FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3Q2ML

Calculation Name: 1Y97-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1Y97

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9BQ50

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptAll
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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2576757.315182
FMO2-HF: Nuclear repulsion 2491649.264724
FMO2-HF: Total energy -85108.050458
FMO2-MP2: Total energy -85354.884869


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:ALA)


Summations of interaction energy for fragment #1(A:-1:ALA)
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.
-1.340.763-0.008-1.045-1.050
Interaction energy analysis for fragmet #1(A:-1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.012
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].
3A1MET0-0.0120.0043.797-0.6361.467-0.008-1.045-1.0500.000
4A2SER0-0.0070.0015.4510.3510.3510.0000.0000.0000.000
5A3GLU-1-0.921-0.9729.252-0.691-0.6910.0000.0000.0000.000
6A4ALA0-0.046-0.00212.0960.0470.0470.0000.0000.0000.000
7A5PRO0-0.038-0.01311.839-0.072-0.0720.0000.0000.0000.000
8A6ARG10.8380.91210.9600.3120.3120.0000.0000.0000.000
9A7ALA0-0.0120.00712.9990.0160.0160.0000.0000.0000.000
10A8GLU-1-0.785-0.90615.808-0.196-0.1960.0000.0000.0000.000
11A9THR0-0.041-0.02918.4230.0250.0250.0000.0000.0000.000
12A10PHE0-0.012-0.01515.891-0.006-0.0060.0000.0000.0000.000
13A11VAL00.001-0.01222.0000.0070.0070.0000.0000.0000.000
14A12PHE00.0240.00822.1970.0010.0010.0000.0000.0000.000
15A13LEU0-0.038-0.03426.483-0.003-0.0030.0000.0000.0000.000
16A14ASP-1-0.874-0.93929.1250.0030.0030.0000.0000.0000.000
17A15LEU0-0.051-0.02931.949-0.005-0.0050.0000.0000.0000.000
18A16GLU-1-0.791-0.88534.8860.0030.0030.0000.0000.0000.000
19A17ALA00.002-0.00537.977-0.003-0.0030.0000.0000.0000.000
20A18THR00.0180.01739.9190.0030.0030.0000.0000.0000.000
21A19GLY00.0390.00941.1910.0020.0020.0000.0000.0000.000
22A20LEU00.0170.02438.561-0.001-0.0010.0000.0000.0000.000
23A21PRO00.0900.01535.735-0.002-0.0020.0000.0000.0000.000
24A22SER0-0.068-0.02438.339-0.002-0.0020.0000.0000.0000.000
25A23VAL0-0.055-0.03041.6020.0010.0010.0000.0000.0000.000
26A24GLU-1-0.912-0.94340.693-0.017-0.0170.0000.0000.0000.000
27A25PRO0-0.0310.00638.559-0.001-0.0010.0000.0000.0000.000
28A26GLU-1-0.728-0.86939.899-0.020-0.0200.0000.0000.0000.000
29A27ILE0-0.009-0.01535.1570.0020.0020.0000.0000.0000.000
30A28ALA0-0.0080.00439.236-0.001-0.0010.0000.0000.0000.000
31A29GLU-1-0.832-0.91438.551-0.010-0.0100.0000.0000.0000.000
32A30LEU0-0.0140.00633.4150.0000.0000.0000.0000.0000.000
33A31SER0-0.024-0.02134.041-0.001-0.0010.0000.0000.0000.000
34A32LEU0-0.003-0.00430.032-0.001-0.0010.0000.0000.0000.000
35A33PHE00.001-0.00229.2220.0010.0010.0000.0000.0000.000
36A34ALA0-0.035-0.01826.582-0.001-0.0010.0000.0000.0000.000
37A35VAL00.0290.01223.3420.0030.0030.0000.0000.0000.000
38A36HIS00.0080.02019.8470.0100.0100.0000.0000.0000.000
39A37ARG10.7340.81912.1710.1750.1750.0000.0000.0000.000
40A38SER00.005-0.01119.4300.0120.0120.0000.0000.0000.000
41A39SER00.011-0.01221.0250.0080.0080.0000.0000.0000.000
42A40LEU0-0.094-0.03219.1630.0120.0120.0000.0000.0000.000
43A41GLU-1-0.843-0.92314.178-0.091-0.0910.0000.0000.0000.000
44A42ASN0-0.107-0.05118.3900.0170.0170.0000.0000.0000.000
45A43PRO00.0170.01021.093-0.005-0.0050.0000.0000.0000.000
46A44GLU-1-0.756-0.85124.297-0.011-0.0110.0000.0000.0000.000
47A45HIS0-0.038-0.03726.1850.0100.0100.0000.0000.0000.000
48A46ASP-1-0.913-0.94230.9580.0040.0040.0000.0000.0000.000
49A47GLU-1-0.938-0.98533.9220.0170.0170.0000.0000.0000.000
50A48SER0-0.082-0.03134.5690.0020.0020.0000.0000.0000.000
51A49GLY0-0.0180.00133.7950.0020.0020.0000.0000.0000.000
52A50ALA0-0.038-0.02332.5440.0050.0050.0000.0000.0000.000
53A51LEU0-0.0130.00026.463-0.002-0.0020.0000.0000.0000.000
54A52VAL0-0.029-0.01129.935-0.002-0.0020.0000.0000.0000.000
55A53LEU0-0.012-0.01529.1360.0000.0000.0000.0000.0000.000
56A54PRO0-0.0020.00026.0300.0000.0000.0000.0000.0000.000
57A55ARG10.9120.95428.6240.0150.0150.0000.0000.0000.000
58A56VAL0-0.066-0.03128.261-0.002-0.0020.0000.0000.0000.000
59A57LEU0-0.009-0.00528.361-0.002-0.0020.0000.0000.0000.000
60A58ASP-1-0.815-0.87729.647-0.050-0.0500.0000.0000.0000.000
61A59LYS10.8200.89331.0780.0170.0170.0000.0000.0000.000
62A60LEU0-0.039-0.01333.667-0.002-0.0020.0000.0000.0000.000
63A61THR00.0300.00434.7060.0000.0000.0000.0000.0000.000
64A62LEU0-0.067-0.02537.401-0.001-0.0010.0000.0000.0000.000
65A63CYS00.019-0.00339.7060.0010.0010.0000.0000.0000.000
66A64MET0-0.098-0.05039.031-0.003-0.0030.0000.0000.0000.000
67A65CYS0-0.028-0.01344.0270.0020.0020.0000.0000.0000.000
68A66PRO0-0.059-0.00844.357-0.001-0.0010.0000.0000.0000.000
69A67GLU-1-0.865-0.93245.225-0.022-0.0220.0000.0000.0000.000
70A68ARG10.8030.90742.5850.0180.0180.0000.0000.0000.000
71A69PRO0-0.048-0.02647.5010.0000.0000.0000.0000.0000.000
72A70PHE00.0560.01644.7070.0000.0000.0000.0000.0000.000
73A71THR0-0.049-0.03144.9350.0010.0010.0000.0000.0000.000
74A72ALA00.005-0.01347.3870.0000.0000.0000.0000.0000.000
75A73LYS10.8100.88344.217-0.012-0.0120.0000.0000.0000.000
76A74ALA00.0720.05143.6120.0010.0010.0000.0000.0000.000
77A75SER0-0.019-0.02044.5420.0000.0000.0000.0000.0000.000
78A76GLU-1-0.911-0.92246.6040.0110.0110.0000.0000.0000.000
79A77ILE0-0.026-0.02340.5890.0010.0010.0000.0000.0000.000
80A78THR00.0360.00941.3810.0000.0000.0000.0000.0000.000
81A79GLY0-0.0120.00243.584-0.001-0.0010.0000.0000.0000.000
82A80LEU0-0.0150.00643.021-0.001-0.0010.0000.0000.0000.000
83A81SER00.0260.00846.8950.0000.0000.0000.0000.0000.000
84A82SER00.0910.02749.4890.0000.0000.0000.0000.0000.000
85A83GLU-1-0.854-0.88550.546-0.007-0.0070.0000.0000.0000.000
86A84GLY00.0560.03251.568-0.001-0.0010.0000.0000.0000.000
87A85LEU00.0320.01345.728-0.001-0.0010.0000.0000.0000.000
88A86ALA00.0340.01649.652-0.001-0.0010.0000.0000.0000.000
89A87ARG10.7740.86152.5630.0050.0050.0000.0000.0000.000
90A88CYS0-0.085-0.04649.8010.0000.0000.0000.0000.0000.000
91A89ARG10.8880.93950.5960.0120.0120.0000.0000.0000.000
92A90LYS10.8950.96845.1630.0180.0180.0000.0000.0000.000
93A91ALA00.0210.01046.3570.0010.0010.0000.0000.0000.000
94A92GLY00.1120.06044.9540.0010.0010.0000.0000.0000.000
95A93PHE00.0550.02435.470-0.002-0.0020.0000.0000.0000.000
96A94ASP-1-0.768-0.88641.513-0.033-0.0330.0000.0000.0000.000
97A95GLY00.0330.01340.513-0.003-0.0030.0000.0000.0000.000
98A96ALA0-0.063-0.05040.642-0.003-0.0030.0000.0000.0000.000
99A97VAL00.0270.03137.722-0.002-0.0020.0000.0000.0000.000
100A98VAL0-0.0010.00835.845-0.003-0.0030.0000.0000.0000.000
101A99ARG10.9450.97035.8300.0380.0380.0000.0000.0000.000
102A100THR0-0.026-0.01636.695-0.002-0.0020.0000.0000.0000.000
103A101LEU00.0230.01532.845-0.002-0.0020.0000.0000.0000.000
104A102GLN0-0.056-0.03831.938-0.002-0.0020.0000.0000.0000.000
105A103ALA0-0.0080.00132.043-0.005-0.0050.0000.0000.0000.000
106A104PHE00.0160.01529.816-0.004-0.0040.0000.0000.0000.000
107A105LEU00.0180.00326.700-0.003-0.0030.0000.0000.0000.000
108A106SER0-0.094-0.06127.996-0.007-0.0070.0000.0000.0000.000
109A107ARG10.8500.92229.8860.0590.0590.0000.0000.0000.000
110A108GLN0-0.081-0.03825.4610.0000.0000.0000.0000.0000.000
111A109ALA0-0.0040.00722.383-0.007-0.0070.0000.0000.0000.000
112A110GLY00.0060.01821.8120.0000.0000.0000.0000.0000.000
113A111PRO00.0510.01616.711-0.003-0.0030.0000.0000.0000.000
114A112ILE0-0.023-0.00819.6710.0080.0080.0000.0000.0000.000
115A113CYS0-0.020-0.00318.191-0.005-0.0050.0000.0000.0000.000
116A114LEU0-0.0110.00120.2540.0140.0140.0000.0000.0000.000
117A115VAL0-0.020-0.01520.9740.0020.0020.0000.0000.0000.000
118A116ALA00.0940.05223.5480.0010.0010.0000.0000.0000.000
119A117HIS0-0.0200.00725.5280.0030.0030.0000.0000.0000.000
120A118ASN0-0.037-0.03826.5370.0050.0050.0000.0000.0000.000
121A119GLY00.0490.03926.634-0.004-0.0040.0000.0000.0000.000
122A120PHE0-0.080-0.07719.569-0.006-0.0060.0000.0000.0000.000
123A121ASP-1-0.954-0.96825.8750.0110.0110.0000.0000.0000.000
124A122TYR0-0.042-0.03529.3260.0000.0000.0000.0000.0000.000
125A123ASP-1-0.803-0.90829.113-0.012-0.0120.0000.0000.0000.000
126A124PHE0-0.007-0.01523.604-0.007-0.0070.0000.0000.0000.000
127A125PRO00.0600.02428.096-0.006-0.0060.0000.0000.0000.000
128A126LEU00.0330.02630.857-0.003-0.0030.0000.0000.0000.000
129A127LEU00.0180.00529.429-0.002-0.0020.0000.0000.0000.000
130A128CYS0-0.111-0.05729.775-0.005-0.0050.0000.0000.0000.000
131A129ALA00.0250.00731.880-0.002-0.0020.0000.0000.0000.000
132A130GLU-1-0.830-0.91835.476-0.027-0.0270.0000.0000.0000.000
133A131LEU0-0.052-0.02731.419-0.002-0.0020.0000.0000.0000.000
134A132ARG10.8240.90030.4390.0570.0570.0000.0000.0000.000
135A133ARG10.7800.87335.7470.0280.0280.0000.0000.0000.000
136A134LEU0-0.056-0.02138.2190.0010.0010.0000.0000.0000.000
137A135GLY0-0.046-0.01236.752-0.002-0.0020.0000.0000.0000.000
138A136ALA0-0.040-0.00734.982-0.006-0.0060.0000.0000.0000.000
139A137ARG10.9250.94930.0240.0840.0840.0000.0000.0000.000
140A138LEU00.0620.04826.4620.0030.0030.0000.0000.0000.000
141A139PRO00.003-0.00425.073-0.004-0.0040.0000.0000.0000.000
142A140ARG10.8650.92221.5890.1980.1980.0000.0000.0000.000
143A141ASP-1-0.823-0.91318.868-0.221-0.2210.0000.0000.0000.000
144A142THR0-0.021-0.00119.211-0.008-0.0080.0000.0000.0000.000
145A143VAL00.0090.00716.409-0.002-0.0020.0000.0000.0000.000
146A144CYS0-0.051-0.00219.5130.0170.0170.0000.0000.0000.000
147A145LEU00.0310.00817.1960.0020.0020.0000.0000.0000.000
148A146ASP-1-0.724-0.85620.0590.0230.0230.0000.0000.0000.000
149A147THR00.054-0.02021.3270.0120.0120.0000.0000.0000.000
150A148LEU0-0.0250.01222.5890.0180.0180.0000.0000.0000.000
151A149PRO0-0.040-0.04121.0670.0160.0160.0000.0000.0000.000
152A150ALA00.0250.03418.2270.0220.0220.0000.0000.0000.000
153A151LEU00.0280.01319.4070.0300.0300.0000.0000.0000.000
154A152ARG10.9560.98221.832-0.054-0.0540.0000.0000.0000.000
155A153GLY0-0.043-0.00218.8460.0090.0090.0000.0000.0000.000
156A154LEU00.0180.00115.1940.0320.0320.0000.0000.0000.000
157A155ASP-1-0.785-0.84718.6930.1480.1480.0000.0000.0000.000
158A156ARG10.8560.90821.455-0.146-0.1460.0000.0000.0000.000
159A157ALA0-0.0120.01916.7000.0090.0090.0000.0000.0000.000
160A158HIS10.8120.90116.079-0.293-0.2930.0000.0000.0000.000
161A169GLY00.0550.02531.7910.0000.0000.0000.0000.0000.000
162A170TYR0-0.069-0.08725.1350.0030.0030.0000.0000.0000.000
163A171SER00.0210.02629.563-0.005-0.0050.0000.0000.0000.000
164A172LEU00.1270.05129.0930.0060.0060.0000.0000.0000.000
165A173GLY00.0880.04931.6600.0020.0020.0000.0000.0000.000
166A174SER0-0.042-0.01832.1520.0020.0020.0000.0000.0000.000
167A175LEU0-0.041-0.01326.8410.0060.0060.0000.0000.0000.000
168A176PHE00.0490.02930.1920.0050.0050.0000.0000.0000.000
169A177HIS0-0.0080.00532.0550.0050.0050.0000.0000.0000.000
170A178ARG10.7660.87526.425-0.094-0.0940.0000.0000.0000.000
171A179TYR0-0.028-0.03224.5750.0110.0110.0000.0000.0000.000
172A180PHE0-0.004-0.00728.1060.0020.0020.0000.0000.0000.000
173A181ARG10.8290.93330.165-0.071-0.0710.0000.0000.0000.000
174A182ALA00.0060.00335.635-0.002-0.0020.0000.0000.0000.000
175A183GLU-1-0.846-0.93736.4670.0300.0300.0000.0000.0000.000
176A184PRO0-0.0090.00535.6720.0000.0000.0000.0000.0000.000
177A185SER0-0.046-0.02836.929-0.002-0.0020.0000.0000.0000.000
178A186ALA0-0.004-0.00237.7940.0000.0000.0000.0000.0000.000
179A187ALA0-0.027-0.02340.3270.0000.0000.0000.0000.0000.000
180A188HIS0-0.050-0.00741.613-0.001-0.0010.0000.0000.0000.000
181A189SER00.0500.01039.759-0.002-0.0020.0000.0000.0000.000
182A190ALA00.0810.04935.0470.0020.0020.0000.0000.0000.000
183A191GLU-1-0.839-0.89134.565-0.013-0.0130.0000.0000.0000.000
184A192GLY0-0.019-0.01335.0580.0010.0010.0000.0000.0000.000
185A193ASP-1-0.848-0.92533.4540.0160.0160.0000.0000.0000.000
186A194VAL0-0.014-0.00429.4560.0030.0030.0000.0000.0000.000
187A195HIS0-0.008-0.00430.0040.0030.0030.0000.0000.0000.000
188A196THR0-0.011-0.02030.8150.0040.0040.0000.0000.0000.000
189A197LEU0-0.0190.00025.4690.0070.0070.0000.0000.0000.000
190A198LEU0-0.0150.00125.8030.0050.0050.0000.0000.0000.000
191A199LEU00.0320.01625.8020.0050.0050.0000.0000.0000.000
192A200ILE0-0.034-0.02825.3550.0100.0100.0000.0000.0000.000
193A201PHE0-0.004-0.02018.1150.0150.0150.0000.0000.0000.000
194A202LEU00.0410.00421.8320.0110.0110.0000.0000.0000.000
195A203HIS0-0.0230.00022.7370.0070.0070.0000.0000.0000.000
196A204ARG10.7310.82919.428-0.152-0.1520.0000.0000.0000.000
197A205ALA00.0410.04318.5140.0180.0180.0000.0000.0000.000
198A206ALA00.0290.00614.888-0.005-0.0050.0000.0000.0000.000
199A207GLU-1-0.788-0.86513.7640.2640.2640.0000.0000.0000.000
200A208LEU0-0.014-0.00414.3170.0160.0160.0000.0000.0000.000
201A209LEU0-0.0050.00613.935-0.024-0.0240.0000.0000.0000.000
202A210ALA00.0000.00810.055-0.045-0.0450.0000.0000.0000.000
203A211TRP0-0.004-0.01810.6010.0180.0180.0000.0000.0000.000
204A212ALA0-0.009-0.01213.212-0.034-0.0340.0000.0000.0000.000
205A213ASP-1-0.765-0.8709.330-0.269-0.2690.0000.0000.0000.000
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