Manual

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

tag_button

FMODB ID: 4JG8N

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1896460.627378
FMO2-HF: Nuclear repulsion 1826880.252384
FMO2-HF: Total energy -69580.374994
FMO2-MP2: Total energy -69785.132174


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.
-21.335-17.79716.819-9.559-10.798-0.078
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 : -0.050 / 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].
3B78PHE0-0.052-0.0203.818-0.8011.025-0.014-0.881-0.9310.002
4B79SER00.0780.0396.015-0.622-0.6220.0000.0000.0000.000
5B80LYS10.7520.8489.014-0.851-0.8510.0000.0000.0000.000
6B81LEU00.0420.0196.965-0.121-0.1210.0000.0000.0000.000
7B82GLN0-0.007-0.0118.577-0.033-0.0330.0000.0000.0000.000
8B83GLU-1-0.849-0.90911.2460.5290.5290.0000.0000.0000.000
9B84LEU0-0.079-0.03413.480-0.076-0.0760.0000.0000.0000.000
10B85ASN0-0.053-0.03012.528-0.022-0.0220.0000.0000.0000.000
11B86PRO0-0.0040.00312.9750.0240.0240.0000.0000.0000.000
12B87GLU-1-0.842-0.92414.7190.2960.2960.0000.0000.0000.000
13B88VAL0-0.049-0.0128.674-0.024-0.0240.0000.0000.0000.000
14B89LEU0-0.0120.00110.5210.0290.0290.0000.0000.0000.000
15B90GLY0-0.021-0.0296.386-0.071-0.0710.0000.0000.0000.000
16B91TRP0-0.038-0.0213.725-0.359-0.1220.005-0.053-0.1890.000
17B92ILE0-0.0100.0045.404-0.181-0.1810.0000.0000.0000.000
18B93ASN0-0.037-0.0285.997-0.224-0.2240.0000.0000.0000.000
19B94VAL00.0360.0267.777-0.284-0.2840.0000.0000.0000.000
20B95TYR00.0420.0226.4190.1060.1060.0000.0000.0000.000
21B96GLY0-0.021-0.01911.2750.0390.0390.0000.0000.0000.000
22B97THR0-0.066-0.03712.9410.0360.0360.0000.0000.0000.000
23B98ASN0-0.080-0.06612.9810.0170.0170.0000.0000.0000.000
24B99ILE0-0.016-0.00511.4610.0390.0390.0000.0000.0000.000
25B100ASP-1-0.820-0.8856.9371.1281.1280.0000.0000.0000.000
26B101TYR00.0100.0028.560-0.149-0.1490.0000.0000.0000.000
27B102PRO00.0150.0298.4070.1380.1380.0000.0000.0000.000
28B103LEU0-0.040-0.0227.922-0.088-0.0880.0000.0000.0000.000
29B104VAL00.0440.01210.7230.0120.0120.0000.0000.0000.000
30B105GLN0-0.067-0.03713.890-0.017-0.0170.0000.0000.0000.000
31B106ALA00.0180.02416.9040.0100.0100.0000.0000.0000.000
32B107LYS10.8950.92520.469-0.100-0.1000.0000.0000.0000.000
33B108ASP-1-0.925-0.97223.6020.0610.0610.0000.0000.0000.000
34B109ASN0-0.0360.00324.5330.0000.0000.0000.0000.0000.000
35B110GLU-1-0.934-0.96322.9570.0730.0730.0000.0000.0000.000
36B120GLU-1-0.962-0.98919.0250.1930.1930.0000.0000.0000.000
37B121PHE00.0310.01013.1930.0150.0150.0000.0000.0000.000
38B122ALA0-0.022-0.00817.323-0.004-0.0040.0000.0000.0000.000
39B123ALA0-0.0220.00116.757-0.017-0.0170.0000.0000.0000.000
40B124THR0-0.055-0.05112.5060.0460.0460.0000.0000.0000.000
41B125GLY00.0480.03513.7290.0220.0220.0000.0000.0000.000
42B126ALA00.027-0.00313.5720.0440.0440.0000.0000.0000.000
43B127ILE0-0.0240.00912.465-0.037-0.0370.0000.0000.0000.000
44B128PHE0-0.007-0.01013.8620.0160.0160.0000.0000.0000.000
45B129LEU0-0.006-0.00212.421-0.020-0.0200.0000.0000.0000.000
46B130ASP-1-0.721-0.82316.5370.0350.0350.0000.0000.0000.000
47B131ALA00.0010.00019.663-0.001-0.0010.0000.0000.0000.000
48B132ARG10.8000.86921.758-0.016-0.0160.0000.0000.0000.000
49B133ASN0-0.021-0.01517.992-0.003-0.0030.0000.0000.0000.000
50B134ASN0-0.035-0.02817.2030.0190.0190.0000.0000.0000.000
51B135PRO00.000-0.00614.798-0.013-0.0130.0000.0000.0000.000
52B136LYS10.8560.93712.738-0.045-0.0450.0000.0000.0000.000
53B137PHE00.0320.00710.439-0.043-0.0430.0000.0000.0000.000
54B138GLU-1-0.889-0.93814.261-0.052-0.0520.0000.0000.0000.000
55B139ASP-1-0.821-0.87017.263-0.023-0.0230.0000.0000.0000.000
56B140PHE0-0.0050.00418.370-0.013-0.0130.0000.0000.0000.000
57B141ASN00.0180.00519.541-0.016-0.0160.0000.0000.0000.000
58B142THR0-0.008-0.01115.0560.0160.0160.0000.0000.0000.000
59B143ILE00.0020.00917.437-0.007-0.0070.0000.0000.0000.000
60B144ILE0-0.029-0.01912.7420.0150.0150.0000.0000.0000.000
61B145TYR0-0.018-0.03216.767-0.012-0.0120.0000.0000.0000.000
62B146GLY00.0590.02617.4470.0260.0260.0000.0000.0000.000
63B147HIS0-0.0120.01018.536-0.021-0.0210.0000.0000.0000.000
64B148HIS00.0320.00721.7220.0140.0140.0000.0000.0000.000
65B149VAL0-0.015-0.01223.066-0.002-0.0020.0000.0000.0000.000
66B150GLU-1-0.959-0.96324.9410.0380.0380.0000.0000.0000.000
67B151ASN0-0.063-0.04126.021-0.007-0.0070.0000.0000.0000.000
68B152GLY00.015-0.02123.276-0.004-0.0040.0000.0000.0000.000
69B153VAL00.0030.01218.3600.0040.0040.0000.0000.0000.000
70B154MET0-0.056-0.02319.1230.0090.0090.0000.0000.0000.000
71B155PHE00.0980.06715.243-0.002-0.0020.0000.0000.0000.000
72B156GLY0-0.021-0.02218.704-0.014-0.0140.0000.0000.0000.000
73B157ASP-1-0.749-0.86217.138-0.021-0.0210.0000.0000.0000.000
74B158VAL00.0210.01417.565-0.017-0.0170.0000.0000.0000.000
75B159ALA00.0480.02419.755-0.013-0.0130.0000.0000.0000.000
76B160LYS10.8290.90920.3670.0130.0130.0000.0000.0000.000
77B161PHE0-0.046-0.01916.154-0.012-0.0120.0000.0000.0000.000
78B162ALA00.0690.03422.203-0.006-0.0060.0000.0000.0000.000
79B163ASP-1-0.898-0.93525.136-0.071-0.0710.0000.0000.0000.000
80B164GLN0-0.033-0.03325.0770.0000.0000.0000.0000.0000.000
81B165GLU-1-0.882-0.94825.352-0.105-0.1050.0000.0000.0000.000
82B166PHE0-0.056-0.03218.561-0.017-0.0170.0000.0000.0000.000
83B167PHE00.005-0.00520.619-0.018-0.0180.0000.0000.0000.000
84B168ASP-1-0.873-0.93120.889-0.140-0.1400.0000.0000.0000.000
85B169GLN0-0.110-0.04720.406-0.026-0.0260.0000.0000.0000.000
86B170HIS10.7720.92515.4270.1290.1290.0000.0000.0000.000
87B171ARG10.8660.91516.4480.2650.2650.0000.0000.0000.000
88B172TYR0-0.042-0.03212.1920.0070.0070.0000.0000.0000.000
89B173GLY00.0420.0129.4180.0840.0840.0000.0000.0000.000
90B174SER0-0.0330.0044.1520.2540.299-0.001-0.007-0.0360.000
91B175ILE00.0140.0105.7580.5250.5250.0000.0000.0000.000
92B176TYR0-0.0020.0101.952-1.460-2.1088.955-4.075-4.232-0.017
93B177TYR00.0810.0293.9880.3360.4350.001-0.088-0.0130.000
94B178ASN0-0.001-0.0047.235-0.026-0.0260.0000.0000.0000.000
95B179GLY00.0060.0116.479-0.004-0.0040.0000.0000.0000.000
96B180VAL0-0.081-0.0396.3840.0940.0940.0000.0000.0000.000
97B181GLU-1-0.832-0.9282.096-19.630-17.6557.874-4.447-5.401-0.063
98B182LYS10.7780.8835.2630.8510.855-0.001-0.0080.0040.000
99B183GLY00.0850.0387.418-0.214-0.2140.0000.0000.0000.000
100B184LEU0-0.054-0.0189.4850.1520.1520.0000.0000.0000.000
101B185GLU-1-0.799-0.88911.612-0.325-0.3250.0000.0000.0000.000
102B186ILE00.0120.00014.6510.0320.0320.0000.0000.0000.000
103B187PHE00.000-0.02317.030-0.011-0.0110.0000.0000.0000.000
104B188GLU-1-0.806-0.92720.536-0.068-0.0680.0000.0000.0000.000
105B189MET0-0.0540.00121.213-0.001-0.0010.0000.0000.0000.000
106B190LEU00.0530.02923.394-0.001-0.0010.0000.0000.0000.000
107B191GLU-1-0.895-0.96125.509-0.008-0.0080.0000.0000.0000.000
108B192VAL00.0050.00926.765-0.002-0.0020.0000.0000.0000.000
109B193ASP-1-0.758-0.87729.5240.0060.0060.0000.0000.0000.000
110B194ALA0-0.048-0.03328.510-0.001-0.0010.0000.0000.0000.000
111B195TYR0-0.109-0.05229.1570.0030.0030.0000.0000.0000.000
112B196ASP-1-0.791-0.88529.905-0.020-0.0200.0000.0000.0000.000
113B197PHE0-0.021-0.03429.427-0.001-0.0010.0000.0000.0000.000
114B198ASN0-0.101-0.04629.914-0.002-0.0020.0000.0000.0000.000
115B199ILE00.0250.02525.332-0.005-0.0050.0000.0000.0000.000
116B200TYR0-0.037-0.02723.239-0.003-0.0030.0000.0000.0000.000
117B201ASP-1-0.936-0.96725.892-0.008-0.0080.0000.0000.0000.000
118B202PRO0-0.038-0.00922.078-0.007-0.0070.0000.0000.0000.000
119B203GLY00.0110.00822.2830.0030.0030.0000.0000.0000.000
120B204ILE0-0.0180.01023.1920.0020.0020.0000.0000.0000.000
121B205GLN0-0.005-0.01025.173-0.009-0.0090.0000.0000.0000.000
122B206GLY0-0.025-0.01527.4860.0040.0040.0000.0000.0000.000
123B207GLU-1-0.879-0.94128.792-0.069-0.0690.0000.0000.0000.000
124B208ASP-1-0.877-0.94329.861-0.048-0.0480.0000.0000.0000.000
125B209ARG10.8580.92430.3990.0290.0290.0000.0000.0000.000
126B210GLN0-0.015-0.01524.890-0.001-0.0010.0000.0000.0000.000
127B211GLN0-0.014-0.01827.626-0.008-0.0080.0000.0000.0000.000
128B212ALA0-0.0020.00229.454-0.001-0.0010.0000.0000.0000.000
129B213TYR0-0.047-0.03723.688-0.003-0.0030.0000.0000.0000.000
130B214LEU00.008-0.00324.093-0.001-0.0010.0000.0000.0000.000
131B215ASP-1-0.855-0.92727.269-0.068-0.0680.0000.0000.0000.000
132B216HIS0-0.046-0.01729.8890.0000.0000.0000.0000.0000.000
133B217LEU00.0080.01123.0720.0010.0010.0000.0000.0000.000
134B218LEU00.0590.03725.253-0.001-0.0010.0000.0000.0000.000
135B219SER0-0.177-0.07828.2280.0010.0010.0000.0000.0000.000
136B220VAL0-0.018-0.00929.1420.0030.0030.0000.0000.0000.000
137B221ALA0-0.0380.00027.2030.0020.0020.0000.0000.0000.000
138B222MET0-0.063-0.02827.4780.0020.0020.0000.0000.0000.000
139B223HIS0-0.057-0.02924.903-0.006-0.0060.0000.0000.0000.000
140B224LYS10.8980.92424.4960.0750.0750.0000.0000.0000.000
141B225ARG10.7690.89019.5170.1700.1700.0000.0000.0000.000
142B226ASP-1-0.937-0.96224.516-0.116-0.1160.0000.0000.0000.000
143B227ILE0-0.031-0.01519.660-0.012-0.0120.0000.0000.0000.000
144B228SER0-0.047-0.02622.7620.0150.0150.0000.0000.0000.000
145B229LEU00.0090.01220.743-0.018-0.0180.0000.0000.0000.000
146B230SER00.0010.00523.4390.0140.0140.0000.0000.0000.000
147B231PRO00.0490.01023.456-0.009-0.0090.0000.0000.0000.000
148B232SER0-0.043-0.02223.4550.0060.0060.0000.0000.0000.000
149B233ASP-1-0.860-0.89519.485-0.199-0.1990.0000.0000.0000.000
150B234ARG10.8860.92312.9720.2400.2400.0000.0000.0000.000
151B235ILE0-0.0090.00016.702-0.033-0.0330.0000.0000.0000.000
152B236ILE0-0.007-0.00511.9700.0170.0170.0000.0000.0000.000
153B237LEU00.0090.01916.157-0.010-0.0100.0000.0000.0000.000
154B238LEU0-0.012-0.00414.1050.0190.0190.0000.0000.0000.000
155B239SER00.0210.01417.314-0.011-0.0110.0000.0000.0000.000
156B240THR00.002-0.03120.0690.0160.0160.0000.0000.0000.000
157B241CYS0-0.042-0.02021.978-0.009-0.0090.0000.0000.0000.000
158B242PHE00.0000.00925.307-0.001-0.0010.0000.0000.0000.000
159B243LEU0-0.015-0.02426.8160.0000.0000.0000.0000.0000.000
160B244ASP-1-0.929-0.95429.721-0.002-0.0020.0000.0000.0000.000
161B245VAL0-0.026-0.00131.837-0.001-0.0010.0000.0000.0000.000
162B246THR0-0.0030.00132.2530.0030.0030.0000.0000.0000.000
163B247ASN0-0.099-0.07631.4290.0020.0020.0000.0000.0000.000
164B248GLY00.1090.06430.440-0.001-0.0010.0000.0000.0000.000
165B249ARG10.8280.92325.173-0.011-0.0110.0000.0000.0000.000
166B250HIS00.0410.02223.483-0.010-0.0100.0000.0000.0000.000
167B251ILE0-0.004-0.01220.6830.0100.0100.0000.0000.0000.000
168B252VAL0-0.0180.00216.991-0.009-0.0090.0000.0000.0000.000
169B253VAL00.0260.00518.4140.0080.0080.0000.0000.0000.000
170B254ALA0-0.006-0.00514.513-0.020-0.0200.0000.0000.0000.000
171B255LYS10.8470.91316.3890.2370.2370.0000.0000.0000.000
172B256ILE0-0.019-0.01411.004-0.054-0.0540.0000.0000.0000.000
173B257THR0-0.016-0.01312.4510.0130.0130.0000.0000.0000.000
174B258ASP-1-0.820-0.90511.956-0.551-0.5510.0000.0000.0000.000
175B259THR0-0.078-0.0279.597-0.097-0.0970.0000.0000.0000.000