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: N29QQ

Calculation Name: 5L0W-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5L0W

Chain ID: B

ChEMBL ID:

UniProt ID: G0SH41

Base Structure: X-ray

Registration Date: 2023-09-26

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2087738.018643
FMO2-HF: Nuclear repulsion 2006087.796508
FMO2-HF: Total energy -81650.222135
FMO2-MP2: Total energy -81889.331215


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:5:ASP)


Summations of interaction energy for fragment #1(B:5:ASP)
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.
-49.776-41.5261.579-4.739-5.0880.016
Interaction energy analysis for fragmet #1(B:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.863 / q_NPA : -0.926
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].
3B7PHE0-0.051-0.0262.456-20.426-12.7911.552-4.390-4.7960.018
4B8THR00.0090.0043.342-0.651-0.1230.028-0.346-0.209-0.002
5B9PHE00.0060.0004.627-1.323-1.236-0.001-0.003-0.0830.000
6B10ILE00.0150.0046.099-2.623-2.6230.0000.0000.0000.000
7B11PRO0-0.0120.0069.8540.2760.2760.0000.0000.0000.000
8B12LEU00.0180.00712.060-1.242-1.2420.0000.0000.0000.000
9B13HIS0-0.046-0.03214.686-0.443-0.4430.0000.0000.0000.000
10B14ILE00.0120.01118.023-0.027-0.0270.0000.0000.0000.000
11B15ASP-1-0.841-0.91820.01111.20711.2070.0000.0000.0000.000
12B16PRO00.0330.01223.814-0.071-0.0710.0000.0000.0000.000
13B17LYS10.9280.96425.174-11.050-11.0500.0000.0000.0000.000
14B18SER0-0.040-0.03326.473-0.093-0.0930.0000.0000.0000.000
15B19LYS10.8130.91723.512-11.302-11.3020.0000.0000.0000.000
16B20ALA00.0140.02822.4250.4730.4730.0000.0000.0000.000
17B21ILE00.017-0.00916.6820.2380.2380.0000.0000.0000.000
18B22SER0-0.008-0.00919.352-0.640-0.6400.0000.0000.0000.000
19B23ALA00.0410.02017.0820.9730.9730.0000.0000.0000.000
20B24ALA0-0.0030.01215.420-0.636-0.6360.0000.0000.0000.000
21B25PRO00.002-0.01317.414-0.249-0.2490.0000.0000.0000.000
22B26ASN0-0.034-0.00618.4750.4650.4650.0000.0000.0000.000
23B27ALA00.0300.02413.7590.3390.3390.0000.0000.0000.000
24B28LEU00.0350.00512.4900.9290.9290.0000.0000.0000.000
25B29GLY00.0060.02014.4630.1080.1080.0000.0000.0000.000
26B30THR0-0.038-0.01217.372-0.822-0.8220.0000.0000.0000.000
27B31PRO00.0390.01719.4950.2790.2790.0000.0000.0000.000
28B32SER00.006-0.00221.4140.0570.0570.0000.0000.0000.000
29B33ALA00.0670.02116.2200.0160.0160.0000.0000.0000.000
30B34ASN00.024-0.00717.6071.0371.0370.0000.0000.0000.000
31B35LYS10.9791.00119.016-11.263-11.2630.0000.0000.0000.000
32B36ALA0-0.003-0.00318.932-0.170-0.1700.0000.0000.0000.000
33B37LEU00.0430.02414.5400.1160.1160.0000.0000.0000.000
34B38GLU-1-0.916-0.96117.85312.95112.9510.0000.0000.0000.000
35B39THR0-0.094-0.05920.959-0.423-0.4230.0000.0000.0000.000
36B40GLU-1-0.922-0.95317.24415.18115.1810.0000.0000.0000.000
37B41LEU00.0390.01316.2270.0610.0610.0000.0000.0000.000
38B42ALA0-0.052-0.02019.891-0.312-0.3120.0000.0000.0000.000
39B43ALA00.007-0.00222.387-0.398-0.3980.0000.0000.0000.000
40B44LEU00.0370.02917.058-0.266-0.2660.0000.0000.0000.000
41B45ASN00.0210.01021.185-0.122-0.1220.0000.0000.0000.000
42B46ALA0-0.071-0.04023.437-0.443-0.4430.0000.0000.0000.000
43B47LEU00.0410.02721.654-0.476-0.4760.0000.0000.0000.000
44B48HIS00.0280.01921.8330.0400.0400.0000.0000.0000.000
45B49ARG10.9430.95924.441-11.454-11.4540.0000.0000.0000.000
46B50ALA00.0010.01927.836-0.372-0.3720.0000.0000.0000.000
47B51LEU00.011-0.00423.636-0.318-0.3180.0000.0000.0000.000
48B52HIS0-0.046-0.02027.634-0.111-0.1110.0000.0000.0000.000
49B53THR0-0.055-0.05029.117-0.368-0.3680.0000.0000.0000.000
50B54GLN0-0.033-0.02031.554-0.376-0.3760.0000.0000.0000.000
51B55ILE0-0.0340.00728.795-0.111-0.1110.0000.0000.0000.000
52B56GLU-1-0.900-0.93932.2718.3178.3170.0000.0000.0000.000
53B57GLY0-0.025-0.00733.877-0.155-0.1550.0000.0000.0000.000
54B58PRO00.0170.00232.8480.1420.1420.0000.0000.0000.000
55B59ILE00.000-0.00827.1920.2780.2780.0000.0000.0000.000
56B60PRO00.0080.01525.159-0.127-0.1270.0000.0000.0000.000
57B61VAL0-0.020-0.01923.1950.5270.5270.0000.0000.0000.000
58B62PRO00.010-0.00125.338-0.397-0.3970.0000.0000.0000.000
59B63PRO0-0.0040.01727.9840.2120.2120.0000.0000.0000.000
60B64PRO00.008-0.00130.0620.0750.0750.0000.0000.0000.000
61B65PRO00.0440.00829.942-0.310-0.3100.0000.0000.0000.000
62B66VAL0-0.020-0.01332.973-0.265-0.2650.0000.0000.0000.000
63B67PRO0-0.043-0.00334.575-0.288-0.2880.0000.0000.0000.000
64B68VAL00.0420.02136.9210.1200.1200.0000.0000.0000.000
65B69ASN0-0.001-0.01338.464-0.461-0.4610.0000.0000.0000.000
66B70PRO00.0310.01540.4590.0070.0070.0000.0000.0000.000
67B71LYS10.9880.99643.192-7.470-7.4700.0000.0000.0000.000
68B72ARG10.8990.94138.113-8.356-8.3560.0000.0000.0000.000
69B73SER00.0670.00843.423-0.051-0.0510.0000.0000.0000.000
70B74ALA0-0.0010.01945.013-0.165-0.1650.0000.0000.0000.000
71B75ASN0-0.006-0.01146.533-0.287-0.2870.0000.0000.0000.000
72B76ILE00.0460.03543.141-0.153-0.1530.0000.0000.0000.000
73B77ASN0-0.009-0.01247.771-0.243-0.2430.0000.0000.0000.000
74B78LYS10.9140.96150.651-6.392-6.3920.0000.0000.0000.000
75B79LEU00.0180.00049.259-0.128-0.1280.0000.0000.0000.000
76B80ARG10.8870.95250.564-6.223-6.2230.0000.0000.0000.000
77B81GLU-1-0.767-0.85952.6875.4135.4130.0000.0000.0000.000
78B82SER00.0020.01555.223-0.121-0.1210.0000.0000.0000.000
79B83GLY00.007-0.00455.267-0.103-0.1030.0000.0000.0000.000
80B84ASN0-0.013-0.01156.092-0.037-0.0370.0000.0000.0000.000
81B85ALA0-0.043-0.01858.499-0.111-0.1110.0000.0000.0000.000
82B86GLU-1-0.822-0.90059.2325.0735.0730.0000.0000.0000.000
83B87TYR00.0010.00659.384-0.024-0.0240.0000.0000.0000.000
84B88ARG10.8210.87660.212-5.365-5.3650.0000.0000.0000.000
85B89LYS10.7960.88763.970-5.121-5.1210.0000.0000.0000.000
86B90GLN0-0.037-0.01464.969-0.076-0.0760.0000.0000.0000.000
87B91ARG10.8690.93360.739-5.211-5.2110.0000.0000.0000.000
88B92TYR00.058-0.00160.1770.0890.0890.0000.0000.0000.000
89B93GLY00.0370.01458.2420.1000.1000.0000.0000.0000.000
90B94ASP-1-0.774-0.86756.9935.4395.4390.0000.0000.0000.000
91B95ALA00.0420.03256.4650.1070.1070.0000.0000.0000.000
92B96ILE00.0220.02553.3630.1350.1350.0000.0000.0000.000
93B97LYS10.8840.94952.614-5.428-5.4280.0000.0000.0000.000
94B98LEU0-0.021-0.00551.5870.1510.1510.0000.0000.0000.000
95B99TYR00.008-0.02650.9790.1230.1230.0000.0000.0000.000
96B100THR0-0.010-0.00947.6740.1740.1740.0000.0000.0000.000
97B101LEU0-0.0070.00946.9570.1680.1680.0000.0000.0000.000
98B102GLY0-0.0030.00246.3110.1610.1610.0000.0000.0000.000
99B103LEU00.009-0.00444.7080.1660.1660.0000.0000.0000.000
100B104GLN00.0070.00442.5400.1450.1450.0000.0000.0000.000
101B105MET0-0.035-0.00441.4010.1910.1910.0000.0000.0000.000
102B106ALA00.0100.00641.6920.1350.1350.0000.0000.0000.000
103B107LEU0-0.022-0.01238.6530.1990.1990.0000.0000.0000.000
104B108THR0-0.042-0.02436.8220.1910.1910.0000.0000.0000.000
105B109ARG10.7170.83236.192-8.082-8.0820.0000.0000.0000.000
106B110PRO00.0320.01932.3360.1250.1250.0000.0000.0000.000
107B111ALA00.0330.01029.227-0.072-0.0720.0000.0000.0000.000
108B112TRP00.0060.00927.7740.2510.2510.0000.0000.0000.000
109B113GLU-1-0.873-0.93229.8558.7078.7070.0000.0000.0000.000
110B114PRO0-0.008-0.00733.4670.0580.0580.0000.0000.0000.000
111B115ALA00.0750.03033.369-0.242-0.2420.0000.0000.0000.000
112B116GLY0-0.007-0.00735.354-0.204-0.2040.0000.0000.0000.000
113B117LEU00.0120.01638.281-0.222-0.2220.0000.0000.0000.000
114B118VAL00.0240.01536.878-0.229-0.2290.0000.0000.0000.000
115B119ARG10.8530.91736.585-8.509-8.5090.0000.0000.0000.000
116B120ASP-1-0.795-0.88141.0026.9606.9600.0000.0000.0000.000
117B121GLU-1-0.794-0.86642.4977.3147.3140.0000.0000.0000.000
118B122ILE00.005-0.01140.410-0.199-0.1990.0000.0000.0000.000
119B123HIS00.0030.01344.496-0.237-0.2370.0000.0000.0000.000
120B124GLN00.0300.03046.323-0.300-0.3000.0000.0000.0000.000
121B125LEU0-0.008-0.00546.175-0.184-0.1840.0000.0000.0000.000
122B126TYR00.0300.01742.655-0.142-0.1420.0000.0000.0000.000
123B127SER00.0200.01648.749-0.178-0.1780.0000.0000.0000.000
124B128ASN0-0.111-0.06251.724-0.232-0.2320.0000.0000.0000.000
125B129ARG10.8050.85147.719-6.640-6.6400.0000.0000.0000.000
126B130ALA00.0610.03552.029-0.094-0.0940.0000.0000.0000.000
127B131GLN00.0040.00453.747-0.122-0.1220.0000.0000.0000.000
128B132ALA0-0.005-0.02056.231-0.112-0.1120.0000.0000.0000.000
129B133TYR0-0.010-0.00752.535-0.059-0.0590.0000.0000.0000.000
130B134MET0-0.026-0.00656.441-0.094-0.0940.0000.0000.0000.000
131B135GLN0-0.058-0.00459.278-0.163-0.1630.0000.0000.0000.000
132B136LEU0-0.043-0.02159.029-0.100-0.1000.0000.0000.0000.000
133B137GLY00.0090.01761.602-0.030-0.0300.0000.0000.0000.000
134B138GLN0-0.076-0.03656.159-0.047-0.0470.0000.0000.0000.000
135B139TRP00.0690.00656.6340.1350.1350.0000.0000.0000.000
136B140PRO00.0220.00653.2650.0850.0850.0000.0000.0000.000
137B141GLU-1-0.799-0.90451.2505.9335.9330.0000.0000.0000.000
138B142ALA00.0020.01451.3210.1170.1170.0000.0000.0000.000
139B143ALA00.011-0.00652.4940.0730.0730.0000.0000.0000.000
140B144ALA00.0290.02047.6750.1170.1170.0000.0000.0000.000
141B145ASP-1-0.756-0.83747.7166.6436.6430.0000.0000.0000.000
142B146ALA0-0.025-0.02348.4480.1020.1020.0000.0000.0000.000
143B147GLU-1-0.843-0.91245.4676.8476.8470.0000.0000.0000.000
144B148CYS0-0.054-0.02544.2990.1930.1930.0000.0000.0000.000
145B149SER0-0.064-0.04944.4450.1190.1190.0000.0000.0000.000
146B150VAL00.0030.00246.1230.0970.0970.0000.0000.0000.000
147B151GLU-1-0.845-0.89139.8398.0008.0000.0000.0000.0000.000
148B152ALA0-0.063-0.00841.4150.2260.2260.0000.0000.0000.000
149B153LYS10.8380.89542.082-6.868-6.8680.0000.0000.0000.000
150B154ARG10.9210.94240.437-7.788-7.7880.0000.0000.0000.000
151B155GLN00.0470.02245.315-0.209-0.2090.0000.0000.0000.000
152B156GLY00.0300.01647.8320.0620.0620.0000.0000.0000.000
153B157ASN0-0.058-0.04747.975-0.172-0.1720.0000.0000.0000.000
154B158ALA00.0980.05251.0610.0220.0220.0000.0000.0000.000
155B159LYS10.8320.90254.113-5.433-5.4330.0000.0000.0000.000
156B160ALA0-0.0140.00550.639-0.069-0.0690.0000.0000.0000.000
157B161TRP00.0490.02547.882-0.027-0.0270.0000.0000.0000.000
158B162TYR00.0670.03253.181-0.038-0.0380.0000.0000.0000.000
159B163ARG10.8650.92154.507-5.829-5.8290.0000.0000.0000.000
160B164ARG10.8430.92548.139-6.567-6.5670.0000.0000.0000.000
161B165GLY00.0480.02654.141-0.025-0.0250.0000.0000.0000.000
162B166LYS10.8700.91256.546-5.107-5.1070.0000.0000.0000.000
163B167CYS0-0.049-0.02155.515-0.064-0.0640.0000.0000.0000.000
164B168LEU0-0.015-0.00452.665-0.039-0.0390.0000.0000.0000.000
165B169MET00.0260.02456.871-0.085-0.0850.0000.0000.0000.000
166B170GLU-1-0.850-0.90160.3974.8894.8890.0000.0000.0000.000
167B171MET0-0.094-0.02154.622-0.025-0.0250.0000.0000.0000.000
168B172ARG10.8620.92459.315-4.909-4.9090.0000.0000.0000.000
169B173ARG10.8180.87850.778-6.014-6.0140.0000.0000.0000.000
170B174LEU00.0640.01357.5250.0740.0740.0000.0000.0000.000
171B175GLN00.008-0.00356.706-0.082-0.0820.0000.0000.0000.000
172B176GLU-1-0.765-0.84351.7626.0966.0960.0000.0000.0000.000
173B177ALA0-0.008-0.00454.2510.0880.0880.0000.0000.0000.000
174B178ARG10.9040.94956.614-5.344-5.3440.0000.0000.0000.000
175B179GLU-1-0.906-0.95852.8485.9685.9680.0000.0000.0000.000
176B180TRP0-0.066-0.03847.9510.1390.1390.0000.0000.0000.000
177B181VAL00.005-0.01653.0600.0740.0740.0000.0000.0000.000
178B182ALA0-0.039-0.00655.4440.0010.0010.0000.0000.0000.000
179B183ARG10.9830.99347.184-6.597-6.5970.0000.0000.0000.000
180B184GLY0-0.036-0.03651.2970.1010.1010.0000.0000.0000.000
181B185LEU0-0.056-0.03052.525-0.011-0.0110.0000.0000.0000.000
182B186GLU-1-0.957-0.95550.3576.3026.3020.0000.0000.0000.000
183B187PHE0-0.073-0.04445.1740.1260.1260.0000.0000.0000.000
184B188GLU-1-0.877-0.92650.1915.8165.8160.0000.0000.0000.000
185B189GLY0-0.081-0.05252.1260.1010.1010.0000.0000.0000.000
186B190GLU-1-0.857-0.92654.1125.1885.1880.0000.0000.0000.000
187B191GLU-1-0.855-0.91857.5495.4775.4770.0000.0000.0000.000
188B192LYS10.8930.91559.318-5.067-5.0670.0000.0000.0000.000
189B193GLU-1-0.814-0.89060.4315.2555.2550.0000.0000.0000.000
190B194LEU00.0240.00355.201-0.032-0.0320.0000.0000.0000.000
191B195ALA00.0240.02359.794-0.013-0.0130.0000.0000.0000.000
192B196GLU-1-0.922-0.95362.3934.7014.7010.0000.0000.0000.000
193B197LEU0-0.035-0.01659.035-0.041-0.0410.0000.0000.0000.000
194B198LEU0-0.0020.00059.413-0.011-0.0110.0000.0000.0000.000
195B199LYS10.9150.96362.145-4.755-4.7550.0000.0000.0000.000
196B200GLU-1-0.871-0.90665.2584.8154.8150.0000.0000.0000.000
197B201ILE0-0.041-0.02159.569-0.035-0.0350.0000.0000.0000.000
198B202ASP-1-0.797-0.91563.2235.0515.0510.0000.0000.0000.000
199B203SER0-0.044-0.02964.753-0.077-0.0770.0000.0000.0000.000
200B204LYS10.8070.87465.622-4.905-4.9050.0000.0000.0000.000
201B205LEU0-0.012-0.00461.216-0.019-0.0190.0000.0000.0000.000
202B206ALA0-0.022-0.00365.867-0.024-0.0240.0000.0000.0000.000
203B207ALA00.002-0.01168.806-0.052-0.0520.0000.0000.0000.000
204B208GLU-1-0.871-0.92265.2004.8634.8630.0000.0000.0000.000
205B209LYS10.7670.86165.155-4.881-4.8810.0000.0000.0000.000
206B210ALA00.0390.03469.315-0.012-0.0120.0000.0000.0000.000
207B211SER0-0.036-0.01872.371-0.084-0.0840.0000.0000.0000.000
208B212ARG10.7570.87165.754-4.724-4.7240.0000.0000.0000.000
209B213ASP-1-0.823-0.87670.7564.5054.5050.0000.0000.0000.000