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: 76L1K

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2607511.407279
FMO2-HF: Nuclear repulsion 2520295.790091
FMO2-HF: Total energy -87215.617189
FMO2-MP2: Total energy -87471.862585


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.
132.084137.9890.584-2.862-3.627-0.015
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 : -0.889 / q_NPA : -0.948
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].
3A5LEU00.0400.0173.793-8.652-6.444-0.018-1.009-1.1820.004
4A6ASP-1-0.888-0.9442.72826.64629.7070.603-1.687-1.976-0.019
5A7THR0-0.006-0.0114.355-2.775-2.383-0.001-0.142-0.2490.000
6A8VAL0-0.0190.0056.395-3.536-3.5360.0000.0000.0000.000
7A9LEU0-0.035-0.0186.835-2.626-2.6260.0000.0000.0000.000
8A10GLY0-0.027-0.0218.573-1.888-1.8880.0000.0000.0000.000
9A11TYR00.0530.00510.208-1.471-1.4710.0000.0000.0000.000
10A12LEU0-0.071-0.02812.090-1.536-1.5360.0000.0000.0000.000
11A13LYS10.9090.94411.890-20.001-20.0010.0000.0000.0000.000
12A14GLU-1-0.931-0.94414.65416.83516.8350.0000.0000.0000.000
13A15PHE0-0.030-0.01316.946-0.901-0.9010.0000.0000.0000.000
14A16PRO00.016-0.00519.7320.0410.0410.0000.0000.0000.000
15A17ASP-1-0.934-0.96022.58610.92210.9220.0000.0000.0000.000
16A18TYR00.0120.00913.397-0.046-0.0460.0000.0000.0000.000
17A19TYR00.000-0.02818.3230.2750.2750.0000.0000.0000.000
18A20LYS10.8890.96820.655-10.603-10.6030.0000.0000.0000.000
19A21TYR00.0240.00720.012-0.475-0.4750.0000.0000.0000.000
20A22VAL0-0.0040.02314.4360.4380.4380.0000.0000.0000.000
21A23THR0-0.019-0.00217.336-0.457-0.4570.0000.0000.0000.000
22A24LYS10.9250.97914.074-14.604-14.6040.0000.0000.0000.000
23A25LYS10.9430.96516.367-12.344-12.3440.0000.0000.0000.000
24A26THR0-0.023-0.01616.1410.6950.6950.0000.0000.0000.000
25A27TYR0-0.040-0.01318.193-0.731-0.7310.0000.0000.0000.000
26A28THR0-0.020-0.04319.5670.3610.3610.0000.0000.0000.000
27A29LEU00.0640.02522.060-0.232-0.2320.0000.0000.0000.000
28A30ASN0-0.052-0.04523.491-0.267-0.2670.0000.0000.0000.000
29A31GLU-1-0.874-0.88723.25411.09011.0900.0000.0000.0000.000
30A32LYS10.8840.93723.956-9.698-9.6980.0000.0000.0000.000
31A33ILE00.0180.01518.505-0.029-0.0290.0000.0000.0000.000
32A34ILE0-0.036-0.02722.652-0.192-0.1920.0000.0000.0000.000
33A35PHE0-0.015-0.01520.2500.1300.1300.0000.0000.0000.000
34A36GLU-1-0.902-0.94624.63110.01210.0120.0000.0000.0000.000
35A37ASP-1-1.026-0.99626.7819.2719.2710.0000.0000.0000.000
36A38GLU-1-0.885-0.95426.4949.9879.9870.0000.0000.0000.000
37A39LYS10.9010.93529.269-8.040-8.0400.0000.0000.0000.000
38A40ALA00.0280.02326.5080.0510.0510.0000.0000.0000.000
39A41LYS10.9650.99324.912-9.812-9.8120.0000.0000.0000.000
40A42SER00.013-0.01819.8180.1330.1330.0000.0000.0000.000
41A43ILE0-0.0120.01715.511-0.198-0.1980.0000.0000.0000.000
42A44PHE0-0.036-0.02415.8290.0130.0130.0000.0000.0000.000
43A45PHE00.0710.03110.1520.1400.1400.0000.0000.0000.000
44A46ILE0-0.0170.00111.425-0.440-0.4400.0000.0000.0000.000
45A47VAL0-0.001-0.0047.6221.6101.6100.0000.0000.0000.000
46A48GLU-1-0.917-0.9578.02621.05521.0550.0000.0000.0000.000
47A49GLY00.0460.01710.619-1.376-1.3760.0000.0000.0000.000
48A50TYR00.0300.00512.6030.6540.6540.0000.0000.0000.000
49A51ALA0-0.001-0.00616.139-0.801-0.8010.0000.0000.0000.000
50A52ALA0-0.018-0.00719.0370.3640.3640.0000.0000.0000.000
51A53VAL00.0140.01821.211-0.394-0.3940.0000.0000.0000.000
52A54GLU-1-0.858-0.95423.76810.09110.0910.0000.0000.0000.000
53A55LEU0-0.005-0.00427.515-0.067-0.0670.0000.0000.0000.000
54A56GLU-1-0.926-0.96230.5279.0849.0840.0000.0000.0000.000
55A57ASP-1-0.857-0.93732.9817.7517.7510.0000.0000.0000.000
56A58ASN00.008-0.00736.3910.1070.1070.0000.0000.0000.000
57A59LEU0-0.0280.00238.752-0.175-0.1750.0000.0000.0000.000
58A60ARG10.8190.91934.582-8.556-8.5560.0000.0000.0000.000
59A61LYS10.9540.99036.855-7.924-7.9240.0000.0000.0000.000
60A62THR0-0.012-0.02432.7510.1020.1020.0000.0000.0000.000
61A63ASN00.0520.04830.963-0.315-0.3150.0000.0000.0000.000
62A64TYR0-0.024-0.00230.6790.1450.1450.0000.0000.0000.000
63A65ILE00.0040.00724.064-0.041-0.0410.0000.0000.0000.000
64A66SER0-0.054-0.05025.636-0.104-0.1040.0000.0000.0000.000
65A67ILE00.0360.01020.0430.0340.0340.0000.0000.0000.000
66A68PHE00.0380.02118.345-0.435-0.4350.0000.0000.0000.000
67A69VAL0-0.0240.01715.1100.2660.2660.0000.0000.0000.000
68A70LEU00.044-0.00312.505-0.391-0.3910.0000.0000.0000.000
69A71PRO00.003-0.0058.627-0.311-0.3110.0000.0000.0000.000
70A72TYR00.022-0.0103.9142.1282.3720.000-0.024-0.2200.000
71A73ASN0-0.0170.0218.512-1.568-1.5680.0000.0000.0000.000
72A74VAL00.0330.01812.230-0.090-0.0900.0000.0000.0000.000
73A75LEU00.003-0.01214.216-0.721-0.7210.0000.0000.0000.000
74A76GLY00.0210.01017.466-0.024-0.0240.0000.0000.0000.000
75A77ILE00.0480.01517.912-0.398-0.3980.0000.0000.0000.000
76A78ASP-1-0.878-0.94021.45511.58511.5850.0000.0000.0000.000
77A79ALA0-0.088-0.03824.092-0.500-0.5000.0000.0000.0000.000
78A80PHE0-0.036-0.02822.310-0.380-0.3800.0000.0000.0000.000
79A81SER0-0.051-0.00826.621-0.276-0.2760.0000.0000.0000.000
80A82SER00.004-0.00528.708-0.102-0.1020.0000.0000.0000.000
81A83TYR0-0.0090.01231.503-0.324-0.3240.0000.0000.0000.000
82A84PRO00.0090.00132.4700.0450.0450.0000.0000.0000.000
83A85LYS10.9990.97928.893-9.349-9.3490.0000.0000.0000.000
84A86LYS10.9330.95931.179-8.359-8.3590.0000.0000.0000.000
85A87LYS10.9630.98231.290-8.075-8.0750.0000.0000.0000.000
86A88HIS00.0260.03326.7880.0290.0290.0000.0000.0000.000
87A89SER0-0.047-0.01626.8560.0480.0480.0000.0000.0000.000
88A90ILE00.0380.01720.5860.1680.1680.0000.0000.0000.000
89A91THR00.0020.00923.458-0.186-0.1860.0000.0000.0000.000
90A92VAL00.0150.02119.0810.4850.4850.0000.0000.0000.000
91A93MET0-0.049-0.02520.011-0.687-0.6870.0000.0000.0000.000
92A94SER0-0.0150.00117.102-0.098-0.0980.0000.0000.0000.000
93A95GLU-1-0.916-0.96219.48411.64111.6410.0000.0000.0000.000
94A96SER0-0.003-0.01816.503-0.441-0.4410.0000.0000.0000.000
95A97LEU00.0110.02714.5800.5470.5470.0000.0000.0000.000
96A98MET00.0000.01411.516-1.498-1.4980.0000.0000.0000.000
97A99LEU0-0.0100.00312.4710.9740.9740.0000.0000.0000.000
98A100TYR00.009-0.00910.209-1.071-1.0710.0000.0000.0000.000
99A101LYS10.8900.94913.974-11.535-11.5350.0000.0000.0000.000
100A102ILE00.014-0.01112.830-0.080-0.0800.0000.0000.0000.000
101A103ASP-1-0.882-0.93517.38311.55511.5550.0000.0000.0000.000
102A104ALA00.0500.00619.8030.4750.4750.0000.0000.0000.000
103A105ASP-1-0.896-0.93521.09111.04911.0490.0000.0000.0000.000
104A106PHE0-0.037-0.02817.0390.2170.2170.0000.0000.0000.000
105A107LEU00.006-0.00614.6750.3440.3440.0000.0000.0000.000
106A108LEU0-0.040-0.04618.2600.4970.4970.0000.0000.0000.000
107A109ASN0-0.0180.00220.859-0.363-0.3630.0000.0000.0000.000
108A110ILE0-0.083-0.02716.2120.0240.0240.0000.0000.0000.000
109A111LEU0-0.051-0.01616.2430.9280.9280.0000.0000.0000.000
110A112SER00.009-0.01217.5700.5760.5760.0000.0000.0000.000
111A113ILE0-0.031-0.01018.6390.1740.1740.0000.0000.0000.000
112A114LYS10.8520.96710.885-22.061-22.0610.0000.0000.0000.000
113A115PRO00.007-0.00913.8210.1330.1330.0000.0000.0000.000
114A116ASP-1-0.860-0.9379.11428.31128.3110.0000.0000.0000.000
115A117VAL00.0690.04011.670-0.114-0.1140.0000.0000.0000.000
116A118ASN00.0150.01514.256-0.131-0.1310.0000.0000.0000.000
117A119ASP-1-0.863-0.94411.96720.28320.2830.0000.0000.0000.000
118A120PHE0-0.0030.0056.9110.0090.0090.0000.0000.0000.000
119A121LEU00.0050.03010.9120.1600.1600.0000.0000.0000.000
120A122LEU0-0.008-0.01613.994-0.541-0.5410.0000.0000.0000.000
121A123THR0-0.001-0.00610.237-0.623-0.6230.0000.0000.0000.000
122A124SER0-0.001-0.03411.4060.4100.4100.0000.0000.0000.000
123A125ILE0-0.089-0.03812.767-0.763-0.7630.0000.0000.0000.000
124A126ALA0-0.0080.00215.330-0.700-0.7000.0000.0000.0000.000
125A127ASP-1-0.835-0.92511.85322.70022.7000.0000.0000.0000.000
126A128VAL0-0.087-0.04415.424-0.657-0.6570.0000.0000.0000.000
127A129PHE0-0.011-0.01617.483-0.860-0.8600.0000.0000.0000.000
128A130ALA00.0170.02217.906-0.780-0.7800.0000.0000.0000.000
129A131ARG10.8580.89815.661-17.810-17.8100.0000.0000.0000.000
130A132HIS0-0.043-0.02419.995-0.845-0.8450.0000.0000.0000.000
131A133TYR0-0.023-0.02323.008-0.660-0.6600.0000.0000.0000.000
132A134ALA00.0470.03622.388-0.494-0.4940.0000.0000.0000.000
133A135LEU0-0.024-0.01722.807-0.592-0.5920.0000.0000.0000.000
134A136LEU0-0.043-0.02125.855-0.575-0.5750.0000.0000.0000.000
135A137GLY00.0230.02627.906-0.467-0.4670.0000.0000.0000.000
136A138MET0-0.072-0.03626.328-0.357-0.3570.0000.0000.0000.000
137A139ILE0-0.064-0.03730.775-0.395-0.3950.0000.0000.0000.000
138A140ALA0-0.049-0.02433.700-0.048-0.0480.0000.0000.0000.000
139A141LYS10.9761.02332.508-9.612-9.6120.0000.0000.0000.000
140A142THR0-0.033-0.03835.883-0.054-0.0540.0000.0000.0000.000
141A143PRO0-0.032-0.03634.9080.2230.2230.0000.0000.0000.000
142A144LYS10.8550.93233.831-8.454-8.4540.0000.0000.0000.000
143A145GLU-1-0.800-0.90133.2069.0769.0760.0000.0000.0000.000
144A146ARG10.8150.89130.782-8.882-8.8820.0000.0000.0000.000
145A147ILE0-0.001-0.00529.1860.3960.3960.0000.0000.0000.000
146A148TYR0-0.029-0.07628.1800.3820.3820.0000.0000.0000.000
147A149MET00.0240.02426.6190.2080.2080.0000.0000.0000.000
148A150ALA0-0.039-0.03224.9330.5030.5030.0000.0000.0000.000
149A151LEU0-0.024-0.01923.5110.5950.5950.0000.0000.0000.000
150A152GLU-1-0.854-0.92622.36513.76013.7600.0000.0000.0000.000
151A153ASN0-0.020-0.00620.6970.8260.8260.0000.0000.0000.000
152A154LEU0-0.064-0.05018.9780.7750.7750.0000.0000.0000.000
153A155ALA00.0170.01417.8550.9360.9360.0000.0000.0000.000
154A156VAL00.0040.00915.7731.1211.1210.0000.0000.0000.000
155A157GLU-1-0.920-0.96314.53617.57017.5700.0000.0000.0000.000
156A158MET0-0.082-0.04113.4470.8210.8210.0000.0000.0000.000
157A159GLY0-0.0280.00115.141-0.259-0.2590.0000.0000.0000.000
158A160THR0-0.066-0.04912.7561.2191.2190.0000.0000.0000.000
159A161GLU-1-0.913-0.96714.57218.28918.2890.0000.0000.0000.000
160A162ASP-1-0.943-0.96716.14515.14415.1440.0000.0000.0000.000
161A163GLU-1-0.906-0.94916.40718.44618.4460.0000.0000.0000.000
162A164GLU-1-0.936-0.96719.53113.50013.5000.0000.0000.0000.000
163A165ARG10.7700.88221.747-13.675-13.6750.0000.0000.0000.000
164A166ASN00.0060.00321.9140.2670.2670.0000.0000.0000.000
165A167GLU-1-0.810-0.88221.38212.22812.2280.0000.0000.0000.000
166A168ILE00.0130.01117.7651.0021.0020.0000.0000.0000.000
167A169VAL0-0.0080.00118.839-0.987-0.9870.0000.0000.0000.000
168A170LEU0-0.0090.00818.3100.9240.9240.0000.0000.0000.000
169A171PRO00.0240.00416.553-0.520-0.5200.0000.0000.0000.000
170A172ASN00.014-0.00819.155-0.697-0.6970.0000.0000.0000.000
171A173PHE0-0.050-0.02717.384-0.669-0.6690.0000.0000.0000.000
172A174ILE00.0150.02220.809-0.604-0.6040.0000.0000.0000.000
173A175ASN00.0610.03023.687-0.202-0.2020.0000.0000.0000.000
174A176GLN00.0660.01727.3440.0660.0660.0000.0000.0000.000
175A177SER0-0.060-0.03530.474-0.149-0.1490.0000.0000.0000.000
176A178VAL00.0410.01824.250-0.178-0.1780.0000.0000.0000.000
177A179LEU00.0520.03926.0480.0080.0080.0000.0000.0000.000
178A180ALA00.012-0.00627.857-0.069-0.0690.0000.0000.0000.000
179A181ARG10.8250.89727.942-10.428-10.4280.0000.0000.0000.000
180A182TYR00.0370.02822.290-0.254-0.2540.0000.0000.0000.000
181A183CYS00.0110.02327.4790.0550.0550.0000.0000.0000.000
182A184ARG10.8560.95326.849-11.082-11.0820.0000.0000.0000.000
183A185THR00.0220.02132.588-0.369-0.3690.0000.0000.0000.000
184A186THR00.0000.00934.7220.1050.1050.0000.0000.0000.000
185A187GLN00.0780.01434.0260.1630.1630.0000.0000.0000.000
186A188PRO0-0.021-0.01636.1220.0920.0920.0000.0000.0000.000
187A189ASN00.001-0.00237.456-0.120-0.1200.0000.0000.0000.000
188A190ILE00.0560.03831.3980.0130.0130.0000.0000.0000.000
189A191SER0-0.018-0.00534.6170.1420.1420.0000.0000.0000.000
190A192ASN0-0.019-0.02636.2930.0330.0330.0000.0000.0000.000
191A193LEU00.0250.01934.6370.0090.0090.0000.0000.0000.000
192A194LEU0-0.004-0.00230.1420.1270.1270.0000.0000.0000.000
193A195THR0-0.042-0.01933.7210.1840.1840.0000.0000.0000.000
194A196GLU-1-0.839-0.91736.6638.2588.2580.0000.0000.0000.000
195A197LEU00.0110.00629.8590.0320.0320.0000.0000.0000.000
196A198VAL0-0.051-0.00232.6900.1780.1780.0000.0000.0000.000
197A199GLU-1-0.974-0.99333.8547.9757.9750.0000.0000.0000.000
198A200GLU-1-0.820-0.85234.3768.9438.9430.0000.0000.0000.000
199A201GLU-1-0.950-0.96432.1199.4549.4540.0000.0000.0000.000
200A202PHE00.0320.02825.8820.3620.3620.0000.0000.0000.000
201A203LEU0-0.061-0.04426.9310.5460.5460.0000.0000.0000.000
202A204ILE00.0670.04626.874-0.415-0.4150.0000.0000.0000.000
203A205ASN0-0.030-0.03529.363-0.662-0.6620.0000.0000.0000.000
204A206LYS10.8840.94530.170-8.380-8.3800.0000.0000.0000.000
205A207LYS10.8820.93830.570-9.838-9.8380.0000.0000.0000.000
206A208SER00.0270.03626.0620.1080.1080.0000.0000.0000.000
207A209PRO0-0.030-0.03922.852-0.443-0.4430.0000.0000.0000.000
208A210TYR0-0.004-0.00724.342-0.257-0.2570.0000.0000.0000.000
209A211ARG10.8510.91623.108-12.357-12.3570.0000.0000.0000.000
210A212ILE0-0.014-0.00821.944-0.611-0.6110.0000.0000.0000.000
211A213ASP-1-0.864-0.93323.44512.28712.2870.0000.0000.0000.000
212A214LYS10.9210.96117.694-17.012-17.0120.0000.0000.0000.000
213A215ASP-1-0.854-0.91822.88212.16612.1660.0000.0000.0000.000
214A216SER0-0.066-0.04225.659-0.074-0.0740.0000.0000.0000.000
215A217LEU0-0.094-0.03720.718-0.088-0.0880.0000.0000.0000.000
216A218ASP-1-0.982-0.98021.14714.21214.2120.0000.0000.0000.000