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: 5J4RZ

Calculation Name: 5DBU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DBU

Chain ID: A

ChEMBL ID:

UniProt ID: D5AHU8

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 OptHSide
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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2281326.265774
FMO2-HF: Nuclear repulsion 2202887.129519
FMO2-HF: Total energy -78439.136255
FMO2-MP2: Total energy -78664.906051


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.
-0.0751.808-0.003-0.911-0.970
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 : -0.025 / q_NPA : -0.026
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].
3A3LEU00.024-0.0033.621-0.4451.438-0.003-0.911-0.9700.000
4A4ASN00.0710.0546.3320.0800.0800.0000.0000.0000.000
5A5LYS10.8000.9028.3150.3710.3710.0000.0000.0000.000
6A6TYR0-0.022-0.0205.619-0.014-0.0140.0000.0000.0000.000
7A7ILE00.0180.01410.8510.0600.0600.0000.0000.0000.000
8A8ASP-1-0.720-0.82014.188-0.088-0.0880.0000.0000.0000.000
9A9HIS0-0.017-0.02617.6130.0190.0190.0000.0000.0000.000
10A10THR0-0.071-0.04620.0320.0010.0010.0000.0000.0000.000
11A11ILE00.0020.00323.1420.0040.0040.0000.0000.0000.000
12A12LEU0-0.001-0.00925.878-0.001-0.0010.0000.0000.0000.000
13A13LYS10.8380.93529.3160.0020.0020.0000.0000.0000.000
14A14PRO00.0380.02932.380-0.002-0.0020.0000.0000.0000.000
15A15GLU-1-0.833-0.91235.537-0.003-0.0030.0000.0000.0000.000
16A16THR0-0.083-0.05330.8000.0000.0000.0000.0000.0000.000
17A17THR0-0.031-0.05734.0640.0000.0000.0000.0000.0000.000
18A18GLN00.010-0.01133.4260.0000.0000.0000.0000.0000.000
19A19GLU-1-0.799-0.87432.738-0.016-0.0160.0000.0000.0000.000
20A20GLN0-0.045-0.01830.976-0.001-0.0010.0000.0000.0000.000
21A21VAL00.0240.01128.558-0.002-0.0020.0000.0000.0000.000
22A22GLU-1-0.831-0.91427.862-0.028-0.0280.0000.0000.0000.000
23A23LYS10.8320.90926.7950.0170.0170.0000.0000.0000.000
24A24ILE0-0.028-0.01523.527-0.003-0.0030.0000.0000.0000.000
25A25LEU00.001-0.00123.469-0.008-0.0080.0000.0000.0000.000
26A26ALA0-0.039-0.01423.372-0.008-0.0080.0000.0000.0000.000
27A27GLU-1-0.772-0.86721.716-0.033-0.0330.0000.0000.0000.000
28A28ALA0-0.004-0.00819.301-0.008-0.0080.0000.0000.0000.000
29A29LYS10.8740.92718.5060.0410.0410.0000.0000.0000.000
30A30GLU-1-0.953-0.95019.153-0.048-0.0480.0000.0000.0000.000
31A31TYR0-0.110-0.06615.7330.0010.0010.0000.0000.0000.000
32A32ASP-1-0.838-0.92013.098-0.287-0.2870.0000.0000.0000.000
33A33PHE0-0.0140.00813.560-0.041-0.0410.0000.0000.0000.000
34A34ALA0-0.019-0.01012.839-0.024-0.0240.0000.0000.0000.000
35A35SER0-0.045-0.03614.2440.0120.0120.0000.0000.0000.000
36A36VAL00.0470.03518.0260.0070.0070.0000.0000.0000.000
37A37CYS0-0.124-0.05921.4090.0040.0040.0000.0000.0000.000
38A38VAL00.0700.03023.4020.0040.0040.0000.0000.0000.000
39A39ASN00.0330.01627.1250.0020.0020.0000.0000.0000.000
40A40PRO00.0890.03630.178-0.003-0.0030.0000.0000.0000.000
41A41THR0-0.028-0.00831.493-0.001-0.0010.0000.0000.0000.000
42A42TRP0-0.016-0.01030.159-0.001-0.0010.0000.0000.0000.000
43A43VAL00.0010.01727.077-0.003-0.0030.0000.0000.0000.000
44A44ALA00.0930.04828.672-0.004-0.0040.0000.0000.0000.000
45A45LEU0-0.021-0.00330.212-0.002-0.0020.0000.0000.0000.000
46A46ALA00.007-0.01325.738-0.002-0.0020.0000.0000.0000.000
47A47ALA00.0320.01225.745-0.006-0.0060.0000.0000.0000.000
48A48GLU-1-0.830-0.89826.218-0.042-0.0420.0000.0000.0000.000
49A49SER0-0.058-0.03426.8810.0010.0010.0000.0000.0000.000
50A50LEU0-0.035-0.01721.523-0.001-0.0010.0000.0000.0000.000
51A51LYS10.8290.94622.0750.0300.0300.0000.0000.0000.000
52A52ASP-1-0.960-0.98422.298-0.058-0.0580.0000.0000.0000.000
53A53SER0-0.046-0.04119.071-0.004-0.0040.0000.0000.0000.000
54A54ASP-1-0.839-0.91312.976-0.297-0.2970.0000.0000.0000.000
55A55VAL0-0.053-0.00615.580-0.026-0.0260.0000.0000.0000.000
56A56LYS10.9030.94514.7210.2180.2180.0000.0000.0000.000
57A57VAL00.0560.02519.1500.0060.0060.0000.0000.0000.000
58A58CYS0-0.0390.01020.4480.0070.0070.0000.0000.0000.000
59A59THR00.021-0.01822.5710.0040.0040.0000.0000.0000.000
60A60VAL0-0.062-0.02925.2330.0020.0020.0000.0000.0000.000
61A61ILE00.002-0.00627.425-0.001-0.0010.0000.0000.0000.000
62A62GLY0-0.005-0.00930.0130.0030.0030.0000.0000.0000.000
63A63PHE0-0.0100.02127.5310.0030.0030.0000.0000.0000.000
64A64PRO0-0.008-0.01931.101-0.001-0.0010.0000.0000.0000.000
65A65LEU00.039-0.01532.0880.0020.0020.0000.0000.0000.000
66A66GLY00.0380.03533.1530.0010.0010.0000.0000.0000.000
67A67ALA0-0.041-0.01933.8360.0010.0010.0000.0000.0000.000
68A68ASN0-0.0030.00135.7900.0000.0000.0000.0000.0000.000
69A69THR00.0260.00137.4960.0010.0010.0000.0000.0000.000
70A70PRO00.1130.04935.904-0.001-0.0010.0000.0000.0000.000
71A71ALA0-0.0020.00436.108-0.001-0.0010.0000.0000.0000.000
72A72VAL0-0.016-0.00637.374-0.001-0.0010.0000.0000.0000.000
73A73LYS10.8030.89232.338-0.011-0.0110.0000.0000.0000.000
74A74ALA00.0330.01732.973-0.002-0.0020.0000.0000.0000.000
75A75PHE0-0.034-0.01933.743-0.002-0.0020.0000.0000.0000.000
76A76GLU-1-0.804-0.90832.738-0.007-0.0070.0000.0000.0000.000
77A77THR0-0.015-0.02329.045-0.002-0.0020.0000.0000.0000.000
78A78LYS10.9270.96630.3160.0060.0060.0000.0000.0000.000
79A79ASP-1-0.924-0.95532.638-0.018-0.0180.0000.0000.0000.000
80A80ALA00.0150.00928.946-0.002-0.0020.0000.0000.0000.000
81A81ILE0-0.017-0.01526.659-0.004-0.0040.0000.0000.0000.000
82A82SER0-0.114-0.04428.989-0.003-0.0030.0000.0000.0000.000
83A83ASN0-0.049-0.03131.182-0.001-0.0010.0000.0000.0000.000
84A84GLY0-0.002-0.00727.670-0.001-0.0010.0000.0000.0000.000
85A85ALA0-0.062-0.01325.358-0.006-0.0060.0000.0000.0000.000
86A86ASP-1-0.858-0.92820.443-0.078-0.0780.0000.0000.0000.000
87A87GLU-1-0.813-0.88616.887-0.085-0.0850.0000.0000.0000.000
88A88ILE00.0170.01321.7810.0030.0030.0000.0000.0000.000
89A89ASP-1-0.710-0.84721.699-0.002-0.0020.0000.0000.0000.000
90A90MET00.0270.04524.393-0.001-0.0010.0000.0000.0000.000
91A91VAL0-0.033-0.00526.8050.0050.0050.0000.0000.0000.000
92A92ILE00.0190.02328.665-0.002-0.0020.0000.0000.0000.000
93A93ASN00.0500.02030.5430.0000.0000.0000.0000.0000.000
94A94ILE00.0530.01631.6670.0010.0010.0000.0000.0000.000
95A95GLY00.0340.02034.5230.0010.0010.0000.0000.0000.000
96A96ALA00.0140.01136.8810.0000.0000.0000.0000.0000.000
97A97LEU00.002-0.01331.6210.0000.0000.0000.0000.0000.000
98A98LYS10.7850.88535.272-0.026-0.0260.0000.0000.0000.000
99A99THR0-0.101-0.04438.042-0.001-0.0010.0000.0000.0000.000
100A100GLY00.0320.01738.9550.0000.0000.0000.0000.0000.000
101A101ASN0-0.052-0.02039.2230.0000.0000.0000.0000.0000.000
102A102TYR00.050-0.00634.9990.0000.0000.0000.0000.0000.000
103A103ASP-1-0.889-0.92835.6060.0160.0160.0000.0000.0000.000
104A104LEU0-0.0020.00637.011-0.001-0.0010.0000.0000.0000.000
105A105VAL0-0.039-0.02432.011-0.001-0.0010.0000.0000.0000.000
106A106LEU00.0180.01130.917-0.001-0.0010.0000.0000.0000.000
107A107GLU-1-0.957-0.98432.7460.0070.0070.0000.0000.0000.000
108A108ASP-1-0.861-0.92932.9050.0090.0090.0000.0000.0000.000
109A109ILE00.004-0.00827.457-0.002-0.0020.0000.0000.0000.000
110A110LYS10.9550.99029.685-0.016-0.0160.0000.0000.0000.000
111A111ALA0-0.035-0.00131.344-0.002-0.0020.0000.0000.0000.000
112A112VAL0-0.021-0.01527.709-0.003-0.0030.0000.0000.0000.000
113A113VAL00.0210.00525.877-0.004-0.0040.0000.0000.0000.000
114A114ALA0-0.044-0.01428.225-0.003-0.0030.0000.0000.0000.000
115A115ALA0-0.125-0.07931.147-0.002-0.0020.0000.0000.0000.000
116A116SER00.0260.02924.641-0.004-0.0040.0000.0000.0000.000
117A117GLY0-0.0050.00026.820-0.004-0.0040.0000.0000.0000.000
118A118ASP-1-0.957-0.98123.326-0.044-0.0440.0000.0000.0000.000
119A119LYS10.8620.94422.1900.0480.0480.0000.0000.0000.000
120A120LEU0-0.0090.00916.0430.0080.0080.0000.0000.0000.000
121A121VAL00.014-0.00820.4550.0000.0000.0000.0000.0000.000
122A122LYS10.7390.84517.7380.0380.0380.0000.0000.0000.000
123A123VAL00.0300.01621.729-0.005-0.0050.0000.0000.0000.000
124A124ILE0-0.038-0.02223.6360.0080.0080.0000.0000.0000.000
125A125ILE00.014-0.01724.832-0.003-0.0030.0000.0000.0000.000
126A126GLU-1-0.799-0.88326.3980.0200.0200.0000.0000.0000.000
127A127ALA00.0390.00325.751-0.002-0.0020.0000.0000.0000.000
128A128CYS0-0.0360.01327.7570.0000.0000.0000.0000.0000.000
129A129LEU0-0.025-0.00430.104-0.002-0.0020.0000.0000.0000.000
130A130LEU0-0.075-0.02929.016-0.002-0.0020.0000.0000.0000.000
131A131THR00.026-0.02232.2150.0020.0020.0000.0000.0000.000
132A132ASP-1-0.831-0.92729.0910.0540.0540.0000.0000.0000.000
133A133ASP-1-0.883-0.94429.4980.0440.0440.0000.0000.0000.000
134A134GLU-1-0.776-0.85031.2970.0290.0290.0000.0000.0000.000
135A135LYS10.7880.89226.409-0.054-0.0540.0000.0000.0000.000
136A136VAL00.0070.00826.5390.0030.0030.0000.0000.0000.000
137A137LYS10.9580.98827.547-0.031-0.0310.0000.0000.0000.000
138A138ALA00.0400.01427.806-0.002-0.0020.0000.0000.0000.000
139A139CYS0-0.054-0.01523.3230.0010.0010.0000.0000.0000.000
140A140GLN00.016-0.00525.017-0.005-0.0050.0000.0000.0000.000
141A141LEU0-0.026-0.00826.931-0.003-0.0030.0000.0000.0000.000
142A142SER0-0.006-0.02724.620-0.005-0.0050.0000.0000.0000.000
143A143GLN0-0.030-0.02820.912-0.006-0.0060.0000.0000.0000.000
144A144GLU-1-0.966-0.97224.5810.0240.0240.0000.0000.0000.000
145A145ALA0-0.086-0.06327.879-0.003-0.0030.0000.0000.0000.000
146A146GLY00.0070.01724.747-0.004-0.0040.0000.0000.0000.000
147A147ALA0-0.0010.00923.279-0.006-0.0060.0000.0000.0000.000
148A148ASP-1-0.798-0.89218.1760.0050.0050.0000.0000.0000.000
149A149TYR0-0.048-0.05612.6640.0020.0020.0000.0000.0000.000
150A150VAL00.0090.03118.942-0.008-0.0080.0000.0000.0000.000
151A151LYS10.8180.88819.4350.0030.0030.0000.0000.0000.000
152A152THR00.0460.00520.418-0.003-0.0030.0000.0000.0000.000
153A153SER0-0.045-0.01423.0530.0000.0000.0000.0000.0000.000
154A154THR0-0.005-0.02824.825-0.003-0.0030.0000.0000.0000.000
155A155GLY0-0.030-0.02426.800-0.003-0.0030.0000.0000.0000.000
156A156PHE0-0.053-0.02427.417-0.002-0.0020.0000.0000.0000.000
157A157SER00.0110.01830.413-0.001-0.0010.0000.0000.0000.000
158A158THR0-0.026-0.01931.5520.0010.0010.0000.0000.0000.000
159A159GLY00.0250.00729.0980.0000.0000.0000.0000.0000.000
160A160GLY0-0.035-0.01825.014-0.002-0.0020.0000.0000.0000.000
161A161ALA0-0.056-0.01420.3320.0020.0020.0000.0000.0000.000
162A162THR00.036-0.00722.4330.0010.0010.0000.0000.0000.000
163A163VAL00.0770.01618.1170.0050.0050.0000.0000.0000.000
164A164ALA00.0030.00520.1830.0120.0120.0000.0000.0000.000
165A165ASP-1-0.770-0.85122.7590.0680.0680.0000.0000.0000.000
166A166VAL0-0.011-0.00616.3130.0000.0000.0000.0000.0000.000
167A167ALA00.0320.01918.3090.0130.0130.0000.0000.0000.000
168A168LEU0-0.051-0.01719.3590.0040.0040.0000.0000.0000.000
169A169MET00.0100.00820.326-0.006-0.0060.0000.0000.0000.000
170A170ARG10.7970.87913.060-0.269-0.2690.0000.0000.0000.000
171A171LYS10.9090.95018.170-0.087-0.0870.0000.0000.0000.000
172A172THR0-0.101-0.05719.834-0.011-0.0110.0000.0000.0000.000
173A173VAL0-0.015-0.00418.333-0.008-0.0080.0000.0000.0000.000
174A174GLY00.0430.04517.964-0.008-0.0080.0000.0000.0000.000
175A175PRO0-0.056-0.03012.6340.0140.0140.0000.0000.0000.000
176A176ASP-1-0.894-0.95313.1170.2040.2040.0000.0000.0000.000
177A177MET0-0.0140.03015.178-0.030-0.0300.0000.0000.0000.000
178A178GLY0-0.028-0.00914.3030.0410.0410.0000.0000.0000.000
179A179VAL00.021-0.00114.583-0.017-0.0170.0000.0000.0000.000
180A180LYS10.7520.87115.0410.0280.0280.0000.0000.0000.000
181A181ALA00.0260.01716.303-0.007-0.0070.0000.0000.0000.000
182A182SER0-0.012-0.02418.043-0.015-0.0150.0000.0000.0000.000
183A183GLY00.012-0.00920.743-0.007-0.0070.0000.0000.0000.000
184A184GLY0-0.026-0.01622.1720.0060.0060.0000.0000.0000.000
185A185ALA00.0340.04618.1140.0020.0020.0000.0000.0000.000
186A186ARG10.8350.90520.022-0.022-0.0220.0000.0000.0000.000
187A187SER00.028-0.00819.217-0.011-0.0110.0000.0000.0000.000
188A188TYR00.0130.00410.0190.0130.0130.0000.0000.0000.000
189A189GLU-1-0.811-0.89814.4080.0690.0690.0000.0000.0000.000
190A190ASP-1-0.806-0.90216.0620.0730.0730.0000.0000.0000.000
191A191ALA0-0.024-0.01412.9470.0170.0170.0000.0000.0000.000
192A192ILE00.0070.00010.3770.0400.0400.0000.0000.0000.000
193A193ALA0-0.0010.01512.0930.0530.0530.0000.0000.0000.000
194A194PHE0-0.020-0.03614.7440.0110.0110.0000.0000.0000.000
195A195ILE0-0.023-0.0137.8080.0130.0130.0000.0000.0000.000
196A196GLU-1-0.954-0.97710.3640.5070.5070.0000.0000.0000.000
197A197ALA0-0.074-0.01812.080-0.027-0.0270.0000.0000.0000.000
198A198GLY00.0080.00412.866-0.026-0.0260.0000.0000.0000.000
199A199ALA0-0.0230.00613.146-0.009-0.0090.0000.0000.0000.000
200A200SER00.0180.00910.0470.0570.0570.0000.0000.0000.000
201A201ARG10.6830.78710.748-0.008-0.0080.0000.0000.0000.000
202A202ILE00.0310.01812.6450.0340.0340.0000.0000.0000.000
203A203GLY0-0.0100.00715.459-0.026-0.0260.0000.0000.0000.000
204A204ALA0-0.040-0.03518.6250.0120.0120.0000.0000.0000.000
205A205SER00.0380.03720.320-0.008-0.0080.0000.0000.0000.000
206A206SER0-0.034-0.03820.3260.0000.0000.0000.0000.0000.000
207A207GLY00.0530.02417.1770.0040.0040.0000.0000.0000.000
208A208VAL0-0.0060.00916.779-0.005-0.0050.0000.0000.0000.000
209A209ALA00.0330.02415.5630.0090.0090.0000.0000.0000.000
210A210ILE0-0.052-0.01014.085-0.002-0.0020.0000.0000.0000.000
211A211MET0-0.018-0.01911.768-0.009-0.0090.0000.0000.0000.000