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: 851MY

Calculation Name: 5WQN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WQN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HWU9

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2402122.703441
FMO2-HF: Nuclear repulsion 2321135.423362
FMO2-HF: Total energy -80987.280079
FMO2-MP2: Total energy -81223.221134


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.
-8.588-0.6921.555-3.142-6.309-0.011
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 : -0.005 / q_NPA : -0.001
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].
3A3ASN0-0.0050.0023.106-2.2530.6580.109-1.455-1.5650.000
4A4VAL00.006-0.0035.3150.5190.606-0.001-0.007-0.0790.000
5A5LEU0-0.0160.0037.9470.2420.2420.0000.0000.0000.000
6A6ILE0-0.0020.00911.1050.0670.0670.0000.0000.0000.000
7A7VAL00.012-0.00713.8330.0630.0630.0000.0000.0000.000
8A8GLY00.0080.01217.1370.0290.0290.0000.0000.0000.000
9A9ALA00.032-0.00215.6490.0160.0160.0000.0000.0000.000
10A10SER0-0.011-0.00117.6010.0360.0360.0000.0000.0000.000
11A11ARG11.0281.01720.4380.1300.1300.0000.0000.0000.000
12A12GLY0-0.012-0.00121.153-0.025-0.0250.0000.0000.0000.000
13A13ILE00.0920.02819.0860.0100.0100.0000.0000.0000.000
14A14GLY00.0500.03417.738-0.021-0.0210.0000.0000.0000.000
15A15LEU0-0.039-0.00416.140-0.032-0.0320.0000.0000.0000.000
16A16GLY00.0400.01015.9200.0240.0240.0000.0000.0000.000
17A17LEU0-0.0020.00114.2640.0210.0210.0000.0000.0000.000
18A18ALA00.0080.00011.704-0.049-0.0490.0000.0000.0000.000
19A19ASP-1-0.851-0.90611.1460.2300.2300.0000.0000.0000.000
20A20ALA00.0570.02212.2460.0950.0950.0000.0000.0000.000
21A21PHE00.000-0.0198.1610.0300.0300.0000.0000.0000.000
22A22LEU0-0.024-0.0027.3800.0760.0760.0000.0000.0000.000
23A23GLN0-0.051-0.0418.1480.3950.3950.0000.0000.0000.000
24A24ARG10.9190.9688.1710.3420.3420.0000.0000.0000.000
25A25GLY0-0.0100.0055.147-0.028-0.0280.0000.0000.0000.000
26A26ALA0-0.055-0.0192.955-1.929-0.1610.317-0.786-1.299-0.007
27A27GLN00.0340.0202.5391.0653.5851.083-0.776-2.827-0.005
28A28VAL0-0.048-0.0243.792-1.104-1.0520.0080.007-0.0670.000
29A29PHE0-0.0010.0006.3300.2730.2730.0000.0000.0000.000
30A30ALA00.0260.01510.248-0.022-0.0220.0000.0000.0000.000
31A31VAL00.0080.01413.4550.0520.0520.0000.0000.0000.000
32A32ALA0-0.009-0.01816.7260.0300.0300.0000.0000.0000.000
33A33ARG11.0021.00420.0540.1620.1620.0000.0000.0000.000
34A34ARG10.9050.94323.1640.1340.1340.0000.0000.0000.000
35A35PRO00.0480.04318.3230.0240.0240.0000.0000.0000.000
36A36GLN00.0800.03420.4530.0120.0120.0000.0000.0000.000
37A37GLY0-0.021-0.00122.4850.0170.0170.0000.0000.0000.000
38A38SER0-0.078-0.04521.0140.0090.0090.0000.0000.0000.000
39A39PRO00.037-0.00121.6630.0100.0100.0000.0000.0000.000
40A40GLY00.0140.00620.5970.0210.0210.0000.0000.0000.000
41A41LEU00.035-0.00115.3750.0200.0200.0000.0000.0000.000
42A42GLN0-0.018-0.00916.8390.0470.0470.0000.0000.0000.000
43A43ALA00.0170.02118.0030.0320.0320.0000.0000.0000.000
44A44LEU0-0.025-0.01213.4140.0480.0480.0000.0000.0000.000
45A45ALA0-0.010-0.00913.1000.0980.0980.0000.0000.0000.000
46A46GLU-1-0.951-0.95713.4030.2860.2860.0000.0000.0000.000
47A47ARG10.8630.93511.279-0.403-0.4030.0000.0000.0000.000
48A48ALA0-0.083-0.0549.0930.1260.1260.0000.0000.0000.000
49A49GLY00.0470.0289.0070.2720.2720.0000.0000.0000.000
50A50GLU-1-0.906-0.9706.9750.0750.0750.0000.0000.0000.000
51A51ARG10.8340.9244.143-3.585-3.0270.039-0.125-0.4720.001
52A52LEU0-0.039-0.0096.171-0.307-0.3070.0000.0000.0000.000
53A53GLN0-0.033-0.0088.047-0.077-0.0770.0000.0000.0000.000
54A54ALA0-0.017-0.00810.630-0.084-0.0840.0000.0000.0000.000
55A55VAL00.0350.01613.635-0.007-0.0070.0000.0000.0000.000
56A56THR0-0.024-0.02816.0780.0330.0330.0000.0000.0000.000
57A57GLY00.0470.01019.884-0.020-0.0200.0000.0000.0000.000
58A58ASP-1-0.877-0.96421.282-0.208-0.2080.0000.0000.0000.000
59A59LEU00.0310.02121.634-0.005-0.0050.0000.0000.0000.000
60A60ASN0-0.019-0.03623.702-0.005-0.0050.0000.0000.0000.000
61A61GLN0-0.0350.00826.3080.0180.0180.0000.0000.0000.000
62A62HIS0-0.002-0.02925.855-0.035-0.0350.0000.0000.0000.000
63A63ASP-1-0.869-0.91624.798-0.275-0.2750.0000.0000.0000.000
64A64CYS0-0.043-0.01519.978-0.021-0.0210.0000.0000.0000.000
65A65ALA00.0390.00719.533-0.038-0.0380.0000.0000.0000.000
66A66GLU-1-0.922-0.95218.692-0.374-0.3740.0000.0000.0000.000
67A67ARG10.8220.89218.8740.2800.2800.0000.0000.0000.000
68A68ILE0-0.033-0.01914.297-0.023-0.0230.0000.0000.0000.000
69A69GLY0-0.016-0.01314.258-0.103-0.1030.0000.0000.0000.000
70A70GLU-1-0.814-0.88414.951-0.392-0.3920.0000.0000.0000.000
71A71MET0-0.0240.00111.7400.0120.0120.0000.0000.0000.000
72A72LEU0-0.048-0.0339.083-0.100-0.1000.0000.0000.0000.000
73A73GLY00.0100.02010.179-0.184-0.1840.0000.0000.0000.000
74A74GLU-1-0.960-1.00210.171-1.320-1.3200.0000.0000.0000.000
75A75ARG10.8800.9635.1501.6361.6360.0000.0000.0000.000
76A76ARG10.8890.9428.0911.6201.6200.0000.0000.0000.000
77A77ILE0-0.008-0.0088.031-0.635-0.6350.0000.0000.0000.000
78A78ASP-1-0.779-0.8715.820-4.673-4.6730.0000.0000.0000.000
79A79ARG10.7820.8589.1431.9901.9900.0000.0000.0000.000
80A80LEU00.0060.01110.830-0.063-0.0630.0000.0000.0000.000
81A81ILE00.0110.01513.5930.1060.1060.0000.0000.0000.000
82A82VAL0-0.001-0.00215.6970.0160.0160.0000.0000.0000.000
83A83ASN0-0.052-0.03618.8810.0440.0440.0000.0000.0000.000
84A84ALA00.0130.00820.5420.0170.0170.0000.0000.0000.000
85A85GLY0-0.020-0.02923.9800.0000.0000.0000.0000.0000.000
86A86ILE0-0.071-0.02027.3610.0100.0100.0000.0000.0000.000
87A87TYR00.0590.01830.703-0.007-0.0070.0000.0000.0000.000
88A88GLY00.0640.03833.787-0.002-0.0020.0000.0000.0000.000
89A89PRO00.0360.01136.3050.0040.0040.0000.0000.0000.000
90A90GLN00.012-0.00938.822-0.005-0.0050.0000.0000.0000.000
91A91GLN00.0210.02140.6790.0020.0020.0000.0000.0000.000
92A92GLN0-0.081-0.04137.115-0.002-0.0020.0000.0000.0000.000
93A93ASP-1-0.816-0.90341.920-0.075-0.0750.0000.0000.0000.000
94A94VAL0-0.027-0.03443.829-0.002-0.0020.0000.0000.0000.000
95A95ALA0-0.052-0.01645.697-0.001-0.0010.0000.0000.0000.000
96A96GLU-1-0.940-0.97846.113-0.070-0.0700.0000.0000.0000.000
97A97ILE0-0.098-0.02439.752-0.002-0.0020.0000.0000.0000.000
98A98ASP-1-0.737-0.85343.122-0.098-0.0980.0000.0000.0000.000
99A99ALA00.002-0.01842.659-0.006-0.0060.0000.0000.0000.000
100A100GLU-1-0.950-0.97640.514-0.106-0.1060.0000.0000.0000.000
101A101GLN00.0390.00538.730-0.009-0.0090.0000.0000.0000.000
102A102THR0-0.033-0.02037.784-0.008-0.0080.0000.0000.0000.000
103A103ALA0-0.016-0.00637.085-0.010-0.0100.0000.0000.0000.000
104A104GLN00.000-0.00233.854-0.009-0.0090.0000.0000.0000.000
105A105LEU0-0.0040.00333.018-0.013-0.0130.0000.0000.0000.000
106A106PHE00.013-0.00732.540-0.014-0.0140.0000.0000.0000.000
107A107LEU0-0.030-0.01131.435-0.018-0.0180.0000.0000.0000.000
108A108THR0-0.031-0.01027.999-0.021-0.0210.0000.0000.0000.000
109A109ASN0-0.034-0.03927.503-0.026-0.0260.0000.0000.0000.000
110A110ALA00.0100.01328.021-0.013-0.0130.0000.0000.0000.000
111A111ILE00.0110.00027.930-0.022-0.0220.0000.0000.0000.000
112A112ALA0-0.033-0.01326.436-0.020-0.0200.0000.0000.0000.000
113A113PRO00.022-0.00123.287-0.034-0.0340.0000.0000.0000.000
114A114LEU00.0410.03322.749-0.045-0.0450.0000.0000.0000.000
115A115ARG10.8950.96224.1200.2500.2500.0000.0000.0000.000
116A116LEU0-0.007-0.00119.128-0.013-0.0130.0000.0000.0000.000
117A117ALA00.0350.00719.315-0.049-0.0490.0000.0000.0000.000
118A118ARG10.9430.96720.0210.2950.2950.0000.0000.0000.000
119A119ALA0-0.0170.01421.873-0.017-0.0170.0000.0000.0000.000
120A120LEU0-0.004-0.01016.007-0.021-0.0210.0000.0000.0000.000
121A121SER0-0.017-0.01216.797-0.102-0.1020.0000.0000.0000.000
122A122GLY00.0160.01517.197-0.050-0.0500.0000.0000.0000.000
123A123ARG10.8910.94013.4040.8760.8760.0000.0000.0000.000
124A124VAL0-0.0100.01412.301-0.257-0.2570.0000.0000.0000.000
125A125SER0-0.082-0.0538.2040.2550.2550.0000.0000.0000.000
126A126ARG10.9700.97411.3790.8670.8670.0000.0000.0000.000
127A127GLY00.0090.01712.177-0.092-0.0920.0000.0000.0000.000
128A128GLY00.0040.01111.710-0.062-0.0620.0000.0000.0000.000
129A129VAL0-0.028-0.01312.5200.1850.1850.0000.0000.0000.000
130A130VAL00.0050.01514.268-0.121-0.1210.0000.0000.0000.000
131A131ALA0-0.010-0.01116.8730.0810.0810.0000.0000.0000.000
132A132PHE0-0.025-0.00718.490-0.016-0.0160.0000.0000.0000.000
133A133MET00.0070.01419.5690.0300.0300.0000.0000.0000.000
134A134SER0-0.020-0.02922.6170.0220.0220.0000.0000.0000.000
135A135SER00.010-0.00826.1820.0160.0160.0000.0000.0000.000
136A136GLN00.0620.02528.893-0.002-0.0020.0000.0000.0000.000
137A137MET0-0.078-0.04431.3040.0050.0050.0000.0000.0000.000
138A138ALA0-0.0050.01331.0080.0050.0050.0000.0000.0000.000
139A139SER0-0.044-0.02832.9350.0030.0030.0000.0000.0000.000
140A140LEU00.003-0.01734.4090.0100.0100.0000.0000.0000.000
141A141ALA0-0.045-0.02437.1050.0070.0070.0000.0000.0000.000
142A142LEU0-0.016-0.00833.4750.0070.0070.0000.0000.0000.000
143A143GLY00.0190.02537.8220.0070.0070.0000.0000.0000.000
144A144LEU00.001-0.01435.1910.0060.0060.0000.0000.0000.000
145A145SER00.018-0.01437.0440.0010.0010.0000.0000.0000.000
146A146ALA0-0.0140.00038.6450.0000.0000.0000.0000.0000.000
147A147THR0-0.005-0.00240.2190.0000.0000.0000.0000.0000.000
148A148MET0-0.0420.00135.771-0.002-0.0020.0000.0000.0000.000
149A149PRO00.0540.03937.917-0.009-0.0090.0000.0000.0000.000
150A150LEU00.0410.02238.600-0.009-0.0090.0000.0000.0000.000
151A151TYR00.0110.00329.604-0.017-0.0170.0000.0000.0000.000
152A152GLY00.0520.03333.796-0.012-0.0120.0000.0000.0000.000
153A153ALA00.0170.01234.514-0.011-0.0110.0000.0000.0000.000
154A154SER0-0.057-0.04432.886-0.012-0.0120.0000.0000.0000.000
155A155LYS10.8660.93026.4710.2130.2130.0000.0000.0000.000
156A156ALA00.0350.02130.641-0.014-0.0140.0000.0000.0000.000
157A157ALA0-0.027-0.01132.763-0.009-0.0090.0000.0000.0000.000
158A158LEU0-0.024-0.00325.241-0.010-0.0100.0000.0000.0000.000
159A159ASN00.0470.02128.307-0.030-0.0300.0000.0000.0000.000
160A160SER0-0.0220.00029.363-0.012-0.0120.0000.0000.0000.000
161A161LEU00.000-0.01029.165-0.006-0.0060.0000.0000.0000.000
162A162VAL00.0030.00024.420-0.013-0.0130.0000.0000.0000.000
163A163ARG10.8800.92027.0650.2350.2350.0000.0000.0000.000
164A164SER0-0.031-0.01729.2410.0060.0060.0000.0000.0000.000
165A165TRP0-0.013-0.00720.756-0.018-0.0180.0000.0000.0000.000
166A166GLU-1-0.833-0.91925.552-0.313-0.3130.0000.0000.0000.000
167A167GLY0-0.020-0.00126.562-0.001-0.0010.0000.0000.0000.000
168A168GLU-1-0.983-0.99427.607-0.305-0.3050.0000.0000.0000.000
169A169PHE0-0.110-0.04822.365-0.017-0.0170.0000.0000.0000.000
170A170GLU-1-0.991-0.98626.420-0.262-0.2620.0000.0000.0000.000
171A171GLU-1-0.864-0.94121.840-0.361-0.3610.0000.0000.0000.000
172A172LEU0-0.072-0.01920.905-0.026-0.0260.0000.0000.0000.000
173A173PRO0-0.021-0.00217.572-0.018-0.0180.0000.0000.0000.000
174A174PHE00.004-0.00915.424-0.114-0.1140.0000.0000.0000.000
175A175SER00.0230.00116.6700.0970.0970.0000.0000.0000.000
176A176LEU0-0.044-0.01118.451-0.056-0.0560.0000.0000.0000.000
177A177LEU0-0.001-0.00618.0540.0490.0490.0000.0000.0000.000
178A178LEU0-0.038-0.00321.444-0.007-0.0070.0000.0000.0000.000
179A179LEU00.0250.00818.5060.0180.0180.0000.0000.0000.000
180A180HIS00.0540.01623.1970.0030.0030.0000.0000.0000.000
181A181PRO00.0240.00523.0140.0020.0020.0000.0000.0000.000
182A182GLY00.0080.02324.2880.0140.0140.0000.0000.0000.000
183A195LEU00.0480.02326.862-0.003-0.0030.0000.0000.0000.000
184A196SER0-0.058-0.02124.8570.0000.0000.0000.0000.0000.000
185A197VAL00.000-0.01920.530-0.015-0.0150.0000.0000.0000.000
186A198GLU-1-0.907-0.94819.9830.0480.0480.0000.0000.0000.000
187A199GLU-1-0.875-0.94619.934-0.052-0.0520.0000.0000.0000.000
188A200SER0-0.040-0.03021.458-0.025-0.0250.0000.0000.0000.000
189A201ALA00.012-0.00716.865-0.031-0.0310.0000.0000.0000.000
190A202ALA00.0210.01116.660-0.045-0.0450.0000.0000.0000.000
191A203GLY0-0.007-0.00517.387-0.024-0.0240.0000.0000.0000.000
192A204LEU0-0.020-0.02318.141-0.032-0.0320.0000.0000.0000.000
193A205VAL0-0.0140.00312.306-0.057-0.0570.0000.0000.0000.000
194A206ALA0-0.032-0.01214.678-0.074-0.0740.0000.0000.0000.000
195A207ALA00.0180.01216.565-0.026-0.0260.0000.0000.0000.000
196A208VAL0-0.023-0.02413.168-0.032-0.0320.0000.0000.0000.000
197A209GLU-1-0.860-0.92310.252-1.279-1.2790.0000.0000.0000.000
198A210ASP-1-0.838-0.90113.552-0.321-0.3210.0000.0000.0000.000
199A211ALA0-0.020-0.00816.5360.0270.0270.0000.0000.0000.000
200A212ALA0-0.0130.00011.916-0.036-0.0360.0000.0000.0000.000
201A213GLY0-0.029-0.01514.0430.0730.0730.0000.0000.0000.000
202A214VAL0-0.078-0.03315.1880.0730.0730.0000.0000.0000.000
203A215ASN00.0230.01517.061-0.034-0.0340.0000.0000.0000.000
204A216ALA00.0740.04419.4780.0470.0470.0000.0000.0000.000
205A217CYS0-0.0150.00221.600-0.032-0.0320.0000.0000.0000.000
206A218ARG10.8770.93020.4070.3650.3650.0000.0000.0000.000
207A219PHE0-0.0050.00124.369-0.019-0.0190.0000.0000.0000.000
208A220VAL00.0320.01522.0440.0190.0190.0000.0000.0000.000
209A221ASP-1-0.808-0.91024.743-0.169-0.1690.0000.0000.0000.000
210A222TYR0-0.035-0.02622.376-0.018-0.0180.0000.0000.0000.000
211A223ARG10.9310.97722.3960.1000.1000.0000.0000.0000.000
212A224ASN0-0.036-0.01920.977-0.013-0.0130.0000.0000.0000.000
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