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: JLZZ9

Calculation Name: 3WHR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WHR

Chain ID: B

ChEMBL ID:

UniProt ID: P54422

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1658909.420027
FMO2-HF: Nuclear repulsion 1589670.974462
FMO2-HF: Total energy -69238.445565
FMO2-MP2: Total energy -69440.434138


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:403:THR)


Summations of interaction energy for fragment #1(B:403:THR)
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.
-27.464-18.95818.568-9.514-17.56-0.078
Interaction energy analysis for fragmet #1(B:403:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : 0.000
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].
3B405HIS00.0870.0752.936-2.5400.2140.284-1.453-1.586-0.004
4B406PHE0-0.0100.0065.1960.1550.166-0.001-0.002-0.0080.000
5B407THR0-0.022-0.0168.934-0.013-0.0130.0000.0000.0000.000
6B408VAL00.011-0.00112.1690.0200.0200.0000.0000.0000.000
7B409ALA00.0290.02015.782-0.008-0.0080.0000.0000.0000.000
8B410ASP-1-0.752-0.86919.165-0.052-0.0520.0000.0000.0000.000
9B411ARG10.9300.96422.6180.0310.0310.0000.0000.0000.000
10B412TRP0-0.107-0.06525.3850.0050.0050.0000.0000.0000.000
11B413GLY00.0350.03624.5300.0010.0010.0000.0000.0000.000
12B414ASN0-0.095-0.05020.673-0.008-0.0080.0000.0000.0000.000
13B415VAL00.003-0.01316.4400.0060.0060.0000.0000.0000.000
14B416VAL0-0.0190.00012.474-0.012-0.0120.0000.0000.0000.000
15B417SER00.0320.00510.9420.0070.0070.0000.0000.0000.000
16B418TYR0-0.051-0.0247.7560.0180.0180.0000.0000.0000.000
17B419THR00.018-0.0042.650-0.222-0.1470.922-0.237-0.760-0.001
18B420THR0-0.042-0.0283.557-0.537-0.0360.012-0.157-0.3560.000
19B421THR0-0.040-0.0612.010-13.839-11.90411.174-6.856-6.253-0.052
20B422ILE0-0.0110.0002.9592.4842.0130.1011.028-0.658-0.001
21B423GLU-1-0.780-0.8703.3520.1190.5670.008-0.138-0.3180.000
22B424GLN0-0.050-0.0212.561-4.863-2.4660.579-1.451-1.525-0.019
23B425LEU0-0.020-0.0173.9270.4620.697-0.001-0.020-0.2140.000
24B426PHE0-0.026-0.0235.589-0.248-0.2480.0000.0000.0000.000
25B427GLY00.0270.0256.185-0.154-0.1540.0000.0000.0000.000
26B428THR0-0.048-0.0517.4290.0360.0360.0000.0000.0000.000
27B429GLY0-0.0280.00210.5230.0160.0160.0000.0000.0000.000
28B430ILE0-0.042-0.01612.4090.0140.0140.0000.0000.0000.000
29B431MET0-0.0210.00013.4500.0060.0060.0000.0000.0000.000
30B432VAL0-0.030-0.01215.737-0.017-0.0170.0000.0000.0000.000
31B433PRO00.0190.00718.3130.0160.0160.0000.0000.0000.000
32B434ASP-1-0.902-0.96621.5240.0070.0070.0000.0000.0000.000
33B435TYR0-0.062-0.02819.773-0.003-0.0030.0000.0000.0000.000
34B436GLY0-0.008-0.00517.7180.0020.0020.0000.0000.0000.000
35B437VAL0-0.015-0.01513.3470.0410.0410.0000.0000.0000.000
36B438ILE00.0050.0099.785-0.024-0.0240.0000.0000.0000.000
37B439LEU0-0.020-0.00211.013-0.034-0.0340.0000.0000.0000.000
38B440ASN00.0100.0247.3590.0500.0500.0000.0000.0000.000
39B441ASN0-0.003-0.0237.5490.0930.0930.0000.0000.0000.000
40B442GLU-1-0.710-0.8664.238-4.731-4.566-0.001-0.042-0.1210.000
41B443LEU0-0.043-0.0148.0070.1490.1490.0000.0000.0000.000
42B444THR0-0.007-0.0079.2570.0480.0480.0000.0000.0000.000
43B445ASP-1-0.860-0.9187.005-0.128-0.1280.0000.0000.0000.000
44B446PHE0-0.077-0.03110.1160.0400.0400.0000.0000.0000.000
45B447ASP-1-0.851-0.92513.824-0.032-0.0320.0000.0000.0000.000
46B448ALA0-0.026-0.02316.786-0.011-0.0110.0000.0000.0000.000
47B449ILE0-0.053-0.02418.1430.0050.0050.0000.0000.0000.000
48B450PRO00.001-0.00321.312-0.002-0.0020.0000.0000.0000.000
49B451GLY00.000-0.00822.9470.0100.0100.0000.0000.0000.000
50B452GLY00.0120.01921.3190.0050.0050.0000.0000.0000.000
51B453ALA00.018-0.00719.918-0.011-0.0110.0000.0000.0000.000
52B454ASN0-0.033-0.03413.485-0.058-0.0580.0000.0000.0000.000
53B455GLU-1-0.838-0.87316.489-0.104-0.1040.0000.0000.0000.000
54B456VAL00.0460.03016.601-0.020-0.0200.0000.0000.0000.000
55B457GLN0-0.029-0.03518.4410.0180.0180.0000.0000.0000.000
56B458PRO00.0060.00619.176-0.026-0.0260.0000.0000.0000.000
57B459ASN0-0.057-0.04019.244-0.001-0.0010.0000.0000.0000.000
58B460LYS10.7800.91017.1070.1320.1320.0000.0000.0000.000
59B461ARG10.9380.95513.0270.2920.2920.0000.0000.0000.000
60B462PRO00.0390.0319.8410.0570.0570.0000.0000.0000.000
61B463LEU0-0.011-0.01211.174-0.071-0.0710.0000.0000.0000.000
62B464SER00.0150.0185.8490.1040.1040.0000.0000.0000.000
63B465SER00.002-0.0036.4260.0550.0550.0000.0000.0000.000
64B466MET0-0.043-0.0132.725-1.401-0.6110.565-0.285-1.071-0.001
65B467THR0-0.012-0.0055.192-0.084-0.072-0.001-0.002-0.0090.000
66B468PRO0-0.0270.0007.0500.0370.0370.0000.0000.0000.000
67B469THR0-0.004-0.0089.2270.0140.0140.0000.0000.0000.000
68B470ILE0-0.013-0.01712.707-0.006-0.0060.0000.0000.0000.000
69B471LEU00.0010.00915.9060.0030.0030.0000.0000.0000.000
70B472PHE00.018-0.00819.048-0.002-0.0020.0000.0000.0000.000
71B473LYS10.8520.90722.6480.0190.0190.0000.0000.0000.000
72B474ASP-1-0.789-0.87026.207-0.019-0.0190.0000.0000.0000.000
73B475ASP-1-0.877-0.92227.221-0.034-0.0340.0000.0000.0000.000
74B476LYS10.8180.89725.6240.0290.0290.0000.0000.0000.000
75B477PRO00.0020.01820.2230.0030.0030.0000.0000.0000.000
76B478VAL00.0370.00521.2000.0020.0020.0000.0000.0000.000
77B479LEU00.0050.01716.8200.0050.0050.0000.0000.0000.000
78B480THR0-0.0070.00612.618-0.006-0.0060.0000.0000.0000.000
79B481VAL00.0140.02111.2440.0090.0090.0000.0000.0000.000
80B482GLY00.0800.0237.823-0.034-0.0340.0000.0000.0000.000
81B483SER00.026-0.0075.674-0.116-0.1160.0000.0000.0000.000
82B484PRO0-0.0190.0092.349-0.650-0.7684.471-1.558-2.7950.001
83B485GLY00.0680.0262.5450.534-1.0550.2502.086-0.747-0.002
84B486GLY00.0740.0533.834-1.382-0.9930.001-0.107-0.2820.001
85B487ALA00.0550.0105.498-0.390-0.362-0.0010.001-0.0270.000
86B488THR0-0.076-0.0537.438-0.182-0.1820.0000.0000.0000.000
87B489ILE0-0.0260.0072.727-0.661-0.1750.206-0.135-0.557-0.001
88B490ILE00.0480.0207.113-0.154-0.1540.0000.0000.0000.000
89B491SER00.001-0.00110.241-0.072-0.0720.0000.0000.0000.000
90B492SER00.013-0.0019.337-0.016-0.0160.0000.0000.0000.000
91B493VAL0-0.0160.0118.946-0.053-0.0530.0000.0000.0000.000
92B494LEU0-0.0170.00011.689-0.031-0.0310.0000.0000.0000.000
93B495GLN0-0.005-0.02114.598-0.029-0.0290.0000.0000.0000.000
94B496THR00.0220.01513.268-0.017-0.0170.0000.0000.0000.000
95B497ILE0-0.020-0.01614.740-0.014-0.0140.0000.0000.0000.000
96B498LEU0-0.009-0.00717.644-0.007-0.0070.0000.0000.0000.000
97B499TYR0-0.005-0.01518.109-0.008-0.0080.0000.0000.0000.000
98B500HIS0-0.040-0.03718.840-0.011-0.0110.0000.0000.0000.000
99B501ILE0-0.066-0.02720.718-0.005-0.0050.0000.0000.0000.000
100B502GLU-1-0.954-0.96922.9950.0190.0190.0000.0000.0000.000
101B503TYR0-0.059-0.03523.6070.0000.0000.0000.0000.0000.000
102B504GLY0-0.024-0.00125.3430.0000.0000.0000.0000.0000.000
103B505MET0-0.049-0.00522.476-0.001-0.0010.0000.0000.0000.000
104B506GLU-1-0.791-0.88722.4320.0130.0130.0000.0000.0000.000
105B507LEU00.0200.01516.6350.0040.0040.0000.0000.0000.000
106B508LYS10.7880.87216.577-0.036-0.0360.0000.0000.0000.000
107B509ALA00.008-0.00718.7510.0060.0060.0000.0000.0000.000
108B510ALA0-0.005-0.00618.9980.0060.0060.0000.0000.0000.000
109B511VAL0-0.032-0.01113.4930.0070.0070.0000.0000.0000.000
110B512GLU-1-0.786-0.87215.6760.0680.0680.0000.0000.0000.000
111B513GLU-1-0.911-0.93717.9210.0610.0610.0000.0000.0000.000
112B514PRO0-0.036-0.00617.9400.0110.0110.0000.0000.0000.000
113B515ARG10.7810.87311.198-0.135-0.1350.0000.0000.0000.000
114B516ILE0-0.031-0.03716.7000.0000.0000.0000.0000.0000.000
115B517TYR0-0.019-0.02012.0960.0410.0410.0000.0000.0000.000
116B518THR00.000-0.01315.527-0.019-0.0190.0000.0000.0000.000
117B519ASN00.0400.05714.9500.0320.0320.0000.0000.0000.000
118B520SER00.000-0.01417.101-0.018-0.0180.0000.0000.0000.000
119B521MET0-0.0070.00520.6080.0080.0080.0000.0000.0000.000
120B522SER0-0.009-0.01421.073-0.009-0.0090.0000.0000.0000.000
121B523SER0-0.050-0.01615.7500.0070.0070.0000.0000.0000.000
122B524TYR00.006-0.01717.857-0.002-0.0020.0000.0000.0000.000
123B525ARG10.8700.92910.998-0.291-0.2910.0000.0000.0000.000
124B526TYR0-0.026-0.03516.349-0.005-0.0050.0000.0000.0000.000
125B527GLU-1-0.711-0.83413.2780.1630.1630.0000.0000.0000.000
126B528ASP-1-0.873-0.96517.1890.0710.0710.0000.0000.0000.000
127B529GLY00.0060.01120.277-0.001-0.0010.0000.0000.0000.000
128B530VAL0-0.0110.00019.990-0.006-0.0060.0000.0000.0000.000
129B531PRO00.000-0.00322.924-0.001-0.0010.0000.0000.0000.000
130B532LYS11.0271.00626.700-0.054-0.0540.0000.0000.0000.000
131B533ASP-1-0.885-0.92527.7700.0450.0450.0000.0000.0000.000
132B534VAL00.0240.00726.290-0.002-0.0020.0000.0000.0000.000
133B535LEU00.0370.02622.334-0.001-0.0010.0000.0000.0000.000
134B536SER0-0.062-0.04326.359-0.001-0.0010.0000.0000.0000.000
135B537LYS10.8900.94929.769-0.039-0.0390.0000.0000.0000.000
136B538LEU00.0060.00024.637-0.003-0.0030.0000.0000.0000.000
137B539ASN00.004-0.01125.6060.0010.0010.0000.0000.0000.000
138B540GLY0-0.021-0.00328.504-0.003-0.0030.0000.0000.0000.000
139B541MET0-0.058-0.02930.573-0.004-0.0040.0000.0000.0000.000
140B542GLY00.0060.01429.841-0.002-0.0020.0000.0000.0000.000
141B543HIS00.0000.02424.4800.0070.0070.0000.0000.0000.000
142B544LYS10.8590.91323.979-0.061-0.0610.0000.0000.0000.000
143B545PHE00.0440.02619.7060.0080.0080.0000.0000.0000.000
144B546GLY00.0500.02921.055-0.009-0.0090.0000.0000.0000.000
145B547THR0-0.008-0.01722.431-0.002-0.0020.0000.0000.0000.000
146B548SER0-0.041-0.01420.188-0.008-0.0080.0000.0000.0000.000
147B549PRO00.0020.02118.7190.0070.0070.0000.0000.0000.000
148B550VAL0-0.065-0.04513.8600.0020.0020.0000.0000.0000.000
149B551ASP-1-0.839-0.91011.3630.1590.1590.0000.0000.0000.000
150B552ILE0-0.091-0.03710.2080.0600.0600.0000.0000.0000.000
151B553GLY00.0630.0617.0820.0080.0080.0000.0000.0000.000
152B554ASN0-0.062-0.0296.731-0.160-0.1600.0000.0000.0000.000
153B555VAL0-0.019-0.0087.387-0.092-0.0920.0000.0000.0000.000
154B556GLN0-0.055-0.0337.9300.0650.0650.0000.0000.0000.000
155B557SER0-0.050-0.04910.587-0.004-0.0040.0000.0000.0000.000
156B558ILE0-0.025-0.01713.4150.0060.0060.0000.0000.0000.000
157B559SER0-0.026-0.01616.5660.0010.0010.0000.0000.0000.000
158B560ILE0-0.045-0.03119.919-0.001-0.0010.0000.0000.0000.000
159B561ASP-1-0.785-0.85823.001-0.011-0.0110.0000.0000.0000.000
160B562HIS0-0.026-0.05024.2070.0000.0000.0000.0000.0000.000
161B563GLU-1-0.978-0.96928.927-0.010-0.0100.0000.0000.0000.000
162B564ASN0-0.101-0.07930.6480.0010.0010.0000.0000.0000.000
163B565GLY0-0.0380.00129.4700.0000.0000.0000.0000.0000.000
164B566THR0-0.068-0.03627.2080.0010.0010.0000.0000.0000.000
165B567PHE00.0250.00321.582-0.003-0.0030.0000.0000.0000.000
166B568LYS10.8680.93020.571-0.001-0.0010.0000.0000.0000.000
167B569GLY00.0210.00517.404-0.008-0.0080.0000.0000.0000.000
168B570VAL0-0.040-0.02114.8380.0100.0100.0000.0000.0000.000
169B571ALA00.0160.01312.745-0.017-0.0170.0000.0000.0000.000
170B572ASP-1-0.746-0.84310.8390.1070.1070.0000.0000.0000.000
171B573SER0-0.022-0.04412.830-0.001-0.0010.0000.0000.0000.000
172B574SER00.0090.0019.719-0.011-0.0110.0000.0000.0000.000
173B575ARG10.8140.8963.4890.5641.0220.000-0.186-0.2730.001
174B576ASN00.0090.01611.733-0.020-0.0200.0000.0000.0000.000
175B577GLY0-0.0080.00212.6060.0020.0020.0000.0000.0000.000
176B578ALA0-0.012-0.02113.3670.0070.0070.0000.0000.0000.000
177B579ALA00.0060.00914.950-0.016-0.0160.0000.0000.0000.000
178B580ILE00.002-0.00817.3710.0080.0080.0000.0000.0000.000
179B581GLY00.0320.02520.420-0.007-0.0070.0000.0000.0000.000
180B582ILE0-0.018-0.01421.6250.0040.0040.0000.0000.0000.000
181B583ASN0-0.0010.00124.570-0.001-0.0010.0000.0000.0000.000
182B584LEU0-0.018-0.00627.2690.0020.0020.0000.0000.0000.000
183B585LYS10.9881.00030.4100.0140.0140.0000.0000.0000.000