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: 85JQY

Calculation Name: 5X5V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X5V

Chain ID: A

ChEMBL ID:

UniProt ID: G3G933

Base Structure: X-ray

Registration Date: 2023-06-21

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3132957.328521
FMO2-HF: Nuclear repulsion 3036793.581705
FMO2-HF: Total energy -96163.746815
FMO2-MP2: Total energy -96442.235228


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:26:PRO)


Summations of interaction energy for fragment #1(A:26:PRO)
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.
-1.8770.404-0.014-1.154-1.1130
Interaction energy analysis for fragmet #1(A:26:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / 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].
3A28PHE0-0.021-0.0033.693-1.1031.178-0.014-1.154-1.1130.000
4A29PRO00.0240.0036.0240.1770.1770.0000.0000.0000.000
5A30PRO00.0260.0258.592-0.041-0.0410.0000.0000.0000.000
6A31PRO0-0.010-0.00611.5860.0420.0420.0000.0000.0000.000
7A32ALA00.0150.00614.9140.0430.0430.0000.0000.0000.000
8A33TYR0-0.032-0.02517.2760.0010.0010.0000.0000.0000.000
9A34PRO0-0.0050.00420.7230.0080.0080.0000.0000.0000.000
10A35TYR0-0.063-0.05720.9430.0040.0040.0000.0000.0000.000
11A36THR0-0.042-0.01925.384-0.001-0.0010.0000.0000.0000.000
12A37GLU-1-0.788-0.87024.446-0.054-0.0540.0000.0000.0000.000
13A38SER0-0.046-0.03427.9640.0000.0000.0000.0000.0000.000
14A39TRP00.0390.01030.1860.0020.0020.0000.0000.0000.000
15A40GLN00.027-0.00932.3870.0080.0080.0000.0000.0000.000
16A41LEU0-0.031-0.00730.104-0.006-0.0060.0000.0000.0000.000
17A42THR0-0.108-0.07334.3820.0010.0010.0000.0000.0000.000
18A43LEU0-0.038-0.00633.7650.0020.0020.0000.0000.0000.000
19A44THR00.0310.01436.192-0.001-0.0010.0000.0000.0000.000
20A45THR0-0.052-0.02338.5810.0010.0010.0000.0000.0000.000
21A46VAL0-0.010-0.00834.0080.0000.0000.0000.0000.0000.000
22A47PRO00.0240.02033.3930.0010.0010.0000.0000.0000.000
23A48SER00.0310.01235.7950.0050.0050.0000.0000.0000.000
24A49PRO0-0.0150.01334.1860.0010.0010.0000.0000.0000.000
25A50PHE0-0.053-0.03535.5070.0050.0050.0000.0000.0000.000
26A51VAL00.0130.01335.974-0.002-0.0020.0000.0000.0000.000
27A52GLY00.0120.00137.378-0.003-0.0030.0000.0000.0000.000
28A53PRO0-0.035-0.01036.4370.0010.0010.0000.0000.0000.000
29A54ALA00.007-0.00732.0210.0000.0000.0000.0000.0000.000
30A55ASP-1-0.884-0.92029.7350.1040.1040.0000.0000.0000.000
31A56VAL0-0.023-0.02230.2710.0030.0030.0000.0000.0000.000
32A57TYR0-0.047-0.02325.1030.0130.0130.0000.0000.0000.000
33A58HIS00.0060.00226.674-0.009-0.0090.0000.0000.0000.000
34A59THR00.003-0.00123.1290.0140.0140.0000.0000.0000.000
35A60ARG10.8770.93819.443-0.337-0.3370.0000.0000.0000.000
36A61PRO00.0350.02122.9460.0020.0020.0000.0000.0000.000
37A62LEU0-0.054-0.01820.9050.0240.0240.0000.0000.0000.000
38A63GLU-1-0.937-0.96318.1700.3790.3790.0000.0000.0000.000
39A64ASP-1-0.771-0.86520.9750.2210.2210.0000.0000.0000.000
40A65PRO00.0450.01722.8560.0100.0100.0000.0000.0000.000
41A66CYS0-0.124-0.01722.055-0.014-0.0140.0000.0000.0000.000
42A67GLY00.0680.05618.9450.0120.0120.0000.0000.0000.000
43A68VAL0-0.032-0.03215.877-0.023-0.0230.0000.0000.0000.000
44A69VAL00.0400.02318.6750.0270.0270.0000.0000.0000.000
45A70ALA00.013-0.00517.318-0.006-0.0060.0000.0000.0000.000
46A71LEU0-0.0280.00019.151-0.003-0.0030.0000.0000.0000.000
47A72ILE00.0350.00915.300-0.013-0.0130.0000.0000.0000.000
48A73SER00.0410.00819.5320.0120.0120.0000.0000.0000.000
49A74ASP-1-0.820-0.89419.5890.1400.1400.0000.0000.0000.000
50A75PRO0-0.040-0.01320.971-0.008-0.0080.0000.0000.0000.000
51A76GLN00.0300.00722.781-0.025-0.0250.0000.0000.0000.000
52A77VAL00.0300.00922.162-0.013-0.0130.0000.0000.0000.000
53A78ASP-1-0.833-0.92621.8210.0640.0640.0000.0000.0000.000
54A79ARG10.9280.97723.808-0.084-0.0840.0000.0000.0000.000
55A80LEU00.0350.01927.251-0.007-0.0070.0000.0000.0000.000
56A81LEU0-0.024-0.00122.793-0.008-0.0080.0000.0000.0000.000
57A82ASN0-0.023-0.03824.695-0.017-0.0170.0000.0000.0000.000
58A83GLU-1-0.933-0.95428.0570.0210.0210.0000.0000.0000.000
59A84ALA0-0.010-0.00429.559-0.004-0.0040.0000.0000.0000.000
60A85VAL0-0.027-0.01027.202-0.007-0.0070.0000.0000.0000.000
61A86ALA0-0.033-0.01330.586-0.004-0.0040.0000.0000.0000.000
62A87HIS0-0.058-0.02933.267-0.003-0.0030.0000.0000.0000.000
63A88ARG10.8690.93733.7580.0210.0210.0000.0000.0000.000
64A89ARG10.9190.95932.9990.0000.0000.0000.0000.0000.000
65A90PRO0-0.039-0.02231.706-0.001-0.0010.0000.0000.0000.000
66A91THR0-0.055-0.03329.685-0.006-0.0060.0000.0000.0000.000
67A92TYR00.0430.03423.3460.0080.0080.0000.0000.0000.000
68A93ARG10.8970.96129.557-0.006-0.0060.0000.0000.0000.000
69A94ALA00.026-0.00626.9250.0050.0050.0000.0000.0000.000
70A95HIS00.0020.00828.161-0.003-0.0030.0000.0000.0000.000
71A96VAL00.0180.01923.8340.0060.0060.0000.0000.0000.000
72A97ALA0-0.0050.00127.064-0.006-0.0060.0000.0000.0000.000
73A98TRP00.0090.00522.5050.0100.0100.0000.0000.0000.000
74A99TYR0-0.041-0.05228.625-0.007-0.0070.0000.0000.0000.000
75A100ARG10.8530.93228.709-0.078-0.0780.0000.0000.0000.000
76A101ILE0-0.029-0.02332.939-0.007-0.0070.0000.0000.0000.000
77A102ALA00.0160.00335.5410.0040.0040.0000.0000.0000.000
78A103ASP-1-0.915-0.96438.7660.0530.0530.0000.0000.0000.000
79A104GLY00.0300.02242.073-0.003-0.0030.0000.0000.0000.000
80A105CYS0-0.120-0.06038.8810.0000.0000.0000.0000.0000.000
81A106ALA00.0300.01535.7990.0040.0040.0000.0000.0000.000
82A107HIS0-0.032-0.00834.780-0.002-0.0020.0000.0000.0000.000
83A108LEU0-0.010-0.00733.8380.0040.0040.0000.0000.0000.000
84A109LEU0-0.027-0.01327.0640.0020.0020.0000.0000.0000.000
85A110TYR00.0300.00223.125-0.002-0.0020.0000.0000.0000.000
86A111PHE00.0320.01328.5010.0020.0020.0000.0000.0000.000
87A112ILE0-0.0080.01823.944-0.004-0.0040.0000.0000.0000.000
88A113GLU-1-0.752-0.85427.822-0.001-0.0010.0000.0000.0000.000
89A114TYR0-0.024-0.05822.074-0.005-0.0050.0000.0000.0000.000
90A115ALA00.013-0.01027.9470.0050.0050.0000.0000.0000.000
91A116ASP-1-0.832-0.89928.710-0.054-0.0540.0000.0000.0000.000
92A117CYS0-0.060-0.00421.401-0.004-0.0040.0000.0000.0000.000
93A118ASP-1-0.790-0.91023.799-0.084-0.0840.0000.0000.0000.000
94A119PRO0-0.034-0.01624.0030.0000.0000.0000.0000.0000.000
95A120ARG10.9190.96023.8860.0630.0630.0000.0000.0000.000
96A121GLN0-0.065-0.01919.294-0.034-0.0340.0000.0000.0000.000
97A122VAL00.0340.01615.1430.0180.0180.0000.0000.0000.000
98A123PHE00.0350.00118.571-0.012-0.0120.0000.0000.0000.000
99A124GLY00.0790.04519.320-0.002-0.0020.0000.0000.0000.000
100A125ARG10.8950.97317.9120.1860.1860.0000.0000.0000.000
101A127ARG10.9370.95324.5710.0620.0620.0000.0000.0000.000
102A128ARG10.8300.90026.9730.0380.0380.0000.0000.0000.000
103A129ARG10.8170.87920.3970.0500.0500.0000.0000.0000.000
104A130THR00.0080.01927.197-0.004-0.0040.0000.0000.0000.000
105A131THR00.0400.01926.217-0.002-0.0020.0000.0000.0000.000
106A132PRO0-0.045-0.01623.0950.0050.0050.0000.0000.0000.000
107A133MET0-0.063-0.00926.298-0.005-0.0050.0000.0000.0000.000
108A134TRP00.0620.00922.6130.0100.0100.0000.0000.0000.000
109A135TRP0-0.0210.00228.907-0.007-0.0070.0000.0000.0000.000
110A136THR00.045-0.00229.0570.0070.0070.0000.0000.0000.000
111A137PRO00.0060.00828.7050.0040.0040.0000.0000.0000.000
112A138SER00.013-0.00427.1720.0070.0070.0000.0000.0000.000
113A139ALA00.0180.02624.6310.0100.0100.0000.0000.0000.000
114A140ASP-1-0.831-0.89923.7240.0490.0490.0000.0000.0000.000
115A141TYR0-0.104-0.07622.133-0.001-0.0010.0000.0000.0000.000
116A142MET0-0.0410.00021.4240.0190.0190.0000.0000.0000.000
117A143PHE00.0130.00514.620-0.013-0.0130.0000.0000.0000.000
118A144PRO00.0310.01618.8570.0240.0240.0000.0000.0000.000
119A145THR0-0.015-0.03614.7530.0030.0030.0000.0000.0000.000
120A146GLU-1-0.948-0.9799.5450.0200.0200.0000.0000.0000.000
121A147ASP-1-0.847-0.90613.5510.1360.1360.0000.0000.0000.000
122A148GLU-1-0.811-0.85915.523-0.037-0.0370.0000.0000.0000.000
123A149LEU0-0.0100.00518.198-0.008-0.0080.0000.0000.0000.000
124A150GLY00.0120.01118.6730.0070.0070.0000.0000.0000.000
125A151LEU0-0.046-0.01319.594-0.020-0.0200.0000.0000.0000.000
126A152LEU0-0.023-0.00214.1120.0320.0320.0000.0000.0000.000
127A153MET0-0.004-0.00318.782-0.028-0.0280.0000.0000.0000.000
128A154VAL0-0.028-0.01517.7490.0210.0210.0000.0000.0000.000
129A155ALA0-0.0050.00220.437-0.021-0.0210.0000.0000.0000.000
130A156PRO0-0.0140.00022.784-0.018-0.0180.0000.0000.0000.000
131A157GLY00.0490.01625.7100.0000.0000.0000.0000.0000.000
132A158ARG10.8600.88729.344-0.103-0.1030.0000.0000.0000.000
133A159PHE0-0.076-0.03329.8230.0000.0000.0000.0000.0000.000
134A160ASN0-0.0250.01128.027-0.007-0.0070.0000.0000.0000.000
135A161GLU-1-0.776-0.85129.8020.1160.1160.0000.0000.0000.000
136A162GLY00.0060.00331.219-0.009-0.0090.0000.0000.0000.000
137A163GLN0-0.048-0.01630.9650.0080.0080.0000.0000.0000.000
138A164TYR0-0.043-0.04727.670-0.011-0.0110.0000.0000.0000.000
139A165ARG10.8280.87528.865-0.067-0.0670.0000.0000.0000.000
140A166ARG10.8060.88421.854-0.138-0.1380.0000.0000.0000.000
141A167LEU0-0.025-0.01427.8000.0000.0000.0000.0000.0000.000
142A168VAL00.0120.00424.596-0.002-0.0020.0000.0000.0000.000
143A169SER0-0.005-0.00927.586-0.001-0.0010.0000.0000.0000.000
144A170VAL00.0400.00926.714-0.006-0.0060.0000.0000.0000.000
145A171ASP-1-0.836-0.93929.909-0.004-0.0040.0000.0000.0000.000
146A172GLY0-0.058-0.02533.1670.0000.0000.0000.0000.0000.000
147A173VAL00.0040.02132.4710.0020.0020.0000.0000.0000.000
148A174ASN00.003-0.00231.807-0.001-0.0010.0000.0000.0000.000
149A175ILE00.0080.01327.1170.0010.0010.0000.0000.0000.000
150A176LEU00.0010.00629.6010.0000.0000.0000.0000.0000.000
151A177THR0-0.047-0.01725.7550.0060.0060.0000.0000.0000.000
152A178ASP-1-0.719-0.81428.8040.0850.0850.0000.0000.0000.000
153A179PHE0-0.024-0.02422.8090.0120.0120.0000.0000.0000.000
154A180MET0-0.007-0.00227.661-0.010-0.0100.0000.0000.0000.000
155A181VAL0-0.013-0.00925.9110.0140.0140.0000.0000.0000.000
156A182ALA00.0180.01328.290-0.012-0.0120.0000.0000.0000.000
157A183LEU0-0.023-0.02426.1260.0140.0140.0000.0000.0000.000
158A184PRO00.0740.03829.015-0.012-0.0120.0000.0000.0000.000
159A185GLU-1-0.847-0.92632.0020.0870.0870.0000.0000.0000.000
160A186GLY0-0.031-0.01634.6410.0020.0020.0000.0000.0000.000
161A187GLN0-0.0170.00429.2900.0040.0040.0000.0000.0000.000
162A188GLU-1-0.865-0.93729.2030.0950.0950.0000.0000.0000.000
163A190PRO00.0340.00226.907-0.008-0.0080.0000.0000.0000.000
164A191PHE00.002-0.00721.236-0.007-0.0070.0000.0000.0000.000
165A192ALA00.0280.02126.224-0.001-0.0010.0000.0000.0000.000
166A193ARG10.7530.84925.845-0.071-0.0710.0000.0000.0000.000
167A194VAL00.0580.01528.4260.0000.0000.0000.0000.0000.000
168A195ASP-1-0.859-0.89531.1190.0500.0500.0000.0000.0000.000
169A196GLN00.039-0.00431.068-0.006-0.0060.0000.0000.0000.000
170A197HIS00.0470.04232.508-0.004-0.0040.0000.0000.0000.000
171A198ARG10.9060.94134.292-0.056-0.0560.0000.0000.0000.000
172A199THR0-0.0150.00437.015-0.001-0.0010.0000.0000.0000.000
173A200TYR00.0070.00035.077-0.003-0.0030.0000.0000.0000.000
174A201LYS10.8820.95436.046-0.052-0.0520.0000.0000.0000.000
175A202PHE00.025-0.00331.7890.0010.0010.0000.0000.0000.000
176A203GLY00.0540.04635.388-0.001-0.0010.0000.0000.0000.000
177A204ALA0-0.035-0.01737.9390.0020.0020.0000.0000.0000.000
178A206TRP00.010-0.00538.514-0.005-0.0050.0000.0000.0000.000
179A207SER00.0950.04240.7980.0020.0020.0000.0000.0000.000
180A208ASP-1-0.760-0.87941.9650.0330.0330.0000.0000.0000.000
181A209ASP-1-0.828-0.90642.9760.0270.0270.0000.0000.0000.000
182A210SER0-0.016-0.01943.352-0.003-0.0030.0000.0000.0000.000
183A211PHE00.003-0.00937.194-0.002-0.0020.0000.0000.0000.000
184A212LYS10.7930.89641.781-0.032-0.0320.0000.0000.0000.000
185A213ARG10.8400.94544.323-0.023-0.0230.0000.0000.0000.000
186A214GLY00.0240.02042.532-0.002-0.0020.0000.0000.0000.000
187A215VAL0-0.044-0.02239.081-0.001-0.0010.0000.0000.0000.000
188A216ASP-1-0.820-0.90439.2720.0100.0100.0000.0000.0000.000
189A217VAL00.0450.01133.5950.0020.0020.0000.0000.0000.000
190A218MET0-0.006-0.01434.0980.0010.0010.0000.0000.0000.000
191A219ARG10.7810.90636.758-0.013-0.0130.0000.0000.0000.000
192A220PHE0-0.022-0.02837.4670.0010.0010.0000.0000.0000.000
193A221LEU0-0.0260.00331.4540.0040.0040.0000.0000.0000.000
194A222THR0-0.014-0.01431.215-0.005-0.0050.0000.0000.0000.000
195A223PRO00.001-0.00129.6500.0040.0040.0000.0000.0000.000
196A224PHE00.002-0.00723.5530.0000.0000.0000.0000.0000.000
197A225TYR0-0.0120.00121.248-0.011-0.0110.0000.0000.0000.000
198A226GLN00.032-0.00219.9170.0160.0160.0000.0000.0000.000
199A227GLN00.011-0.00613.728-0.036-0.0360.0000.0000.0000.000
200A228PRO00.0380.02913.6910.0150.0150.0000.0000.0000.000
201A229PRO00.011-0.00615.3650.0120.0120.0000.0000.0000.000
202A230HIS0-0.029-0.01417.7390.0090.0090.0000.0000.0000.000
203A231ARG10.9300.9519.691-0.171-0.1710.0000.0000.0000.000
204A232GLU-1-0.828-0.90011.7170.0480.0480.0000.0000.0000.000
205A233VAL0-0.0260.00515.8610.0040.0040.0000.0000.0000.000
206A234VAL00.0010.00518.1980.0070.0070.0000.0000.0000.000
207A235ASN0-0.038-0.04812.2960.0550.0550.0000.0000.0000.000
208A236TYR00.0030.01116.1510.0080.0080.0000.0000.0000.000
209A237TRP0-0.022-0.00918.3020.0010.0010.0000.0000.0000.000
210A238TYR0-0.037-0.04415.4910.0130.0130.0000.0000.0000.000
211A239ARG10.9440.96812.689-0.145-0.1450.0000.0000.0000.000
212A240LYS10.8730.95217.536-0.042-0.0420.0000.0000.0000.000
213A241ASN0-0.081-0.03920.962-0.011-0.0110.0000.0000.0000.000
214A242GLY00.0030.00719.5560.0080.0080.0000.0000.0000.000
215A243ARG10.7990.88017.388-0.235-0.2350.0000.0000.0000.000
216A244THR0-0.012-0.02510.957-0.036-0.0360.0000.0000.0000.000
217A245LEU0-0.0030.00711.3830.0280.0280.0000.0000.0000.000
218A246PRO00.0390.02410.5590.0820.0820.0000.0000.0000.000
219A247ARG10.9490.9725.362-1.447-1.4470.0000.0000.0000.000
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