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: 89YLY

Calculation Name: 1Q6H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Q6H

Chain ID: A

ChEMBL ID:

UniProt ID: P45523

Base Structure: X-ray

Registration Date: 2023-09-24

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1962059.235883
FMO2-HF: Nuclear repulsion 1882915.42165
FMO2-HF: Total energy -79143.814233
FMO2-MP2: Total energy -79378.706875


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:15:ALA)


Summations of interaction energy for fragment #1(A:15: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.
-0.7061.0220.203-0.659-1.2720.003
Interaction energy analysis for fragmet #1(A:15:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.001
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].
3A17LYS10.9240.9652.7931.2012.9290.203-0.659-1.2720.003
4A18ASN00.0390.0176.1200.1930.1930.0000.0000.0000.000
5A19ASP-1-0.831-0.9048.9590.2500.2500.0000.0000.0000.000
6A20ASP-1-0.824-0.89611.517-0.048-0.0480.0000.0000.0000.000
7A21GLN0-0.053-0.0286.298-0.495-0.4950.0000.0000.0000.000
8A22LYS10.9220.9546.812-1.604-1.6040.0000.0000.0000.000
9A23SER00.021-0.0118.289-0.004-0.0040.0000.0000.0000.000
10A24ALA00.0300.03011.285-0.024-0.0240.0000.0000.0000.000
11A25TYR0-0.021-0.0157.951-0.041-0.0410.0000.0000.0000.000
12A26ALA0-0.014-0.0079.8160.0120.0120.0000.0000.0000.000
13A27LEU00.0340.01711.461-0.007-0.0070.0000.0000.0000.000
14A28GLY00.0370.02413.3880.0010.0010.0000.0000.0000.000
15A29ALA0-0.018-0.01511.4170.0060.0060.0000.0000.0000.000
16A30SER0-0.048-0.01913.5050.0120.0120.0000.0000.0000.000
17A31LEU00.0330.00816.4230.0020.0020.0000.0000.0000.000
18A32GLY00.0280.01516.7450.0020.0020.0000.0000.0000.000
19A33ARG10.9210.96617.0150.0060.0060.0000.0000.0000.000
20A34TYR00.0200.01918.6780.0100.0100.0000.0000.0000.000
21A35MET00.0400.02621.1590.0070.0070.0000.0000.0000.000
22A36GLU-1-0.974-0.99320.024-0.090-0.0900.0000.0000.0000.000
23A37ASN0-0.036-0.04622.1610.0150.0150.0000.0000.0000.000
24A38SER00.0480.02224.3770.0070.0070.0000.0000.0000.000
25A39LEU0-0.011-0.00925.0910.0030.0030.0000.0000.0000.000
26A40LYS10.8900.96423.0160.0670.0670.0000.0000.0000.000
27A41GLU-1-0.892-0.95327.786-0.015-0.0150.0000.0000.0000.000
28A42GLN00.0290.00529.760-0.001-0.0010.0000.0000.0000.000
29A43GLU-1-0.936-0.96528.948-0.053-0.0530.0000.0000.0000.000
30A44LYS10.8320.92331.0220.0200.0200.0000.0000.0000.000
31A45LEU0-0.044-0.02834.2750.0030.0030.0000.0000.0000.000
32A46GLY0-0.0010.00935.7700.0010.0010.0000.0000.0000.000
33A47ILE0-0.094-0.03632.968-0.003-0.0030.0000.0000.0000.000
34A48LYS10.9460.96531.1430.0530.0530.0000.0000.0000.000
35A49LEU0-0.011-0.00228.981-0.001-0.0010.0000.0000.0000.000
36A50ASP-1-0.825-0.90728.037-0.107-0.1070.0000.0000.0000.000
37A51LYS10.9550.94522.5950.1050.1050.0000.0000.0000.000
38A52ASP-1-0.888-0.92723.705-0.160-0.1600.0000.0000.0000.000
39A53GLN0-0.016-0.01524.522-0.008-0.0080.0000.0000.0000.000
40A54LEU0-0.054-0.01422.8640.0000.0000.0000.0000.0000.000
41A55ILE0-0.019-0.02018.934-0.004-0.0040.0000.0000.0000.000
42A56ALA00.0480.03121.831-0.009-0.0090.0000.0000.0000.000
43A57GLY00.0410.02924.0350.0020.0020.0000.0000.0000.000
44A58VAL0-0.055-0.02619.7140.0020.0020.0000.0000.0000.000
45A59GLN0-0.029-0.02917.9310.0160.0160.0000.0000.0000.000
46A60ASP-1-0.870-0.93921.371-0.131-0.1310.0000.0000.0000.000
47A61ALA0-0.013-0.01124.9010.0060.0060.0000.0000.0000.000
48A62PHE0-0.071-0.01517.2790.0010.0010.0000.0000.0000.000
49A63ALA0-0.033-0.01222.242-0.003-0.0030.0000.0000.0000.000
50A64ASP-1-0.932-0.96023.614-0.094-0.0940.0000.0000.0000.000
51A65LYS10.8610.91526.4790.1210.1210.0000.0000.0000.000
52A66SER0-0.005-0.01628.478-0.004-0.0040.0000.0000.0000.000
53A67LYS10.8770.93128.6200.1110.1110.0000.0000.0000.000
54A68LEU0-0.0360.00331.7530.0050.0050.0000.0000.0000.000
55A69SER00.0380.02132.683-0.002-0.0020.0000.0000.0000.000
56A70ASP-1-0.831-0.93032.599-0.058-0.0580.0000.0000.0000.000
57A71GLN0-0.022-0.01634.8070.0010.0010.0000.0000.0000.000
58A72GLU-1-0.860-0.91836.342-0.054-0.0540.0000.0000.0000.000
59A73ILE00.0020.00930.4280.0010.0010.0000.0000.0000.000
60A74GLU-1-0.885-0.93334.372-0.031-0.0310.0000.0000.0000.000
61A75GLN00.0260.01036.4270.0000.0000.0000.0000.0000.000
62A76THR0-0.037-0.02534.9240.0010.0010.0000.0000.0000.000
63A77LEU0-0.033-0.02931.2440.0010.0010.0000.0000.0000.000
64A78GLN0-0.0060.00335.3710.0040.0040.0000.0000.0000.000
65A79ALA0-0.028-0.00638.7290.0020.0020.0000.0000.0000.000
66A80PHE0-0.037-0.03132.3050.0010.0010.0000.0000.0000.000
67A81GLU-1-0.910-0.96335.759-0.029-0.0290.0000.0000.0000.000
68A82ALA0-0.013-0.00137.5410.0030.0030.0000.0000.0000.000
69A83ARG10.9600.98435.8720.0480.0480.0000.0000.0000.000
70A84VAL0-0.011-0.00734.6830.0010.0010.0000.0000.0000.000
71A85LYS10.9850.98137.8440.0220.0220.0000.0000.0000.000
72A86SER0-0.0300.00340.6600.0020.0020.0000.0000.0000.000
73A87SER00.002-0.01438.9130.0000.0000.0000.0000.0000.000
74A88ALA0-0.012-0.00239.1510.0010.0010.0000.0000.0000.000
75A89GLN0-0.0060.00340.5770.0020.0020.0000.0000.0000.000
76A90ALA00.011-0.00243.2390.0010.0010.0000.0000.0000.000
77A91LYS10.8480.90937.7420.0180.0180.0000.0000.0000.000
78A92MET00.0020.00142.6350.0020.0020.0000.0000.0000.000
79A93GLU-1-0.848-0.91944.645-0.011-0.0110.0000.0000.0000.000
80A94LYS10.8590.91943.8580.0200.0200.0000.0000.0000.000
81A95ASP-1-0.848-0.90842.126-0.015-0.0150.0000.0000.0000.000
82A96ALA0-0.0060.00345.6840.0010.0010.0000.0000.0000.000
83A97ALA0-0.014-0.00548.9140.0010.0010.0000.0000.0000.000
84A98ASP-1-0.821-0.90146.394-0.015-0.0150.0000.0000.0000.000
85A99ASN0-0.074-0.03745.2830.0000.0000.0000.0000.0000.000
86A100GLH0-0.043-0.03249.3260.0010.0010.0000.0000.0000.000
87A101ALA0-0.054-0.02452.4010.0010.0010.0000.0000.0000.000
88A102LYS11.0050.99245.0170.0110.0110.0000.0000.0000.000
89A103GLY00.0320.01451.8700.0010.0010.0000.0000.0000.000
90A104LYS10.9420.97753.3020.0070.0070.0000.0000.0000.000
91A105GLU-1-0.950-0.96753.731-0.008-0.0080.0000.0000.0000.000
92A106TYR0-0.019-0.01952.1270.0010.0010.0000.0000.0000.000
93A107ARG10.9240.94155.2300.0030.0030.0000.0000.0000.000
94A108GLU-1-0.942-0.96558.037-0.003-0.0030.0000.0000.0000.000
95A109LYS10.9320.97156.4250.0030.0030.0000.0000.0000.000
96A110PHE00.0330.00957.6080.0000.0000.0000.0000.0000.000
97A111ALA00.023-0.00259.6300.0010.0010.0000.0000.0000.000
98A112LYS10.8880.95162.8130.0040.0040.0000.0000.0000.000
99A113GLU-1-0.973-0.96859.3250.0000.0000.0000.0000.0000.000
100A114LYS10.9820.97563.970-0.002-0.0020.0000.0000.0000.000
101A115GLY0-0.035-0.02964.9190.0000.0000.0000.0000.0000.000
102A116VAL0-0.0410.01261.9590.0010.0010.0000.0000.0000.000
103A117LYS10.9320.96564.831-0.003-0.0030.0000.0000.0000.000
104A118THR00.0370.01264.3840.0000.0000.0000.0000.0000.000
105A119SER0-0.060-0.04665.4100.0000.0000.0000.0000.0000.000
106A120SER00.020-0.00867.1020.0000.0000.0000.0000.0000.000
107A121THR0-0.080-0.06064.501-0.001-0.0010.0000.0000.0000.000
108A122GLY00.0160.01063.2530.0000.0000.0000.0000.0000.000
109A123LEU0-0.0270.00659.9410.0000.0000.0000.0000.0000.000
110A124VAL0-0.0130.00359.9340.0000.0000.0000.0000.0000.000
111A125TYR0-0.029-0.02160.4170.0000.0000.0000.0000.0000.000
112A126GLN00.0460.01960.3480.0000.0000.0000.0000.0000.000
113A127VAL0-0.0220.00362.1950.0010.0010.0000.0000.0000.000
114A128VAL0-0.034-0.01360.2200.0000.0000.0000.0000.0000.000
115A129GLU-1-0.892-0.95563.6330.0090.0090.0000.0000.0000.000
116A130ALA00.0070.00465.6740.0000.0000.0000.0000.0000.000
117A131GLY00.0550.03567.6860.0000.0000.0000.0000.0000.000
118A132LYS10.8790.91668.318-0.008-0.0080.0000.0000.0000.000
119A133GLY00.0160.01070.6950.0000.0000.0000.0000.0000.000
120A134GLU-1-0.891-0.94671.7870.0070.0070.0000.0000.0000.000
121A135ALA0-0.079-0.05070.3720.0000.0000.0000.0000.0000.000
122A136PRO00.0530.03166.0400.0000.0000.0000.0000.0000.000
123A137LYS10.8570.91768.213-0.007-0.0070.0000.0000.0000.000
124A138ASP-1-0.802-0.88366.8240.0050.0050.0000.0000.0000.000
125A139SER00.0270.01666.0680.0000.0000.0000.0000.0000.000
126A140ASP-1-0.895-0.91566.7280.0080.0080.0000.0000.0000.000
127A141THR0-0.059-0.04461.4690.0000.0000.0000.0000.0000.000
128A142VAL00.0010.00759.9330.0000.0000.0000.0000.0000.000
129A143VAL0-0.027-0.01558.1880.0010.0010.0000.0000.0000.000
130A144VAL00.0140.00255.5360.0000.0000.0000.0000.0000.000
131A145ASN00.0400.03454.1050.0020.0020.0000.0000.0000.000
132A146TYR0-0.054-0.08849.716-0.001-0.0010.0000.0000.0000.000
133A147LYS10.9840.99747.670-0.010-0.0100.0000.0000.0000.000
134A148GLY00.0150.01048.587-0.001-0.0010.0000.0000.0000.000
135A149THR0-0.003-0.00546.5440.0010.0010.0000.0000.0000.000
136A150LEU00.0120.00443.390-0.001-0.0010.0000.0000.0000.000
137A151ILE0-0.009-0.01647.3320.0000.0000.0000.0000.0000.000
138A152ASP-1-0.903-0.94742.838-0.001-0.0010.0000.0000.0000.000
139A153GLY0-0.0020.00345.0150.0000.0000.0000.0000.0000.000
140A154LYS10.8920.95138.431-0.007-0.0070.0000.0000.0000.000
141A155GLU-1-0.881-0.94942.8720.0150.0150.0000.0000.0000.000
142A156PHE0-0.066-0.05042.4310.0010.0010.0000.0000.0000.000
143A157ASP-1-0.770-0.83444.1120.0150.0150.0000.0000.0000.000
144A158ASN00.0330.01345.435-0.001-0.0010.0000.0000.0000.000
145A159SER00.0640.05146.8610.0010.0010.0000.0000.0000.000
146A160TYR00.0110.02548.7390.0010.0010.0000.0000.0000.000
147A161THR0-0.090-0.05843.7210.0020.0020.0000.0000.0000.000
148A162ARG10.8460.90345.016-0.017-0.0170.0000.0000.0000.000
149A163GLY0-0.0270.00146.8210.0010.0010.0000.0000.0000.000
150A164GLU-1-0.986-0.98649.2520.0220.0220.0000.0000.0000.000
151A165PRO0-0.035-0.01351.710-0.001-0.0010.0000.0000.0000.000
152A166LEU0-0.0060.00151.5840.0010.0010.0000.0000.0000.000
153A167SER00.005-0.01254.301-0.001-0.0010.0000.0000.0000.000
154A168PHE0-0.050-0.03256.1430.0000.0000.0000.0000.0000.000
155A169ARG10.9900.99658.596-0.010-0.0100.0000.0000.0000.000
156A170LEU00.0120.02260.7070.0000.0000.0000.0000.0000.000
157A171ASP-1-0.892-0.93561.8740.0060.0060.0000.0000.0000.000
158A172GLY0-0.030-0.00859.7940.0000.0000.0000.0000.0000.000
159A173VAL0-0.062-0.02555.9490.0000.0000.0000.0000.0000.000
160A174ILE0-0.027-0.00153.761-0.001-0.0010.0000.0000.0000.000
161A175PRO00.1010.03357.0750.0000.0000.0000.0000.0000.000
162A176GLY00.0490.02158.6040.0000.0000.0000.0000.0000.000
163A177TRP0-0.019-0.01554.2100.0000.0000.0000.0000.0000.000
164A178THR0-0.027-0.03959.2820.0000.0000.0000.0000.0000.000
165A179GLU-1-0.781-0.85662.3660.0020.0020.0000.0000.0000.000
166A180GLY00.022-0.00161.8000.0000.0000.0000.0000.0000.000
167A181LEU0-0.003-0.01159.7770.0000.0000.0000.0000.0000.000
168A182LYS10.8090.89663.445-0.004-0.0040.0000.0000.0000.000
169A183ASN0-0.080-0.03065.0330.0000.0000.0000.0000.0000.000
170A184ILE0-0.068-0.01662.5570.0000.0000.0000.0000.0000.000
171A185LYS10.9030.95367.112-0.006-0.0060.0000.0000.0000.000
172A186LYS10.9530.97965.862-0.011-0.0110.0000.0000.0000.000
173A187GLY0-0.001-0.00164.5580.0000.0000.0000.0000.0000.000
174A188GLY0-0.011-0.00264.5800.0000.0000.0000.0000.0000.000
175A189LYS10.8660.94359.869-0.010-0.0100.0000.0000.0000.000
176A190ILE0-0.018-0.01460.101-0.001-0.0010.0000.0000.0000.000
177A191LYS10.9901.02555.203-0.003-0.0030.0000.0000.0000.000
178A192LEU0-0.032-0.01957.096-0.001-0.0010.0000.0000.0000.000
179A193VAL0-0.010-0.00855.4180.0000.0000.0000.0000.0000.000
180A194ILE00.002-0.00555.253-0.001-0.0010.0000.0000.0000.000
181A195PRO00.0190.01554.9630.0000.0000.0000.0000.0000.000
182A196PRO00.0260.02752.6980.0010.0010.0000.0000.0000.000
183A197GLU-1-0.836-0.91254.492-0.003-0.0030.0000.0000.0000.000
184A198LEU0-0.046-0.01057.5480.0000.0000.0000.0000.0000.000
185A199ALA00.012-0.01253.0740.0010.0010.0000.0000.0000.000
186A200TYR00.0280.01050.1340.0000.0000.0000.0000.0000.000
187A201GLY0-0.0090.01051.499-0.001-0.0010.0000.0000.0000.000
188A202LYS10.8990.93250.5840.0100.0100.0000.0000.0000.000
189A203ALA0-0.0080.00248.474-0.001-0.0010.0000.0000.0000.000
190A204GLY00.0090.02046.8250.0000.0000.0000.0000.0000.000
191A205VAL00.000-0.01045.8470.0000.0000.0000.0000.0000.000
192A206PRO00.0250.00640.693-0.001-0.0010.0000.0000.0000.000
193A207GLY0-0.0050.00140.9860.0010.0010.0000.0000.0000.000
194A208ILE0-0.062-0.03041.9050.0000.0000.0000.0000.0000.000
195A209PRO00.0180.00942.509-0.001-0.0010.0000.0000.0000.000
196A210PRO00.0550.05744.5310.0010.0010.0000.0000.0000.000
197A211ASN0-0.014-0.04147.6050.0000.0000.0000.0000.0000.000
198A212SER0-0.023-0.02747.3200.0000.0000.0000.0000.0000.000
199A213THR0-0.014-0.00649.7720.0000.0000.0000.0000.0000.000
200A214LEU0-0.047-0.01749.3050.0000.0000.0000.0000.0000.000
201A215VAL00.0020.00650.9520.0000.0000.0000.0000.0000.000
202A216PHE00.0010.00751.1400.0010.0010.0000.0000.0000.000
203A217ASP-1-0.906-0.94453.0470.0070.0070.0000.0000.0000.000
204A218VAL0-0.030-0.03054.3920.0010.0010.0000.0000.0000.000
205A219GLU-1-0.891-0.95656.9780.0120.0120.0000.0000.0000.000
206A220LEU0-0.010-0.00258.7120.0010.0010.0000.0000.0000.000
207A221LEU0-0.015-0.01857.5240.0000.0000.0000.0000.0000.000
208A222ASP-1-0.855-0.95261.8210.0120.0120.0000.0000.0000.000
209A223VAL0-0.007-0.00463.6170.0000.0000.0000.0000.0000.000
210A224LYS10.9531.00361.543-0.013-0.0130.0000.0000.0000.000