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: 721YK

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2053377.917112
FMO2-HF: Nuclear repulsion 1980191.286732
FMO2-HF: Total energy -73186.63038
FMO2-MP2: Total energy -73405.373079


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.
-6.7110.7863.356-4.33-6.522-0.025
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 : -0.008 / 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].
3A3VAL0-0.047-0.0463.662-0.8291.355-0.006-1.214-0.9630.003
4A4SER0-0.046-0.0315.7910.3240.3240.0000.0000.0000.000
5A5VAL00.0200.0088.7330.1410.1410.0000.0000.0000.000
6A6LEU0-0.004-0.00211.2540.1760.1760.0000.0000.0000.000
7A7ILE00.029-0.00113.8450.0160.0160.0000.0000.0000.000
8A8PRO0-0.003-0.00217.0650.0720.0720.0000.0000.0000.000
9A9ALA0-0.048-0.02220.6200.0280.0280.0000.0000.0000.000
10A10ALA00.0590.01822.2710.0260.0260.0000.0000.0000.000
11A11GLY0-0.0080.00125.5020.0230.0230.0000.0000.0000.000
12A19GLY00.0570.02831.4700.0060.0060.0000.0000.0000.000
13A20PRO0-0.025-0.02126.716-0.008-0.0080.0000.0000.0000.000
14A21LYS10.8930.93925.0150.2040.2040.0000.0000.0000.000
15A22ALA00.0250.00921.922-0.003-0.0030.0000.0000.0000.000
16A23PHE0-0.004-0.01322.555-0.001-0.0010.0000.0000.0000.000
17A24LEU00.0120.01625.4360.0190.0190.0000.0000.0000.000
18A25GLN00.002-0.01624.438-0.010-0.0100.0000.0000.0000.000
19A26VAL00.0090.00522.750-0.004-0.0040.0000.0000.0000.000
20A27GLY00.0290.01422.966-0.002-0.0020.0000.0000.0000.000
21A28GLY0-0.029-0.00423.3990.0110.0110.0000.0000.0000.000
22A29ARG10.9140.96614.3710.0570.0570.0000.0000.0000.000
23A30THR0-0.041-0.04221.687-0.022-0.0220.0000.0000.0000.000
24A31LEU0-0.035-0.01920.302-0.014-0.0140.0000.0000.0000.000
25A32LEU00.0100.00817.309-0.041-0.0410.0000.0000.0000.000
26A33GLU-1-0.803-0.87316.876-0.125-0.1250.0000.0000.0000.000
27A34TRP0-0.016-0.02215.757-0.014-0.0140.0000.0000.0000.000
28A35THR0-0.058-0.02614.313-0.054-0.0540.0000.0000.0000.000
29A36LEU00.0290.00212.454-0.127-0.1270.0000.0000.0000.000
30A37ALA0-0.047-0.01411.077-0.038-0.0380.0000.0000.0000.000
31A38ALA0-0.020-0.0099.6750.0210.0210.0000.0000.0000.000
32A39PHE00.003-0.0057.731-0.132-0.1320.0000.0000.0000.000
33A40ARG10.9330.9696.894-0.511-0.5110.0000.0000.0000.000
34A41ASP-1-0.858-0.9152.214-0.6780.3961.897-0.748-2.223-0.004
35A42ALA0-0.049-0.0192.805-8.354-5.3720.613-1.948-1.646-0.022
36A43ALA0-0.031-0.0073.1830.1770.6960.017-0.123-0.4140.000
37A44GLU-1-0.732-0.8014.404-0.0350.0870.000-0.017-0.1050.000
38A45VAL00.0070.0148.147-0.191-0.1910.0000.0000.0000.000
39A46LEU0-0.0040.01210.7120.1910.1910.0000.0000.0000.000
40A47VAL00.008-0.00714.311-0.037-0.0370.0000.0000.0000.000
41A48ALA0-0.028-0.00517.2640.0450.0450.0000.0000.0000.000
42A49LEU0-0.002-0.01020.9250.0010.0010.0000.0000.0000.000
43A50PRO0-0.021-0.00123.6460.0020.0020.0000.0000.0000.000
44A51PRO00.0450.01827.4020.0070.0070.0000.0000.0000.000
45A52GLY0-0.0190.00529.1360.0070.0070.0000.0000.0000.000
46A53ALA0-0.078-0.03126.6180.0120.0120.0000.0000.0000.000
47A54GLU-1-0.828-0.91826.264-0.081-0.0810.0000.0000.0000.000
48A55PRO00.0000.00720.753-0.003-0.0030.0000.0000.0000.000
49A56PRO0-0.0030.00320.2110.0250.0250.0000.0000.0000.000
50A57LYS10.8190.89019.9930.0440.0440.0000.0000.0000.000
51A58GLY00.0130.00517.7000.0060.0060.0000.0000.0000.000
52A59LEU0-0.0020.01715.2480.0310.0310.0000.0000.0000.000
53A60GLY00.0120.00511.0410.0290.0290.0000.0000.0000.000
54A61ALA0-0.029-0.02411.071-0.168-0.1680.0000.0000.0000.000
55A62VAL00.0010.01713.0940.0980.0980.0000.0000.0000.000
56A63PHE00.016-0.00615.407-0.061-0.0610.0000.0000.0000.000
57A64LEU00.0190.01318.7960.0250.0250.0000.0000.0000.000
58A65GLU-1-0.859-0.92921.584-0.161-0.1610.0000.0000.0000.000
59A66GLY0-0.003-0.00324.499-0.019-0.0190.0000.0000.0000.000
60A67GLY0-0.053-0.03125.1690.0230.0230.0000.0000.0000.000
61A68ALA00.0120.00028.214-0.002-0.0020.0000.0000.0000.000
62A69THR00.0470.03029.303-0.004-0.0040.0000.0000.0000.000
63A70ARG10.8710.91020.4500.4480.4480.0000.0000.0000.000
64A71GLN00.0720.02424.396-0.030-0.0300.0000.0000.0000.000
65A72ALA00.0230.01125.173-0.017-0.0170.0000.0000.0000.000
66A73SER0-0.005-0.01222.9080.0010.0010.0000.0000.0000.000
67A74VAL0-0.012-0.00519.747-0.019-0.0190.0000.0000.0000.000
68A75ALA0-0.0130.00320.653-0.033-0.0330.0000.0000.0000.000
69A76ARG10.8670.92322.2080.2270.2270.0000.0000.0000.000
70A77LEU0-0.009-0.00817.3310.0000.0000.0000.0000.0000.000
71A78LEU0-0.010-0.00717.024-0.039-0.0390.0000.0000.0000.000
72A79GLU-1-1.004-0.99617.943-0.312-0.3120.0000.0000.0000.000
73A80ALA0-0.013-0.00317.1530.0190.0190.0000.0000.0000.000
74A81ALA0-0.0330.00513.662-0.020-0.0200.0000.0000.0000.000
75A82SER0-0.032-0.06010.9450.0460.0460.0000.0000.0000.000
76A83LEU0-0.026-0.0016.339-0.054-0.0540.0000.0000.0000.000
77A84PRO0-0.0040.0019.8990.0570.0570.0000.0000.0000.000
78A85LEU0-0.028-0.00410.0040.0680.0680.0000.0000.0000.000
79A86VAL00.0130.00510.783-0.133-0.1330.0000.0000.0000.000
80A87LEU0-0.0090.0039.0490.0670.0670.0000.0000.0000.000
81A88VAL00.0060.02013.1190.0390.0390.0000.0000.0000.000
82A89HIS00.0660.01014.456-0.015-0.0150.0000.0000.0000.000
83A90ASP-1-0.806-0.88616.571-0.362-0.3620.0000.0000.0000.000
84A91VAL00.0570.01118.602-0.004-0.0040.0000.0000.0000.000
85A92ALA0-0.049-0.02619.6830.0290.0290.0000.0000.0000.000
86A93ARG10.8850.98418.5290.4190.4190.0000.0000.0000.000
87A94PRO00.0530.03317.288-0.059-0.0590.0000.0000.0000.000
88A95PHE0-0.0040.00715.921-0.019-0.0190.0000.0000.0000.000
89A96VAL0-0.0140.00312.7430.0110.0110.0000.0000.0000.000
90A97SER0-0.025-0.03811.834-0.031-0.0310.0000.0000.0000.000
91A98ARG10.8560.8772.9242.1462.7620.835-0.280-1.171-0.002
92A99GLY00.0060.0057.919-0.227-0.2270.0000.0000.0000.000
93A100LEU00.0000.00710.289-0.082-0.0820.0000.0000.0000.000
94A101VAL00.0180.0087.219-0.006-0.0060.0000.0000.0000.000
95A102ALA00.0090.0086.507-0.161-0.1610.0000.0000.0000.000
96A103ARG10.8050.9108.0670.4930.4930.0000.0000.0000.000
97A104VAL0-0.030-0.01511.7630.0480.0480.0000.0000.0000.000
98A105LEU0-0.004-0.0106.3130.0590.0590.0000.0000.0000.000
99A106GLU-1-0.841-0.8999.755-0.717-0.7170.0000.0000.0000.000
100A107ALA00.0600.02510.9020.1170.1170.0000.0000.0000.000
101A108ALA0-0.0340.01013.0130.1030.1030.0000.0000.0000.000
102A109GLN0-0.029-0.0207.8070.2790.2790.0000.0000.0000.000
103A110ARG10.8160.90513.3990.7530.7530.0000.0000.0000.000
104A111SER0-0.035-0.04716.3720.0840.0840.0000.0000.0000.000
105A112GLY00.0340.01817.2650.0740.0740.0000.0000.0000.000
106A113ALA0-0.009-0.02018.580-0.006-0.0060.0000.0000.0000.000
107A114ALA0-0.0230.01015.9810.0490.0490.0000.0000.0000.000
108A115VAL00.0290.00417.412-0.063-0.0630.0000.0000.0000.000
109A116PRO00.0110.03116.4840.0450.0450.0000.0000.0000.000
110A117VAL0-0.011-0.01118.7410.0340.0340.0000.0000.0000.000
111A118LEU0-0.0080.01121.3940.0020.0020.0000.0000.0000.000
112A119PRO00.011-0.00324.0320.0060.0060.0000.0000.0000.000
113A120VAL00.0250.01727.551-0.001-0.0010.0000.0000.0000.000
114A121PRO0-0.048-0.01028.8470.0080.0080.0000.0000.0000.000
115A122ASP-1-0.860-0.91831.040-0.121-0.1210.0000.0000.0000.000
116A123THR0-0.049-0.04934.588-0.007-0.0070.0000.0000.0000.000
117A124LEU00.0210.02634.125-0.001-0.0010.0000.0000.0000.000
118A125MET0-0.050-0.02137.3350.0040.0040.0000.0000.0000.000
119A126ALA0-0.009-0.00439.969-0.004-0.0040.0000.0000.0000.000
120A127PRO0-0.007-0.03441.3010.0050.0050.0000.0000.0000.000
121A128GLU-1-0.936-0.96444.491-0.092-0.0920.0000.0000.0000.000
122A129GLY00.0130.00047.2220.0040.0040.0000.0000.0000.000
123A130GLU-1-1.036-0.98547.302-0.071-0.0710.0000.0000.0000.000
124A131ALA0-0.029-0.03845.522-0.001-0.0010.0000.0000.0000.000
125A132TYR00.021-0.03143.3800.0020.0020.0000.0000.0000.000
126A133GLY00.0940.08446.106-0.001-0.0010.0000.0000.0000.000
127A134ARG10.9670.99441.9380.1190.1190.0000.0000.0000.000
128A135VAL0-0.0130.00040.921-0.005-0.0050.0000.0000.0000.000
129A136VAL0-0.046-0.02437.7790.0010.0010.0000.0000.0000.000
130A137PRO00.0410.00738.009-0.002-0.0020.0000.0000.0000.000
131A138ARG10.9520.98432.2940.1290.1290.0000.0000.0000.000
132A139GLU-1-0.853-0.93632.887-0.145-0.1450.0000.0000.0000.000
133A140ALA0-0.056-0.01232.679-0.011-0.0110.0000.0000.0000.000
134A141PHE0-0.016-0.00331.662-0.010-0.0100.0000.0000.0000.000
135A142ARG10.8310.89626.1940.2280.2280.0000.0000.0000.000
136A143LEU00.0070.01325.6760.0050.0050.0000.0000.0000.000
137A144VAL00.0430.02522.801-0.018-0.0180.0000.0000.0000.000
138A145GLN0-0.056-0.05219.541-0.002-0.0020.0000.0000.0000.000
139A146THR0-0.064-0.02917.5800.0140.0140.0000.0000.0000.000
140A147PRO00.0440.00412.2090.0570.0570.0000.0000.0000.000
141A148GLN0-0.053-0.05415.2610.0190.0190.0000.0000.0000.000
142A149GLY00.0270.01414.376-0.074-0.0740.0000.0000.0000.000
143A150PHE00.018-0.00715.0860.1220.1220.0000.0000.0000.000
144A151PHE00.0360.04914.856-0.124-0.1240.0000.0000.0000.000
145A152THR0-0.029-0.04413.3160.0700.0700.0000.0000.0000.000
146A153ALA0-0.007-0.01616.1870.0720.0720.0000.0000.0000.000
147A154LEU00.0130.03019.1160.0530.0530.0000.0000.0000.000
148A155LEU00.0210.01518.3610.0480.0480.0000.0000.0000.000
149A156ARG10.8780.93116.3740.5850.5850.0000.0000.0000.000
150A157GLU-1-0.894-0.94422.015-0.271-0.2710.0000.0000.0000.000
151A158ALA0-0.015-0.00223.8820.0320.0320.0000.0000.0000.000
152A159HIS0-0.010-0.02622.8830.0570.0570.0000.0000.0000.000
153A160ALA0-0.036-0.01025.8220.0300.0300.0000.0000.0000.000
154A161TYR0-0.038-0.03727.9440.0360.0360.0000.0000.0000.000
155A162ALA00.0280.01028.7080.0190.0190.0000.0000.0000.000
156A163ARG10.9460.97225.6960.2880.2880.0000.0000.0000.000
157A164ARG10.9170.96030.6150.2350.2350.0000.0000.0000.000
158A165LYS10.8970.96233.7770.1940.1940.0000.0000.0000.000
159A166GLY00.0170.02834.5260.0090.0090.0000.0000.0000.000
160A167LEU0-0.056-0.01030.9270.0050.0050.0000.0000.0000.000
161A168GLU-1-0.899-0.95631.175-0.228-0.2280.0000.0000.0000.000
162A169ALA0-0.006-0.00428.8040.0120.0120.0000.0000.0000.000
163A170SER0-0.0120.00027.649-0.004-0.0040.0000.0000.0000.000
164A171ASP-1-0.857-0.91323.205-0.400-0.4000.0000.0000.0000.000
165A172ASP-1-0.728-0.86521.193-0.481-0.4810.0000.0000.0000.000
166A173ALA00.0300.01522.4460.0050.0050.0000.0000.0000.000
167A174GLN0-0.042-0.05123.7470.0380.0380.0000.0000.0000.000
168A175LEU0-0.036-0.00925.1180.0220.0220.0000.0000.0000.000
169A176VAL00.000-0.00422.2280.0130.0130.0000.0000.0000.000
170A177GLN00.0120.01125.6580.0110.0110.0000.0000.0000.000
171A178ALA0-0.042-0.01428.3660.0200.0200.0000.0000.0000.000
172A179LEU0-0.060-0.02625.6290.0180.0180.0000.0000.0000.000
173A180GLY0-0.029-0.00329.7240.0130.0130.0000.0000.0000.000
174A181TYR0-0.071-0.05621.5460.0140.0140.0000.0000.0000.000
175A182PRO0-0.025-0.00424.8620.0000.0000.0000.0000.0000.000
176A183VAL00.012-0.00721.700-0.039-0.0390.0000.0000.0000.000
177A184ALA00.0010.01519.7710.0350.0350.0000.0000.0000.000
178A185LEU0-0.022-0.01820.753-0.027-0.0270.0000.0000.0000.000
179A186VAL0-0.008-0.00615.6670.0070.0070.0000.0000.0000.000
180A187GLU-1-0.872-0.93517.228-0.346-0.3460.0000.0000.0000.000
181A188GLY00.038-0.00217.269-0.059-0.0590.0000.0000.0000.000
182A189GLU-1-0.757-0.87114.815-0.437-0.4370.0000.0000.0000.000
183A190ALA0-0.0040.00918.878-0.006-0.0060.0000.0000.0000.000
184A191THR00.0330.01017.1290.0150.0150.0000.0000.0000.000
185A192ALA0-0.0170.01616.9790.0040.0040.0000.0000.0000.000
186A193PHE0-0.023-0.01318.794-0.020-0.0200.0000.0000.0000.000
187A194LYS10.8550.90721.8110.2970.2970.0000.0000.0000.000
188A195ILE00.0170.00523.0690.0220.0220.0000.0000.0000.000
189A196THR0-0.097-0.05225.800-0.015-0.0150.0000.0000.0000.000
190A197HIS00.0130.00329.0070.0140.0140.0000.0000.0000.000
191A198PRO00.026-0.00630.927-0.002-0.0020.0000.0000.0000.000
192A199GLN00.016-0.00332.1320.0010.0010.0000.0000.0000.000
193A200ASP-1-0.730-0.84827.473-0.163-0.1630.0000.0000.0000.000
194A201LEU0-0.0020.00127.107-0.006-0.0060.0000.0000.0000.000
195A202VAL00.0110.00727.9130.0050.0050.0000.0000.0000.000
196A203LEU00.0040.00726.3310.0090.0090.0000.0000.0000.000
197A204ALA0-0.027-0.02123.8440.0000.0000.0000.0000.0000.000
198A205GLU-1-0.822-0.93324.016-0.073-0.0730.0000.0000.0000.000
199A206ALA0-0.075-0.01626.1080.0160.0160.0000.0000.0000.000
200A207LEU0-0.004-0.00619.7880.0110.0110.0000.0000.0000.000
201A208ALA0-0.0010.00820.8800.0070.0070.0000.0000.0000.000
202A209ARG10.8520.92221.3690.0490.0490.0000.0000.0000.000
203A210VAL0-0.0210.01118.4050.0160.0160.0000.0000.0000.000