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: 2J1JR

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2265550.311962
FMO2-HF: Nuclear repulsion 2189865.251123
FMO2-HF: Total energy -75685.060839
FMO2-MP2: Total energy -75910.169763


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.
-195.236-211.61474.884-33.314-25.1920.173
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 : -0.734 / q_NPA : -0.807
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].
3A3ASN0-0.018-0.0082.138-25.087-18.9952.979-4.563-4.5080.028
4A4VAL0-0.0160.0033.615-1.685-1.5760.0100.100-0.2200.000
5A5LYS10.8480.9166.709-40.501-40.5010.0000.0000.0000.000
6A6GLU-1-0.744-0.8299.86616.11416.1140.0000.0000.0000.000
7A7ILE0-0.016-0.00811.873-0.261-0.2610.0000.0000.0000.000
8A8THR0-0.026-0.02715.283-1.394-1.3940.0000.0000.0000.000
9A9ASP-1-0.777-0.88018.52013.32413.3240.0000.0000.0000.000
10A10ALA0-0.002-0.00218.6660.7770.7770.0000.0000.0000.000
11A11THR00.000-0.01019.659-0.183-0.1830.0000.0000.0000.000
12A12LYS10.8210.90518.135-16.605-16.6050.0000.0000.0000.000
13A13GLU-1-0.806-0.87419.58414.97814.9780.0000.0000.0000.000
14A14PRO00.005-0.00814.5740.2270.2270.0000.0000.0000.000
15A15TYR0-0.048-0.05911.697-1.481-1.4810.0000.0000.0000.000
16A16ASN00.0230.02017.639-0.033-0.0330.0000.0000.0000.000
17A17SER0-0.0060.00419.748-0.535-0.5350.0000.0000.0000.000
18A18VAL0-0.0020.00116.354-0.219-0.2190.0000.0000.0000.000
19A19VAL0-0.024-0.01919.745-0.647-0.6470.0000.0000.0000.000
20A20ALA0-0.015-0.00220.8890.5780.5780.0000.0000.0000.000
21A21PHE00.0650.00922.155-0.700-0.7000.0000.0000.0000.000
22A22VAL00.0350.01623.0970.3780.3780.0000.0000.0000.000
23A23GLY00.0090.00922.1120.0880.0880.0000.0000.0000.000
24A24GLY0-0.048-0.02518.8910.3860.3860.0000.0000.0000.000
25A25THR0-0.0190.00616.2330.0500.0500.0000.0000.0000.000
26A26GLY00.0420.03119.025-0.480-0.4800.0000.0000.0000.000
27A27VAL00.0010.00118.3790.5390.5390.0000.0000.0000.000
28A28VAL0-0.0200.00820.967-0.618-0.6180.0000.0000.0000.000
29A29VAL0-0.002-0.00922.4980.5930.5930.0000.0000.0000.000
30A30GLY00.0280.00624.798-0.162-0.1620.0000.0000.0000.000
31A31LYS10.8740.94728.382-8.786-8.7860.0000.0000.0000.000
32A32ASN0-0.034-0.01431.5290.0380.0380.0000.0000.0000.000
33A33THR00.009-0.01628.114-0.222-0.2220.0000.0000.0000.000
34A34ILE0-0.0020.00323.7830.4100.4100.0000.0000.0000.000
35A35VAL00.0000.00520.906-0.417-0.4170.0000.0000.0000.000
36A36THR0-0.001-0.02520.7070.5830.5830.0000.0000.0000.000
37A37ASN0-0.006-0.01917.9390.1510.1510.0000.0000.0000.000
38A38LYS10.8560.92821.641-11.413-11.4130.0000.0000.0000.000
39A39HIS00.0300.01319.480-0.774-0.7740.0000.0000.0000.000
40A40ILE0-0.0220.01720.345-0.375-0.3750.0000.0000.0000.000
41A41ALA00.0350.01923.796-0.319-0.3190.0000.0000.0000.000
42A42LYS10.8400.89726.861-10.144-10.1440.0000.0000.0000.000
43A43SER0-0.047-0.04525.922-0.287-0.2870.0000.0000.0000.000
44A44ASN0-0.009-0.01827.267-0.034-0.0340.0000.0000.0000.000
45A45ASP-1-0.826-0.92129.1788.5658.5650.0000.0000.0000.000
46A46ILE0-0.042-0.01331.518-0.299-0.2990.0000.0000.0000.000
47A47PHE0-0.037-0.01531.395-0.215-0.2150.0000.0000.0000.000
48A48LYS10.7900.89234.070-8.597-8.5970.0000.0000.0000.000
49A49ASN00.0100.02630.343-0.104-0.1040.0000.0000.0000.000
50A50ARG10.7910.85531.064-8.747-8.7470.0000.0000.0000.000
51A51VAL0-0.0010.01526.2990.2790.2790.0000.0000.0000.000
52A52SER0-0.045-0.03725.109-0.215-0.2150.0000.0000.0000.000
53A53ALA00.0030.00724.4150.6180.6180.0000.0000.0000.000
54A54HIS00.0130.01421.326-0.614-0.6140.0000.0000.0000.000
55A55HIS0-0.020-0.00321.957-0.338-0.3380.0000.0000.0000.000
56A56SER00.0320.00519.7690.8180.8180.0000.0000.0000.000
57A57SER0-0.046-0.04219.371-0.642-0.6420.0000.0000.0000.000
58A58LYS10.8860.93021.078-14.803-14.8030.0000.0000.0000.000
59A59GLY00.0170.01823.113-0.359-0.3590.0000.0000.0000.000
60A60LYS10.8840.96124.111-11.625-11.6250.0000.0000.0000.000
61A61GLY00.0270.01425.6680.2350.2350.0000.0000.0000.000
62A62GLY00.0320.01626.491-0.396-0.3960.0000.0000.0000.000
63A63GLY00.0310.02628.150-0.334-0.3340.0000.0000.0000.000
64A64ASN0-0.086-0.05529.0280.8070.8070.0000.0000.0000.000
65A65TYR0-0.027-0.03929.597-0.439-0.4390.0000.0000.0000.000
66A66ASP-1-0.780-0.84531.5468.9308.9300.0000.0000.0000.000
67A67VAL00.0180.00330.4730.1390.1390.0000.0000.0000.000
68A68LYS10.7930.89833.182-8.862-8.8620.0000.0000.0000.000
69A69ASP-1-0.817-0.89734.0588.7398.7390.0000.0000.0000.000
70A70ILE00.004-0.00429.4900.3810.3810.0000.0000.0000.000
71A71VAL00.0120.01630.711-0.296-0.2960.0000.0000.0000.000
72A72GLU-1-0.800-0.89528.50910.36310.3630.0000.0000.0000.000
73A73TYR0-0.015-0.00226.288-0.307-0.3070.0000.0000.0000.000
74A74PRO0-0.005-0.01328.5590.0850.0850.0000.0000.0000.000
75A75GLY00.0040.02328.042-0.180-0.1800.0000.0000.0000.000
76A76LYS10.9240.95223.576-11.844-11.8440.0000.0000.0000.000
77A77GLU-1-0.808-0.89322.07912.20812.2080.0000.0000.0000.000
78A78ASP-1-0.795-0.89019.82712.78112.7810.0000.0000.0000.000
79A79LEU0-0.021-0.01220.9000.6290.6290.0000.0000.0000.000
80A80ALA00.011-0.00123.323-0.623-0.6230.0000.0000.0000.000
81A81ILE0-0.025-0.00325.0030.5450.5450.0000.0000.0000.000
82A82VAL00.008-0.00227.126-0.351-0.3510.0000.0000.0000.000
83A83HIS10.7860.87329.183-9.328-9.3280.0000.0000.0000.000
84A84VAL00.0260.01230.019-0.051-0.0510.0000.0000.0000.000
85A85HIS00.0390.02232.988-0.008-0.0080.0000.0000.0000.000
86A86GLU-1-0.780-0.87233.9458.9438.9430.0000.0000.0000.000
87A87THR0-0.017-0.01735.0030.1590.1590.0000.0000.0000.000
88A88SER00.0280.00533.794-0.208-0.2080.0000.0000.0000.000
89A89THR00.0330.00935.865-0.143-0.1430.0000.0000.0000.000
90A90GLU-1-0.835-0.87433.5389.3689.3680.0000.0000.0000.000
91A91GLY00.0100.01137.430-0.122-0.1220.0000.0000.0000.000
92A92LEU0-0.041-0.00532.428-0.042-0.0420.0000.0000.0000.000
93A93ASN00.000-0.01434.8200.0450.0450.0000.0000.0000.000
94A94PHE00.0650.03227.6630.2130.2130.0000.0000.0000.000
95A95ASN0-0.013-0.02429.9890.6500.6500.0000.0000.0000.000
96A96LYS10.8580.93031.482-8.999-8.9990.0000.0000.0000.000
97A97ASN0-0.061-0.02928.7510.1080.1080.0000.0000.0000.000
98A98VAL0-0.0020.01225.0860.3890.3890.0000.0000.0000.000
99A99SER0-0.016-0.01022.124-0.230-0.2300.0000.0000.0000.000
100A100TYR0-0.038-0.03824.271-0.043-0.0430.0000.0000.0000.000
101A101THR00.0130.00118.3190.3390.3390.0000.0000.0000.000
102A102LYS10.8210.90920.697-14.685-14.6850.0000.0000.0000.000
103A103PHE00.011-0.00120.0210.7520.7520.0000.0000.0000.000
104A104ALA00.0290.03317.525-0.124-0.1240.0000.0000.0000.000
105A105ASP-1-0.975-0.99319.57614.18014.1800.0000.0000.0000.000
106A106GLY00.0030.00019.789-0.430-0.4300.0000.0000.0000.000
107A107ALA0-0.037-0.02214.4450.9910.9910.0000.0000.0000.000
108A108LYS10.8610.91214.920-22.249-22.2490.0000.0000.0000.000
109A109VAL00.0280.00812.7191.6771.6770.0000.0000.0000.000
110A110LYS10.9190.9539.958-27.176-27.1760.0000.0000.0000.000
111A111ASP-1-0.796-0.8689.70325.72225.7220.0000.0000.0000.000
112A112ARG10.7890.8521.710-128.224-143.32633.372-10.806-7.4640.121
113A113ILE0-0.050-0.0236.237-5.630-5.6300.0000.0000.0000.000
114A114SER00.009-0.0205.97310.57110.5710.0000.0000.0000.000
115A115VAL0-0.0210.0007.535-4.414-4.4140.0000.0000.0000.000
116A116ILE00.0350.0149.4451.2131.2130.0000.0000.0000.000
117A117GLY00.0250.01212.246-1.309-1.3090.0000.0000.0000.000
118A118TYR0-0.048-0.02114.6320.4690.4690.0000.0000.0000.000
119A119PRO0-0.0320.00211.733-0.947-0.9470.0000.0000.0000.000
120A120LYS10.8530.88713.905-17.051-17.0510.0000.0000.0000.000
121A121GLY00.0450.04017.663-0.350-0.3500.0000.0000.0000.000
122A122ALA00.0570.03819.764-0.349-0.3490.0000.0000.0000.000
123A123GLN0-0.006-0.00919.858-0.183-0.1830.0000.0000.0000.000
124A124THR0-0.011-0.01516.410-0.560-0.5600.0000.0000.0000.000
125A125LYS10.8460.92019.859-11.850-11.8500.0000.0000.0000.000
126A126TYR0-0.014-0.02719.909-0.141-0.1410.0000.0000.0000.000
127A127LYS10.8330.92316.927-15.659-15.6590.0000.0000.0000.000
128A128MET00.0020.02914.9430.6540.6540.0000.0000.0000.000
129A129PHE0-0.036-0.03210.8550.0530.0530.0000.0000.0000.000
130A130GLU-1-0.783-0.8587.80831.02831.0280.0000.0000.0000.000
131A131SER0-0.046-0.0355.2892.8182.8180.0000.0000.0000.000
132A132THR0-0.009-0.0151.530-21.912-36.41826.897-9.303-3.0880.068
133A133GLY00.0440.0072.8380.7624.1252.475-2.898-2.9410.004
134A134THR0-0.065-0.0293.501-3.927-3.8300.0280.378-0.5030.001
135A135ILE0-0.0080.0126.331-2.813-2.8130.0000.0000.0000.000
136A136ASN0-0.051-0.0506.464-1.603-1.6030.0000.0000.0000.000
137A137HIS0-0.009-0.01510.088-2.423-2.4230.0000.0000.0000.000
138A138ILE00.0190.00913.4070.6070.6070.0000.0000.0000.000
139A139SER0-0.0190.00416.271-0.827-0.8270.0000.0000.0000.000
140A140GLY00.0380.02419.517-0.307-0.3070.0000.0000.0000.000
141A141THR0-0.052-0.06821.0960.1050.1050.0000.0000.0000.000
142A142PHE0-0.0260.00614.2720.2680.2680.0000.0000.0000.000
143A143MET0-0.0220.00013.1800.3410.3410.0000.0000.0000.000
144A144GLU-1-0.804-0.8868.87321.49021.4900.0000.0000.0000.000
145A145PHE00.031-0.0036.6690.6400.6400.0000.0000.0000.000
146A146ASP-1-0.735-0.8522.71553.28355.1840.314-0.949-1.2660.000
147A147ALA00.0050.0271.913-7.324-9.0148.440-3.750-2.999-0.037
148A148TYR0-0.081-0.0543.463-6.421-5.7610.005-0.141-0.5240.000
149A149ALA00.0040.0174.7620.8370.954-0.001-0.011-0.1050.000
150A150GLN00.0080.0068.442-2.035-2.0350.0000.0000.0000.000
151A151PRO00.0330.01711.8060.0170.0170.0000.0000.0000.000
152A152GLY00.0540.02715.344-0.080-0.0800.0000.0000.0000.000
153A153ASN00.003-0.01411.3880.1650.1650.0000.0000.0000.000
154A154SER00.0070.01614.0930.3120.3120.0000.0000.0000.000
155A155GLY00.0500.03016.605-0.527-0.5270.0000.0000.0000.000
156A156SER0-0.048-0.04512.850-0.227-0.2270.0000.0000.0000.000
157A157PRO0-0.0140.00614.4770.1330.1330.0000.0000.0000.000
158A158VAL00.003-0.00210.1081.6761.6760.0000.0000.0000.000
159A159LEU0-0.009-0.00311.459-1.962-1.9620.0000.0000.0000.000
160A160ASN00.0490.00110.7773.3393.3390.0000.0000.0000.000
161A161SER00.008-0.00911.201-0.233-0.2330.0000.0000.0000.000
162A162LYS10.8090.89512.115-18.044-18.0440.0000.0000.0000.000
163A163HIS00.0290.01211.985-1.106-1.1060.0000.0000.0000.000
164A164GLU-1-0.787-0.85315.04716.24916.2490.0000.0000.0000.000
165A165LEU0-0.036-0.03015.5841.4861.4860.0000.0000.0000.000
166A166ILE00.002-0.00612.682-1.060-1.0600.0000.0000.0000.000
167A167GLY00.026-0.00815.941-1.032-1.0320.0000.0000.0000.000
168A168ILE0-0.0350.00115.3650.6460.6460.0000.0000.0000.000
169A169LEU0-0.0020.00610.093-0.044-0.0440.0000.0000.0000.000
170A170TYR0-0.043-0.01913.841-0.873-0.8730.0000.0000.0000.000
171A171ALA0-0.030-0.00614.096-0.658-0.6580.0000.0000.0000.000
172A172GLY00.0820.03810.6731.3551.3550.0000.0000.0000.000
173A173SER0-0.067-0.0259.256-1.363-1.3630.0000.0000.0000.000
174A174GLY00.0370.01911.0100.5120.5120.0000.0000.0000.000
175A175LYS10.8680.93713.683-15.371-15.3710.0000.0000.0000.000
176A176ASP-1-0.759-0.90213.00216.13616.1360.0000.0000.0000.000
177A177GLU-1-0.883-0.8788.88720.88020.8800.0000.0000.0000.000
178A178SER0-0.025-0.0167.755-0.278-0.2780.0000.0000.0000.000
179A179GLU-1-0.826-0.9412.59826.96029.2600.365-1.328-1.336-0.012
180A180LYS10.8190.9094.091-19.606-19.3250.000-0.043-0.2380.000
181A181ASN0-0.055-0.0215.842-4.273-4.2730.0000.0000.0000.000
182A182PHE00.0200.0048.6290.7520.7520.0000.0000.0000.000
183A183GLY00.0480.00612.003-0.164-0.1640.0000.0000.0000.000
184A184VAL0-0.024-0.01214.138-0.494-0.4940.0000.0000.0000.000
185A185TYR00.0150.00016.2070.5850.5850.0000.0000.0000.000
186A186PHE00.0410.01418.051-0.953-0.9530.0000.0000.0000.000
187A187THR00.0460.02120.855-0.116-0.1160.0000.0000.0000.000
188A188PRO00.0410.00323.616-0.065-0.0650.0000.0000.0000.000
189A189GLN00.0220.02726.788-0.300-0.3000.0000.0000.0000.000
190A190LEU00.0000.00122.287-0.204-0.2040.0000.0000.0000.000
191A191LYS10.8420.93021.098-14.789-14.7890.0000.0000.0000.000
192A192GLU-1-0.835-0.91626.2349.5179.5170.0000.0000.0000.000
193A193PHE0-0.0240.00427.067-0.249-0.2490.0000.0000.0000.000
194A194ILE00.0220.01323.546-0.219-0.2190.0000.0000.0000.000
195A195GLN00.004-0.01327.973-0.150-0.1500.0000.0000.0000.000
196A196ASN0-0.039-0.02630.166-0.533-0.5330.0000.0000.0000.000
197A197ASN0-0.023-0.01730.698-0.517-0.5170.0000.0000.0000.000
198A198ILE0-0.0370.01027.789-0.036-0.0360.0000.0000.0000.000
199A199GLU-1-0.825-0.88431.7478.4828.4820.0000.0000.0000.000
200A200LYS10.8110.89433.853-9.274-9.2740.0000.0000.0000.000