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: R8RK8

Calculation Name: 4FHR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FHR

Chain ID: B

ChEMBL ID:

UniProt ID: Q9WY63

Base Structure: X-ray

Registration Date: 2023-09-24

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2313224.407066
FMO2-HF: Nuclear repulsion 2230404.569841
FMO2-HF: Total energy -82819.837225
FMO2-MP2: Total energy -83062.439898


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:113:HIS)


Summations of interaction energy for fragment #1(B:113:HIS)
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.
1.193.7550.101-1.013-1.6520.004
Interaction energy analysis for fragmet #1(B:113:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.025
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].
3B115ASP-1-0.823-0.9043.714-2.504-0.9750.001-0.614-0.9160.002
4B116PRO00.0400.0075.0240.5200.5200.0000.0000.0000.000
5B117VAL00.0340.0237.9040.1620.1620.0000.0000.0000.000
6B118GLN00.0130.0128.9810.1000.1000.0000.0000.0000.000
7B119LEU00.0180.0017.4170.1180.1180.0000.0000.0000.000
8B120VAL00.0050.00910.8490.0500.0500.0000.0000.0000.000
9B121ASN0-0.065-0.05213.6090.0250.0250.0000.0000.0000.000
10B122PHE0-0.0210.00013.7130.0180.0180.0000.0000.0000.000
11B123LEU00.004-0.01913.079-0.009-0.0090.0000.0000.0000.000
12B124GLN0-0.022-0.00316.612-0.023-0.0230.0000.0000.0000.000
13B125SER0-0.042-0.01219.188-0.033-0.0330.0000.0000.0000.000
14B126GLU-1-0.963-0.97217.7490.3970.3970.0000.0000.0000.000
15B127HIS00.0250.01321.025-0.007-0.0070.0000.0000.0000.000
16B128PRO00.0730.01521.6190.0340.0340.0000.0000.0000.000
17B129GLN00.0390.02921.660-0.009-0.0090.0000.0000.0000.000
18B130THR0-0.004-0.00517.9530.0250.0250.0000.0000.0000.000
19B131ILE00.0180.01516.8240.0680.0680.0000.0000.0000.000
20B132ALA00.0160.01316.8300.0520.0520.0000.0000.0000.000
21B133VAL0-0.042-0.01616.8790.0300.0300.0000.0000.0000.000
22B134VAL00.002-0.00712.0690.0660.0660.0000.0000.0000.000
23B135LEU0-0.011-0.01112.8250.1260.1260.0000.0000.0000.000
24B136SER00.000-0.01814.0710.0140.0140.0000.0000.0000.000
25B137TYR0-0.060-0.02912.134-0.079-0.0790.0000.0000.0000.000
26B138LEU0-0.063-0.0217.6520.2720.2720.0000.0000.0000.000
27B139ASP-1-0.850-0.9348.6700.7080.7080.0000.0000.0000.000
28B140PRO00.0470.02710.568-0.025-0.0250.0000.0000.0000.000
29B141PRO00.0350.02010.718-0.056-0.0560.0000.0000.0000.000
30B142VAL0-0.0080.0046.435-0.086-0.0860.0000.0000.0000.000
31B143ALA0-0.008-0.0089.388-0.138-0.1380.0000.0000.0000.000
32B144ALA00.0290.01012.282-0.082-0.0820.0000.0000.0000.000
33B145GLN0-0.015-0.0058.5820.0040.0040.0000.0000.0000.000
34B146ILE0-0.056-0.0279.021-0.072-0.0720.0000.0000.0000.000
35B147LEU0-0.015-0.00112.812-0.050-0.0500.0000.0000.0000.000
36B148GLY00.013-0.00515.961-0.028-0.0280.0000.0000.0000.000
37B149ALA0-0.052-0.01914.452-0.037-0.0370.0000.0000.0000.000
38B150LEU0-0.039-0.00816.067-0.006-0.0060.0000.0000.0000.000
39B151PRO00.0120.00218.166-0.017-0.0170.0000.0000.0000.000
40B152GLU-1-0.870-0.93121.9310.0910.0910.0000.0000.0000.000
41B153GLU-1-0.922-0.96924.0550.1070.1070.0000.0000.0000.000
42B154LEU0-0.028-0.01721.1320.0100.0100.0000.0000.0000.000
43B155GLN00.0220.02319.7070.0090.0090.0000.0000.0000.000
44B156THR00.0650.01722.3510.0170.0170.0000.0000.0000.000
45B157GLU-1-0.795-0.87225.3260.1920.1920.0000.0000.0000.000
46B158VAL0-0.009-0.01018.8400.0150.0150.0000.0000.0000.000
47B159LEU00.0060.01720.0360.0260.0260.0000.0000.0000.000
48B160LYS10.8550.91022.196-0.149-0.1490.0000.0000.0000.000
49B161ARG10.7880.86523.404-0.228-0.2280.0000.0000.0000.000
50B162ILE0-0.0060.00517.8190.0120.0120.0000.0000.0000.000
51B163ALA0-0.036-0.01321.5110.0100.0100.0000.0000.0000.000
52B164LEU0-0.029-0.01724.467-0.016-0.0160.0000.0000.0000.000
53B165LEU0-0.068-0.01219.879-0.005-0.0050.0000.0000.0000.000
54B166GLU-1-0.918-0.94623.2770.2510.2510.0000.0000.0000.000
55B167ARG10.8810.92021.077-0.429-0.4290.0000.0000.0000.000
56B168THR00.0530.03019.990-0.033-0.0330.0000.0000.0000.000
57B169SER00.0060.00822.9960.0150.0150.0000.0000.0000.000
58B170PRO00.0600.01521.8940.0300.0300.0000.0000.0000.000
59B171GLU-1-0.803-0.89321.4780.4830.4830.0000.0000.0000.000
60B172VAL0-0.0110.00021.7330.0110.0110.0000.0000.0000.000
61B173VAL0-0.0130.00016.8740.0070.0070.0000.0000.0000.000
62B174LYS10.8740.92817.657-0.448-0.4480.0000.0000.0000.000
63B175GLU-1-0.862-0.90518.2630.5230.5230.0000.0000.0000.000
64B176ILE00.0090.00815.3410.0050.0050.0000.0000.0000.000
65B177GLU-1-0.898-0.96213.6381.0341.0340.0000.0000.0000.000
66B178ARG10.9210.95113.876-0.481-0.4810.0000.0000.0000.000
67B179ASN0-0.071-0.05316.195-0.045-0.0450.0000.0000.0000.000
68B180LEU00.0050.00610.945-0.058-0.0580.0000.0000.0000.000
69B181GLU-1-0.918-0.96311.3761.1231.1230.0000.0000.0000.000
70B182LYS10.7990.89012.399-0.541-0.5410.0000.0000.0000.000
71B183LYS10.8190.92613.314-0.563-0.5630.0000.0000.0000.000
72B184ILE0-0.034-0.0077.420-0.181-0.1810.0000.0000.0000.000
73B185SER00.0090.0025.9770.4110.4110.0000.0000.0000.000
74B186GLY00.006-0.0063.356-1.186-0.6200.095-0.312-0.3480.002
75B187PHE00.0000.0023.9601.3341.8040.005-0.087-0.3880.000
76B195VAL0-0.022-0.00416.9510.0020.0020.0000.0000.0000.000
77B196GLY00.0200.01018.6580.0110.0110.0000.0000.0000.000
78B197GLY00.0020.00720.724-0.012-0.0120.0000.0000.0000.000
79B198ILE0-0.015-0.02023.0010.0090.0090.0000.0000.0000.000
80B199ASP-1-0.816-0.89722.2440.1900.1900.0000.0000.0000.000
81B200THR00.0170.00717.313-0.019-0.0190.0000.0000.0000.000
82B201ALA00.0050.00219.0450.0090.0090.0000.0000.0000.000
83B202ALA00.0110.00421.129-0.016-0.0160.0000.0000.0000.000
84B203GLU-1-0.910-0.96115.7890.2550.2550.0000.0000.0000.000
85B204ILE0-0.0030.00215.527-0.016-0.0160.0000.0000.0000.000
86B205MET0-0.041-0.02717.748-0.029-0.0290.0000.0000.0000.000
87B206ASN0-0.064-0.04520.607-0.031-0.0310.0000.0000.0000.000
88B207ASN0-0.072-0.03715.239-0.053-0.0530.0000.0000.0000.000
89B208LEU0-0.0380.00016.568-0.008-0.0080.0000.0000.0000.000
90B209ASP-1-0.810-0.86618.784-0.019-0.0190.0000.0000.0000.000
91B210ARG10.7980.86121.031-0.003-0.0030.0000.0000.0000.000
92B211THR0-0.045-0.03924.3800.0060.0060.0000.0000.0000.000
93B212THR0-0.035-0.04120.3170.0110.0110.0000.0000.0000.000
94B213GLU-1-0.817-0.90622.7170.0680.0680.0000.0000.0000.000
95B214LYS10.8760.92423.983-0.024-0.0240.0000.0000.0000.000
96B215LYS10.8030.91624.354-0.086-0.0860.0000.0000.0000.000
97B216ILE00.013-0.00621.9970.0060.0060.0000.0000.0000.000
98B217MET00.0080.01126.4640.0050.0050.0000.0000.0000.000
99B218ASP-1-0.815-0.89928.6820.0440.0440.0000.0000.0000.000
100B219LYS10.7540.87429.286-0.090-0.0900.0000.0000.0000.000
101B220LEU00.0520.01326.5990.0030.0030.0000.0000.0000.000
102B221VAL0-0.013-0.01230.961-0.001-0.0010.0000.0000.0000.000
103B222GLN0-0.051-0.01334.1230.0010.0010.0000.0000.0000.000
104B223GLU-1-0.861-0.92231.0000.1220.1220.0000.0000.0000.000
105B224ASN0-0.039-0.02832.398-0.002-0.0020.0000.0000.0000.000
106B225PRO00.0650.02933.3620.0050.0050.0000.0000.0000.000
107B226GLU-1-0.919-0.94534.6470.0900.0900.0000.0000.0000.000
108B227LEU0-0.016-0.00628.1790.0030.0030.0000.0000.0000.000
109B228ALA0-0.003-0.00130.0530.0060.0060.0000.0000.0000.000
110B229ASP-1-0.759-0.87930.5180.0660.0660.0000.0000.0000.000
111B230GLU-1-0.772-0.85030.4110.1210.1210.0000.0000.0000.000
112B231ILE00.001-0.00925.1630.0030.0030.0000.0000.0000.000
113B232ARG10.8580.90927.291-0.070-0.0700.0000.0000.0000.000
114B233ARG10.8160.88829.371-0.108-0.1080.0000.0000.0000.000
115B234ARG10.7390.84325.333-0.161-0.1610.0000.0000.0000.000
116B235MET0-0.0510.00124.1420.0030.0030.0000.0000.0000.000
117B236PHE0-0.019-0.00725.600-0.018-0.0180.0000.0000.0000.000
118B237VAL00.0300.01627.2920.0030.0030.0000.0000.0000.000
119B238PHE00.0450.00529.886-0.011-0.0110.0000.0000.0000.000
120B239GLU-1-0.720-0.85228.565-0.024-0.0240.0000.0000.0000.000
121B240ASP-1-0.767-0.85625.4430.0140.0140.0000.0000.0000.000
122B241ILE0-0.021-0.01728.152-0.010-0.0100.0000.0000.0000.000
123B242LEU0-0.044-0.02027.646-0.009-0.0090.0000.0000.0000.000
124B243LYS10.8430.92323.611-0.030-0.0300.0000.0000.0000.000
125B244LEU00.0130.01927.105-0.009-0.0090.0000.0000.0000.000
126B245ASP-1-0.811-0.89930.397-0.099-0.0990.0000.0000.0000.000
127B246ASP-1-0.749-0.86032.001-0.072-0.0720.0000.0000.0000.000
128B247ARG10.9280.96334.2530.0880.0880.0000.0000.0000.000
129B248SER00.0530.02533.9910.0020.0020.0000.0000.0000.000
130B249ILE00.0070.01533.0140.0060.0060.0000.0000.0000.000
131B250GLN0-0.063-0.05536.8880.0050.0050.0000.0000.0000.000
132B251LEU0-0.055-0.01738.3520.0020.0020.0000.0000.0000.000
133B252VAL00.0610.03336.7190.0030.0030.0000.0000.0000.000
134B253LEU0-0.046-0.03140.0780.0030.0030.0000.0000.0000.000
135B254ARG10.8430.93842.3670.0340.0340.0000.0000.0000.000
136B255GLU-1-0.792-0.85643.067-0.001-0.0010.0000.0000.0000.000
137B256VAL0-0.025-0.01341.4720.0040.0040.0000.0000.0000.000
138B257ASP-1-0.890-0.93244.967-0.005-0.0050.0000.0000.0000.000
139B258THR0-0.014-0.02646.5040.0010.0010.0000.0000.0000.000
140B259ARG10.9470.97146.680-0.008-0.0080.0000.0000.0000.000
141B260ASP-1-0.803-0.90744.7370.0110.0110.0000.0000.0000.000
142B261LEU00.0160.00740.4110.0020.0020.0000.0000.0000.000
143B262ALA00.006-0.00142.022-0.001-0.0010.0000.0000.0000.000
144B263LEU0-0.032-0.02243.2730.0010.0010.0000.0000.0000.000
145B264ALA00.0080.00438.8880.0020.0020.0000.0000.0000.000
146B265LEU00.014-0.00237.6430.0000.0000.0000.0000.0000.000
147B266LYS10.8120.90839.5310.0020.0020.0000.0000.0000.000
148B267GLY0-0.053-0.01337.9920.0010.0010.0000.0000.0000.000
149B268ALA00.0110.02434.6140.0040.0040.0000.0000.0000.000
150B269SER0-0.028-0.05831.432-0.006-0.0060.0000.0000.0000.000
151B270ASP-1-0.845-0.93133.532-0.033-0.0330.0000.0000.0000.000
152B271GLU-1-0.936-0.96128.576-0.089-0.0890.0000.0000.0000.000
153B272LEU00.0160.00632.262-0.004-0.0040.0000.0000.0000.000
154B273LYS10.8220.90833.6960.0220.0220.0000.0000.0000.000
155B274GLU-1-0.823-0.89536.327-0.049-0.0490.0000.0000.0000.000
156B275LYS10.7900.91330.8520.0670.0670.0000.0000.0000.000
157B276ILE00.0240.01535.2310.0000.0000.0000.0000.0000.000
158B277PHE00.040-0.01138.1340.0000.0000.0000.0000.0000.000
159B278LYS10.8000.89534.0210.0840.0840.0000.0000.0000.000
160B279ASN0-0.084-0.04335.929-0.005-0.0050.0000.0000.0000.000
161B280MET00.0140.02240.2700.0040.0040.0000.0000.0000.000
162B281SER00.0120.00643.923-0.003-0.0030.0000.0000.0000.000
163B282LYS11.0150.99247.2650.0430.0430.0000.0000.0000.000
164B283ARG10.9460.97448.4980.0250.0250.0000.0000.0000.000
165B284ALA00.0280.01547.4330.0020.0020.0000.0000.0000.000
166B285ALA00.0500.02044.8410.0020.0020.0000.0000.0000.000
167B286ALA0-0.047-0.01746.1790.0010.0010.0000.0000.0000.000
168B287LEU00.0330.01049.1520.0010.0010.0000.0000.0000.000
169B288LEU0-0.0050.01242.7280.0020.0020.0000.0000.0000.000
170B289LYS10.8090.88641.9470.0440.0440.0000.0000.0000.000
171B290ASP-1-0.883-0.93846.958-0.021-0.0210.0000.0000.0000.000
172B291GLU-1-0.915-0.97248.399-0.003-0.0030.0000.0000.0000.000
173B292LEU0-0.022-0.02442.9140.0020.0020.0000.0000.0000.000
174B293GLU-1-0.938-0.94146.880-0.019-0.0190.0000.0000.0000.000
175B294TYR0-0.085-0.06049.2180.0030.0030.0000.0000.0000.000
176B295MET0-0.0700.00047.0700.0020.0020.0000.0000.0000.000
177B296GLY00.017-0.00349.6920.0000.0000.0000.0000.0000.000
178B297PRO0-0.035-0.01848.0240.0000.0000.0000.0000.0000.000
179B298VAL00.0130.00344.6730.0010.0010.0000.0000.0000.000
180B299ARG10.9080.95645.183-0.027-0.0270.0000.0000.0000.000
181B300LEU00.0550.03337.131-0.002-0.0020.0000.0000.0000.000
182B301LYS10.8870.93740.752-0.033-0.0330.0000.0000.0000.000
183B302ASP-1-0.852-0.93342.1890.0260.0260.0000.0000.0000.000
184B303VAL0-0.0090.00938.831-0.002-0.0020.0000.0000.0000.000
185B304GLU-1-0.871-0.95236.7510.0470.0470.0000.0000.0000.000
186B305GLU-1-0.856-0.90738.8630.0280.0280.0000.0000.0000.000
187B306ALA0-0.008-0.01241.437-0.001-0.0010.0000.0000.0000.000
188B307GLN0-0.042-0.03235.4210.0020.0020.0000.0000.0000.000
189B308GLN0-0.015-0.00735.5080.0020.0020.0000.0000.0000.000
190B309LYS10.7990.89838.126-0.021-0.0210.0000.0000.0000.000
191B310ILE00.0160.00837.152-0.002-0.0020.0000.0000.0000.000
192B311ILE00.0140.00633.135-0.003-0.0030.0000.0000.0000.000
193B312ASN0-0.0040.00035.9090.0040.0040.0000.0000.0000.000
194B313ILE0-0.0290.00238.3780.0000.0000.0000.0000.0000.000
195B314ILE00.0050.00132.828-0.003-0.0030.0000.0000.0000.000
196B315ARG10.7820.88633.839-0.050-0.0500.0000.0000.0000.000
197B316ARG10.8350.88335.061-0.006-0.0060.0000.0000.0000.000
198B317LEU0-0.004-0.01237.370-0.002-0.0020.0000.0000.0000.000
199B318GLU-1-0.876-0.91729.4420.0140.0140.0000.0000.0000.000
200B319GLU-1-0.884-0.94133.7020.0350.0350.0000.0000.0000.000
201B320ALA0-0.053-0.02435.385-0.001-0.0010.0000.0000.0000.000
202B321GLY0-0.0100.00634.589-0.003-0.0030.0000.0000.0000.000
203B322GLU-1-0.976-0.98835.548-0.027-0.0270.0000.0000.0000.000
204B323ILE0-0.085-0.04832.235-0.007-0.0070.0000.0000.0000.000
205B324VAL00.0440.01428.0120.0050.0050.0000.0000.0000.000
206B325ILE0-0.0040.00826.377-0.013-0.0130.0000.0000.0000.000
207B326ALA0-0.027-0.00824.9630.0070.0070.0000.0000.0000.000
208B327ARG10.8350.91121.3180.0870.0870.0000.0000.0000.000