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: N1RLQ

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2571140.880746
FMO2-HF: Nuclear repulsion 2486035.00686
FMO2-HF: Total energy -85105.873885
FMO2-MP2: Total energy -85352.988659


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.
-1.9820.51-0.023-1.131-1.339-0.001
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 : 0.019 / 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].
3A1MET0-0.0230.0083.537-1.4261.019-0.022-1.126-1.298-0.001
4A2SER0-0.013-0.0025.0020.1600.207-0.001-0.005-0.0410.000
5A3GLU-1-0.907-0.9688.669-0.567-0.5670.0000.0000.0000.000
6A4ALA0-0.085-0.02711.728-0.006-0.0060.0000.0000.0000.000
7A5PRO0-0.0160.00611.428-0.055-0.0550.0000.0000.0000.000
8A6ARG10.9720.9799.3740.2870.2870.0000.0000.0000.000
9A7ALA0-0.0020.00412.6860.0000.0000.0000.0000.0000.000
10A8GLU-1-0.890-0.94615.824-0.150-0.1500.0000.0000.0000.000
11A9THR0-0.023-0.01518.2810.0170.0170.0000.0000.0000.000
12A10PHE0-0.046-0.03515.6350.0010.0010.0000.0000.0000.000
13A11VAL00.009-0.00321.5720.0010.0010.0000.0000.0000.000
14A12PHE0-0.004-0.00222.1080.0050.0050.0000.0000.0000.000
15A13LEU0-0.061-0.05226.134-0.007-0.0070.0000.0000.0000.000
16A14ASP-1-0.819-0.91628.9790.0350.0350.0000.0000.0000.000
17A15LEU0-0.069-0.03731.741-0.006-0.0060.0000.0000.0000.000
18A16GLU-1-0.810-0.88234.6080.0250.0250.0000.0000.0000.000
19A17ALA0-0.015-0.02137.541-0.003-0.0030.0000.0000.0000.000
20A18THR00.0130.01239.4580.0020.0020.0000.0000.0000.000
21A19GLY00.0370.00040.7350.0000.0000.0000.0000.0000.000
22A20LEU00.0140.03937.6820.0010.0010.0000.0000.0000.000
23A21PRO00.1150.02835.322-0.002-0.0020.0000.0000.0000.000
24A22SER0-0.058-0.01838.060-0.002-0.0020.0000.0000.0000.000
25A23VAL0-0.071-0.03741.257-0.001-0.0010.0000.0000.0000.000
26A24GLU-1-0.938-0.94939.9860.0050.0050.0000.0000.0000.000
27A25PRO0-0.0270.00038.031-0.002-0.0020.0000.0000.0000.000
28A26GLU-1-0.741-0.83839.5220.0020.0020.0000.0000.0000.000
29A27ILE0-0.005-0.01134.7860.0020.0020.0000.0000.0000.000
30A28ALA0-0.033-0.01638.784-0.002-0.0020.0000.0000.0000.000
31A29GLU-1-0.904-0.98038.3820.0090.0090.0000.0000.0000.000
32A30LEU00.0180.03233.8780.0020.0020.0000.0000.0000.000
33A31SER00.024-0.01733.659-0.002-0.0020.0000.0000.0000.000
34A32LEU0-0.019-0.01329.4050.0010.0010.0000.0000.0000.000
35A33PHE00.0200.00028.672-0.001-0.0010.0000.0000.0000.000
36A34ALA0-0.037-0.02526.3640.0020.0020.0000.0000.0000.000
37A35VAL00.0220.00223.3750.0000.0000.0000.0000.0000.000
38A36HIS00.0860.08520.3380.0080.0080.0000.0000.0000.000
39A37ARG10.8180.86711.9790.0750.0750.0000.0000.0000.000
40A38SER00.023-0.02719.2090.0110.0110.0000.0000.0000.000
41A39SER0-0.011-0.01120.7800.0060.0060.0000.0000.0000.000
42A40LEU0-0.059-0.01219.1420.0110.0110.0000.0000.0000.000
43A41GLU-1-0.943-0.97715.092-0.040-0.0400.0000.0000.0000.000
44A42ASN0-0.105-0.04418.9260.0090.0090.0000.0000.0000.000
45A43PRO00.0100.01021.545-0.005-0.0050.0000.0000.0000.000
46A44GLU-1-0.836-0.91024.6970.0040.0040.0000.0000.0000.000
47A45HIS00.023-0.01126.7620.0090.0090.0000.0000.0000.000
48A46ASP-1-0.951-0.96831.3830.0110.0110.0000.0000.0000.000
49A47GLU-1-0.936-0.97834.2860.0180.0180.0000.0000.0000.000
50A48SER0-0.077-0.03335.1510.0020.0020.0000.0000.0000.000
51A49GLY0-0.028-0.01233.8100.0020.0020.0000.0000.0000.000
52A50ALA0-0.014-0.00732.4250.0050.0050.0000.0000.0000.000
53A51LEU0-0.0170.01026.523-0.002-0.0020.0000.0000.0000.000
54A52VAL0-0.039-0.01730.000-0.001-0.0010.0000.0000.0000.000
55A53LEU0-0.031-0.02529.2330.0010.0010.0000.0000.0000.000
56A54PRO00.0170.02226.139-0.002-0.0020.0000.0000.0000.000
57A55ARG10.9330.96728.5810.0030.0030.0000.0000.0000.000
58A56VAL0-0.080-0.04828.459-0.002-0.0020.0000.0000.0000.000
59A57LEU0-0.006-0.00828.1990.0010.0010.0000.0000.0000.000
60A58ASP-1-0.856-0.87729.601-0.027-0.0270.0000.0000.0000.000
61A59LYS10.9040.94430.736-0.002-0.0020.0000.0000.0000.000
62A60LEU0-0.042-0.01533.355-0.003-0.0030.0000.0000.0000.000
63A61THR00.0580.05534.6280.0020.0020.0000.0000.0000.000
64A62LEU0-0.086-0.03237.322-0.002-0.0020.0000.0000.0000.000
65A63CYS00.0340.02239.5110.0020.0020.0000.0000.0000.000
66A64MET0-0.069-0.03738.118-0.003-0.0030.0000.0000.0000.000
67A65CYS0-0.036-0.02943.4260.0020.0020.0000.0000.0000.000
68A66PRO0-0.025-0.00443.460-0.001-0.0010.0000.0000.0000.000
69A67GLU-1-1.011-1.00745.126-0.003-0.0030.0000.0000.0000.000
70A68ARG10.8400.90642.414-0.004-0.0040.0000.0000.0000.000
71A69PRO0-0.053-0.03047.1510.0000.0000.0000.0000.0000.000
72A70PHE00.0770.04443.9440.0000.0000.0000.0000.0000.000
73A71THR0-0.040-0.01844.7590.0000.0000.0000.0000.0000.000
74A72ALA00.020-0.01647.2380.0000.0000.0000.0000.0000.000
75A73LYS10.8960.96143.893-0.028-0.0280.0000.0000.0000.000
76A74ALA00.0520.04043.0630.0010.0010.0000.0000.0000.000
77A75SER00.0080.00444.1390.0000.0000.0000.0000.0000.000
78A76GLU-1-0.941-0.96846.7300.0230.0230.0000.0000.0000.000
79A77ILE0-0.054-0.04140.2780.0010.0010.0000.0000.0000.000
80A78THR00.0170.00040.6310.0000.0000.0000.0000.0000.000
81A79GLY0-0.0060.01043.006-0.001-0.0010.0000.0000.0000.000
82A80LEU0-0.019-0.00142.332-0.002-0.0020.0000.0000.0000.000
83A81SER00.014-0.00146.3390.0000.0000.0000.0000.0000.000
84A82SER00.1030.03749.010-0.001-0.0010.0000.0000.0000.000
85A83GLU-1-0.972-0.97150.1360.0050.0050.0000.0000.0000.000
86A84GLY00.0130.01150.737-0.001-0.0010.0000.0000.0000.000
87A85LEU00.0340.01045.007-0.001-0.0010.0000.0000.0000.000
88A86ALA00.0390.01449.080-0.001-0.0010.0000.0000.0000.000
89A87ARG10.9110.96452.002-0.005-0.0050.0000.0000.0000.000
90A88CYS0-0.089-0.04749.630-0.001-0.0010.0000.0000.0000.000
91A89ARG10.8930.93950.5390.0020.0020.0000.0000.0000.000
92A90LYS10.8930.96945.1780.0020.0020.0000.0000.0000.000
93A91ALA00.0410.02246.1690.0010.0010.0000.0000.0000.000
94A92GLY00.0930.05544.6250.0010.0010.0000.0000.0000.000
95A93PHE00.0580.02135.129-0.002-0.0020.0000.0000.0000.000
96A94ASP-1-0.795-0.91541.227-0.012-0.0120.0000.0000.0000.000
97A95GLY00.003-0.01240.253-0.001-0.0010.0000.0000.0000.000
98A96ALA0-0.052-0.02940.241-0.002-0.0020.0000.0000.0000.000
99A97VAL00.0540.04937.288-0.002-0.0020.0000.0000.0000.000
100A98VAL00.0190.00835.247-0.001-0.0010.0000.0000.0000.000
101A99ARG10.9290.96235.5690.0200.0200.0000.0000.0000.000
102A100THR0-0.024-0.00936.246-0.003-0.0030.0000.0000.0000.000
103A101LEU00.0140.01132.471-0.001-0.0010.0000.0000.0000.000
104A102GLN0-0.030-0.02631.530-0.002-0.0020.0000.0000.0000.000
105A103ALA0-0.0050.00631.776-0.004-0.0040.0000.0000.0000.000
106A104PHE00.0100.03329.539-0.004-0.0040.0000.0000.0000.000
107A105LEU00.0320.00126.808-0.002-0.0020.0000.0000.0000.000
108A106SER0-0.125-0.07327.648-0.006-0.0060.0000.0000.0000.000
109A107ARG10.9210.95229.3870.0380.0380.0000.0000.0000.000
110A108GLN0-0.068-0.04125.1010.0000.0000.0000.0000.0000.000
111A109ALA0-0.0240.00722.320-0.007-0.0070.0000.0000.0000.000
112A110GLY00.0090.01421.4680.0070.0070.0000.0000.0000.000
113A111PRO00.0460.00516.624-0.007-0.0070.0000.0000.0000.000
114A112ILE0-0.0060.00219.5560.0070.0070.0000.0000.0000.000
115A113CYS0-0.0090.00117.6700.0010.0010.0000.0000.0000.000
116A114LEU0-0.042-0.01819.7530.0070.0070.0000.0000.0000.000
117A115VAL0-0.013-0.01220.5730.0110.0110.0000.0000.0000.000
118A116ALA00.0890.04223.065-0.005-0.0050.0000.0000.0000.000
119A117HIS00.0060.02524.9140.0130.0130.0000.0000.0000.000
120A118ASN0-0.022-0.01825.8600.0000.0000.0000.0000.0000.000
121A119GLY00.0510.03025.690-0.006-0.0060.0000.0000.0000.000
122A120PHE0-0.069-0.07719.520-0.005-0.0050.0000.0000.0000.000
123A121ASP-1-0.925-0.94725.6690.0580.0580.0000.0000.0000.000
124A122TYR0-0.089-0.08329.123-0.005-0.0050.0000.0000.0000.000
125A123ASP-1-0.807-0.90928.7150.0260.0260.0000.0000.0000.000
126A124PHE0-0.030-0.02022.959-0.007-0.0070.0000.0000.0000.000
127A125PRO00.0650.02828.103-0.008-0.0080.0000.0000.0000.000
128A126LEU00.0590.03330.382-0.005-0.0050.0000.0000.0000.000
129A127LEU00.0000.00528.783-0.004-0.0040.0000.0000.0000.000
130A128CYS0-0.099-0.04429.161-0.006-0.0060.0000.0000.0000.000
131A129ALA0-0.0020.00131.256-0.004-0.0040.0000.0000.0000.000
132A130GLU-1-0.814-0.91034.807-0.003-0.0030.0000.0000.0000.000
133A131LEU0-0.043-0.02330.759-0.003-0.0030.0000.0000.0000.000
134A132ARG10.9170.96330.5070.0190.0190.0000.0000.0000.000
135A133ARG10.9230.97335.3080.0070.0070.0000.0000.0000.000
136A134LEU0-0.072-0.04537.846-0.001-0.0010.0000.0000.0000.000
137A135GLY0-0.0290.00735.976-0.002-0.0020.0000.0000.0000.000
138A136ALA0-0.058-0.01734.176-0.005-0.0050.0000.0000.0000.000
139A137ARG10.9540.96229.5940.0550.0550.0000.0000.0000.000
140A138LEU00.0360.03226.2480.0010.0010.0000.0000.0000.000
141A139PRO0-0.019-0.01124.447-0.005-0.0050.0000.0000.0000.000
142A140ARG10.9000.94121.8900.1390.1390.0000.0000.0000.000
143A141ASP-1-0.851-0.94218.293-0.161-0.1610.0000.0000.0000.000
144A142THR0-0.0250.02618.919-0.003-0.0030.0000.0000.0000.000
145A143VAL00.022-0.00515.8260.0000.0000.0000.0000.0000.000
146A144CYS0-0.0270.00119.0030.0050.0050.0000.0000.0000.000
147A145LEU00.0370.01216.5930.0160.0160.0000.0000.0000.000
148A146ASP-1-0.710-0.84219.5530.0710.0710.0000.0000.0000.000
149A147THR00.026-0.05221.0320.0180.0180.0000.0000.0000.000
150A148LEU0-0.0090.02122.1480.0160.0160.0000.0000.0000.000
151A149PRO0-0.043-0.02920.6750.0160.0160.0000.0000.0000.000
152A150ALA00.0010.01217.8350.0250.0250.0000.0000.0000.000
153A151LEU00.0410.01718.9910.0310.0310.0000.0000.0000.000
154A152ARG10.9580.99021.366-0.105-0.1050.0000.0000.0000.000
155A153GLY0-0.051-0.00918.5990.0050.0050.0000.0000.0000.000
156A154LEU00.0210.00715.2030.0320.0320.0000.0000.0000.000
157A155ASP-1-0.791-0.87818.4260.1890.1890.0000.0000.0000.000
158A156ARG10.7910.88521.060-0.212-0.2120.0000.0000.0000.000
159A157ALA0-0.0160.01516.5880.0100.0100.0000.0000.0000.000
160A158HIS10.9080.96715.657-0.371-0.3710.0000.0000.0000.000
161A169GLY00.0140.00431.438-0.002-0.0020.0000.0000.0000.000
162A170TYR0-0.067-0.08725.1590.0010.0010.0000.0000.0000.000
163A171SER00.0420.04729.224-0.002-0.0020.0000.0000.0000.000
164A172LEU00.1470.05029.3310.0060.0060.0000.0000.0000.000
165A173GLY00.0790.04131.5450.0010.0010.0000.0000.0000.000
166A174SER0-0.015-0.02532.180-0.001-0.0010.0000.0000.0000.000
167A175LEU0-0.078-0.02526.6180.0040.0040.0000.0000.0000.000
168A176PHE00.0570.03829.9860.0040.0040.0000.0000.0000.000
169A177HIS00.0370.03431.8270.0020.0020.0000.0000.0000.000
170A178ARG10.8370.92427.805-0.110-0.1100.0000.0000.0000.000
171A179TYR0-0.010-0.02124.9290.0090.0090.0000.0000.0000.000
172A180PHE00.002-0.00428.0400.0010.0010.0000.0000.0000.000
173A181ARG10.8160.92230.696-0.079-0.0790.0000.0000.0000.000
174A182ALA0-0.015-0.00935.518-0.003-0.0030.0000.0000.0000.000
175A183GLU-1-0.854-0.95236.1410.0420.0420.0000.0000.0000.000
176A184PRO0-0.0160.02235.4970.0000.0000.0000.0000.0000.000
177A185SER0-0.033-0.03836.847-0.003-0.0030.0000.0000.0000.000
178A186ALA00.0020.00638.0860.0010.0010.0000.0000.0000.000
179A187ALA0-0.043-0.02740.840-0.001-0.0010.0000.0000.0000.000
180A188HIS0-0.061-0.02341.209-0.001-0.0010.0000.0000.0000.000
181A189SER00.0700.06039.077-0.002-0.0020.0000.0000.0000.000
182A190ALA00.1130.06135.5390.0020.0020.0000.0000.0000.000
183A191GLU-1-0.911-0.97234.4220.0100.0100.0000.0000.0000.000
184A192GLY0-0.010-0.00234.4620.0020.0020.0000.0000.0000.000
185A193ASP-1-0.831-0.91533.1260.0370.0370.0000.0000.0000.000
186A194VAL0-0.066-0.03029.0870.0050.0050.0000.0000.0000.000
187A195HIS0-0.058-0.02629.9130.0050.0050.0000.0000.0000.000
188A196THR0-0.010-0.02330.9700.0050.0050.0000.0000.0000.000
189A197LEU0-0.0260.00125.3100.0080.0080.0000.0000.0000.000
190A198LEU00.005-0.00724.9470.0080.0080.0000.0000.0000.000
191A199LEU00.0270.02325.8610.0050.0050.0000.0000.0000.000
192A200ILE0-0.028-0.02024.8550.0100.0100.0000.0000.0000.000
193A201PHE0-0.012-0.03418.1440.0160.0160.0000.0000.0000.000
194A202LEU00.029-0.00221.8090.0100.0100.0000.0000.0000.000
195A203HIS0-0.055-0.00423.0280.0040.0040.0000.0000.0000.000
196A204ARG10.7070.82719.844-0.184-0.1840.0000.0000.0000.000
197A205ALA00.0340.03418.6880.0250.0250.0000.0000.0000.000
198A206ALA00.0330.01115.3850.0050.0050.0000.0000.0000.000
199A207GLU-1-0.839-0.90514.1830.2840.2840.0000.0000.0000.000
200A208LEU0-0.033-0.01214.4330.0410.0410.0000.0000.0000.000
201A209LEU00.0080.02213.809-0.004-0.0040.0000.0000.0000.000
202A210ALA00.0350.0289.955-0.013-0.0130.0000.0000.0000.000
203A211TRP0-0.004-0.01210.4870.0760.0760.0000.0000.0000.000
204A212ALA00.0120.00312.656-0.011-0.0110.0000.0000.0000.000
205A213ASP-1-0.841-0.9128.966-0.063-0.0630.0000.0000.0000.000
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