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: MV7VZ

Calculation Name: 2W7U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W7U

Chain ID: A

ChEMBL ID:

UniProt ID: Q2FXC2

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2252466.008928
FMO2-HF: Nuclear repulsion 2176782.726611
FMO2-HF: Total energy -75683.282317
FMO2-MP2: Total energy -75908.182317


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:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-172.138-163.67344.14-27.921-24.6820.144
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.749 / q_NPA : -0.834
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].
3A3ASN0-0.047-0.0242.707-16.196-10.8270.460-2.875-2.9540.015
4A4VAL00.000-0.0023.933-0.205-0.0800.0010.013-0.1390.000
5A5LYS10.9380.9687.198-32.856-32.8560.0000.0000.0000.000
6A6GLU-1-0.836-0.91110.25416.46816.4680.0000.0000.0000.000
7A7ILE0-0.028-0.01012.402-0.108-0.1080.0000.0000.0000.000
8A8THR0-0.024-0.01815.693-1.166-1.1660.0000.0000.0000.000
9A9ASP-1-0.766-0.87718.97412.72012.7200.0000.0000.0000.000
10A10ALA0-0.0010.00219.5770.7030.7030.0000.0000.0000.000
11A11THR00.006-0.01620.547-0.205-0.2050.0000.0000.0000.000
12A12LYS10.7830.89518.767-15.713-15.7130.0000.0000.0000.000
13A13GLU-1-0.934-0.94720.27714.28114.2810.0000.0000.0000.000
14A14PRO00.023-0.00315.4610.1560.1560.0000.0000.0000.000
15A15TYR0-0.007-0.03312.488-1.078-1.0780.0000.0000.0000.000
16A16ASN00.0630.04018.2200.2670.2670.0000.0000.0000.000
17A17SER0-0.0040.01119.514-0.620-0.6200.0000.0000.0000.000
18A18VAL00.0050.01016.727-0.128-0.1280.0000.0000.0000.000
19A19VAL0-0.015-0.00820.151-0.544-0.5440.0000.0000.0000.000
20A20ALA0-0.017-0.01821.0510.5850.5850.0000.0000.0000.000
21A21PHE00.0280.00322.226-0.720-0.7200.0000.0000.0000.000
22A22VAL00.0340.01223.3030.3080.3080.0000.0000.0000.000
23A23GLY0-0.007-0.01222.8900.2030.2030.0000.0000.0000.000
24A24GLY0-0.004-0.00819.2890.4310.4310.0000.0000.0000.000
25A25THR0-0.057-0.01116.7140.0040.0040.0000.0000.0000.000
26A26GLY00.0480.03619.254-0.307-0.3070.0000.0000.0000.000
27A27VAL00.0080.00118.6490.5340.5340.0000.0000.0000.000
28A28VAL0-0.0130.00321.061-0.694-0.6940.0000.0000.0000.000
29A29VAL0-0.015-0.01323.1590.4160.4160.0000.0000.0000.000
30A30GLY00.0330.00325.269-0.093-0.0930.0000.0000.0000.000
31A31LYS10.9630.99428.814-8.633-8.6330.0000.0000.0000.000
32A32ASN00.0280.03431.5320.0940.0940.0000.0000.0000.000
33A33THR0-0.012-0.01928.055-0.241-0.2410.0000.0000.0000.000
34A34ILE00.0050.00223.8930.4220.4220.0000.0000.0000.000
35A35VAL0-0.0060.00521.198-0.399-0.3990.0000.0000.0000.000
36A36THR00.008-0.01121.0430.6210.6210.0000.0000.0000.000
37A37ASN00.018-0.00518.5290.1420.1420.0000.0000.0000.000
38A38LYS10.9040.95622.056-11.320-11.3200.0000.0000.0000.000
39A39HIS00.0210.00719.993-0.631-0.6310.0000.0000.0000.000
40A40ILE0-0.0230.00520.717-0.296-0.2960.0000.0000.0000.000
41A41ALA00.0270.01424.463-0.294-0.2940.0000.0000.0000.000
42A42LYS10.9040.94927.486-10.256-10.2560.0000.0000.0000.000
43A43SER0-0.053-0.03026.624-0.321-0.3210.0000.0000.0000.000
44A44ASN00.003-0.00727.934-0.057-0.0570.0000.0000.0000.000
45A45ASP-1-0.902-0.95329.9098.5998.5990.0000.0000.0000.000
46A46ILE0-0.043-0.02632.473-0.298-0.2980.0000.0000.0000.000
47A47PHE0-0.031-0.01532.190-0.180-0.1800.0000.0000.0000.000
48A48LYS10.8590.95034.132-8.454-8.4540.0000.0000.0000.000
49A49ASN00.0210.02430.552-0.101-0.1010.0000.0000.0000.000
50A50ARG10.9220.96631.449-8.634-8.6340.0000.0000.0000.000
51A51VAL0-0.0120.00826.6540.2800.2800.0000.0000.0000.000
52A52SER0-0.014-0.00325.420-0.141-0.1410.0000.0000.0000.000
53A53ALA00.0200.01024.8260.6150.6150.0000.0000.0000.000
54A54HIS00.0110.00921.778-0.473-0.4730.0000.0000.0000.000
55A55HIS0-0.055-0.01122.462-0.555-0.5550.0000.0000.0000.000
56A56SER00.035-0.00320.3650.7930.7930.0000.0000.0000.000
57A57SER0-0.066-0.04719.973-0.711-0.7110.0000.0000.0000.000
58A58LYS10.8990.93921.199-14.693-14.6930.0000.0000.0000.000
59A59GLY00.0230.03424.052-0.198-0.1980.0000.0000.0000.000
60A60LYS10.9270.98924.675-11.306-11.3060.0000.0000.0000.000
61A61GLY00.009-0.00126.7860.2040.2040.0000.0000.0000.000
62A62GLY00.0450.02027.178-0.347-0.3470.0000.0000.0000.000
63A63GLY00.0220.04028.660-0.303-0.3030.0000.0000.0000.000
64A64ASN0-0.039-0.03329.4840.6960.6960.0000.0000.0000.000
65A65TYR0-0.033-0.04729.960-0.410-0.4100.0000.0000.0000.000
66A66ASP-1-0.850-0.92231.8918.8708.8700.0000.0000.0000.000
67A67VAL00.001-0.00630.7940.1210.1210.0000.0000.0000.000
68A68LYS10.8300.91633.472-8.674-8.6740.0000.0000.0000.000
69A69ASP-1-0.842-0.92534.5918.6108.6100.0000.0000.0000.000
70A70ILE00.012-0.00130.2320.3680.3680.0000.0000.0000.000
71A71VAL0-0.0090.00731.179-0.270-0.2700.0000.0000.0000.000
72A72GLU-1-0.865-0.94829.25210.23210.2320.0000.0000.0000.000
73A73TYR0-0.020-0.00626.969-0.321-0.3210.0000.0000.0000.000
74A74PRO00.0130.00129.1790.0820.0820.0000.0000.0000.000
75A75GLY0-0.0030.01828.789-0.155-0.1550.0000.0000.0000.000
76A76LYS10.9470.96424.071-11.711-11.7110.0000.0000.0000.000
77A77GLU-1-0.861-0.94322.79112.11812.1180.0000.0000.0000.000
78A78ASP-1-0.831-0.91620.24112.73912.7390.0000.0000.0000.000
79A79LEU0-0.028-0.02421.4740.5810.5810.0000.0000.0000.000
80A80ALA0-0.008-0.01323.896-0.604-0.6040.0000.0000.0000.000
81A81ILE0-0.025-0.00525.3530.4990.4990.0000.0000.0000.000
82A82VAL00.009-0.00527.365-0.375-0.3750.0000.0000.0000.000
83A83HIS10.8010.90129.258-9.303-9.3030.0000.0000.0000.000
84A84VAL00.0100.02030.203-0.074-0.0740.0000.0000.0000.000
85A85HIS00.0260.00533.022-0.064-0.0640.0000.0000.0000.000
86A86GLU-1-0.885-0.95834.5988.7618.7610.0000.0000.0000.000
87A87THR0-0.019-0.00535.4590.0820.0820.0000.0000.0000.000
88A88SER00.0610.03934.581-0.139-0.1390.0000.0000.0000.000
89A89THR0-0.002-0.01436.599-0.163-0.1630.0000.0000.0000.000
90A90GLU-1-0.955-0.98434.4159.1969.1960.0000.0000.0000.000
91A91GLY0-0.0050.00638.441-0.134-0.1340.0000.0000.0000.000
92A92LEU0-0.042-0.00633.204-0.023-0.0230.0000.0000.0000.000
93A93ASN0-0.021-0.02435.2410.1790.1790.0000.0000.0000.000
94A94PHE00.0600.03227.6840.2660.2660.0000.0000.0000.000
95A95ASN00.009-0.01430.4260.6860.6860.0000.0000.0000.000
96A96LYS10.8980.96131.404-8.662-8.6620.0000.0000.0000.000
97A97ASN0-0.053-0.03729.1250.1460.1460.0000.0000.0000.000
98A98VAL0-0.0180.01825.7170.4250.4250.0000.0000.0000.000
99A99SER0-0.020-0.01622.693-0.189-0.1890.0000.0000.0000.000
100A100TYR0-0.049-0.04324.5250.0280.0280.0000.0000.0000.000
101A101THR00.0110.00118.5010.1180.1180.0000.0000.0000.000
102A102LYS10.9360.97221.131-14.614-14.6140.0000.0000.0000.000
103A103PHE0-0.007-0.00120.4290.7870.7870.0000.0000.0000.000
104A104ALA00.0210.00417.908-0.330-0.3300.0000.0000.0000.000
105A105ASP-1-1.005-0.98719.38014.75414.7540.0000.0000.0000.000
106A106GLY0-0.0050.01719.792-0.176-0.1760.0000.0000.0000.000
107A107ALA00.008-0.01114.3700.8300.8300.0000.0000.0000.000
108A108LYS10.9350.96514.606-19.557-19.5570.0000.0000.0000.000
109A109VAL00.0130.00312.3911.6261.6260.0000.0000.0000.000
110A110LYS10.9110.9539.240-27.303-27.3030.0000.0000.0000.000
111A111ASP-1-0.854-0.9169.28126.99926.9990.0000.0000.0000.000
112A112ARG10.7690.8481.662-132.560-137.60324.866-11.944-7.8780.147
113A113ILE0-0.040-0.0216.506-6.282-6.2820.0000.0000.0000.000
114A114SER0-0.014-0.0246.3379.4639.4630.0000.0000.0000.000
115A115VAL0-0.018-0.0067.840-4.263-4.2630.0000.0000.0000.000
116A116ILE00.0130.0119.8170.5920.5920.0000.0000.0000.000
117A117GLY00.007-0.01812.826-1.364-1.3640.0000.0000.0000.000
118A118TYR0-0.076-0.03214.8780.3380.3380.0000.0000.0000.000
119A119PRO0-0.0350.00112.157-0.962-0.9620.0000.0000.0000.000
120A120LYS10.9680.97314.269-17.093-17.0930.0000.0000.0000.000
121A121GLY00.0240.02017.927-0.311-0.3110.0000.0000.0000.000
122A122ALA00.0710.03620.020-0.431-0.4310.0000.0000.0000.000
123A123GLN0-0.031-0.03220.423-0.107-0.1070.0000.0000.0000.000
124A124THR00.0010.00917.213-0.454-0.4540.0000.0000.0000.000
125A125LYS10.8680.93120.658-11.854-11.8540.0000.0000.0000.000
126A126TYR0-0.0080.00320.453-0.179-0.1790.0000.0000.0000.000
127A127LYS10.9180.97317.588-14.711-14.7110.0000.0000.0000.000
128A128MET0-0.0010.02315.3810.5640.5640.0000.0000.0000.000
129A129PHE0-0.018-0.02011.1360.0740.0740.0000.0000.0000.000
130A130GLU-1-0.806-0.8998.40729.63729.6370.0000.0000.0000.000
131A131SER0-0.048-0.0305.6953.7763.7760.0000.0000.0000.000
132A132THR0-0.0090.0061.993-21.358-19.5284.232-3.172-2.8890.046
133A133GLY00.0150.0062.6472.8446.3332.210-3.022-2.6770.009
134A134THR0-0.037-0.0233.450-5.624-5.2180.0160.262-0.6850.002
135A135ILE0-0.0020.0175.671-3.876-3.874-0.0010.0000.0000.000
136A136ASN0-0.008-0.0107.114-0.066-0.0660.0000.0000.0000.000
137A137HIS0-0.020-0.01810.352-2.695-2.6950.0000.0000.0000.000
138A138ILE00.0290.01613.5430.4510.4510.0000.0000.0000.000
139A139SER0-0.0220.00316.420-0.890-0.8900.0000.0000.0000.000
140A140GLY00.0300.01019.498-0.322-0.3220.0000.0000.0000.000
141A141THR0-0.014-0.01521.0920.5110.5110.0000.0000.0000.000
142A142PHE0-0.0250.00413.9860.3640.3640.0000.0000.0000.000
143A143MET0-0.022-0.00513.1770.4750.4750.0000.0000.0000.000
144A144GLU-1-0.920-0.9618.93423.17723.1770.0000.0000.0000.000
145A145PHE00.038-0.0057.0220.7860.7860.0000.0000.0000.000
146A146ASP-1-0.802-0.8892.94557.16258.6860.098-0.552-1.070-0.001
147A147ALA00.0200.0251.920-4.107-5.5577.222-3.148-2.624-0.032
148A148TYR0-0.109-0.0973.685-6.610-6.1990.000-0.073-0.3380.000
149A149ALA00.0070.0145.3690.2210.323-0.001-0.006-0.0950.000
150A150GLN0-0.0100.0018.849-2.173-2.1730.0000.0000.0000.000
151A151PRO00.1190.03312.1480.0800.0800.0000.0000.0000.000
152A152GLY0-0.0200.01715.469-0.223-0.2230.0000.0000.0000.000
153A153ASN0-0.025-0.04011.5550.0560.0560.0000.0000.0000.000
154A154SER00.0340.02714.3280.5260.5260.0000.0000.0000.000
155A155GLY00.0320.02016.813-0.564-0.5640.0000.0000.0000.000
156A156SER0-0.025-0.01813.334-0.197-0.1970.0000.0000.0000.000
157A157PRO00.0200.01614.6000.3070.3070.0000.0000.0000.000
158A158VAL0-0.0030.00310.3551.5411.5410.0000.0000.0000.000
159A159LEU0-0.005-0.00311.826-1.847-1.8470.0000.0000.0000.000
160A160ASN00.0720.02911.0103.4523.4520.0000.0000.0000.000
161A161SER0-0.001-0.01211.265-0.394-0.3940.0000.0000.0000.000
162A162LYS10.9070.95412.263-18.791-18.7910.0000.0000.0000.000
163A163HIS00.0210.01913.235-1.005-1.0050.0000.0000.0000.000
164A164GLU-1-0.897-0.94015.66215.81215.8120.0000.0000.0000.000
165A165LEU0-0.025-0.03715.8341.4011.4010.0000.0000.0000.000
166A166ILE0-0.020-0.01512.927-0.908-0.9080.0000.0000.0000.000
167A167GLY00.017-0.00715.700-1.053-1.0530.0000.0000.0000.000
168A168ILE0-0.043-0.00115.4060.5920.5920.0000.0000.0000.000
169A169LEU00.0000.00810.446-0.036-0.0360.0000.0000.0000.000
170A170TYR0-0.044-0.02114.248-0.879-0.8790.0000.0000.0000.000
171A171ALA0-0.0200.00914.530-0.712-0.7120.0000.0000.0000.000
172A172GLY00.0740.04811.1691.3241.3240.0000.0000.0000.000
173A173SER0-0.079-0.0199.851-1.381-1.3810.0000.0000.0000.000
174A174GLY00.0860.03711.5110.4870.4870.0000.0000.0000.000
175A175LYS10.8130.90013.856-15.159-15.1590.0000.0000.0000.000
176A176ASP-1-0.799-0.93013.50915.79015.7900.0000.0000.0000.000
177A177GLU-1-0.916-0.9049.47319.83919.8390.0000.0000.0000.000
178A178SER0-0.035-0.0198.285-0.350-0.3500.0000.0000.0000.000
179A179GLU-1-0.836-0.9472.06023.88825.4175.038-3.379-3.188-0.042
180A180LYS10.9040.9824.199-19.427-19.256-0.001-0.025-0.1450.000
181A181ASN0-0.046-0.0216.435-4.149-4.1490.0000.0000.0000.000
182A182PHE00.022-0.0039.1250.8330.8330.0000.0000.0000.000
183A183GLY00.017-0.01012.402-0.117-0.1170.0000.0000.0000.000
184A184VAL0-0.028-0.02314.343-0.638-0.6380.0000.0000.0000.000
185A185TYR00.0190.00716.3450.5510.5510.0000.0000.0000.000
186A186PHE00.0350.00818.070-0.989-0.9890.0000.0000.0000.000
187A187THR00.0200.00520.996-0.125-0.1250.0000.0000.0000.000
188A188PRO00.034-0.00723.705-0.109-0.1090.0000.0000.0000.000
189A189GLN00.0280.02326.876-0.321-0.3210.0000.0000.0000.000
190A190LEU00.0160.01322.602-0.244-0.2440.0000.0000.0000.000
191A191LYS10.8980.94522.189-14.308-14.3080.0000.0000.0000.000
192A192GLU-1-0.897-0.94426.4299.5519.5510.0000.0000.0000.000
193A193PHE0-0.025-0.00527.613-0.258-0.2580.0000.0000.0000.000
194A194ILE00.0080.00423.855-0.236-0.2360.0000.0000.0000.000
195A195GLN00.0230.00328.245-0.297-0.2970.0000.0000.0000.000
196A196ASN00.0220.01230.420-0.279-0.2790.0000.0000.0000.000
197A197ASN0-0.074-0.03131.146-0.586-0.5860.0000.0000.0000.000
198A198ILE0-0.0120.01728.6980.0840.0840.0000.0000.0000.000
199A199GLU-1-0.852-0.91732.3638.4338.4330.0000.0000.0000.000
200A200LYS10.8570.92834.464-9.165-9.1650.0000.0000.0000.000