FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: Q19RY

Calculation Name: 2WD5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WD5

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CU62

Base Structure: X-ray

Registration Date: 2023-06-21

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2136105.835675
FMO2-HF: Nuclear repulsion 2057451.893787
FMO2-HF: Total energy -78653.941888
FMO2-MP2: Total energy -78879.989315


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(B:492:LYS)


Summations of interaction energy for fragment #1(B:492:LYS)
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.
35.03638.5070.829-1.645-2.654-0.001
Interaction energy analysis for fragmet #1(B:492:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.023 / q_NPA : 0.990
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].
3B494GLN0-0.055-0.0333.0770.6632.7820.005-0.984-1.1390.003
4B495LEU00.0310.0132.5412.0133.0600.826-0.617-1.256-0.004
5B496LEU00.0750.0555.5632.9252.9250.0000.0000.0000.000
6B497ARG10.9710.9817.63923.73523.7350.0000.0000.0000.000
7B498ALA00.0300.0238.5351.8451.8450.0000.0000.0000.000
8B499ALA0-0.021-0.00610.2401.4391.4390.0000.0000.0000.000
9B500THR0-0.072-0.03912.2891.0751.0750.0000.0000.0000.000
10B501GLY00.0330.02814.1520.9450.9450.0000.0000.0000.000
11B502LYS10.9740.95916.13912.95012.9500.0000.0000.0000.000
12B503ALA0-0.0080.00517.1050.0940.0940.0000.0000.0000.000
13B504ILE00.0420.03317.0590.2860.2860.0000.0000.0000.000
14B505LEU0-0.025-0.01912.324-0.185-0.1850.0000.0000.0000.000
15B506ASN00.0180.00416.327-0.577-0.5770.0000.0000.0000.000
16B507GLY00.0920.05919.1360.3200.3200.0000.0000.0000.000
17B508ILE0-0.036-0.02115.4290.1610.1610.0000.0000.0000.000
18B509ASP-1-0.911-0.97215.249-16.695-16.6950.0000.0000.0000.000
19B510SER0-0.047-0.03117.9220.2050.2050.0000.0000.0000.000
20B511ILE00.0030.01120.0830.4110.4110.0000.0000.0000.000
21B512ASN00.0360.01016.3950.7400.7400.0000.0000.0000.000
22B513LYS10.9210.96919.22913.82113.8210.0000.0000.0000.000
23B514VAL00.0190.01322.3540.3260.3260.0000.0000.0000.000
24B515LEU0-0.0140.00021.0120.4240.4240.0000.0000.0000.000
25B516GLU-1-0.850-0.92319.915-13.973-13.9730.0000.0000.0000.000
26B517HIS0-0.036-0.00123.4830.1730.1730.0000.0000.0000.000
27B518PHE00.010-0.02026.7900.4010.4010.0000.0000.0000.000
28B519ARG10.8780.94119.96213.81613.8160.0000.0000.0000.000
29B520ARG10.9080.95123.79212.25412.2540.0000.0000.0000.000
30B521LYS10.8990.94227.7639.6119.6110.0000.0000.0000.000
31B522GLY00.0250.04230.1190.2960.2960.0000.0000.0000.000
32B523ILE0-0.033-0.01631.3950.3500.3500.0000.0000.0000.000
33B524ASN0-0.032-0.02831.221-0.046-0.0460.0000.0000.0000.000
34B525GLN00.0710.03530.519-0.384-0.3840.0000.0000.0000.000
35B526HIS00.0250.00530.041-0.337-0.3370.0000.0000.0000.000
36B527VAL00.0160.01127.307-0.116-0.1160.0000.0000.0000.000
37B528GLN0-0.005-0.00522.616-0.581-0.5810.0000.0000.0000.000
38B529ASN0-0.013-0.00425.510-0.708-0.7080.0000.0000.0000.000
39B530GLY00.0590.03927.7510.0710.0710.0000.0000.0000.000
40B531TYR0-0.058-0.02519.546-0.062-0.0620.0000.0000.0000.000
41B532HIS0-0.020-0.03122.294-0.627-0.6270.0000.0000.0000.000
42B533GLY00.0360.04618.763-0.507-0.5070.0000.0000.0000.000
43B534ILE0-0.045-0.02314.9480.5590.5590.0000.0000.0000.000
44B535VAL00.015-0.00118.881-0.274-0.2740.0000.0000.0000.000
45B536MET0-0.042-0.02312.728-0.116-0.1160.0000.0000.0000.000
46B537ASN0-0.022-0.00613.124-1.190-1.1900.0000.0000.0000.000
47B538ASN0-0.048-0.04615.676-0.200-0.2000.0000.0000.0000.000
48B539PHE0-0.031-0.01618.1460.6400.6400.0000.0000.0000.000
49B540GLU-1-0.922-0.96716.158-17.107-17.1070.0000.0000.0000.000
50B541CYS00.014-0.00318.4720.6830.6830.0000.0000.0000.000
51B542GLU-1-0.921-0.95318.834-13.813-13.8130.0000.0000.0000.000
52B543PRO00.0590.00717.2670.3730.3730.0000.0000.0000.000
53B544ALA0-0.0040.01919.3340.0180.0180.0000.0000.0000.000
54B545PHE00.000-0.02122.1400.4070.4070.0000.0000.0000.000
55B546TYR00.0180.01115.321-0.161-0.1610.0000.0000.0000.000
56B547THR00.0730.02819.764-0.290-0.2900.0000.0000.0000.000
57B548CYS00.0130.02821.6440.0980.0980.0000.0000.0000.000
58B549VAL00.0350.00521.2540.2330.2330.0000.0000.0000.000
59B550GLU-1-0.786-0.87917.183-15.193-15.1930.0000.0000.0000.000
60B551VAL0-0.064-0.03921.0020.0280.0280.0000.0000.0000.000
61B552THR0-0.0060.01523.8090.3050.3050.0000.0000.0000.000
62B553ALA00.0120.01722.7040.2660.2660.0000.0000.0000.000
63B554GLY00.0200.00922.6340.0700.0700.0000.0000.0000.000
64B555ASN00.010-0.01821.132-1.024-1.0240.0000.0000.0000.000
65B556ARG10.9460.97822.3399.5319.5310.0000.0000.0000.000
66B557LEU00.0390.00917.854-0.051-0.0510.0000.0000.0000.000
67B558PHE0-0.026-0.04015.290-0.581-0.5810.0000.0000.0000.000
68B559TYR0-0.0030.02120.0310.3350.3350.0000.0000.0000.000
69B560HIS00.0660.02920.087-0.626-0.6260.0000.0000.0000.000
70B561ILE00.0100.01922.0780.5460.5460.0000.0000.0000.000
71B562VAL0-0.034-0.01324.385-0.307-0.3070.0000.0000.0000.000
72B563ASP-1-0.804-0.90727.105-9.749-9.7490.0000.0000.0000.000
73B564SER0-0.046-0.05430.1520.3450.3450.0000.0000.0000.000
74B565ASP-1-0.798-0.92032.145-8.232-8.2320.0000.0000.0000.000
75B566GLU-1-0.879-0.93634.374-7.998-7.9980.0000.0000.0000.000
76B567VAL0-0.090-0.03228.643-0.087-0.0870.0000.0000.0000.000
77B568SER0-0.037-0.04629.711-0.330-0.3300.0000.0000.0000.000
78B569THR00.0030.01030.698-0.196-0.1960.0000.0000.0000.000
79B570LYS10.9590.99732.2548.3128.3120.0000.0000.0000.000
80B571ILE00.025-0.00125.882-0.081-0.0810.0000.0000.0000.000
81B572LEU00.0230.00528.893-0.207-0.2070.0000.0000.0000.000
82B573MET0-0.0200.00330.8610.0490.0490.0000.0000.0000.000
83B574GLU-1-0.912-0.98530.301-8.788-8.7880.0000.0000.0000.000
84B575PHE00.0130.02424.197-0.146-0.1460.0000.0000.0000.000
85B576ASN00.004-0.01929.005-0.250-0.2500.0000.0000.0000.000
86B577LYS10.9210.98831.7448.5358.5350.0000.0000.0000.000
87B578MET0-0.130-0.05828.825-0.011-0.0110.0000.0000.0000.000
88B579ASN0-0.020-0.00329.400-0.153-0.1530.0000.0000.0000.000
89B580LEU0-0.029-0.00624.571-0.301-0.3010.0000.0000.0000.000
90B581PRO0-0.067-0.04222.6620.1810.1810.0000.0000.0000.000
91B582GLY00.0270.03323.670-0.307-0.3070.0000.0000.0000.000
92B583GLU-1-0.919-0.97723.566-10.350-10.3500.0000.0000.0000.000
93B584VAL0-0.043-0.02523.648-0.508-0.5080.0000.0000.0000.000
94B585THR0-0.0200.00124.9700.3780.3780.0000.0000.0000.000
95B586PHE00.0370.00225.491-0.417-0.4170.0000.0000.0000.000
96B587LEU0-0.0160.00125.0320.3150.3150.0000.0000.0000.000
97B588PRO00.009-0.00128.126-0.208-0.2080.0000.0000.0000.000
98B589LEU00.0170.00227.8890.2860.2860.0000.0000.0000.000
99B590ASN0-0.0300.00731.5560.0550.0550.0000.0000.0000.000
100B591LYS10.9010.95534.3177.8767.8760.0000.0000.0000.000
101B592LEU0-0.067-0.01930.0010.1380.1380.0000.0000.0000.000
102B593ASP-1-0.915-0.96034.666-7.289-7.2890.0000.0000.0000.000
103B594VAL0-0.049-0.01633.077-0.057-0.0570.0000.0000.0000.000
104B595ARG10.9460.96636.5037.1157.1150.0000.0000.0000.000
105B596ASP-1-0.916-0.95738.235-7.493-7.4930.0000.0000.0000.000
106B597THR0-0.061-0.02737.6220.1230.1230.0000.0000.0000.000
107B598ALA00.0290.02239.218-0.112-0.1120.0000.0000.0000.000
108B599TYR0-0.042-0.05434.052-0.034-0.0340.0000.0000.0000.000
109B600PRO00.0270.01639.5240.1050.1050.0000.0000.0000.000
110B601GLU-1-0.931-0.94040.774-6.930-6.9300.0000.0000.0000.000
111B602THR0-0.081-0.05339.3000.0490.0490.0000.0000.0000.000
112B603ASN00.0560.01439.953-0.186-0.1860.0000.0000.0000.000
113B604ASP-1-0.975-0.99138.329-7.435-7.4350.0000.0000.0000.000
114B605ALA0-0.006-0.00735.579-0.153-0.1530.0000.0000.0000.000
115B606ILE00.0030.01430.7350.0710.0710.0000.0000.0000.000
116B607PRO00.0570.02232.664-0.182-0.1820.0000.0000.0000.000
117B608MET00.0340.06226.111-0.257-0.2570.0000.0000.0000.000
118B609ILE00.023-0.00927.460-0.367-0.3670.0000.0000.0000.000
119B610SER0-0.096-0.05728.137-0.193-0.1930.0000.0000.0000.000
120B611LYS10.9230.96425.9339.8649.8640.0000.0000.0000.000
121B612LEU0-0.0280.01322.329-0.532-0.5320.0000.0000.0000.000
122B613ARG10.9230.97920.58913.23213.2320.0000.0000.0000.000
123B614TYR00.010-0.04221.770-0.670-0.6700.0000.0000.0000.000
124B615ASN00.0210.01123.3500.8190.8190.0000.0000.0000.000
125B616PRO00.0910.04225.1530.0500.0500.0000.0000.0000.000
126B617ARG10.9330.98424.98911.26711.2670.0000.0000.0000.000
127B618PHE0-0.058-0.03822.3660.2010.2010.0000.0000.0000.000
128B619ASP-1-0.770-0.86127.207-9.364-9.3640.0000.0000.0000.000
129B620LYS10.9730.98329.7258.0538.0530.0000.0000.0000.000
130B621ALA00.0340.01926.5730.0760.0760.0000.0000.0000.000
131B622PHE00.0160.00921.438-0.015-0.0150.0000.0000.0000.000
132B623LYS10.9550.97027.1578.6178.6170.0000.0000.0000.000
133B624HIS0-0.0220.00829.2240.2940.2940.0000.0000.0000.000
134B625VAL0-0.104-0.05724.9250.1040.1040.0000.0000.0000.000
135B626PHE00.021-0.00622.752-0.058-0.0580.0000.0000.0000.000
136B627GLY00.0040.01628.8470.1260.1260.0000.0000.0000.000
137B628LYS10.8880.95932.1658.1108.1100.0000.0000.0000.000
138B629THR00.0170.01429.4030.1610.1610.0000.0000.0000.000
139B630LEU00.0140.00431.863-0.120-0.1200.0000.0000.0000.000
140B631ILE0-0.009-0.01927.314-0.173-0.1730.0000.0000.0000.000
141B632CYS0-0.033-0.00731.6880.1840.1840.0000.0000.0000.000
142B633ARG10.9600.98033.1647.5247.5240.0000.0000.0000.000
143B634SER00.0480.01434.729-0.097-0.0970.0000.0000.0000.000
144B635MET00.0500.01734.7180.0340.0340.0000.0000.0000.000
145B636GLU-1-0.981-0.99035.964-6.984-6.9840.0000.0000.0000.000
146B637VAL00.0890.04337.9000.1060.1060.0000.0000.0000.000
147B638SER00.002-0.01535.187-0.006-0.0060.0000.0000.0000.000
148B639THR0-0.025-0.00937.5270.0970.0970.0000.0000.0000.000
149B640GLN0-0.0150.00340.4740.0380.0380.0000.0000.0000.000
150B641LEU00.023-0.00538.6190.1300.1300.0000.0000.0000.000
151B642ALA0-0.016-0.01138.1180.0540.0540.0000.0000.0000.000
152B643ARG10.9050.96640.0936.7526.7520.0000.0000.0000.000
153B644ALA0-0.026-0.01643.6360.0980.0980.0000.0000.0000.000
154B645PHE00.0040.00541.7760.1130.1130.0000.0000.0000.000
155B646THR0-0.014-0.01241.346-0.097-0.0970.0000.0000.0000.000
156B647MET0-0.052-0.02736.641-0.121-0.1210.0000.0000.0000.000
157B648ASP-1-0.841-0.90233.346-8.264-8.2640.0000.0000.0000.000
158B649CYS0-0.017-0.00133.930-0.008-0.0080.0000.0000.0000.000
159B650ILE0-0.032-0.00426.869-0.087-0.0870.0000.0000.0000.000
160B651THR00.0470.04330.558-0.053-0.0530.0000.0000.0000.000
161B652LEU00.038-0.00426.222-0.260-0.2600.0000.0000.0000.000
162B653GLU-1-0.943-0.97325.557-10.211-10.2110.0000.0000.0000.000
163B654GLY0-0.030-0.01526.311-0.190-0.1900.0000.0000.0000.000
164B655ASP-1-0.929-0.96127.098-9.059-9.0590.0000.0000.0000.000
165B656GLN0-0.002-0.02528.811-0.025-0.0250.0000.0000.0000.000
166B657VAL0-0.009-0.00832.1420.1780.1780.0000.0000.0000.000
167B658SER0-0.0130.00635.4770.0500.0500.0000.0000.0000.000
168B659HIS0-0.014-0.02436.4430.2930.2930.0000.0000.0000.000
169B660ARG10.8870.93139.1437.4157.4150.0000.0000.0000.000
170B661GLY00.0160.01339.8980.1380.1380.0000.0000.0000.000
171B662ALA0-0.051-0.01436.068-0.008-0.0080.0000.0000.0000.000
172B663LEU00.0500.02835.769-0.083-0.0830.0000.0000.0000.000
173B664THR0-0.075-0.04629.493-0.114-0.1140.0000.0000.0000.000
174B665GLY00.0710.03030.101-0.034-0.0340.0000.0000.0000.000
175B666GLY0-0.012-0.00128.6850.1350.1350.0000.0000.0000.000
176B667TYR0-0.0250.00523.0310.1550.1550.0000.0000.0000.000
177B668TYR0-0.001-0.00622.108-0.367-0.3670.0000.0000.0000.000
178B669ASP-1-0.873-0.93418.366-13.461-13.4610.0000.0000.0000.000
179B670THR00.0100.00415.408-0.129-0.1290.0000.0000.0000.000
180B671ARG10.8970.92612.53316.81216.8120.0000.0000.0000.000
181B672LYS10.8120.93814.97413.31813.3180.0000.0000.0000.000
182B673SER00.0720.00814.841-0.426-0.4260.0000.0000.0000.000
183B674ARG10.9080.94713.03913.92913.9290.0000.0000.0000.000
184B675LEU0-0.040-0.03112.422-1.322-1.3220.0000.0000.0000.000
185B676GLU-1-0.932-0.94511.397-19.431-19.4310.0000.0000.0000.000
186B677LEU00.0480.0167.615-1.141-1.1410.0000.0000.0000.000
187B678GLN0-0.068-0.0357.840-2.215-2.2150.0000.0000.0000.000
188B679LYS10.9620.9939.82519.40919.4090.0000.0000.0000.000
189B680ASP-1-0.845-0.9476.870-27.223-27.2230.0000.0000.0000.000
190B681VAL0-0.101-0.0564.176-3.837-3.660-0.001-0.022-0.1530.000
191B682ARG10.8850.9645.62217.89417.8940.0000.0000.0000.000
192B683LYS10.8810.9417.56523.70223.7020.0000.0000.0000.000
193B684ALA0-0.070-0.0094.083-0.957-0.829-0.001-0.022-0.1060.000
194B685GLU-1-0.960-0.9676.186-21.991-21.9910.0000.0000.0000.000