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: G54Y1

Calculation Name: 1R5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q99ZQ5

Base Structure: X-ray

Registration Date: 2023-09-23

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 329
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4778431.296697
FMO2-HF: Nuclear repulsion 4653194.551946
FMO2-HF: Total energy -125236.744752
FMO2-MP2: Total energy -125601.567103


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-7.082-6.63112.378-4.614-8.2140
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.029
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].
3A3ILE00.0720.0283.877-0.7691.208-0.015-1.072-0.8900.004
4A4ARG10.8960.9407.0320.6150.6150.0000.0000.0000.000
5A5SER00.009-0.0012.9520.0190.7720.162-0.340-0.574-0.001
6A6LEU00.0150.0204.9650.1610.321-0.001-0.012-0.1470.000
7A7PHE00.027-0.0076.2130.0990.0990.0000.0000.0000.000
8A8GLY0-0.0270.0078.0920.0090.0090.0000.0000.0000.000
9A9GLY00.0620.0328.0390.0070.0070.0000.0000.0000.000
10A10LEU0-0.012-0.0169.471-0.039-0.0390.0000.0000.0000.000
11A11ARG10.8500.90511.252-0.014-0.0140.0000.0000.0000.000
12A12GLU-1-0.943-0.95312.5990.1360.1360.0000.0000.0000.000
13A13LYS10.8530.90412.434-0.109-0.1090.0000.0000.0000.000
14A14ILE0-0.009-0.00615.321-0.011-0.0110.0000.0000.0000.000
15A15LEU00.0040.01517.340-0.008-0.0080.0000.0000.0000.000
16A16GLY0-0.0080.00019.1510.0030.0030.0000.0000.0000.000
17A17LYS10.7960.89517.929-0.064-0.0640.0000.0000.0000.000
18A18ASN0-0.056-0.02822.904-0.001-0.0010.0000.0000.0000.000
19A19MET00.0240.03421.763-0.002-0.0020.0000.0000.0000.000
20A20LYS10.8660.92124.707-0.023-0.0230.0000.0000.0000.000
21A21ILE0-0.005-0.00122.5700.0020.0020.0000.0000.0000.000
22A22VAL0-0.011-0.00626.044-0.003-0.0030.0000.0000.0000.000
23A23PHE00.0400.00723.5340.0020.0020.0000.0000.0000.000
24A24PRO00.020-0.01629.010-0.002-0.0020.0000.0000.0000.000
25A25GLU-1-0.738-0.84529.0500.0050.0050.0000.0000.0000.000
26A26GLY00.0610.01631.824-0.002-0.0020.0000.0000.0000.000
27A27ASN0-0.016-0.00833.415-0.001-0.0010.0000.0000.0000.000
28A28ASP-1-0.780-0.86929.461-0.011-0.0110.0000.0000.0000.000
29A29GLU-1-0.762-0.85629.558-0.019-0.0190.0000.0000.0000.000
30A30ARG10.7660.85126.0070.0100.0100.0000.0000.0000.000
31A31VAL00.008-0.00326.089-0.001-0.0010.0000.0000.0000.000
32A32VAL0-0.0040.00827.1220.0010.0010.0000.0000.0000.000
33A33ARG10.8080.87025.1700.0230.0230.0000.0000.0000.000
34A34ALA0-0.040-0.01922.756-0.001-0.0010.0000.0000.0000.000
35A35ALA00.0090.00223.5870.0020.0020.0000.0000.0000.000
36A36ALA00.0190.00925.8290.0020.0020.0000.0000.0000.000
37A37ARG10.7910.88816.3000.0480.0480.0000.0000.0000.000
38A38LEU0-0.027-0.02319.6070.0030.0030.0000.0000.0000.000
39A39LYS10.8180.91122.312-0.007-0.0070.0000.0000.0000.000
40A40PHE0-0.034-0.01925.0810.0030.0030.0000.0000.0000.000
41A41GLU-1-0.804-0.86316.865-0.009-0.0090.0000.0000.0000.000
42A42GLY00.0110.00620.4560.0050.0050.0000.0000.0000.000
43A43LEU0-0.059-0.03817.1570.0050.0050.0000.0000.0000.000
44A44LEU00.001-0.00520.5160.0050.0050.0000.0000.0000.000
45A45GLU-1-0.794-0.88923.4090.0110.0110.0000.0000.0000.000
46A46PRO0-0.040-0.01826.1000.0010.0010.0000.0000.0000.000
47A47ILE0-0.021-0.00428.013-0.001-0.0010.0000.0000.0000.000
48A48ILE0-0.0240.00730.2540.0000.0000.0000.0000.0000.000
49A49LEU0-0.028-0.00532.2260.0000.0000.0000.0000.0000.000
50A50GLY00.0330.00135.016-0.001-0.0010.0000.0000.0000.000
51A51GLN00.0170.00437.9690.0010.0010.0000.0000.0000.000
52A52SER00.0360.00940.0230.0000.0000.0000.0000.0000.000
53A53GLU-1-0.947-0.97040.0940.0010.0010.0000.0000.0000.000
54A54GLU-1-0.859-0.91440.247-0.002-0.0020.0000.0000.0000.000
55A55VAL0-0.017-0.01634.280-0.001-0.0010.0000.0000.0000.000
56A56ARG10.8700.95635.785-0.004-0.0040.0000.0000.0000.000
57A57ASN00.0280.00337.575-0.001-0.0010.0000.0000.0000.000
58A58LEU0-0.025-0.01833.576-0.001-0.0010.0000.0000.0000.000
59A59LEU0-0.019-0.00731.274-0.002-0.0020.0000.0000.0000.000
60A60THR00.0320.01133.926-0.002-0.0020.0000.0000.0000.000
61A61LYS10.8460.94436.6130.0080.0080.0000.0000.0000.000
62A62LEU0-0.073-0.04930.286-0.002-0.0020.0000.0000.0000.000
63A63GLY0-0.034-0.00331.859-0.002-0.0020.0000.0000.0000.000
64A64PHE0-0.041-0.01626.9990.0000.0000.0000.0000.0000.000
65A65ALA00.0360.01232.3310.0000.0000.0000.0000.0000.000
66A66ASP-1-0.797-0.90634.3270.0000.0000.0000.0000.0000.000
67A67GLN0-0.090-0.06035.7890.0000.0000.0000.0000.0000.000
68A68ASP-1-0.855-0.92134.2610.0080.0080.0000.0000.0000.000
69A69TYR0-0.027-0.02529.9140.0010.0010.0000.0000.0000.000
70A70THR0-0.0060.00232.097-0.001-0.0010.0000.0000.0000.000
71A71ILE0-0.017-0.00533.9900.0010.0010.0000.0000.0000.000
72A72ILE0-0.027-0.01535.8500.0000.0000.0000.0000.0000.000
73A73ASN00.015-0.01137.8410.0000.0000.0000.0000.0000.000
74A74PRO0-0.012-0.01338.4140.0000.0000.0000.0000.0000.000
75A75ASN0-0.053-0.03641.1330.0000.0000.0000.0000.0000.000
76A76GLU-1-0.882-0.91843.9600.0040.0040.0000.0000.0000.000
77A77TYR0-0.065-0.05139.9270.0000.0000.0000.0000.0000.000
78A78ALA00.0520.01343.4470.0000.0000.0000.0000.0000.000
79A79ASP-1-0.788-0.85742.0630.0090.0090.0000.0000.0000.000
80A80PHE0-0.051-0.03442.1480.0000.0000.0000.0000.0000.000
81A81ASP-1-0.821-0.88644.9380.0060.0060.0000.0000.0000.000
82A82LYS10.8640.91940.954-0.010-0.0100.0000.0000.0000.000
83A83MET0-0.0020.00138.3070.0010.0010.0000.0000.0000.000
84A84LYS10.8410.90842.346-0.006-0.0060.0000.0000.0000.000
85A85GLU-1-0.924-0.97144.9220.0070.0070.0000.0000.0000.000
86A86ALA0-0.001-0.00840.9960.0000.0000.0000.0000.0000.000
87A87PHE00.005-0.01340.0040.0010.0010.0000.0000.0000.000
88A88VAL0-0.006-0.00242.0750.0000.0000.0000.0000.0000.000
89A89GLU-1-0.802-0.88343.2910.0090.0090.0000.0000.0000.000
90A90VAL0-0.0340.00737.9240.0000.0000.0000.0000.0000.000
91A91ARG10.8300.90040.243-0.010-0.0100.0000.0000.0000.000
92A92LYS10.7840.86943.321-0.010-0.0100.0000.0000.0000.000
93A93GLY00.0280.02146.6870.0000.0000.0000.0000.0000.000
94A94LYS10.8880.94644.027-0.009-0.0090.0000.0000.0000.000
95A95ALA0-0.018-0.00545.5790.0010.0010.0000.0000.0000.000
96A96THR00.0490.01147.2290.0000.0000.0000.0000.0000.000
97A97LEU00.0650.03348.4230.0000.0000.0000.0000.0000.000
98A98GLU-1-0.842-0.92949.3060.0050.0050.0000.0000.0000.000
99A99ASP-1-0.900-0.92247.0350.0060.0060.0000.0000.0000.000
100A100ALA0-0.010-0.00144.6820.0000.0000.0000.0000.0000.000
101A101ASP-1-0.826-0.90044.6540.0060.0060.0000.0000.0000.000
102A102LYS10.8490.90246.118-0.005-0.0050.0000.0000.0000.000
103A103MET0-0.050-0.01841.2880.0000.0000.0000.0000.0000.000
104A104LEU0-0.008-0.00439.3990.0010.0010.0000.0000.0000.000
105A105ARG10.8760.92740.538-0.005-0.0050.0000.0000.0000.000
106A106ASP-1-0.805-0.88337.1870.0090.0090.0000.0000.0000.000
107A107VAL00.0300.01534.8540.0010.0010.0000.0000.0000.000
108A108ASN0-0.001-0.00632.3790.0020.0020.0000.0000.0000.000
109A109TYR0-0.007-0.04033.7980.0020.0020.0000.0000.0000.000
110A110PHE0-0.0050.01135.9490.0010.0010.0000.0000.0000.000
111A111GLY00.0490.00932.4950.0010.0010.0000.0000.0000.000
112A112VAL00.020-0.00730.6530.0020.0020.0000.0000.0000.000
113A113MET0-0.044-0.00932.5490.0010.0010.0000.0000.0000.000
114A114LEU00.007-0.00133.2030.0000.0000.0000.0000.0000.000
115A115VAL0-0.032-0.00728.3590.0000.0000.0000.0000.0000.000
116A116LYS10.8400.92231.308-0.017-0.0170.0000.0000.0000.000
117A117MET0-0.049-0.02033.735-0.001-0.0010.0000.0000.0000.000
118A118GLY0-0.0130.00232.358-0.001-0.0010.0000.0000.0000.000
119A119LEU0-0.012-0.00732.5950.0010.0010.0000.0000.0000.000
120A120ALA0-0.0040.00529.3860.0000.0000.0000.0000.0000.000
121A121ASP-1-0.814-0.89325.7660.0260.0260.0000.0000.0000.000
122A122GLY00.0570.02124.5650.0040.0040.0000.0000.0000.000
123A123MET0-0.084-0.01525.418-0.005-0.0050.0000.0000.0000.000
124A124VAL00.0100.00422.1660.0040.0040.0000.0000.0000.000
125A125SER0-0.006-0.01125.201-0.005-0.0050.0000.0000.0000.000
126A126GLY00.0700.04226.3490.0030.0030.0000.0000.0000.000
127A127ALA0-0.088-0.04527.350-0.002-0.0020.0000.0000.0000.000
128A128ILE0-0.080-0.04028.430-0.003-0.0030.0000.0000.0000.000
129A129HIS0-0.044-0.01531.550-0.001-0.0010.0000.0000.0000.000
130A130SER0-0.034-0.04431.0670.0000.0000.0000.0000.0000.000
131A131THR00.016-0.03527.1680.0000.0000.0000.0000.0000.000
132A132ALA0-0.027-0.01029.5660.0020.0020.0000.0000.0000.000
133A133ASP-1-0.845-0.89832.6590.0100.0100.0000.0000.0000.000
134A134THR00.005-0.00727.173-0.001-0.0010.0000.0000.0000.000
135A135VAL00.002-0.00828.1610.0010.0010.0000.0000.0000.000
136A136ARG10.8630.93030.307-0.011-0.0110.0000.0000.0000.000
137A137PRO00.012-0.00833.1300.0000.0000.0000.0000.0000.000
138A138ALA00.0150.00629.1540.0000.0000.0000.0000.0000.000
139A139LEU00.0170.02729.6170.0010.0010.0000.0000.0000.000
140A140GLN0-0.0390.00132.750-0.002-0.0020.0000.0000.0000.000
141A141ILE00.0110.00634.914-0.001-0.0010.0000.0000.0000.000
142A142ILE0-0.025-0.00329.106-0.001-0.0010.0000.0000.0000.000
143A143LYS10.8850.95231.784-0.016-0.0160.0000.0000.0000.000
144A144THR00.0390.00528.6000.0020.0020.0000.0000.0000.000
145A145LYS10.8590.93322.334-0.045-0.0450.0000.0000.0000.000
146A146PRO00.006-0.02227.9030.0000.0000.0000.0000.0000.000
147A147GLY00.0080.02727.624-0.002-0.0020.0000.0000.0000.000
148A148ILE0-0.032-0.00324.0260.0010.0010.0000.0000.0000.000
149A149SER0-0.056-0.04427.817-0.001-0.0010.0000.0000.0000.000
150A150ARG10.8620.91028.692-0.022-0.0220.0000.0000.0000.000
151A151THR00.0260.01725.5460.0020.0020.0000.0000.0000.000
152A152SER00.0170.01322.1780.0010.0010.0000.0000.0000.000
153A153GLY00.012-0.00321.0330.0010.0010.0000.0000.0000.000
154A154VAL0-0.0210.01214.863-0.003-0.0030.0000.0000.0000.000
155A155PHE00.0280.00215.354-0.018-0.0180.0000.0000.0000.000
156A156LEU0-0.0010.0158.1980.0220.0220.0000.0000.0000.000
157A157MET0-0.048-0.01410.667-0.115-0.1150.0000.0000.0000.000
158A158ASN0-0.031-0.0355.1420.3210.348-0.001-0.006-0.0200.000
159A159ARG10.8700.9116.355-0.076-0.0760.0000.0000.0000.000
160A160GLU-1-0.776-0.8904.287-2.174-1.940-0.001-0.041-0.1920.000
161A161ASN0-0.064-0.0325.038-0.301-0.227-0.001-0.003-0.0700.000
162A162THR0-0.039-0.0217.2040.1580.1580.0000.0000.0000.000
163A163SER0-0.057-0.0253.446-0.541-0.0760.016-0.083-0.3980.000
164A164GLU-1-0.757-0.8294.3791.1461.7200.031-0.128-0.477-0.001
165A165ARG10.8250.8951.880-4.679-9.28712.186-2.798-4.781-0.001
166A166TYR0-0.035-0.0385.553-0.228-0.113-0.001-0.004-0.1100.000
167A167VAL0-0.0040.0038.869-0.029-0.0290.0000.0000.0000.000
168A168PHE0-0.007-0.00712.068-0.057-0.0570.0000.0000.0000.000
169A169ALA00.0470.01615.599-0.007-0.0070.0000.0000.0000.000
170A170ASP-1-0.727-0.85318.4730.0430.0430.0000.0000.0000.000
171A171CYS0-0.0480.01019.752-0.007-0.0070.0000.0000.0000.000
172A172ALA0-0.051-0.04021.871-0.007-0.0070.0000.0000.0000.000
173A173ILE0-0.061-0.01824.408-0.005-0.0050.0000.0000.0000.000
174A174ASN0-0.060-0.05626.225-0.009-0.0090.0000.0000.0000.000
175A175ILE00.003-0.00928.0100.0010.0010.0000.0000.0000.000
176A176ASP-1-0.830-0.91629.7130.0210.0210.0000.0000.0000.000
177A177PRO0-0.0420.00626.312-0.002-0.0020.0000.0000.0000.000
178A178THR00.016-0.01329.544-0.002-0.0020.0000.0000.0000.000
179A179ALA00.0180.00629.3930.0020.0020.0000.0000.0000.000
180A180GLN0-0.020-0.02428.4430.0000.0000.0000.0000.0000.000
181A181GLU-1-0.761-0.84227.7800.0230.0230.0000.0000.0000.000
182A182LEU00.006-0.00224.2030.0040.0040.0000.0000.0000.000
183A183ALA00.0410.03123.6860.0060.0060.0000.0000.0000.000
184A184GLU-1-0.770-0.85823.1990.0260.0260.0000.0000.0000.000
185A185ILE0-0.046-0.02921.3970.0060.0060.0000.0000.0000.000
186A186ALA00.0160.03019.3980.0140.0140.0000.0000.0000.000
187A187VAL00.0270.01718.3220.0080.0080.0000.0000.0000.000
188A188ASN0-0.041-0.04018.6400.0060.0060.0000.0000.0000.000
189A189THR0-0.014-0.02214.9960.0130.0130.0000.0000.0000.000
190A190ALA00.0130.01314.1770.0320.0320.0000.0000.0000.000
191A191GLU-1-0.861-0.90714.0990.0160.0160.0000.0000.0000.000
192A192THR0-0.010-0.04414.3160.0040.0040.0000.0000.0000.000
193A193ALA0-0.020-0.01210.5390.0490.0490.0000.0000.0000.000
194A194LYS10.8380.9069.5430.0640.0640.0000.0000.0000.000
195A195ILE0-0.049-0.00510.2770.0010.0010.0000.0000.0000.000
196A196PHE0-0.058-0.0428.474-0.030-0.0300.0000.0000.0000.000
197A197ASP-1-0.913-0.9553.820-0.2290.2060.004-0.113-0.325-0.001
198A198ILE0-0.0100.0024.596-0.1270.118-0.001-0.014-0.2300.000
199A199ASP-1-0.803-0.8866.307-0.298-0.2980.0000.0000.0000.000
200A200PRO0-0.014-0.0018.3630.0390.0390.0000.0000.0000.000
201A201LYS10.8540.9239.5420.1840.1840.0000.0000.0000.000
202A202ILE0-0.007-0.01012.7990.0480.0480.0000.0000.0000.000
203A203ALA00.0510.03015.772-0.015-0.0150.0000.0000.0000.000
204A204MET0-0.066-0.02218.2200.0140.0140.0000.0000.0000.000
205A205LEU0-0.020-0.00218.629-0.006-0.0060.0000.0000.0000.000
206A206SER00.0240.00222.557-0.004-0.0040.0000.0000.0000.000
207A207PHE0-0.023-0.01125.5020.0010.0010.0000.0000.0000.000
208A208SER0-0.056-0.03828.089-0.003-0.0030.0000.0000.0000.000
209A209THR00.013-0.01924.7390.0050.0050.0000.0000.0000.000
210A210LYS10.8500.92424.474-0.006-0.0060.0000.0000.0000.000
211A211GLY00.0300.01228.503-0.002-0.0020.0000.0000.0000.000
212A212SER0-0.121-0.06230.3710.0000.0000.0000.0000.0000.000
213A213GLY0-0.005-0.01132.210-0.001-0.0010.0000.0000.0000.000
214A214LYS10.9370.96433.185-0.001-0.0010.0000.0000.0000.000
215A215ALA00.0370.01235.020-0.001-0.0010.0000.0000.0000.000
216A216PRO00.0630.03234.7230.0010.0010.0000.0000.0000.000
217A217GLN00.0420.01731.6260.0000.0000.0000.0000.0000.000
218A218VAL0-0.042-0.00630.0230.0020.0020.0000.0000.0000.000
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