Manual

About

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

tag_button

FMODB ID: ZY8NN

Calculation Name: 1YQ8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ8

Chain ID: A

ChEMBL ID:

UniProt ID: P22536

Base Structure: X-ray

Registration Date: 2023-06-20

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1571621.633538
FMO2-HF: Nuclear repulsion 1503469.212615
FMO2-HF: Total energy -68152.420923
FMO2-MP2: Total energy -68350.622841


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:142:VAL)


Summations of interaction energy for fragment #1(A:142:VAL)
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.
-2.939-0.347-0.01-1.416-1.1650.004
Interaction energy analysis for fragmet #1(A:142:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.003
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].
3A144VAL0-0.012-0.0063.795-1.1781.414-0.010-1.416-1.1650.004
4A145GLU-1-0.885-0.9225.693-1.231-1.2310.0000.0000.0000.000
5A146ASP-1-0.882-0.9318.396-0.312-0.3120.0000.0000.0000.000
6A147SER00.015-0.00311.8250.0180.0180.0000.0000.0000.000
7A148GLY0-0.0630.00015.0290.0510.0510.0000.0000.0000.000
8A149ALA0-0.037-0.01818.0780.0370.0370.0000.0000.0000.000
9A150SER0-0.045-0.02817.602-0.051-0.0510.0000.0000.0000.000
10A151PHE00.0590.00619.2820.0290.0290.0000.0000.0000.000
11A152GLY00.0080.01318.116-0.031-0.0310.0000.0000.0000.000
12A153GLH0-0.020-0.05510.943-0.024-0.0240.0000.0000.0000.000
13A154SER00.0110.03313.302-0.091-0.0910.0000.0000.0000.000
14A155LEU00.011-0.0387.8100.0460.0460.0000.0000.0000.000
15A156LEU00.0280.02410.5510.0280.0280.0000.0000.0000.000
16A157ASP-1-0.824-0.89312.914-0.149-0.1490.0000.0000.0000.000
17A158THR0-0.025-0.0058.4780.0450.0450.0000.0000.0000.000
18A159THR0-0.051-0.03311.4760.1090.1090.0000.0000.0000.000
19A160SER0-0.053-0.04314.4110.0050.0050.0000.0000.0000.000
20A161GLU-1-0.818-0.90315.2480.0650.0650.0000.0000.0000.000
21A162PRO00.0240.00412.6660.0130.0130.0000.0000.0000.000
22A163GLY0-0.017-0.00210.0040.0190.0190.0000.0000.0000.000
23A164LYS10.7930.89910.088-0.025-0.0250.0000.0000.0000.000
24A165ILE00.023-0.0035.9980.0070.0070.0000.0000.0000.000
25A166LEU0-0.012-0.0129.496-0.039-0.0390.0000.0000.0000.000
26A167VAL0-0.0330.00810.8500.0160.0160.0000.0000.0000.000
27A168LYS10.8420.93013.6480.3070.3070.0000.0000.0000.000
28A169ARG10.9790.98616.7860.1630.1630.0000.0000.0000.000
29A170ILE00.0350.02619.5590.0030.0030.0000.0000.0000.000
30A171SER0-0.022-0.01722.0740.0140.0140.0000.0000.0000.000
31A172GLY00.0380.02825.792-0.006-0.0060.0000.0000.0000.000
32A173GLY0-0.009-0.01529.2260.0020.0020.0000.0000.0000.000
33A174SER0-0.052-0.04331.5430.0070.0070.0000.0000.0000.000
34A175GLY00.0200.01834.8020.0000.0000.0000.0000.0000.000
35A176ILE0-0.039-0.01128.848-0.004-0.0040.0000.0000.0000.000
36A177THR00.0030.00331.4400.0090.0090.0000.0000.0000.000
37A178VAL0-0.005-0.01225.828-0.009-0.0090.0000.0000.0000.000
38A179THR0-0.014-0.00427.8130.0140.0140.0000.0000.0000.000
39A180ASP-1-0.935-0.97023.901-0.234-0.2340.0000.0000.0000.000
40A181TYR0-0.081-0.04625.9520.0240.0240.0000.0000.0000.000
41A182GLY0-0.015-0.02223.190-0.017-0.0170.0000.0000.0000.000
42A183ASP-1-0.990-0.98021.519-0.304-0.3040.0000.0000.0000.000
43A184GLN0-0.028-0.02820.641-0.051-0.0510.0000.0000.0000.000
44A185VAL0-0.018-0.00220.7160.0270.0270.0000.0000.0000.000
45A186GLU-1-0.827-0.88523.496-0.202-0.2020.0000.0000.0000.000
46A187ILE0-0.045-0.03523.4050.0070.0070.0000.0000.0000.000
47A188GLU-1-0.913-0.94727.828-0.139-0.1390.0000.0000.0000.000
48A189ALA0-0.020-0.01931.5840.0000.0000.0000.0000.0000.000
49A190SER0-0.024-0.00933.9250.0080.0080.0000.0000.0000.000
50A199VAL00.0030.00037.473-0.001-0.0010.0000.0000.0000.000
51A200THR0-0.003-0.01937.4800.0000.0000.0000.0000.0000.000
52A201ASP-1-0.764-0.85139.887-0.078-0.0780.0000.0000.0000.000
53A202ALA00.005-0.00543.5920.0000.0000.0000.0000.0000.000
54A203LEU0-0.0190.00146.6050.0010.0010.0000.0000.0000.000
55A204SER0-0.026-0.01650.0340.0010.0010.0000.0000.0000.000
56A205LEU00.0170.00452.7080.0010.0010.0000.0000.0000.000
57A206MET00.0190.01356.1910.0000.0000.0000.0000.0000.000
58A207TYR0-0.039-0.01659.5960.0010.0010.0000.0000.0000.000
59A208SER00.0790.01562.6050.0010.0010.0000.0000.0000.000
60A209THR0-0.023-0.00366.1540.0000.0000.0000.0000.0000.000
61A210SER0-0.030-0.01166.5320.0010.0010.0000.0000.0000.000
62A211THR0-0.053-0.03261.9750.0000.0000.0000.0000.0000.000
63A212GLY00.0550.01363.281-0.001-0.0010.0000.0000.0000.000
64A213GLY00.0310.03664.6840.0000.0000.0000.0000.0000.000
65A214PRO0-0.020-0.00166.8580.0010.0010.0000.0000.0000.000
66A215ALA00.0360.00570.5020.0000.0000.0000.0000.0000.000
67A216SER0-0.016-0.02773.2610.0000.0000.0000.0000.0000.000
68A217ILE0-0.0320.01068.7640.0000.0000.0000.0000.0000.000
69A218ALA00.020-0.00272.8300.0000.0000.0000.0000.0000.000
70A219ALA00.0200.00774.547-0.001-0.0010.0000.0000.0000.000
71A220ASN0-0.084-0.05575.0990.0000.0000.0000.0000.0000.000
72A221ALA00.0510.03573.9440.0010.0010.0000.0000.0000.000
73A222LEU00.0070.01767.921-0.001-0.0010.0000.0000.0000.000
74A223THR00.0170.02468.8090.0010.0010.0000.0000.0000.000
75A224ASP-1-0.826-0.89763.787-0.037-0.0370.0000.0000.0000.000
76A225PHE0-0.009-0.01162.9440.0010.0010.0000.0000.0000.000
77A226ASP-1-0.792-0.84962.563-0.037-0.0370.0000.0000.0000.000
78A227LEU0-0.009-0.00858.1810.0000.0000.0000.0000.0000.000
79A228SER0-0.054-0.04958.771-0.001-0.0010.0000.0000.0000.000
80A229GLY00.0300.01159.252-0.001-0.0010.0000.0000.0000.000
81A230ALA0-0.0310.00058.5750.0000.0000.0000.0000.0000.000
82A231LEU00.0100.01456.857-0.001-0.0010.0000.0000.0000.000
83A232THR00.017-0.01651.4420.0000.0000.0000.0000.0000.000
84A233VAL0-0.0250.00153.2370.0000.0000.0000.0000.0000.000
85A234ASN0-0.021-0.02146.663-0.003-0.0030.0000.0000.0000.000
86A235SER00.0110.00047.3920.0040.0040.0000.0000.0000.000
87A236VAL00.0180.01941.650-0.002-0.0020.0000.0000.0000.000
88A237GLY00.0470.03941.6640.0010.0010.0000.0000.0000.000
89A238THR0-0.023-0.02642.5890.0020.0020.0000.0000.0000.000
90A239GLY0-0.045-0.02344.4090.0040.0040.0000.0000.0000.000
91A240LEU00.0050.01545.7420.0020.0020.0000.0000.0000.000
92A241THR0-0.002-0.00148.8760.0000.0000.0000.0000.0000.000
93A242LYS10.8220.91651.5890.0460.0460.0000.0000.0000.000
94A243SER0-0.010-0.03755.3160.0010.0010.0000.0000.0000.000
95A244ALA00.0540.01357.9110.0000.0000.0000.0000.0000.000
96A245ALA0-0.051-0.01560.0510.0010.0010.0000.0000.0000.000
97A246GLY00.0180.00758.4840.0000.0000.0000.0000.0000.000
98A247ILE0-0.019-0.00752.1720.0000.0000.0000.0000.0000.000
99A248GLN0-0.0150.01452.3300.0010.0010.0000.0000.0000.000
100A249LEU00.0310.00448.538-0.002-0.0020.0000.0000.0000.000
101A250ALA0-0.024-0.00545.8550.0020.0020.0000.0000.0000.000
102A251ALA00.0610.00645.781-0.002-0.0020.0000.0000.0000.000
103A252GLY00.0140.00842.626-0.002-0.0020.0000.0000.0000.000
104A253LYS10.8230.90840.7530.0750.0750.0000.0000.0000.000
105A254SER00.0540.03843.8030.0010.0010.0000.0000.0000.000
106A255GLY0-0.006-0.00842.996-0.005-0.0050.0000.0000.0000.000
107A256LEU00.0000.00443.3740.0040.0040.0000.0000.0000.000
108A257TYR0-0.017-0.04545.116-0.003-0.0030.0000.0000.0000.000
109A258GLN00.0300.02947.5870.0010.0010.0000.0000.0000.000
110A259ILE00.015-0.01249.1990.0000.0000.0000.0000.0000.000
111A260THR0-0.060-0.03252.6310.0000.0000.0000.0000.0000.000
112A261MET0-0.0310.01755.5210.0000.0000.0000.0000.0000.000
113A262THR0-0.021-0.00858.6760.0010.0010.0000.0000.0000.000
114A263VAL00.0350.01561.4210.0010.0010.0000.0000.0000.000
115A264LYS10.8580.93164.7850.0390.0390.0000.0000.0000.000
116A265ASN00.0840.03067.1080.0000.0000.0000.0000.0000.000
117A266ASN00.0470.00769.6030.0000.0000.0000.0000.0000.000
118A267THR0-0.0060.01772.4890.0000.0000.0000.0000.0000.000
119A268VAL00.0060.01874.2370.0010.0010.0000.0000.0000.000
120A269THR0-0.0080.00674.008-0.001-0.0010.0000.0000.0000.000
121A270THR00.0350.02075.9400.0000.0000.0000.0000.0000.000
122A271GLY00.0330.02976.3010.0000.0000.0000.0000.0000.000
123A272ASN0-0.060-0.05671.940-0.002-0.0020.0000.0000.0000.000
124A273TYR00.010-0.01768.6850.0000.0000.0000.0000.0000.000
125A274LEU0-0.025-0.00968.803-0.001-0.0010.0000.0000.0000.000
126A275LEU0-0.009-0.01563.0830.0000.0000.0000.0000.0000.000
127A276ARG10.8570.91263.4460.0350.0350.0000.0000.0000.000
128A277VAL00.0030.00056.8930.0000.0000.0000.0000.0000.000
129A278LYS10.8430.90559.2960.0370.0370.0000.0000.0000.000
130A279TYR00.008-0.01151.445-0.002-0.0020.0000.0000.0000.000
131A280GLY00.0540.03956.7520.0000.0000.0000.0000.0000.000
132A281SER0-0.053-0.03257.6560.0010.0010.0000.0000.0000.000
133A282SER0-0.049-0.01157.3420.0000.0000.0000.0000.0000.000
134A283ASP-1-0.906-0.97459.467-0.038-0.0380.0000.0000.0000.000
135A284PHE00.0200.02056.2120.0000.0000.0000.0000.0000.000
136A285VAL00.014-0.00761.0370.0000.0000.0000.0000.0000.000
137A286VAL0-0.013-0.00462.899-0.001-0.0010.0000.0000.0000.000
138A287ALA00.0150.01165.2770.0010.0010.0000.0000.0000.000
139A288CYS0-0.037-0.00765.906-0.002-0.0020.0000.0000.0000.000
140A289PRO00.0360.02368.5780.0010.0010.0000.0000.0000.000
141A290ALA00.0030.01971.168-0.001-0.0010.0000.0000.0000.000
142A291SER00.010-0.01072.2760.0010.0010.0000.0000.0000.000
143A292SER00.012-0.03073.4690.0000.0000.0000.0000.0000.000
144A293LEU0-0.0220.00670.510-0.001-0.0010.0000.0000.0000.000
145A294THR0-0.029-0.00268.038-0.001-0.0010.0000.0000.0000.000
146A295ALA00.0260.03269.8460.0000.0000.0000.0000.0000.000
147A296GLY00.000-0.01767.4190.0000.0000.0000.0000.0000.000
148A297GLY00.0380.02165.6970.0010.0010.0000.0000.0000.000
149A298THR0-0.059-0.05659.339-0.002-0.0020.0000.0000.0000.000
150A299ILE00.0070.02559.3390.0010.0010.0000.0000.0000.000
151A300SER0-0.035-0.03354.532-0.002-0.0020.0000.0000.0000.000
152A301LEU00.0050.00154.3370.0010.0010.0000.0000.0000.000
153A302LEU00.0150.01947.046-0.002-0.0020.0000.0000.0000.000
154A303ILE0-0.0030.00450.5030.0010.0010.0000.0000.0000.000
155A304TYR0-0.010-0.01545.046-0.004-0.0040.0000.0000.0000.000
156A305CYS0-0.0340.00548.4400.0030.0030.0000.0000.0000.000
157A306ASN00.0170.00347.948-0.004-0.0040.0000.0000.0000.000
158A307VAL0-0.025-0.01346.7900.0030.0030.0000.0000.0000.000
159A308LEU0-0.046-0.03148.0280.0000.0000.0000.0000.0000.000
160A309GLY0-0.015-0.00349.2030.0010.0010.0000.0000.0000.000
161A310VAL0-0.047-0.02049.8230.0020.0020.0000.0000.0000.000
162A311VAL00.0670.02952.1620.0000.0000.0000.0000.0000.000
163A312SER0-0.021-0.00754.362-0.001-0.0010.0000.0000.0000.000
164A313LEU0-0.036-0.02555.7520.0010.0010.0000.0000.0000.000
165A314ASP-1-0.729-0.83451.358-0.049-0.0490.0000.0000.0000.000
166A315VAL0-0.032-0.02753.206-0.001-0.0010.0000.0000.0000.000
167A316LEU00.0080.01351.7340.0010.0010.0000.0000.0000.000
168A317LYS10.9410.98855.7940.0370.0370.0000.0000.0000.000
169A318PHE00.0490.00355.359-0.001-0.0010.0000.0000.0000.000
170A319SER0-0.026-0.02961.3380.0020.0020.0000.0000.0000.000
171A320LEU00.006-0.00563.938-0.001-0.0010.0000.0000.0000.000
172A321CYS0-0.008-0.01067.1640.0010.0010.0000.0000.0000.000
173A322ASN0-0.0010.00170.5060.0000.0000.0000.0000.0000.000
174A323ASP-1-0.789-0.88073.309-0.029-0.0290.0000.0000.0000.000
175A324GLY00.0360.02475.8460.0010.0010.0000.0000.0000.000
176A325ALA0-0.048-0.02177.0090.0010.0010.0000.0000.0000.000
177A326ALA00.0060.00775.988-0.001-0.0010.0000.0000.0000.000
178A327LEU0-0.047-0.02070.3650.0000.0000.0000.0000.0000.000
179A328SER00.0350.01572.9910.0000.0000.0000.0000.0000.000
180A329ASN0-0.080-0.04872.7640.0000.0000.0000.0000.0000.000
181A330TYR0-0.039-0.03066.746-0.001-0.0010.0000.0000.0000.000
182A331ILE0-0.0020.00263.1010.0000.0000.0000.0000.0000.000
183A332ILE0-0.0040.00361.9860.0000.0000.0000.0000.0000.000
184A333ASN0-0.048-0.02157.9280.0000.0000.0000.0000.0000.000
185A334ILE00.0400.02156.0420.0000.0000.0000.0000.0000.000
186A335THR0-0.032-0.01551.056-0.002-0.0020.0000.0000.0000.000
187A336ALA00.0200.01950.7220.0010.0010.0000.0000.0000.000
188A337ALA00.0370.00945.621-0.001-0.0010.0000.0000.0000.000
189A338LYS10.8500.93539.8680.0890.0890.0000.0000.0000.000
190A339ILE0-0.002-0.00342.318-0.004-0.0040.0000.0000.0000.000
191A340ASN0-0.0030.02537.943-0.002-0.0020.0000.0000.0000.000