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

tag_button

FMODB ID: 395ML

Calculation Name: 3DEL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DEL

Chain ID: B

ChEMBL ID:

UniProt ID: O84385

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2793965.718128
FMO2-HF: Nuclear repulsion 2703747.256767
FMO2-HF: Total energy -90218.461361
FMO2-MP2: Total energy -90486.395967


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:34:GLU)


Summations of interaction energy for fragment #1(B:34: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.
6.083.23316.733-7.202-6.6820.058
Interaction energy analysis for fragmet #1(B:34:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.864 / q_NPA : -0.916
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].
3B36PHE00.0060.0083.801-1.1681.750-0.008-1.544-1.3660.005
4B37ILE0-0.019-0.0175.308-4.878-4.8780.0000.0000.0000.000
5B38VAL00.0030.0018.550-1.901-1.9010.0000.0000.0000.000
6B39GLY00.0020.00712.335-0.391-0.3910.0000.0000.0000.000
7B40THR00.000-0.04114.962-1.195-1.1950.0000.0000.0000.000
8B41ASN00.003-0.01018.406-0.489-0.4890.0000.0000.0000.000
9B42ALA00.0250.02321.339-0.441-0.4410.0000.0000.0000.000
10B43THR0-0.056-0.05123.069-0.531-0.5310.0000.0000.0000.000
11B44TYR0-0.085-0.05026.061-0.426-0.4260.0000.0000.0000.000
12B45PRO00.0410.03926.9490.3650.3650.0000.0000.0000.000
13B46PRO00.0240.01528.199-0.256-0.2560.0000.0000.0000.000
14B47PHE0-0.023-0.01023.9110.3870.3870.0000.0000.0000.000
15B48GLH0-0.054-0.05921.4650.5060.5060.0000.0000.0000.000
16B49PHE0-0.034-0.01523.490-0.550-0.5500.0000.0000.0000.000
17B50VAL00.0520.03323.3800.4770.4770.0000.0000.0000.000
18B51ASP-1-0.799-0.90724.50812.15212.1520.0000.0000.0000.000
19B52LYS10.9210.94126.451-10.051-10.0510.0000.0000.0000.000
20B53ARG10.9020.95823.631-12.956-12.9560.0000.0000.0000.000
21B54GLY0-0.044-0.01424.1480.1810.1810.0000.0000.0000.000
22B55GLU-1-0.931-0.95818.59817.26817.2680.0000.0000.0000.000
23B56VAL0-0.017-0.00718.723-0.671-0.6710.0000.0000.0000.000
24B57VAL0-0.030-0.01819.7330.6680.6680.0000.0000.0000.000
25B58GLY00.0530.01222.092-0.231-0.2310.0000.0000.0000.000
26B59PHE00.0260.00821.6490.7330.7330.0000.0000.0000.000
27B60ASP-1-0.696-0.82519.42815.21015.2100.0000.0000.0000.000
28B61ILE0-0.064-0.01616.9901.2731.2730.0000.0000.0000.000
29B62ASP-1-0.780-0.87916.67215.69015.6900.0000.0000.0000.000
30B63LEU0-0.0070.00217.3540.5890.5890.0000.0000.0000.000
31B64ALA00.000-0.01013.7810.8540.8540.0000.0000.0000.000
32B65ARG10.9410.97812.610-17.895-17.8950.0000.0000.0000.000
33B66GLU-1-0.804-0.89012.59618.30918.3090.0000.0000.0000.000
34B67ILE0-0.004-0.00711.6800.5600.5600.0000.0000.0000.000
35B68SER0-0.103-0.0598.6041.3651.3650.0000.0000.0000.000
36B69ASN0-0.016-0.0168.7503.4553.4550.0000.0000.0000.000
37B70LYS10.7590.86210.682-16.038-16.0380.0000.0000.0000.000
38B71LEU0-0.066-0.0248.0150.3380.3380.0000.0000.0000.000
39B72GLY00.0010.0257.4202.0812.0810.0000.0000.0000.000
40B73LYS10.7420.8371.861-73.584-79.82016.742-5.538-4.9670.053
41B74THR00.0140.0123.973-6.364-5.893-0.001-0.120-0.3490.000
42B75LEU00.0100.0055.7874.6904.6900.0000.0000.0000.000
43B76ASP-1-0.834-0.8907.32336.71736.7170.0000.0000.0000.000
44B77VAL00.0390.0229.3540.2780.2780.0000.0000.0000.000
45B78ARG10.8510.9007.112-36.042-36.0420.0000.0000.0000.000
46B79GLU-1-0.877-0.94314.13215.18815.1880.0000.0000.0000.000
47B80PHE0-0.050-0.02514.0140.3550.3550.0000.0000.0000.000
48B81SER00.0480.03219.678-0.386-0.3860.0000.0000.0000.000
49B82PHE00.0340.00021.8410.5200.5200.0000.0000.0000.000
50B83ASP-1-0.902-0.95622.74413.12313.1230.0000.0000.0000.000
51B84ALA00.0040.00720.4480.0600.0600.0000.0000.0000.000
52B85LEU0-0.0330.00317.4781.0301.0300.0000.0000.0000.000
53B86ILE00.0280.00517.3501.0581.0580.0000.0000.0000.000
54B87LEU00.0130.01018.1240.5750.5750.0000.0000.0000.000
55B88ASN00.006-0.02614.5361.2381.2380.0000.0000.0000.000
56B89LEU0-0.0160.01613.0161.5161.5160.0000.0000.0000.000
57B90LYS10.8420.89413.781-13.365-13.3650.0000.0000.0000.000
58B91GLN0-0.048-0.01914.7000.3610.3610.0000.0000.0000.000
59B92HIS0-0.091-0.0489.6442.1512.1510.0000.0000.0000.000
60B93ARG10.9080.9719.071-17.147-17.1470.0000.0000.0000.000
61B94ILE0-0.053-0.0179.5351.9631.9630.0000.0000.0000.000
62B95ASP-1-0.797-0.8916.41844.92844.9280.0000.0000.0000.000
63B96ALA0-0.017-0.0149.603-2.014-2.0140.0000.0000.0000.000
64B97VAL0-0.025-0.00113.0580.3500.3500.0000.0000.0000.000
65B98ILE00.0100.01414.657-0.574-0.5740.0000.0000.0000.000
66B99THR0-0.011-0.00418.0760.2190.2190.0000.0000.0000.000
67B100GLY00.1030.06321.378-0.642-0.6420.0000.0000.0000.000
68B101MET0-0.072-0.03221.255-0.567-0.5670.0000.0000.0000.000
69B102SER00.0080.01024.441-0.076-0.0760.0000.0000.0000.000
70B103ILE00.0440.02523.9760.3220.3220.0000.0000.0000.000
71B104THR00.0490.02026.746-0.340-0.3400.0000.0000.0000.000
72B105PRO00.0820.03228.1910.4570.4570.0000.0000.0000.000
73B106SER0-0.045-0.02229.4120.2750.2750.0000.0000.0000.000
74B107ARG10.8990.92124.384-12.000-12.0000.0000.0000.0000.000
75B108LEU00.0040.00424.3250.5110.5110.0000.0000.0000.000
76B109LYS10.8940.96725.268-10.286-10.2860.0000.0000.0000.000
77B110GLU-1-0.885-0.91023.07612.78812.7880.0000.0000.0000.000
78B111ILE0-0.094-0.04219.1580.8080.8080.0000.0000.0000.000
79B112LEU00.0310.02117.508-0.681-0.6810.0000.0000.0000.000
80B113MET0-0.043-0.02419.3880.4700.4700.0000.0000.0000.000
81B114ILE0-0.0040.02017.320-0.510-0.5100.0000.0000.0000.000
82B115PRO00.0470.01420.2940.3010.3010.0000.0000.0000.000
83B116TYR0-0.096-0.07620.7980.2200.2200.0000.0000.0000.000
84B117TYR00.0330.01922.993-0.167-0.1670.0000.0000.0000.000
85B118GLY00.0010.00926.3770.1060.1060.0000.0000.0000.000
86B119GLU-1-0.885-0.93829.8219.4589.4580.0000.0000.0000.000
87B120GLU-1-0.865-0.92831.01210.02110.0210.0000.0000.0000.000
88B121ILE0-0.032-0.01633.007-0.298-0.2980.0000.0000.0000.000
89B122LYS10.8170.89032.980-9.346-9.3460.0000.0000.0000.000
90B123HIS00.0110.00437.752-0.254-0.2540.0000.0000.0000.000
91B124LEU0-0.006-0.00440.0710.1500.1500.0000.0000.0000.000
92B125VAL00.0100.01143.112-0.144-0.1440.0000.0000.0000.000
93B126LEU00.0070.00746.2120.0160.0160.0000.0000.0000.000
94B127VAL0-0.004-0.01048.874-0.086-0.0860.0000.0000.0000.000
95B128PHE00.0520.01351.652-0.027-0.0270.0000.0000.0000.000
96B129LYS10.8770.94255.447-5.370-5.3700.0000.0000.0000.000
97B130GLY0-0.0120.00158.820-0.056-0.0560.0000.0000.0000.000
98B131GLU-1-0.912-0.95959.4595.2485.2480.0000.0000.0000.000
99B132ASN0-0.040-0.03155.657-0.042-0.0420.0000.0000.0000.000
100B133LYS10.9390.96757.824-5.001-5.0010.0000.0000.0000.000
101B134HIS00.0080.00457.2150.0660.0660.0000.0000.0000.000
102B135PRO00.0840.05452.6980.0210.0210.0000.0000.0000.000
103B136LEU0-0.0040.03549.2060.0870.0870.0000.0000.0000.000
104B137PRO00.0360.00752.081-0.095-0.0950.0000.0000.0000.000
105B138LEU00.050-0.00347.531-0.109-0.1090.0000.0000.0000.000
106B139THR00.0180.00851.619-0.033-0.0330.0000.0000.0000.000
107B140GLN0-0.102-0.03753.601-0.198-0.1980.0000.0000.0000.000
108B141TYR0-0.037-0.02153.140-0.159-0.1590.0000.0000.0000.000
109B142ARG10.8960.94556.031-5.438-5.4380.0000.0000.0000.000
110B143SER0-0.034-0.04754.200-0.032-0.0320.0000.0000.0000.000
111B144VAL00.0040.00749.090-0.061-0.0610.0000.0000.0000.000
112B145ALA0-0.0100.00050.2190.0900.0900.0000.0000.0000.000
113B146VAL00.005-0.00343.8940.0580.0580.0000.0000.0000.000
114B147GLN00.011-0.00241.987-0.109-0.1090.0000.0000.0000.000
115B148THR00.0320.00641.6000.0930.0930.0000.0000.0000.000
116B149GLY00.0250.02238.5580.0800.0800.0000.0000.0000.000
117B150THR0-0.056-0.03236.9980.3010.3010.0000.0000.0000.000
118B151TYR0-0.020-0.04434.9540.0650.0650.0000.0000.0000.000
119B152GLN00.0780.02337.2460.1090.1090.0000.0000.0000.000
120B153GLU-1-0.825-0.91140.8407.5497.5490.0000.0000.0000.000
121B154ALA00.0230.01537.744-0.118-0.1180.0000.0000.0000.000
122B155TYR00.0200.00039.714-0.153-0.1530.0000.0000.0000.000
123B156LEU0-0.0010.00040.893-0.154-0.1540.0000.0000.0000.000
124B157GLN0-0.024-0.01941.2460.0020.0020.0000.0000.0000.000
125B158SER0-0.103-0.04640.442-0.054-0.0540.0000.0000.0000.000
126B159LEU0-0.050-0.01442.429-0.095-0.0950.0000.0000.0000.000
127B160SER0-0.025-0.03045.808-0.033-0.0330.0000.0000.0000.000
128B161GLU-1-0.935-0.96448.6156.0866.0860.0000.0000.0000.000
129B162VAL00.0190.01248.667-0.122-0.1220.0000.0000.0000.000
130B163HIS0-0.029-0.00350.0520.1460.1460.0000.0000.0000.000
131B164ILE00.0330.01345.833-0.043-0.0430.0000.0000.0000.000
132B165ARG10.7840.87250.115-6.120-6.1200.0000.0000.0000.000
133B166SER00.0160.00946.014-0.033-0.0330.0000.0000.0000.000
134B167PHE0-0.044-0.02546.939-0.175-0.1750.0000.0000.0000.000
135B168ASP-1-0.818-0.89544.6447.3657.3650.0000.0000.0000.000
136B169SER0-0.061-0.06843.9160.1560.1560.0000.0000.0000.000
137B170THR00.0420.00043.897-0.100-0.1000.0000.0000.0000.000
138B171LEU0-0.0010.00546.363-0.143-0.1430.0000.0000.0000.000
139B172GLU-1-0.839-0.89248.5516.5426.5420.0000.0000.0000.000
140B173VAL0-0.0180.00546.585-0.134-0.1340.0000.0000.0000.000
141B174LEU00.0130.00648.819-0.128-0.1280.0000.0000.0000.000
142B175MET0-0.019-0.01351.908-0.159-0.1590.0000.0000.0000.000
143B176GLU-1-0.740-0.83353.2725.7415.7410.0000.0000.0000.000
144B177VAL00.0010.00653.245-0.131-0.1310.0000.0000.0000.000
145B178MET0-0.023-0.00655.866-0.148-0.1480.0000.0000.0000.000
146B179HIS0-0.018-0.00758.059-0.186-0.1860.0000.0000.0000.000
147B180GLY0-0.030-0.00459.436-0.094-0.0940.0000.0000.0000.000
148B181LYS10.8460.93657.648-5.640-5.6400.0000.0000.0000.000
149B182SER00.0150.00354.7480.0190.0190.0000.0000.0000.000
150B183PRO0-0.061-0.01856.336-0.029-0.0290.0000.0000.0000.000
151B184VAL0-0.0020.00952.353-0.015-0.0150.0000.0000.0000.000
152B185ALA00.0050.00549.3890.0130.0130.0000.0000.0000.000
153B186VAL00.0070.00944.364-0.022-0.0220.0000.0000.0000.000
154B187LEU0-0.042-0.01644.0550.0740.0740.0000.0000.0000.000
155B188GLU-1-0.746-0.84737.5588.3878.3870.0000.0000.0000.000
156B189PRO0-0.010-0.01239.599-0.139-0.1390.0000.0000.0000.000
157B190SER0-0.025-0.04037.835-0.152-0.1520.0000.0000.0000.000
158B191ILE00.0220.00938.817-0.131-0.1310.0000.0000.0000.000
159B192ALA0-0.028-0.02241.856-0.195-0.1950.0000.0000.0000.000
160B193GLN0-0.031-0.02342.650-0.200-0.2000.0000.0000.0000.000
161B194VAL0-0.0090.01941.582-0.122-0.1220.0000.0000.0000.000
162B195VAL00.002-0.02144.753-0.169-0.1690.0000.0000.0000.000
163B196LEU00.0160.00247.255-0.164-0.1640.0000.0000.0000.000
164B197LYS10.8180.91747.615-6.720-6.7200.0000.0000.0000.000
165B198ASP-1-0.871-0.91650.1086.2806.2800.0000.0000.0000.000
166B199PHE0-0.058-0.04550.956-0.123-0.1230.0000.0000.0000.000
167B200PRO00.0420.01854.697-0.001-0.0010.0000.0000.0000.000
168B201ALA0-0.055-0.02557.141-0.051-0.0510.0000.0000.0000.000
169B202LEU0-0.042-0.02052.973-0.049-0.0490.0000.0000.0000.000
170B203SER0-0.0050.00354.856-0.008-0.0080.0000.0000.0000.000
171B204THR0-0.014-0.02849.6520.1000.1000.0000.0000.0000.000
172B205ALA0-0.0090.00450.794-0.110-0.1100.0000.0000.0000.000
173B206THR00.0090.00745.2480.0490.0490.0000.0000.0000.000
174B207ILE0-0.034-0.00445.197-0.135-0.1350.0000.0000.0000.000
175B208ASP-1-0.887-0.94943.4307.3927.3920.0000.0000.0000.000
176B209LEU0-0.055-0.01838.446-0.057-0.0570.0000.0000.0000.000
177B210PRO00.0290.01840.4150.0490.0490.0000.0000.0000.000
178B211GLU-1-0.863-0.94034.5699.3859.3850.0000.0000.0000.000
179B212ASP-1-0.953-0.97835.0788.7768.7760.0000.0000.0000.000
180B213GLN0-0.034-0.02335.4730.1690.1690.0000.0000.0000.000
181B214TRP0-0.034-0.00834.0810.1670.1670.0000.0000.0000.000
182B215VAL0-0.043-0.01631.1810.3490.3490.0000.0000.0000.000
183B216LEU0-0.057-0.03228.688-0.273-0.2730.0000.0000.0000.000
184B217GLY00.0830.05628.2420.2810.2810.0000.0000.0000.000
185B218TYR0-0.031-0.02924.740-0.060-0.0600.0000.0000.0000.000
186B219GLY00.0240.00022.0280.0130.0130.0000.0000.0000.000
187B220ILE0-0.046-0.01315.2980.3170.3170.0000.0000.0000.000
188B221GLY00.0050.00118.077-0.335-0.3350.0000.0000.0000.000
189B222VAL00.003-0.02413.3531.6351.6350.0000.0000.0000.000
190B223ALA00.0390.02614.014-1.328-1.3280.0000.0000.0000.000
191B224SER00.050-0.00315.7840.2560.2560.0000.0000.0000.000
192B225ASP-1-0.881-0.91815.21519.78519.7850.0000.0000.0000.000
193B226ARG10.8210.9017.549-31.961-31.9610.0000.0000.0000.000
194B227PRO00.0620.02514.3500.5830.5830.0000.0000.0000.000
195B228ALA00.0120.00113.244-0.122-0.1220.0000.0000.0000.000
196B229LEU0-0.044-0.0258.7640.5090.5090.0000.0000.0000.000
197B230ALA00.0690.03011.992-0.023-0.0230.0000.0000.0000.000
198B231LEU00.0090.01515.305-0.580-0.5800.0000.0000.0000.000
199B232LYS10.9340.9668.370-29.390-29.3900.0000.0000.0000.000
200B233ILE00.0140.00711.616-0.021-0.0210.0000.0000.0000.000
201B234GLU-1-0.828-0.90414.43613.53913.5390.0000.0000.0000.000
202B235ALA0-0.034-0.01916.015-0.660-0.6600.0000.0000.0000.000
203B236ALA0-0.0010.00114.026-0.533-0.5330.0000.0000.0000.000
204B237VAL00.0190.00216.186-0.650-0.6500.0000.0000.0000.000
205B238GLN0-0.079-0.04819.008-0.959-0.9590.0000.0000.0000.000
206B239GLU-1-0.850-0.89117.84014.86314.8630.0000.0000.0000.000
207B240ILE00.0440.00616.274-0.446-0.4460.0000.0000.0000.000
208B241ARG10.9120.96020.566-13.333-13.3330.0000.0000.0000.000
209B242LYS10.7920.90021.416-13.939-13.9390.0000.0000.0000.000
210B243GLU-1-0.844-0.91820.08514.01414.0140.0000.0000.0000.000
211B244GLY00.0010.01224.205-0.218-0.2180.0000.0000.0000.000
212B245VAL00.0470.02520.106-0.192-0.1920.0000.0000.0000.000
213B246LEU0-0.047-0.02321.9380.0660.0660.0000.0000.0000.000
214B247ALA00.0630.02924.167-0.150-0.1500.0000.0000.0000.000
215B248GLU-1-0.943-0.96624.96211.38411.3840.0000.0000.0000.000
216B249LEU0-0.059-0.03320.348-0.170-0.1700.0000.0000.0000.000
217B250GLU-1-0.894-0.96525.06911.03811.0380.0000.0000.0000.000
218B251GLN0-0.0230.00128.001-0.406-0.4060.0000.0000.0000.000
219B252LYS10.8100.90022.386-13.255-13.2550.0000.0000.0000.000
220B253TRP0-0.078-0.05122.849-0.270-0.2700.0000.0000.0000.000
221B254GLY00.0230.01728.268-0.079-0.0790.0000.0000.0000.000
222B255LEU0-0.004-0.00426.403-0.216-0.2160.0000.0000.0000.000
223B256ASN0-0.031-0.02230.856-0.014-0.0140.0000.0000.0000.000
224B257ASN0-0.050-0.02434.147-0.412-0.4120.0000.0000.0000.000
225B258LEU0-0.0240.00630.692-0.037-0.0370.0000.0000.0000.000
226B259GLU-1-0.871-0.93033.8798.4878.4870.0000.0000.0000.000
227B260HIS0-0.039-0.01533.181-0.123-0.1230.0000.0000.0000.000
228B261HIS00.0170.00832.4250.6140.6140.0000.0000.0000.000
229B262HIS10.8430.90729.713-10.576-10.5760.0000.0000.0000.000
230B263HIS00.0850.05829.354-0.277-0.2770.0000.0000.0000.000
231B264HIS10.8770.95925.915-12.186-12.1860.0000.0000.0000.000
232B265HIS00.0370.02628.0940.4180.4180.0000.0000.0000.000