FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2N1KR

Calculation Name: 5HQP-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HQP

Chain ID: D

ChEMBL ID:

UniProt ID: Q9BS26

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2371253.762092
FMO2-HF: Nuclear repulsion 2286432.118155
FMO2-HF: Total energy -84821.643937
FMO2-MP2: Total energy -85065.573407


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(D:2:ILE)


Summations of interaction energy for fragment #1(D:2:ILE)
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.
-15.285-3.85510.748-8.509-13.67-0.042
Interaction energy analysis for fragmet #1(D:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.032
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].
3D4SER0-0.030-0.0223.854-2.0831.067-0.026-1.726-1.3990.009
4D5LEU0-0.0020.0226.7900.0210.0210.0000.0000.0000.000
5D6ASP-1-0.829-0.9319.641-0.314-0.3140.0000.0000.0000.000
6D7THR0-0.044-0.05313.3220.0380.0380.0000.0000.0000.000
7D8GLU-1-1.019-0.97615.748-0.046-0.0460.0000.0000.0000.000
8D9ASN0-0.010-0.02411.4540.0170.0170.0000.0000.0000.000
9D10ILE00.0230.00612.2080.0300.0300.0000.0000.0000.000
10D11ASP-1-0.888-0.94713.1010.0230.0230.0000.0000.0000.000
11D12GLU-1-0.908-0.92512.3970.1800.1800.0000.0000.0000.000
12D13ILE0-0.001-0.0187.4910.0300.0300.0000.0000.0000.000
13D14LEU0-0.064-0.02210.9590.0330.0330.0000.0000.0000.000
14D15ASN0-0.059-0.06712.6700.0050.0050.0000.0000.0000.000
15D16ASN0-0.072-0.02711.5380.0500.0500.0000.0000.0000.000
16D17ALA00.0510.0399.9850.0340.0340.0000.0000.0000.000
17D18ASP-1-0.816-0.89712.0060.1820.1820.0000.0000.0000.000
18D19VAL0-0.070-0.04510.500-0.055-0.0550.0000.0000.0000.000
19D20ALA00.0600.0508.3850.0250.0250.0000.0000.0000.000
20D21LEU0-0.043-0.0197.566-0.039-0.0390.0000.0000.0000.000
21D22VAL00.0320.0036.838-0.102-0.1020.0000.0000.0000.000
22D23ASN0-0.009-0.0177.0810.0620.0620.0000.0000.0000.000
23D24PHE00.0230.0068.909-0.037-0.0370.0000.0000.0000.000
24D25TYR0-0.064-0.0518.583-0.022-0.0220.0000.0000.0000.000
25D26ALA00.0640.03512.0510.0060.0060.0000.0000.0000.000
26D27ASP-1-0.752-0.89711.087-0.414-0.4140.0000.0000.0000.000
27D28TRP0-0.111-0.06414.2100.0130.0130.0000.0000.0000.000
28D29CYS0-0.079-0.01016.2870.0230.0230.0000.0000.0000.000
29D30ARG10.9330.95315.7900.1430.1430.0000.0000.0000.000
30D31PHE00.017-0.02216.119-0.006-0.0060.0000.0000.0000.000
31D32SER00.012-0.00612.0130.0040.0040.0000.0000.0000.000
32D33GLN00.0160.02611.311-0.007-0.0070.0000.0000.0000.000
33D34MET0-0.057-0.04112.259-0.010-0.0100.0000.0000.0000.000
34D35LEU0-0.0020.0088.7160.0150.0150.0000.0000.0000.000
35D36HIS0-0.0140.0066.843-0.055-0.0550.0000.0000.0000.000
36D37PRO00.0200.0146.538-0.060-0.0600.0000.0000.0000.000
37D38ILE00.0140.0107.9970.0110.0110.0000.0000.0000.000
38D39PHE0-0.033-0.0243.761-0.383-0.0210.008-0.061-0.3080.000
39D40GLU-1-0.890-0.9612.275-2.357-1.6251.191-0.458-1.4650.000
40D41GLU-1-0.926-0.9574.097-0.0390.1610.000-0.023-0.1760.000
41D42ALA0-0.042-0.0457.1450.1150.1150.0000.0000.0000.000
42D43SER-1-0.678-0.8212.626-7.115-2.9541.962-2.961-3.162-0.035
43D44ASP-1-0.964-0.9764.6401.3781.604-0.001-0.019-0.2060.000
44D45VAL0-0.061-0.0115.7550.0840.0840.0000.0000.0000.000
45D46ILE00.0180.0076.4820.0660.0660.0000.0000.0000.000
46D47LYS10.7450.8452.161-2.205-3.3555.447-1.186-3.1120.011
47D48GLU-1-1.025-1.0095.9510.6200.6200.0000.0000.0000.000
48D49GLU-1-0.808-0.8829.0850.1030.1030.0000.0000.0000.000
49D50PHE0-0.042-0.0019.638-0.033-0.0330.0000.0000.0000.000
50D51PRO0-0.023-0.0158.812-0.055-0.0550.0000.0000.0000.000
51D52ASN00.008-0.0288.6470.2220.2220.0000.0000.0000.000
52D53GLU-1-0.977-0.9599.8970.4290.4290.0000.0000.0000.000
53D54ASN0-0.032-0.0468.4580.2930.2930.0000.0000.0000.000
54D55GLN0-0.044-0.0089.502-0.112-0.1120.0000.0000.0000.000
55D56VAL0-0.029-0.0086.437-0.101-0.1010.0000.0000.0000.000
56D57VAL00.0200.0194.5040.0860.227-0.001-0.010-0.1290.000
57D58PHE0-0.0100.0052.765-0.957-0.0390.167-0.237-0.8490.000
58D59ALA00.0370.0162.539-3.671-1.1962.002-1.824-2.653-0.027
59D60ARG10.8220.9134.0050.5800.795-0.001-0.004-0.2110.000
60D61VAL00.0460.0126.469-0.042-0.0420.0000.0000.0000.000
61D62ASP-1-0.718-0.83510.019-0.327-0.3270.0000.0000.0000.000
62D63CYS0-0.069-0.03712.3150.0450.0450.0000.0000.0000.000
63D64ASP-1-0.831-0.89515.372-0.190-0.1900.0000.0000.0000.000
64D65GLN0-0.114-0.07714.2270.0170.0170.0000.0000.0000.000
65D66HIS00.0870.05512.0790.0150.0150.0000.0000.0000.000
66D67SER0-0.026-0.01816.4050.0160.0160.0000.0000.0000.000
67D68ASP-1-0.829-0.89418.560-0.129-0.1290.0000.0000.0000.000
68D69ILE00.0450.01513.8540.0190.0190.0000.0000.0000.000
69D70ALA0-0.0040.00617.2570.0120.0120.0000.0000.0000.000
70D71GLN0-0.057-0.04118.3030.0120.0120.0000.0000.0000.000
71D72ARG10.8560.92317.7510.1100.1100.0000.0000.0000.000
72D73TYR00.0440.01516.3840.0080.0080.0000.0000.0000.000
73D74ARG10.8060.90619.3560.0580.0580.0000.0000.0000.000
74D75ILE00.0390.03015.7330.0040.0040.0000.0000.0000.000
75D76SER0-0.053-0.03019.1650.0030.0030.0000.0000.0000.000
76D77LYS10.8450.91118.6920.0820.0820.0000.0000.0000.000
77D78TYR00.0330.04815.641-0.002-0.0020.0000.0000.0000.000
78D79PRO0-0.026-0.02012.2650.0130.0130.0000.0000.0000.000
79D80THR0-0.042-0.06013.4980.0200.0200.0000.0000.0000.000
80D81LEU0-0.0290.0149.127-0.013-0.0130.0000.0000.0000.000
81D82LYN0-0.028-0.02911.6810.0290.0290.0000.0000.0000.000
82D83LEU00.0350.02811.610-0.019-0.0190.0000.0000.0000.000
83D84PHE0-0.041-0.02512.632-0.013-0.0130.0000.0000.0000.000
84D85ARG10.8790.94213.264-0.063-0.0630.0000.0000.0000.000
85D86ASN0-0.040-0.02814.800-0.030-0.0300.0000.0000.0000.000
86D87GLY00.0580.05215.079-0.011-0.0110.0000.0000.0000.000
87D88MET0-0.062-0.03616.652-0.026-0.0260.0000.0000.0000.000
88D89MET0-0.020-0.00117.1520.0030.0030.0000.0000.0000.000
89D90MET00.0470.04416.9310.0040.0040.0000.0000.0000.000
90D91LYS10.8370.90119.2640.0050.0050.0000.0000.0000.000
91D92ARG00.0670.05219.426-0.016-0.0160.0000.0000.0000.000
92D93GLU-1-0.762-0.86516.562-0.079-0.0790.0000.0000.0000.000
93D94TYR0-0.008-0.00814.2070.0130.0130.0000.0000.0000.000
94D95ARG10.7930.87916.3220.0390.0390.0000.0000.0000.000
95D96GLY00.0260.02617.5590.0060.0060.0000.0000.0000.000
96D97GLN0-0.003-0.00417.047-0.023-0.0230.0000.0000.0000.000
97D98ARG10.9770.99013.2800.1550.1550.0000.0000.0000.000
98D99SER0-0.019-0.01113.7540.0050.0050.0000.0000.0000.000
99D100VAL00.0990.04710.116-0.004-0.0040.0000.0000.0000.000
100D101LYS10.8890.93912.0850.0050.0050.0000.0000.0000.000
101D102ALA0-0.035-0.01415.0550.0110.0110.0000.0000.0000.000
102D103LEU0-0.0010.0028.8920.0080.0080.0000.0000.0000.000
103D104ALA00.0720.04111.1170.0070.0070.0000.0000.0000.000
104D105ASP-1-0.819-0.91012.0810.0520.0520.0000.0000.0000.000
105D106TYR0-0.050-0.02112.8380.0140.0140.0000.0000.0000.000
106D107ILE00.0260.0048.8110.0050.0050.0000.0000.0000.000
107D108ARG10.7790.85712.708-0.070-0.0700.0000.0000.0000.000
108D109GLN0-0.037-0.01414.7530.0060.0060.0000.0000.0000.000
109D110GLN0-0.025-0.00914.4220.0090.0090.0000.0000.0000.000
110D111LYN00.0100.01513.1390.0020.0020.0000.0000.0000.000
111D112SER0-0.046-0.03316.9140.0050.0050.0000.0000.0000.000
112D113ASP-1-0.918-0.94620.6220.0820.0820.0000.0000.0000.000
113D114PRO0-0.044-0.01821.5940.0030.0030.0000.0000.0000.000
114D115ILE0-0.071-0.03224.108-0.009-0.0090.0000.0000.0000.000
115D116GLN00.0250.00427.5140.0000.0000.0000.0000.0000.000
116D117GLU-1-0.823-0.87530.3980.0550.0550.0000.0000.0000.000
117D118ILE0-0.047-0.02432.549-0.002-0.0020.0000.0000.0000.000
118D119ARG10.7430.84433.372-0.049-0.0490.0000.0000.0000.000
119D120ASP-1-0.898-0.95939.3070.0290.0290.0000.0000.0000.000
120D121LEU00.0170.03240.621-0.001-0.0010.0000.0000.0000.000
121D122ALA0-0.025-0.02442.889-0.002-0.0020.0000.0000.0000.000
122D123GLU-1-0.782-0.89737.5980.0320.0320.0000.0000.0000.000
123D124ILE00.0030.00140.266-0.002-0.0020.0000.0000.0000.000
124D125THR0-0.046-0.02541.698-0.002-0.0020.0000.0000.0000.000
125D126THR0-0.104-0.06441.834-0.001-0.0010.0000.0000.0000.000
126D127LEU00.0140.01636.3440.0000.0000.0000.0000.0000.000
127D128ASP-1-0.759-0.86238.0200.0120.0120.0000.0000.0000.000
128D129ARG10.8720.93338.017-0.011-0.0110.0000.0000.0000.000
129D130SER0-0.037-0.03737.0570.0010.0010.0000.0000.0000.000
130D131LYS10.8480.93233.734-0.018-0.0180.0000.0000.0000.000
131D132ARG10.7930.87932.623-0.015-0.0150.0000.0000.0000.000
132D133ASN00.0000.00332.9570.0000.0000.0000.0000.0000.000
133D134ILE00.0390.03031.495-0.002-0.0020.0000.0000.0000.000
134D135ILE00.0130.00932.7160.0030.0030.0000.0000.0000.000
135D136GLY00.0410.01233.663-0.002-0.0020.0000.0000.0000.000
136D137TYR0-0.040-0.01734.6410.0020.0020.0000.0000.0000.000
137D138PHE00.0480.00932.8250.0000.0000.0000.0000.0000.000
138D139GLU-1-0.829-0.90336.1860.0450.0450.0000.0000.0000.000
139D140GLN0-0.010-0.00332.9090.0040.0040.0000.0000.0000.000
140D141LYS10.9090.96130.493-0.057-0.0570.0000.0000.0000.000
141D142ASP-1-0.836-0.89828.5960.1000.1000.0000.0000.0000.000
142D143SER0-0.103-0.05929.3380.0040.0040.0000.0000.0000.000
143D144ASP-1-0.817-0.92328.9830.0860.0860.0000.0000.0000.000
144D145ASN0-0.039-0.03829.2500.0040.0040.0000.0000.0000.000
145D146TYR0-0.0080.00827.390-0.004-0.0040.0000.0000.0000.000
146D147ARG10.8900.93424.601-0.099-0.0990.0000.0000.0000.000
147D148VAL0-0.067-0.02725.0540.0020.0020.0000.0000.0000.000
148D149PHE0-0.012-0.01026.638-0.004-0.0040.0000.0000.0000.000
149D150GLU-1-0.849-0.93422.9960.1000.1000.0000.0000.0000.000
150D151ARG10.8900.95121.277-0.063-0.0630.0000.0000.0000.000
151D152VAL0-0.069-0.04722.441-0.004-0.0040.0000.0000.0000.000
152D153ALA00.0270.00824.710-0.006-0.0060.0000.0000.0000.000
153D154ASN0-0.021-0.03219.079-0.002-0.0020.0000.0000.0000.000
154D155ILE0-0.072-0.02319.936-0.004-0.0040.0000.0000.0000.000
155D156LEU0-0.001-0.00821.546-0.008-0.0080.0000.0000.0000.000
156D157HIS00.0080.00319.8880.0040.0040.0000.0000.0000.000
157D158ASP-1-0.970-0.96221.9160.0060.0060.0000.0000.0000.000
158D159ASP-1-0.943-0.96625.0090.0070.0070.0000.0000.0000.000
159D160CYS0-0.120-0.05827.8200.0000.0000.0000.0000.0000.000
160D161ALA00.0270.01828.1860.0030.0030.0000.0000.0000.000
161D162PHE00.0580.02227.042-0.001-0.0010.0000.0000.0000.000
162D163LEU0-0.039-0.02329.9180.0010.0010.0000.0000.0000.000
163D164SER0-0.015-0.00331.4250.0020.0020.0000.0000.0000.000
164D165ALA00.0590.01933.4290.0000.0000.0000.0000.0000.000
165D166PHE0-0.105-0.06436.0020.0040.0040.0000.0000.0000.000
166D167GLY00.0340.02438.762-0.002-0.0020.0000.0000.0000.000
167D168ASP-1-0.924-0.95741.5340.0310.0310.0000.0000.0000.000
168D169VAL0-0.115-0.08440.799-0.001-0.0010.0000.0000.0000.000
169D178ASP-1-0.835-0.89537.0520.0460.0460.0000.0000.0000.000
170D179ASN0-0.047-0.03538.124-0.002-0.0020.0000.0000.0000.000
171D180ILE00.0220.00432.8520.0020.0020.0000.0000.0000.000
172D181ILE0-0.044-0.02036.805-0.003-0.0030.0000.0000.0000.000
173D182TYR-1-0.777-0.88435.4250.0150.0150.0000.0000.0000.000
174D183LYS10.8550.90837.582-0.020-0.0200.0000.0000.0000.000
175D184PRO00.0510.03938.627-0.001-0.0010.0000.0000.0000.000
176D185PRO0-0.041-0.00838.8610.0010.0010.0000.0000.0000.000
177D186GLY00.0090.00540.434-0.002-0.0020.0000.0000.0000.000
178D187HIS0-0.028-0.02743.4220.0010.0010.0000.0000.0000.000
179D188SER0-0.088-0.04346.074-0.001-0.0010.0000.0000.0000.000
180D189ALA0-0.0070.00244.341-0.001-0.0010.0000.0000.0000.000
181D190PRO0-0.005-0.00545.0780.0010.0010.0000.0000.0000.000
182D191ASP-1-0.738-0.84142.3110.0180.0180.0000.0000.0000.000
183D192MET0-0.073-0.03140.2390.0000.0000.0000.0000.0000.000
184D193VAL00.0270.00540.1210.0010.0010.0000.0000.0000.000
185D194TYR0-0.048-0.04235.349-0.002-0.0020.0000.0000.0000.000
186D195LEU0-0.015-0.02139.0500.0010.0010.0000.0000.0000.000
187D196GLY00.0230.00938.481-0.002-0.0020.0000.0000.0000.000
188D197ALA0-0.042-0.00936.0640.0020.0020.0000.0000.0000.000
189D198MET00.0550.03932.8240.0000.0000.0000.0000.0000.000
190D199THR00.0220.00931.4860.0010.0010.0000.0000.0000.000
191D200ASN00.000-0.00130.3090.0040.0040.0000.0000.0000.000
192D201PHE00.0540.03126.427-0.002-0.0020.0000.0000.0000.000
193D202ASP-1-0.809-0.91526.8690.0390.0390.0000.0000.0000.000
194D203VAL0-0.060-0.02229.611-0.004-0.0040.0000.0000.0000.000
195D204THR00.0120.00930.211-0.002-0.0020.0000.0000.0000.000
196D205TYR00.0220.01825.648-0.002-0.0020.0000.0000.0000.000
197D206ASN00.0230.00328.997-0.004-0.0040.0000.0000.0000.000
198D207TRP0-0.022-0.00331.293-0.003-0.0030.0000.0000.0000.000
199D208ILE00.0480.01829.820-0.002-0.0020.0000.0000.0000.000
200D209GLN0-0.003-0.00428.482-0.004-0.0040.0000.0000.0000.000
201D210ASP-1-0.860-0.91330.3880.0080.0080.0000.0000.0000.000
202D211LYS10.7480.87633.971-0.019-0.0190.0000.0000.0000.000
203D212CYS0-0.034-0.00530.0500.0020.0020.0000.0000.0000.000
204D213VAL0-0.123-0.05330.143-0.005-0.0050.0000.0000.0000.000