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: 72R2K

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2256985.413504
FMO2-HF: Nuclear repulsion 2181301.164194
FMO2-HF: Total energy -75684.24931
FMO2-MP2: Total energy -75909.282013


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.
-188.871-201.59367.805-30.633-24.450.161
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 : -0.760 / q_NPA : -0.815
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].
3A3ASN0-0.046-0.0342.418-22.341-16.3621.491-3.590-3.8800.024
4A4VAL00.0050.0063.8250.4990.6580.0020.031-0.1920.000
5A5LYS10.9230.9696.934-38.820-38.8200.0000.0000.0000.000
6A6GLU-1-0.767-0.84410.06016.27616.2760.0000.0000.0000.000
7A7ILE0-0.018-0.00611.957-0.083-0.0830.0000.0000.0000.000
8A8THR0-0.033-0.01815.184-1.290-1.2900.0000.0000.0000.000
9A9ASP-1-0.750-0.87218.48613.25313.2530.0000.0000.0000.000
10A10ALA0-0.026-0.00719.0810.7500.7500.0000.0000.0000.000
11A11THR00.012-0.00820.078-0.311-0.3110.0000.0000.0000.000
12A12LYS10.8130.90318.232-16.476-16.4760.0000.0000.0000.000
13A13GLU-1-0.856-0.90119.88714.61214.6120.0000.0000.0000.000
14A14PRO00.018-0.00314.9610.1540.1540.0000.0000.0000.000
15A15TYR0-0.023-0.05111.981-1.200-1.2000.0000.0000.0000.000
16A16ASN00.0310.02817.8090.1410.1410.0000.0000.0000.000
17A17SER00.0010.01219.107-0.607-0.6070.0000.0000.0000.000
18A18VAL0-0.0060.00216.348-0.160-0.1600.0000.0000.0000.000
19A19VAL0-0.017-0.01319.745-0.538-0.5380.0000.0000.0000.000
20A20ALA0-0.027-0.01620.9730.5880.5880.0000.0000.0000.000
21A21PHE00.0350.00222.245-0.723-0.7230.0000.0000.0000.000
22A22VAL00.0330.01323.2570.3080.3080.0000.0000.0000.000
23A23GLY00.0110.00122.8930.2100.2100.0000.0000.0000.000
24A24GLY0-0.002-0.00619.4580.4230.4230.0000.0000.0000.000
25A25THR0-0.054-0.00616.5970.0720.0720.0000.0000.0000.000
26A26GLY00.0500.04319.413-0.334-0.3340.0000.0000.0000.000
27A27VAL00.0040.00518.6800.5570.5570.0000.0000.0000.000
28A28VAL0-0.025-0.00521.092-0.700-0.7000.0000.0000.0000.000
29A29VAL0-0.026-0.01922.8750.4130.4130.0000.0000.0000.000
30A30GLY00.0360.00825.011-0.093-0.0930.0000.0000.0000.000
31A31LYS10.8750.94028.551-8.704-8.7040.0000.0000.0000.000
32A32ASN0-0.0030.01331.1640.0050.0050.0000.0000.0000.000
33A33THR0-0.010-0.02228.291-0.240-0.2400.0000.0000.0000.000
34A34ILE00.0070.00624.0780.4310.4310.0000.0000.0000.000
35A35VAL0-0.0120.00021.378-0.403-0.4030.0000.0000.0000.000
36A36THR0-0.005-0.02921.1430.6020.6020.0000.0000.0000.000
37A37ASN00.014-0.01118.3650.1360.1360.0000.0000.0000.000
38A38LYS10.8680.92422.056-11.372-11.3720.0000.0000.0000.000
39A39HIS00.0250.00820.032-0.703-0.7030.0000.0000.0000.000
40A40ILE0-0.0300.00720.853-0.315-0.3150.0000.0000.0000.000
41A41ALA00.0290.01724.465-0.297-0.2970.0000.0000.0000.000
42A42LYS10.8340.89027.574-10.145-10.1450.0000.0000.0000.000
43A43SER0-0.042-0.03326.622-0.306-0.3060.0000.0000.0000.000
44A44ASN0-0.002-0.01528.032-0.012-0.0120.0000.0000.0000.000
45A45ASP-1-0.838-0.92329.9698.5428.5420.0000.0000.0000.000
46A46ILE0-0.031-0.01432.364-0.292-0.2920.0000.0000.0000.000
47A47PHE0-0.035-0.01431.863-0.177-0.1770.0000.0000.0000.000
48A48LYS10.7900.90734.256-8.545-8.5450.0000.0000.0000.000
49A49ASN00.0130.02430.713-0.140-0.1400.0000.0000.0000.000
50A50ARG10.7980.86631.374-8.661-8.6610.0000.0000.0000.000
51A51VAL0-0.0120.00326.6170.2820.2820.0000.0000.0000.000
52A52SER0-0.018-0.01725.058-0.169-0.1690.0000.0000.0000.000
53A53ALA00.0000.00924.4560.6390.6390.0000.0000.0000.000
54A54HIS00.0100.00921.309-0.573-0.5730.0000.0000.0000.000
55A55HIS0-0.0210.00522.152-0.574-0.5740.0000.0000.0000.000
56A56SER00.0260.00119.9470.8360.8360.0000.0000.0000.000
57A57SER0-0.052-0.05319.637-0.667-0.6670.0000.0000.0000.000
58A58LYS10.8960.93421.090-14.930-14.9300.0000.0000.0000.000
59A59GLY00.0160.03023.570-0.200-0.2000.0000.0000.0000.000
60A60LYS10.9240.98224.175-11.513-11.5130.0000.0000.0000.000
61A61GLY00.0090.00326.3270.2060.2060.0000.0000.0000.000
62A62GLY00.0530.02526.692-0.354-0.3540.0000.0000.0000.000
63A63GLY00.0100.02528.198-0.318-0.3180.0000.0000.0000.000
64A64ASN0-0.072-0.04329.1190.7490.7490.0000.0000.0000.000
65A65TYR0-0.025-0.03629.631-0.424-0.4240.0000.0000.0000.000
66A66ASP-1-0.773-0.84931.8318.9058.9050.0000.0000.0000.000
67A67VAL00.0200.00530.8750.1080.1080.0000.0000.0000.000
68A68LYS10.7950.89933.619-8.790-8.7900.0000.0000.0000.000
69A69ASP-1-0.831-0.90134.6818.6968.6960.0000.0000.0000.000
70A70ILE00.005-0.00930.0230.3540.3540.0000.0000.0000.000
71A71VAL00.0060.01531.284-0.268-0.2680.0000.0000.0000.000
72A72GLU-1-0.807-0.89229.22910.32810.3280.0000.0000.0000.000
73A73TYR0-0.024-0.00826.898-0.319-0.3190.0000.0000.0000.000
74A74PRO00.007-0.00129.1810.0990.0990.0000.0000.0000.000
75A75GLY00.0020.02128.794-0.155-0.1550.0000.0000.0000.000
76A76LYS10.9370.96524.084-11.673-11.6730.0000.0000.0000.000
77A77GLU-1-0.838-0.93022.69712.02712.0270.0000.0000.0000.000
78A78ASP-1-0.805-0.89220.27812.73912.7390.0000.0000.0000.000
79A79LEU0-0.014-0.01721.4740.5870.5870.0000.0000.0000.000
80A80ALA00.005-0.00623.927-0.609-0.6090.0000.0000.0000.000
81A81ILE0-0.024-0.00625.4360.4970.4970.0000.0000.0000.000
82A82VAL00.004-0.00827.255-0.371-0.3710.0000.0000.0000.000
83A83HIS10.7920.87829.368-9.318-9.3180.0000.0000.0000.000
84A84VAL00.0130.01930.225-0.075-0.0750.0000.0000.0000.000
85A85HIS00.0320.01133.162-0.030-0.0300.0000.0000.0000.000
86A86GLU-1-0.778-0.88234.2488.9338.9330.0000.0000.0000.000
87A87THR0-0.022-0.00635.0500.0970.0970.0000.0000.0000.000
88A88SER00.0470.00334.212-0.154-0.1540.0000.0000.0000.000
89A89THR00.0230.00036.217-0.170-0.1700.0000.0000.0000.000
90A90GLU-1-0.872-0.90933.8489.2709.2700.0000.0000.0000.000
91A91GLY00.0000.00938.057-0.139-0.1390.0000.0000.0000.000
92A92LEU0-0.042-0.00732.825-0.031-0.0310.0000.0000.0000.000
93A93ASN0-0.021-0.03634.8090.1710.1710.0000.0000.0000.000
94A94PHE00.0650.03527.4540.2440.2440.0000.0000.0000.000
95A95ASN0-0.007-0.01830.0360.6450.6450.0000.0000.0000.000
96A96LYS10.8890.95531.050-8.757-8.7570.0000.0000.0000.000
97A97ASN0-0.052-0.03628.6980.1640.1640.0000.0000.0000.000
98A98VAL0-0.0170.01525.3260.4300.4300.0000.0000.0000.000
99A99SER0-0.018-0.01322.313-0.220-0.2200.0000.0000.0000.000
100A100TYR0-0.045-0.04324.1990.0110.0110.0000.0000.0000.000
101A101THR00.0210.00618.3700.0090.0090.0000.0000.0000.000
102A102LYS10.8550.93020.961-14.903-14.9030.0000.0000.0000.000
103A103PHE00.000-0.00320.2920.8210.8210.0000.0000.0000.000
104A104ALA00.0090.00217.881-0.268-0.2680.0000.0000.0000.000
105A105ASP-1-0.974-0.96319.61514.64514.6450.0000.0000.0000.000
106A106GLY0-0.029-0.00120.137-0.144-0.1440.0000.0000.0000.000
107A107ALA00.002-0.01514.7330.7950.7950.0000.0000.0000.000
108A108LYS10.9200.95414.990-19.943-19.9430.0000.0000.0000.000
109A109VAL00.010-0.00112.6671.5721.5720.0000.0000.0000.000
110A110LYS10.9110.9529.727-27.359-27.3590.0000.0000.0000.000
111A111ASP-1-0.831-0.8989.66526.18126.1810.0000.0000.0000.000
112A112ARG10.7790.8401.656-131.548-146.17333.970-11.567-7.7780.130
113A113ILE0-0.050-0.0226.463-5.675-5.6750.0000.0000.0000.000
114A114SER00.000-0.0316.2119.8949.8940.0000.0000.0000.000
115A115VAL0-0.028-0.0147.756-4.455-4.4550.0000.0000.0000.000
116A116ILE00.0150.0099.8120.8230.8230.0000.0000.0000.000
117A117GLY00.023-0.00812.517-1.461-1.4610.0000.0000.0000.000
118A118TYR0-0.074-0.04314.6780.3920.3920.0000.0000.0000.000
119A119PRO0-0.042-0.00811.676-0.972-0.9720.0000.0000.0000.000
120A120LYS10.8750.91114.087-17.039-17.0390.0000.0000.0000.000
121A121GLY00.0330.02617.645-0.259-0.2590.0000.0000.0000.000
122A122ALA00.0670.03719.614-0.435-0.4350.0000.0000.0000.000
123A123GLN0-0.003-0.01619.982-0.191-0.1910.0000.0000.0000.000
124A124THR0-0.009-0.00316.836-0.373-0.3730.0000.0000.0000.000
125A125LYS10.8400.91620.309-11.909-11.9090.0000.0000.0000.000
126A126TYR0-0.012-0.00120.029-0.155-0.1550.0000.0000.0000.000
127A127LYS10.8390.91917.045-15.708-15.7080.0000.0000.0000.000
128A128MET00.0040.02515.0070.6000.6000.0000.0000.0000.000
129A129PHE0-0.023-0.02510.8150.1160.1160.0000.0000.0000.000
130A130GLU-1-0.784-0.8597.95030.52930.5290.0000.0000.0000.000
131A131SER0-0.050-0.0365.5183.9543.9540.0000.0000.0000.000
132A132THR0-0.022-0.0071.587-23.045-33.44820.959-7.382-3.1740.065
133A133GLY00.0240.0032.8214.4297.0872.832-2.559-2.9310.001
134A134THR0-0.049-0.0243.597-2.259-1.9240.0110.164-0.5110.001
135A135ILE00.0110.0206.188-3.343-3.3430.0000.0000.0000.000
136A136ASN0-0.053-0.0476.581-1.251-1.2510.0000.0000.0000.000
137A137HIS0-0.017-0.01710.349-2.507-2.5070.0000.0000.0000.000
138A138ILE00.0170.01413.5430.4460.4460.0000.0000.0000.000
139A139SER0-0.0130.00916.417-0.870-0.8700.0000.0000.0000.000
140A140GLY00.0270.00919.498-0.308-0.3080.0000.0000.0000.000
141A141THR0-0.021-0.02321.0750.4580.4580.0000.0000.0000.000
142A142PHE0-0.0270.00014.3480.3820.3820.0000.0000.0000.000
143A143MET0-0.0200.00313.3810.4380.4380.0000.0000.0000.000
144A144GLU-1-0.809-0.8808.99421.11421.1140.0000.0000.0000.000
145A145PHE00.032-0.0046.9480.8160.8160.0000.0000.0000.000
146A146ASP-1-0.774-0.8722.91150.24051.5320.093-0.515-0.869-0.001
147A147ALA00.0330.0311.917-4.727-6.1677.299-3.249-2.609-0.034
148A148TYR0-0.097-0.0733.834-6.108-5.7150.000-0.072-0.3210.000
149A149ALA00.0130.0205.3700.5240.630-0.001-0.006-0.0990.000
150A150GLN00.0120.0188.853-2.265-2.2650.0000.0000.0000.000
151A151PRO00.1130.02712.1560.1010.1010.0000.0000.0000.000
152A152GLY0-0.0150.02015.477-0.165-0.1650.0000.0000.0000.000
153A153ASN0-0.031-0.04211.761-0.041-0.0410.0000.0000.0000.000
154A154SER00.0120.01814.4790.4880.4880.0000.0000.0000.000
155A155GLY00.0500.03016.870-0.537-0.5370.0000.0000.0000.000
156A156SER0-0.031-0.01813.440-0.132-0.1320.0000.0000.0000.000
157A157PRO00.0180.01414.6960.2660.2660.0000.0000.0000.000
158A158VAL0-0.010-0.00210.3681.6081.6080.0000.0000.0000.000
159A159LEU00.0050.00111.620-1.930-1.9300.0000.0000.0000.000
160A160ASN00.0520.00210.9043.2743.2740.0000.0000.0000.000
161A161SER00.007-0.00511.316-0.178-0.1780.0000.0000.0000.000
162A162LYS10.8130.89112.261-18.300-18.3000.0000.0000.0000.000
163A163HIS00.0210.01312.501-1.132-1.1320.0000.0000.0000.000
164A164GLU-1-0.799-0.86015.49216.17716.1770.0000.0000.0000.000
165A165LEU0-0.030-0.03215.7251.4301.4300.0000.0000.0000.000
166A166ILE0-0.013-0.01313.123-0.957-0.9570.0000.0000.0000.000
167A167GLY00.013-0.01715.704-1.087-1.0870.0000.0000.0000.000
168A168ILE0-0.0360.00415.4610.6550.6550.0000.0000.0000.000
169A169LEU0-0.0080.00910.573-0.092-0.0920.0000.0000.0000.000
170A170TYR0-0.037-0.01614.290-0.892-0.8920.0000.0000.0000.000
171A171ALA0-0.0180.00714.527-0.704-0.7040.0000.0000.0000.000
172A172GLY00.0770.05011.1941.2691.2690.0000.0000.0000.000
173A173SER0-0.073-0.0339.660-1.307-1.3070.0000.0000.0000.000
174A174GLY00.0540.04011.5130.4830.4830.0000.0000.0000.000
175A175LYS10.8370.91413.809-15.012-15.0120.0000.0000.0000.000
176A176ASP-1-0.769-0.91213.42815.89715.8970.0000.0000.0000.000
177A177GLU-1-0.884-0.8869.24720.39120.3910.0000.0000.0000.000
178A178SER0-0.024-0.0288.226-0.413-0.4130.0000.0000.0000.000
179A179GLU-1-0.832-0.9502.42424.19526.8451.150-1.864-1.936-0.025
180A180LYS10.8060.9024.221-19.453-19.279-0.001-0.024-0.1500.000
181A181ASN0-0.0240.0026.432-3.893-3.8930.0000.0000.0000.000
182A182PHE00.0270.0009.1350.7870.7870.0000.0000.0000.000
183A183GLY00.026-0.00912.408-0.077-0.0770.0000.0000.0000.000
184A184VAL0-0.030-0.02314.343-0.650-0.6500.0000.0000.0000.000
185A185TYR00.0360.01216.2990.4800.4800.0000.0000.0000.000
186A186PHE00.0380.01518.026-0.968-0.9680.0000.0000.0000.000
187A187THR00.0300.00920.966-0.056-0.0560.0000.0000.0000.000
188A188PRO00.0560.00523.647-0.085-0.0850.0000.0000.0000.000
189A189GLN00.0240.02226.826-0.312-0.3120.0000.0000.0000.000
190A190LEU00.0000.00622.569-0.234-0.2340.0000.0000.0000.000
191A191LYS10.8750.93021.158-14.759-14.7590.0000.0000.0000.000
192A192GLU-1-0.854-0.92826.4229.5049.5040.0000.0000.0000.000
193A193PHE0-0.0170.00427.422-0.266-0.2660.0000.0000.0000.000
194A194ILE00.0120.00723.900-0.223-0.2230.0000.0000.0000.000
195A195GLN00.0100.00128.279-0.244-0.2440.0000.0000.0000.000
196A196ASN0-0.031-0.02130.451-0.483-0.4830.0000.0000.0000.000
197A197ASN0-0.060-0.02431.197-0.549-0.5490.0000.0000.0000.000
198A198ILE0-0.0160.01628.3820.0930.0930.0000.0000.0000.000
199A199GLU-1-0.819-0.89432.4358.4528.4520.0000.0000.0000.000
200A200LYS10.8580.92934.356-9.188-9.1880.0000.0000.0000.000