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: N967Q

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2164751.31404
FMO2-HF: Nuclear repulsion 2083976.163662
FMO2-HF: Total energy -80775.150377
FMO2-MP2: Total energy -81012.086326


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.
-1.904-0.291-0.006-0.711-0.8990.002
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 : 0.043 / 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].
3A3GLN0-0.034-0.0103.783-1.0310.292-0.007-0.632-0.6850.002
4A4LEU00.0280.0076.559-0.016-0.0160.0000.0000.0000.000
5A5VAL00.012-0.00110.2820.1320.1320.0000.0000.0000.000
6A6GLU-1-0.775-0.87113.2550.1020.1020.0000.0000.0000.000
7A7SER0-0.066-0.05416.8360.0620.0620.0000.0000.0000.000
8A8GLY00.0300.00419.856-0.026-0.0260.0000.0000.0000.000
9A9GLY0-0.0040.01722.943-0.016-0.0160.0000.0000.0000.000
10A10ARG10.9360.95924.648-0.070-0.0700.0000.0000.0000.000
11A11LEU0-0.0160.00028.180-0.007-0.0070.0000.0000.0000.000
12A12VAL0-0.054-0.02831.295-0.001-0.0010.0000.0000.0000.000
13A13THR00.0630.01833.6900.0010.0010.0000.0000.0000.000
14A14PRO00.004-0.02236.074-0.001-0.0010.0000.0000.0000.000
15A15GLY0-0.0010.00736.959-0.001-0.0010.0000.0000.0000.000
16A16THR0-0.063-0.01735.577-0.002-0.0020.0000.0000.0000.000
17A17ALA00.0310.01332.7390.0050.0050.0000.0000.0000.000
18A18LEU0-0.044-0.00526.2710.0040.0040.0000.0000.0000.000
19A19THR0-0.039-0.03424.917-0.014-0.0140.0000.0000.0000.000
20A20LEU0-0.0190.01221.7160.0150.0150.0000.0000.0000.000
21A21THR0-0.007-0.01619.162-0.010-0.0100.0000.0000.0000.000
22A22CYS0-0.0080.00414.4800.0100.0100.0000.0000.0000.000
23A23LYS10.8640.93012.788-0.334-0.3340.0000.0000.0000.000
24A24VAL00.0500.02110.3010.0540.0540.0000.0000.0000.000
25A25SER0-0.054-0.0377.4110.1810.1810.0000.0000.0000.000
26A26GLY00.0590.0313.779-0.0050.0960.001-0.047-0.0560.000
27A27PHE0-0.027-0.0184.262-1.068-0.8790.000-0.032-0.1580.000
28A28SER0-0.027-0.0036.1460.3780.3780.0000.0000.0000.000
29A29LEU0-0.0130.0147.7050.1910.1910.0000.0000.0000.000
30A30SER00.0260.00110.8410.0010.0010.0000.0000.0000.000
31A31GLY0-0.036-0.01913.8150.0230.0230.0000.0000.0000.000
32A32PHE00.0370.00210.784-0.036-0.0360.0000.0000.0000.000
33A33TRP00.0250.02715.0940.0490.0490.0000.0000.0000.000
34A34LEU0-0.014-0.01413.353-0.032-0.0320.0000.0000.0000.000
35A35ASN00.003-0.00316.2600.0540.0540.0000.0000.0000.000
36A36TRP00.0150.00417.5070.0150.0150.0000.0000.0000.000
37A37VAL00.0010.00319.055-0.001-0.0010.0000.0000.0000.000
38A38ARG10.8070.90520.852-0.017-0.0170.0000.0000.0000.000
39A39GLN00.015-0.01222.1760.0020.0020.0000.0000.0000.000
40A40ALA00.0440.02824.7930.0120.0120.0000.0000.0000.000
41A41PRO00.000-0.02227.5720.0060.0060.0000.0000.0000.000
42A42GLY00.0030.01228.052-0.006-0.0060.0000.0000.0000.000
43A43LYS10.9000.96327.997-0.074-0.0740.0000.0000.0000.000
44A44GLY00.0500.02426.3130.0080.0080.0000.0000.0000.000
45A45LEU00.0070.00720.3530.0000.0000.0000.0000.0000.000
46A46GLU-1-0.841-0.91124.0650.0290.0290.0000.0000.0000.000
47A47TRP0-0.031-0.02120.9900.0120.0120.0000.0000.0000.000
48A48VAL0-0.074-0.05023.2310.0040.0040.0000.0000.0000.000
49A49GLY00.022-0.00823.1280.0020.0020.0000.0000.0000.000
50A50ALA0-0.050-0.01120.014-0.003-0.0030.0000.0000.0000.000
51A51ILE0-0.022-0.01419.0210.0150.0150.0000.0000.0000.000
52A52TYR0-0.038-0.01417.368-0.023-0.0230.0000.0000.0000.000
53A53ARG10.7740.87813.8280.3340.3340.0000.0000.0000.000
54A54GLY00.0050.01318.0680.0150.0150.0000.0000.0000.000
55A55SER0-0.086-0.03919.7220.0230.0230.0000.0000.0000.000
56A56GLY00.0830.03522.7480.0000.0000.0000.0000.0000.000
57A57SER0-0.048-0.01123.6700.0160.0160.0000.0000.0000.000
58A58GLU-1-0.829-0.87823.633-0.080-0.0800.0000.0000.0000.000
59A59TRP0-0.030-0.01624.4780.0120.0120.0000.0000.0000.000
60A60TYR0-0.020-0.04325.3050.0030.0030.0000.0000.0000.000
61A61ALA00.0410.03027.659-0.002-0.0020.0000.0000.0000.000
62A62SER0-0.049-0.04829.3680.0030.0030.0000.0000.0000.000
63A63TRP00.0380.01127.2130.0010.0010.0000.0000.0000.000
64A64ALA00.0120.01728.8510.0020.0020.0000.0000.0000.000
65A65LYS10.9380.96930.8750.0260.0260.0000.0000.0000.000
66A66GLY00.0410.02332.4840.0040.0040.0000.0000.0000.000
67A67ARG10.8100.87032.397-0.015-0.0150.0000.0000.0000.000
68A68PHE0-0.007-0.00726.9620.0070.0070.0000.0000.0000.000
69A69THR0-0.005-0.00528.046-0.002-0.0020.0000.0000.0000.000
70A70ILE0-0.0010.01621.7660.0100.0100.0000.0000.0000.000
71A71SER0-0.014-0.00723.2690.0000.0000.0000.0000.0000.000
72A72ASP-1-0.783-0.88418.210-0.206-0.2060.0000.0000.0000.000
73A73THR0-0.020-0.01618.7340.0130.0130.0000.0000.0000.000
74A74SER00.0580.02417.128-0.021-0.0210.0000.0000.0000.000
75A75THR00.032-0.00512.931-0.047-0.0470.0000.0000.0000.000
76A76THR0-0.042-0.00413.4330.0370.0370.0000.0000.0000.000
77A77VAL0-0.0060.02415.9560.0210.0210.0000.0000.0000.000
78A78THR0-0.0080.00318.3160.0300.0300.0000.0000.0000.000
79A79LEU00.0350.01921.445-0.014-0.0140.0000.0000.0000.000
80A80LYS10.9010.95223.8840.0090.0090.0000.0000.0000.000
81A81LEU0-0.0060.00626.266-0.005-0.0050.0000.0000.0000.000
82A82THR00.013-0.01029.8440.0070.0070.0000.0000.0000.000
83A83SER00.0530.02433.0650.0030.0030.0000.0000.0000.000
84A84PRO0-0.073-0.00632.153-0.001-0.0010.0000.0000.0000.000
85A85THR00.014-0.00234.065-0.001-0.0010.0000.0000.0000.000
86A86THR00.048-0.01234.3160.0030.0030.0000.0000.0000.000
87A87GLU-1-0.888-0.92534.2040.0400.0400.0000.0000.0000.000
88A88ASP-1-0.793-0.85230.3940.0270.0270.0000.0000.0000.000
89A89THR0-0.0200.00629.2300.0060.0060.0000.0000.0000.000
90A90ALA0-0.002-0.00126.084-0.002-0.0020.0000.0000.0000.000
91A91THR0-0.032-0.00720.9620.0110.0110.0000.0000.0000.000
92A92TYR0-0.058-0.04721.588-0.014-0.0140.0000.0000.0000.000
93A93PHE00.0190.00816.3890.0230.0230.0000.0000.0000.000
94A95ALA00.017-0.00312.9530.0120.0120.0000.0000.0000.000
95A96ALA00.0190.01610.1770.0180.0180.0000.0000.0000.000
96A97ASP-1-0.759-0.88212.175-0.265-0.2650.0000.0000.0000.000
97A98THR0-0.027-0.0107.5140.0800.0800.0000.0000.0000.000
98A99THR0-0.056-0.03510.828-0.006-0.0060.0000.0000.0000.000
99A100ASP-1-0.825-0.89613.858-0.311-0.3110.0000.0000.0000.000
100A101ASN0-0.109-0.05916.7320.0380.0380.0000.0000.0000.000
101A102GLY00.0190.02018.3850.0260.0260.0000.0000.0000.000
102A103TYR0-0.040-0.02913.5950.0310.0310.0000.0000.0000.000
103A104PHE0-0.043-0.02313.820-0.035-0.0350.0000.0000.0000.000
104A105THR00.0270.0079.4800.0560.0560.0000.0000.0000.000
105A106ILE0-0.0010.0065.8100.0840.0840.0000.0000.0000.000
106A107TRP00.005-0.0129.0340.0440.0440.0000.0000.0000.000
107A108GLY00.0150.02910.2900.0200.0200.0000.0000.0000.000
108A109PRO0-0.049-0.03912.1900.0110.0110.0000.0000.0000.000
109A110GLY00.0270.02614.744-0.010-0.0100.0000.0000.0000.000
110A111THR0-0.068-0.05217.9410.0250.0250.0000.0000.0000.000
111A112LEU00.005-0.00320.922-0.020-0.0200.0000.0000.0000.000
112A113VAL0-0.0060.01424.4290.0020.0020.0000.0000.0000.000
113A114THR0-0.038-0.02827.1680.0010.0010.0000.0000.0000.000
114A115VAL00.0110.01530.678-0.001-0.0010.0000.0000.0000.000
115A116SER00.014-0.00633.660-0.003-0.0030.0000.0000.0000.000
116A117SER00.0240.01336.9240.0010.0010.0000.0000.0000.000
117A118ALA0-0.0230.00738.583-0.001-0.0010.0000.0000.0000.000
118A119SER00.0280.00638.3050.0010.0010.0000.0000.0000.000
119A120THR0-0.070-0.03033.9440.0010.0010.0000.0000.0000.000
120A121LYS10.8580.93336.554-0.099-0.0990.0000.0000.0000.000
121A122GLY00.0610.03035.5650.0060.0060.0000.0000.0000.000
122A123PRO0-0.010-0.01633.704-0.006-0.0060.0000.0000.0000.000
123A124SER0-0.040-0.01736.777-0.004-0.0040.0000.0000.0000.000
124A125VAL0-0.022-0.01335.4770.0020.0020.0000.0000.0000.000
125A126PHE0-0.0010.00238.685-0.003-0.0030.0000.0000.0000.000
126A127PRO00.0460.02239.9520.0050.0050.0000.0000.0000.000
127A128LEU0-0.042-0.00738.842-0.006-0.0060.0000.0000.0000.000
128A129ALA00.027-0.01341.9520.0030.0030.0000.0000.0000.000
129A130PRO00.0740.05842.461-0.004-0.0040.0000.0000.0000.000
130A131SER0-0.050-0.02344.699-0.007-0.0070.0000.0000.0000.000
131A132ALA00.0860.04347.5670.0010.0010.0000.0000.0000.000
132A133LYS10.8750.93349.088-0.072-0.0720.0000.0000.0000.000
133A134SER00.0590.03143.903-0.001-0.0010.0000.0000.0000.000
134A135THR00.0000.00544.7340.0050.0050.0000.0000.0000.000
135A136SER00.0280.02144.068-0.004-0.0040.0000.0000.0000.000
136A137GLY0-0.025-0.00446.163-0.001-0.0010.0000.0000.0000.000
137A138GLY00.0370.01044.178-0.001-0.0010.0000.0000.0000.000
138A139THR0-0.049-0.02739.4550.0050.0050.0000.0000.0000.000
139A140ALA00.0220.00740.801-0.007-0.0070.0000.0000.0000.000
140A141ALA00.0070.01838.8310.0070.0070.0000.0000.0000.000
141A142LEU0-0.036-0.00536.913-0.009-0.0090.0000.0000.0000.000
142A143GLY00.0410.00136.7970.0080.0080.0000.0000.0000.000
143A144CYS0-0.065-0.01932.1270.0060.0060.0000.0000.0000.000
144A145LEU0-0.0240.01636.1210.0040.0040.0000.0000.0000.000
145A146VAL0-0.016-0.01833.4240.0010.0010.0000.0000.0000.000
146A147LYS10.8770.90936.625-0.085-0.0850.0000.0000.0000.000
147A148ASP-1-0.786-0.88139.0140.0870.0870.0000.0000.0000.000
148A149TYR0-0.033-0.02031.3600.0000.0000.0000.0000.0000.000
149A150PHE00.0560.02734.733-0.003-0.0030.0000.0000.0000.000
150A151PRO00.0040.01430.641-0.001-0.0010.0000.0000.0000.000
151A152GLU-1-0.777-0.88028.3810.1590.1590.0000.0000.0000.000
152A153PRO0-0.028-0.01524.693-0.001-0.0010.0000.0000.0000.000
153A154VAL00.021-0.02427.704-0.006-0.0060.0000.0000.0000.000
154A155THR0-0.061-0.03623.4870.0070.0070.0000.0000.0000.000
155A156VAL0-0.0190.00226.5820.0080.0080.0000.0000.0000.000
156A157SER00.0010.01225.3490.0190.0190.0000.0000.0000.000
157A158TRP00.0210.00227.417-0.024-0.0240.0000.0000.0000.000
158A159ASN00.022-0.00128.6470.0120.0120.0000.0000.0000.000
159A160SER0-0.008-0.02626.3540.0030.0030.0000.0000.0000.000
160A161GLY0-0.015-0.00124.1990.0230.0230.0000.0000.0000.000
161A162ALA0-0.0070.01624.6030.0200.0200.0000.0000.0000.000
162A163LEU0-0.046-0.01726.785-0.006-0.0060.0000.0000.0000.000
163A164THR00.0280.00523.974-0.006-0.0060.0000.0000.0000.000
164A165SER00.009-0.01227.131-0.003-0.0030.0000.0000.0000.000
165A166GLY00.0500.02529.262-0.011-0.0110.0000.0000.0000.000
166A167VAL0-0.0200.00928.311-0.014-0.0140.0000.0000.0000.000
167A168HIS0-0.063-0.04029.018-0.002-0.0020.0000.0000.0000.000
168A169THR00.0160.00027.747-0.016-0.0160.0000.0000.0000.000
169A170PHE0-0.0100.00829.3860.0020.0020.0000.0000.0000.000
170A171PRO0-0.002-0.00429.5950.0030.0030.0000.0000.0000.000
171A172ALA00.0070.01630.864-0.007-0.0070.0000.0000.0000.000
172A173VAL0-0.026-0.02132.806-0.004-0.0040.0000.0000.0000.000
173A174LEU0-0.0220.00036.1070.0000.0000.0000.0000.0000.000
174A175GLN0-0.028-0.02137.841-0.004-0.0040.0000.0000.0000.000
175A176SER00.0360.00241.523-0.001-0.0010.0000.0000.0000.000
176A177SER0-0.026-0.00943.344-0.002-0.0020.0000.0000.0000.000
177A178GLY00.0390.02440.995-0.002-0.0020.0000.0000.0000.000
178A179LEU0-0.091-0.03338.7430.0040.0040.0000.0000.0000.000
179A180TYR00.0440.02632.678-0.004-0.0040.0000.0000.0000.000
180A181SER00.007-0.00936.314-0.001-0.0010.0000.0000.0000.000
181A182LEU00.0320.03430.520-0.001-0.0010.0000.0000.0000.000
182A183SER00.014-0.01534.210-0.007-0.0070.0000.0000.0000.000
183A184SER00.0090.01630.3670.0000.0000.0000.0000.0000.000
184A185VAL0-0.001-0.01633.099-0.010-0.0100.0000.0000.0000.000
185A186VAL00.0430.02932.5930.0110.0110.0000.0000.0000.000
186A187THR0-0.034-0.00834.507-0.011-0.0110.0000.0000.0000.000
187A188VAL00.0290.00635.4150.0090.0090.0000.0000.0000.000
188A189PRO00.0420.01737.330-0.008-0.0080.0000.0000.0000.000
189A190SER0-0.001-0.01540.5890.0010.0010.0000.0000.0000.000
190A191SER00.0010.00743.071-0.001-0.0010.0000.0000.0000.000
191A192SER0-0.019-0.00640.016-0.001-0.0010.0000.0000.0000.000
192A193LEU0-0.004-0.02041.2120.0040.0040.0000.0000.0000.000
193A194GLY00.0140.01643.205-0.001-0.0010.0000.0000.0000.000
194A195THR00.005-0.00840.9050.0010.0010.0000.0000.0000.000
195A196GLN0-0.0220.00035.0880.0080.0080.0000.0000.0000.000
196A197THR0-0.0150.00437.8390.0000.0000.0000.0000.0000.000
197A198TYR00.0290.01334.8750.0120.0120.0000.0000.0000.000
198A199ILE00.011-0.00832.885-0.011-0.0110.0000.0000.0000.000
199A201ASN00.020-0.00728.2590.0000.0000.0000.0000.0000.000
200A202VAL0-0.019-0.01128.5980.0140.0140.0000.0000.0000.000
201A203ASN00.000-0.01626.156-0.004-0.0040.0000.0000.0000.000
202A204HIS00.0380.06027.9030.0060.0060.0000.0000.0000.000
203A205LYS11.0311.00421.218-0.336-0.3360.0000.0000.0000.000
204A206PRO0-0.0120.00027.130-0.007-0.0070.0000.0000.0000.000
205A207SER00.0240.00029.618-0.011-0.0110.0000.0000.0000.000
206A208ASN0-0.042-0.01830.1510.0070.0070.0000.0000.0000.000
207A209THR00.0060.00430.9130.0070.0070.0000.0000.0000.000
208A210LYS10.8490.90627.408-0.185-0.1850.0000.0000.0000.000
209A211VAL0-0.0080.00131.0750.0010.0010.0000.0000.0000.000
210A212ASP-1-0.770-0.87731.0450.2080.2080.0000.0000.0000.000
211A213LYS10.8960.96934.058-0.121-0.1210.0000.0000.0000.000
212A214LYS10.9000.93536.338-0.115-0.1150.0000.0000.0000.000
213A215ALA0-0.026-0.01538.538-0.008-0.0080.0000.0000.0000.000
214A216GLU-1-0.793-0.89340.2820.1180.1180.0000.0000.0000.000
215A217PRO0-0.028-0.02543.265-0.004-0.0040.0000.0000.0000.000
216A218LYS10.7950.89446.106-0.090-0.0900.0000.0000.0000.000
217A219SER00.0120.01248.6940.0000.0000.0000.0000.0000.000
218A220CYS00.0320.02851.6810.0000.0000.0000.0000.0000.000