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: 85K6Y

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2164883.233935
FMO2-HF: Nuclear repulsion 2084109.272124
FMO2-HF: Total energy -80773.961811
FMO2-MP2: Total energy -81010.961724


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.
-2.994-1.464-0.005-0.652-0.8730.001
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 : 0.001 / q_NPA : -0.031
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].
3A3GLN0-0.029-0.0113.728-2.299-1.122-0.006-0.572-0.5990.001
4A4LEU00.0300.0026.5000.0340.0340.0000.0000.0000.000
5A5VAL00.000-0.00610.220-0.009-0.0090.0000.0000.0000.000
6A6GLU-1-0.774-0.86313.2030.4120.4120.0000.0000.0000.000
7A7SER0-0.068-0.05316.7870.0230.0230.0000.0000.0000.000
8A8GLY00.021-0.00319.805-0.013-0.0130.0000.0000.0000.000
9A9GLY0-0.0010.01922.899-0.022-0.0220.0000.0000.0000.000
10A10ARG10.9350.95924.607-0.169-0.1690.0000.0000.0000.000
11A11LEU0-0.026-0.00128.129-0.003-0.0030.0000.0000.0000.000
12A12VAL0-0.053-0.02831.3020.0000.0000.0000.0000.0000.000
13A13THR00.0780.03433.645-0.003-0.0030.0000.0000.0000.000
14A14PRO0-0.002-0.01936.0190.0040.0040.0000.0000.0000.000
15A15GLY00.0050.00636.907-0.004-0.0040.0000.0000.0000.000
16A16THR0-0.090-0.04435.5500.0010.0010.0000.0000.0000.000
17A17ALA00.0410.01832.6060.0070.0070.0000.0000.0000.000
18A18LEU0-0.0480.00126.0970.0010.0010.0000.0000.0000.000
19A19THR0-0.046-0.05024.883-0.009-0.0090.0000.0000.0000.000
20A20LEU0-0.0190.00321.6570.0080.0080.0000.0000.0000.000
21A21THR0-0.022-0.01918.7610.0000.0000.0000.0000.0000.000
22A22CYS0-0.028-0.00514.3430.0220.0220.0000.0000.0000.000
23A23LYS10.9000.95212.938-0.602-0.6020.0000.0000.0000.000
24A24VAL00.0620.02910.2740.1150.1150.0000.0000.0000.000
25A25SER0-0.051-0.0447.2520.0340.0340.0000.0000.0000.000
26A26GLY00.0420.0273.7410.0930.2320.001-0.045-0.0950.000
27A27PHE0-0.019-0.0144.1780.0160.2300.000-0.035-0.1790.000
28A28SER00.0100.0076.425-0.158-0.1580.0000.0000.0000.000
29A29LEU0-0.0440.0017.946-0.184-0.1840.0000.0000.0000.000
30A30SER00.0200.00711.0980.0310.0310.0000.0000.0000.000
31A31GLY0-0.045-0.02613.9570.0200.0200.0000.0000.0000.000
32A32PHE00.0530.00611.1780.0220.0220.0000.0000.0000.000
33A33TRP00.0300.03115.728-0.024-0.0240.0000.0000.0000.000
34A34LEU0-0.002-0.01213.0350.0420.0420.0000.0000.0000.000
35A35ASN0-0.002-0.00216.266-0.057-0.0570.0000.0000.0000.000
36A36TRP00.0220.01517.4190.0270.0270.0000.0000.0000.000
37A37VAL00.0020.00119.130-0.022-0.0220.0000.0000.0000.000
38A38ARG10.8470.92920.790-0.135-0.1350.0000.0000.0000.000
39A39GLN00.0310.00621.9990.0080.0080.0000.0000.0000.000
40A40ALA00.0420.02224.7480.0050.0050.0000.0000.0000.000
41A41PRO0-0.024-0.02227.5400.0030.0030.0000.0000.0000.000
42A42GLY00.0040.01128.031-0.009-0.0090.0000.0000.0000.000
43A43LYS10.9160.96627.971-0.117-0.1170.0000.0000.0000.000
44A44GLY00.0350.01126.2760.0060.0060.0000.0000.0000.000
45A45LEU00.0030.00320.0810.0020.0020.0000.0000.0000.000
46A46GLU-1-0.898-0.95324.0130.1300.1300.0000.0000.0000.000
47A47TRP0-0.028-0.02020.9760.0030.0030.0000.0000.0000.000
48A48VAL0-0.080-0.05123.148-0.013-0.0130.0000.0000.0000.000
49A49GLY00.021-0.01423.040-0.015-0.0150.0000.0000.0000.000
50A50ALA0-0.050-0.01219.9960.0180.0180.0000.0000.0000.000
51A51ILE0-0.021-0.01519.346-0.017-0.0170.0000.0000.0000.000
52A52TYR0-0.0170.00618.1000.0200.0200.0000.0000.0000.000
53A53ARG10.8220.90813.790-0.355-0.3550.0000.0000.0000.000
54A54GLY00.0190.02218.187-0.012-0.0120.0000.0000.0000.000
55A55SER0-0.083-0.03219.679-0.023-0.0230.0000.0000.0000.000
56A56GLY00.0790.03022.6810.0080.0080.0000.0000.0000.000
57A57SER0-0.053-0.02424.185-0.009-0.0090.0000.0000.0000.000
58A58GLU-1-0.888-0.93523.9390.1570.1570.0000.0000.0000.000
59A59TRP0-0.0100.00224.382-0.016-0.0160.0000.0000.0000.000
60A60TYR00.0150.01625.2480.0150.0150.0000.0000.0000.000
61A61ALA00.0410.02927.587-0.006-0.0060.0000.0000.0000.000
62A62SER0-0.040-0.04929.274-0.001-0.0010.0000.0000.0000.000
63A63TRP00.0230.01127.244-0.006-0.0060.0000.0000.0000.000
64A64ALA00.0130.01728.783-0.003-0.0030.0000.0000.0000.000
65A65LYS10.9350.96930.787-0.093-0.0930.0000.0000.0000.000
66A66GLY00.0350.02232.388-0.006-0.0060.0000.0000.0000.000
67A67ARG10.8550.91932.416-0.118-0.1180.0000.0000.0000.000
68A68PHE0-0.009-0.01226.7800.0080.0080.0000.0000.0000.000
69A69THR0-0.025-0.01827.964-0.009-0.0090.0000.0000.0000.000
70A70ILE00.0040.01221.6600.0110.0110.0000.0000.0000.000
71A71SER0-0.006-0.00523.246-0.014-0.0140.0000.0000.0000.000
72A72ASP-1-0.803-0.90118.0000.2900.2900.0000.0000.0000.000
73A73THR0-0.032-0.01718.687-0.019-0.0190.0000.0000.0000.000
74A74SER00.0660.02617.0940.0280.0280.0000.0000.0000.000
75A75THR00.034-0.01012.5220.0250.0250.0000.0000.0000.000
76A76THR0-0.093-0.01713.3240.0210.0210.0000.0000.0000.000
77A77VAL00.0090.01815.871-0.028-0.0280.0000.0000.0000.000
78A78THR0-0.0180.00418.2800.0180.0180.0000.0000.0000.000
79A79LEU00.0420.02121.445-0.010-0.0100.0000.0000.0000.000
80A80LYS10.9170.96823.800-0.148-0.1480.0000.0000.0000.000
81A81LEU0-0.0090.00126.251-0.005-0.0050.0000.0000.0000.000
82A82THR00.007-0.01629.768-0.005-0.0050.0000.0000.0000.000
83A83SER00.0360.01732.984-0.003-0.0030.0000.0000.0000.000
84A84PRO0-0.0470.00632.070-0.001-0.0010.0000.0000.0000.000
85A85THR00.010-0.00333.998-0.008-0.0080.0000.0000.0000.000
86A86THR00.0350.00634.2580.0050.0050.0000.0000.0000.000
87A87GLU-1-0.875-0.92034.1550.1050.1050.0000.0000.0000.000
88A88ASP-1-0.797-0.87930.3230.1340.1340.0000.0000.0000.000
89A89THR0-0.058-0.03429.1750.0120.0120.0000.0000.0000.000
90A90ALA00.0130.00826.031-0.005-0.0050.0000.0000.0000.000
91A91THR0-0.063-0.02221.5660.0140.0140.0000.0000.0000.000
92A92TYR0-0.031-0.03121.532-0.007-0.0070.0000.0000.0000.000
93A93PHE00.0450.02115.9360.0150.0150.0000.0000.0000.000
94A95ALA00.0280.00112.8730.0240.0240.0000.0000.0000.000
95A96ALA00.0150.01110.084-0.033-0.0330.0000.0000.0000.000
96A97ASP-1-0.790-0.91112.0800.3050.3050.0000.0000.0000.000
97A98THR0-0.014-0.0238.011-0.034-0.0340.0000.0000.0000.000
98A99THR0-0.067-0.02511.3980.0220.0220.0000.0000.0000.000
99A100ASP-1-0.863-0.91214.5180.2340.2340.0000.0000.0000.000
100A101ASN0-0.097-0.05917.162-0.024-0.0240.0000.0000.0000.000
101A102GLY00.0250.02118.749-0.014-0.0140.0000.0000.0000.000
102A103TYR0-0.046-0.03213.737-0.003-0.0030.0000.0000.0000.000
103A104PHE0-0.036-0.02213.7250.0280.0280.0000.0000.0000.000
104A105THR00.0300.0289.420-0.045-0.0450.0000.0000.0000.000
105A106ILE00.0040.0085.571-0.045-0.0450.0000.0000.0000.000
106A107TRP00.024-0.0018.962-0.005-0.0050.0000.0000.0000.000
107A108GLY00.0170.02510.2460.0340.0340.0000.0000.0000.000
108A109PRO0-0.076-0.05012.304-0.040-0.0400.0000.0000.0000.000
109A110GLY00.0620.05514.725-0.039-0.0390.0000.0000.0000.000
110A111THR0-0.080-0.06217.9070.0090.0090.0000.0000.0000.000
111A112LEU00.002-0.00920.887-0.014-0.0140.0000.0000.0000.000
112A113VAL0-0.0130.01324.397-0.002-0.0020.0000.0000.0000.000
113A114THR0-0.030-0.03227.125-0.007-0.0070.0000.0000.0000.000
114A115VAL00.0300.02530.640-0.001-0.0010.0000.0000.0000.000
115A116SER00.012-0.00533.614-0.007-0.0070.0000.0000.0000.000
116A117SER00.0330.01236.8840.0030.0030.0000.0000.0000.000
117A118ALA0-0.0270.01138.530-0.004-0.0040.0000.0000.0000.000
118A119SER00.0300.00238.2750.0040.0040.0000.0000.0000.000
119A120THR0-0.089-0.03433.994-0.003-0.0030.0000.0000.0000.000
120A121LYS10.9260.97636.501-0.101-0.1010.0000.0000.0000.000
121A122GLY00.0500.03235.5220.0060.0060.0000.0000.0000.000
122A123PRO0-0.010-0.02833.517-0.006-0.0060.0000.0000.0000.000
123A124SER0-0.059-0.01636.734-0.004-0.0040.0000.0000.0000.000
124A125VAL0-0.019-0.01435.3160.0010.0010.0000.0000.0000.000
125A126PHE0-0.014-0.00338.648-0.004-0.0040.0000.0000.0000.000
126A127PRO00.0410.01939.9200.0030.0030.0000.0000.0000.000
127A128LEU0-0.056-0.00538.594-0.003-0.0030.0000.0000.0000.000
128A129ALA00.012-0.01841.9220.0000.0000.0000.0000.0000.000
129A130PRO00.0980.06742.261-0.002-0.0020.0000.0000.0000.000
130A131SER0-0.067-0.04744.674-0.003-0.0030.0000.0000.0000.000
131A132ALA00.0670.03347.5440.0000.0000.0000.0000.0000.000
132A133LYS10.8850.93649.178-0.042-0.0420.0000.0000.0000.000
133A134SER00.0390.02343.9660.0020.0020.0000.0000.0000.000
134A135THR0-0.0020.00344.8020.0010.0010.0000.0000.0000.000
135A136SER00.0310.02644.125-0.001-0.0010.0000.0000.0000.000
136A137GLY0-0.033-0.01146.236-0.001-0.0010.0000.0000.0000.000
137A138GLY00.0480.01744.263-0.001-0.0010.0000.0000.0000.000
138A139THR0-0.056-0.03139.4610.0010.0010.0000.0000.0000.000
139A140ALA00.0240.00540.840-0.002-0.0020.0000.0000.0000.000
140A141ALA00.0070.01738.8390.0030.0030.0000.0000.0000.000
141A142LEU0-0.0220.00637.175-0.003-0.0030.0000.0000.0000.000
142A143GLY00.040-0.00736.7670.0040.0040.0000.0000.0000.000
143A144CYS0-0.083-0.02932.0990.0030.0030.0000.0000.0000.000
144A145LEU0-0.0260.01536.0870.0050.0050.0000.0000.0000.000
145A146VAL0-0.017-0.01833.3620.0000.0000.0000.0000.0000.000
146A147LYS10.9430.97036.586-0.074-0.0740.0000.0000.0000.000
147A148ASP-1-0.835-0.93738.9730.0840.0840.0000.0000.0000.000
148A149TYR0-0.046-0.01931.189-0.003-0.0030.0000.0000.0000.000
149A150PHE00.0480.02534.729-0.001-0.0010.0000.0000.0000.000
150A151PRO0-0.0020.00430.630-0.002-0.0020.0000.0000.0000.000
151A152GLU-1-0.783-0.90128.1820.1650.1650.0000.0000.0000.000
152A153PRO0-0.025-0.01224.8410.0060.0060.0000.0000.0000.000
153A154VAL00.011-0.03327.721-0.006-0.0060.0000.0000.0000.000
154A155THR0-0.064-0.03323.4320.0060.0060.0000.0000.0000.000
155A156VAL0-0.0170.00126.5430.0030.0030.0000.0000.0000.000
156A157SER00.0030.01325.4360.0080.0080.0000.0000.0000.000
157A158TRP00.0390.00427.388-0.013-0.0130.0000.0000.0000.000
158A159ASN00.0450.01228.6260.0050.0050.0000.0000.0000.000
159A160SER0-0.012-0.03226.287-0.002-0.0020.0000.0000.0000.000
160A161GLY0-0.0070.00624.2130.0110.0110.0000.0000.0000.000
161A162ALA0-0.0050.01624.6080.0030.0030.0000.0000.0000.000
162A163LEU0-0.057-0.01826.883-0.010-0.0100.0000.0000.0000.000
163A164THR00.0360.00523.8470.0030.0030.0000.0000.0000.000
164A165SER0-0.001-0.01427.1140.0020.0020.0000.0000.0000.000
165A166GLY00.0500.02729.342-0.004-0.0040.0000.0000.0000.000
166A167VAL0-0.029-0.00128.415-0.003-0.0030.0000.0000.0000.000
167A168HIS0-0.046-0.02429.0770.0000.0000.0000.0000.0000.000
168A169THR0-0.019-0.01727.879-0.009-0.0090.0000.0000.0000.000
169A170PHE00.0060.01729.4220.0020.0020.0000.0000.0000.000
170A171PRO00.0100.00029.6970.0050.0050.0000.0000.0000.000
171A172ALA00.0050.01230.875-0.008-0.0080.0000.0000.0000.000
172A173VAL0-0.010-0.01632.816-0.001-0.0010.0000.0000.0000.000
173A174LEU0-0.0210.00636.111-0.001-0.0010.0000.0000.0000.000
174A175GLN0-0.013-0.01437.835-0.005-0.0050.0000.0000.0000.000
175A176SER00.028-0.00541.5200.0010.0010.0000.0000.0000.000
176A177SER0-0.026-0.00343.2770.0000.0000.0000.0000.0000.000
177A178GLY00.0350.02140.978-0.001-0.0010.0000.0000.0000.000
178A179LEU0-0.112-0.03838.7290.0060.0060.0000.0000.0000.000
179A180TYR00.0330.01132.595-0.002-0.0020.0000.0000.0000.000
180A181SER0-0.001-0.00636.356-0.002-0.0020.0000.0000.0000.000
181A182LEU00.0430.03330.833-0.001-0.0010.0000.0000.0000.000
182A183SER00.025-0.01834.250-0.005-0.0050.0000.0000.0000.000
183A184SER0-0.0020.02530.425-0.002-0.0020.0000.0000.0000.000
184A185VAL00.010-0.00733.152-0.006-0.0060.0000.0000.0000.000
185A186VAL00.0510.02932.4930.0050.0050.0000.0000.0000.000
186A187THR0-0.045-0.01434.547-0.006-0.0060.0000.0000.0000.000
187A188VAL00.0280.00735.4260.0020.0020.0000.0000.0000.000
188A189PRO00.0450.01937.323-0.002-0.0020.0000.0000.0000.000
189A190SER0-0.035-0.02440.5760.0000.0000.0000.0000.0000.000
190A191SER00.0530.02643.1680.0010.0010.0000.0000.0000.000
191A192SER0-0.030-0.01539.9450.0000.0000.0000.0000.0000.000
192A193LEU0-0.007-0.02141.2460.0030.0030.0000.0000.0000.000
193A194GLY00.0260.02543.1880.0010.0010.0000.0000.0000.000
194A195THR0-0.015-0.01641.0480.0010.0010.0000.0000.0000.000
195A196GLN0-0.0030.00835.3090.0040.0040.0000.0000.0000.000
196A197THR0-0.0010.00438.0250.0020.0020.0000.0000.0000.000
197A198TYR00.0320.01134.7510.0050.0050.0000.0000.0000.000
198A199ILE00.004-0.01032.463-0.003-0.0030.0000.0000.0000.000
199A201ASN00.0230.01528.178-0.004-0.0040.0000.0000.0000.000
200A202VAL00.0090.00028.5650.0120.0120.0000.0000.0000.000
201A203ASN00.009-0.00824.814-0.002-0.0020.0000.0000.0000.000
202A204HIS00.0500.04427.8620.0030.0030.0000.0000.0000.000
203A205LYS11.0130.99320.860-0.326-0.3260.0000.0000.0000.000
204A206PRO0-0.0160.00227.256-0.004-0.0040.0000.0000.0000.000
205A207SER00.0050.01729.571-0.011-0.0110.0000.0000.0000.000
206A208ASN0-0.054-0.02329.7690.0040.0040.0000.0000.0000.000
207A209THR0-0.031-0.03430.540-0.001-0.0010.0000.0000.0000.000
208A210LYS10.9220.95125.461-0.198-0.1980.0000.0000.0000.000
209A211VAL0-0.0020.01030.787-0.004-0.0040.0000.0000.0000.000
210A212ASP-1-0.795-0.89930.9480.1430.1430.0000.0000.0000.000
211A213LYS10.8930.96533.884-0.087-0.0870.0000.0000.0000.000
212A214LYS10.9610.97836.234-0.062-0.0620.0000.0000.0000.000
213A215ALA0-0.023-0.01538.453-0.003-0.0030.0000.0000.0000.000
214A216GLU-1-0.879-0.95040.2550.0550.0550.0000.0000.0000.000
215A217PRO0-0.031-0.01943.2410.0000.0000.0000.0000.0000.000
216A218LYS10.8290.92946.082-0.049-0.0490.0000.0000.0000.000
217A219SER00.0320.01748.6670.0010.0010.0000.0000.0000.000
218A220CYS00.0070.01951.655-0.001-0.0010.0000.0000.0000.000