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: 6Y91Z

Calculation Name: 4RFA-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: 4RFA

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8Y902

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2611710.619591
FMO2-HF: Nuclear repulsion 2524492.871163
FMO2-HF: Total energy -87217.748428
FMO2-MP2: Total energy -87473.991158


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:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
129.241129.38311.022-5.597-5.567-0.046
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.820 / q_NPA : -0.905
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].
3A5LEU00.0440.0263.733-8.558-6.840-0.006-0.759-0.9540.002
4A6ASP-1-0.851-0.9251.85926.05623.05310.940-4.313-3.624-0.048
5A7THR0-0.003-0.0143.948-3.384-2.7970.000-0.250-0.3360.001
6A8VAL0-0.036-0.0106.006-3.462-3.4620.0000.0000.0000.000
7A9LEU0-0.037-0.0296.813-2.577-2.5770.0000.0000.0000.000
8A10GLY0-0.021-0.0038.389-1.677-1.6770.0000.0000.0000.000
9A11TYR00.0550.00910.014-0.945-0.9450.0000.0000.0000.000
10A12LEU0-0.064-0.03411.774-1.471-1.4710.0000.0000.0000.000
11A13LYS10.8980.94511.331-19.616-19.6160.0000.0000.0000.000
12A14GLU-1-0.923-0.94214.58016.65916.6590.0000.0000.0000.000
13A15PHE0-0.013-0.00315.977-1.004-1.0040.0000.0000.0000.000
14A16PRO00.006-0.01419.5920.0070.0070.0000.0000.0000.000
15A17ASP-1-0.792-0.88222.35510.86610.8660.0000.0000.0000.000
16A18TYR0-0.0030.01213.7550.0040.0040.0000.0000.0000.000
17A19TYR00.009-0.02118.6550.2490.2490.0000.0000.0000.000
18A20LYS10.7690.89620.814-10.985-10.9850.0000.0000.0000.000
19A21TYR0-0.010-0.00919.850-0.444-0.4440.0000.0000.0000.000
20A22VAL00.0010.01714.4680.5160.5160.0000.0000.0000.000
21A23THR0-0.022-0.00817.283-0.654-0.6540.0000.0000.0000.000
22A24LYS10.8860.93213.660-14.488-14.4880.0000.0000.0000.000
23A25LYS10.8180.92016.419-12.686-12.6860.0000.0000.0000.000
24A26THR00.0130.01016.4670.6570.6570.0000.0000.0000.000
25A27TYR0-0.033-0.03518.031-0.623-0.6230.0000.0000.0000.000
26A28THR00.005-0.01219.4840.3460.3460.0000.0000.0000.000
27A29LEU00.0450.02322.025-0.076-0.0760.0000.0000.0000.000
28A30ASN0-0.056-0.03823.611-0.292-0.2920.0000.0000.0000.000
29A31GLU-1-0.802-0.87623.01411.19311.1930.0000.0000.0000.000
30A32LYS10.8170.89623.682-10.086-10.0860.0000.0000.0000.000
31A33ILE0-0.010-0.00118.059-0.061-0.0610.0000.0000.0000.000
32A34ILE0-0.056-0.03822.315-0.242-0.2420.0000.0000.0000.000
33A35PHE00.0180.01119.6250.1780.1780.0000.0000.0000.000
34A36GLU-1-0.828-0.90424.14510.78410.7840.0000.0000.0000.000
35A37ASP-1-0.909-0.92626.6479.6989.6980.0000.0000.0000.000
36A38GLU-1-0.875-0.92825.29710.36610.3660.0000.0000.0000.000
37A39LYS10.9090.93328.530-8.112-8.1120.0000.0000.0000.000
38A40ALA00.0280.02926.2120.0210.0210.0000.0000.0000.000
39A41LYS10.9170.96924.457-10.085-10.0850.0000.0000.0000.000
40A42SER00.0330.00219.9560.2010.2010.0000.0000.0000.000
41A43ILE0-0.031-0.00515.306-0.157-0.1570.0000.0000.0000.000
42A44PHE0-0.005-0.01515.701-0.041-0.0410.0000.0000.0000.000
43A45PHE00.0510.0149.8170.1570.1570.0000.0000.0000.000
44A46ILE0-0.0250.00011.082-0.583-0.5830.0000.0000.0000.000
45A47VAL0-0.024-0.0227.1681.7441.7440.0000.0000.0000.000
46A48GLU-1-0.846-0.9118.17219.01619.0160.0000.0000.0000.000
47A49GLY00.0220.00810.909-1.122-1.1220.0000.0000.0000.000
48A50TYR00.0530.00912.2520.6930.6930.0000.0000.0000.000
49A51ALA0-0.011-0.00416.001-0.928-0.9280.0000.0000.0000.000
50A52ALA00.0020.00418.9300.4530.4530.0000.0000.0000.000
51A53VAL00.0060.01020.802-0.491-0.4910.0000.0000.0000.000
52A54GLU-1-0.814-0.88323.38710.21510.2150.0000.0000.0000.000
53A55LEU0-0.005-0.00927.064-0.075-0.0750.0000.0000.0000.000
54A56GLU-1-0.877-0.90229.7529.4659.4650.0000.0000.0000.000
55A57ASP-1-0.845-0.92732.5087.9757.9750.0000.0000.0000.000
56A58ASN0-0.026-0.02835.8680.0280.0280.0000.0000.0000.000
57A59LEU0-0.0230.00638.565-0.208-0.2080.0000.0000.0000.000
58A60ARG10.8210.91834.639-8.740-8.7400.0000.0000.0000.000
59A61LYS10.9540.97737.249-7.828-7.8280.0000.0000.0000.000
60A62THR0-0.008-0.01532.7270.0470.0470.0000.0000.0000.000
61A63ASN00.0450.03430.374-0.306-0.3060.0000.0000.0000.000
62A64TYR00.0040.01130.4930.1180.1180.0000.0000.0000.000
63A65ILE0-0.022-0.01223.741-0.010-0.0100.0000.0000.0000.000
64A66SER0-0.017-0.02625.515-0.045-0.0450.0000.0000.0000.000
65A67ILE00.0410.02619.451-0.001-0.0010.0000.0000.0000.000
66A68PHE00.0280.02018.185-0.528-0.5280.0000.0000.0000.000
67A69VAL0-0.022-0.00614.6470.3170.3170.0000.0000.0000.000
68A70LEU00.0270.01412.061-0.600-0.6000.0000.0000.0000.000
69A71PRO00.023-0.0028.180-0.164-0.1640.0000.0000.0000.000
70A72TYR00.001-0.0082.8822.2633.1030.088-0.275-0.653-0.001
71A73ASN0-0.0230.0037.894-1.866-1.8660.0000.0000.0000.000
72A74VAL00.0330.02011.670-0.450-0.4500.0000.0000.0000.000
73A75LEU0-0.019-0.01513.892-0.755-0.7550.0000.0000.0000.000
74A76GLY00.0440.02317.1580.0960.0960.0000.0000.0000.000
75A77ILE00.0400.01517.800-0.600-0.6000.0000.0000.0000.000
76A78ASP-1-0.865-0.93421.01812.43912.4390.0000.0000.0000.000
77A79ALA0-0.071-0.02123.852-0.587-0.5870.0000.0000.0000.000
78A80PHE0-0.018-0.01622.067-0.429-0.4290.0000.0000.0000.000
79A81SER0-0.0230.00126.138-0.276-0.2760.0000.0000.0000.000
80A82SER0-0.002-0.00628.014-0.148-0.1480.0000.0000.0000.000
81A83TYR0-0.026-0.01630.518-0.462-0.4620.0000.0000.0000.000
82A84PRO0-0.0130.00031.3130.1010.1010.0000.0000.0000.000
83A85LYS10.9220.92428.665-9.538-9.5380.0000.0000.0000.000
84A86LYS10.8990.94931.141-8.510-8.5100.0000.0000.0000.000
85A87LYS10.9860.98131.255-8.292-8.2920.0000.0000.0000.000
86A88HIS00.0330.03926.4920.0710.0710.0000.0000.0000.000
87A89SER0-0.055-0.03926.319-0.070-0.0700.0000.0000.0000.000
88A90ILE00.0550.02420.0590.1950.1950.0000.0000.0000.000
89A91THR0-0.022-0.01623.302-0.290-0.2900.0000.0000.0000.000
90A92VAL00.0270.01719.0380.4870.4870.0000.0000.0000.000
91A93MET0-0.058-0.03619.863-0.733-0.7330.0000.0000.0000.000
92A94SER0-0.026-0.02117.3070.0730.0730.0000.0000.0000.000
93A95GLU-1-0.906-0.96719.73911.51611.5160.0000.0000.0000.000
94A96SER0-0.031-0.02015.936-0.512-0.5120.0000.0000.0000.000
95A97LEU00.0080.02614.7020.3980.3980.0000.0000.0000.000
96A98MET0-0.0010.02911.561-1.431-1.4310.0000.0000.0000.000
97A99LEU00.0080.01612.3801.1151.1150.0000.0000.0000.000
98A100TYR00.016-0.00510.013-1.137-1.1370.0000.0000.0000.000
99A101LYS10.7900.88113.982-11.411-11.4110.0000.0000.0000.000
100A102ILE00.000-0.01112.629-0.093-0.0930.0000.0000.0000.000
101A103ASP-1-0.841-0.92317.33911.75211.7520.0000.0000.0000.000
102A104ALA00.0330.00419.5830.5560.5560.0000.0000.0000.000
103A105ASP-1-0.895-0.93320.91011.50211.5020.0000.0000.0000.000
104A106PHE0-0.032-0.01516.6780.2490.2490.0000.0000.0000.000
105A107LEU0-0.005-0.01214.1850.4240.4240.0000.0000.0000.000
106A108LEU0-0.009-0.02317.9410.5570.5570.0000.0000.0000.000
107A109ASN0-0.071-0.04020.452-0.229-0.2290.0000.0000.0000.000
108A110ILE0-0.022-0.00815.2860.1350.1350.0000.0000.0000.000
109A111LEU0-0.074-0.01916.0810.8820.8820.0000.0000.0000.000
110A112SER00.005-0.00916.9350.7780.7780.0000.0000.0000.000
111A113ILE0-0.057-0.01118.664-0.200-0.2000.0000.0000.0000.000
112A114LYS10.8100.89611.008-22.875-22.8750.0000.0000.0000.000
113A115PRO00.0160.00412.6990.1120.1120.0000.0000.0000.000
114A116ASP-1-0.813-0.8939.19529.83529.8350.0000.0000.0000.000
115A117VAL00.0340.03211.288-0.643-0.6430.0000.0000.0000.000
116A118ASN00.027-0.01113.955-0.359-0.3590.0000.0000.0000.000
117A119ASP-1-0.861-0.92611.61022.32122.3210.0000.0000.0000.000
118A120PHE00.0330.0336.6650.3480.3480.0000.0000.0000.000
119A121LEU0-0.0260.00710.1050.1260.1260.0000.0000.0000.000
120A122LEU0-0.014-0.01813.122-0.792-0.7920.0000.0000.0000.000
121A123THR0-0.002-0.01210.251-0.873-0.8730.0000.0000.0000.000
122A124SER00.004-0.01210.258-0.042-0.0420.0000.0000.0000.000
123A125ILE0-0.071-0.03312.241-1.163-1.1630.0000.0000.0000.000
124A126ALA00.0020.00615.452-0.985-0.9850.0000.0000.0000.000
125A127ASP-1-0.839-0.92411.85925.50225.5020.0000.0000.0000.000
126A128VAL0-0.067-0.03314.859-1.021-1.0210.0000.0000.0000.000
127A129PHE0-0.011-0.01917.095-1.010-1.0100.0000.0000.0000.000
128A130ALA00.0190.01617.780-0.895-0.8950.0000.0000.0000.000
129A131ARG10.8100.87415.655-18.673-18.6730.0000.0000.0000.000
130A132HIS0-0.044-0.02019.869-1.155-1.1550.0000.0000.0000.000
131A133TYR0-0.022-0.02222.854-0.710-0.7100.0000.0000.0000.000
132A134ALA00.0420.02922.190-0.586-0.5860.0000.0000.0000.000
133A135LEU0-0.038-0.02922.332-0.629-0.6290.0000.0000.0000.000
134A136LEU0-0.052-0.02625.604-0.637-0.6370.0000.0000.0000.000
135A137GLY00.0300.02627.552-0.495-0.4950.0000.0000.0000.000
136A138MET0-0.041-0.02226.274-0.460-0.4600.0000.0000.0000.000
137A139ILE0-0.032-0.02030.699-0.452-0.4520.0000.0000.0000.000
138A140ALA0-0.063-0.03833.549-0.044-0.0440.0000.0000.0000.000
139A141LYS10.8750.96632.313-9.992-9.9920.0000.0000.0000.000
140A142THR0-0.016-0.03935.450-0.072-0.0720.0000.0000.0000.000
141A143PRO0-0.031-0.03534.8680.2600.2600.0000.0000.0000.000
142A144LYS10.8010.88533.930-8.631-8.6310.0000.0000.0000.000
143A145GLU-1-0.731-0.82932.7479.4679.4670.0000.0000.0000.000
144A146ARG10.8010.88530.564-9.112-9.1120.0000.0000.0000.000
145A147ILE0-0.012-0.01729.1880.3940.3940.0000.0000.0000.000
146A148TYR00.008-0.01328.3770.4250.4250.0000.0000.0000.000
147A149MET00.0440.01926.3780.2220.2220.0000.0000.0000.000
148A150ALA0-0.058-0.02424.9550.5660.5660.0000.0000.0000.000
149A151LEU00.000-0.01823.5790.6240.6240.0000.0000.0000.000
150A152GLU-1-0.886-0.93022.42613.84813.8480.0000.0000.0000.000
151A153ASN00.007-0.00720.6261.0521.0520.0000.0000.0000.000
152A154LEU0-0.074-0.04519.0420.9560.9560.0000.0000.0000.000
153A155ALA00.0460.01118.1730.8900.8900.0000.0000.0000.000
154A156VAL00.0150.01915.3041.0231.0230.0000.0000.0000.000
155A157GLU-1-0.859-0.91914.39718.16318.1630.0000.0000.0000.000
156A158MET0-0.107-0.06913.6720.8200.8200.0000.0000.0000.000
157A159GLY00.0150.02815.270-0.476-0.4760.0000.0000.0000.000
158A160THR0-0.080-0.03813.4581.4131.4130.0000.0000.0000.000
159A161GLU-1-0.804-0.88614.60717.23817.2380.0000.0000.0000.000
160A162ASP-1-0.823-0.90316.12714.76014.7600.0000.0000.0000.000
161A163GLU-1-0.927-0.95016.66818.38318.3830.0000.0000.0000.000
162A164GLU-1-0.969-0.97919.26712.60412.6040.0000.0000.0000.000
163A165ARG10.7690.86522.004-13.756-13.7560.0000.0000.0000.000
164A166ASN0-0.026-0.01422.3330.0330.0330.0000.0000.0000.000
165A167GLU-1-0.821-0.89721.65712.22412.2240.0000.0000.0000.000
166A168ILE00.0180.00917.3400.9770.9770.0000.0000.0000.000
167A169VAL0-0.034-0.00918.948-0.979-0.9790.0000.0000.0000.000
168A170LEU00.0040.00818.5840.9640.9640.0000.0000.0000.000
169A171PRO00.0250.00416.620-0.664-0.6640.0000.0000.0000.000
170A172ASN0-0.001-0.01419.331-0.764-0.7640.0000.0000.0000.000
171A173PHE00.0020.01017.489-0.702-0.7020.0000.0000.0000.000
172A174ILE0-0.0050.00220.707-0.658-0.6580.0000.0000.0000.000
173A175ASN00.0310.00323.749-0.573-0.5730.0000.0000.0000.000
174A176GLN00.0930.03327.474-0.033-0.0330.0000.0000.0000.000
175A177SER0-0.055-0.02530.194-0.187-0.1870.0000.0000.0000.000
176A178VAL00.0170.00524.016-0.161-0.1610.0000.0000.0000.000
177A179LEU00.0770.04426.2540.0950.0950.0000.0000.0000.000
178A180ALA00.0090.00527.907-0.059-0.0590.0000.0000.0000.000
179A181ARG10.7870.87027.640-10.556-10.5560.0000.0000.0000.000
180A182TYR00.0390.04321.769-0.332-0.3320.0000.0000.0000.000
181A183CYS00.0280.03227.2810.0790.0790.0000.0000.0000.000
182A184ARG10.8110.90826.229-11.680-11.6800.0000.0000.0000.000
183A185THR00.0160.02032.259-0.397-0.3970.0000.0000.0000.000
184A186THR0-0.003-0.00634.6990.0590.0590.0000.0000.0000.000
185A187GLN00.0680.03133.6690.1110.1110.0000.0000.0000.000
186A188PRO00.001-0.00335.8580.0850.0850.0000.0000.0000.000
187A189ASN0-0.008-0.00337.133-0.113-0.1130.0000.0000.0000.000
188A190ILE00.0500.02531.5860.0100.0100.0000.0000.0000.000
189A191SER0-0.007-0.01434.6910.0500.0500.0000.0000.0000.000
190A192ASN0-0.046-0.02836.413-0.027-0.0270.0000.0000.0000.000
191A193LEU00.0350.02634.7840.0260.0260.0000.0000.0000.000
192A194LEU0-0.013-0.01630.1420.1180.1180.0000.0000.0000.000
193A195THR0-0.066-0.02633.9320.1010.1010.0000.0000.0000.000
194A196GLU-1-0.778-0.87736.4808.4738.4730.0000.0000.0000.000
195A197LEU00.005-0.00429.7050.0490.0490.0000.0000.0000.000
196A198VAL0-0.037-0.00131.9480.2440.2440.0000.0000.0000.000
197A199GLU-1-0.984-0.99333.6368.0488.0480.0000.0000.0000.000
198A200GLU-1-0.838-0.89333.9809.1079.1070.0000.0000.0000.000
199A201GLU-1-0.955-0.96632.0109.5489.5480.0000.0000.0000.000
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