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: 2N3JR

Calculation Name: 1YPY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YPY

Chain ID: A

ChEMBL ID:

UniProt ID: P07612

Base Structure: X-ray

Registration Date: 2023-09-23

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1790160.209824
FMO2-HF: Nuclear repulsion 1720621.141709
FMO2-HF: Total energy -69539.068115
FMO2-MP2: Total energy -69737.107369


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:4:ALA)


Summations of interaction energy for fragment #1(A:4: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.
-6.822-4.0858.961-4.107-7.5930.013
Interaction energy analysis for fragmet #1(A:4:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.025
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].
3A6SER00.0520.0303.054-1.4930.2430.015-0.795-0.9580.001
4A7ILE00.0150.0102.185-2.239-1.5003.607-1.696-2.6500.008
5A8GLN00.0090.0043.616-1.452-0.8550.001-0.238-0.3590.000
6A9THR00.0190.0035.3300.2030.322-0.001-0.007-0.1110.000
7A10THR0-0.017-0.0117.5110.0120.0120.0000.0000.0000.000
8A11VAL0-0.002-0.0016.730-0.035-0.0350.0000.0000.0000.000
9A12ASN00.0140.0188.958-0.083-0.0830.0000.0000.0000.000
10A13THR0-0.014-0.00711.1630.0310.0310.0000.0000.0000.000
11A14LEU00.0010.00211.9890.0050.0050.0000.0000.0000.000
12A15SER0-0.0020.00512.8870.0140.0140.0000.0000.0000.000
13A16GLU-1-0.889-0.93514.600-0.077-0.0770.0000.0000.0000.000
14A17ARG10.8230.90316.630-0.019-0.0190.0000.0000.0000.000
15A18ILE00.0180.00315.7940.0060.0060.0000.0000.0000.000
16A19SER0-0.027-0.02118.287-0.005-0.0050.0000.0000.0000.000
17A20SER00.031-0.00720.6930.0100.0100.0000.0000.0000.000
18A21LYS10.7830.92322.052-0.029-0.0290.0000.0000.0000.000
19A22LEU0-0.007-0.01321.8850.0020.0020.0000.0000.0000.000
20A23GLU-1-0.976-0.98924.884-0.048-0.0480.0000.0000.0000.000
21A24GLN0-0.074-0.03625.6980.0080.0080.0000.0000.0000.000
22A25GLU-1-0.902-0.95427.1680.0240.0240.0000.0000.0000.000
23A26ALA0-0.023-0.00427.2950.0020.0020.0000.0000.0000.000
24A27ASN0-0.069-0.03129.224-0.004-0.0040.0000.0000.0000.000
25A28ALA00.0120.01926.736-0.002-0.0020.0000.0000.0000.000
26A29SER00.0690.01427.6810.0000.0000.0000.0000.0000.000
27A30ALA00.0190.01025.398-0.002-0.0020.0000.0000.0000.000
28A31GLN0-0.037-0.02226.897-0.001-0.0010.0000.0000.0000.000
29A32THR0-0.045-0.01229.9200.0050.0050.0000.0000.0000.000
30A33LYS10.8980.94130.1420.0470.0470.0000.0000.0000.000
31A34CYS0-0.0340.01124.5730.0080.0080.0000.0000.0000.000
32A35ASP-1-0.831-0.88130.245-0.037-0.0370.0000.0000.0000.000
33A36ILE0-0.059-0.03027.067-0.001-0.0010.0000.0000.0000.000
34A37GLU-1-0.807-0.89926.743-0.088-0.0880.0000.0000.0000.000
35A38ILE0-0.026-0.02020.6840.0030.0030.0000.0000.0000.000
36A39GLY0-0.002-0.00724.157-0.002-0.0020.0000.0000.0000.000
37A40ASN0-0.069-0.04222.508-0.016-0.0160.0000.0000.0000.000
38A41PHE00.0270.00313.5630.0120.0120.0000.0000.0000.000
39A42TYR0-0.013-0.01016.619-0.019-0.0190.0000.0000.0000.000
40A43ILE00.0270.00911.3700.0170.0170.0000.0000.0000.000
41A44ARG10.9000.94315.4100.1180.1180.0000.0000.0000.000
42A45GLN0-0.038-0.01012.933-0.027-0.0270.0000.0000.0000.000
43A46ASN00.003-0.00911.892-0.117-0.1170.0000.0000.0000.000
44A47HIS0-0.044-0.03110.6710.0830.0830.0000.0000.0000.000
45A48GLY00.0720.0368.791-0.101-0.1010.0000.0000.0000.000
46A49CYS0-0.068-0.0257.876-0.324-0.3240.0000.0000.0000.000
47A50ASN00.0050.0179.5560.1870.1870.0000.0000.0000.000
48A51LEU0-0.012-0.01011.487-0.050-0.0500.0000.0000.0000.000
49A52THR00.0040.00713.8210.0280.0280.0000.0000.0000.000
50A53VAL00.005-0.00416.169-0.005-0.0050.0000.0000.0000.000
51A54LYS10.8380.93317.5780.1540.1540.0000.0000.0000.000
52A55ASN0-0.013-0.02920.3490.0030.0030.0000.0000.0000.000
53A56MET0-0.0130.00822.7730.0010.0010.0000.0000.0000.000
54A58SER00.0400.02127.4580.0010.0010.0000.0000.0000.000
55A59ALA0-0.022-0.01930.289-0.001-0.0010.0000.0000.0000.000
56A60ASP-1-0.860-0.91432.372-0.005-0.0050.0000.0000.0000.000
57A61ALA00.0270.00429.3040.0000.0000.0000.0000.0000.000
58A62ASP-1-0.826-0.90428.7060.0040.0040.0000.0000.0000.000
59A63ALA00.0550.03029.2930.0040.0040.0000.0000.0000.000
60A64GLN00.0230.02625.5730.0010.0010.0000.0000.0000.000
61A65LEU0-0.038-0.01924.0940.0020.0020.0000.0000.0000.000
62A66ASP-1-0.876-0.93524.4380.0330.0330.0000.0000.0000.000
63A67ALA0-0.014-0.00524.2430.0080.0080.0000.0000.0000.000
64A68VAL0-0.006-0.01719.0300.0060.0060.0000.0000.0000.000
65A69LEU0-0.006-0.01219.9190.0160.0160.0000.0000.0000.000
66A70SER0-0.0060.01321.0330.0150.0150.0000.0000.0000.000
67A71ALA00.0490.02318.5600.0150.0150.0000.0000.0000.000
68A72ALA00.0080.00516.4180.0210.0210.0000.0000.0000.000
69A73THR0-0.001-0.00516.9800.0430.0430.0000.0000.0000.000
70A74GLU-1-0.816-0.87419.1380.0830.0830.0000.0000.0000.000
71A75THR0-0.020-0.02513.1390.0100.0100.0000.0000.0000.000
72A76TYR0-0.023-0.03414.4280.0660.0660.0000.0000.0000.000
73A77SER0-0.023-0.04015.7300.0360.0360.0000.0000.0000.000
74A78GLY00.0060.02017.190-0.001-0.0010.0000.0000.0000.000
75A79LEU0-0.0350.00810.7400.0250.0250.0000.0000.0000.000
76A80THR00.0390.01112.235-0.037-0.0370.0000.0000.0000.000
77A81PRO00.028-0.01113.7130.0520.0520.0000.0000.0000.000
78A82GLU-1-0.937-0.95910.1980.6530.6530.0000.0000.0000.000
79A83GLN00.0280.0058.228-0.025-0.0250.0000.0000.0000.000
80A84LYS10.8120.90210.384-0.226-0.2260.0000.0000.0000.000
81A85ALA0-0.002-0.00312.715-0.030-0.0300.0000.0000.0000.000
82A86TYR0-0.0090.0018.2300.0240.0240.0000.0000.0000.000
83A87VAL0-0.002-0.01310.911-0.021-0.0210.0000.0000.0000.000
84A88PRO0-0.021-0.00312.705-0.066-0.0660.0000.0000.0000.000
85A89ALA00.0200.01012.131-0.058-0.0580.0000.0000.0000.000
86A90MET00.0080.0348.194-0.096-0.0960.0000.0000.0000.000
87A91PHE00.020-0.01412.408-0.086-0.0860.0000.0000.0000.000
88A92THR0-0.057-0.01416.014-0.040-0.0400.0000.0000.0000.000
89A93ALA0-0.012-0.01113.612-0.029-0.0290.0000.0000.0000.000
90A94ALA0-0.029-0.01013.471-0.037-0.0370.0000.0000.0000.000
91A95LEU0-0.056-0.03815.549-0.028-0.0280.0000.0000.0000.000
92A96ASN0-0.0340.00618.738-0.003-0.0030.0000.0000.0000.000
93A97ILE0-0.0120.00519.576-0.006-0.0060.0000.0000.0000.000
94A98GLN00.0070.00319.6330.0280.0280.0000.0000.0000.000
95A99THR0-0.021-0.03718.660-0.004-0.0040.0000.0000.0000.000
96A100SER0-0.0030.00019.7900.0170.0170.0000.0000.0000.000
97A101VAL00.0590.01216.244-0.008-0.0080.0000.0000.0000.000
98A102ASN0-0.0080.00618.7830.0050.0050.0000.0000.0000.000
99A103THR0-0.057-0.02921.906-0.014-0.0140.0000.0000.0000.000
100A104VAL00.0240.04116.443-0.016-0.0160.0000.0000.0000.000
101A105VAL00.0260.01219.822-0.012-0.0120.0000.0000.0000.000
102A106ARG10.8950.92821.360-0.123-0.1230.0000.0000.0000.000
103A107ASP-1-0.738-0.83921.8030.1190.1190.0000.0000.0000.000
104A108PHE00.0150.01017.920-0.009-0.0090.0000.0000.0000.000
105A109GLU-1-0.856-0.92021.0700.0590.0590.0000.0000.0000.000
106A110ASN0-0.011-0.01624.076-0.016-0.0160.0000.0000.0000.000
107A111TYR00.0300.02520.618-0.010-0.0100.0000.0000.0000.000
108A112VAL00.0330.00921.372-0.013-0.0130.0000.0000.0000.000
109A113LYS10.8650.93824.077-0.062-0.0620.0000.0000.0000.000
110A114GLN0-0.013-0.00727.319-0.002-0.0020.0000.0000.0000.000
111A115THR0-0.041-0.01523.815-0.006-0.0060.0000.0000.0000.000
112A116CYS0-0.109-0.04220.826-0.011-0.0110.0000.0000.0000.000
113A117ASN0-0.029-0.02226.666-0.009-0.0090.0000.0000.0000.000
114A118SER00.0440.00729.6480.0030.0030.0000.0000.0000.000
115A119SER00.0330.01230.856-0.002-0.0020.0000.0000.0000.000
116A120ALA0-0.125-0.04230.871-0.003-0.0030.0000.0000.0000.000
117A121VAL0-0.010-0.02026.763-0.005-0.0050.0000.0000.0000.000
118A122VAL0-0.024-0.02929.701-0.005-0.0050.0000.0000.0000.000
119A123ASP-1-0.818-0.88731.797-0.012-0.0120.0000.0000.0000.000
120A124ASN0-0.050-0.01428.400-0.003-0.0030.0000.0000.0000.000
121A125LYS10.9820.99132.4170.0250.0250.0000.0000.0000.000
122A126LEU0-0.006-0.01330.590-0.001-0.0010.0000.0000.0000.000
123A127LYS10.7780.88130.7260.0370.0370.0000.0000.0000.000
124A128ILE00.0280.02127.632-0.004-0.0040.0000.0000.0000.000
125A129GLN00.0050.01224.613-0.001-0.0010.0000.0000.0000.000
126A130ASN00.0190.02723.366-0.015-0.0150.0000.0000.0000.000
127A131VAL0-0.019-0.01017.3560.0120.0120.0000.0000.0000.000
128A132ILE0-0.023-0.01518.642-0.019-0.0190.0000.0000.0000.000
129A133ILE0-0.016-0.00612.8050.0280.0280.0000.0000.0000.000
130A134ASP-1-0.855-0.91814.738-0.141-0.1410.0000.0000.0000.000
131A135GLU-1-0.849-0.92311.756-0.163-0.1630.0000.0000.0000.000
132A137TYR00.0180.0064.0530.0570.220-0.001-0.023-0.1390.000
133A138GLY00.0470.0264.743-0.861-0.793-0.001-0.007-0.0600.000
134A139ALA0-0.0150.0054.9620.3600.3600.0000.0000.0000.000
135A140PRO00.0440.0016.788-0.060-0.0600.0000.0000.0000.000
136A141GLY0-0.012-0.0029.7600.0130.0130.0000.0000.0000.000
137A142SER0-0.069-0.0435.2950.1770.1770.0000.0000.0000.000
138A143PRO0-0.0150.0195.738-0.373-0.3730.0000.0000.0000.000
139A144THR0-0.009-0.0224.303-0.620-0.515-0.001-0.022-0.0820.000
140A145ASN0-0.048-0.0256.1880.5100.5100.0000.0000.0000.000
141A146LEU00.007-0.0076.8260.0030.0030.0000.0000.0000.000
142A147GLU-1-0.783-0.89510.318-0.179-0.1790.0000.0000.0000.000
143A148PHE0-0.023-0.01813.8170.0330.0330.0000.0000.0000.000
144A149ILE00.0200.00416.1980.0050.0050.0000.0000.0000.000
145A150ASN0-0.028-0.03018.7680.0220.0220.0000.0000.0000.000
146A151THR00.050-0.00822.0670.0020.0020.0000.0000.0000.000
147A152GLY00.0400.01524.3940.0060.0060.0000.0000.0000.000
148A153SER0-0.006-0.01926.5520.0050.0050.0000.0000.0000.000
149A154SER00.023-0.00526.066-0.005-0.0050.0000.0000.0000.000
150A155LYS10.8100.90925.737-0.001-0.0010.0000.0000.0000.000
151A156GLY00.0490.03024.5170.0050.0050.0000.0000.0000.000
152A157ASN00.0490.00221.665-0.001-0.0010.0000.0000.0000.000
153A159ALA00.0600.02720.5570.0060.0060.0000.0000.0000.000
154A160ILE0-0.0100.01016.8240.0120.0120.0000.0000.0000.000
155A161LYS10.9260.96116.2000.0530.0530.0000.0000.0000.000
156A162ALA00.0050.01116.092-0.006-0.0060.0000.0000.0000.000
157A163LEU00.0390.01713.8780.0250.0250.0000.0000.0000.000
158A164MET0-0.0100.01911.858-0.003-0.0030.0000.0000.0000.000
159A165GLN0-0.007-0.00811.548-0.052-0.0520.0000.0000.0000.000
160A166LEU0-0.0160.00711.9320.0100.0100.0000.0000.0000.000
161A167THR0-0.017-0.0187.0350.1350.1350.0000.0000.0000.000
162A168THR0-0.033-0.0396.8860.0080.0080.0000.0000.0000.000
163A169LYS10.8920.9567.931-0.017-0.0170.0000.0000.0000.000
164A170ALA00.0470.0236.1990.0420.0420.0000.0000.0000.000
165A171THR0-0.060-0.0413.100-0.0540.4460.042-0.140-0.4030.000
166A172THR0-0.028-0.0244.273-0.513-0.414-0.001-0.007-0.0900.000
167A173GLN0-0.053-0.0467.1180.0960.0960.0000.0000.0000.000
168A174ILE0-0.042-0.0192.401-0.111-1.6035.302-1.167-2.6440.004
169A175ALA0-0.0300.0104.893-0.379-0.276-0.001-0.005-0.0970.000
170A176PRO0-0.036-0.0106.1640.2480.2480.0000.0000.0000.000
171A177LYS10.9730.9868.708-0.169-0.1690.0000.0000.0000.000
172A178GLN0-0.013-0.02211.9940.0370.0370.0000.0000.0000.000
173A179VAL00.0280.01714.896-0.017-0.0170.0000.0000.0000.000
174A180ALA0-0.007-0.00317.9050.0120.0120.0000.0000.0000.000
175A181GLY00.0150.00716.6860.0080.0080.0000.0000.0000.000
176A182THR0-0.038-0.00217.7080.0140.0140.0000.0000.0000.000
177A183GLY00.0110.00116.101-0.006-0.0060.0000.0000.0000.000
178A184VAL0-0.0010.00315.4720.0050.0050.0000.0000.0000.000
179A185GLN00.0130.00515.8620.0220.0220.0000.0000.0000.000