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: 6Y9RZ

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2301373.913849
FMO2-HF: Nuclear repulsion 2218555.70906
FMO2-HF: Total energy -82818.204789
FMO2-MP2: Total energy -83060.796461


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.
-0.321.9640.033-0.898-1.4170.006
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 : -0.032 / q_NPA : -0.031
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-1-0.863-0.9273.742-3.298-1.881-0.007-0.509-0.9010.003
4B116PRO00.0270.0035.0180.6280.6280.0000.0000.0000.000
5B117VAL00.0400.0258.0090.1860.1860.0000.0000.0000.000
6B118GLN0-0.003-0.0128.7920.2140.2140.0000.0000.0000.000
7B119LEU00.0100.0028.7700.1120.1120.0000.0000.0000.000
8B120VAL00.0150.01911.1330.0400.0400.0000.0000.0000.000
9B121ASN0-0.031-0.01613.6830.0030.0030.0000.0000.0000.000
10B122PHE0-0.068-0.03113.6650.0280.0280.0000.0000.0000.000
11B123LEU00.011-0.02013.167-0.010-0.0100.0000.0000.0000.000
12B124GLN0-0.0190.00616.627-0.036-0.0360.0000.0000.0000.000
13B125SER0-0.036-0.01719.313-0.036-0.0360.0000.0000.0000.000
14B126GLU-1-0.985-0.97718.3190.4110.4110.0000.0000.0000.000
15B127HIS00.0090.01121.354-0.020-0.0200.0000.0000.0000.000
16B128PRO00.0890.02321.7630.0340.0340.0000.0000.0000.000
17B129GLN00.0290.01021.766-0.009-0.0090.0000.0000.0000.000
18B130THR0-0.019-0.01118.3030.0230.0230.0000.0000.0000.000
19B131ILE00.0310.02216.9100.0680.0680.0000.0000.0000.000
20B132ALA00.0230.01416.9520.0440.0440.0000.0000.0000.000
21B133VAL0-0.046-0.00917.3560.0220.0220.0000.0000.0000.000
22B134VAL0-0.005-0.00612.3500.0660.0660.0000.0000.0000.000
23B135LEU00.005-0.01213.1520.1190.1190.0000.0000.0000.000
24B136SER0-0.025-0.02614.014-0.009-0.0090.0000.0000.0000.000
25B137TYR0-0.055-0.02312.365-0.071-0.0710.0000.0000.0000.000
26B138LEU0-0.077-0.0268.0110.2180.2180.0000.0000.0000.000
27B139ASP-1-0.856-0.9368.372-0.158-0.1580.0000.0000.0000.000
28B140PRO00.0510.02810.4730.0040.0040.0000.0000.0000.000
29B141PRO00.0350.02710.925-0.012-0.0120.0000.0000.0000.000
30B142VAL00.0080.0056.876-0.063-0.0630.0000.0000.0000.000
31B143ALA0-0.010-0.0099.670-0.051-0.0510.0000.0000.0000.000
32B144ALA00.0350.01112.662-0.036-0.0360.0000.0000.0000.000
33B145GLN0-0.0230.0028.780-0.012-0.0120.0000.0000.0000.000
34B146ILE0-0.053-0.0289.239-0.017-0.0170.0000.0000.0000.000
35B147LEU0-0.002-0.00312.868-0.016-0.0160.0000.0000.0000.000
36B148GLY00.011-0.00416.032-0.007-0.0070.0000.0000.0000.000
37B149ALA0-0.059-0.02214.553-0.024-0.0240.0000.0000.0000.000
38B150LEU0-0.047-0.01916.5290.0230.0230.0000.0000.0000.000
39B151PRO00.0140.00218.571-0.026-0.0260.0000.0000.0000.000
40B152GLU-1-0.854-0.91122.2110.0270.0270.0000.0000.0000.000
41B153GLU-1-0.919-0.97424.3690.0810.0810.0000.0000.0000.000
42B154LEU0-0.022-0.01021.6150.0100.0100.0000.0000.0000.000
43B155GLN00.0290.04719.8870.0130.0130.0000.0000.0000.000
44B156THR00.0690.01222.7830.0080.0080.0000.0000.0000.000
45B157GLU-1-0.856-0.91325.6040.1470.1470.0000.0000.0000.000
46B158VAL0-0.005-0.01219.1160.0180.0180.0000.0000.0000.000
47B159LEU00.0140.01920.5240.0250.0250.0000.0000.0000.000
48B160LYS10.9420.96722.576-0.106-0.1060.0000.0000.0000.000
49B161ARG10.8290.89423.641-0.196-0.1960.0000.0000.0000.000
50B162ILE0-0.0010.01118.1380.0200.0200.0000.0000.0000.000
51B163ALA0-0.048-0.02021.8620.0080.0080.0000.0000.0000.000
52B164LEU0-0.045-0.03024.653-0.007-0.0070.0000.0000.0000.000
53B165LEU0-0.075-0.00320.2010.0060.0060.0000.0000.0000.000
54B166GLU-1-0.917-0.95124.3660.1780.1780.0000.0000.0000.000
55B167ARG10.9330.94821.707-0.389-0.3890.0000.0000.0000.000
56B168THR00.0110.01220.643-0.033-0.0330.0000.0000.0000.000
57B169SER00.0010.00823.2970.0210.0210.0000.0000.0000.000
58B170PRO00.054-0.00222.0520.0320.0320.0000.0000.0000.000
59B171GLU-1-0.919-0.96321.7380.5150.5150.0000.0000.0000.000
60B172VAL0-0.0180.00121.4770.0170.0170.0000.0000.0000.000
61B173VAL00.0090.00216.9230.0140.0140.0000.0000.0000.000
62B174LYS10.9870.98917.693-0.523-0.5230.0000.0000.0000.000
63B175GLU-1-0.897-0.92818.5580.5980.5980.0000.0000.0000.000
64B176ILE0-0.003-0.01415.5050.0160.0160.0000.0000.0000.000
65B177GLU-1-0.940-0.97913.6611.2551.2550.0000.0000.0000.000
66B178ARG10.9250.96414.321-0.529-0.5290.0000.0000.0000.000
67B179ASN0-0.086-0.05516.1690.0020.0020.0000.0000.0000.000
68B180LEU0-0.0030.01011.292-0.032-0.0320.0000.0000.0000.000
69B181GLU-1-0.925-0.95111.2951.4831.4830.0000.0000.0000.000
70B182LYS10.8490.92712.228-0.637-0.6370.0000.0000.0000.000
71B183LYS10.8770.92913.526-0.619-0.6190.0000.0000.0000.000
72B184ILE00.0100.0257.586-0.211-0.2110.0000.0000.0000.000
73B185SER0-0.018-0.0116.0370.3450.3450.0000.0000.0000.000
74B186GLY00.0140.0053.554-0.940-0.3910.039-0.332-0.2550.003
75B187PHE00.0330.0204.1091.1461.4640.001-0.057-0.2610.000
76B195VAL0-0.034-0.03216.907-0.003-0.0030.0000.0000.0000.000
77B196GLY00.0370.02618.6570.0030.0030.0000.0000.0000.000
78B197GLY00.0290.02420.820-0.014-0.0140.0000.0000.0000.000
79B198ILE0-0.005-0.02722.874-0.002-0.0020.0000.0000.0000.000
80B199ASP-1-0.855-0.91821.2130.0520.0520.0000.0000.0000.000
81B200THR00.0310.02017.183-0.036-0.0360.0000.0000.0000.000
82B201ALA0-0.005-0.00219.261-0.014-0.0140.0000.0000.0000.000
83B202ALA00.0110.00721.633-0.023-0.0230.0000.0000.0000.000
84B203GLU-1-0.899-0.95515.482-0.051-0.0510.0000.0000.0000.000
85B204ILE0-0.012-0.01116.096-0.040-0.0400.0000.0000.0000.000
86B205MET0-0.037-0.03018.146-0.035-0.0350.0000.0000.0000.000
87B206ASN0-0.052-0.02920.382-0.023-0.0230.0000.0000.0000.000
88B207ASN0-0.090-0.04915.578-0.104-0.1040.0000.0000.0000.000
89B208LEU0-0.0540.00117.239-0.027-0.0270.0000.0000.0000.000
90B209ASP-1-0.824-0.88519.062-0.163-0.1630.0000.0000.0000.000
91B210ARG10.9600.96321.0390.1250.1250.0000.0000.0000.000
92B211THR0-0.047-0.02124.5680.0190.0190.0000.0000.0000.000
93B212THR0-0.030-0.04120.7290.0260.0260.0000.0000.0000.000
94B213GLU-1-0.833-0.90823.001-0.064-0.0640.0000.0000.0000.000
95B214LYS10.9310.96124.2770.0740.0740.0000.0000.0000.000
96B215LYS10.7730.87324.4320.0100.0100.0000.0000.0000.000
97B216ILE00.009-0.00522.3510.0140.0140.0000.0000.0000.000
98B217MET00.0090.00626.8270.0160.0160.0000.0000.0000.000
99B218ASP-1-0.872-0.94629.036-0.025-0.0250.0000.0000.0000.000
100B219LYS10.8200.92029.506-0.029-0.0290.0000.0000.0000.000
101B220LEU00.0430.00526.9830.0070.0070.0000.0000.0000.000
102B221VAL0-0.0090.00531.3260.0030.0030.0000.0000.0000.000
103B222GLN0-0.076-0.03534.4000.0050.0050.0000.0000.0000.000
104B223GLU-1-0.951-0.98331.5800.0790.0790.0000.0000.0000.000
105B224ASN0-0.071-0.04032.6000.0000.0000.0000.0000.0000.000
106B225PRO00.0830.03433.6650.0010.0010.0000.0000.0000.000
107B226GLU-1-0.886-0.93135.2330.0360.0360.0000.0000.0000.000
108B227LEU0-0.0180.00128.5210.0000.0000.0000.0000.0000.000
109B228ALA0-0.015-0.01130.481-0.002-0.0020.0000.0000.0000.000
110B229ASP-1-0.918-0.95831.119-0.001-0.0010.0000.0000.0000.000
111B230GLU-1-0.783-0.88730.1160.0250.0250.0000.0000.0000.000
112B231ILE0-0.020-0.01725.518-0.003-0.0030.0000.0000.0000.000
113B232ARG10.9550.97027.2970.0050.0050.0000.0000.0000.000
114B233ARG10.8030.89029.285-0.029-0.0290.0000.0000.0000.000
115B234ARG10.7850.88025.283-0.059-0.0590.0000.0000.0000.000
116B235MET0-0.0560.00024.243-0.002-0.0020.0000.0000.0000.000
117B236PHE0-0.0020.00625.371-0.027-0.0270.0000.0000.0000.000
118B237VAL00.0460.02426.7660.0140.0140.0000.0000.0000.000
119B238PHE00.0390.00329.390-0.013-0.0130.0000.0000.0000.000
120B239GLU-1-0.754-0.90528.379-0.132-0.1320.0000.0000.0000.000
121B240ASP-1-0.816-0.89125.479-0.157-0.1570.0000.0000.0000.000
122B241ILE0-0.014-0.00627.963-0.014-0.0140.0000.0000.0000.000
123B242LEU0-0.030-0.01427.924-0.006-0.0060.0000.0000.0000.000
124B243LYS10.8740.94423.6890.1550.1550.0000.0000.0000.000
125B244LEU0-0.029-0.00427.029-0.012-0.0120.0000.0000.0000.000
126B245ASP-1-0.900-0.95329.624-0.218-0.2180.0000.0000.0000.000
127B246ASP-1-0.842-0.94231.629-0.168-0.1680.0000.0000.0000.000
128B247ARG10.9330.95734.8070.1700.1700.0000.0000.0000.000
129B248SER00.0830.03532.8020.0100.0100.0000.0000.0000.000
130B249ILE00.0400.03033.1100.0100.0100.0000.0000.0000.000
131B250GLN0-0.081-0.05136.6870.0130.0130.0000.0000.0000.000
132B251LEU0-0.027-0.02037.9730.0070.0070.0000.0000.0000.000
133B252VAL00.0290.02636.6110.0070.0070.0000.0000.0000.000
134B253LEU0-0.036-0.02739.9530.0070.0070.0000.0000.0000.000
135B254ARG10.8510.93841.9480.0990.0990.0000.0000.0000.000
136B255GLU-1-0.870-0.91842.715-0.059-0.0590.0000.0000.0000.000
137B256VAL0-0.037-0.00541.4030.0040.0040.0000.0000.0000.000
138B257ASP-1-0.874-0.92544.836-0.050-0.0500.0000.0000.0000.000
139B258THR0-0.003-0.02946.405-0.002-0.0020.0000.0000.0000.000
140B259ARG10.9780.99346.9260.0350.0350.0000.0000.0000.000
141B260ASP-1-0.879-0.94244.384-0.042-0.0420.0000.0000.0000.000
142B261LEU0-0.011-0.00440.515-0.002-0.0020.0000.0000.0000.000
143B262ALA00.003-0.00842.168-0.004-0.0040.0000.0000.0000.000
144B263LEU00.000-0.01543.357-0.001-0.0010.0000.0000.0000.000
145B264ALA00.0190.02338.8830.0010.0010.0000.0000.0000.000
146B265LEU00.0120.00037.888-0.003-0.0030.0000.0000.0000.000
147B266LYS10.8400.92139.5210.0560.0560.0000.0000.0000.000
148B267GLY0-0.054-0.01337.7590.0020.0020.0000.0000.0000.000
149B268ALA0-0.0050.01034.676-0.001-0.0010.0000.0000.0000.000
150B269SER0-0.034-0.02331.4850.0000.0000.0000.0000.0000.000
151B270ASP-1-0.886-0.96233.716-0.113-0.1130.0000.0000.0000.000
152B271GLU-1-0.964-0.97828.236-0.221-0.2210.0000.0000.0000.000
153B272LEU0-0.0010.00232.306-0.003-0.0030.0000.0000.0000.000
154B273LYS10.9490.96733.6560.0910.0910.0000.0000.0000.000
155B274GLU-1-0.905-0.95535.333-0.124-0.1240.0000.0000.0000.000
156B275LYS10.8030.93830.6000.1890.1890.0000.0000.0000.000
157B276ILE00.0210.00735.0750.0010.0010.0000.0000.0000.000
158B277PHE00.015-0.01238.0360.0050.0050.0000.0000.0000.000
159B278LYS10.8830.95932.6580.1850.1850.0000.0000.0000.000
160B279ASN0-0.078-0.03735.617-0.002-0.0020.0000.0000.0000.000
161B280MET00.0170.02439.8730.0060.0060.0000.0000.0000.000
162B281SER00.0060.00443.478-0.002-0.0020.0000.0000.0000.000
163B282LYS11.0360.99846.6310.0850.0850.0000.0000.0000.000
164B283ARG10.9330.95948.1330.0640.0640.0000.0000.0000.000
165B284ALA00.0240.01147.1940.0030.0030.0000.0000.0000.000
166B285ALA00.0640.03444.7580.0020.0020.0000.0000.0000.000
167B286ALA0-0.060-0.02646.2440.0010.0010.0000.0000.0000.000
168B287LEU00.0340.01349.1840.0020.0020.0000.0000.0000.000
169B288LEU00.0110.02342.6810.0030.0030.0000.0000.0000.000
170B289LYS10.9290.95543.8180.0980.0980.0000.0000.0000.000
171B290ASP-1-0.864-0.92847.076-0.063-0.0630.0000.0000.0000.000
172B291GLU-1-0.959-0.98148.411-0.047-0.0470.0000.0000.0000.000
173B292LEU0-0.058-0.05142.9230.0020.0020.0000.0000.0000.000
174B293GLU-1-1.000-0.99446.952-0.064-0.0640.0000.0000.0000.000
175B294TYR0-0.030-0.01249.1660.0040.0040.0000.0000.0000.000
176B295MET0-0.0660.00646.4490.0020.0020.0000.0000.0000.000
177B296GLY00.000-0.00650.3370.0000.0000.0000.0000.0000.000
178B297PRO0-0.020-0.01548.121-0.002-0.0020.0000.0000.0000.000
179B298VAL00.0210.01444.4820.0020.0020.0000.0000.0000.000
180B299ARG10.9140.94945.1160.0120.0120.0000.0000.0000.000
181B300LEU00.0880.04437.326-0.001-0.0010.0000.0000.0000.000
182B301LYS10.9820.98440.6230.0040.0040.0000.0000.0000.000
183B302ASP-1-0.876-0.94042.218-0.020-0.0200.0000.0000.0000.000
184B303VAL0-0.050-0.01638.940-0.002-0.0020.0000.0000.0000.000
185B304GLU-1-0.904-0.96836.171-0.026-0.0260.0000.0000.0000.000
186B305GLU-1-0.975-0.97438.720-0.022-0.0220.0000.0000.0000.000
187B306ALA0-0.010-0.01041.309-0.001-0.0010.0000.0000.0000.000
188B307GLN0-0.050-0.03635.528-0.001-0.0010.0000.0000.0000.000
189B308GLN0-0.0110.00635.144-0.004-0.0040.0000.0000.0000.000
190B309LYS10.9220.96137.9830.0310.0310.0000.0000.0000.000
191B310ILE00.0160.01137.029-0.002-0.0020.0000.0000.0000.000
192B311ILE00.0190.01032.671-0.005-0.0050.0000.0000.0000.000
193B312ASN0-0.015-0.01535.710-0.001-0.0010.0000.0000.0000.000
194B313ILE0-0.0160.00638.0860.0000.0000.0000.0000.0000.000
195B314ILE00.0030.00432.837-0.003-0.0030.0000.0000.0000.000
196B315ARG10.9070.95933.9940.0240.0240.0000.0000.0000.000
197B316ARG10.8780.93335.2590.0570.0570.0000.0000.0000.000
198B317LEU0-0.004-0.01837.453-0.001-0.0010.0000.0000.0000.000
199B318GLU-1-0.951-0.97429.560-0.100-0.1000.0000.0000.0000.000
200B319GLU-1-0.943-0.96934.228-0.041-0.0410.0000.0000.0000.000
201B320ALA0-0.072-0.03735.7100.0000.0000.0000.0000.0000.000
202B321GLY0-0.022-0.00334.833-0.001-0.0010.0000.0000.0000.000
203B322GLU-1-0.991-0.99535.913-0.094-0.0940.0000.0000.0000.000
204B323ILE0-0.058-0.02832.479-0.009-0.0090.0000.0000.0000.000
205B324VAL00.005-0.00328.3530.0050.0050.0000.0000.0000.000
206B325ILE0-0.024-0.01526.270-0.014-0.0140.0000.0000.0000.000
207B326ALA0-0.0120.00424.780-0.002-0.0020.0000.0000.0000.000
208B327ARG10.9370.97321.5320.2680.2680.0000.0000.0000.000