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: 76V2K

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1790083.419326
FMO2-HF: Nuclear repulsion 1720545.42072
FMO2-HF: Total energy -69537.998606
FMO2-MP2: Total energy -69736.176754


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.
11.086-4.95635.171-8.568-10.5591.7347234759768E-18
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 : 0.094 / q_NPA : 0.054
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].
3A6SER00.0090.0093.108-2.5630.2450.016-1.449-1.3740.006
4A7ILE00.0280.0162.126-0.036-1.1776.835-2.321-3.3740.006
5A8GLN00.0260.0143.6590.9651.6250.002-0.260-0.4010.000
6A9THR00.0250.0085.3670.8450.953-0.001-0.005-0.1020.000
7A10THR0-0.008-0.0067.3340.5250.5250.0000.0000.0000.000
8A11VAL0-0.0170.0006.3120.3000.3000.0000.0000.0000.000
9A12ASN00.0210.0128.9970.2530.2530.0000.0000.0000.000
10A13THR0-0.0140.00311.2000.1990.1990.0000.0000.0000.000
11A14LEU0-0.005-0.00512.0410.1150.1150.0000.0000.0000.000
12A15SER0-0.008-0.00112.9220.1210.1210.0000.0000.0000.000
13A16GLU-1-0.889-0.94514.633-0.309-0.3090.0000.0000.0000.000
14A17ARG10.7910.86616.6670.3890.3890.0000.0000.0000.000
15A18ILE00.0160.00315.7810.0470.0470.0000.0000.0000.000
16A19SER0-0.006-0.00218.4690.0500.0500.0000.0000.0000.000
17A20SER0-0.0030.00020.7970.0350.0350.0000.0000.0000.000
18A21LYS10.8710.96922.0940.2500.2500.0000.0000.0000.000
19A22LEU0-0.018-0.01921.9560.0230.0230.0000.0000.0000.000
20A23GLU-1-0.978-0.98924.918-0.176-0.1760.0000.0000.0000.000
21A24GLN0-0.078-0.03826.2340.0150.0150.0000.0000.0000.000
22A25GLU-1-0.951-0.98127.104-0.164-0.1640.0000.0000.0000.000
23A26ALA0-0.032-0.00927.3630.0090.0090.0000.0000.0000.000
24A27ASN0-0.078-0.03229.2560.0060.0060.0000.0000.0000.000
25A28ALA00.0070.01226.7560.0080.0080.0000.0000.0000.000
26A29SER00.0770.03827.729-0.003-0.0030.0000.0000.0000.000
27A30ALA00.0170.00825.4380.0030.0030.0000.0000.0000.000
28A31GLN0-0.036-0.01926.9150.0040.0040.0000.0000.0000.000
29A32THR0-0.057-0.03929.9200.0140.0140.0000.0000.0000.000
30A33LYS10.8930.93930.1560.0710.0710.0000.0000.0000.000
31A34CYS0-0.0240.01424.592-0.005-0.0050.0000.0000.0000.000
32A35ASP-1-0.861-0.91030.255-0.059-0.0590.0000.0000.0000.000
33A36ILE0-0.072-0.03426.9120.0080.0080.0000.0000.0000.000
34A37GLU-1-0.863-0.94226.768-0.107-0.1070.0000.0000.0000.000
35A38ILE0-0.029-0.02320.7100.0070.0070.0000.0000.0000.000
36A39GLY00.006-0.00224.1520.0020.0020.0000.0000.0000.000
37A40ASN0-0.049-0.03522.450-0.007-0.0070.0000.0000.0000.000
38A41PHE00.0300.00513.5640.0080.0080.0000.0000.0000.000
39A42TYR0-0.012-0.01216.588-0.001-0.0010.0000.0000.0000.000
40A43ILE00.0180.00211.188-0.006-0.0060.0000.0000.0000.000
41A44ARG10.8890.94215.378-0.119-0.1190.0000.0000.0000.000
42A45GLN00.0010.01914.0950.0380.0380.0000.0000.0000.000
43A46ASN0-0.012-0.01112.0290.1440.1440.0000.0000.0000.000
44A47HIS0-0.032-0.02411.053-0.055-0.0550.0000.0000.0000.000
45A48GLY00.0700.0368.8130.2450.2450.0000.0000.0000.000
46A49CYS0-0.090-0.0397.918-0.167-0.1670.0000.0000.0000.000
47A50ASN00.0220.0179.5200.1190.1190.0000.0000.0000.000
48A51LEU0-0.017-0.01311.471-0.103-0.1030.0000.0000.0000.000
49A52THR00.0010.00913.8050.0300.0300.0000.0000.0000.000
50A53VAL00.007-0.00116.167-0.018-0.0180.0000.0000.0000.000
51A54LYS10.9210.98618.8540.3120.3120.0000.0000.0000.000
52A55ASN00.005-0.00220.358-0.007-0.0070.0000.0000.0000.000
53A56MET0-0.0150.00222.7820.0000.0000.0000.0000.0000.000
54A58SER00.0700.03627.4760.0000.0000.0000.0000.0000.000
55A59ALA0-0.022-0.02130.3110.0040.0040.0000.0000.0000.000
56A60ASP-1-0.848-0.90732.408-0.085-0.0850.0000.0000.0000.000
57A61ALA00.022-0.00229.327-0.008-0.0080.0000.0000.0000.000
58A62ASP-1-0.923-0.96628.731-0.087-0.0870.0000.0000.0000.000
59A63ALA00.0540.02729.324-0.007-0.0070.0000.0000.0000.000
60A64GLN0-0.0010.01125.638-0.014-0.0140.0000.0000.0000.000
61A65LEU0-0.023-0.01323.908-0.017-0.0170.0000.0000.0000.000
62A66ASP-1-0.887-0.93824.469-0.130-0.1300.0000.0000.0000.000
63A67ALA00.004-0.00124.200-0.014-0.0140.0000.0000.0000.000
64A68VAL0-0.008-0.01719.083-0.028-0.0280.0000.0000.0000.000
65A69LEU0-0.011-0.02119.955-0.027-0.0270.0000.0000.0000.000
66A70SER0-0.0020.01920.840-0.021-0.0210.0000.0000.0000.000
67A71ALA00.0380.01918.534-0.016-0.0160.0000.0000.0000.000
68A72ALA00.001-0.00316.263-0.047-0.0470.0000.0000.0000.000
69A73THR0-0.017-0.00516.590-0.023-0.0230.0000.0000.0000.000
70A74GLU-1-0.792-0.88418.563-0.276-0.2760.0000.0000.0000.000
71A75THR0-0.028-0.01812.756-0.029-0.0290.0000.0000.0000.000
72A76TYR0-0.026-0.03313.558-0.039-0.0390.0000.0000.0000.000
73A77SER0-0.051-0.04415.0230.0130.0130.0000.0000.0000.000
74A78GLY0-0.0060.00616.5690.0280.0280.0000.0000.0000.000
75A79LEU0-0.049-0.00310.361-0.029-0.0290.0000.0000.0000.000
76A80THR00.0390.01412.0860.0750.0750.0000.0000.0000.000
77A81PRO00.020-0.01513.662-0.015-0.0150.0000.0000.0000.000
78A82GLU-1-0.930-0.95810.252-0.114-0.1140.0000.0000.0000.000
79A83GLN00.0250.0008.0560.1920.1920.0000.0000.0000.000
80A84LYS10.8840.95010.2830.2620.2620.0000.0000.0000.000
81A85ALA00.001-0.00112.5980.0390.0390.0000.0000.0000.000
82A86TYR0-0.0100.0008.1290.1170.1170.0000.0000.0000.000
83A87VAL0-0.005-0.01210.4120.0560.0560.0000.0000.0000.000
84A88PRO0-0.014-0.00311.8210.0400.0400.0000.0000.0000.000
85A89ALA00.0180.01211.7750.0140.0140.0000.0000.0000.000
86A90MET00.0060.0277.482-0.005-0.0050.0000.0000.0000.000
87A91PHE00.033-0.00412.0490.0010.0010.0000.0000.0000.000
88A92THR0-0.0470.00215.5600.0120.0120.0000.0000.0000.000
89A93ALA0-0.014-0.01513.7510.0060.0060.0000.0000.0000.000
90A94ALA0-0.053-0.02613.4820.0100.0100.0000.0000.0000.000
91A95LEU0-0.030-0.01515.596-0.020-0.0200.0000.0000.0000.000
92A96ASN0-0.0360.00618.631-0.001-0.0010.0000.0000.0000.000
93A97ILE0-0.0130.00119.322-0.013-0.0130.0000.0000.0000.000
94A98GLN0-0.001-0.01019.2090.0190.0190.0000.0000.0000.000
95A99THR0-0.002-0.00217.743-0.014-0.0140.0000.0000.0000.000
96A100SER00.002-0.00219.0340.0170.0170.0000.0000.0000.000
97A101VAL00.0590.01415.715-0.012-0.0120.0000.0000.0000.000
98A102ASN0-0.017-0.00418.116-0.035-0.0350.0000.0000.0000.000
99A103THR0-0.053-0.02420.977-0.001-0.0010.0000.0000.0000.000
100A104VAL00.0140.03515.7310.0030.0030.0000.0000.0000.000
101A105VAL00.0370.01718.954-0.003-0.0030.0000.0000.0000.000
102A106ARG10.9090.95220.6470.0570.0570.0000.0000.0000.000
103A107ASP-1-0.762-0.88721.030-0.045-0.0450.0000.0000.0000.000
104A108PHE00.0080.00617.7780.0060.0060.0000.0000.0000.000
105A109GLU-1-0.929-0.96920.619-0.121-0.1210.0000.0000.0000.000
106A110ASN00.013-0.01123.7040.0020.0020.0000.0000.0000.000
107A111TYR00.0180.02220.6300.0120.0120.0000.0000.0000.000
108A112VAL00.0290.00621.5010.0080.0080.0000.0000.0000.000
109A113LYS10.9120.97123.9980.1150.1150.0000.0000.0000.000
110A114GLN00.0290.01427.1560.0010.0010.0000.0000.0000.000
111A115THR0-0.0330.01123.8610.0120.0120.0000.0000.0000.000
112A116CYS0-0.111-0.04020.836-0.004-0.0040.0000.0000.0000.000
113A117ASN0-0.049-0.03626.682-0.003-0.0030.0000.0000.0000.000
114A118SER00.033-0.01529.6950.0060.0060.0000.0000.0000.000
115A119SER00.0700.04430.866-0.003-0.0030.0000.0000.0000.000
116A120ALA0-0.089-0.02730.8230.0010.0010.0000.0000.0000.000
117A121VAL0-0.025-0.02127.1260.0000.0000.0000.0000.0000.000
118A122VAL0-0.032-0.04229.708-0.004-0.0040.0000.0000.0000.000
119A123ASP-1-0.846-0.90931.807-0.035-0.0350.0000.0000.0000.000
120A124ASN0-0.057-0.00728.6560.0050.0050.0000.0000.0000.000
121A125LYS10.9790.98432.4190.0380.0380.0000.0000.0000.000
122A126LEU0-0.015-0.02630.3640.0000.0000.0000.0000.0000.000
123A127LYS10.8340.92530.7250.0510.0510.0000.0000.0000.000
124A128ILE00.0360.02427.593-0.005-0.0050.0000.0000.0000.000
125A129GLN0-0.0140.01324.5180.0010.0010.0000.0000.0000.000
126A130ASN00.0170.03323.351-0.011-0.0110.0000.0000.0000.000
127A131VAL0-0.033-0.01717.3260.0090.0090.0000.0000.0000.000
128A132ILE0-0.015-0.01018.6480.0000.0000.0000.0000.0000.000
129A133ILE0-0.034-0.01612.901-0.006-0.0060.0000.0000.0000.000
130A134ASP-1-0.893-0.95614.8340.2740.2740.0000.0000.0000.000
131A135GLU-1-0.901-0.95212.3710.5140.5140.0000.0000.0000.000
132A137TYR00.0280.0094.309-0.571-0.449-0.001-0.020-0.1010.000
133A138GLY00.0430.0254.7660.1250.194-0.001-0.007-0.0610.000
134A139ALA0-0.0190.0044.978-0.032-0.0320.0000.0000.0000.000
135A140PRO00.0360.0026.785-0.249-0.2490.0000.0000.0000.000
136A141GLY0-0.005-0.0059.749-0.090-0.0900.0000.0000.0000.000
137A142SER0-0.064-0.0355.3480.0040.0040.0000.0000.0000.000
138A143PRO0-0.0270.0105.748-0.133-0.1330.0000.0000.0000.000
139A144THR0-0.004-0.0214.419-0.828-0.736-0.001-0.017-0.0740.000
140A145ASN0-0.043-0.0236.1660.5610.5610.0000.0000.0000.000
141A146LEU0-0.003-0.0156.975-0.208-0.2080.0000.0000.0000.000
142A147GLU-1-0.836-0.93110.319-0.296-0.2960.0000.0000.0000.000
143A148PHE0-0.036-0.02013.823-0.017-0.0170.0000.0000.0000.000
144A149ILE00.0330.00916.2040.0290.0290.0000.0000.0000.000
145A150ASN0-0.033-0.03218.7830.0190.0190.0000.0000.0000.000
146A151THR00.048-0.00122.0780.0040.0040.0000.0000.0000.000
147A152GLY00.0440.01324.4110.0070.0070.0000.0000.0000.000
148A153SER00.002-0.01726.5950.0150.0150.0000.0000.0000.000
149A154SER00.020-0.01426.078-0.008-0.0080.0000.0000.0000.000
150A155LYS10.9090.97325.7480.0760.0760.0000.0000.0000.000
151A156GLY00.0620.03624.540-0.004-0.0040.0000.0000.0000.000
152A157ASN00.0440.00921.674-0.033-0.0330.0000.0000.0000.000
153A159ALA00.0630.02720.5930.0020.0020.0000.0000.0000.000
154A160ILE0-0.0150.00916.942-0.023-0.0230.0000.0000.0000.000
155A161LYS10.9420.96216.2140.0100.0100.0000.0000.0000.000
156A162ALA00.0040.01416.0980.0080.0080.0000.0000.0000.000
157A163LEU00.0360.01413.8700.0040.0040.0000.0000.0000.000
158A164MET0-0.0120.02011.855-0.072-0.0720.0000.0000.0000.000
159A165GLN00.000-0.01211.5480.0140.0140.0000.0000.0000.000
160A166LEU0-0.0170.00311.7680.0780.0780.0000.0000.0000.000
161A167THR0-0.008-0.0157.017-0.011-0.0110.0000.0000.0000.000
162A168THR0-0.029-0.0286.8890.0370.0370.0000.0000.0000.000
163A169LYS10.9721.0148.090-0.018-0.0180.0000.0000.0000.000
164A170ALA00.0360.0135.7500.2690.2690.0000.0000.0000.000
165A171THR0-0.050-0.0403.1950.0700.6240.027-0.192-0.3890.001
166A172THR0-0.027-0.0194.7980.8820.982-0.001-0.006-0.0930.000
167A173GLN0-0.048-0.0427.714-0.111-0.1110.0000.0000.0000.000
168A174ILE0-0.028-0.0112.02511.028-8.48228.297-4.288-4.498-0.013
169A175ALA0-0.0320.0065.0570.0790.175-0.001-0.003-0.0920.000
170A176PRO0-0.037-0.0116.317-0.515-0.5150.0000.0000.0000.000
171A177LYS10.9800.9858.763-0.733-0.7330.0000.0000.0000.000
172A178GLN00.003-0.02212.106-0.154-0.1540.0000.0000.0000.000
173A179VAL00.0340.02614.9710.0220.0220.0000.0000.0000.000
174A180ALA0-0.008-0.00317.991-0.031-0.0310.0000.0000.0000.000
175A181GLY00.0100.00416.669-0.031-0.0310.0000.0000.0000.000
176A182THR0-0.036-0.00517.698-0.013-0.0130.0000.0000.0000.000
177A183GLY00.001-0.00316.1370.0360.0360.0000.0000.0000.000
178A184VAL0-0.0160.01015.312-0.046-0.0460.0000.0000.0000.000
179A185GLN00.007-0.00115.3770.0260.0260.0000.0000.0000.000