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: R8M98

Calculation Name: 3R89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R89

Chain ID: A

ChEMBL ID:

UniProt ID: C7RH50

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 289
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4291099.898504
FMO2-HF: Nuclear repulsion 4175797.417256
FMO2-HF: Total energy -115302.481248
FMO2-MP2: Total energy -115637.789386


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-0.960.0559999999999990.003-0.463-0.5560.001
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.028
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].
3A0ALA00.0090.0223.7320.2461.2620.003-0.463-0.5560.001
4A1MET0-0.050-0.0176.4340.4140.4140.0000.0000.0000.000
5A2LYS10.9730.9797.9240.9430.9430.0000.0000.0000.000
6A3ILE00.0750.04111.106-0.145-0.1450.0000.0000.0000.000
7A4ILE00.0000.00213.598-0.013-0.0130.0000.0000.0000.000
8A5ASP-1-0.780-0.8809.048-1.069-1.0690.0000.0000.0000.000
9A6LYS10.9510.9799.7891.0031.0030.0000.0000.0000.000
10A7LEU0-0.0080.01211.0530.0590.0590.0000.0000.0000.000
11A8TYR00.0160.01210.8810.0550.0550.0000.0000.0000.000
12A9GLU-1-0.894-0.9725.502-3.051-3.0510.0000.0000.0000.000
13A10LYS10.8900.95210.0630.7360.7360.0000.0000.0000.000
14A11VAL0-0.0070.00512.7570.0830.0830.0000.0000.0000.000
15A12SER0-0.061-0.01811.0830.0870.0870.0000.0000.0000.000
16A13LYS10.8840.9406.4821.2841.2840.0000.0000.0000.000
17A14ASN0-0.021-0.01112.7980.0410.0410.0000.0000.0000.000
18A15GLY00.0220.03116.1170.0350.0350.0000.0000.0000.000
19A16PHE00.017-0.00818.066-0.035-0.0350.0000.0000.0000.000
20A17VAL00.0060.00920.1980.0040.0040.0000.0000.0000.000
21A18CYS0-0.0170.00921.203-0.029-0.0290.0000.0000.0000.000
22A19ILE00.0220.00323.3390.0230.0230.0000.0000.0000.000
23A20GLY00.0360.01925.545-0.012-0.0120.0000.0000.0000.000
24A21LEU00.0140.00526.0880.0130.0130.0000.0000.0000.000
25A22ASP-1-0.864-0.89329.662-0.126-0.1260.0000.0000.0000.000
26A23SER0-0.055-0.06332.2570.0080.0080.0000.0000.0000.000
27A24SER00.0320.01434.6770.0020.0020.0000.0000.0000.000
28A25ILE00.0730.02338.4090.0000.0000.0000.0000.0000.000
29A26ASP-1-0.926-0.96540.587-0.057-0.0570.0000.0000.0000.000
30A27TYR0-0.101-0.05935.8590.0050.0050.0000.0000.0000.000
31A28ILE0-0.0240.00036.951-0.001-0.0010.0000.0000.0000.000
32A29PRO00.0300.01938.0770.0030.0030.0000.0000.0000.000
33A30GLU-1-0.910-0.96441.058-0.042-0.0420.0000.0000.0000.000
34A31ASN00.016-0.00940.115-0.001-0.0010.0000.0000.0000.000
35A32MET00.0110.02835.010-0.002-0.0020.0000.0000.0000.000
36A33LYS10.8810.93939.5300.0530.0530.0000.0000.0000.000
37A34ALA00.0020.01141.5520.0010.0010.0000.0000.0000.000
38A35GLY0-0.050-0.02343.4240.0000.0000.0000.0000.0000.000
39A36LYS10.8560.94837.3930.0590.0590.0000.0000.0000.000
40A37SER00.0170.02140.7350.0010.0010.0000.0000.0000.000
41A38VAL00.028-0.00639.877-0.002-0.0020.0000.0000.0000.000
42A39SER0-0.023-0.02137.017-0.004-0.0040.0000.0000.0000.000
43A40GLU-1-0.851-0.92136.058-0.066-0.0660.0000.0000.0000.000
44A41ALA0-0.040-0.02236.176-0.003-0.0030.0000.0000.0000.000
45A42LEU0-0.011-0.01834.881-0.003-0.0030.0000.0000.0000.000
46A43PHE00.0150.02028.219-0.004-0.0040.0000.0000.0000.000
47A44SER0-0.007-0.01231.386-0.004-0.0040.0000.0000.0000.000
48A45TYR0-0.022-0.01232.359-0.002-0.0020.0000.0000.0000.000
49A46ASN00.0290.00828.7670.0020.0020.0000.0000.0000.000
50A47LYS10.8900.95327.4060.0940.0940.0000.0000.0000.000
51A48GLU-1-0.858-0.92127.548-0.079-0.0790.0000.0000.0000.000
52A49ILE0-0.025-0.02427.0240.0000.0000.0000.0000.0000.000
53A50ILE00.0000.01922.544-0.004-0.0040.0000.0000.0000.000
54A51ASP-1-0.803-0.87923.294-0.138-0.1380.0000.0000.0000.000
55A52GLN0-0.054-0.01823.8940.0020.0020.0000.0000.0000.000
56A53THR0-0.017-0.04123.3450.0000.0000.0000.0000.0000.000
57A54TYR00.0170.01817.008-0.010-0.0100.0000.0000.0000.000
58A55ASP-1-0.859-0.91417.137-0.183-0.1830.0000.0000.0000.000
59A56VAL0-0.049-0.01818.1300.0130.0130.0000.0000.0000.000
60A57CYS0-0.059-0.01819.3140.0120.0120.0000.0000.0000.000
61A58ALA00.0240.02316.634-0.029-0.0290.0000.0000.0000.000
62A59ILE0-0.038-0.03016.824-0.057-0.0570.0000.0000.0000.000
63A60TYR00.0260.00719.5850.0320.0320.0000.0000.0000.000
64A61LYS10.8660.92823.0460.1440.1440.0000.0000.0000.000
65A62LEU0-0.0030.00825.8200.0150.0150.0000.0000.0000.000
66A63GLN0-0.033-0.00128.9000.0000.0000.0000.0000.0000.000
67A64ILE00.0380.02232.1370.0070.0070.0000.0000.0000.000
68A65ALA00.0300.01533.5340.0070.0070.0000.0000.0000.000
69A66TYR0-0.032-0.02035.2000.0080.0080.0000.0000.0000.000
70A67TYR0-0.040-0.03331.2770.0050.0050.0000.0000.0000.000
71A68GLU-1-0.823-0.93636.414-0.099-0.0990.0000.0000.0000.000
72A69SER0-0.113-0.04438.8650.0070.0070.0000.0000.0000.000
73A70TYR00.0280.01638.6980.0060.0060.0000.0000.0000.000
74A71GLY00.0040.00541.5790.0030.0030.0000.0000.0000.000
75A72ILE00.012-0.01139.966-0.004-0.0040.0000.0000.0000.000
76A73GLU-1-0.815-0.90139.015-0.073-0.0730.0000.0000.0000.000
77A74GLY00.0240.00837.508-0.003-0.0030.0000.0000.0000.000
78A75MET0-0.016-0.01333.946-0.007-0.0070.0000.0000.0000.000
79A76ILE00.0010.00534.305-0.007-0.0070.0000.0000.0000.000
80A77ALA00.0370.02133.436-0.005-0.0050.0000.0000.0000.000
81A78TYR0-0.029-0.00929.352-0.010-0.0100.0000.0000.0000.000
82A79ARG10.8980.95329.5670.0930.0930.0000.0000.0000.000
83A80ASP-1-0.849-0.91328.678-0.114-0.1140.0000.0000.0000.000
84A81THR0-0.036-0.03526.754-0.004-0.0040.0000.0000.0000.000
85A82LEU0-0.0060.00024.849-0.014-0.0140.0000.0000.0000.000
86A83SER00.0080.00923.733-0.022-0.0220.0000.0000.0000.000
87A84TYR0-0.062-0.05123.565-0.009-0.0090.0000.0000.0000.000
88A85LEU0-0.020-0.02121.255-0.011-0.0110.0000.0000.0000.000
89A86ARG10.9340.96418.4700.2880.2880.0000.0000.0000.000
90A87GLU-1-0.979-0.98318.522-0.172-0.1720.0000.0000.0000.000
91A88LYS10.8200.92118.7700.1780.1780.0000.0000.0000.000
92A89ASP-1-0.929-0.95412.176-0.707-0.7070.0000.0000.0000.000
93A90LEU0-0.096-0.04714.728-0.065-0.0650.0000.0000.0000.000
94A91LEU00.0110.01414.2420.0000.0000.0000.0000.0000.000
95A92SER00.007-0.00518.0070.0480.0480.0000.0000.0000.000
96A93ILE00.001-0.02021.642-0.015-0.0150.0000.0000.0000.000
97A94GLY00.0900.04123.9480.0180.0180.0000.0000.0000.000
98A95ASP-1-0.838-0.89727.344-0.148-0.1480.0000.0000.0000.000
99A96VAL00.0250.00129.7060.0130.0130.0000.0000.0000.000
100A97LYS10.8340.90831.5020.1410.1410.0000.0000.0000.000
101A98ARG10.8520.94732.3360.1300.1300.0000.0000.0000.000
102A99SER00.034-0.00233.755-0.004-0.0040.0000.0000.0000.000
103A100ASP-1-0.909-0.95136.018-0.095-0.0950.0000.0000.0000.000
104A101ILE00.0780.03434.920-0.007-0.0070.0000.0000.0000.000
105A102ALA00.007-0.00135.1580.0030.0030.0000.0000.0000.000
106A103ALA00.014-0.00334.594-0.005-0.0050.0000.0000.0000.000
107A104SER00.0280.01135.542-0.002-0.0020.0000.0000.0000.000
108A105ALA00.0200.01632.263-0.004-0.0040.0000.0000.0000.000
109A106LYS10.8190.89928.5290.1440.1440.0000.0000.0000.000
110A107MET0-0.062-0.02931.183-0.004-0.0040.0000.0000.0000.000
111A108TYR00.016-0.00431.682-0.002-0.0020.0000.0000.0000.000
112A109ALA00.0030.00827.275-0.008-0.0080.0000.0000.0000.000
113A110LYS10.9730.99227.4230.1050.1050.0000.0000.0000.000
114A111ALA0-0.062-0.02628.979-0.002-0.0020.0000.0000.0000.000
115A112HIS0-0.013-0.02427.8200.0080.0080.0000.0000.0000.000
116A113PHE00.0120.01323.340-0.018-0.0180.0000.0000.0000.000
117A114GLU-1-0.845-0.89023.646-0.178-0.1780.0000.0000.0000.000
118A115GLY0-0.012-0.00325.9890.0080.0080.0000.0000.0000.000
119A116ASP-1-0.914-0.96427.571-0.124-0.1240.0000.0000.0000.000
120A117PHE0-0.059-0.04729.3000.0000.0000.0000.0000.0000.000
121A118GLU-1-0.863-0.88621.363-0.268-0.2680.0000.0000.0000.000
122A119THR0-0.039-0.02423.340-0.005-0.0050.0000.0000.0000.000
123A120ASP-1-0.819-0.91418.459-0.408-0.4080.0000.0000.0000.000
124A121PHE00.0080.01417.119-0.014-0.0140.0000.0000.0000.000
125A122ILE00.0130.02322.3730.0200.0200.0000.0000.0000.000
126A123THR0-0.019-0.03226.092-0.005-0.0050.0000.0000.0000.000
127A124LEU0-0.0090.00227.8660.0080.0080.0000.0000.0000.000
128A125ASN00.006-0.01430.7140.0010.0010.0000.0000.0000.000
129A126PRO00.0550.03132.6620.0010.0010.0000.0000.0000.000
130A127TYR0-0.044-0.01334.3640.0050.0050.0000.0000.0000.000
131A128MET0-0.025-0.01837.6110.0040.0040.0000.0000.0000.000
132A129GLY00.0610.05036.6330.0040.0040.0000.0000.0000.000
133A130MET00.0140.01530.625-0.003-0.0030.0000.0000.0000.000
134A131ASP-1-0.832-0.89632.258-0.110-0.1100.0000.0000.0000.000
135A132SER0-0.062-0.04833.646-0.002-0.0020.0000.0000.0000.000
136A133ILE0-0.032-0.04427.575-0.008-0.0080.0000.0000.0000.000
137A134GLU-1-0.868-0.95528.228-0.136-0.1360.0000.0000.0000.000
138A135PRO0-0.066-0.02528.147-0.008-0.0080.0000.0000.0000.000
139A136TYR00.0470.01925.680-0.002-0.0020.0000.0000.0000.000
140A137GLU-1-0.770-0.87123.738-0.210-0.2100.0000.0000.0000.000
141A138GLU-1-0.899-0.91822.712-0.177-0.1770.0000.0000.0000.000
142A139TYR0-0.085-0.09521.671-0.013-0.0130.0000.0000.0000.000
143A140ILE0-0.022-0.00819.554-0.028-0.0280.0000.0000.0000.000
144A141GLU-1-0.982-0.99118.144-0.313-0.3130.0000.0000.0000.000
145A142LYS10.9420.97217.3460.2210.2210.0000.0000.0000.000
146A143GLY0-0.046-0.00814.037-0.042-0.0420.0000.0000.0000.000
147A144ASP-1-0.902-0.96113.869-0.615-0.6150.0000.0000.0000.000
148A145LYS10.7300.84915.9230.3270.3270.0000.0000.0000.000
149A146GLY00.023-0.00219.022-0.014-0.0140.0000.0000.0000.000
150A147VAL0-0.032-0.01120.3360.0260.0260.0000.0000.0000.000
151A148PHE0-0.025-0.00720.853-0.010-0.0100.0000.0000.0000.000
152A149VAL00.0150.00225.8590.0130.0130.0000.0000.0000.000
153A150LEU0-0.048-0.03528.9970.0020.0020.0000.0000.0000.000
154A151LEU00.0230.02630.5880.0020.0020.0000.0000.0000.000
155A152ARG10.8500.94732.8420.0900.0900.0000.0000.0000.000
156A153THR00.004-0.02433.812-0.006-0.0060.0000.0000.0000.000
157A154SER0-0.024-0.02335.6700.0040.0040.0000.0000.0000.000
158A155ASN00.0200.03537.5300.0020.0020.0000.0000.0000.000
159A156PRO00.037-0.00340.1830.0000.0000.0000.0000.0000.000
160A157GLY00.0430.02343.2920.0010.0010.0000.0000.0000.000
161A158ALA0-0.0040.01639.6970.0000.0000.0000.0000.0000.000
162A159LYS10.8960.92441.5990.0620.0620.0000.0000.0000.000
163A160ASP-1-0.913-0.92944.702-0.058-0.0580.0000.0000.0000.000
164A161PHE0-0.007-0.03542.9800.0010.0010.0000.0000.0000.000
165A162GLU-1-0.833-0.91237.882-0.094-0.0940.0000.0000.0000.000
166A163VAL0-0.003-0.01240.180-0.002-0.0020.0000.0000.0000.000
167A164LEU0-0.0330.01042.0320.0030.0030.0000.0000.0000.000
168A165PRO00.011-0.00243.530-0.003-0.0030.0000.0000.0000.000
169A166VAL0-0.003-0.00542.2210.0010.0010.0000.0000.0000.000
170A167ASP-1-0.878-0.93542.867-0.064-0.0640.0000.0000.0000.000
171A168GLY0-0.055-0.03843.529-0.001-0.0010.0000.0000.0000.000
172A169GLU-1-0.785-0.86237.692-0.076-0.0760.0000.0000.0000.000
173A170GLU-1-0.896-0.93339.037-0.070-0.0700.0000.0000.0000.000
174A171PHE0-0.001-0.00539.077-0.004-0.0040.0000.0000.0000.000
175A172PHE00.016-0.00634.432-0.004-0.0040.0000.0000.0000.000
176A173TYR00.0280.00533.518-0.010-0.0100.0000.0000.0000.000
177A174LYS10.8500.93634.4980.0720.0720.0000.0000.0000.000
178A175VAL0-0.0020.00332.517-0.004-0.0040.0000.0000.0000.000
179A176GLY00.0600.00630.695-0.009-0.0090.0000.0000.0000.000
180A177ASP-1-0.817-0.87129.732-0.116-0.1160.0000.0000.0000.000
181A178LYS10.8830.94230.2710.1020.1020.0000.0000.0000.000
182A179MET00.0070.01127.319-0.010-0.0100.0000.0000.0000.000
183A180ARG10.9520.97925.8270.1090.1090.0000.0000.0000.000
184A181GLU-1-0.924-0.97925.258-0.154-0.1540.0000.0000.0000.000
185A182LEU0-0.063-0.01724.953-0.007-0.0070.0000.0000.0000.000
186A183ASN0-0.004-0.01020.505-0.039-0.0390.0000.0000.0000.000
187A184GLU-1-0.875-0.93920.556-0.239-0.2390.0000.0000.0000.000
188A185LYS10.7970.90920.5350.1820.1820.0000.0000.0000.000
189A186TYR0-0.089-0.07317.524-0.020-0.0200.0000.0000.0000.000
190A187ILE0-0.039-0.00315.296-0.052-0.0520.0000.0000.0000.000
191A188GLY0-0.018-0.01812.385-0.039-0.0390.0000.0000.0000.000
192A189LYS10.8590.9036.8751.1471.1470.0000.0000.0000.000
193A190SER0-0.035-0.0309.9900.1600.1600.0000.0000.0000.000
194A191GLY0-0.0130.01211.6000.0900.0900.0000.0000.0000.000
195A192PHE00.0210.01914.6380.0510.0510.0000.0000.0000.000
196A193GLY00.0110.00915.476-0.073-0.0730.0000.0000.0000.000
197A194PRO0-0.055-0.02416.8630.0060.0060.0000.0000.0000.000
198A195ILE00.0040.00118.7640.0230.0230.0000.0000.0000.000
199A196GLY00.0520.02722.4460.0070.0070.0000.0000.0000.000
200A197LEU0-0.034-0.01423.6110.0180.0180.0000.0000.0000.000
201A198VAL0-0.045-0.02026.621-0.006-0.0060.0000.0000.0000.000
202A199VAL00.0270.01128.3360.0100.0100.0000.0000.0000.000
203A200GLY0-0.018-0.02430.010-0.003-0.0030.0000.0000.0000.000
204A201ALA00.0150.00331.9110.0010.0010.0000.0000.0000.000
205A202THR0-0.079-0.05633.4070.0050.0050.0000.0000.0000.000
206A203HIS00.014-0.00636.7790.0060.0060.0000.0000.0000.000
207A204SER00.0580.02035.552-0.002-0.0020.0000.0000.0000.000
208A205GLU-1-0.951-0.96635.189-0.056-0.0560.0000.0000.0000.000
209A206GLU-1-0.811-0.89335.425-0.081-0.0810.0000.0000.0000.000
210A207VAL0-0.026-0.01431.470-0.006-0.0060.0000.0000.0000.000
211A208GLU-1-0.837-0.91530.917-0.065-0.0650.0000.0000.0000.000
212A209LYS10.8410.93330.8550.0690.0690.0000.0000.0000.000
213A210ILE0-0.024-0.01829.263-0.005-0.0050.0000.0000.0000.000
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215A212LYS10.9570.98626.1780.0610.0610.0000.0000.0000.000
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