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: 8N5MY

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2087354.909393
FMO2-HF: Nuclear repulsion 2005705.936799
FMO2-HF: Total energy -81648.972595
FMO2-MP2: Total energy -81888.120337


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.
-40.703-36.0271.535-2.535-3.674-0.002
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 : -0.920 / q_NPA : -0.970
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].
3B7PHE0-0.045-0.0032.442-14.649-10.7331.503-2.113-3.3040.001
4B8THR00.0190.0083.2560.8481.5370.033-0.420-0.301-0.003
5B9PHE00.0020.0034.673-1.836-1.765-0.001-0.002-0.0690.000
6B10ILE00.0250.0066.101-2.264-2.2640.0000.0000.0000.000
7B11PRO0-0.0170.0039.8650.1940.1940.0000.0000.0000.000
8B12LEU00.0120.00212.099-1.152-1.1520.0000.0000.0000.000
9B13HIS0-0.045-0.02514.740-0.405-0.4050.0000.0000.0000.000
10B14ILE00.0120.00818.090-0.018-0.0180.0000.0000.0000.000
11B15ASP-1-0.854-0.93020.17710.95010.9500.0000.0000.0000.000
12B16PRO00.0240.00523.972-0.038-0.0380.0000.0000.0000.000
13B17LYS10.9350.97225.403-11.014-11.0140.0000.0000.0000.000
14B18SER0-0.023-0.02026.749-0.065-0.0650.0000.0000.0000.000
15B19LYS10.8520.93323.698-11.125-11.1250.0000.0000.0000.000
16B20ALA00.0020.01922.5690.4540.4540.0000.0000.0000.000
17B21ILE00.0340.00316.7420.1970.1970.0000.0000.0000.000
18B22SER0-0.023-0.01619.383-0.626-0.6260.0000.0000.0000.000
19B23ALA00.0390.01917.1060.9050.9050.0000.0000.0000.000
20B24ALA00.0010.01215.513-0.606-0.6060.0000.0000.0000.000
21B25PRO00.006-0.01017.436-0.221-0.2210.0000.0000.0000.000
22B26ASN0-0.035-0.01618.4510.6420.6420.0000.0000.0000.000
23B27ALA00.0360.02313.6780.3430.3430.0000.0000.0000.000
24B28LEU00.026-0.00212.4570.9400.9400.0000.0000.0000.000
25B29GLY00.0190.02614.4120.1730.1730.0000.0000.0000.000
26B30THR0-0.044-0.01817.308-0.772-0.7720.0000.0000.0000.000
27B31PRO00.0330.01919.4240.2450.2450.0000.0000.0000.000
28B32SER0-0.004-0.00721.3170.0390.0390.0000.0000.0000.000
29B33ALA00.0700.02416.182-0.007-0.0070.0000.0000.0000.000
30B34ASN00.0290.00617.5830.8930.8930.0000.0000.0000.000
31B35LYS10.9901.00218.978-10.997-10.9970.0000.0000.0000.000
32B36ALA00.0030.00218.854-0.182-0.1820.0000.0000.0000.000
33B37LEU00.0400.02014.4940.1110.1110.0000.0000.0000.000
34B38GLU-1-0.925-0.96717.83512.65712.6570.0000.0000.0000.000
35B39THR0-0.081-0.05120.954-0.364-0.3640.0000.0000.0000.000
36B40GLU-1-0.933-0.95917.24114.84714.8470.0000.0000.0000.000
37B41LEU00.0280.01416.2220.0330.0330.0000.0000.0000.000
38B42ALA0-0.046-0.01719.913-0.312-0.3120.0000.0000.0000.000
39B43ALA00.006-0.00322.313-0.399-0.3990.0000.0000.0000.000
40B44LEU00.0390.03217.205-0.262-0.2620.0000.0000.0000.000
41B45ASN00.0250.00421.182-0.020-0.0200.0000.0000.0000.000
42B46ALA0-0.070-0.04023.492-0.424-0.4240.0000.0000.0000.000
43B47LEU00.0370.02621.548-0.461-0.4610.0000.0000.0000.000
44B48HIS00.0280.01722.5110.0790.0790.0000.0000.0000.000
45B49ARG10.9390.95524.454-11.213-11.2130.0000.0000.0000.000
46B50ALA0-0.0090.00327.744-0.358-0.3580.0000.0000.0000.000
47B51LEU00.008-0.00623.486-0.299-0.2990.0000.0000.0000.000
48B52HIS0-0.069-0.02927.683-0.254-0.2540.0000.0000.0000.000
49B53THR0-0.064-0.03429.130-0.365-0.3650.0000.0000.0000.000
50B54GLN0-0.020-0.01731.523-0.395-0.3950.0000.0000.0000.000
51B55ILE0-0.0380.00428.823-0.101-0.1010.0000.0000.0000.000
52B56GLU-1-0.937-0.96432.2388.2298.2290.0000.0000.0000.000
53B57GLY0-0.031-0.01034.166-0.149-0.1490.0000.0000.0000.000
54B58PRO00.0140.00233.1140.1360.1360.0000.0000.0000.000
55B59ILE00.004-0.00627.5010.2780.2780.0000.0000.0000.000
56B60PRO00.0070.01525.352-0.136-0.1360.0000.0000.0000.000
57B61VAL0-0.021-0.02223.5540.5130.5130.0000.0000.0000.000
58B62PRO00.009-0.00525.493-0.391-0.3910.0000.0000.0000.000
59B63PRO00.0000.01928.3060.2140.2140.0000.0000.0000.000
60B64PRO00.005-0.00230.3500.0730.0730.0000.0000.0000.000
61B65PRO00.0490.01230.261-0.304-0.3040.0000.0000.0000.000
62B66VAL0-0.010-0.00433.301-0.252-0.2520.0000.0000.0000.000
63B67PRO0-0.049-0.01234.883-0.292-0.2920.0000.0000.0000.000
64B68VAL00.0470.02437.2360.1220.1220.0000.0000.0000.000
65B69ASN00.0410.00838.692-0.429-0.4290.0000.0000.0000.000
66B70PRO00.0230.01640.6750.0060.0060.0000.0000.0000.000
67B71LYS10.9890.99543.222-7.305-7.3050.0000.0000.0000.000
68B72ARG10.9070.94538.456-8.173-8.1730.0000.0000.0000.000
69B73SER00.0930.03843.205-0.060-0.0600.0000.0000.0000.000
70B74ALA0-0.0020.02044.996-0.160-0.1600.0000.0000.0000.000
71B75ASN0-0.048-0.03346.369-0.191-0.1910.0000.0000.0000.000
72B76ILE00.0300.02343.024-0.156-0.1560.0000.0000.0000.000
73B77ASN00.014-0.00147.637-0.182-0.1820.0000.0000.0000.000
74B78LYS10.9480.97450.545-6.203-6.2030.0000.0000.0000.000
75B79LEU0-0.008-0.01149.059-0.130-0.1300.0000.0000.0000.000
76B80ARG10.9350.98550.699-6.108-6.1080.0000.0000.0000.000
77B81GLU-1-0.859-0.94852.5445.3935.3930.0000.0000.0000.000
78B82SER0-0.0140.01355.001-0.149-0.1490.0000.0000.0000.000
79B83GLY00.0410.01055.147-0.098-0.0980.0000.0000.0000.000
80B84ASN00.0210.01955.994-0.022-0.0220.0000.0000.0000.000
81B85ALA0-0.032-0.00758.352-0.111-0.1110.0000.0000.0000.000
82B86GLU-1-0.889-0.96359.0855.0685.0680.0000.0000.0000.000
83B87TYR0-0.027-0.00259.298-0.040-0.0400.0000.0000.0000.000
84B88ARG10.8580.92560.126-5.308-5.3080.0000.0000.0000.000
85B89LYS10.8730.94864.219-5.021-5.0210.0000.0000.0000.000
86B90GLN0-0.021-0.00664.871-0.054-0.0540.0000.0000.0000.000
87B91ARG10.9581.02160.748-5.169-5.1690.0000.0000.0000.000
88B92TYR00.0880.01960.0700.1060.1060.0000.0000.0000.000
89B93GLY00.026-0.01058.1460.0960.0960.0000.0000.0000.000
90B94ASP-1-0.870-0.95056.9125.3985.3980.0000.0000.0000.000
91B95ALA00.0450.02756.3780.1080.1080.0000.0000.0000.000
92B96ILE00.0090.02053.2250.1320.1320.0000.0000.0000.000
93B97LYS10.8950.95952.517-5.383-5.3830.0000.0000.0000.000
94B98LEU0-0.0030.00751.5070.1580.1580.0000.0000.0000.000
95B99TYR00.001-0.02950.8770.1160.1160.0000.0000.0000.000
96B100THR0-0.019-0.01147.5120.1750.1750.0000.0000.0000.000
97B101LEU0-0.0220.00146.8630.1680.1680.0000.0000.0000.000
98B102GLY00.0000.00246.2190.1550.1550.0000.0000.0000.000
99B103LEU00.007-0.00544.5750.1570.1570.0000.0000.0000.000
100B104GLN00.0060.00642.4520.1850.1850.0000.0000.0000.000
101B105MET0-0.043-0.00641.3090.1920.1920.0000.0000.0000.000
102B106ALA00.0200.01041.7690.1030.1030.0000.0000.0000.000
103B107LEU0-0.032-0.01738.6060.1940.1940.0000.0000.0000.000
104B108THR0-0.041-0.02536.7330.1800.1800.0000.0000.0000.000
105B109ARG10.7710.89535.986-8.012-8.0120.0000.0000.0000.000
106B110PRO00.0370.02132.2850.1220.1220.0000.0000.0000.000
107B111ALA00.0280.00729.073-0.065-0.0650.0000.0000.0000.000
108B112TRP00.0090.01327.7150.2690.2690.0000.0000.0000.000
109B113GLU-1-0.908-0.95929.8738.7278.7270.0000.0000.0000.000
110B114PRO0-0.008-0.00533.5180.0600.0600.0000.0000.0000.000
111B115ALA00.0810.03033.376-0.238-0.2380.0000.0000.0000.000
112B116GLY0-0.012-0.01035.361-0.197-0.1970.0000.0000.0000.000
113B117LEU00.0500.03738.392-0.205-0.2050.0000.0000.0000.000
114B118VAL00.0210.01036.606-0.226-0.2260.0000.0000.0000.000
115B119ARG10.8850.94735.951-8.515-8.5150.0000.0000.0000.000
116B120ASP-1-0.859-0.92140.9047.1407.1400.0000.0000.0000.000
117B121GLU-1-0.862-0.93942.7217.1557.1550.0000.0000.0000.000
118B122ILE0-0.009-0.01640.306-0.198-0.1980.0000.0000.0000.000
119B123HIS0-0.016-0.01444.318-0.236-0.2360.0000.0000.0000.000
120B124GLN0-0.0030.01246.120-0.310-0.3100.0000.0000.0000.000
121B125LEU00.0060.00646.239-0.189-0.1890.0000.0000.0000.000
122B126TYR00.0330.01942.496-0.150-0.1500.0000.0000.0000.000
123B127SER00.0230.01648.580-0.171-0.1710.0000.0000.0000.000
124B128ASN0-0.121-0.08351.535-0.226-0.2260.0000.0000.0000.000
125B129ARG10.8310.87247.175-6.613-6.6130.0000.0000.0000.000
126B130ALA00.0520.03451.864-0.093-0.0930.0000.0000.0000.000
127B131GLN0-0.018-0.02553.587-0.170-0.1700.0000.0000.0000.000
128B132ALA0-0.009-0.02056.093-0.109-0.1090.0000.0000.0000.000
129B133TYR00.0100.00152.185-0.065-0.0650.0000.0000.0000.000
130B134MET0-0.030-0.00756.337-0.091-0.0910.0000.0000.0000.000
131B135GLN0-0.066-0.01759.170-0.145-0.1450.0000.0000.0000.000
132B136LEU0-0.065-0.03159.077-0.097-0.0970.0000.0000.0000.000
133B137GLY00.0130.01861.583-0.029-0.0290.0000.0000.0000.000
134B138GLN0-0.043-0.01156.7610.0300.0300.0000.0000.0000.000
135B139TRP00.0710.01156.6130.1430.1430.0000.0000.0000.000
136B140PRO00.012-0.00153.2220.0840.0840.0000.0000.0000.000
137B141GLU-1-0.834-0.92851.2265.9175.9170.0000.0000.0000.000
138B142ALA0-0.0010.01251.3020.1120.1120.0000.0000.0000.000
139B143ALA0-0.001-0.01552.3840.0720.0720.0000.0000.0000.000
140B144ALA00.0300.02247.6920.1140.1140.0000.0000.0000.000
141B145ASP-1-0.783-0.86147.6336.5706.5700.0000.0000.0000.000
142B146ALA0-0.025-0.02448.2700.0990.0990.0000.0000.0000.000
143B147GLU-1-0.890-0.94945.5926.8316.8310.0000.0000.0000.000
144B148CYS0-0.034-0.00844.1040.1940.1940.0000.0000.0000.000
145B149SER0-0.064-0.03644.2430.1100.1100.0000.0000.0000.000
146B150VAL0-0.005-0.00345.9050.0940.0940.0000.0000.0000.000
147B151GLU-1-0.918-0.95139.6397.9477.9470.0000.0000.0000.000
148B152ALA0-0.065-0.02141.2190.2060.2060.0000.0000.0000.000
149B153LYS10.9110.95242.004-6.706-6.7060.0000.0000.0000.000
150B154ARG10.9470.97741.061-7.613-7.6130.0000.0000.0000.000
151B155GLN00.0540.03045.652-0.180-0.1800.0000.0000.0000.000
152B156GLY00.0310.01047.9270.0650.0650.0000.0000.0000.000
153B157ASN0-0.055-0.04547.945-0.164-0.1640.0000.0000.0000.000
154B158ALA00.1080.05951.0380.0260.0260.0000.0000.0000.000
155B159LYS10.8710.93454.053-5.426-5.4260.0000.0000.0000.000
156B160ALA0-0.0120.00450.417-0.070-0.0700.0000.0000.0000.000
157B161TRP00.0490.02647.833-0.026-0.0260.0000.0000.0000.000
158B162TYR00.0700.03552.941-0.033-0.0330.0000.0000.0000.000
159B163ARG10.8830.95054.636-5.769-5.7690.0000.0000.0000.000
160B164ARG10.9100.95849.151-6.452-6.4520.0000.0000.0000.000
161B165GLY00.0440.02854.006-0.024-0.0240.0000.0000.0000.000
162B166LYS10.9700.98056.432-5.087-5.0870.0000.0000.0000.000
163B167CYS0-0.035-0.00755.524-0.061-0.0610.0000.0000.0000.000
164B168LEU0-0.017-0.00352.773-0.037-0.0370.0000.0000.0000.000
165B169MET0-0.010-0.00456.829-0.074-0.0740.0000.0000.0000.000
166B170GLU-1-0.946-0.96760.3694.8984.8980.0000.0000.0000.000
167B171MET0-0.103-0.02954.619-0.022-0.0220.0000.0000.0000.000
168B172ARG10.8990.94459.156-4.883-4.8830.0000.0000.0000.000
169B173ARG10.8490.91150.758-5.974-5.9740.0000.0000.0000.000
170B174LEU00.0620.01557.4730.0750.0750.0000.0000.0000.000
171B175GLN00.0180.01156.574-0.075-0.0750.0000.0000.0000.000
172B176GLU-1-0.795-0.87851.7246.1166.1160.0000.0000.0000.000
173B177ALA0-0.008-0.00754.1980.0850.0850.0000.0000.0000.000
174B178ARG10.9380.98356.564-5.332-5.3320.0000.0000.0000.000
175B179GLU-1-0.929-0.97752.9125.9655.9650.0000.0000.0000.000
176B180TRP0-0.070-0.03447.8920.1410.1410.0000.0000.0000.000
177B181VAL00.004-0.01552.8690.0740.0740.0000.0000.0000.000
178B182ALA0-0.032-0.00555.2090.0010.0010.0000.0000.0000.000
179B183ARG11.0010.99546.460-6.630-6.6300.0000.0000.0000.000
180B184GLY0-0.033-0.03751.2210.1020.1020.0000.0000.0000.000
181B185LEU0-0.046-0.02752.405-0.009-0.0090.0000.0000.0000.000
182B186GLU-1-0.976-0.95850.5936.2536.2530.0000.0000.0000.000
183B187PHE0-0.083-0.05045.0590.1330.1330.0000.0000.0000.000
184B188GLU-1-0.860-0.91850.2795.7525.7520.0000.0000.0000.000
185B189GLY0-0.117-0.07352.3200.1030.1030.0000.0000.0000.000
186B190GLU-1-0.922-0.96854.2415.2305.2300.0000.0000.0000.000
187B191GLU-1-0.844-0.91057.5935.5155.5150.0000.0000.0000.000
188B192LYS10.9770.96759.384-4.882-4.8820.0000.0000.0000.000
189B193GLU-1-0.856-0.91960.6355.1835.1830.0000.0000.0000.000
190B194LEU00.010-0.00654.936-0.028-0.0280.0000.0000.0000.000
191B195ALA00.0110.01759.673-0.013-0.0130.0000.0000.0000.000
192B196GLU-1-1.001-1.00362.3134.7624.7620.0000.0000.0000.000
193B197LEU0-0.018-0.01458.969-0.039-0.0390.0000.0000.0000.000
194B198LEU0-0.011-0.00459.202-0.011-0.0110.0000.0000.0000.000
195B199LYS10.9811.00461.941-4.730-4.7300.0000.0000.0000.000
196B200GLU-1-0.970-0.98065.1324.7884.7880.0000.0000.0000.000
197B201ILE0-0.037-0.02359.529-0.036-0.0360.0000.0000.0000.000
198B202ASP-1-0.812-0.94463.2555.0155.0150.0000.0000.0000.000
199B203SER0-0.050-0.00964.696-0.086-0.0860.0000.0000.0000.000
200B204LYS10.9290.95965.746-4.838-4.8380.0000.0000.0000.000
201B205LEU0-0.008-0.00461.120-0.020-0.0200.0000.0000.0000.000
202B206ALA0-0.0180.00165.807-0.024-0.0240.0000.0000.0000.000
203B207ALA0-0.003-0.01468.742-0.052-0.0520.0000.0000.0000.000
204B208GLU-1-0.970-0.98264.9984.8734.8730.0000.0000.0000.000
205B209LYS10.8520.90665.990-4.765-4.7650.0000.0000.0000.000
206B210ALA00.0640.05069.247-0.010-0.0100.0000.0000.0000.000
207B211SER0-0.026-0.01272.311-0.083-0.0830.0000.0000.0000.000
208B212ARG10.8350.93665.384-4.748-4.7480.0000.0000.0000.000
209B213ASP-1-0.915-0.94570.9954.4834.4830.0000.0000.0000.000