Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: JLKR9

Calculation Name: 2X7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X7L

Chain ID: A

ChEMBL ID:

UniProt ID: P04616

Base Structure: X-ray

Registration Date: 2023-06-26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2169097.227961
FMO2-HF: Nuclear repulsion 2088321.03791
FMO2-HF: Total energy -80776.190052
FMO2-MP2: Total energy -81013.071769


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:1:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-2.18-0.2830.018-0.768-1.1450.002
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.009
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].
3A3GLN0-0.023-0.0103.877-0.9340.387-0.009-0.596-0.7150.002
4A4LEU00.0120.0146.2600.2560.2560.0000.0000.0000.000
5A5VAL00.0200.00510.0900.1170.1170.0000.0000.0000.000
6A6GLU-1-0.767-0.86412.6520.1330.1330.0000.0000.0000.000
7A7SER0-0.040-0.04416.3920.0840.0840.0000.0000.0000.000
8A8GLY00.0240.01619.520-0.026-0.0260.0000.0000.0000.000
9A9GLY0-0.0150.00922.719-0.017-0.0170.0000.0000.0000.000
10A10ARG10.8970.94524.584-0.102-0.1020.0000.0000.0000.000
11A11LEU00.0070.01527.984-0.009-0.0090.0000.0000.0000.000
12A12VAL0-0.021-0.01531.5040.0060.0060.0000.0000.0000.000
13A13THR00.0520.02833.786-0.001-0.0010.0000.0000.0000.000
14A14PRO00.009-0.01636.4790.0000.0000.0000.0000.0000.000
15A15GLY00.0150.02037.1250.0000.0000.0000.0000.0000.000
16A16THR0-0.045-0.02835.872-0.001-0.0010.0000.0000.0000.000
17A17ALA00.0120.01132.6890.0050.0050.0000.0000.0000.000
18A18LEU0-0.033-0.00226.3610.0070.0070.0000.0000.0000.000
19A19THR0-0.040-0.02624.697-0.015-0.0150.0000.0000.0000.000
20A20LEU0-0.0180.01821.5630.0210.0210.0000.0000.0000.000
21A21THR00.005-0.00418.981-0.001-0.0010.0000.0000.0000.000
22A22CYS0-0.0030.00714.4310.0050.0050.0000.0000.0000.000
23A23LYS10.8300.92912.488-0.427-0.4270.0000.0000.0000.000
24A24VAL00.0290.00810.0200.0250.0250.0000.0000.0000.000
25A25SER0-0.021-0.0166.9970.3010.3010.0000.0000.0000.000
26A26GLY00.0350.0063.306-0.517-0.2660.024-0.110-0.1640.000
27A27PHE0-0.039-0.0303.980-1.155-0.8300.003-0.062-0.2660.000
28A28SER0-0.048-0.0165.6900.4450.4450.0000.0000.0000.000
29A29LEU0-0.0140.0067.0770.2120.2120.0000.0000.0000.000
30A30SER00.002-0.01010.5430.0220.0220.0000.0000.0000.000
31A31GLY0-0.032-0.02213.2030.0660.0660.0000.0000.0000.000
32A32PHE00.0140.00910.937-0.054-0.0540.0000.0000.0000.000
33A33TRP0-0.0060.00115.4390.0610.0610.0000.0000.0000.000
34A34LEU0-0.024-0.01113.682-0.045-0.0450.0000.0000.0000.000
35A35ASN00.004-0.00116.5140.0650.0650.0000.0000.0000.000
36A36TRP00.008-0.00217.7490.0120.0120.0000.0000.0000.000
37A37VAL0-0.004-0.00219.283-0.003-0.0030.0000.0000.0000.000
38A38ARG10.7580.86121.109-0.005-0.0050.0000.0000.0000.000
39A39GLN0-0.004-0.00522.731-0.006-0.0060.0000.0000.0000.000
40A40ALA00.0560.03724.9800.0140.0140.0000.0000.0000.000
41A41PRO00.008-0.00428.1280.0010.0010.0000.0000.0000.000
42A42GLY00.0210.02228.417-0.005-0.0050.0000.0000.0000.000
43A43LYS10.8390.91628.381-0.050-0.0500.0000.0000.0000.000
44A44GLY00.0660.03326.8140.0040.0040.0000.0000.0000.000
45A45LEU00.0010.00220.6580.0050.0050.0000.0000.0000.000
46A46GLU-1-0.829-0.90124.4850.0100.0100.0000.0000.0000.000
47A47TRP0-0.007-0.00821.5150.0150.0150.0000.0000.0000.000
48A48VAL0-0.030-0.02223.7410.0070.0070.0000.0000.0000.000
49A49GLY00.0260.00023.7070.0060.0060.0000.0000.0000.000
50A50ALA0-0.058-0.01520.574-0.008-0.0080.0000.0000.0000.000
51A51ILE0-0.021-0.00919.5080.0210.0210.0000.0000.0000.000
52A52TYR0-0.041-0.01417.676-0.014-0.0140.0000.0000.0000.000
53A53ARG10.8390.91413.4140.2020.2020.0000.0000.0000.000
54A54GLY0-0.0170.01217.8710.0190.0190.0000.0000.0000.000
55A55SER0-0.070-0.04819.3550.0160.0160.0000.0000.0000.000
56A56GLY00.0530.02522.5470.0050.0050.0000.0000.0000.000
57A57SER0-0.0230.00023.8600.0080.0080.0000.0000.0000.000
58A58GLU-1-0.826-0.89024.119-0.050-0.0500.0000.0000.0000.000
59A59TRP0-0.039-0.01924.9360.0040.0040.0000.0000.0000.000
60A60TYR0-0.040-0.05625.8670.0040.0040.0000.0000.0000.000
61A61ALA00.0220.02027.828-0.004-0.0040.0000.0000.0000.000
62A62SER0-0.039-0.03429.4090.0060.0060.0000.0000.0000.000
63A63TRP00.0330.01127.6430.0050.0050.0000.0000.0000.000
64A64ALA00.0110.01429.1580.0060.0060.0000.0000.0000.000
65A65LYS10.9640.97631.2100.0300.0300.0000.0000.0000.000
66A66GLY00.0230.02232.5530.0030.0030.0000.0000.0000.000
67A67ARG10.8150.86932.651-0.011-0.0110.0000.0000.0000.000
68A68PHE0-0.002-0.00527.2720.0080.0080.0000.0000.0000.000
69A69THR0-0.025-0.01928.122-0.003-0.0030.0000.0000.0000.000
70A70ILE0-0.0060.01522.0830.0140.0140.0000.0000.0000.000
71A71SER0-0.007-0.00523.1980.0000.0000.0000.0000.0000.000
72A72ASP-1-0.768-0.88318.426-0.095-0.0950.0000.0000.0000.000
73A73THR0-0.008-0.00618.6020.0230.0230.0000.0000.0000.000
74A74SER00.0740.02416.397-0.029-0.0290.0000.0000.0000.000
75A75THR0-0.021-0.01512.766-0.023-0.0230.0000.0000.0000.000
76A76THR0-0.033-0.01913.1350.0580.0580.0000.0000.0000.000
77A77VAL0-0.0180.01416.0000.0130.0130.0000.0000.0000.000
78A78THR0-0.055-0.02718.2870.0340.0340.0000.0000.0000.000
79A79LEU00.0320.01221.228-0.022-0.0220.0000.0000.0000.000
80A80LYS10.9080.94723.787-0.038-0.0380.0000.0000.0000.000
81A81LEU00.0250.01626.644-0.009-0.0090.0000.0000.0000.000
82A82THR00.000-0.02129.8920.0080.0080.0000.0000.0000.000
83A83SER00.0200.00532.9860.0020.0020.0000.0000.0000.000
84A84PRO0-0.068-0.00132.146-0.004-0.0040.0000.0000.0000.000
85A85THR00.022-0.01133.9910.0000.0000.0000.0000.0000.000
86A86THR00.029-0.01834.3010.0040.0040.0000.0000.0000.000
87A87GLU-1-0.881-0.92334.2700.0370.0370.0000.0000.0000.000
88A88ASP-1-0.770-0.82930.4450.0240.0240.0000.0000.0000.000
89A89THR0-0.030-0.01029.4320.0090.0090.0000.0000.0000.000
90A90ALA00.0160.00626.305-0.005-0.0050.0000.0000.0000.000
91A91THR0-0.042-0.00421.0080.0180.0180.0000.0000.0000.000
92A92TYR0-0.007-0.02821.722-0.023-0.0230.0000.0000.0000.000
93A93PHE00.0260.00416.6030.0300.0300.0000.0000.0000.000
94A95ALA00.0230.00113.475-0.003-0.0030.0000.0000.0000.000
95A96ALA00.0080.01110.8370.0380.0380.0000.0000.0000.000
96A97ASP-1-0.734-0.85012.330-0.417-0.4170.0000.0000.0000.000
97A98THR0-0.036-0.0088.0880.1060.1060.0000.0000.0000.000
98A99THR0-0.048-0.04411.221-0.028-0.0280.0000.0000.0000.000
99A100ASP-1-0.802-0.88214.240-0.325-0.3250.0000.0000.0000.000
100A101ASN0-0.073-0.04917.2050.0310.0310.0000.0000.0000.000
101A102GLY0-0.0070.00718.5000.0300.0300.0000.0000.0000.000
102A103TYR0-0.060-0.03514.2290.0310.0310.0000.0000.0000.000
103A104PHE0-0.046-0.02814.414-0.038-0.0380.0000.0000.0000.000
104A105THR00.0390.0089.8800.0700.0700.0000.0000.0000.000
105A106ILE0-0.0070.0036.194-0.005-0.0050.0000.0000.0000.000
106A107TRP0-0.006-0.0199.4630.1220.1220.0000.0000.0000.000
107A108GLY00.0270.03010.461-0.001-0.0010.0000.0000.0000.000
108A109PRO0-0.049-0.03312.084-0.009-0.0090.0000.0000.0000.000
109A110GLY00.0250.00814.682-0.018-0.0180.0000.0000.0000.000
110A111THR0-0.072-0.04517.8620.0400.0400.0000.0000.0000.000
111A112LEU00.001-0.00220.906-0.023-0.0230.0000.0000.0000.000
112A113VAL00.0100.01724.5300.0080.0080.0000.0000.0000.000
113A114THR0-0.077-0.05127.255-0.002-0.0020.0000.0000.0000.000
114A115VAL00.0110.02030.8430.0030.0030.0000.0000.0000.000
115A116SER00.024-0.00133.995-0.006-0.0060.0000.0000.0000.000
116A117SER00.0250.00837.2880.0030.0030.0000.0000.0000.000
117A118ALA0-0.0240.00638.2970.0000.0000.0000.0000.0000.000
118A119SER00.0320.00637.7340.0040.0040.0000.0000.0000.000
119A120THR0-0.064-0.04833.501-0.001-0.0010.0000.0000.0000.000
120A121LYS10.8470.91636.017-0.105-0.1050.0000.0000.0000.000
121A122GLY00.0590.03134.9490.0040.0040.0000.0000.0000.000
122A123PRO0-0.033-0.02033.285-0.008-0.0080.0000.0000.0000.000
123A124SER0-0.009-0.00636.450-0.001-0.0010.0000.0000.0000.000
124A125VAL0-0.027-0.00735.538-0.001-0.0010.0000.0000.0000.000
125A126PHE00.001-0.00838.685-0.002-0.0020.0000.0000.0000.000
126A127PRO00.0260.01939.9890.0030.0030.0000.0000.0000.000
127A128LEU0-0.039-0.01838.513-0.006-0.0060.0000.0000.0000.000
128A129ALA00.0270.00641.7790.0020.0020.0000.0000.0000.000
129A130PRO00.0740.05442.189-0.005-0.0050.0000.0000.0000.000
130A131SER0-0.009-0.01744.501-0.006-0.0060.0000.0000.0000.000
131A132ALA00.0340.02047.3300.0010.0010.0000.0000.0000.000
132A133LYS10.8690.92248.427-0.061-0.0610.0000.0000.0000.000
133A134SER00.0170.02443.344-0.002-0.0020.0000.0000.0000.000
134A135THR00.0030.00444.4350.0030.0030.0000.0000.0000.000
135A136SER00.0220.02643.713-0.005-0.0050.0000.0000.0000.000
136A137GLY00.0070.00445.6900.0000.0000.0000.0000.0000.000
137A138GLY00.0200.02844.2180.0000.0000.0000.0000.0000.000
138A139THR0-0.029-0.01739.3720.0040.0040.0000.0000.0000.000
139A140ALA00.0190.00240.735-0.006-0.0060.0000.0000.0000.000
140A141ALA00.0180.01838.8270.0060.0060.0000.0000.0000.000
141A142LEU0-0.0190.00036.898-0.007-0.0070.0000.0000.0000.000
142A143GLY00.0430.00736.4790.0050.0050.0000.0000.0000.000
143A144CYS0-0.077-0.00132.1950.0040.0040.0000.0000.0000.000
144A145LEU00.0150.02636.0460.0030.0030.0000.0000.0000.000
145A146VAL0-0.016-0.02033.4020.0030.0030.0000.0000.0000.000
146A147LYS10.8910.91636.331-0.079-0.0790.0000.0000.0000.000
147A148ASP-1-0.790-0.86738.9680.0860.0860.0000.0000.0000.000
148A149TYR0-0.043-0.03631.3320.0010.0010.0000.0000.0000.000
149A150PHE00.0560.02834.666-0.005-0.0050.0000.0000.0000.000
150A151PRO00.0110.02130.6260.0010.0010.0000.0000.0000.000
151A152GLU-1-0.777-0.87628.4230.1480.1480.0000.0000.0000.000
152A153PRO0-0.016-0.00824.4350.0000.0000.0000.0000.0000.000
153A154VAL00.003-0.01327.4980.0070.0070.0000.0000.0000.000
154A155THR0-0.047-0.02223.2610.0060.0060.0000.0000.0000.000
155A156VAL0-0.006-0.01026.4440.0020.0020.0000.0000.0000.000
156A157SER0-0.019-0.00125.4890.0100.0100.0000.0000.0000.000
157A158TRP00.0570.01427.605-0.019-0.0190.0000.0000.0000.000
158A159ASN00.0260.00528.5800.0110.0110.0000.0000.0000.000
159A160SER0-0.011-0.01827.1050.0030.0030.0000.0000.0000.000
160A161GLY0-0.0060.00424.2860.0270.0270.0000.0000.0000.000
161A162ALA0-0.025-0.00524.9950.0080.0080.0000.0000.0000.000
162A163LEU0-0.042-0.00927.190-0.014-0.0140.0000.0000.0000.000
163A164THR00.0190.00223.846-0.002-0.0020.0000.0000.0000.000
164A165SER00.029-0.00426.978-0.005-0.0050.0000.0000.0000.000
165A166GLY00.0590.03628.951-0.007-0.0070.0000.0000.0000.000
166A167VAL0-0.039-0.00528.145-0.009-0.0090.0000.0000.0000.000
167A168HIS0-0.061-0.03729.070-0.008-0.0080.0000.0000.0000.000
168A169THR00.0180.01027.801-0.011-0.0110.0000.0000.0000.000
169A170PHE0-0.0180.00429.1430.0000.0000.0000.0000.0000.000
170A171PRO00.011-0.00729.3180.0060.0060.0000.0000.0000.000
171A172ALA0-0.0040.01730.510-0.004-0.0040.0000.0000.0000.000
172A173VAL0-0.015-0.01132.462-0.006-0.0060.0000.0000.0000.000
173A174LEU0-0.027-0.01035.9380.0020.0020.0000.0000.0000.000
174A175GLN0-0.029-0.02337.653-0.006-0.0060.0000.0000.0000.000
175A176SER00.030-0.00241.2950.0000.0000.0000.0000.0000.000
176A177SER0-0.0110.00143.074-0.002-0.0020.0000.0000.0000.000
177A178GLY00.0150.01440.8470.0000.0000.0000.0000.0000.000
178A179LEU0-0.046-0.01338.5390.0040.0040.0000.0000.0000.000
179A180TYR00.0250.00932.648-0.004-0.0040.0000.0000.0000.000
180A181SER0-0.004-0.00436.4810.0010.0010.0000.0000.0000.000
181A182LEU00.0100.02530.470-0.002-0.0020.0000.0000.0000.000
182A183SER00.0260.00034.274-0.004-0.0040.0000.0000.0000.000
183A184SER0-0.009-0.00330.3930.0010.0010.0000.0000.0000.000
184A185VAL00.015-0.00733.102-0.006-0.0060.0000.0000.0000.000
185A186VAL00.0310.01732.4470.0090.0090.0000.0000.0000.000
186A187THR0-0.027-0.00734.232-0.008-0.0080.0000.0000.0000.000
187A188VAL0-0.001-0.00135.1180.0080.0080.0000.0000.0000.000
188A189PRO00.0520.01737.021-0.007-0.0070.0000.0000.0000.000
189A190SER0-0.045-0.03540.2470.0020.0020.0000.0000.0000.000
190A191SER00.0100.00043.4200.0010.0010.0000.0000.0000.000
191A192SER00.0190.00739.199-0.002-0.0020.0000.0000.0000.000
192A193LEU0-0.032-0.01641.1380.0060.0060.0000.0000.0000.000
193A194GLY00.011-0.00243.011-0.002-0.0020.0000.0000.0000.000
194A195THR0-0.0140.00042.2870.0020.0020.0000.0000.0000.000
195A196GLN00.0080.00535.7030.0060.0060.0000.0000.0000.000
196A197THR0-0.035-0.00237.626-0.004-0.0040.0000.0000.0000.000
197A198TYR00.033-0.00235.1210.0100.0100.0000.0000.0000.000
198A199ILE00.002-0.01533.306-0.009-0.0090.0000.0000.0000.000
199A201ASN00.025-0.01228.452-0.001-0.0010.0000.0000.0000.000
200A202VAL0-0.002-0.00528.8470.0090.0090.0000.0000.0000.000
201A203ASN0-0.056-0.03826.1170.0190.0190.0000.0000.0000.000
202A204HIS00.0370.04128.1780.0010.0010.0000.0000.0000.000
203A205LYS11.0191.00621.262-0.362-0.3620.0000.0000.0000.000
204A206PRO00.0190.01927.140-0.001-0.0010.0000.0000.0000.000
205A207SER00.0030.00429.639-0.012-0.0120.0000.0000.0000.000
206A208ASN0-0.013-0.00729.4630.0120.0120.0000.0000.0000.000
207A209THR00.0240.01330.4950.0090.0090.0000.0000.0000.000
208A210LYS10.8390.90127.372-0.224-0.2240.0000.0000.0000.000
209A211VAL00.0140.01831.028-0.001-0.0010.0000.0000.0000.000
210A212ASP-1-0.787-0.88031.2580.2070.2070.0000.0000.0000.000
211A213LYS10.8880.94633.976-0.126-0.1260.0000.0000.0000.000
212A214LYS10.8850.93636.358-0.114-0.1140.0000.0000.0000.000
213A215ALA0-0.024-0.01438.546-0.006-0.0060.0000.0000.0000.000
214A216GLU-1-0.772-0.87540.1800.1110.1110.0000.0000.0000.000
215A217PRO00.0110.00543.267-0.003-0.0030.0000.0000.0000.000
216A218LYS10.7890.87246.092-0.079-0.0790.0000.0000.0000.000
217A219SER0-0.0020.01048.5850.0010.0010.0000.0000.0000.000
218A220CYS00.0340.02651.463-0.001-0.0010.0000.0000.0000.000