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: R5RQ8

Calculation Name: 3R8C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R8C

Chain ID: A

ChEMBL ID:

UniProt ID: B1MB31

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017080.456216
FMO2-HF: Nuclear repulsion 1943692.63987
FMO2-HF: Total energy -73387.816346
FMO2-MP2: Total energy -73602.94519


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:-1:SER)


Summations of interaction energy for fragment #1(A:-1: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.
-16.612-1610.526-4.388-6.75-0.047
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.038
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].
3A1VAL00.007-0.0013.887-0.3891.172-0.006-0.783-0.7720.003
4A2VAL0-0.015-0.0146.2621.0221.0220.0000.0000.0000.000
5A3ALA00.0300.0249.5630.2460.2460.0000.0000.0000.000
6A4VAL00.011-0.00412.5120.1940.1940.0000.0000.0000.000
7A5ASP-1-0.756-0.86515.676-0.914-0.9140.0000.0000.0000.000
8A6GLY00.0840.02518.8360.0400.0400.0000.0000.0000.000
9A7PRO0-0.068-0.01922.6450.0100.0100.0000.0000.0000.000
10A8SER00.0190.01424.968-0.009-0.0090.0000.0000.0000.000
11A9GLY00.026-0.00726.7160.0120.0120.0000.0000.0000.000
12A10THR00.003-0.01424.2530.0260.0260.0000.0000.0000.000
13A11GLY00.0020.01224.401-0.001-0.0010.0000.0000.0000.000
14A12LYS10.7930.89518.8090.6540.6540.0000.0000.0000.000
15A13SER00.000-0.02419.081-0.008-0.0080.0000.0000.0000.000
16A14SER0-0.084-0.04119.5800.0260.0260.0000.0000.0000.000
17A15VAL00.019-0.00217.8060.0120.0120.0000.0000.0000.000
18A16ALA00.0180.00414.851-0.007-0.0070.0000.0000.0000.000
19A17LYS10.8540.93913.8820.3030.3030.0000.0000.0000.000
20A18GLU-1-0.814-0.88814.732-0.008-0.0080.0000.0000.0000.000
21A19LEU0-0.020-0.01711.9550.0540.0540.0000.0000.0000.000
22A20ALA00.0220.01210.266-0.021-0.0210.0000.0000.0000.000
23A21ARG10.8030.86410.6920.1940.1940.0000.0000.0000.000
24A22GLN0-0.094-0.05412.8750.1630.1630.0000.0000.0000.000
25A23LEU0-0.047-0.0328.194-0.017-0.0170.0000.0000.0000.000
26A24GLY0-0.045-0.0088.1670.2280.2280.0000.0000.0000.000
27A25ALA0-0.054-0.0186.4910.4330.4330.0000.0000.0000.000
28A26SER00.0360.0146.8320.0880.0880.0000.0000.0000.000
29A27TYR0-0.065-0.0698.707-0.346-0.3460.0000.0000.0000.000
30A28LEU00.0380.01511.2930.0910.0910.0000.0000.0000.000
31A29ASP-1-0.749-0.84813.290-0.495-0.4950.0000.0000.0000.000
32A30THR00.007-0.04214.9420.0870.0870.0000.0000.0000.000
33A31GLY0-0.011-0.00317.4170.0570.0570.0000.0000.0000.000
34A32ALA0-0.025-0.02019.9360.0520.0520.0000.0000.0000.000
35A33MET00.0270.02516.4490.0110.0110.0000.0000.0000.000
36A34TYR00.0410.01419.5760.0550.0550.0000.0000.0000.000
37A35ARG10.8250.90223.2430.3040.3040.0000.0000.0000.000
38A36ILE00.0110.01321.7530.0300.0300.0000.0000.0000.000
39A37VAL00.0250.01523.7350.0280.0280.0000.0000.0000.000
40A38THR0-0.034-0.02526.4570.0200.0200.0000.0000.0000.000
41A39LEU0-0.013-0.00828.7040.0180.0180.0000.0000.0000.000
42A40TRP0-0.014-0.02228.8830.0210.0210.0000.0000.0000.000
43A41VAL00.0180.00230.1650.0120.0120.0000.0000.0000.000
44A42LEU0-0.030-0.01932.5110.0100.0100.0000.0000.0000.000
45A43ARG10.7540.83332.4680.1120.1120.0000.0000.0000.000
46A44ALA0-0.030-0.00334.5330.0100.0100.0000.0000.0000.000
47A45GLY0-0.027-0.00636.3410.0040.0040.0000.0000.0000.000
48A46VAL0-0.045-0.02035.1760.0030.0030.0000.0000.0000.000
49A47ASP-1-0.820-0.88637.695-0.140-0.1400.0000.0000.0000.000
50A48LEU0-0.012-0.02634.307-0.009-0.0090.0000.0000.0000.000
51A49THR0-0.103-0.07036.815-0.011-0.0110.0000.0000.0000.000
52A50ASP-1-0.831-0.91038.255-0.156-0.1560.0000.0000.0000.000
53A51PRO0-0.003-0.02833.542-0.004-0.0040.0000.0000.0000.000
54A52ALA0-0.0090.01033.492-0.011-0.0110.0000.0000.0000.000
55A53ALA00.0200.01735.0030.0000.0000.0000.0000.0000.000
56A54ILE0-0.013-0.00530.735-0.002-0.0020.0000.0000.0000.000
57A55ALA0-0.0230.00330.327-0.009-0.0090.0000.0000.0000.000
58A56ALA00.0590.03730.643-0.004-0.0040.0000.0000.0000.000
59A57ALA0-0.028-0.00232.5760.0070.0070.0000.0000.0000.000
60A58THR0-0.056-0.05627.335-0.007-0.0070.0000.0000.0000.000
61A59ASP-1-0.820-0.90226.881-0.225-0.2250.0000.0000.0000.000
62A60GLN0-0.081-0.04226.1870.0140.0140.0000.0000.0000.000
63A61VAL00.0050.01824.9860.0170.0170.0000.0000.0000.000
64A62PRO0-0.0040.02224.710-0.012-0.0120.0000.0000.0000.000
65A63MET0-0.031-0.01720.4690.0010.0010.0000.0000.0000.000
66A64SER0-0.032-0.01219.821-0.002-0.0020.0000.0000.0000.000
67A65VAL00.018-0.00716.143-0.001-0.0010.0000.0000.0000.000
68A66SER00.0000.01616.5180.0130.0130.0000.0000.0000.000
69A67SER00.0340.01910.967-0.036-0.0360.0000.0000.0000.000
70A68ASP-1-0.797-0.87811.8280.1720.1720.0000.0000.0000.000
71A69PRO0-0.004-0.01012.125-0.093-0.0930.0000.0000.0000.000
72A70ASP-1-0.844-0.89214.9170.0260.0260.0000.0000.0000.000
73A71ALA0-0.031-0.01117.465-0.019-0.0190.0000.0000.0000.000
74A72GLN0-0.084-0.06316.063-0.070-0.0700.0000.0000.0000.000
75A73THR0-0.0140.00219.515-0.006-0.0060.0000.0000.0000.000
76A74ALA0-0.029-0.02520.563-0.025-0.0250.0000.0000.0000.000
77A75LEU0-0.014-0.01022.5490.0220.0220.0000.0000.0000.000
78A76LEU0-0.010-0.01224.136-0.028-0.0280.0000.0000.0000.000
79A77ALA0-0.025-0.02626.8890.0140.0140.0000.0000.0000.000
80A78GLY0-0.0030.01027.2400.0150.0150.0000.0000.0000.000
81A79GLU-1-0.814-0.85528.183-0.069-0.0690.0000.0000.0000.000
82A80ASP-1-0.790-0.87326.844-0.085-0.0850.0000.0000.0000.000
83A81VAL0-0.017-0.01026.003-0.002-0.0020.0000.0000.0000.000
84A82SER0-0.007-0.04824.969-0.025-0.0250.0000.0000.0000.000
85A83VAL00.0000.00326.320-0.015-0.0150.0000.0000.0000.000
86A84PRO00.0260.01329.711-0.013-0.0130.0000.0000.0000.000
87A85ILE0-0.0010.00924.040-0.011-0.0110.0000.0000.0000.000
88A86ARG10.8120.88321.5740.2550.2550.0000.0000.0000.000
89A87GLY00.0510.04628.8680.0000.0000.0000.0000.0000.000
90A88ASN0-0.006-0.00132.148-0.025-0.0250.0000.0000.0000.000
91A89GLU-1-0.863-0.94034.752-0.145-0.1450.0000.0000.0000.000
92A90VAL00.0230.01228.764-0.007-0.0070.0000.0000.0000.000
93A91THR0-0.079-0.04930.386-0.026-0.0260.0000.0000.0000.000
94A92GLY0-0.037-0.00831.434-0.012-0.0120.0000.0000.0000.000
95A93ALA00.0330.02032.792-0.005-0.0050.0000.0000.0000.000
96A94VAL00.0030.00526.269-0.010-0.0100.0000.0000.0000.000
97A95SER0-0.039-0.00828.329-0.021-0.0210.0000.0000.0000.000
98A96ALA00.0440.02129.944-0.013-0.0130.0000.0000.0000.000
99A97VAL00.0270.00827.851-0.005-0.0050.0000.0000.0000.000
100A98SER0-0.005-0.01925.048-0.017-0.0170.0000.0000.0000.000
101A99ALA0-0.0220.00126.292-0.032-0.0320.0000.0000.0000.000
102A100VAL00.0140.01728.951-0.007-0.0070.0000.0000.0000.000
103A101PRO0-0.008-0.01226.980-0.020-0.0200.0000.0000.0000.000
104A102ALA00.0630.03125.621-0.029-0.0290.0000.0000.0000.000
105A103VAL0-0.0030.01024.882-0.012-0.0120.0000.0000.0000.000
106A104ARG10.8950.93321.9740.4170.4170.0000.0000.0000.000
107A105GLU-1-0.869-0.90921.006-0.430-0.4300.0000.0000.0000.000
108A106ARG10.8100.88620.3650.2180.2180.0000.0000.0000.000
109A107LEU00.0070.00619.181-0.032-0.0320.0000.0000.0000.000
110A108VAL00.006-0.00316.494-0.074-0.0740.0000.0000.0000.000
111A109ARG10.8070.90215.2760.3060.3060.0000.0000.0000.000
112A110GLN00.0410.01714.461-0.088-0.0880.0000.0000.0000.000
113A111GLN0-0.008-0.02113.444-0.091-0.0910.0000.0000.0000.000
114A112ARG10.8300.91210.6780.8950.8950.0000.0000.0000.000
115A113GLU-1-0.853-0.9289.576-0.824-0.8240.0000.0000.0000.000
116A114LEU0-0.0080.00310.0580.0520.0520.0000.0000.0000.000
117A115ALA0-0.025-0.0027.3590.0570.0570.0000.0000.0000.000
118A116GLU-1-0.945-0.9745.534-1.904-1.9040.0000.0000.0000.000
119A117SER0-0.073-0.0605.3420.2900.2900.0000.0000.0000.000
120A118SER0-0.039-0.0286.5160.8070.8070.0000.0000.0000.000
121A119GLY0-0.0030.0072.6310.4801.4840.501-0.587-0.9190.001
122A120ALA00.0150.0231.979-14.114-14.3519.825-4.861-4.727-0.050
123A121VAL0-0.011-0.0082.7793.3781.6620.2061.843-0.332-0.001
124A122VAL00.0010.0096.272-0.534-0.5340.0000.0000.0000.000
125A123VAL00.0040.0008.8000.3280.3280.0000.0000.0000.000
126A124GLU-1-0.713-0.80211.518-0.523-0.5230.0000.0000.0000.000
127A125GLY00.0450.02715.3050.0560.0560.0000.0000.0000.000
128A126ARG10.8060.88418.0260.5250.5250.0000.0000.0000.000
129A127ASP-1-0.850-0.92419.149-0.686-0.6860.0000.0000.0000.000
130A128ILE00.0020.00912.635-0.042-0.0420.0000.0000.0000.000
131A129GLY00.0440.01214.554-0.132-0.1320.0000.0000.0000.000
132A130THR0-0.065-0.04415.5760.0020.0020.0000.0000.0000.000
133A131VAL0-0.027-0.01217.5140.0620.0620.0000.0000.0000.000
134A132VAL0-0.0220.00013.422-0.028-0.0280.0000.0000.0000.000
135A133LEU00.0270.0068.801-0.058-0.0580.0000.0000.0000.000
136A134PRO0-0.0220.00112.031-0.134-0.1340.0000.0000.0000.000
137A135ASP-1-0.880-0.9439.696-1.536-1.5360.0000.0000.0000.000
138A136ALA0-0.051-0.0128.359-0.336-0.3360.0000.0000.0000.000
139A137ASP-1-0.793-0.8856.178-5.408-5.4080.0000.0000.0000.000
140A138VAL0-0.024-0.0119.1920.7350.7350.0000.0000.0000.000
141A139LYS10.7850.89011.6551.2361.2360.0000.0000.0000.000
142A140ILE00.0080.01014.3960.1750.1750.0000.0000.0000.000
143A141TYR0-0.040-0.04116.8950.0100.0100.0000.0000.0000.000
144A142LEU00.0230.02019.4150.0640.0640.0000.0000.0000.000
145A143THR00.033-0.00221.9970.0220.0220.0000.0000.0000.000
146A144ALA00.0100.00725.7480.0130.0130.0000.0000.0000.000
147A145SER00.0500.03129.1000.0030.0030.0000.0000.0000.000
148A146ALA00.0200.00032.469-0.003-0.0030.0000.0000.0000.000
149A147GLN00.0210.00334.464-0.004-0.0040.0000.0000.0000.000
150A148ALA00.0670.04731.6840.0080.0080.0000.0000.0000.000
151A149ARG10.7530.84528.4860.2980.2980.0000.0000.0000.000
152A150ALA0-0.044-0.02331.8180.0030.0030.0000.0000.0000.000
153A151GLN0-0.0050.00334.8240.0130.0130.0000.0000.0000.000
154A152ARG10.8440.91027.8460.2580.2580.0000.0000.0000.000
155A153ARG10.8090.89331.6430.1970.1970.0000.0000.0000.000
156A154ASN0-0.051-0.02334.2510.0160.0160.0000.0000.0000.000
157A170LEU00.0710.02337.7180.0020.0020.0000.0000.0000.000
158A171ALA00.0800.04038.119-0.011-0.0110.0000.0000.0000.000
159A172ASP-1-0.813-0.87135.667-0.200-0.2000.0000.0000.0000.000
160A173VAL0-0.0100.00632.646-0.011-0.0110.0000.0000.0000.000
161A174GLN00.0400.01034.581-0.008-0.0080.0000.0000.0000.000
162A175ARG10.9240.93736.6600.1630.1630.0000.0000.0000.000
163A176ARG10.8610.93031.2180.2370.2370.0000.0000.0000.000
164A177ASP-1-0.809-0.86131.105-0.316-0.3160.0000.0000.0000.000
165A178HIS0-0.045-0.01232.606-0.015-0.0150.0000.0000.0000.000
166A179LEU0-0.037-0.01232.234-0.010-0.0100.0000.0000.0000.000
167A187PRO00.0330.01022.2640.0170.0170.0000.0000.0000.000
168A188LEU00.0000.01022.121-0.039-0.0390.0000.0000.0000.000
169A189ARG10.8730.94123.8810.4130.4130.0000.0000.0000.000
170A190PRO00.0340.03421.422-0.041-0.0410.0000.0000.0000.000
171A191ALA00.0300.01018.2010.0360.0360.0000.0000.0000.000
172A192GLU-1-0.930-0.96620.286-0.529-0.5290.0000.0000.0000.000
173A193ASP-1-0.824-0.89315.322-1.175-1.1750.0000.0000.0000.000
174A194ALA0-0.058-0.02117.314-0.089-0.0890.0000.0000.0000.000
175A195LEU0-0.010-0.00316.5090.0950.0950.0000.0000.0000.000
176A196GLU-1-0.916-0.97219.709-0.473-0.4730.0000.0000.0000.000
177A197VAL0-0.013-0.01020.4470.0250.0250.0000.0000.0000.000
178A198ASP-1-0.794-0.86423.352-0.286-0.2860.0000.0000.0000.000
179A199THR00.027-0.00723.7210.0190.0190.0000.0000.0000.000
180A200SER0-0.115-0.08426.6920.0190.0190.0000.0000.0000.000
181A201ASP-1-0.932-0.96030.423-0.174-0.1740.0000.0000.0000.000
182A202MET0-0.0280.00423.9460.0020.0020.0000.0000.0000.000
183A203THR0-0.060-0.06227.285-0.006-0.0060.0000.0000.0000.000
184A204GLN00.0280.01922.444-0.027-0.0270.0000.0000.0000.000
185A205GLU-1-0.777-0.87722.182-0.161-0.1610.0000.0000.0000.000
186A206GLN00.0220.02222.168-0.019-0.0190.0000.0000.0000.000
187A207VAL00.0110.00320.405-0.023-0.0230.0000.0000.0000.000
188A208VAL00.0010.00217.080-0.048-0.0480.0000.0000.0000.000
189A209ALA0-0.0030.00017.624-0.033-0.0330.0000.0000.0000.000
190A210HIS00.0060.00618.8310.0100.0100.0000.0000.0000.000
191A211LEU0-0.003-0.01315.548-0.041-0.0410.0000.0000.0000.000
192A212LEU0-0.012-0.00413.071-0.086-0.0860.0000.0000.0000.000
193A213ASP-1-0.929-0.95314.471-0.311-0.3110.0000.0000.0000.000
194A214LEU0-0.0120.00415.886-0.036-0.0360.0000.0000.0000.000
195A215VAL0-0.023-0.0149.824-0.105-0.1050.0000.0000.0000.000
196A216ARG10.8720.93411.3550.0390.0390.0000.0000.0000.000
197A217THR0-0.050-0.03212.5830.0190.0190.0000.0000.0000.000
198A218ARG10.7710.89410.6151.1271.1270.0000.0000.0000.000