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: J38V9

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 OptHSide
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 -2573626.241338
FMO2-HF: Nuclear repulsion 2488519.137429
FMO2-HF: Total energy -85107.103909
FMO2-MP2: Total energy -85354.108482


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.
-1.9690.494-0.023-1.094-1.346-0.001
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 : 0.015 / 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].
3A1MET0-0.0250.0073.579-1.3291.084-0.022-1.088-1.303-0.001
4A2SER0-0.012-0.0014.9550.2210.271-0.001-0.006-0.0430.000
5A3GLU-1-0.920-0.9738.611-0.595-0.5950.0000.0000.0000.000
6A4ALA0-0.071-0.02411.6910.0020.0020.0000.0000.0000.000
7A5PRO0-0.0150.00211.391-0.059-0.0590.0000.0000.0000.000
8A6ARG10.9260.9729.9330.2850.2850.0000.0000.0000.000
9A7ALA0-0.018-0.00612.6680.0050.0050.0000.0000.0000.000
10A8GLU-1-0.830-0.93015.814-0.161-0.1610.0000.0000.0000.000
11A9THR0-0.030-0.02918.2760.0190.0190.0000.0000.0000.000
12A10PHE0-0.027-0.02715.4810.0000.0000.0000.0000.0000.000
13A11VAL00.014-0.00121.5490.0020.0020.0000.0000.0000.000
14A12PHE0-0.007-0.00422.1060.0050.0050.0000.0000.0000.000
15A13LEU0-0.050-0.04926.101-0.006-0.0060.0000.0000.0000.000
16A14ASP-1-0.873-0.93828.9400.0300.0300.0000.0000.0000.000
17A15LEU0-0.039-0.02031.697-0.006-0.0060.0000.0000.0000.000
18A16GLU-1-0.801-0.88734.5600.0210.0210.0000.0000.0000.000
19A17ALA0-0.008-0.01937.456-0.003-0.0030.0000.0000.0000.000
20A18THR00.0320.02139.4050.0020.0020.0000.0000.0000.000
21A19GLY00.0300.00040.6780.0000.0000.0000.0000.0000.000
22A20LEU00.0130.02537.7640.0010.0010.0000.0000.0000.000
23A21PRO00.1180.02935.298-0.002-0.0020.0000.0000.0000.000
24A22SER0-0.064-0.01737.995-0.001-0.0010.0000.0000.0000.000
25A23VAL0-0.071-0.04241.191-0.001-0.0010.0000.0000.0000.000
26A24GLU-1-0.933-0.94439.9060.0010.0010.0000.0000.0000.000
27A25PRO0-0.055-0.01237.882-0.002-0.0020.0000.0000.0000.000
28A26GLU-1-0.732-0.86839.464-0.002-0.0020.0000.0000.0000.000
29A27ILE0-0.016-0.01434.5360.0020.0020.0000.0000.0000.000
30A28ALA0-0.040-0.01938.735-0.002-0.0020.0000.0000.0000.000
31A29GLU-1-0.885-0.96438.3700.0050.0050.0000.0000.0000.000
32A30LEU00.0040.02533.3240.0010.0010.0000.0000.0000.000
33A31SER00.012-0.00533.729-0.002-0.0020.0000.0000.0000.000
34A32LEU0-0.014-0.01129.5300.0010.0010.0000.0000.0000.000
35A33PHE00.0120.00028.624-0.001-0.0010.0000.0000.0000.000
36A34ALA0-0.057-0.02826.3290.0010.0010.0000.0000.0000.000
37A35VAL00.0320.00523.5230.0010.0010.0000.0000.0000.000
38A36HIS00.0280.04220.1430.0100.0100.0000.0000.0000.000
39A37ARG10.7670.83312.0920.1030.1030.0000.0000.0000.000
40A38SER00.015-0.02219.2070.0110.0110.0000.0000.0000.000
41A39SER00.0020.00820.7910.0070.0070.0000.0000.0000.000
42A40LEU0-0.067-0.01819.1410.0120.0120.0000.0000.0000.000
43A41GLU-1-0.894-0.94714.633-0.047-0.0470.0000.0000.0000.000
44A42ASN0-0.115-0.05518.9330.0070.0070.0000.0000.0000.000
45A43PRO00.0160.01221.526-0.005-0.0050.0000.0000.0000.000
46A44GLU-1-0.802-0.89324.698-0.001-0.0010.0000.0000.0000.000
47A45HIS00.000-0.01926.4960.0100.0100.0000.0000.0000.000
48A46ASP-1-0.943-0.95831.3860.0080.0080.0000.0000.0000.000
49A47GLU-1-0.925-0.97234.2700.0170.0170.0000.0000.0000.000
50A48SER0-0.086-0.03835.0370.0030.0030.0000.0000.0000.000
51A49GLY0-0.025-0.01133.8140.0020.0020.0000.0000.0000.000
52A50ALA0-0.029-0.01732.4240.0050.0050.0000.0000.0000.000
53A51LEU0-0.0040.01526.554-0.002-0.0020.0000.0000.0000.000
54A52VAL0-0.040-0.02129.991-0.001-0.0010.0000.0000.0000.000
55A53LEU0-0.017-0.01829.2250.0010.0010.0000.0000.0000.000
56A54PRO00.0080.01526.002-0.002-0.0020.0000.0000.0000.000
57A55ARG10.9110.94828.5770.0060.0060.0000.0000.0000.000
58A56VAL0-0.082-0.04228.463-0.001-0.0010.0000.0000.0000.000
59A57LEU00.000-0.00328.0230.0000.0000.0000.0000.0000.000
60A58ASP-1-0.865-0.89429.594-0.033-0.0330.0000.0000.0000.000
61A59LYS10.8540.91130.7180.0020.0020.0000.0000.0000.000
62A60LEU0-0.042-0.02033.335-0.003-0.0030.0000.0000.0000.000
63A61THR00.0470.02034.5980.0020.0020.0000.0000.0000.000
64A62LEU0-0.080-0.03237.291-0.002-0.0020.0000.0000.0000.000
65A63CYS00.0140.00339.4730.0010.0010.0000.0000.0000.000
66A64MET0-0.076-0.03838.195-0.003-0.0030.0000.0000.0000.000
67A65CYS0-0.042-0.02543.4050.0020.0020.0000.0000.0000.000
68A66PRO0-0.0160.00343.535-0.001-0.0010.0000.0000.0000.000
69A67GLU-1-0.922-0.96745.136-0.007-0.0070.0000.0000.0000.000
70A68ARG10.8310.92342.1050.0000.0000.0000.0000.0000.000
71A69PRO0-0.051-0.03447.0970.0000.0000.0000.0000.0000.000
72A70PHE00.0650.04044.0390.0000.0000.0000.0000.0000.000
73A71THR0-0.040-0.02344.6140.0010.0010.0000.0000.0000.000
74A72ALA00.004-0.02047.1820.0000.0000.0000.0000.0000.000
75A73LYS10.8210.89243.985-0.024-0.0240.0000.0000.0000.000
76A74ALA00.0660.04943.0750.0010.0010.0000.0000.0000.000
77A75SER0-0.009-0.01044.0840.0000.0000.0000.0000.0000.000
78A76GLU-1-0.905-0.92346.3630.0220.0220.0000.0000.0000.000
79A77ILE0-0.016-0.02240.2090.0010.0010.0000.0000.0000.000
80A78THR00.018-0.01040.7340.0000.0000.0000.0000.0000.000
81A79GLY0-0.0110.00742.958-0.001-0.0010.0000.0000.0000.000
82A80LEU0-0.0190.00242.434-0.002-0.0020.0000.0000.0000.000
83A81SER00.0170.01046.2930.0000.0000.0000.0000.0000.000
84A82SER00.1080.04048.962-0.001-0.0010.0000.0000.0000.000
85A83GLU-1-0.866-0.89450.0880.0020.0020.0000.0000.0000.000
86A84GLY00.0440.03150.696-0.001-0.0010.0000.0000.0000.000
87A85LEU00.0450.01745.098-0.001-0.0010.0000.0000.0000.000
88A86ALA00.0200.00649.038-0.001-0.0010.0000.0000.0000.000
89A87ARG10.7970.88151.960-0.003-0.0030.0000.0000.0000.000
90A88CYS0-0.097-0.05249.5780.0000.0000.0000.0000.0000.000
91A89ARG10.8870.93450.5040.0040.0040.0000.0000.0000.000
92A90LYS10.9090.97945.0230.0050.0050.0000.0000.0000.000
93A91ALA00.0350.01346.1530.0010.0010.0000.0000.0000.000
94A92GLY00.0980.05644.5810.0010.0010.0000.0000.0000.000
95A93PHE00.0580.01635.050-0.002-0.0020.0000.0000.0000.000
96A94ASP-1-0.762-0.89141.183-0.018-0.0180.0000.0000.0000.000
97A95GLY00.0090.00240.215-0.002-0.0020.0000.0000.0000.000
98A96ALA0-0.066-0.04540.209-0.002-0.0020.0000.0000.0000.000
99A97VAL00.0410.03637.215-0.002-0.0020.0000.0000.0000.000
100A98VAL00.0170.00935.274-0.002-0.0020.0000.0000.0000.000
101A99ARG10.9330.96835.5390.0240.0240.0000.0000.0000.000
102A100THR0-0.028-0.01036.221-0.003-0.0030.0000.0000.0000.000
103A101LEU00.0170.01132.368-0.002-0.0020.0000.0000.0000.000
104A102GLN0-0.040-0.03031.504-0.002-0.0020.0000.0000.0000.000
105A103ALA0-0.0080.00431.755-0.005-0.0050.0000.0000.0000.000
106A104PHE00.0140.02429.559-0.004-0.0040.0000.0000.0000.000
107A105LEU00.0310.00126.559-0.003-0.0030.0000.0000.0000.000
108A106SER0-0.104-0.05727.632-0.007-0.0070.0000.0000.0000.000
109A107ARG10.8960.95129.3790.0430.0430.0000.0000.0000.000
110A108GLN0-0.073-0.04525.0600.0000.0000.0000.0000.0000.000
111A109ALA0-0.0030.01622.364-0.007-0.0070.0000.0000.0000.000
112A110GLY00.0120.02521.4560.0060.0060.0000.0000.0000.000
113A111PRO00.0400.00216.487-0.007-0.0070.0000.0000.0000.000
114A112ILE0-0.013-0.00319.5390.0070.0070.0000.0000.0000.000
115A113CYS00.0020.00817.6280.0000.0000.0000.0000.0000.000
116A114LEU0-0.038-0.01219.7190.0090.0090.0000.0000.0000.000
117A115VAL0-0.022-0.02220.4840.0090.0090.0000.0000.0000.000
118A116ALA00.0940.04723.022-0.004-0.0040.0000.0000.0000.000
119A117HIS00.0000.00724.8620.0110.0110.0000.0000.0000.000
120A118ASN0-0.035-0.02925.8150.0010.0010.0000.0000.0000.000
121A119GLY00.0520.03025.638-0.005-0.0050.0000.0000.0000.000
122A120PHE0-0.073-0.07719.365-0.005-0.0050.0000.0000.0000.000
123A121ASP-1-0.937-0.95825.6060.0530.0530.0000.0000.0000.000
124A122TYR0-0.060-0.05029.058-0.004-0.0040.0000.0000.0000.000
125A123ASP-1-0.801-0.90728.7230.0190.0190.0000.0000.0000.000
126A124PHE0-0.017-0.01823.011-0.007-0.0070.0000.0000.0000.000
127A125PRO00.0660.03227.795-0.007-0.0070.0000.0000.0000.000
128A126LEU00.0520.03230.322-0.004-0.0040.0000.0000.0000.000
129A127LEU00.0090.00728.745-0.004-0.0040.0000.0000.0000.000
130A128CYS0-0.100-0.05028.955-0.006-0.0060.0000.0000.0000.000
131A129ALA00.0040.00131.203-0.004-0.0040.0000.0000.0000.000
132A130GLU-1-0.824-0.91134.751-0.008-0.0080.0000.0000.0000.000
133A131LEU0-0.044-0.02730.903-0.003-0.0030.0000.0000.0000.000
134A132ARG10.9000.96030.2430.0240.0240.0000.0000.0000.000
135A133ARG10.8060.90335.2580.0100.0100.0000.0000.0000.000
136A134LEU0-0.059-0.03637.8030.0000.0000.0000.0000.0000.000
137A135GLY0-0.0300.00435.931-0.002-0.0020.0000.0000.0000.000
138A136ALA0-0.061-0.02034.171-0.005-0.0050.0000.0000.0000.000
139A137ARG10.9500.96329.4500.0610.0610.0000.0000.0000.000
140A138LEU00.0480.03726.3540.0020.0020.0000.0000.0000.000
141A139PRO0-0.008-0.01024.414-0.005-0.0050.0000.0000.0000.000
142A140ARG10.8530.91021.2160.1610.1610.0000.0000.0000.000
143A141ASP-1-0.822-0.91918.350-0.179-0.1790.0000.0000.0000.000
144A142THR00.0060.04318.888-0.004-0.0040.0000.0000.0000.000
145A143VAL0-0.021-0.03015.8290.0020.0020.0000.0000.0000.000
146A144CYS0-0.0370.00318.9580.0070.0070.0000.0000.0000.000
147A145LEU00.0470.01716.6570.0130.0130.0000.0000.0000.000
148A146ASP-1-0.719-0.84919.5010.0640.0640.0000.0000.0000.000
149A147THR00.046-0.02920.9750.0170.0170.0000.0000.0000.000
150A148LEU0-0.0320.01022.0970.0180.0180.0000.0000.0000.000
151A149PRO0-0.029-0.02520.6730.0170.0170.0000.0000.0000.000
152A150ALA0-0.0050.01317.8250.0250.0250.0000.0000.0000.000
153A151LEU00.0470.01918.9360.0320.0320.0000.0000.0000.000
154A152ARG10.9540.98721.315-0.097-0.0970.0000.0000.0000.000
155A153GLY0-0.044-0.00718.5380.0070.0070.0000.0000.0000.000
156A154LEU00.0130.00315.1410.0330.0330.0000.0000.0000.000
157A155ASP-1-0.780-0.86218.3770.1820.1820.0000.0000.0000.000
158A156ARG10.8040.89421.040-0.208-0.2080.0000.0000.0000.000
159A157ALA0-0.0180.01516.5450.0110.0110.0000.0000.0000.000
160A158HIS10.8620.94715.602-0.362-0.3620.0000.0000.0000.000
161A169GLY00.0160.01031.388-0.002-0.0020.0000.0000.0000.000
162A170TYR0-0.067-0.08124.8790.0010.0010.0000.0000.0000.000
163A171SER00.0340.04429.171-0.003-0.0030.0000.0000.0000.000
164A172LEU00.1320.04629.1020.0070.0070.0000.0000.0000.000
165A173GLY00.0810.03931.4990.0010.0010.0000.0000.0000.000
166A174SER0-0.007-0.02032.7990.0000.0000.0000.0000.0000.000
167A175LEU0-0.054-0.01626.4790.0040.0040.0000.0000.0000.000
168A176PHE00.0570.02929.9500.0040.0040.0000.0000.0000.000
169A177HIS00.0190.03131.7910.0020.0020.0000.0000.0000.000
170A178ARG10.7940.89926.530-0.114-0.1140.0000.0000.0000.000
171A179TYR0-0.007-0.02424.6060.0100.0100.0000.0000.0000.000
172A180PHE0-0.008-0.01028.0310.0010.0010.0000.0000.0000.000
173A181ARG10.8220.92730.662-0.078-0.0780.0000.0000.0000.000
174A182ALA0-0.008-0.01035.486-0.003-0.0030.0000.0000.0000.000
175A183GLU-1-0.862-0.95036.1100.0400.0400.0000.0000.0000.000
176A184PRO00.0030.03435.2290.0000.0000.0000.0000.0000.000
177A185SER0-0.053-0.04936.808-0.003-0.0030.0000.0000.0000.000
178A186ALA00.0000.00138.0510.0010.0010.0000.0000.0000.000
179A187ALA0-0.033-0.02140.648-0.001-0.0010.0000.0000.0000.000
180A188HIS0-0.058-0.02041.263-0.001-0.0010.0000.0000.0000.000
181A189SER00.0570.05238.990-0.002-0.0020.0000.0000.0000.000
182A190ALA00.1220.07035.4870.0020.0020.0000.0000.0000.000
183A191GLU-1-0.839-0.89934.3840.0040.0040.0000.0000.0000.000
184A192GLY0-0.001-0.00234.4300.0010.0010.0000.0000.0000.000
185A193ASP-1-0.820-0.91833.2490.0340.0340.0000.0000.0000.000
186A194VAL0-0.046-0.01228.9800.0040.0040.0000.0000.0000.000
187A195HIS0-0.049-0.02729.8820.0040.0040.0000.0000.0000.000
188A196THR0-0.019-0.02430.9430.0050.0050.0000.0000.0000.000
189A197LEU0-0.026-0.00425.2300.0080.0080.0000.0000.0000.000
190A198LEU0-0.002-0.00625.1500.0080.0080.0000.0000.0000.000
191A199LEU00.0330.02525.8370.0050.0050.0000.0000.0000.000
192A200ILE0-0.037-0.02024.9420.0100.0100.0000.0000.0000.000
193A201PHE0-0.005-0.02918.0130.0160.0160.0000.0000.0000.000
194A202LEU00.031-0.00221.7850.0100.0100.0000.0000.0000.000
195A203HIS0-0.0420.00223.0130.0050.0050.0000.0000.0000.000
196A204ARG10.7070.82119.615-0.183-0.1830.0000.0000.0000.000
197A205ALA00.0390.03718.6620.0240.0240.0000.0000.0000.000
198A206ALA00.0340.01215.4010.0030.0030.0000.0000.0000.000
199A207GLU-1-0.807-0.89714.1650.3000.3000.0000.0000.0000.000
200A208LEU0-0.022-0.01014.3980.0380.0380.0000.0000.0000.000
201A209LEU00.0060.02113.849-0.007-0.0070.0000.0000.0000.000
202A210ALA00.0330.0249.913-0.019-0.0190.0000.0000.0000.000
203A211TRP00.001-0.00810.4430.0620.0620.0000.0000.0000.000
204A212ALA00.0090.00112.602-0.016-0.0160.0000.0000.0000.000
205A213ASP-1-0.799-0.8828.951-0.136-0.1360.0000.0000.0000.000
206A214GLH0-0.095-0.0615.517-0.267-0.2670.0000.0000.0000.000
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