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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: KGQM3

Calculation Name: 4Y4Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y4Q

Chain ID: B

ChEMBL ID:

UniProt ID: A0A0M3

Base Structure: X-ray

Registration Date: 2023-09-23

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1895603.434909
FMO2-HF: Nuclear repulsion 1826023.976103
FMO2-HF: Total energy -69579.458806
FMO2-MP2: Total energy -69784.246194


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:76:SER)


Summations of interaction energy for fragment #1(B:76:SER)
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.
-21.164-16.56113.367-8.607-9.363-0.06
Interaction energy analysis for fragmet #1(B:76:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.021
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].
3B78PHE0-0.054-0.0173.8180.5602.186-0.017-0.752-0.8570.002
4B79SER00.0830.0335.665-1.046-1.020-0.001-0.002-0.0220.000
5B80LYS10.9160.9498.746-1.449-1.4490.0000.0000.0000.000
6B81LEU00.0510.0256.935-0.152-0.1520.0000.0000.0000.000
7B82GLN0-0.029-0.0298.7260.0770.0770.0000.0000.0000.000
8B83GLU-1-1.012-0.99811.3480.6580.6580.0000.0000.0000.000
9B84LEU0-0.064-0.02913.142-0.093-0.0930.0000.0000.0000.000
10B85ASN0-0.036-0.01312.394-0.032-0.0320.0000.0000.0000.000
11B86PRO00.0140.00812.975-0.013-0.0130.0000.0000.0000.000
12B87GLU-1-0.899-0.95814.699-0.005-0.0050.0000.0000.0000.000
13B88VAL0-0.035-0.0038.670-0.091-0.0910.0000.0000.0000.000
14B89LEU0-0.0130.00410.5020.1540.1540.0000.0000.0000.000
15B90GLY0-0.026-0.0336.3670.1630.1630.0000.0000.0000.000
16B91TRP0-0.069-0.0453.615-0.2010.1280.008-0.104-0.2330.000
17B92ILE0-0.0110.0055.399-0.266-0.2660.0000.0000.0000.000
18B93ASN00.0310.0145.1240.5990.5990.0000.0000.0000.000
19B94VAL00.0360.0307.0420.0490.0490.0000.0000.0000.000
20B95TYR00.0270.0326.7930.0400.0400.0000.0000.0000.000
21B96GLY0-0.002-0.01311.1690.1080.1080.0000.0000.0000.000
22B97THR0-0.083-0.06712.1150.1020.1020.0000.0000.0000.000
23B98ASN0-0.085-0.04812.179-0.035-0.0350.0000.0000.0000.000
24B99ILE0-0.025-0.01610.4520.0310.0310.0000.0000.0000.000
25B100ASP-1-0.826-0.8846.032-2.232-2.2320.0000.0000.0000.000
26B101TYR0-0.004-0.0147.5560.3630.3630.0000.0000.0000.000
27B102PRO00.0260.0377.728-0.425-0.4250.0000.0000.0000.000
28B103LEU0-0.035-0.0267.9810.1360.1360.0000.0000.0000.000
29B104VAL00.0560.01910.7080.1130.1130.0000.0000.0000.000
30B105GLN0-0.070-0.03713.873-0.013-0.0130.0000.0000.0000.000
31B106ALA00.0250.02816.8890.0420.0420.0000.0000.0000.000
32B107LYS10.8920.92120.4530.0630.0630.0000.0000.0000.000
33B108ASP-1-0.944-0.98623.586-0.101-0.1010.0000.0000.0000.000
34B109ASN0-0.0040.02624.5860.0010.0010.0000.0000.0000.000
35B110GLU-1-0.954-0.97322.942-0.151-0.1510.0000.0000.0000.000
36B120GLU-1-0.955-0.98318.562-0.015-0.0150.0000.0000.0000.000
37B121PHE00.0280.00413.512-0.001-0.0010.0000.0000.0000.000
38B122ALA0-0.019-0.00516.483-0.042-0.0420.0000.0000.0000.000
39B123ALA0-0.0110.01116.288-0.007-0.0070.0000.0000.0000.000
40B124THR0-0.077-0.06511.764-0.031-0.0310.0000.0000.0000.000
41B125GLY00.0500.03012.756-0.095-0.0950.0000.0000.0000.000
42B126ALA00.026-0.00112.813-0.047-0.0470.0000.0000.0000.000
43B127ILE0-0.0230.00812.1600.0510.0510.0000.0000.0000.000
44B128PHE0-0.016-0.01513.849-0.008-0.0080.0000.0000.0000.000
45B129LEU0-0.006-0.00312.511-0.011-0.0110.0000.0000.0000.000
46B130ASP-1-0.714-0.81316.526-0.176-0.1760.0000.0000.0000.000
47B131ALA0-0.003-0.00419.652-0.002-0.0020.0000.0000.0000.000
48B132ARG10.7990.86021.7450.2080.2080.0000.0000.0000.000
49B133ASN0-0.0090.00217.968-0.013-0.0130.0000.0000.0000.000
50B134ASN00.0320.01016.845-0.002-0.0020.0000.0000.0000.000
51B135PRO0-0.008-0.00714.817-0.042-0.0420.0000.0000.0000.000
52B136LYS10.8530.92812.721-0.030-0.0300.0000.0000.0000.000
53B137PHE00.0310.01210.621-0.044-0.0440.0000.0000.0000.000
54B138GLU-1-0.953-0.97314.256-0.116-0.1160.0000.0000.0000.000
55B139ASP-1-0.823-0.88217.259-0.203-0.2030.0000.0000.0000.000
56B140PHE00.0000.00718.369-0.035-0.0350.0000.0000.0000.000
57B141ASN00.0150.00219.535-0.028-0.0280.0000.0000.0000.000
58B142THR0-0.005-0.00814.9940.0340.0340.0000.0000.0000.000
59B143ILE0-0.0010.00717.435-0.049-0.0490.0000.0000.0000.000
60B144ILE0-0.031-0.01812.8570.0040.0040.0000.0000.0000.000
61B145TYR0-0.016-0.03216.760-0.006-0.0060.0000.0000.0000.000
62B146GLY00.0610.03217.106-0.037-0.0370.0000.0000.0000.000
63B147HIS0-0.0110.00717.8500.0240.0240.0000.0000.0000.000
64B148HIS00.011-0.00520.778-0.022-0.0220.0000.0000.0000.000
65B149VAL0-0.0210.02022.0910.0180.0180.0000.0000.0000.000
66B150GLU-1-0.913-0.95923.947-0.120-0.1200.0000.0000.0000.000
67B151ASN0-0.101-0.06824.9570.0120.0120.0000.0000.0000.000
68B152GLY00.012-0.02522.4090.0090.0090.0000.0000.0000.000
69B153VAL00.0090.01917.449-0.006-0.0060.0000.0000.0000.000
70B154MET0-0.049-0.01418.113-0.037-0.0370.0000.0000.0000.000
71B155PHE00.0980.05214.1010.0060.0060.0000.0000.0000.000
72B156GLY0-0.026-0.02217.708-0.013-0.0130.0000.0000.0000.000
73B157ASP-1-0.752-0.89116.175-0.473-0.4730.0000.0000.0000.000
74B158VAL00.0040.00716.8190.0000.0000.0000.0000.0000.000
75B159ALA00.0450.01818.8720.0150.0150.0000.0000.0000.000
76B160LYS10.8820.95319.8970.3750.3750.0000.0000.0000.000
77B161PHE0-0.043-0.01715.6660.0040.0040.0000.0000.0000.000
78B162ALA00.0620.02921.6690.0100.0100.0000.0000.0000.000
79B163ASP-1-0.910-0.93624.592-0.231-0.2310.0000.0000.0000.000
80B164GLN0-0.006-0.01324.738-0.004-0.0040.0000.0000.0000.000
81B165GLU-1-0.908-0.95725.230-0.234-0.2340.0000.0000.0000.000
82B166PHE0-0.051-0.03217.786-0.024-0.0240.0000.0000.0000.000
83B167PHE0-0.009-0.01020.402-0.056-0.0560.0000.0000.0000.000
84B168ASP-1-0.882-0.94520.778-0.314-0.3140.0000.0000.0000.000
85B169GLN0-0.095-0.05420.321-0.021-0.0210.0000.0000.0000.000
86B170HIS10.7830.94215.4070.4950.4950.0000.0000.0000.000
87B171ARG10.8610.92116.3540.4310.4310.0000.0000.0000.000
88B172TYR0-0.011-0.01312.1370.0130.0130.0000.0000.0000.000
89B173GLY00.0350.0099.3130.0610.0610.0000.0000.0000.000
90B174SER0-0.070-0.0143.9740.3530.420-0.001-0.009-0.0570.000
91B175ILE00.0420.0185.756-0.055-0.0550.0000.0000.0000.000
92B176TYR0-0.0010.0131.938-0.097-1.6429.945-4.224-4.178-0.015
93B177TYR00.0960.0333.9830.1140.2430.002-0.109-0.0210.000
94B178ASN00.003-0.0017.2250.1920.1920.0000.0000.0000.000
95B179GLY00.0010.0116.4790.0170.0170.0000.0000.0000.000
96B180VAL0-0.086-0.0416.1930.3470.3470.0000.0000.0000.000
97B181GLU-1-0.858-0.9492.198-17.363-13.3983.432-3.399-3.998-0.047
98B182LYS10.8600.9395.2650.9220.928-0.001-0.0080.0030.000
99B183GLY00.0410.0227.322-0.544-0.5440.0000.0000.0000.000
100B184LEU0-0.029-0.0069.3040.1430.1430.0000.0000.0000.000
101B185GLU-1-0.816-0.90211.493-0.485-0.4850.0000.0000.0000.000
102B186ILE00.0170.00014.4860.0430.0430.0000.0000.0000.000
103B187PHE0-0.013-0.01816.9000.0340.0340.0000.0000.0000.000
104B188GLU-1-0.785-0.91920.400-0.255-0.2550.0000.0000.0000.000
105B189MET0-0.059-0.00220.951-0.040-0.0400.0000.0000.0000.000
106B190LEU00.0440.02523.0150.0280.0280.0000.0000.0000.000
107B191GLU-1-0.915-0.96224.916-0.222-0.2220.0000.0000.0000.000
108B192VAL00.0140.01426.5130.0110.0110.0000.0000.0000.000
109B193ASP-1-0.774-0.90429.028-0.160-0.1600.0000.0000.0000.000
110B194ALA0-0.053-0.04028.259-0.008-0.0080.0000.0000.0000.000
111B195TYR0-0.109-0.05129.106-0.003-0.0030.0000.0000.0000.000
112B196ASP-1-0.815-0.90729.774-0.169-0.1690.0000.0000.0000.000
113B197PHE0-0.021-0.03829.423-0.010-0.0100.0000.0000.0000.000
114B198ASN0-0.062-0.01029.9110.0040.0040.0000.0000.0000.000
115B199ILE00.0200.02425.199-0.007-0.0070.0000.0000.0000.000
116B200TYR0-0.038-0.03423.164-0.019-0.0190.0000.0000.0000.000
117B201ASP-1-0.956-0.96825.895-0.152-0.1520.0000.0000.0000.000
118B202PRO0-0.039-0.01122.147-0.009-0.0090.0000.0000.0000.000
119B203GLY00.0180.00722.2680.0190.0190.0000.0000.0000.000
120B204ILE0-0.0060.02023.1870.0280.0280.0000.0000.0000.000
121B205GLN0-0.002-0.00625.171-0.003-0.0030.0000.0000.0000.000
122B206GLY0-0.022-0.02227.4840.0080.0080.0000.0000.0000.000
123B207GLU-1-0.885-0.94428.796-0.135-0.1350.0000.0000.0000.000
124B208ASP-1-0.871-0.94029.863-0.120-0.1200.0000.0000.0000.000
125B209ARG10.8570.93430.1330.1160.1160.0000.0000.0000.000
126B210GLN0-0.015-0.02024.833-0.002-0.0020.0000.0000.0000.000
127B211GLN0-0.013-0.02227.629-0.014-0.0140.0000.0000.0000.000
128B212ALA0-0.0080.00229.458-0.006-0.0060.0000.0000.0000.000
129B213TYR0-0.051-0.04623.662-0.013-0.0130.0000.0000.0000.000
130B214LEU00.003-0.00323.647-0.014-0.0140.0000.0000.0000.000
131B215ASP-1-0.855-0.92527.273-0.179-0.1790.0000.0000.0000.000
132B216HIS0-0.043-0.01730.1320.0060.0060.0000.0000.0000.000
133B217LEU00.0040.00423.101-0.002-0.0020.0000.0000.0000.000
134B218LEU00.0450.02625.038-0.004-0.0040.0000.0000.0000.000
135B219SER0-0.190-0.09528.2350.0070.0070.0000.0000.0000.000
136B220VAL0-0.028-0.01228.9370.0110.0110.0000.0000.0000.000
137B221ALA0-0.0330.00926.995-0.005-0.0050.0000.0000.0000.000
138B222MET0-0.078-0.03527.1610.0120.0120.0000.0000.0000.000
139B223HIS0-0.055-0.03024.5890.0080.0080.0000.0000.0000.000
140B224LYS10.9560.96724.3760.2020.2020.0000.0000.0000.000
141B225ARG10.7740.88919.4590.4400.4400.0000.0000.0000.000
142B226ASP-1-0.939-0.96424.399-0.228-0.2280.0000.0000.0000.000
143B227ILE0-0.018-0.01119.653-0.003-0.0030.0000.0000.0000.000
144B228SER0-0.064-0.03522.6570.0150.0150.0000.0000.0000.000
145B229LEU00.0430.02420.802-0.032-0.0320.0000.0000.0000.000
146B230SER0-0.0040.01723.4410.0310.0310.0000.0000.0000.000
147B231PRO00.0440.00823.462-0.022-0.0220.0000.0000.0000.000
148B232SER0-0.083-0.03923.5160.0040.0040.0000.0000.0000.000
149B233ASP-1-0.865-0.92219.442-0.314-0.3140.0000.0000.0000.000
150B234ARG10.8710.91112.7550.4560.4560.0000.0000.0000.000
151B235ILE0-0.011-0.00216.708-0.061-0.0610.0000.0000.0000.000
152B236ILE0-0.010-0.00711.9250.0070.0070.0000.0000.0000.000
153B237LEU00.0100.01516.158-0.014-0.0140.0000.0000.0000.000
154B238LEU0-0.0100.00013.423-0.007-0.0070.0000.0000.0000.000
155B239SER00.0400.02217.0550.0420.0420.0000.0000.0000.000
156B240THR0-0.027-0.03319.252-0.005-0.0050.0000.0000.0000.000
157B241CYS0-0.055-0.02721.2260.0190.0190.0000.0000.0000.000
158B242PHE0-0.0050.01124.351-0.015-0.0150.0000.0000.0000.000
159B243LEU0-0.003-0.02425.5020.0150.0150.0000.0000.0000.000
160B244ASP-1-0.932-0.95228.746-0.168-0.1680.0000.0000.0000.000
161B245VAL0-0.0270.00030.8890.0140.0140.0000.0000.0000.000
162B246THR0-0.010-0.01131.370-0.004-0.0040.0000.0000.0000.000
163B247ASN0-0.054-0.02930.8220.0010.0010.0000.0000.0000.000
164B248GLY00.0860.05729.741-0.004-0.0040.0000.0000.0000.000
165B249ARG10.8390.91824.4520.2170.2170.0000.0000.0000.000
166B250HIS00.0440.02722.5890.0010.0010.0000.0000.0000.000
167B251ILE00.001-0.00920.502-0.029-0.0290.0000.0000.0000.000
168B252VAL0-0.0170.00216.4150.0150.0150.0000.0000.0000.000
169B253VAL00.0310.00418.149-0.037-0.0370.0000.0000.0000.000
170B254ALA0-0.011-0.00914.449-0.010-0.0100.0000.0000.0000.000
171B255LYS10.8930.94716.3840.4020.4020.0000.0000.0000.000
172B256ILE0-0.023-0.01711.063-0.102-0.1020.0000.0000.0000.000
173B257THR0-0.011-0.00912.4720.0910.0910.0000.0000.0000.000
174B258ASP-1-0.935-0.97111.969-0.472-0.4720.0000.0000.0000.000
175B259THR0-0.044-0.0199.660-0.066-0.0660.0000.0000.0000.000