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: 9G362

Calculation Name: 2YN7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YN7

Chain ID: A

ChEMBL ID:

UniProt ID: O50955

Base Structure: X-ray

Registration Date: 2023-06-20

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2708975.20438
FMO2-HF: Nuclear repulsion 2619326.671362
FMO2-HF: Total energy -89648.533018
FMO2-MP2: Total energy -89909.779676


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(A:193:SER)


Summations of interaction energy for fragment #1(A:193: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.
-0.252-5.65417.744-5.732-6.609-0.015
Interaction energy analysis for fragmet #1(A:193:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.004
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].
3A195LEU0-0.0010.0143.154-3.670-0.5850.200-1.297-1.9890.004
4A196GLN00.0940.0221.5492.059-5.42317.539-6.015-4.040-0.018
5A197THR00.0090.0193.0111.3320.2340.0061.583-0.491-0.001
6A198LEU0-0.021-0.0025.1840.4380.531-0.001-0.003-0.0890.000
7A199LYS10.8850.9336.200-0.391-0.3910.0000.0000.0000.000
8A200ASN00.0180.0006.9210.2840.2840.0000.0000.0000.000
9A201GLU-1-0.956-0.9788.719-0.500-0.5000.0000.0000.0000.000
10A202LEU0-0.040-0.01810.5480.0530.0530.0000.0000.0000.000
11A203ILE00.0320.01910.3890.0200.0200.0000.0000.0000.000
12A204ARG10.8640.94012.8290.4190.4190.0000.0000.0000.000
13A205ALA0-0.003-0.00714.6250.0260.0260.0000.0000.0000.000
14A206ILE00.0230.00316.1860.0190.0190.0000.0000.0000.000
15A207SER00.0240.00317.2500.0200.0200.0000.0000.0000.000
16A208GLU-1-0.901-0.93917.792-0.245-0.2450.0000.0000.0000.000
17A209GLU-1-0.882-0.95820.631-0.056-0.0560.0000.0000.0000.000
18A210LYS10.9320.95821.2790.0500.0500.0000.0000.0000.000
19A211ASN00.0030.01322.1130.0140.0140.0000.0000.0000.000
20A212LYS10.9230.97224.0930.0900.0900.0000.0000.0000.000
21A213THR0-0.077-0.02426.3330.0050.0050.0000.0000.0000.000
22A214GLN0-0.036-0.02826.3140.0070.0070.0000.0000.0000.000
23A215ASN0-0.037-0.01228.761-0.004-0.0040.0000.0000.0000.000
24A216ASN0-0.0040.01030.730-0.002-0.0020.0000.0000.0000.000
25A217PHE0-0.038-0.03431.952-0.002-0.0020.0000.0000.0000.000
26A218GLY00.0010.01235.0120.0010.0010.0000.0000.0000.000
27A219PHE00.0040.01437.2460.0020.0020.0000.0000.0000.000
28A220ARG10.9090.94238.9580.0370.0370.0000.0000.0000.000
29A221GLU-1-0.749-0.79842.213-0.023-0.0230.0000.0000.0000.000
30A222THR0-0.0090.00843.682-0.001-0.0010.0000.0000.0000.000
31A223TYR00.019-0.00947.0970.0010.0010.0000.0000.0000.000
32A224ASP-1-0.856-0.93850.093-0.018-0.0180.0000.0000.0000.000
33A225GLN00.005-0.03446.2350.0030.0030.0000.0000.0000.000
34A226PHE00.012-0.01842.5840.0000.0000.0000.0000.0000.000
35A227LYS10.8730.93947.0350.0190.0190.0000.0000.0000.000
36A228MET0-0.038-0.00643.4540.0030.0030.0000.0000.0000.000
37A229LYS10.8630.95548.6920.0150.0150.0000.0000.0000.000
38A230ASP-1-0.861-0.92350.201-0.010-0.0100.0000.0000.0000.000
39A231SER00.0660.01250.7050.0010.0010.0000.0000.0000.000
40A232ALA0-0.025-0.01646.5890.0010.0010.0000.0000.0000.000
41A233PHE0-0.041-0.02542.5130.0020.0020.0000.0000.0000.000
42A234GLU-1-0.860-0.91247.238-0.005-0.0050.0000.0000.0000.000
43A235LEU0-0.086-0.02348.8390.0020.0020.0000.0000.0000.000
44A236LEU0-0.037-0.02943.1060.0030.0030.0000.0000.0000.000
45A237ASP-1-0.860-0.91246.0910.0010.0010.0000.0000.0000.000
46A238VAL0-0.082-0.04840.2740.0010.0010.0000.0000.0000.000
47A239ILE00.0350.01437.6930.0030.0030.0000.0000.0000.000
48A240SER0-0.156-0.07735.4930.0030.0030.0000.0000.0000.000
49A241SER0-0.069-0.06337.5070.0000.0000.0000.0000.0000.000
50A242ALA00.0690.04638.0190.0030.0030.0000.0000.0000.000
51A243LYS10.9410.95433.048-0.007-0.0070.0000.0000.0000.000
52A244VAL0-0.053-0.03637.788-0.003-0.0030.0000.0000.0000.000
53A245TYR0-0.0130.00440.531-0.001-0.0010.0000.0000.0000.000
54A246ASP-1-0.845-0.91843.0430.0110.0110.0000.0000.0000.000
55A247ARG10.9860.97742.759-0.020-0.0200.0000.0000.0000.000
56A248SER0-0.034-0.01845.746-0.001-0.0010.0000.0000.0000.000
57A249TYR0-0.053-0.01946.610-0.002-0.0020.0000.0000.0000.000
58A250ALA0-0.029-0.00444.371-0.002-0.0020.0000.0000.0000.000
59A251PRO00.0330.02444.3550.0000.0000.0000.0000.0000.000
60A252GLN00.0490.02546.1770.0020.0020.0000.0000.0000.000
61A253LEU0-0.0130.01641.771-0.002-0.0020.0000.0000.0000.000
62A254ASN00.0520.03145.250-0.002-0.0020.0000.0000.0000.000
63A255SER0-0.039-0.02947.516-0.002-0.0020.0000.0000.0000.000
64A256ASN0-0.028-0.02347.114-0.001-0.0010.0000.0000.0000.000
65A257THR00.0060.01045.9020.0000.0000.0000.0000.0000.000
66A258PRO00.0320.00042.208-0.001-0.0010.0000.0000.0000.000
67A259GLU-1-0.896-0.95040.396-0.013-0.0130.0000.0000.0000.000
68A260ALA00.0200.01440.6650.0010.0010.0000.0000.0000.000
69A261GLU-1-0.927-0.95241.396-0.032-0.0320.0000.0000.0000.000
70A262ASN0-0.065-0.03434.6380.0020.0020.0000.0000.0000.000
71A263GLU-1-0.706-0.84936.978-0.001-0.0010.0000.0000.0000.000
72A264ARG10.8020.86438.2850.0190.0190.0000.0000.0000.000
73A265ASN0-0.026-0.03436.269-0.003-0.0030.0000.0000.0000.000
74A266LYS10.8820.96732.1420.0150.0150.0000.0000.0000.000
75A267PHE00.0350.00934.9630.0010.0010.0000.0000.0000.000
76A268TYR0-0.027-0.06036.9870.0000.0000.0000.0000.0000.000
77A269ALA00.0450.03231.623-0.003-0.0030.0000.0000.0000.000
78A270LEU0-0.090-0.02032.464-0.002-0.0020.0000.0000.0000.000
79A271MET0-0.082-0.02733.7860.0020.0020.0000.0000.0000.000
80A272ASP-1-0.894-0.94431.230-0.046-0.0460.0000.0000.0000.000
81A273PHE0-0.082-0.05231.682-0.005-0.0050.0000.0000.0000.000
82A274ASP-1-0.874-0.91536.043-0.041-0.0410.0000.0000.0000.000
83A275GLN00.020-0.01438.1080.0060.0060.0000.0000.0000.000
84A276TYR0-0.011-0.01441.5400.0020.0020.0000.0000.0000.000
85A277LYS10.9100.97536.5930.0250.0250.0000.0000.0000.000
86A278ILE0-0.040-0.02438.4220.0040.0040.0000.0000.0000.000
87A279GLU-1-0.867-0.91742.226-0.017-0.0170.0000.0000.0000.000
88A280GLN00.0380.01044.2380.0020.0020.0000.0000.0000.000
89A281PHE00.004-0.01942.7150.0030.0030.0000.0000.0000.000
90A282GLY00.028-0.00745.0210.0020.0020.0000.0000.0000.000
91A283SER0-0.0240.00047.0970.0020.0020.0000.0000.0000.000
92A284ILE00.0010.00346.8400.0010.0010.0000.0000.0000.000
93A285MET0-0.078-0.03846.1860.0030.0030.0000.0000.0000.000
94A286GLU-1-0.893-0.95449.568-0.010-0.0100.0000.0000.0000.000
95A287ALA0-0.021-0.00252.6350.0010.0010.0000.0000.0000.000
96A288LEU0-0.039-0.02949.7850.0010.0010.0000.0000.0000.000
97A289TYR0-0.016-0.03052.8360.0020.0020.0000.0000.0000.000
98A290ASN0-0.0150.01254.7640.0000.0000.0000.0000.0000.000
99A291GLU-1-0.931-0.95257.6630.0020.0020.0000.0000.0000.000
100A292ASN00.0470.00157.0760.0010.0010.0000.0000.0000.000
101A293GLN0-0.0210.00056.7080.0000.0000.0000.0000.0000.000
102A294ASN0-0.060-0.04653.2800.0030.0030.0000.0000.0000.000
103A295HIS0-0.016-0.01052.1010.0010.0010.0000.0000.0000.000
104A296SER0-0.025-0.02450.6140.0000.0000.0000.0000.0000.000
105A297LEU00.0350.03347.6770.0010.0010.0000.0000.0000.000
106A298ILE00.0350.03447.2020.0000.0000.0000.0000.0000.000
107A299ARG10.9270.95246.230-0.008-0.0080.0000.0000.0000.000
108A300GLU-1-0.902-0.93743.8920.0200.0200.0000.0000.0000.000
109A301LEU0-0.031-0.03342.9230.0010.0010.0000.0000.0000.000
110A302MET00.0210.01741.540-0.001-0.0010.0000.0000.0000.000
111A303ILE00.0150.02340.3550.0000.0000.0000.0000.0000.000
112A304SER0-0.052-0.01738.5290.0010.0010.0000.0000.0000.000
113A305GLY00.0740.03636.7460.0020.0020.0000.0000.0000.000
114A306LEU00.0330.01335.688-0.001-0.0010.0000.0000.0000.000
115A307GLY0-0.019-0.01135.3630.0000.0000.0000.0000.0000.000
116A308THR0-0.072-0.07031.7550.0050.0050.0000.0000.0000.000
117A309GLN0-0.004-0.01629.6890.0040.0040.0000.0000.0000.000
118A310ILE00.0330.02130.572-0.001-0.0010.0000.0000.0000.000
119A311SER0-0.004-0.00329.8420.0040.0040.0000.0000.0000.000
120A312PHE0-0.028-0.01124.6760.0070.0070.0000.0000.0000.000
121A313GLU-1-0.794-0.90225.796-0.023-0.0230.0000.0000.0000.000
122A314LEU0-0.020-0.00725.987-0.001-0.0010.0000.0000.0000.000
123A315ALA00.0220.01224.1260.0090.0090.0000.0000.0000.000
124A316LEU0-0.017-0.00821.2720.0110.0110.0000.0000.0000.000
125A317GLU-1-0.879-0.94420.769-0.004-0.0040.0000.0000.0000.000
126A318GLU-1-0.928-0.97821.7240.0960.0960.0000.0000.0000.000
127A319ILE0-0.045-0.03316.7830.0270.0270.0000.0000.0000.000
128A320ASN00.0070.00117.0760.0240.0240.0000.0000.0000.000
129A321LYS10.9800.99217.142-0.033-0.0330.0000.0000.0000.000
130A322LYS10.8690.95817.535-0.141-0.1410.0000.0000.0000.000
131A323ILE0-0.013-0.00511.7830.0720.0720.0000.0000.0000.000
132A324GLU-1-0.963-0.97113.4770.0890.0890.0000.0000.0000.000
133A325ILE00.002-0.00215.5270.0240.0240.0000.0000.0000.000
134A326PHE00.024-0.00113.4290.0360.0360.0000.0000.0000.000
135A327ASN00.0500.0179.5950.3220.3220.0000.0000.0000.000
136A328GLN00.0200.00912.1390.0530.0530.0000.0000.0000.000
137A329ASP-1-0.893-0.93514.9250.3320.3320.0000.0000.0000.000
138A330TYR0-0.071-0.0425.5720.2550.2550.0000.0000.0000.000
139A331LEU0-0.043-0.02010.1270.0000.0000.0000.0000.0000.000
140A332ASN0-0.074-0.03612.406-0.078-0.0780.0000.0000.0000.000
141A333ALA0-0.031-0.01613.600-0.029-0.0290.0000.0000.0000.000
142A334LYS10.9490.97814.580-0.248-0.2480.0000.0000.0000.000
143A335ILE0-0.036-0.00912.572-0.007-0.0070.0000.0000.0000.000
144A336ASN00.0990.06411.6010.1770.1770.0000.0000.0000.000
145A337SER00.033-0.0156.670-0.138-0.1380.0000.0000.0000.000
146A338PHE00.0180.0188.7690.1050.1050.0000.0000.0000.000
147A339ASP-1-0.853-0.93511.3460.5560.5560.0000.0000.0000.000
148A340PHE00.0340.0067.911-0.088-0.0880.0000.0000.0000.000
149A341THR0-0.038-0.0328.249-0.041-0.0410.0000.0000.0000.000
150A342MET0-0.042-0.02110.030-0.166-0.1660.0000.0000.0000.000
151A343LYS10.9801.00413.640-0.542-0.5420.0000.0000.0000.000
152A344LEU00.0000.0068.382-0.088-0.0880.0000.0000.0000.000
153A345LYS10.9230.96111.707-0.736-0.7360.0000.0000.0000.000
154A346GLU-1-0.925-0.96313.6240.2070.2070.0000.0000.0000.000
155A347LEU00.0030.00114.254-0.044-0.0440.0000.0000.0000.000
156A348LYS10.9510.97612.954-0.076-0.0760.0000.0000.0000.000
157A349SER0-0.074-0.03715.829-0.045-0.0450.0000.0000.0000.000
158A350LYS10.9530.97218.859-0.180-0.1800.0000.0000.0000.000
159A351LEU00.0250.01417.258-0.016-0.0160.0000.0000.0000.000
160A352ASN0-0.007-0.02317.878-0.036-0.0360.0000.0000.0000.000
161A353GLN00.0260.03221.3420.0000.0000.0000.0000.0000.000
162A354ILE0-0.014-0.01022.953-0.008-0.0080.0000.0000.0000.000
163A355LEU0-0.0270.00020.851-0.009-0.0090.0000.0000.0000.000
164A356ASP-1-0.913-0.95425.0960.0150.0150.0000.0000.0000.000
165A357LYS10.8980.95527.111-0.048-0.0480.0000.0000.0000.000
166A358ARG10.8620.92928.0360.0270.0270.0000.0000.0000.000
167A359LYS10.8810.93925.3570.0310.0310.0000.0000.0000.000
168A360GLU-1-0.927-0.98030.7270.0140.0140.0000.0000.0000.000
169A361TRP0-0.004-0.00333.058-0.003-0.0030.0000.0000.0000.000
170A362SER00.0370.00933.496-0.001-0.0010.0000.0000.0000.000
171A363ARG10.9600.98829.0870.0040.0040.0000.0000.0000.000
172A364GLN0-0.0030.01136.5850.0000.0000.0000.0000.0000.000
173A365ALA0-0.010-0.00138.5790.0000.0000.0000.0000.0000.000
174A366ASP-1-0.829-0.90537.123-0.021-0.0210.0000.0000.0000.000
175A367GLY0-0.037-0.01140.4070.0000.0000.0000.0000.0000.000
176A368LEU0-0.016-0.01342.5570.0000.0000.0000.0000.0000.000
177A369ILE00.0240.01541.8430.0000.0000.0000.0000.0000.000
178A370ALA0-0.014-0.00244.028-0.001-0.0010.0000.0000.0000.000
179A371ASN0-0.132-0.06045.8690.0000.0000.0000.0000.0000.000
180A372ALA00.0690.01948.2810.0000.0000.0000.0000.0000.000
181A373SER0-0.050-0.02347.510-0.001-0.0010.0000.0000.0000.000
182A374SER0-0.019-0.00549.570-0.001-0.0010.0000.0000.0000.000
183A375ASN00.010-0.00752.4390.0000.0000.0000.0000.0000.000
184A376SER00.0900.05852.1000.0010.0010.0000.0000.0000.000
185A377SER0-0.010-0.01054.2230.0010.0010.0000.0000.0000.000
186A378LEU0-0.041-0.01157.0900.0000.0000.0000.0000.0000.000
187A379SER0-0.089-0.04356.4540.0010.0010.0000.0000.0000.000
188A380ASP-1-0.805-0.88458.5870.0030.0030.0000.0000.0000.000
189A381SER00.0830.03756.9630.0000.0000.0000.0000.0000.000
190A382LYS10.9971.00956.113-0.007-0.0070.0000.0000.0000.000
191A383SER0-0.090-0.09156.0430.0010.0010.0000.0000.0000.000
192A384LEU00.0440.04151.1170.0010.0010.0000.0000.0000.000
193A385ALA00.0610.03051.7730.0010.0010.0000.0000.0000.000
194A386GLU-1-0.905-0.96351.2860.0130.0130.0000.0000.0000.000
195A387TYR00.0300.02347.6110.0020.0020.0000.0000.0000.000
196A388ILE00.0560.03046.1020.0010.0010.0000.0000.0000.000
197A389LYS10.8340.89846.700-0.011-0.0110.0000.0000.0000.000
198A390LYS10.8460.94447.542-0.013-0.0130.0000.0000.0000.000
199A391ARG10.8740.92745.731-0.012-0.0120.0000.0000.0000.000
200A392TYR0-0.002-0.00442.1370.0000.0000.0000.0000.0000.000
201A393LEU00.0210.02842.0250.0000.0000.0000.0000.0000.000
202A394ASP-1-0.853-0.92341.8350.0260.0260.0000.0000.0000.000
203A395ASN0-0.054-0.03238.2290.0060.0060.0000.0000.0000.000
204A396MET0-0.044-0.01337.2800.0010.0010.0000.0000.0000.000
205A397GLN0-0.007-0.03237.3480.0010.0010.0000.0000.0000.000
206A398ASN00.0020.00136.1530.0040.0040.0000.0000.0000.000
207A399ALA0-0.0220.00133.2040.0040.0040.0000.0000.0000.000
208A400ARG10.9870.99832.592-0.024-0.0240.0000.0000.0000.000
209A401GLN00.002-0.01033.383-0.002-0.0020.0000.0000.0000.000
210A402SER0-0.035-0.00730.1480.0060.0060.0000.0000.0000.000
211A403VAL0-0.0140.00127.8280.0070.0070.0000.0000.0000.000
212A404LEU0-0.0210.00328.6190.0050.0050.0000.0000.0000.000
213A405GLU-1-0.901-0.96730.0990.0750.0750.0000.0000.0000.000
214A406ALA0-0.0220.00025.0710.0110.0110.0000.0000.0000.000
215A407TYR00.0280.00425.3890.0110.0110.0000.0000.0000.000
216A408ILE00.0140.00126.3810.0080.0080.0000.0000.0000.000
217A409SER0-0.093-0.04325.2440.0130.0130.0000.0000.0000.000
218A410ILE0-0.0050.00320.6740.0200.0200.0000.0000.0000.000
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