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

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FMODB ID: JQ279

Calculation Name: 5D50-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5D50

Chain ID: A

ChEMBL ID:
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UniProt ID: T1S9Z0

Base Structure: X-ray

Registration Date: 2023-09-22

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 171
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1528398.67231
FMO2-HF: Nuclear repulsion 1459812.299803
FMO2-HF: Total energy -68586.372506
FMO2-MP2: Total energy -68786.386138


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:0:ALA)


Summations of interaction energy for fragment #1(A:0: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.
-0.4321.515-0.001-1.052-0.8940.006
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.018
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].
3A2LYS10.8520.9383.8020.2192.166-0.001-1.052-0.8940.006
4A3SER00.0230.0196.1000.8830.8830.0000.0000.0000.000
5A4ILE00.0720.0117.614-0.045-0.0450.0000.0000.0000.000
6A5TYR0-0.057-0.0399.3390.1010.1010.0000.0000.0000.000
7A6ASP-1-0.830-0.9046.476-2.648-2.6480.0000.0000.0000.000
8A7ILE00.0380.0309.3330.1190.1190.0000.0000.0000.000
9A8ARG10.8560.92811.8920.7080.7080.0000.0000.0000.000
10A9ARG10.9450.9848.3461.2261.2260.0000.0000.0000.000
11A10LYS10.8940.97211.0471.0901.0900.0000.0000.0000.000
12A11ASN00.002-0.02513.4550.0950.0950.0000.0000.0000.000
13A12LEU0-0.085-0.05316.5210.0740.0740.0000.0000.0000.000
14A13ASN0-0.071-0.06814.7710.1170.1170.0000.0000.0000.000
15A14GLU-1-0.864-0.92816.583-0.421-0.4210.0000.0000.0000.000
16A15ILE0-0.042-0.00919.2000.0440.0440.0000.0000.0000.000
17A16ILE0-0.038-0.02020.9880.0360.0360.0000.0000.0000.000
18A17LEU00.0220.03820.9250.0310.0310.0000.0000.0000.000
19A18ARG10.8810.93318.6490.3930.3930.0000.0000.0000.000
20A19ASP-1-0.927-0.94624.997-0.238-0.2380.0000.0000.0000.000
21A20PHE0-0.130-0.08725.9840.0230.0230.0000.0000.0000.000
22A21ASP-1-0.859-0.92827.360-0.149-0.1490.0000.0000.0000.000
23A22ASP-1-0.929-0.98921.451-0.248-0.2480.0000.0000.0000.000
24A23THR0-0.044-0.00524.1710.0120.0120.0000.0000.0000.000
25A24GLN00.0890.01820.9440.0140.0140.0000.0000.0000.000
26A25LEU0-0.011-0.01724.838-0.002-0.0020.0000.0000.0000.000
27A26ARG11.0131.02028.5210.1250.1250.0000.0000.0000.000
28A27PHE00.0370.03123.776-0.001-0.0010.0000.0000.0000.000
29A28ALA0-0.044-0.03027.126-0.001-0.0010.0000.0000.0000.000
30A29GLU-1-0.934-0.97428.134-0.114-0.1140.0000.0000.0000.000
31A30ARG10.8980.96829.7020.1660.1660.0000.0000.0000.000
32A31VAL0-0.022-0.00626.0140.0040.0040.0000.0000.0000.000
33A32LYS10.9550.98429.1870.1240.1240.0000.0000.0000.000
34A33ARG10.8720.94126.6600.1710.1710.0000.0000.0000.000
35A34SER00.0600.02827.827-0.001-0.0010.0000.0000.0000.000
36A35GLN00.1130.03926.274-0.022-0.0220.0000.0000.0000.000
37A36ASN00.0300.02124.931-0.013-0.0130.0000.0000.0000.000
38A37LEU0-0.071-0.03321.781-0.006-0.0060.0000.0000.0000.000
39A38VAL00.0380.01721.480-0.025-0.0250.0000.0000.0000.000
40A39ASN00.0200.00020.556-0.026-0.0260.0000.0000.0000.000
41A40ARG10.9140.96018.8490.1470.1470.0000.0000.0000.000
42A41TRP0-0.026-0.01716.976-0.018-0.0180.0000.0000.0000.000
43A42CYS00.0090.01315.628-0.067-0.0670.0000.0000.0000.000
44A43THR00.021-0.00215.131-0.049-0.0490.0000.0000.0000.000
45A44GLY00.0090.00212.556-0.040-0.0400.0000.0000.0000.000
46A45ILE0-0.041-0.00313.385-0.002-0.0020.0000.0000.0000.000
47A46LYS10.8830.94615.8270.2620.2620.0000.0000.0000.000
48A47ASN00.0450.02611.933-0.107-0.1070.0000.0000.0000.000
49A48ILE00.0020.01314.5180.0720.0720.0000.0000.0000.000
50A49GLY0-0.006-0.00316.241-0.032-0.0320.0000.0000.0000.000
51A50PRO00.0550.00718.533-0.017-0.0170.0000.0000.0000.000
52A51ASN00.0480.01119.9740.0050.0050.0000.0000.0000.000
53A52ALA0-0.0110.00820.8850.0100.0100.0000.0000.0000.000
54A53ALA00.0680.02318.9050.0080.0080.0000.0000.0000.000
55A54ARG10.8320.92919.1270.3750.3750.0000.0000.0000.000
56A55ILE00.0210.01724.3050.0110.0110.0000.0000.0000.000
57A56ILE0-0.065-0.02720.5190.0130.0130.0000.0000.0000.000
58A57GLU-1-0.745-0.88221.854-0.344-0.3440.0000.0000.0000.000
59A58GLU-1-0.902-0.94425.053-0.179-0.1790.0000.0000.0000.000
60A59ALA0-0.077-0.04426.9850.0110.0110.0000.0000.0000.000
61A60ALA0-0.054-0.03424.7720.0110.0110.0000.0000.0000.000
62A61ARG10.8890.94726.7410.1700.1700.0000.0000.0000.000
63A62LYS10.9090.96823.6290.2900.2900.0000.0000.0000.000
64A63GLU-1-0.838-0.92826.583-0.207-0.2070.0000.0000.0000.000
65A64LYS10.9370.96825.1170.1930.1930.0000.0000.0000.000
66A65PHE0-0.070-0.05319.8970.0070.0070.0000.0000.0000.000
67A66TRP00.0910.05620.239-0.052-0.0520.0000.0000.0000.000
68A67LEU0-0.029-0.00317.684-0.045-0.0450.0000.0000.0000.000
69A68ASP-1-0.813-0.91716.054-0.583-0.5830.0000.0000.0000.000
70A69VAL0-0.0150.01315.421-0.081-0.0810.0000.0000.0000.000
71A70ASP-1-0.841-0.91911.488-1.198-1.1980.0000.0000.0000.000
72A71HIS0-0.006-0.01814.7100.0710.0710.0000.0000.0000.000
73A72GLU-1-0.906-0.96211.491-0.978-0.9780.0000.0000.0000.000
74A73LEU0-0.031-0.02014.9430.0450.0450.0000.0000.0000.000
75A74ASP-1-0.979-0.97117.885-0.275-0.2750.0000.0000.0000.000
76A75ALA0-0.020-0.00519.683-0.008-0.0080.0000.0000.0000.000
77A76VAL0-0.013-0.00521.1210.0020.0020.0000.0000.0000.000
78A90TRP0-0.045-0.04529.996-0.003-0.0030.0000.0000.0000.000
79A91THR0-0.036-0.01033.5190.0030.0030.0000.0000.0000.000
80A92VAL00.0770.04432.477-0.001-0.0010.0000.0000.0000.000
81A93GLU-1-0.823-0.88634.000-0.013-0.0130.0000.0000.0000.000
82A94LYS11.0090.98036.2480.0370.0370.0000.0000.0000.000
83A95GLN00.0370.03227.216-0.005-0.0050.0000.0000.0000.000
84A96ALA00.0390.02431.8950.0030.0030.0000.0000.0000.000
85A97ALA0-0.004-0.01333.7340.0050.0050.0000.0000.0000.000
86A98ALA00.011-0.00131.6730.0000.0000.0000.0000.0000.000
87A99THR00.0310.01628.674-0.004-0.0040.0000.0000.0000.000
88A100LEU00.0240.02630.3760.0030.0030.0000.0000.0000.000
89A101ASN0-0.054-0.01033.2290.0040.0040.0000.0000.0000.000
90A102ALA0-0.058-0.04228.5950.0000.0000.0000.0000.0000.000
91A103TRP0-0.017-0.00726.3460.0030.0030.0000.0000.0000.000
92A104MET0-0.049-0.00230.6810.0070.0070.0000.0000.0000.000
93A105ARG10.9030.94228.0820.0460.0460.0000.0000.0000.000
94A106LYS10.9150.98529.425-0.035-0.0350.0000.0000.0000.000
95A120ALA00.013-0.02739.4580.0010.0010.0000.0000.0000.000
96A121GLY00.0140.00939.974-0.001-0.0010.0000.0000.0000.000
97A122ILE0-0.0420.01140.4350.0010.0010.0000.0000.0000.000
98A123GLY00.043-0.04039.257-0.001-0.0010.0000.0000.0000.000
99A124PRO00.004-0.01538.892-0.001-0.0010.0000.0000.0000.000
100A125ALA00.0540.02840.0150.0010.0010.0000.0000.0000.000
101A126THR0-0.018-0.01241.626-0.002-0.0020.0000.0000.0000.000
102A127VAL00.0010.05440.868-0.002-0.0020.0000.0000.0000.000
103A128ASN00.0210.00543.541-0.002-0.0020.0000.0000.0000.000
104A129ARG10.8980.95742.615-0.011-0.0110.0000.0000.0000.000
105A130ILE0-0.0090.01842.1810.0010.0010.0000.0000.0000.000
106A131MET00.0190.01137.3820.0020.0020.0000.0000.0000.000
107A132LYS10.9690.95640.3940.0080.0080.0000.0000.0000.000
108A133ALA0-0.0020.00337.885-0.003-0.0030.0000.0000.0000.000
109A134GLU-1-0.904-0.94839.359-0.024-0.0240.0000.0000.0000.000
110A135VAL0-0.047-0.03041.8340.0000.0000.0000.0000.0000.000
111A136SER0-0.014-0.04040.5050.0010.0010.0000.0000.0000.000
112A137THR0-0.061-0.02038.5410.0020.0020.0000.0000.0000.000
113A138THR00.0430.01739.9510.0010.0010.0000.0000.0000.000
114A139ILE00.1150.03735.9620.0000.0000.0000.0000.0000.000
115A140GLY00.0360.02337.0510.0040.0040.0000.0000.0000.000
116A141VAL0-0.026-0.01639.2230.0020.0020.0000.0000.0000.000
117A142LEU00.0290.01334.0950.0010.0010.0000.0000.0000.000
118A143SER00.0020.01034.4860.0040.0040.0000.0000.0000.000
119A144SER0-0.056-0.03135.4670.0050.0050.0000.0000.0000.000
120A145LEU0-0.027-0.02435.9770.0010.0010.0000.0000.0000.000
121A146ALA0-0.0190.00131.2030.0000.0000.0000.0000.0000.000
122A147ARG11.0141.00431.951-0.079-0.0790.0000.0000.0000.000
123A148ALA0-0.052-0.01933.3700.0040.0040.0000.0000.0000.000
124A149PHE0-0.063-0.03730.5340.0000.0000.0000.0000.0000.000
125A150GLY0-0.0060.00129.8640.0030.0030.0000.0000.0000.000
126A151HIS0-0.027-0.00426.0300.0130.0130.0000.0000.0000.000
127A152GLU-1-0.867-0.93526.0510.1010.1010.0000.0000.0000.000
128A153ALA0-0.030-0.03728.737-0.009-0.0090.0000.0000.0000.000
129A154TYR0-0.023-0.01123.269-0.011-0.0110.0000.0000.0000.000
130A155GLU-1-0.892-0.93123.4500.0630.0630.0000.0000.0000.000
131A156MET0-0.002-0.00322.649-0.002-0.0020.0000.0000.0000.000
132A157ILE0-0.012-0.01126.575-0.010-0.0100.0000.0000.0000.000
133A158ILE00.014-0.00524.151-0.006-0.0060.0000.0000.0000.000
134A159PRO0-0.061-0.01124.749-0.001-0.0010.0000.0000.0000.000
135A160VAL00.0090.00021.530-0.009-0.0090.0000.0000.0000.000
136A161GLY00.0240.00620.290-0.017-0.0170.0000.0000.0000.000
137A162ALA00.0360.00818.4170.0090.0090.0000.0000.0000.000
138A163PRO0-0.057-0.03818.9140.0050.0050.0000.0000.0000.000
139A164GLY00.0060.02319.0840.0190.0190.0000.0000.0000.000
140A165ILE00.0040.01213.051-0.023-0.0230.0000.0000.0000.000
141A166ILE00.004-0.01215.7920.0330.0330.0000.0000.0000.000
142A167ASP-1-0.954-0.9739.5070.2530.2530.0000.0000.0000.000
143A168TYR0-0.041-0.00412.2460.0960.0960.0000.0000.0000.000
144A169ASP-1-0.775-0.90913.1690.3330.3330.0000.0000.0000.000
145A170HIS00.0250.00315.4480.0120.0120.0000.0000.0000.000
146A171ARG10.9230.96418.758-0.256-0.2560.0000.0000.0000.000
147A172MET00.0160.01211.4860.0110.0110.0000.0000.0000.000
148A173TYR00.0670.02716.547-0.005-0.0050.0000.0000.0000.000
149A174ALA0-0.105-0.06517.817-0.027-0.0270.0000.0000.0000.000
150A175ALA0-0.006-0.00619.387-0.021-0.0210.0000.0000.0000.000
151A176LEU0-0.0390.00515.709-0.003-0.0030.0000.0000.0000.000
152A177PRO00.0670.02719.911-0.045-0.0450.0000.0000.0000.000
153A178GLN00.0450.00721.8580.0220.0220.0000.0000.0000.000
154A179GLU-1-0.958-0.97923.3780.2620.2620.0000.0000.0000.000
155A180GLU-1-0.894-0.96817.9310.4770.4770.0000.0000.0000.000
156A181LYS10.8430.95018.550-0.288-0.2880.0000.0000.0000.000
157A182ASN00.0170.01019.978-0.012-0.0120.0000.0000.0000.000
158A183LYS10.9430.98418.171-0.364-0.3640.0000.0000.0000.000
159A184ILE00.0210.01714.692-0.014-0.0140.0000.0000.0000.000
160A185THR0-0.048-0.03217.073-0.038-0.0380.0000.0000.0000.000
161A186SER0-0.021-0.01519.946-0.036-0.0360.0000.0000.0000.000
162A187PHE00.0270.01213.166-0.022-0.0220.0000.0000.0000.000
163A188ILE00.0100.01116.201-0.031-0.0310.0000.0000.0000.000
164A189ASN00.002-0.01118.171-0.041-0.0410.0000.0000.0000.000
165A190PHE0-0.0130.00419.353-0.021-0.0210.0000.0000.0000.000
166A191VAL00.0160.00315.766-0.024-0.0240.0000.0000.0000.000
167A192PHE0-0.039-0.02119.146-0.026-0.0260.0000.0000.0000.000
168A193GLU-1-0.954-0.97121.7810.0130.0130.0000.0000.0000.000
169A194GLN0-0.046-0.01721.175-0.019-0.0190.0000.0000.0000.000
170A195ASN0-0.091-0.03019.030-0.039-0.0390.0000.0000.0000.000
171A196LYS10.9510.97923.0160.0640.0640.0000.0000.0000.000