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: 4J26N

Calculation Name: 2FY8-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FY8

Chain ID: H

ChEMBL ID:

UniProt ID: O27564

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2434940.590617
FMO2-HF: Nuclear repulsion 2348455.57568
FMO2-HF: Total energy -86485.014937
FMO2-MP2: Total energy -86736.670694


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(H:115:SER)


Summations of interaction energy for fragment #1(H:115: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.
-10.978-6.4424.714-4.505-4.744-0.022
Interaction energy analysis for fragmet #1(H:115:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.008
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].
3H117HIS00.0200.0172.268-4.492-2.0434.567-3.440-3.576-0.014
4H118VAL00.0120.0164.646-1.504-1.476-0.001-0.006-0.0210.000
5H119VAL0-0.0040.0057.1540.2820.2820.0000.0000.0000.000
6H120ILE00.0190.0139.539-0.018-0.0180.0000.0000.0000.000
7H121CYS0-0.047-0.02013.2760.0200.0200.0000.0000.0000.000
8H122GLY00.0560.01615.8240.0180.0180.0000.0000.0000.000
9H123TRP00.017-0.01018.5910.0090.0090.0000.0000.0000.000
10H124SER00.030-0.00721.1150.0130.0130.0000.0000.0000.000
11H125GLU-1-0.901-0.98122.891-0.073-0.0730.0000.0000.0000.000
12H126SER0-0.014-0.02521.6260.0250.0250.0000.0000.0000.000
13H127THR0-0.024-0.01517.500-0.008-0.0080.0000.0000.0000.000
14H128LEU0-0.078-0.03519.1890.0200.0200.0000.0000.0000.000
15H129GLU-1-0.867-0.94121.145-0.002-0.0020.0000.0000.0000.000
16H130CYS0-0.034-0.02316.045-0.003-0.0030.0000.0000.0000.000
17H131LEU0-0.039-0.02714.8810.0160.0160.0000.0000.0000.000
18H132ARG10.7590.87317.2730.0070.0070.0000.0000.0000.000
19H133GLU-1-0.795-0.90218.0600.0820.0820.0000.0000.0000.000
20H134LEU0-0.048-0.01212.0950.0350.0350.0000.0000.0000.000
21H135ARG10.9120.96313.888-0.104-0.1040.0000.0000.0000.000
22H136GLY0-0.032-0.01314.4080.0350.0350.0000.0000.0000.000
23H137SER0-0.051-0.0459.5940.1140.1140.0000.0000.0000.000
24H138GLU-1-0.954-0.9696.7571.4941.4940.0000.0000.0000.000
25H139VAL00.0200.0168.150-0.100-0.1000.0000.0000.0000.000
26H140PHE0-0.016-0.0117.0890.0500.0500.0000.0000.0000.000
27H141VAL00.0120.00110.995-0.115-0.1150.0000.0000.0000.000
28H142LEU0-0.0240.00413.9440.0490.0490.0000.0000.0000.000
29H143ALA0-0.003-0.01315.661-0.012-0.0120.0000.0000.0000.000
30H144GLU-1-0.875-0.93419.458-0.185-0.1850.0000.0000.0000.000
31H145ASP-1-0.799-0.89622.706-0.078-0.0780.0000.0000.0000.000
32H146GLU-1-0.725-0.84723.473-0.069-0.0690.0000.0000.0000.000
33H147ASN0-0.143-0.07524.3960.0270.0270.0000.0000.0000.000
34H148VAL00.0390.02820.4630.0180.0180.0000.0000.0000.000
35H149ARG10.8640.91320.3120.0540.0540.0000.0000.0000.000
36H150LYS10.8550.91921.3590.0500.0500.0000.0000.0000.000
37H151LYS10.8770.94122.8410.0900.0900.0000.0000.0000.000
38H152VAL00.0600.03416.6870.0090.0090.0000.0000.0000.000
39H153LEU0-0.0100.00118.2600.0230.0230.0000.0000.0000.000
40H154ARG10.8880.95019.957-0.007-0.0070.0000.0000.0000.000
41H155SER0-0.016-0.01419.1360.0150.0150.0000.0000.0000.000
42H156GLY0-0.055-0.01217.7930.0090.0090.0000.0000.0000.000
43H157ALA00.0010.01313.9330.0540.0540.0000.0000.0000.000
44H158ASN0-0.0070.00010.4140.0050.0050.0000.0000.0000.000
45H159PHE00.014-0.00914.035-0.061-0.0610.0000.0000.0000.000
46H160VAL0-0.035-0.02012.5820.0280.0280.0000.0000.0000.000
47H161HIS0-0.0020.00815.914-0.036-0.0360.0000.0000.0000.000
48H162GLY00.026-0.00818.419-0.010-0.0100.0000.0000.0000.000
49H163ASP-1-0.804-0.85619.360-0.307-0.3070.0000.0000.0000.000
50H164PRO00.002-0.02916.994-0.034-0.0340.0000.0000.0000.000
51H165THR0-0.014-0.02518.041-0.049-0.0490.0000.0000.0000.000
52H166ARG10.8820.95519.5870.2920.2920.0000.0000.0000.000
53H167VAL00.0220.00116.345-0.012-0.0120.0000.0000.0000.000
54H168SER00.0490.01115.773-0.038-0.0380.0000.0000.0000.000
55H169ASP-1-0.830-0.90915.860-0.309-0.3090.0000.0000.0000.000
56H170LEU00.0350.01613.342-0.015-0.0150.0000.0000.0000.000
57H171GLU-1-0.942-0.98311.527-0.870-0.8700.0000.0000.0000.000
58H172LYS10.7530.86910.9970.2360.2360.0000.0000.0000.000
59H173ALA0-0.037-0.01011.0670.0650.0650.0000.0000.0000.000
60H174ASN0-0.030-0.0076.030-0.097-0.0970.0000.0000.0000.000
61H175VAL00.0640.0296.145-0.694-0.6940.0000.0000.0000.000
62H176ARG10.8730.9427.4000.9030.9030.0000.0000.0000.000
63H177GLY00.0080.0033.664-0.0140.1220.003-0.048-0.0900.000
64H178ALA0-0.055-0.0103.116-4.037-2.3410.146-0.965-0.877-0.008
65H179ARG10.9380.9704.2340.5160.743-0.001-0.046-0.1800.000
66H180ALA0-0.023-0.0175.4110.6600.6600.0000.0000.0000.000
67H181VAL00.005-0.0058.333-0.051-0.0510.0000.0000.0000.000
68H182ILE0-0.008-0.00310.7040.0970.0970.0000.0000.0000.000
69H183VAL0-0.010-0.01413.9960.0230.0230.0000.0000.0000.000
70H184ASN0-0.0160.00216.8820.0460.0460.0000.0000.0000.000
71H185LEU0-0.017-0.00118.9960.0200.0200.0000.0000.0000.000
72H186GLU-1-0.927-0.95722.287-0.163-0.1630.0000.0000.0000.000
73H187SER0-0.006-0.03725.6060.0150.0150.0000.0000.0000.000
74H188ASP-1-0.692-0.85025.307-0.261-0.2610.0000.0000.0000.000
75H189SER0-0.043-0.01825.188-0.026-0.0260.0000.0000.0000.000
76H190GLU-1-0.838-0.87923.860-0.246-0.2460.0000.0000.0000.000
77H191THR00.0010.00620.405-0.041-0.0410.0000.0000.0000.000
78H192ILE00.014-0.01520.641-0.048-0.0480.0000.0000.0000.000
79H193HIS0-0.049-0.01521.618-0.050-0.0500.0000.0000.0000.000
80H194CYS0-0.014-0.01417.157-0.049-0.0490.0000.0000.0000.000
81H195ILE0-0.023-0.00317.010-0.072-0.0720.0000.0000.0000.000
82H196LEU00.0020.00417.180-0.065-0.0650.0000.0000.0000.000
83H197GLY0-0.016-0.00517.921-0.020-0.0200.0000.0000.0000.000
84H198ILE00.001-0.01511.925-0.051-0.0510.0000.0000.0000.000
85H199ARG10.8210.90812.5260.9060.9060.0000.0000.0000.000
86H200LYS10.8940.96416.0050.4490.4490.0000.0000.0000.000
87H201ILE0-0.083-0.02611.1920.0170.0170.0000.0000.0000.000
88H202ASP-1-0.821-0.9358.533-2.197-2.1970.0000.0000.0000.000
89H203GLU-1-0.939-0.96612.037-0.699-0.6990.0000.0000.0000.000
90H204SER0-0.104-0.0569.9420.0300.0300.0000.0000.0000.000
91H205VAL00.0080.0337.7090.0110.0110.0000.0000.0000.000
92H206ARG10.9620.9809.1441.0101.0100.0000.0000.0000.000
93H207ILE0-0.028-0.01211.210-0.073-0.0730.0000.0000.0000.000
94H208ILE0-0.036-0.01713.1460.0950.0950.0000.0000.0000.000
95H209ALA00.0110.00116.042-0.008-0.0080.0000.0000.0000.000
96H210GLU-1-0.879-0.90918.918-0.192-0.1920.0000.0000.0000.000
97H211ALA0-0.033-0.00721.9520.0020.0020.0000.0000.0000.000
98H212GLU-1-0.828-0.90625.369-0.161-0.1610.0000.0000.0000.000
99H213ARG10.8220.88428.2410.1790.1790.0000.0000.0000.000
100H214TYR00.005-0.00829.883-0.012-0.0120.0000.0000.0000.000
101H215GLU-1-0.960-0.99831.120-0.160-0.1600.0000.0000.0000.000
102H216ASN0-0.039-0.02828.067-0.002-0.0020.0000.0000.0000.000
103H217ILE0-0.0090.00626.093-0.021-0.0210.0000.0000.0000.000
104H218GLU-1-0.804-0.90725.908-0.281-0.2810.0000.0000.0000.000
105H219GLN0-0.010-0.00926.191-0.026-0.0260.0000.0000.0000.000
106H220LEU00.0110.01522.090-0.026-0.0260.0000.0000.0000.000
107H221ARG10.8950.94121.8430.2550.2550.0000.0000.0000.000
108H222MET0-0.093-0.04422.014-0.025-0.0250.0000.0000.0000.000
109H223ALA0-0.030-0.00921.796-0.016-0.0160.0000.0000.0000.000
110H224GLY00.0280.01218.623-0.039-0.0390.0000.0000.0000.000
111H225ALA0-0.030-0.01017.181-0.086-0.0860.0000.0000.0000.000
112H226ASP-1-0.820-0.90514.350-0.838-0.8380.0000.0000.0000.000
113H227GLN0-0.010-0.00317.3770.0190.0190.0000.0000.0000.000
114H228VAL0-0.0090.00319.189-0.022-0.0220.0000.0000.0000.000
115H229ILE00.0020.00719.3370.0300.0300.0000.0000.0000.000
116H230SER00.031-0.00323.022-0.001-0.0010.0000.0000.0000.000
117H231PRO00.0680.04524.9470.0190.0190.0000.0000.0000.000
118H232PHE00.0450.00927.4730.0180.0180.0000.0000.0000.000
119H233VAL0-0.0110.00629.8100.0110.0110.0000.0000.0000.000
120H234ILE00.0040.00027.2080.0120.0120.0000.0000.0000.000
121H235SER00.0340.01930.6400.0140.0140.0000.0000.0000.000
122H236GLY00.0190.01132.7590.0090.0090.0000.0000.0000.000
123H237ARG10.9320.95430.7940.1330.1330.0000.0000.0000.000
124H238LEU00.0580.03931.5300.0080.0080.0000.0000.0000.000
125H239MET0-0.036-0.00135.6360.0060.0060.0000.0000.0000.000
126H240SER0-0.095-0.05738.4710.0050.0050.0000.0000.0000.000
127H241ARG10.8740.91636.6500.0640.0640.0000.0000.0000.000
128H242SER0-0.072-0.04638.2020.0060.0060.0000.0000.0000.000
129H243ILE0-0.085-0.03740.7930.0020.0020.0000.0000.0000.000
130H244ASP-1-0.920-0.95444.192-0.029-0.0290.0000.0000.0000.000
131H245ASP-1-0.904-0.95642.411-0.016-0.0160.0000.0000.0000.000
132H246GLY0-0.006-0.00538.9560.0020.0020.0000.0000.0000.000
133H247TYR00.0060.00438.3470.0040.0040.0000.0000.0000.000
134H248GLU-1-0.846-0.90936.166-0.048-0.0480.0000.0000.0000.000
135H249ALA00.0140.00534.086-0.002-0.0020.0000.0000.0000.000
136H250MET0-0.0080.00233.2440.0010.0010.0000.0000.0000.000
137H251PHE00.0210.00831.2150.0040.0040.0000.0000.0000.000
138H252VAL0-0.012-0.01128.6820.0020.0020.0000.0000.0000.000
139H253GLN0-0.036-0.02928.479-0.008-0.0080.0000.0000.0000.000
140H254ASP-1-0.855-0.90628.3610.0180.0180.0000.0000.0000.000
141H255VAL0-0.083-0.04127.4480.0100.0100.0000.0000.0000.000
142H256LEU0-0.022-0.01423.9350.0020.0020.0000.0000.0000.000
143H257ALA00.0280.04423.3000.0000.0000.0000.0000.0000.000
144H258GLU-1-0.860-0.92620.4320.1530.1530.0000.0000.0000.000
145H259GLU-1-0.891-0.93223.5330.0990.0990.0000.0000.0000.000
146H260SER0-0.050-0.02726.7240.0090.0090.0000.0000.0000.000
147H261THR0-0.056-0.04128.4610.0070.0070.0000.0000.0000.000
148H262ARG10.7770.88029.555-0.052-0.0520.0000.0000.0000.000
149H263ARG10.9030.95621.884-0.141-0.1410.0000.0000.0000.000
150H264MET0-0.001-0.00724.0450.0000.0000.0000.0000.0000.000
151H265VAL0-0.028-0.01420.6970.0130.0130.0000.0000.0000.000
152H266GLU-1-0.900-0.94417.147-0.174-0.1740.0000.0000.0000.000
153H267VAL0-0.060-0.04018.1870.0480.0480.0000.0000.0000.000
154H268PRO0-0.007-0.00614.165-0.020-0.0200.0000.0000.0000.000
155H269ILE00.0210.02317.1380.0580.0580.0000.0000.0000.000
156H270PRO0-0.053-0.03216.106-0.015-0.0150.0000.0000.0000.000
157H271GLU-1-0.952-0.98013.3280.1380.1380.0000.0000.0000.000
158H272GLY0-0.039-0.02117.4530.0020.0020.0000.0000.0000.000
159H273SER0-0.021-0.01819.584-0.023-0.0230.0000.0000.0000.000
160H274LYS10.9210.97523.115-0.211-0.2110.0000.0000.0000.000
161H275LEU00.0560.02424.414-0.009-0.0090.0000.0000.0000.000
162H276GLU-1-0.918-0.95122.663-0.013-0.0130.0000.0000.0000.000
163H277GLY0-0.0060.00825.2810.0030.0030.0000.0000.0000.000
164H278VAL0-0.080-0.03228.284-0.004-0.0040.0000.0000.0000.000
165H279SER0-0.026-0.04929.378-0.006-0.0060.0000.0000.0000.000
166H280VAL00.0370.00929.8480.0100.0100.0000.0000.0000.000
167H281LEU0-0.060-0.02732.0470.0050.0050.0000.0000.0000.000
168H282ASP-1-0.901-0.92033.3650.0270.0270.0000.0000.0000.000
169H283ALA0-0.039-0.01229.7760.0070.0070.0000.0000.0000.000
170H284ASP-1-0.884-0.92331.8210.0450.0450.0000.0000.0000.000
171H285ILE00.013-0.00227.0930.0070.0070.0000.0000.0000.000
172H286HIS00.0330.00831.0100.0080.0080.0000.0000.0000.000
173H287ASP-1-0.928-0.94932.7840.0580.0580.0000.0000.0000.000
174H288VAL0-0.0320.00230.9810.0080.0080.0000.0000.0000.000
175H289THR0-0.040-0.04928.0510.0160.0160.0000.0000.0000.000
176H290GLY0-0.082-0.04430.3970.0110.0110.0000.0000.0000.000
177H291VAL0-0.064-0.01726.455-0.004-0.0040.0000.0000.0000.000
178H292ILE00.0450.02529.798-0.004-0.0040.0000.0000.0000.000
179H293ILE0-0.025-0.02627.0500.0000.0000.0000.0000.0000.000
180H294ILE00.002-0.00527.992-0.006-0.0060.0000.0000.0000.000
181H295GLY00.0490.01427.178-0.010-0.0100.0000.0000.0000.000
182H296VAL0-0.055-0.01523.8640.0150.0150.0000.0000.0000.000
183H297GLY00.0120.01821.686-0.012-0.0120.0000.0000.0000.000
184H298ARG10.7570.82121.2270.0850.0850.0000.0000.0000.000
185H299GLY0-0.025-0.01620.4770.0010.0010.0000.0000.0000.000
186H300ASP-1-0.957-0.98318.965-0.378-0.3780.0000.0000.0000.000
187H301GLU-1-0.930-0.94321.635-0.142-0.1420.0000.0000.0000.000
188H302LEU0-0.055-0.03124.0930.0050.0050.0000.0000.0000.000
189H303ILE0-0.009-0.00625.9430.0070.0070.0000.0000.0000.000
190H304ILE0-0.019-0.02328.5920.0090.0090.0000.0000.0000.000
191H305ASP-1-0.982-0.97730.666-0.022-0.0220.0000.0000.0000.000
192H306PRO0-0.0200.00629.470-0.003-0.0030.0000.0000.0000.000
193H307PRO00.0340.00832.1240.0070.0070.0000.0000.0000.000
194H308ARG10.9590.95633.8410.0100.0100.0000.0000.0000.000
195H309ASP-1-0.914-0.96734.839-0.025-0.0250.0000.0000.0000.000
196H310TYR0-0.037-0.00625.282-0.009-0.0090.0000.0000.0000.000
197H311SER00.008-0.00129.7400.0050.0050.0000.0000.0000.000
198H312PHE0-0.0070.00524.575-0.014-0.0140.0000.0000.0000.000
199H313ARG10.9300.97622.7890.0930.0930.0000.0000.0000.000
200H314ALA00.027-0.00118.5230.0020.0020.0000.0000.0000.000
201H315GLY0-0.061-0.02916.567-0.033-0.0330.0000.0000.0000.000
202H316ASP-1-0.710-0.82017.636-0.101-0.1010.0000.0000.0000.000
203H317ILE0-0.022-0.00815.6660.0380.0380.0000.0000.0000.000
204H318ILE0-0.0090.00219.669-0.014-0.0140.0000.0000.0000.000
205H319LEU00.0310.01721.8310.0100.0100.0000.0000.0000.000
206H320GLY00.0330.01323.9910.0000.0000.0000.0000.0000.000
207H321ILE0-0.002-0.00225.696-0.002-0.0020.0000.0000.0000.000
208H322GLY00.008-0.00927.7270.0020.0020.0000.0000.0000.000
209H323LYS10.8460.90627.695-0.095-0.0950.0000.0000.0000.000
210H324PRO00.0100.00725.4470.0050.0050.0000.0000.0000.000
211H325GLU-1-0.810-0.91025.4800.1390.1390.0000.0000.0000.000
212H326GLU-1-0.808-0.87027.6580.0840.0840.0000.0000.0000.000
213H327ILE00.0620.03522.2880.0090.0090.0000.0000.0000.000
214H328GLU-1-0.868-0.92321.3760.3210.3210.0000.0000.0000.000
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