.1510.0000.0000.0000.0000.0000.000
69A66THR00.000-0.00690.9740.0000.0000.0000.0000.0000.000
70A67ASN0-0.077-0.04993.6600.0000.0000.0000.0000.0000.000
71A68THR0-0.064-0.03996.2280.0000.0000.0000.0000.0000.000
72A69ARG10.9460.95398.5750.0020.0020.0000.0000.0000.000
73A70GLY00.0670.03899.7460.0000.0000.0000.0000.0000.000
74A71GLY00.0880.04697.0730.0000.0000.0000.0000.0000.000
75A72THR0-0.041-0.02095.1160.0000.0000.0000.0000.0000.000
76A73ARG10.8620.94894.1470.0010.0010.0000.0000.0000.000
77A74GLU-1-0.844-0.89893.1180.0000.0000.0000.0000.0000.000
78A75ILE00.0220.01689.7460.0000.0000.0000.0000.0000.000
79A76GLY00.0240.00189.2270.0000.0000.0000.0000.0000.000
80A77SER0-0.021-0.01688.8030.0000.0000.0000.0000.0000.000
81A78ALA00.0140.00886.6540.0000.0000.0000.0000.0000.000
82A79LEU0-0.014-0.00684.8580.0000.0000.0000.0000.0000.000
83A80THR00.0170.00883.9090.0000.0000.0000.0000.0000.000
84A81ARG10.8020.87783.3080.0000.0000.0000.0000.0000.000
85A82MET0-0.0070.01679.2350.0000.0000.0000.0000.0000.000
86A83CYS0-0.043-0.01379.2080.0000.0000.0000.0000.0000.000
87A84MET0-0.001-0.00478.8930.0000.0000.0000.0000.0000.000
88A85ARG10.8300.91473.4920.0000.0000.0000.0000.0000.000
89A86HIS0-0.005-0.02874.6740.0000.0000.0000.0000.0000.000
90A87ARG10.8230.90174.1450.0020.0020.0000.0000.0000.000
91A88SER0-0.056-0.03372.2370.0000.0000.0000.0000.0000.000
92A89ILE00.0140.00569.5200.0000.0000.0000.0000.0000.000
93A90GLU-1-0.756-0.86669.393-0.002-0.0020.0000.0000.0000.000
94A91ALA0-0.031-0.01769.4990.0000.0000.0000.0000.0000.000
95A92LYS10.9040.92666.2940.0000.0000.0000.0000.0000.000
96A93LEU00.0090.01264.6110.0000.0000.0000.0000.0000.000
97A94ARG10.8120.88464.7720.0020.0020.0000.0000.0000.000
98A95GLN0-0.060-0.02463.5580.0000.0000.0000.0000.0000.000
99A96PHE00.0330.02058.2990.0000.0000.0000.0000.0000.000
100A97SER0-0.022-0.01859.8830.0000.0000.0000.0000.0000.000
101A98SER0-0.002-0.00860.2700.0000.0000.0000.0000.0000.000
102A99ALA00.0510.02157.4460.0000.0000.0000.0000.0000.000
103A100LEU0-0.012-0.00254.5650.0000.0000.0000.0000.0000.000
104A101ILE0-0.025-0.01954.803-0.001-0.0010.0000.0000.0000.000
105A102ASP-1-0.889-0.95054.702-0.002-0.0020.0000.0000.0000.000
106A103CYS0-0.077-0.03853.1180.0010.0010.0000.0000.0000.000
107A104LEU0-0.022-0.01048.8280.0000.0000.0000.0000.0000.000
108A105ILE0-0.039-0.01649.995-0.001-0.0010.0000.0000.0000.000
109A106ASN00.0330.01550.383-0.001-0.0010.0000.0000.0000.000
110A107PRO0-0.008-0.00648.7490.0000.0000.0000.0000.0000.000
111A108LEU00.0120.00144.2140.0000.0000.0000.0000.0000.000
112A109GLN0-0.019-0.01945.320-0.002-0.0020.0000.0000.0000.000
113A110GLU-1-0.905-0.94645.807-0.008-0.0080.0000.0000.0000.000
114A111GLN0-0.057-0.02340.3290.0010.0010.0000.0000.0000.000
115A112MET0-0.044-0.01140.892-0.001-0.0010.0000.0000.0000.000
116A113GLU-1-0.898-0.95039.250-0.018-0.0180.0000.0000.0000.000
117A114GLU-1-0.798-0.88238.701-0.005-0.0050.0000.0000.0000.000
118A115TRP00.0060.00036.7060.0000.0000.0000.0000.0000.000
119A116LYS10.8670.95035.1130.0170.0170.0000.0000.0000.000
120A117LYS10.7660.86034.0350.0040.0040.0000.0000.0000.000
121A118VAL00.0080.00532.667-0.001-0.0010.0000.0000.0000.000
122A119ALA00.0230.01730.6440.0000.0000.0000.0000.0000.000
123A120ASN00.0340.00629.137-0.006-0.0060.0000.0000.0000.000
124A121GLN0-0.070-0.03628.736-0.005-0.0050.0000.0000.0000.000
125A122LEU00.0260.00825.5650.0010.0010.0000.0000.0000.000
126A123ASP-1-0.786-0.87424.606-0.045-0.0450.0000.0000.0000.000
127A124LYS10.8700.92823.4400.0140.0140.0000.0000.0000.000
128A125ASP-1-0.850-0.90023.624-0.001-0.0010.0000.0000.0000.000
129A126HIS0-0.052-0.03617.2210.0050.0050.0000.0000.0000.000
130A127ALA00.0420.01919.071-0.002-0.0020.0000.0000.0000.000
131A128LYS10.7860.88918.771-0.005-0.0050.0000.0000.0000.000
132A129GLU-1-0.762-0.88018.4630.0330.0330.0000.0000.0000.000
133A130TYR00.0800.04912.357-0.008-0.0080.0000.0000.0000.000
134A131LYS10.9460.97513.7200.0610.0610.0000.0000.0000.000
135A132LYS10.7650.86314.316-0.046-0.0460.0000.0000.0000.000
136A133ALA00.0550.03312.4360.0090.0090.0000.0000.0000.000
137A134ARG10.8310.8766.1600.3920.3920.0000.0000.0000.000
138A135GLN0-0.0060.0089.504-0.079-0.0790.0000.0000.0000.000
139A136GLU-1-0.777-0.87911.1790.1930.1930.0000.0000.0000.000
140A137ILE00.0600.0465.1110.0530.0530.0000.0000.0000.000
141A138LYS10.9000.9636.3080.0610.0610.0000.0000.0000.000
142A139LYS10.7990.8868.188-0.134-0.1340.0000.0000.0000.000
143A140LYS10.8820.9407.519-0.508-0.5080.0000.0000.0000.000
144A141SER00.0280.0133.898-0.345-0.1110.000-0.062-0.1720.000
145A142SER0-0.066-0.0475.2720.0660.062-0.0010.0000.0040.000
146A143ASP-1-0.885-0.9498.7660.2550.2550.0000.0000.0000.000
147A144THR00.0550.0225.0230.0630.0630.0000.0000.0000.000
148A145LEU0-0.0210.0007.372-0.052-0.0520.0000.0000.0000.000
149A146LYS10.8090.8908.446-0.147-0.1470.0000.0000.0000.000
150A147LEU00.0310.01510.621-0.051-0.0510.0000.0000.0000.000
151A148GLN00.0330.0225.320-0.413-0.4130.0000.0000.0000.000
152A149LYS10.9100.96310.6750.0020.0020.0000.0000.0000.000
153A150LYS10.9320.96313.307-0.111-0.1110.0000.0000.0000.000
154A151ALA00.0560.03813.412-0.026-0.0260.0000.0000.0000.000
155A152LYS10.8290.89712.567-0.159-0.1590.0000.0000.0000.000
156A153LYS10.9590.99216.950-0.057-0.0570.0000.0000.0000.000
157A154VAL00.0250.00319.2900.0120.0120.0000.0000.0000.000
158A155ASP-1-0.883-0.94721.4040.0600.0600.0000.0000.0000.000
159A156ALA0-0.058-0.02423.068-0.003-0.0030.0000.0000.0000.000
160A157GLN00.0770.03524.1280.0170.0170.0000.0000.0000.000
161A158GLY00.0310.04420.1950.0180.0180.0000.0000.0000.000
162A159ARG10.8170.86818.099-0.222-0.2220.0000.0000.0000.000
163A160GLY00.0260.03419.6090.0200.0200.0000.0000.0000.000
164A161ASP-1-0.832-0.91820.3840.2100.2100.0000.0000.0000.000
165A162ILE0-0.052-0.02815.3650.0270.0270.0000.0000.0000.000
166A163GLN0-0.093-0.05111.996-0.027-0.0270.0000.0000.0000.000
167A164PRO00.1080.05414.0940.0960.0960.0000.0000.0000.000
168A165GLN0-0.0230.00214.8240.0600.0600.0000.0000.0000.000
169A166LEU0-0.043-0.0238.3430.0790.0790.0000.0000.0000.000
170A167ASP-1-0.820-0.9089.7990.9510.9510.0000.0000.0000.000
171A168SER00.003-0.01110.6290.1650.1650.0000.0000.0000.000
172A169ALA0-0.049-0.0239.0040.0420.0420.0000.0000.0000.000
173A170LEU0-0.017-0.0174.7040.2330.333-0.001-0.011-0.0880.000
174A171GLN0-0.022-0.0096.6560.4380.4380.0000.0000.0000.000
175A172ASP-1-0.738-0.8579.0860.5460.5460.0000.0000.0000.000
176A173VAL0-0.036-0.0212.333-1.177-0.5570.741-0.482-0.8780.001
177A174ASN00.0050.0005.814-0.474-0.4740.0000.0000.0000.000
178A175ASP-1-0.808-0.8956.7650.3870.3870.0000.0000.0000.000
179A176LYS10.7600.8757.781-0.593-0.5930.0000.0000.0000.000
180A177TYR0-0.043-0.0482.914-1.755-0.4870.199-0.503-0.964-0.003
181A178LEU00.0420.0267.987-0.152-0.1520.0000.0000.0000.000
182A179LEU0-0.016-0.00511.129-0.085-0.0850.0000.0000.0000.000
183A180LEU0-0.042-0.0059.275-0.061-0.0610.0000.0000.0000.000
184A181GLU-1-0.813-0.91811.5880.1040.1040.0000.0000.0000.000
185A182GLU-1-0.862-0.93013.2740.1030.1030.0000.0000.0000.000
186A183THR0-0.086-0.04915.436-0.020-0.0200.0000.0000.0000.000
187A184GLU-1-0.820-0.90714.423-0.053-0.0530.0000.0000.0000.000
188A185LYS10.8430.91015.966-0.129-0.1290.0000.0000.0000.000
189A186GLN00.004-0.00619.395-0.015-0.0150.0000.0000.0000.000
190A187ALA0-0.036-0.00120.060-0.004-0.0040.0000.0000.0000.000
191A188VAL00.0440.01720.581-0.002-0.0020.0000.0000.0000.000
192A189ARG10.9340.97723.116-0.038-0.0380.0000.0000.0000.000
193A190LYS10.8680.91223.208-0.021-0.0210.0000.0000.0000.000
194A191ALA00.0220.02425.830-0.001-0.0010.0000.0000.0000.000
195A192LEU00.0510.02726.3750.0000.0000.0000.0000.0000.000
196A193ILE0-0.078-0.03229.1460.0010.0010.0000.0000.0000.000
197A194GLU-1-0.831-0.90630.867-0.005-0.0050.0000.0000.0000.000
198A195GLU-1-0.889-0.96230.757-0.017-0.0170.0000.0000.0000.000
199A196ARG10.9390.96433.186-0.006-0.0060.0000.0000.0000.000
200A197GLY00.0380.01935.0300.0010.0010.0000.0000.0000.000
201A198ARG10.8410.92034.4840.0150.0150.0000.0000.0000.000
202A199PHE00.0530.01736.0100.0000.0000.0000.0000.0000.000
203A200CYS0-0.078-0.04538.9200.0010.0010.0000.0000.0000.000
204A201THR0-0.0130.00240.2280.0010.0010.0000.0000.0000.000
205A202PHE00.0380.01942.5520.0000.0000.0000.0000.0000.000
206A203ILE00.016-0.00142.7560.0000.0000.0000.0000.0000.000
207A204SER0-0.091-0.05744.7870.0010.0010.0000.0000.0000.000
208A205MET0-0.0010.02345.1870.0000.0000.0000.0000.0000.000
209A206LEU00.0150.01148.5600.0000.0000.0000.0000.0000.000
210A207ARG10.8810.92346.900-0.003-0.0030.0000.0000.0000.000
211A208PRO00.0170.01051.5700.0000.0000.0000.0000.0000.000
212A209VAL0-0.030-0.00353.5540.0000.0000.0000.0000.0000.000
213A210ILE00.0210.00253.2790.0000.0000.0000.0000.0000.000
214A211GLU-1-0.924-0.95256.3030.0020.0020.0000.0000.0000.000
215A212GLU-1-0.840-0.91658.2680.0010.0010.0000.0000.0000.000
216A213GLU-1-0.931-0.95057.831-0.004-0.0040.0000.0000.0000.000
217A214ILE0-0.0070.00056.9670.0000.0000.0000.0000.0000.000
218A215SER0-0.040-0.03161.3290.0000.0000.0000.0000.0000.000
219A216MET0-0.030-0.01663.5570.0000.0000.0000.0000.0000.000
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