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: KGY83

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2433075.376538
FMO2-HF: Nuclear repulsion 2346591.906096
FMO2-HF: Total energy -86483.470442
FMO2-MP2: Total energy -86735.16099


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.
-7.617-2.1842.989-4.022-4.399-0.022
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 : 0.010 / q_NPA : -0.007
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].
3H117HIS00.0180.0102.405-5.098-1.6212.851-3.037-3.291-0.015
4H118VAL00.0100.0184.652-1.195-1.168-0.001-0.005-0.0200.000
5H119VAL0-0.0030.0057.1870.1700.1700.0000.0000.0000.000
6H120ILE00.0200.0179.5410.0130.0130.0000.0000.0000.000
7H121CYS0-0.062-0.03113.279-0.001-0.0010.0000.0000.0000.000
8H122GLY00.0570.01915.8260.0150.0150.0000.0000.0000.000
9H123TRP0-0.028-0.03418.5950.0080.0080.0000.0000.0000.000
10H124SER00.033-0.03021.1190.0040.0040.0000.0000.0000.000
11H125GLU-1-0.934-0.98622.8940.0020.0020.0000.0000.0000.000
12H126SER00.002-0.00521.5040.0140.0140.0000.0000.0000.000
13H127THR0-0.019-0.00817.4620.0000.0000.0000.0000.0000.000
14H128LEU0-0.071-0.03319.1930.0140.0140.0000.0000.0000.000
15H129GLU-1-0.890-0.94521.1500.0560.0560.0000.0000.0000.000
16H130CYS0-0.002-0.01316.1170.0050.0050.0000.0000.0000.000
17H131LEU0-0.022-0.01614.8070.0170.0170.0000.0000.0000.000
18H132ARG10.8970.95417.278-0.038-0.0380.0000.0000.0000.000
19H133GLU-1-0.843-0.91817.8270.1180.1180.0000.0000.0000.000
20H134LEU0-0.038-0.00912.1380.0310.0310.0000.0000.0000.000
21H135ARG10.9360.97013.894-0.104-0.1040.0000.0000.0000.000
22H136GLY0-0.043-0.01714.4160.0090.0090.0000.0000.0000.000
23H137SER0-0.068-0.0549.0790.0450.0450.0000.0000.0000.000
24H138GLU-1-0.983-0.9746.7651.8611.8610.0000.0000.0000.000
25H139VAL00.0310.0218.158-0.039-0.0390.0000.0000.0000.000
26H140PHE00.002-0.0076.8740.0000.0000.0000.0000.0000.000
27H141VAL00.0050.00211.002-0.073-0.0730.0000.0000.0000.000
28H142LEU0-0.0280.00114.0970.0240.0240.0000.0000.0000.000
29H143ALA0-0.007-0.01515.666-0.003-0.0030.0000.0000.0000.000
30H144GLU-1-0.848-0.91919.462-0.091-0.0910.0000.0000.0000.000
31H145ASP-1-0.840-0.92722.710-0.024-0.0240.0000.0000.0000.000
32H146GLU-1-0.781-0.89523.479-0.018-0.0180.0000.0000.0000.000
33H147ASN0-0.084-0.03524.4040.0140.0140.0000.0000.0000.000
34H148VAL00.000-0.00120.4700.0120.0120.0000.0000.0000.000
35H149ARG10.8980.96219.9260.0110.0110.0000.0000.0000.000
36H150LYS10.8950.94121.3670.0050.0050.0000.0000.0000.000
37H151LYS10.9100.95322.7280.0150.0150.0000.0000.0000.000
38H152VAL00.0590.03516.6790.0080.0080.0000.0000.0000.000
39H153LEU00.0030.00318.3190.0160.0160.0000.0000.0000.000
40H154ARG10.8670.94319.966-0.035-0.0350.0000.0000.0000.000
41H155SER0-0.006-0.01018.9550.0040.0040.0000.0000.0000.000
42H156GLY0-0.066-0.01417.8020.0080.0080.0000.0000.0000.000
43H157ALA00.0200.02413.9380.0420.0420.0000.0000.0000.000
44H158ASN0-0.010-0.00911.8630.0110.0110.0000.0000.0000.000
45H159PHE00.031-0.00614.043-0.034-0.0340.0000.0000.0000.000
46H160VAL0-0.040-0.02112.6060.0170.0170.0000.0000.0000.000
47H161HIS0-0.042-0.01815.921-0.018-0.0180.0000.0000.0000.000
48H162GLY00.013-0.01818.428-0.008-0.0080.0000.0000.0000.000
49H163ASP-1-0.798-0.86719.364-0.139-0.1390.0000.0000.0000.000
50H164PRO00.000-0.03117.105-0.024-0.0240.0000.0000.0000.000
51H165THR0-0.023-0.02118.040-0.026-0.0260.0000.0000.0000.000
52H166ARG10.9020.96219.5770.1510.1510.0000.0000.0000.000
53H167VAL00.017-0.00416.162-0.008-0.0080.0000.0000.0000.000
54H168SER00.0280.00115.773-0.027-0.0270.0000.0000.0000.000
55H169ASP-1-0.858-0.92915.861-0.175-0.1750.0000.0000.0000.000
56H170LEU00.000-0.00113.317-0.013-0.0130.0000.0000.0000.000
57H171GLU-1-0.942-0.98311.554-0.497-0.4970.0000.0000.0000.000
58H172LYS10.8430.93511.0000.0930.0930.0000.0000.0000.000
59H173ALA0-0.039-0.00811.0720.0440.0440.0000.0000.0000.000
60H174ASN0-0.035-0.0056.017-0.049-0.0490.0000.0000.0000.000
61H175VAL00.0710.0346.146-0.559-0.5590.0000.0000.0000.000
62H176ARG10.8990.9607.3960.5110.5110.0000.0000.0000.000
63H177GLY00.0120.0063.6420.0570.1860.003-0.047-0.0850.000
64H178ALA0-0.053-0.0073.138-2.871-1.2900.137-0.889-0.829-0.007
65H179ARG10.9560.9764.2310.2660.485-0.001-0.044-0.1740.000
66H180ALA0-0.034-0.0265.4180.5880.5880.0000.0000.0000.000
67H181VAL00.0090.0028.331-0.127-0.1270.0000.0000.0000.000
68H182ILE0-0.010-0.00510.7010.0790.0790.0000.0000.0000.000
69H183VAL0-0.010-0.01413.995-0.003-0.0030.0000.0000.0000.000
70H184ASN00.0300.05016.8810.0310.0310.0000.0000.0000.000
71H185LEU0-0.016-0.00619.2810.0070.0070.0000.0000.0000.000
72H186GLU-1-0.930-0.95822.288-0.056-0.0560.0000.0000.0000.000
73H187SER00.0100.00425.6080.0080.0080.0000.0000.0000.000
74H188ASP-1-0.684-0.83525.305-0.091-0.0910.0000.0000.0000.000
75H189SER0-0.044-0.01825.185-0.011-0.0110.0000.0000.0000.000
76H190GLU-1-0.845-0.91423.845-0.104-0.1040.0000.0000.0000.000
77H191THR00.0130.01120.301-0.022-0.0220.0000.0000.0000.000
78H192ILE00.005-0.01820.638-0.023-0.0230.0000.0000.0000.000
79H193HIS0-0.051-0.01521.614-0.025-0.0250.0000.0000.0000.000
80H194CYS00.0060.00117.011-0.026-0.0260.0000.0000.0000.000
81H195ILE0-0.025-0.00517.008-0.041-0.0410.0000.0000.0000.000
82H196LEU00.0060.00217.175-0.032-0.0320.0000.0000.0000.000
83H197GLY0-0.016-0.00417.919-0.012-0.0120.0000.0000.0000.000
84H198ILE00.010-0.01112.019-0.035-0.0350.0000.0000.0000.000
85H199ARG10.8410.92212.5310.3250.3250.0000.0000.0000.000
86H200LYS10.8930.96516.0140.2270.2270.0000.0000.0000.000
87H201ILE0-0.084-0.02511.0650.0020.0020.0000.0000.0000.000
88H202ASP-1-0.859-0.9538.427-0.980-0.9800.0000.0000.0000.000
89H203GLU-1-0.921-0.96712.055-0.265-0.2650.0000.0000.0000.000
90H204SER0-0.096-0.04710.0810.0710.0710.0000.0000.0000.000
91H205VAL0-0.0160.0207.6230.0830.0830.0000.0000.0000.000
92H206ARG10.9870.9899.1480.2490.2490.0000.0000.0000.000
93H207ILE0-0.030-0.01811.216-0.090-0.0900.0000.0000.0000.000
94H208ILE0-0.038-0.01613.0330.0590.0590.0000.0000.0000.000
95H209ALA00.009-0.00116.038-0.018-0.0180.0000.0000.0000.000
96H210GLU-1-0.893-0.93718.915-0.043-0.0430.0000.0000.0000.000
97H211ALA0-0.043-0.01521.950-0.004-0.0040.0000.0000.0000.000
98H212GLU-1-0.928-0.97525.366-0.051-0.0510.0000.0000.0000.000
99H213ARG10.9190.94628.2390.0600.0600.0000.0000.0000.000
100H214TYR00.005-0.01129.879-0.004-0.0040.0000.0000.0000.000
101H215GLU-1-0.966-1.00431.116-0.050-0.0500.0000.0000.0000.000
102H216ASN0-0.068-0.03728.022-0.001-0.0010.0000.0000.0000.000
103H217ILE0-0.011-0.00325.983-0.008-0.0080.0000.0000.0000.000
104H218GLU-1-0.883-0.94825.919-0.081-0.0810.0000.0000.0000.000
105H219GLN00.0370.00926.202-0.009-0.0090.0000.0000.0000.000
106H220LEU00.0100.01422.180-0.012-0.0120.0000.0000.0000.000
107H221ARG10.9650.98521.8480.0620.0620.0000.0000.0000.000
108H222MET0-0.084-0.04122.023-0.010-0.0100.0000.0000.0000.000
109H223ALA0-0.033-0.00921.734-0.008-0.0080.0000.0000.0000.000
110H224GLY00.0220.00718.634-0.022-0.0220.0000.0000.0000.000
111H225ALA0-0.038-0.01117.191-0.030-0.0300.0000.0000.0000.000
112H226ASP-1-0.821-0.90414.366-0.242-0.2420.0000.0000.0000.000
113H227GLN0-0.023-0.01817.3810.0270.0270.0000.0000.0000.000
114H228VAL0-0.0090.00619.194-0.017-0.0170.0000.0000.0000.000
115H229ILE0-0.0050.00419.4470.0160.0160.0000.0000.0000.000
116H230SER00.031-0.00223.019-0.007-0.0070.0000.0000.0000.000
117H231PRO00.0660.04424.9130.0090.0090.0000.0000.0000.000
118H232PHE00.0250.00027.4720.0080.0080.0000.0000.0000.000
119H233VAL0-0.0230.00229.7960.0030.0030.0000.0000.0000.000
120H234ILE00.0120.00327.1890.0040.0040.0000.0000.0000.000
121H235SER00.0010.00530.6380.0050.0050.0000.0000.0000.000
122H236GLY00.0680.03232.7570.0020.0020.0000.0000.0000.000
123H237ARG10.9190.94731.2300.0170.0170.0000.0000.0000.000
124H238LEU00.0450.03431.7860.0020.0020.0000.0000.0000.000
125H239MET0-0.027-0.00735.6340.0010.0010.0000.0000.0000.000
126H240SER0-0.101-0.06338.4700.0010.0010.0000.0000.0000.000
127H241ARG10.8790.93336.880-0.005-0.0050.0000.0000.0000.000
128H242SER0-0.041-0.01538.1200.0030.0030.0000.0000.0000.000
129H243ILE0-0.091-0.04140.7930.0000.0000.0000.0000.0000.000
130H244ASP-1-0.907-0.94044.1790.0070.0070.0000.0000.0000.000
131H245ASP-1-0.936-0.96942.5860.0160.0160.0000.0000.0000.000
132H246GLY00.0030.00238.9580.0010.0010.0000.0000.0000.000
133H247TYR00.0150.00238.3470.0030.0030.0000.0000.0000.000
134H248GLU-1-0.859-0.93136.1910.0150.0150.0000.0000.0000.000
135H249ALA00.005-0.00634.0870.0010.0010.0000.0000.0000.000
136H250MET0-0.028-0.00533.2450.0020.0020.0000.0000.0000.000
137H251PHE00.0130.00830.9740.0040.0040.0000.0000.0000.000
138H252VAL0-0.019-0.01628.6300.0040.0040.0000.0000.0000.000
139H253GLN0-0.036-0.02928.479-0.002-0.0020.0000.0000.0000.000
140H254ASP-1-0.894-0.94128.3620.0480.0480.0000.0000.0000.000
141H255VAL0-0.098-0.05327.4950.0080.0080.0000.0000.0000.000
142H256LEU0-0.016-0.01923.7380.0070.0070.0000.0000.0000.000
143H257ALA00.0510.05723.3020.0050.0050.0000.0000.0000.000
144H258GLU-1-0.946-0.98420.1200.1600.1600.0000.0000.0000.000
145H259GLU-1-1.011-1.01723.5360.0930.0930.0000.0000.0000.000
146H260SER0-0.0110.00926.728-0.002-0.0020.0000.0000.0000.000
147H261THR0-0.039-0.03328.4610.0050.0050.0000.0000.0000.000
148H262ARG10.8970.93929.616-0.057-0.0570.0000.0000.0000.000
149H263ARG10.9961.03422.326-0.144-0.1440.0000.0000.0000.000
150H264MET00.004-0.00824.2200.0000.0000.0000.0000.0000.000
151H265VAL0-0.043-0.01920.7730.0120.0120.0000.0000.0000.000
152H266GLU-1-0.891-0.94217.0940.0920.0920.0000.0000.0000.000
153H267VAL0-0.086-0.04918.2360.0340.0340.0000.0000.0000.000
154H268PRO00.0070.00214.392-0.018-0.0180.0000.0000.0000.000
155H269ILE00.0300.02417.3320.0110.0110.0000.0000.0000.000
156H270PRO0-0.055-0.02816.2090.0050.0050.0000.0000.0000.000
157H271GLU-1-0.937-0.98013.1600.1350.1350.0000.0000.0000.000
158H272GLY0-0.050-0.02117.539-0.015-0.0150.0000.0000.0000.000
159H273SER0-0.018-0.02019.470-0.015-0.0150.0000.0000.0000.000
160H274LYS10.9410.98323.062-0.114-0.1140.0000.0000.0000.000
161H275LEU00.0530.02424.477-0.006-0.0060.0000.0000.0000.000
162H276GLU-1-0.941-0.96122.7790.0550.0550.0000.0000.0000.000
163H277GLY00.0050.01425.455-0.005-0.0050.0000.0000.0000.000
164H278VAL0-0.061-0.02328.497-0.005-0.0050.0000.0000.0000.000
165H279SER00.000-0.00929.6900.0020.0020.0000.0000.0000.000
166H280VAL00.0470.01930.3340.0040.0040.0000.0000.0000.000
167H281LEU0-0.070-0.03932.3160.0010.0010.0000.0000.0000.000
168H282ASP-1-0.920-0.95633.8060.0390.0390.0000.0000.0000.000
169H283ALA0-0.061-0.02129.9760.0020.0020.0000.0000.0000.000
170H284ASP-1-0.867-0.91432.0020.0510.0510.0000.0000.0000.000
171H285ILE00.011-0.00327.2730.0020.0020.0000.0000.0000.000
172H286HIS00.0250.00031.1000.0050.0050.0000.0000.0000.000
173H287ASP-1-0.940-0.94832.8450.0520.0520.0000.0000.0000.000
174H288VAL0-0.0250.00630.8710.0030.0030.0000.0000.0000.000
175H289THR0-0.046-0.05228.4370.0070.0070.0000.0000.0000.000
176H290GLY0-0.075-0.03830.4880.0060.0060.0000.0000.0000.000
177H291VAL0-0.054-0.00926.597-0.002-0.0020.0000.0000.0000.000
178H292ILE00.0320.01629.866-0.003-0.0030.0000.0000.0000.000
179H293ILE0-0.031-0.02827.3110.0040.0040.0000.0000.0000.000
180H294ILE0-0.001-0.00628.052-0.006-0.0060.0000.0000.0000.000
181H295GLY00.0490.01327.377-0.008-0.0080.0000.0000.0000.000
182H296VAL0-0.054-0.01424.0960.0110.0110.0000.0000.0000.000
183H297GLY00.0080.01622.058-0.011-0.0110.0000.0000.0000.000
184H298ARG10.8050.86221.645-0.028-0.0280.0000.0000.0000.000
185H299GLY0-0.029-0.01620.955-0.007-0.0070.0000.0000.0000.000
186H300ASP-1-0.963-0.98719.279-0.031-0.0310.0000.0000.0000.000
187H301GLU-1-0.934-0.93921.727-0.011-0.0110.0000.0000.0000.000
188H302LEU0-0.042-0.03224.1640.0090.0090.0000.0000.0000.000
189H303ILE0-0.016-0.01026.208-0.004-0.0040.0000.0000.0000.000
190H304ILE0-0.016-0.02128.9200.0060.0060.0000.0000.0000.000
191H305ASP-1-0.989-0.98230.9700.0270.0270.0000.0000.0000.000
192H306PRO0-0.0090.00929.526-0.003-0.0030.0000.0000.0000.000
193H307PRO00.0280.01232.4560.0010.0010.0000.0000.0000.000
194H308ARG10.9610.95134.185-0.022-0.0220.0000.0000.0000.000
195H309ASP-1-0.923-0.96735.1740.0230.0230.0000.0000.0000.000
196H310TYR0-0.0150.00825.863-0.004-0.0040.0000.0000.0000.000
197H311SER00.001-0.00530.1370.0030.0030.0000.0000.0000.000
198H312PHE0-0.024-0.00424.864-0.002-0.0020.0000.0000.0000.000
199H313ARG10.9400.97523.373-0.031-0.0310.0000.0000.0000.000
200H314ALA00.0420.00918.7770.0080.0080.0000.0000.0000.000
201H315GLY0-0.073-0.03217.012-0.013-0.0130.0000.0000.0000.000
202H316ASP-1-0.762-0.85818.0770.0610.0610.0000.0000.0000.000
203H317ILE0-0.022-0.00816.1580.0230.0230.0000.0000.0000.000
204H318ILE0-0.0100.00019.960-0.019-0.0190.0000.0000.0000.000
205H319LEU00.0430.01621.9740.0120.0120.0000.0000.0000.000
206H320GLY00.0220.01524.140-0.009-0.0090.0000.0000.0000.000
207H321ILE0-0.0050.00125.7380.0030.0030.0000.0000.0000.000
208H322GLY00.006-0.00527.789-0.004-0.0040.0000.0000.0000.000
209H323LYS10.9060.94727.776-0.069-0.0690.0000.0000.0000.000
210H324PRO00.0110.00325.5840.0040.0040.0000.0000.0000.000
211H325GLU-1-0.894-0.95625.5930.1010.1010.0000.0000.0000.000
212H326GLU-1-0.865-0.91927.7710.0780.0780.0000.0000.0000.000
213H327ILE00.0210.01222.3110.0050.0050.0000.0000.0000.000
214H328GLU-1-0.963-0.97922.0810.2050.2050.0000.0000.0000.000
215H329ARG10.8870.93924.275-0.084-0.0840.0000.0000.0000.000
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