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: 945V2

Calculation Name: 5JD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JD6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2734296.02842
FMO2-HF: Nuclear repulsion 2647362.588283
FMO2-HF: Total energy -86933.440137
FMO2-MP2: Total energy -87186.530042


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:3:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
41.88256.0777.304-9.4-12.0990.061
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.858 / q_NPA : -0.934
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].
3A5LEU00.0050.0003.7930.2933.777-0.041-1.776-1.6670.009
4A6LYS10.8240.9186.166-36.696-36.6960.0000.0000.0000.000
5A7GLN0-0.027-0.0368.838-1.291-1.2910.0000.0000.0000.000
6A8GLU-1-0.796-0.84711.52424.08524.0850.0000.0000.0000.000
7A9GLY00.0160.00414.823-0.359-0.3590.0000.0000.0000.000
8A10LYS10.7430.85117.456-14.845-14.8450.0000.0000.0000.000
9A11PHE0-0.0030.00113.6980.0510.0510.0000.0000.0000.000
10A12THR00.0230.01410.5350.1650.1650.0000.0000.0000.000
11A13TYR0-0.040-0.0527.821-0.945-0.9450.0000.0000.0000.000
12A14LEU00.0690.0553.100-8.317-5.1550.197-1.702-1.6570.015
13A15GLU-1-0.778-0.8963.52521.55522.0410.010-0.220-0.2760.001
14A16LYS10.8440.9352.006-52.956-48.0706.433-4.573-6.7460.023
15A17GLY00.0490.0273.704-6.785-6.6820.011-0.049-0.0650.000
16A18GLU-1-1.008-1.0107.04325.28025.2800.0000.0000.0000.000
17A19GLY0-0.012-0.00110.173-1.558-1.5580.0000.0000.0000.000
18A20THR00.0390.01613.1520.3000.3000.0000.0000.0000.000
19A21PRO0-0.0090.02112.1131.8171.8170.0000.0000.0000.000
20A22ILE0-0.013-0.00511.064-1.694-1.6940.0000.0000.0000.000
21A23VAL0-0.049-0.02010.5252.9452.9450.0000.0000.0000.000
22A24ILE00.0080.0008.814-2.163-2.1630.0000.0000.0000.000
23A25LEU0-0.028-0.02412.0080.2160.2160.0000.0000.0000.000
24A26HIS00.012-0.00911.987-2.157-2.1570.0000.0000.0000.000
25A27GLY0-0.033-0.02514.720-1.186-1.1860.0000.0000.0000.000
26A28LEU0-0.045-0.03217.1190.3280.3280.0000.0000.0000.000
27A29MET0-0.013-0.01017.423-0.196-0.1960.0000.0000.0000.000
28A30GLY0-0.0200.00914.7330.1590.1590.0000.0000.0000.000
29A31GLY00.0820.05412.405-0.174-0.1740.0000.0000.0000.000
30A32LEU0-0.020-0.0347.145-0.180-0.1800.0000.0000.0000.000
31A33SER0-0.032-0.0217.5501.9381.9380.0000.0000.0000.000
32A34ASN0-0.076-0.0539.267-2.388-2.3880.0000.0000.0000.000
33A35PHE00.0590.0008.346-2.652-2.6520.0000.0000.0000.000
34A36ASP-1-0.776-0.8656.20842.47742.4770.0000.0000.0000.000
35A37GLY00.0120.0067.2880.5820.5820.0000.0000.0000.000
36A38VAL0-0.021-0.0129.460-0.891-0.8910.0000.0000.0000.000
37A39ILE00.000-0.0052.730-6.064-4.1120.695-1.077-1.5700.013
38A40ASP-1-0.819-0.9154.91249.32149.443-0.001-0.003-0.1180.000
39A41TYR0-0.097-0.0476.751-2.996-2.9960.0000.0000.0000.000
40A42PHE00.025-0.0079.672-1.367-1.3670.0000.0000.0000.000
41A43PRO00.0230.0305.553-2.524-2.5240.0000.0000.0000.000
42A44GLU-1-0.877-0.9286.43635.52535.5250.0000.0000.0000.000
43A45LYS10.7350.87110.082-26.357-26.3570.0000.0000.0000.000
44A46GLY00.0220.02112.011-1.544-1.5440.0000.0000.0000.000
45A47TYR0-0.036-0.03211.417-1.281-1.2810.0000.0000.0000.000
46A48LYS10.8660.9378.269-25.716-25.7160.0000.0000.0000.000
47A49VAL00.0370.0146.189-3.164-3.1640.0000.0000.0000.000
48A50LEU0-0.035-0.0286.1115.6645.6640.0000.0000.0000.000
49A51ILE00.0060.0056.181-4.362-4.3620.0000.0000.0000.000
50A52PRO0-0.026-0.0038.4111.0901.0900.0000.0000.0000.000
51A53GLU-1-0.786-0.88610.04828.37728.3770.0000.0000.0000.000
52A54LEU0-0.023-0.01613.034-1.920-1.9200.0000.0000.0000.000
53A55PRO0-0.0060.00716.581-0.206-0.2060.0000.0000.0000.000
54A56LEU00.011-0.00917.715-1.222-1.2220.0000.0000.0000.000
55A57TYR00.058-0.01021.151-0.820-0.8200.0000.0000.0000.000
56A58SER00.0420.01720.623-0.480-0.4800.0000.0000.0000.000
57A59MET0-0.0250.01522.900-0.385-0.3850.0000.0000.0000.000
58A60SER0-0.026-0.01625.279-0.589-0.5890.0000.0000.0000.000
59A61LEU00.0250.00228.3960.2020.2020.0000.0000.0000.000
60A62LEU0-0.039-0.04930.7410.0480.0480.0000.0000.0000.000
61A63LYS11.0101.03626.965-11.879-11.8790.0000.0000.0000.000
62A64THR00.0050.01825.4880.3760.3760.0000.0000.0000.000
63A65SER0-0.011-0.00326.668-0.358-0.3580.0000.0000.0000.000
64A66VAL00.0940.03424.7340.3770.3770.0000.0000.0000.000
65A67GLY00.0700.03224.7520.3540.3540.0000.0000.0000.000
66A68THR0-0.146-0.08224.198-0.052-0.0520.0000.0000.0000.000
67A69PHE00.0320.02320.6570.2150.2150.0000.0000.0000.000
68A70ALA00.0750.04420.6140.6850.6850.0000.0000.0000.000
69A71ARG10.8930.92921.904-11.299-11.2990.0000.0000.0000.000
70A72TYR0-0.0060.00215.854-0.474-0.4740.0000.0000.0000.000
71A73LEU00.0410.02016.0280.5130.5130.0000.0000.0000.000
72A74LYS10.8140.89818.166-12.964-12.9640.0000.0000.0000.000
73A75GLU-1-0.812-0.88720.35314.45514.4550.0000.0000.0000.000
74A76PHE0-0.030-0.00510.7600.0840.0840.0000.0000.0000.000
75A77VAL00.0200.00216.2290.7240.7240.0000.0000.0000.000
76A78ASP-1-0.799-0.88817.37413.95013.9500.0000.0000.0000.000
77A79PHE0-0.102-0.04313.818-0.291-0.2910.0000.0000.0000.000
78A80LYS10.7890.88010.406-26.951-26.9510.0000.0000.0000.000
79A81GLY0-0.0110.01616.1980.0760.0760.0000.0000.0000.000
80A82TYR0-0.031-0.02411.6780.0290.0290.0000.0000.0000.000
81A83GLU-1-0.910-0.95818.78913.01613.0160.0000.0000.0000.000
82A84ASN0-0.036-0.02120.262-0.241-0.2410.0000.0000.0000.000
83A85VAL0-0.0010.00515.7400.8670.8670.0000.0000.0000.000
84A86ILE00.0300.03415.648-1.011-1.0110.0000.0000.0000.000
85A87LEU0-0.026-0.00315.1771.5271.5270.0000.0000.0000.000
86A88LEU00.0410.03312.604-0.912-0.9120.0000.0000.0000.000
87A89GLY0-0.0040.00415.0431.0591.0590.0000.0000.0000.000
88A90ASN00.0420.02116.314-0.486-0.4860.0000.0000.0000.000
89A91SER0-0.045-0.03318.218-0.291-0.2910.0000.0000.0000.000
90A92LEU0-0.011-0.01420.821-0.516-0.5160.0000.0000.0000.000
91A93GLY00.0630.03517.735-0.424-0.4240.0000.0000.0000.000
92A94GLY00.0490.00918.6970.0460.0460.0000.0000.0000.000
93A95HIS0-0.059-0.00820.627-0.301-0.3010.0000.0000.0000.000
94A96ILE0-0.056-0.03819.695-0.594-0.5940.0000.0000.0000.000
95A97ALA00.0590.02918.718-0.312-0.3120.0000.0000.0000.000
96A98LEU00.0520.03720.605-0.498-0.4980.0000.0000.0000.000
97A99LEU0-0.045-0.01024.205-0.578-0.5780.0000.0000.0000.000
98A100ALA00.010-0.00221.574-0.474-0.4740.0000.0000.0000.000
99A101THR00.0340.01222.428-0.176-0.1760.0000.0000.0000.000
100A102LYS10.7920.88924.673-10.983-10.9830.0000.0000.0000.000
101A103MET0-0.146-0.07826.513-0.382-0.3820.0000.0000.0000.000
102A104PHE0-0.016-0.02324.111-0.348-0.3480.0000.0000.0000.000
103A105PRO00.0390.03024.6890.5190.5190.0000.0000.0000.000
104A106GLU-1-0.919-0.96625.73212.04712.0470.0000.0000.0000.000
105A107ILE0-0.0080.00720.9240.1360.1360.0000.0000.0000.000
106A108VAL0-0.070-0.03820.3210.9640.9640.0000.0000.0000.000
107A109GLN0-0.025-0.01119.853-0.527-0.5270.0000.0000.0000.000
108A110ALA00.0200.00820.239-0.579-0.5790.0000.0000.0000.000
109A111LEU0-0.043-0.01920.0020.8730.8730.0000.0000.0000.000
110A112VAL00.0150.00517.561-0.539-0.5390.0000.0000.0000.000
111A113ILE0-0.006-0.01619.0060.7010.7010.0000.0000.0000.000
112A114THR0-0.029-0.02717.603-0.150-0.1500.0000.0000.0000.000
113A115GLY00.0730.05420.1560.6290.6290.0000.0000.0000.000
114A116SER0-0.040-0.01121.8730.4200.4200.0000.0000.0000.000
115A117SER0-0.035-0.02423.105-0.488-0.4880.0000.0000.0000.000
116A118GLY00.0480.00725.8230.2380.2380.0000.0000.0000.000
117A119LEU0-0.036-0.00528.229-0.454-0.4540.0000.0000.0000.000
118A153LYS10.9570.97620.293-14.016-14.0160.0000.0000.0000.000
119A154GLU-1-0.858-0.96720.02612.92312.9230.0000.0000.0000.000
120A155ILE00.0020.01518.2010.0510.0510.0000.0000.0000.000
121A156VAL0-0.008-0.00720.765-0.285-0.2850.0000.0000.0000.000
122A157ASP-1-0.905-0.95522.38012.43712.4370.0000.0000.0000.000
123A158GLU-1-0.949-0.97318.96715.81215.8120.0000.0000.0000.000
124A159VAL0-0.076-0.04122.2370.1050.1050.0000.0000.0000.000
125A160TYR0-0.009-0.01424.919-0.769-0.7690.0000.0000.0000.000
126A161GLU-1-0.778-0.88122.66112.66012.6600.0000.0000.0000.000
127A162THR0-0.044-0.03925.202-0.156-0.1560.0000.0000.0000.000
128A163VAL0-0.066-0.03227.073-0.374-0.3740.0000.0000.0000.000
129A164SER00.0000.00529.540-0.585-0.5850.0000.0000.0000.000
130A165ASP-1-0.728-0.84726.56511.79811.7980.0000.0000.0000.000
131A166ARG10.8560.94629.187-9.802-9.8020.0000.0000.0000.000
132A167ASN0-0.040-0.03629.204-0.503-0.5030.0000.0000.0000.000
133A168LYS10.8050.91023.020-13.383-13.3830.0000.0000.0000.000
134A169LEU00.0570.03727.8050.2400.2400.0000.0000.0000.000
135A170VAL00.0310.00630.086-0.023-0.0230.0000.0000.0000.000
136A171LYS10.8970.95526.049-12.154-12.1540.0000.0000.0000.000
137A172THR00.0420.02626.0630.3630.3630.0000.0000.0000.000
138A173LEU0-0.010-0.00527.607-0.030-0.0300.0000.0000.0000.000
139A174ALA0-0.058-0.02729.636-0.198-0.1980.0000.0000.0000.000
140A175ILE00.002-0.00223.679-0.158-0.1580.0000.0000.0000.000
141A176ALA00.0390.02427.826-0.041-0.0410.0000.0000.0000.000
142A177LYS10.9720.98929.656-9.162-9.1620.0000.0000.0000.000
143A178SER0-0.039-0.02729.091-0.143-0.1430.0000.0000.0000.000
144A179ALA0-0.014-0.01727.435-0.058-0.0580.0000.0000.0000.000
145A180ILE00.0330.01829.209-0.070-0.0700.0000.0000.0000.000
146A181ARG10.9140.96332.424-9.344-9.3440.0000.0000.0000.000
147A182HIS0-0.089-0.03630.040-0.296-0.2960.0000.0000.0000.000
148A183ASN00.0660.02830.6860.5600.5600.0000.0000.0000.000
149A184MET00.0560.03127.175-0.201-0.2010.0000.0000.0000.000
150A185ALA00.0120.01231.401-0.096-0.0960.0000.0000.0000.000
151A186LYS10.8480.90534.283-9.380-9.3800.0000.0000.0000.000
152A187ASP-1-0.824-0.90431.9269.5999.5990.0000.0000.0000.000
153A188LEU00.0390.01428.8540.0460.0460.0000.0000.0000.000
154A189PRO00.0110.00532.3590.0830.0830.0000.0000.0000.000
155A190LYS10.9090.95534.189-9.082-9.0820.0000.0000.0000.000
156A191MET0-0.0160.02027.038-0.161-0.1610.0000.0000.0000.000
157A192LYS10.9220.93429.771-9.601-9.6010.0000.0000.0000.000
158A193THR00.0180.03425.124-0.119-0.1190.0000.0000.0000.000
159A194PRO00.0720.04824.895-0.065-0.0650.0000.0000.0000.000
160A195THR0-0.046-0.02623.9910.7100.7100.0000.0000.0000.000
161A196CYS0-0.0230.01521.393-0.376-0.3760.0000.0000.0000.000
162A197ILE0-0.015-0.01422.4250.6120.6120.0000.0000.0000.000
163A198ILE00.0610.03619.377-0.465-0.4650.0000.0000.0000.000
164A199TRP0-0.002-0.01122.3370.6320.6320.0000.0000.0000.000
165A200GLY00.0490.03723.928-0.137-0.1370.0000.0000.0000.000
166A201LYS10.8590.92124.759-10.771-10.7710.0000.0000.0000.000
167A202ASN0-0.0070.00427.159-0.509-0.5090.0000.0000.0000.000
168A203ASP-1-0.704-0.84524.89113.19813.1980.0000.0000.0000.000
169A204ASN0-0.019-0.01927.030-0.713-0.7130.0000.0000.0000.000
170A205VAL0-0.026-0.00424.758-0.271-0.2710.0000.0000.0000.000
171A206THR0-0.078-0.04625.367-0.056-0.0560.0000.0000.0000.000
172A207PRO00.0340.03227.4820.3210.3210.0000.0000.0000.000
173A208PRO00.0080.00629.3730.1940.1940.0000.0000.0000.000
174A209GLU-1-0.836-0.93030.3649.6369.6360.0000.0000.0000.000
175A210VAL0-0.016-0.01428.737-0.065-0.0650.0000.0000.0000.000
176A211ALA00.0020.00727.8910.0920.0920.0000.0000.0000.000
177A212GLU-1-0.876-0.95629.1189.5899.5890.0000.0000.0000.000
178A213ASP-1-0.860-0.90532.4829.0539.0530.0000.0000.0000.000
179A214PHE0-0.042-0.03527.094-0.091-0.0910.0000.0000.0000.000
180A215LYS10.8900.94330.513-10.233-10.2330.0000.0000.0000.000
181A216ARG10.7830.87931.634-9.098-9.0980.0000.0000.0000.000
182A217LEU0-0.071-0.03133.258-0.218-0.2180.0000.0000.0000.000
183A218LEU00.0120.01027.635-0.114-0.1140.0000.0000.0000.000
184A219PRO0-0.073-0.01031.531-0.130-0.1300.0000.0000.0000.000
185A220ASP-1-0.815-0.89029.53610.93310.9330.0000.0000.0000.000
186A221ALA00.0210.00827.9980.4680.4680.0000.0000.0000.000
187A222ASP-1-0.780-0.84226.72111.11511.1150.0000.0000.0000.000
188A223LEU0-0.029-0.01726.6520.4500.4500.0000.0000.0000.000
189A224TYR00.0180.01024.498-0.242-0.2420.0000.0000.0000.000
190A225TRP0-0.004-0.02425.3660.2390.2390.0000.0000.0000.000
191A226ILE00.0340.02120.6950.0960.0960.0000.0000.0000.000
192A227ASP-1-0.817-0.90524.85010.64210.6420.0000.0000.0000.000
193A228LYS10.8450.91125.830-10.262-10.2620.0000.0000.0000.000
194A229CYS0-0.0330.02421.8960.7910.7910.0000.0000.0000.000
195A230GLY00.003-0.00223.011-0.539-0.5390.0000.0000.0000.000
196A231HIS10.7320.84221.329-14.165-14.1650.0000.0000.0000.000
197A232ALA00.0270.00416.8510.4870.4870.0000.0000.0000.000
198A233ALA00.0760.02917.9950.4210.4210.0000.0000.0000.000
199A234MET0-0.041-0.00913.2580.1630.1630.0000.0000.0000.000
200A235MET00.0010.00613.8271.3801.3800.0000.0000.0000.000
201A236GLU-1-0.875-0.93714.93114.56614.5660.0000.0000.0000.000
202A237HIS10.8210.88117.841-15.117-15.1170.0000.0000.0000.000
203A238PRO00.0560.03313.144-0.141-0.1410.0000.0000.0000.000
204A239GLU-1-0.955-0.97815.04616.35316.3530.0000.0000.0000.000
205A240GLU-1-0.826-0.91317.30614.02314.0230.0000.0000.0000.000
206A241PHE0-0.014-0.00514.812-0.307-0.3070.0000.0000.0000.000
207A242ASN00.020-0.01111.9380.3890.3890.0000.0000.0000.000
208A243GLN0-0.0060.00915.824-0.166-0.1660.0000.0000.0000.000
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210A245LEU00.0050.00515.335-0.382-0.3820.0000.0000.0000.000
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