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: 2JV4R

Calculation Name: 2PX7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PX7

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX2

Base Structure: X-ray

Registration Date: 2023-09-20

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2058980.105029
FMO2-HF: Nuclear repulsion 1985792.752895
FMO2-HF: Total energy -73187.352134
FMO2-MP2: Total energy -73406.084942


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-9.549-5.1969.506-5.705-8.152-0.048
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.002
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].
3A3VAL0-0.031-0.0253.885-0.3311.573-0.012-1.082-0.8090.004
4A4SER0-0.030-0.0336.283-0.024-0.0240.0000.0000.0000.000
5A5VAL00.000-0.0058.315-0.001-0.0010.0000.0000.0000.000
6A6LEU00.0020.01111.0130.1770.1770.0000.0000.0000.000
7A7ILE00.0260.00113.4700.0300.0300.0000.0000.0000.000
8A8PRO00.0190.01016.7020.0730.0730.0000.0000.0000.000
9A9ALA0-0.042-0.02519.9630.0390.0390.0000.0000.0000.000
10A10ALA00.0100.00221.7300.0340.0340.0000.0000.0000.000
11A11GLY00.0050.01724.8380.0250.0250.0000.0000.0000.000
12A19GLY00.0600.03030.6320.0070.0070.0000.0000.0000.000
13A20PRO0-0.025-0.02426.075-0.009-0.0090.0000.0000.0000.000
14A21LYS10.8880.94025.0690.2270.2270.0000.0000.0000.000
15A22ALA00.0180.00421.376-0.006-0.0060.0000.0000.0000.000
16A23PHE0-0.001-0.02022.010-0.003-0.0030.0000.0000.0000.000
17A24LEU00.0030.00824.5840.0210.0210.0000.0000.0000.000
18A25GLN00.019-0.00524.288-0.014-0.0140.0000.0000.0000.000
19A26VAL00.011-0.00222.653-0.006-0.0060.0000.0000.0000.000
20A27GLY00.0270.01522.969-0.003-0.0030.0000.0000.0000.000
21A28GLY0-0.0280.00023.6560.0170.0170.0000.0000.0000.000
22A29ARG10.8910.96014.5710.0760.0760.0000.0000.0000.000
23A30THR0-0.029-0.04020.977-0.026-0.0260.0000.0000.0000.000
24A31LEU0-0.020-0.01420.004-0.014-0.0140.0000.0000.0000.000
25A32LEU00.0150.02116.612-0.058-0.0580.0000.0000.0000.000
26A33GLU-1-0.801-0.87016.210-0.142-0.1420.0000.0000.0000.000
27A34TRP0-0.040-0.03415.516-0.012-0.0120.0000.0000.0000.000
28A35THR0-0.037-0.02514.136-0.056-0.0560.0000.0000.0000.000
29A36LEU00.0150.00211.840-0.154-0.1540.0000.0000.0000.000
30A37ALA0-0.029-0.00910.716-0.065-0.0650.0000.0000.0000.000
31A38ALA0-0.032-0.00710.0990.0670.0670.0000.0000.0000.000
32A39PHE00.010-0.0087.766-0.121-0.1210.0000.0000.0000.000
33A40ARG10.8740.9356.627-0.611-0.6110.0000.0000.0000.000
34A41ASP-1-0.831-0.8992.175-1.245-0.2592.136-0.889-2.234-0.005
35A42ALA0-0.025-0.0072.006-10.938-10.9906.083-3.115-2.916-0.044
36A43ALA0-0.0180.0063.0260.0940.7890.031-0.186-0.5400.000
37A44GLU-1-0.758-0.8294.1370.0040.1450.001-0.025-0.1160.000
38A45VAL00.0050.0007.940-0.238-0.2380.0000.0000.0000.000
39A46LEU0-0.0070.01310.3540.2130.2130.0000.0000.0000.000
40A47VAL00.011-0.00114.101-0.037-0.0370.0000.0000.0000.000
41A48ALA0-0.022-0.00116.9460.0480.0480.0000.0000.0000.000
42A49LEU0-0.001-0.00720.689-0.001-0.0010.0000.0000.0000.000
43A50PRO0-0.009-0.00823.4180.0000.0000.0000.0000.0000.000
44A51PRO00.0220.00327.2410.0060.0060.0000.0000.0000.000
45A52GLY0-0.0070.00928.9100.0090.0090.0000.0000.0000.000
46A53ALA0-0.079-0.03726.0840.0140.0140.0000.0000.0000.000
47A54GLU-1-0.793-0.89525.312-0.096-0.0960.0000.0000.0000.000
48A55PRO00.0040.01220.369-0.002-0.0020.0000.0000.0000.000
49A56PRO0-0.0090.00320.1420.0270.0270.0000.0000.0000.000
50A57LYS10.8030.87719.4950.0620.0620.0000.0000.0000.000
51A58GLY00.0090.00317.7040.0110.0110.0000.0000.0000.000
52A59LEU0-0.019-0.00215.0630.0350.0350.0000.0000.0000.000
53A60GLY00.0080.01110.9260.0170.0170.0000.0000.0000.000
54A61ALA0-0.038-0.02210.424-0.183-0.1830.0000.0000.0000.000
55A62VAL00.0070.01312.6150.1130.1130.0000.0000.0000.000
56A63PHE00.009-0.00815.072-0.067-0.0670.0000.0000.0000.000
57A64LEU00.0070.00518.4300.0280.0280.0000.0000.0000.000
58A65GLU-1-0.830-0.91121.391-0.181-0.1810.0000.0000.0000.000
59A66GLY0-0.008-0.01024.294-0.023-0.0230.0000.0000.0000.000
60A67GLY0-0.036-0.02525.0330.0220.0220.0000.0000.0000.000
61A68ALA0-0.010-0.01328.062-0.004-0.0040.0000.0000.0000.000
62A69THR00.007-0.00829.035-0.002-0.0020.0000.0000.0000.000
63A70ARG10.8580.90120.6990.4870.4870.0000.0000.0000.000
64A71GLN00.0580.01824.116-0.035-0.0350.0000.0000.0000.000
65A72ALA00.0230.00624.878-0.022-0.0220.0000.0000.0000.000
66A73SER0-0.013-0.01122.9710.0040.0040.0000.0000.0000.000
67A74VAL0-0.022-0.01119.338-0.022-0.0220.0000.0000.0000.000
68A75ALA0-0.0080.00620.536-0.036-0.0360.0000.0000.0000.000
69A76ARG10.8980.94722.0780.2570.2570.0000.0000.0000.000
70A77LEU0-0.011-0.00416.970-0.006-0.0060.0000.0000.0000.000
71A78LEU0-0.007-0.00417.042-0.061-0.0610.0000.0000.0000.000
72A79GLU-1-0.864-0.92318.430-0.353-0.3530.0000.0000.0000.000
73A80ALA0-0.028-0.00817.1570.0090.0090.0000.0000.0000.000
74A81ALA0-0.0190.00713.814-0.018-0.0180.0000.0000.0000.000
75A82SER0-0.022-0.03911.3450.0370.0370.0000.0000.0000.000
76A83LEU0-0.0060.0116.942-0.021-0.0210.0000.0000.0000.000
77A84PRO00.0030.00010.5740.0710.0710.0000.0000.0000.000
78A85LEU0-0.039-0.01410.3190.0970.0970.0000.0000.0000.000
79A86VAL00.0240.01310.746-0.218-0.2180.0000.0000.0000.000
80A87LEU00.0000.0089.0720.1190.1190.0000.0000.0000.000
81A88VAL00.0000.00213.1170.0410.0410.0000.0000.0000.000
82A89HIS00.0510.01114.778-0.009-0.0090.0000.0000.0000.000
83A90ASP-1-0.783-0.86516.907-0.397-0.3970.0000.0000.0000.000
84A91VAL00.0400.00018.4010.0020.0020.0000.0000.0000.000
85A92ALA0-0.029-0.01219.6480.0240.0240.0000.0000.0000.000
86A93ARG10.8300.93918.4060.4720.4720.0000.0000.0000.000
87A94PRO00.0420.01817.117-0.070-0.0700.0000.0000.0000.000
88A95PHE00.0000.01016.002-0.014-0.0140.0000.0000.0000.000
89A96VAL0-0.0040.00912.2910.0310.0310.0000.0000.0000.000
90A97SER0-0.018-0.03511.944-0.040-0.0400.0000.0000.0000.000
91A98ARG10.8240.8492.9712.3763.0551.267-0.408-1.537-0.003
92A99GLY00.0150.0167.845-0.212-0.2120.0000.0000.0000.000
93A100LEU00.0000.00110.168-0.093-0.0930.0000.0000.0000.000
94A101VAL0-0.015-0.0097.171-0.020-0.0200.0000.0000.0000.000
95A102ALA00.0260.0116.461-0.194-0.1940.0000.0000.0000.000
96A103ARG10.7380.8667.8760.5260.5260.0000.0000.0000.000
97A104VAL0-0.024-0.01711.5860.0540.0540.0000.0000.0000.000
98A105LEU00.0020.0065.9470.0670.0670.0000.0000.0000.000
99A106GLU-1-0.840-0.9009.697-0.707-0.7070.0000.0000.0000.000
100A107ALA00.0690.02710.8730.1090.1090.0000.0000.0000.000
101A108ALA0-0.0350.00512.7910.0960.0960.0000.0000.0000.000
102A109GLN0-0.037-0.0287.7320.3270.3270.0000.0000.0000.000
103A110ARG10.8260.90513.3400.7360.7360.0000.0000.0000.000
104A111SER0-0.039-0.03416.2110.0950.0950.0000.0000.0000.000
105A112GLY00.0390.02217.2830.0720.0720.0000.0000.0000.000
106A113ALA0-0.010-0.02018.592-0.011-0.0110.0000.0000.0000.000
107A114ALA0-0.0110.02315.8540.0610.0610.0000.0000.0000.000
108A115VAL00.0260.00217.454-0.064-0.0640.0000.0000.0000.000
109A116PRO00.0120.02416.6210.0480.0480.0000.0000.0000.000
110A117VAL0-0.020-0.01818.7260.0320.0320.0000.0000.0000.000
111A118LEU0-0.0040.01321.4590.0050.0050.0000.0000.0000.000
112A119PRO00.016-0.01024.2230.0040.0040.0000.0000.0000.000
113A120VAL00.0180.02427.872-0.003-0.0030.0000.0000.0000.000
114A121PRO0-0.036-0.00128.9040.0100.0100.0000.0000.0000.000
115A122ASP-1-0.854-0.93131.244-0.129-0.1290.0000.0000.0000.000
116A123THR0-0.043-0.04934.664-0.007-0.0070.0000.0000.0000.000
117A124LEU00.0150.02434.3240.0010.0010.0000.0000.0000.000
118A125MET0-0.0180.00137.3130.0050.0050.0000.0000.0000.000
119A126ALA0-0.0130.00340.019-0.005-0.0050.0000.0000.0000.000
120A127PRO0-0.021-0.03241.5450.0050.0050.0000.0000.0000.000
121A128GLU-1-0.915-0.95144.650-0.099-0.0990.0000.0000.0000.000
122A129GLY0-0.017-0.00746.8520.0040.0040.0000.0000.0000.000
123A130GLU-1-1.011-0.99647.605-0.075-0.0750.0000.0000.0000.000
124A131ALA0-0.046-0.00345.4750.0000.0000.0000.0000.0000.000
125A132TYR00.025-0.01343.8140.0030.0030.0000.0000.0000.000
126A133GLY00.0850.01645.971-0.001-0.0010.0000.0000.0000.000
127A134ARG10.9540.99141.8550.1260.1260.0000.0000.0000.000
128A135VAL00.0010.00041.267-0.006-0.0060.0000.0000.0000.000
129A136VAL0-0.054-0.02837.9770.0010.0010.0000.0000.0000.000
130A137PRO00.0420.01237.992-0.001-0.0010.0000.0000.0000.000
131A138ARG10.9280.97932.1860.1330.1330.0000.0000.0000.000
132A139GLU-1-0.849-0.93232.905-0.150-0.1500.0000.0000.0000.000
133A140ALA0-0.038-0.00532.581-0.011-0.0110.0000.0000.0000.000
134A141PHE0-0.017-0.00331.701-0.011-0.0110.0000.0000.0000.000
135A142ARG10.8170.88526.2910.2340.2340.0000.0000.0000.000
136A143LEU0-0.0010.00925.8000.0010.0010.0000.0000.0000.000
137A144VAL00.0370.01722.884-0.019-0.0190.0000.0000.0000.000
138A145GLN0-0.049-0.03519.373-0.009-0.0090.0000.0000.0000.000
139A146THR0-0.034-0.01017.5120.0140.0140.0000.0000.0000.000
140A147PRO00.0470.00512.0160.0620.0620.0000.0000.0000.000
141A148GLN0-0.060-0.04615.1000.0410.0410.0000.0000.0000.000
142A149GLY00.0280.01214.276-0.087-0.0870.0000.0000.0000.000
143A150PHE00.012-0.00915.1490.1260.1260.0000.0000.0000.000
144A151PHE00.0370.04615.120-0.123-0.1230.0000.0000.0000.000
145A152THR0-0.019-0.03413.6580.0820.0820.0000.0000.0000.000
146A153ALA0-0.010-0.00416.5920.0780.0780.0000.0000.0000.000
147A154LEU00.0110.02219.6870.0540.0540.0000.0000.0000.000
148A155LEU00.0220.01518.3080.0490.0490.0000.0000.0000.000
149A156ARG10.8550.91316.1590.6840.6840.0000.0000.0000.000
150A157GLU-1-0.761-0.85622.055-0.271-0.2710.0000.0000.0000.000
151A158ALA0-0.0010.01323.9820.0330.0330.0000.0000.0000.000
152A159HIS00.004-0.02622.6420.0580.0580.0000.0000.0000.000
153A160ALA0-0.042-0.00625.7720.0310.0310.0000.0000.0000.000
154A161TYR0-0.019-0.02627.9350.0370.0370.0000.0000.0000.000
155A162ALA00.013-0.00228.6180.0200.0200.0000.0000.0000.000
156A163ARG10.8190.89025.3320.3380.3380.0000.0000.0000.000
157A164ARG10.7460.84829.6050.2880.2880.0000.0000.0000.000
158A165LYS10.8910.95533.7660.2180.2180.0000.0000.0000.000
159A166GLY0-0.0010.01834.7360.0090.0090.0000.0000.0000.000
160A167LEU0-0.0380.00231.0790.0050.0050.0000.0000.0000.000
161A168GLU-1-0.837-0.90530.749-0.268-0.2680.0000.0000.0000.000
162A169ALA00.0100.00928.5880.0130.0130.0000.0000.0000.000
163A170SER0-0.011-0.00127.406-0.002-0.0020.0000.0000.0000.000
164A171ASP-1-0.870-0.92223.109-0.433-0.4330.0000.0000.0000.000
165A172ASP-1-0.711-0.85221.274-0.534-0.5340.0000.0000.0000.000
166A173ALA00.0300.02022.5300.0040.0040.0000.0000.0000.000
167A174GLN0-0.027-0.04123.8790.0380.0380.0000.0000.0000.000
168A175LEU0-0.0200.00025.1170.0220.0220.0000.0000.0000.000
169A176VAL00.002-0.00522.2260.0140.0140.0000.0000.0000.000
170A177GLN00.0050.00525.6850.0110.0110.0000.0000.0000.000
171A178ALA0-0.035-0.01328.1500.0230.0230.0000.0000.0000.000
172A179LEU0-0.069-0.02925.9310.0190.0190.0000.0000.0000.000
173A180GLY0-0.027-0.00930.0130.0110.0110.0000.0000.0000.000
174A181TYR0-0.061-0.04521.6160.0160.0160.0000.0000.0000.000
175A182PRO0-0.019-0.01225.0230.0020.0020.0000.0000.0000.000
176A183VAL0-0.014-0.00821.674-0.039-0.0390.0000.0000.0000.000
177A184ALA00.0130.01319.5100.0390.0390.0000.0000.0000.000
178A185LEU0-0.031-0.02520.738-0.023-0.0230.0000.0000.0000.000
179A186VAL0-0.013-0.00515.5410.0070.0070.0000.0000.0000.000
180A187GLU-1-0.812-0.90917.081-0.348-0.3480.0000.0000.0000.000
181A188GLY00.0240.00917.160-0.072-0.0720.0000.0000.0000.000
182A189GLU-1-0.752-0.85514.691-0.457-0.4570.0000.0000.0000.000
183A190ALA00.0010.00318.791-0.007-0.0070.0000.0000.0000.000
184A191THR00.011-0.00516.8020.0160.0160.0000.0000.0000.000
185A192ALA0-0.0220.00817.171-0.003-0.0030.0000.0000.0000.000
186A193PHE0-0.003-0.01319.032-0.014-0.0140.0000.0000.0000.000
187A194LYS10.8540.91222.0110.3260.3260.0000.0000.0000.000
188A195ILE00.0240.02122.8790.0220.0220.0000.0000.0000.000
189A196THR0-0.097-0.05125.730-0.016-0.0160.0000.0000.0000.000
190A197HIS00.004-0.00328.8580.0150.0150.0000.0000.0000.000
191A198PRO00.020-0.00630.813-0.003-0.0030.0000.0000.0000.000
192A199GLN00.0200.01032.0720.0040.0040.0000.0000.0000.000
193A200ASP-1-0.713-0.85227.574-0.174-0.1740.0000.0000.0000.000
194A201LEU00.0100.01127.027-0.008-0.0080.0000.0000.0000.000
195A202VAL00.0090.00827.9420.0060.0060.0000.0000.0000.000
196A203LEU0-0.0060.00425.9640.0100.0100.0000.0000.0000.000
197A204ALA0-0.024-0.02123.7890.0010.0010.0000.0000.0000.000
198A205GLU-1-0.843-0.92524.105-0.074-0.0740.0000.0000.0000.000
199A206ALA0-0.052-0.00826.5030.0190.0190.0000.0000.0000.000
200A207LEU0-0.004-0.00620.0060.0110.0110.0000.0000.0000.000
201A208ALA0-0.003-0.00820.6550.0070.0070.0000.0000.0000.000
202A209ARG10.8410.91921.2880.0530.0530.0000.0000.0000.000
203A210VAL0-0.0340.00117.9210.0150.0150.0000.0000.0000.000