FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2NY4R

Calculation Name: 2EAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EAY

Chain ID: A

ChEMBL ID:

UniProt ID: O66837

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2721246.336886
FMO2-HF: Nuclear repulsion 2635133.427146
FMO2-HF: Total energy -86112.90974
FMO2-MP2: Total energy -86369.550876


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.742-0.5763.981-3.202-5.945-0.021
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / 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].
3A3LYS10.9140.9572.281-2.6510.5142.772-1.971-3.967-0.007
4A4ASN00.0050.0013.4510.8221.0200.0100.149-0.3570.000
5A5LEU00.0160.0196.840-0.002-0.0020.0000.0000.0000.000
6A6ILE00.0060.0199.4860.1400.1400.0000.0000.0000.000
7A7TRP0-0.026-0.05011.950-0.033-0.0330.0000.0000.0000.000
8A8LEU0-0.016-0.00715.2490.0520.0520.0000.0000.0000.000
9A9LYS10.9670.98318.9040.2730.2730.0000.0000.0000.000
10A10GLU-1-0.969-0.98921.723-0.189-0.1890.0000.0000.0000.000
11A11VAL00.0010.00620.767-0.009-0.0090.0000.0000.0000.000
12A12ASP-1-0.786-0.86423.796-0.198-0.1980.0000.0000.0000.000
13A13SER0-0.007-0.03222.5230.0000.0000.0000.0000.0000.000
14A14THR00.031-0.00516.9610.0040.0040.0000.0000.0000.000
15A15GLN00.0460.03217.116-0.050-0.0500.0000.0000.0000.000
16A16GLU-1-0.955-0.97919.290-0.125-0.1250.0000.0000.0000.000
17A17ARG10.8910.91619.8210.2080.2080.0000.0000.0000.000
18A18LEU0-0.0440.00814.082-0.008-0.0080.0000.0000.0000.000
19A19LYS10.8850.93818.1510.1300.1300.0000.0000.0000.000
20A20GLU-1-0.939-0.93421.076-0.149-0.1490.0000.0000.0000.000
21A21TRP0-0.004-0.01418.634-0.005-0.0050.0000.0000.0000.000
22A22ASN0-0.089-0.05416.613-0.026-0.0260.0000.0000.0000.000
23A23VAL00.0400.03412.499-0.025-0.0250.0000.0000.0000.000
24A24SER00.0260.00910.6640.0590.0590.0000.0000.0000.000
25A25TYR00.0480.0067.938-0.085-0.0850.0000.0000.0000.000
26A26GLY0-0.019-0.0125.575-0.092-0.0920.0000.0000.0000.000
27A27THR0-0.0070.0016.349-0.947-0.9470.0000.0000.0000.000
28A28ALA0-0.028-0.0058.7530.2560.2560.0000.0000.0000.000
29A29LEU0-0.023-0.00510.431-0.033-0.0330.0000.0000.0000.000
30A30VAL0-0.002-0.01511.9780.0530.0530.0000.0000.0000.000
31A31ALA00.0240.00614.9390.0280.0280.0000.0000.0000.000
32A32ASP-1-0.824-0.86718.525-0.419-0.4190.0000.0000.0000.000
33A33ARG10.9440.96720.3680.2270.2270.0000.0000.0000.000
34A34GLN00.0450.02620.674-0.023-0.0230.0000.0000.0000.000
35A35THR0-0.062-0.03224.4910.0140.0140.0000.0000.0000.000
36A36LYS11.0001.00627.2260.1290.1290.0000.0000.0000.000
37A49GLU-1-0.933-0.98324.480-0.243-0.2430.0000.0000.0000.000
38A50GLY00.0420.01923.1080.0140.0140.0000.0000.0000.000
39A51GLY00.0250.02922.062-0.004-0.0040.0000.0000.0000.000
40A52LEU0-0.015-0.00714.178-0.030-0.0300.0000.0000.0000.000
41A53TYR0-0.0090.00117.5320.0360.0360.0000.0000.0000.000
42A54PHE00.0390.00910.449-0.088-0.0880.0000.0000.0000.000
43A55SER00.0240.00413.8200.0750.0750.0000.0000.0000.000
44A56PHE0-0.013-0.0179.332-0.162-0.1620.0000.0000.0000.000
45A57LEU0-0.0200.00411.0330.1180.1180.0000.0000.0000.000
46A58LEU0-0.0040.0018.9330.0960.0960.0000.0000.0000.000
47A59ASN00.0430.01211.525-0.160-0.1600.0000.0000.0000.000
48A60PRO00.018-0.01013.2870.0450.0450.0000.0000.0000.000
49A61LYS10.9520.97216.384-0.162-0.1620.0000.0000.0000.000
50A62GLU-1-0.939-0.95611.6000.7880.7880.0000.0000.0000.000
51A63PHE0-0.057-0.03810.2730.0470.0470.0000.0000.0000.000
52A64GLU-1-0.888-0.94116.2220.1670.1670.0000.0000.0000.000
53A65ASN0-0.0270.00919.264-0.044-0.0440.0000.0000.0000.000
54A66LEU00.010-0.02218.2330.0190.0190.0000.0000.0000.000
55A67LEU0-0.0030.01520.271-0.022-0.0220.0000.0000.0000.000
56A68GLN0-0.023-0.02918.9010.0180.0180.0000.0000.0000.000
57A69LEU00.0020.01112.8810.0110.0110.0000.0000.0000.000
58A70PRO00.021-0.00115.4180.0100.0100.0000.0000.0000.000
59A71LEU00.0370.03917.198-0.018-0.0180.0000.0000.0000.000
60A72VAL0-0.0040.00612.569-0.009-0.0090.0000.0000.0000.000
61A73LEU0-0.036-0.01511.0350.0080.0080.0000.0000.0000.000
62A74GLY00.0760.03213.572-0.050-0.0500.0000.0000.0000.000
63A75LEU0-0.0130.00115.451-0.027-0.0270.0000.0000.0000.000
64A76SER00.002-0.00210.6430.0240.0240.0000.0000.0000.000
65A77VAL0-0.0110.01012.736-0.059-0.0590.0000.0000.0000.000
66A78SER0-0.030-0.02414.293-0.021-0.0210.0000.0000.0000.000
67A79GLU-1-0.877-0.95013.6980.1640.1640.0000.0000.0000.000
68A80ALA0-0.0010.00211.907-0.015-0.0150.0000.0000.0000.000
69A81LEU00.012-0.00613.951-0.032-0.0320.0000.0000.0000.000
70A82GLU-1-0.898-0.92217.228-0.013-0.0130.0000.0000.0000.000
71A83GLU-1-0.940-0.96714.047-0.027-0.0270.0000.0000.0000.000
72A84ILE0-0.084-0.03013.879-0.020-0.0200.0000.0000.0000.000
73A85THR0-0.064-0.06617.6650.0100.0100.0000.0000.0000.000
74A86GLU-1-0.940-0.96420.736-0.058-0.0580.0000.0000.0000.000
75A87ILE0-0.053-0.01622.4330.0160.0160.0000.0000.0000.000
76A88PRO0-0.0020.01322.034-0.004-0.0040.0000.0000.0000.000
77A89PHE0-0.013-0.02920.681-0.008-0.0080.0000.0000.0000.000
78A90SER0-0.025-0.02522.5970.0130.0130.0000.0000.0000.000
79A91LEU0-0.054-0.02918.832-0.009-0.0090.0000.0000.0000.000
80A92LYS10.9300.99222.7490.0250.0250.0000.0000.0000.000
81A93TRP0-0.0300.00524.040-0.003-0.0030.0000.0000.0000.000
82A94PRO00.010-0.03123.544-0.008-0.0080.0000.0000.0000.000
83A95ASN0-0.040-0.04920.3230.0080.0080.0000.0000.0000.000
84A96ASP-1-0.791-0.87620.407-0.067-0.0670.0000.0000.0000.000
85A97VAL0-0.027-0.01717.8780.0180.0180.0000.0000.0000.000
86A98TYR00.033-0.00721.240-0.016-0.0160.0000.0000.0000.000
87A99PHE00.0460.04224.1880.0050.0050.0000.0000.0000.000
88A100GLN0-0.006-0.00926.273-0.004-0.0040.0000.0000.0000.000
89A101GLU-1-0.841-0.94029.045-0.015-0.0150.0000.0000.0000.000
90A102LYS10.8120.92629.0450.0620.0620.0000.0000.0000.000
91A103LYS10.9080.96523.0360.0840.0840.0000.0000.0000.000
92A104VAL0-0.008-0.00520.855-0.009-0.0090.0000.0000.0000.000
93A105SER0-0.054-0.04917.938-0.023-0.0230.0000.0000.0000.000
94A106GLY0-0.023-0.00619.7130.0260.0260.0000.0000.0000.000
95A107VAL0-0.025-0.00515.835-0.030-0.0300.0000.0000.0000.000
96A108LEU00.0170.01817.5690.0210.0210.0000.0000.0000.000
97A109CYS0-0.042-0.01216.688-0.012-0.0120.0000.0000.0000.000
98A110GLU-1-0.842-0.91718.176-0.079-0.0790.0000.0000.0000.000
99A111LEU00.0080.00619.1500.0040.0040.0000.0000.0000.000
100A112SER0-0.005-0.00820.717-0.009-0.0090.0000.0000.0000.000
101A113LYS10.9220.94821.7450.0480.0480.0000.0000.0000.000
102A114ASP-1-0.895-0.94319.5630.0560.0560.0000.0000.0000.000
103A115LYS10.8690.94517.1920.1530.1530.0000.0000.0000.000
104A116LEU00.0080.02714.578-0.004-0.0040.0000.0000.0000.000
105A117ILE0-0.025-0.03014.6370.0080.0080.0000.0000.0000.000
106A118VAL00.0120.00912.3300.0280.0280.0000.0000.0000.000
107A119GLY00.0440.02114.066-0.080-0.0800.0000.0000.0000.000
108A120ILE0-0.031-0.01812.1840.0510.0510.0000.0000.0000.000
109A121GLY00.0060.00716.012-0.051-0.0510.0000.0000.0000.000
110A122ILE0-0.0140.00314.7280.0300.0300.0000.0000.0000.000
111A123ASN0-0.037-0.01519.123-0.036-0.0360.0000.0000.0000.000
112A124VAL0-0.001-0.00118.3260.0090.0090.0000.0000.0000.000
113A125ASN00.029-0.00321.0330.0280.0280.0000.0000.0000.000
114A126GLN0-0.0010.00024.2100.0010.0010.0000.0000.0000.000
115A127ARG10.7810.85526.7960.1660.1660.0000.0000.0000.000
116A128GLU-1-0.912-0.94630.395-0.094-0.0940.0000.0000.0000.000
117A129ILE0-0.034-0.00329.900-0.007-0.0070.0000.0000.0000.000
118A130PRO0-0.044-0.03532.3080.0060.0060.0000.0000.0000.000
119A131GLU-1-0.830-0.93235.282-0.060-0.0600.0000.0000.0000.000
120A132GLU-1-1.001-0.99036.514-0.049-0.0490.0000.0000.0000.000
121A133ILE0-0.053-0.03130.4040.0010.0010.0000.0000.0000.000
122A134LYN00.1250.08032.7380.0000.0000.0000.0000.0000.000
123A135ASP-1-0.926-0.96933.717-0.049-0.0490.0000.0000.0000.000
124A136ARG10.9650.98930.7680.0650.0650.0000.0000.0000.000
125A137ALA0-0.058-0.03628.158-0.002-0.0020.0000.0000.0000.000
126A138THR00.0610.02726.2680.0000.0000.0000.0000.0000.000
127A139THR0-0.006-0.01424.759-0.010-0.0100.0000.0000.0000.000
128A140LEU00.0500.02119.3790.0080.0080.0000.0000.0000.000
129A141TYR0-0.0050.01924.0780.0100.0100.0000.0000.0000.000
130A142GLU-1-0.952-0.96626.451-0.081-0.0810.0000.0000.0000.000
131A143ILE0-0.062-0.01324.8070.0080.0080.0000.0000.0000.000
132A144THR0-0.031-0.03824.2460.0030.0030.0000.0000.0000.000
133A145GLY00.0160.01227.5370.0050.0050.0000.0000.0000.000
134A146LYS10.8830.94124.3300.1420.1420.0000.0000.0000.000
135A147ASP-1-0.793-0.86023.660-0.194-0.1940.0000.0000.0000.000
136A148TRP0-0.026-0.03118.956-0.008-0.0080.0000.0000.0000.000
137A149ASP-1-0.822-0.91415.462-0.513-0.5130.0000.0000.0000.000
138A150ARG10.8570.88015.9940.3520.3520.0000.0000.0000.000
139A151LYS10.9690.99510.0990.9600.9600.0000.0000.0000.000
140A152GLU-1-0.923-0.96411.196-0.894-0.8940.0000.0000.0000.000
141A153VAL0-0.0010.00111.796-0.032-0.0320.0000.0000.0000.000
142A154LEU0-0.012-0.0069.621-0.016-0.0160.0000.0000.0000.000
143A155LEU0-0.023-0.0166.052-0.195-0.1950.0000.0000.0000.000
144A156LYS10.8940.9727.5200.0630.0630.0000.0000.0000.000
145A157VAL00.0370.0059.4360.1220.1220.0000.0000.0000.000
146A158LEU0-0.041-0.0225.7000.1230.1230.0000.0000.0000.000
147A159LYN00.0130.0084.7390.0590.218-0.001-0.008-0.1500.000
148A160ARG10.9210.9775.8020.3110.3110.0000.0000.0000.000
149A161ILE0-0.0040.0006.7720.2400.2400.0000.0000.0000.000
150A162SER0-0.062-0.0442.540-1.736-0.1371.201-1.356-1.443-0.014
151A163GLU-1-0.965-0.9694.5401.0311.076-0.001-0.016-0.0280.000
152A164ASN0-0.033-0.0477.1750.0570.0570.0000.0000.0000.000
153A165LEU00.007-0.0027.366-0.057-0.0570.0000.0000.0000.000
154A166LYS10.8370.9365.683-1.088-1.0880.0000.0000.0000.000
155A167LYS10.9620.9848.333-0.580-0.5800.0000.0000.0000.000
156A168PHE0-0.090-0.04311.603-0.117-0.1170.0000.0000.0000.000
157A169LYS10.9130.9647.325-1.769-1.7690.0000.0000.0000.000
158A170GLU-1-0.897-0.93610.8300.7380.7380.0000.0000.0000.000
159A171LYS10.9040.96313.780-0.431-0.4310.0000.0000.0000.000
160A172SER00.0580.02016.660-0.028-0.0280.0000.0000.0000.000
161A173PHE00.0900.03417.9300.0100.0100.0000.0000.0000.000
162A174LYS10.8910.96319.253-0.185-0.1850.0000.0000.0000.000
163A175GLU-1-0.916-0.95316.9950.2730.2730.0000.0000.0000.000
164A176PHE0-0.038-0.03713.048-0.011-0.0110.0000.0000.0000.000
165A177LYS10.8200.91918.709-0.139-0.1390.0000.0000.0000.000
166A178GLY00.0600.03022.163-0.015-0.0150.0000.0000.0000.000
167A179LYS10.9740.98016.848-0.223-0.2230.0000.0000.0000.000
168A180ILE00.0080.00618.167-0.017-0.0170.0000.0000.0000.000
169A181GLU-1-0.785-0.90321.6140.0820.0820.0000.0000.0000.000
170A182SER0-0.081-0.03523.669-0.011-0.0110.0000.0000.0000.000
171A183LYS10.9580.97618.553-0.043-0.0430.0000.0000.0000.000
172A184MET0-0.0400.00324.380-0.007-0.0070.0000.0000.0000.000
173A185LEU00.0100.01826.132-0.001-0.0010.0000.0000.0000.000
174A186TYR0-0.046-0.04128.5810.0030.0030.0000.0000.0000.000
175A187LEU00.0080.02528.9180.0030.0030.0000.0000.0000.000
176A188GLY0-0.057-0.04131.424-0.003-0.0030.0000.0000.0000.000
177A189GLU-1-0.938-0.97134.5050.0060.0060.0000.0000.0000.000
178A190GLU-1-0.908-0.95536.3500.0220.0220.0000.0000.0000.000
179A191VAL0-0.033-0.02433.884-0.004-0.0040.0000.0000.0000.000
180A192LYS10.9190.95036.9520.0080.0080.0000.0000.0000.000
181A193LEU0-0.020-0.01433.011-0.001-0.0010.0000.0000.0000.000
182A194LEU0-0.037-0.00833.880-0.001-0.0010.0000.0000.0000.000
183A195GLY00.0260.01936.5760.0000.0000.0000.0000.0000.000
184A196GLU-1-0.932-0.97536.5270.0070.0070.0000.0000.0000.000
185A197GLY0-0.020-0.01940.1550.0020.0020.0000.0000.0000.000
186A198LYS10.9130.96541.857-0.019-0.0190.0000.0000.0000.000
187A199ILE0-0.040-0.02436.9380.0020.0020.0000.0000.0000.000
188A200THR00.0380.00439.322-0.003-0.0030.0000.0000.0000.000
189A201GLY00.0340.01039.2780.0020.0020.0000.0000.0000.000
190A202LYS10.9831.02836.606-0.035-0.0350.0000.0000.0000.000
191A203LEU00.0000.01329.7670.0050.0050.0000.0000.0000.000
192A204VAL0-0.043-0.03133.3700.0000.0000.0000.0000.0000.000
193A205GLY00.0520.03229.3050.0030.0030.0000.0000.0000.000
194A206LEU0-0.037-0.01623.746-0.003-0.0030.0000.0000.0000.000
195A207SER0-0.044-0.04527.8900.0070.0070.0000.0000.0000.000
196A208GLU-1-0.904-0.97626.0630.1490.1490.0000.0000.0000.000
197A209LYS10.8710.93624.606-0.078-0.0780.0000.0000.0000.000
198A210GLY00.0430.01323.5840.0060.0060.0000.0000.0000.000
199A211GLY00.0300.02524.482-0.009-0.0090.0000.0000.0000.000
200A212ALA00.0170.02727.7770.0040.0040.0000.0000.0000.000
201A213LEU0-0.037-0.02029.517-0.002-0.0020.0000.0000.0000.000
202A214ILE00.0300.02332.627-0.002-0.0020.0000.0000.0000.000
203A215LEU0-0.014-0.01335.7580.0020.0020.0000.0000.0000.000
204A216THR0-0.067-0.05738.887-0.004-0.0040.0000.0000.0000.000
205A217GLU-1-0.894-0.96641.6350.0210.0210.0000.0000.0000.000
206A218GLU-1-0.956-0.96144.5520.0270.0270.0000.0000.0000.000
207A219GLY0-0.0010.01242.3970.0020.0020.0000.0000.0000.000
208A220ILE0-0.031-0.01635.713-0.002-0.0020.0000.0000.0000.000
209A221LYS10.9000.96837.186-0.027-0.0270.0000.0000.0000.000
210A222GLU-1-0.793-0.88530.0870.0840.0840.0000.0000.0000.000
211A223ILE0-0.037-0.01131.212-0.002-0.0020.0000.0000.0000.000
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213A225SER0-0.043-0.01728.0860.0010.0010.0000.0000.0000.000
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