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: 5JGMZ

Calculation Name: 5VO5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VO5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VKJ9

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1579316.483832
FMO2-HF: Nuclear repulsion 1507908.811691
FMO2-HF: Total energy -71407.672141
FMO2-MP2: Total energy -71614.0646


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-23.638-14.4984.9-6.333-7.7060.005
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.021
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].
3A5LEU0-0.029-0.0012.787-2.7201.0960.086-2.036-1.8670.007
4A6GLU-1-0.852-0.9292.411-13.372-8.7434.808-4.184-5.254-0.003
5A7ALA00.0490.0323.642-3.956-3.4690.008-0.104-0.3890.001
6A8LEU0-0.047-0.0235.769-1.204-1.142-0.001-0.002-0.0580.000
7A9GLN0-0.025-0.0206.757-0.578-0.5780.0000.0000.0000.000
8A10GLN00.011-0.0047.026-0.467-0.4670.0000.0000.0000.000
9A11ARG10.8920.9448.922-1.082-1.0820.0000.0000.0000.000
10A12LEU00.0060.01511.209-0.177-0.1770.0000.0000.0000.000
11A13GLU-1-0.878-0.93411.3770.4650.4650.0000.0000.0000.000
12A14LYS10.9410.99813.772-0.418-0.4180.0000.0000.0000.000
13A15TYR0-0.007-0.00215.260-0.103-0.1030.0000.0000.0000.000
14A16GLN00.0360.00615.915-0.028-0.0280.0000.0000.0000.000
15A17SER0-0.089-0.07318.040-0.044-0.0440.0000.0000.0000.000
16A18VAL0-0.004-0.01419.888-0.032-0.0320.0000.0000.0000.000
17A19GLU-1-0.868-0.94321.6310.1750.1750.0000.0000.0000.000
18A20ALA0-0.007-0.01222.654-0.025-0.0250.0000.0000.0000.000
19A21ALA00.0290.01624.139-0.018-0.0180.0000.0000.0000.000
20A22ALA0-0.006-0.00825.903-0.013-0.0130.0000.0000.0000.000
21A23LYS10.7590.87526.353-0.154-0.1540.0000.0000.0000.000
22A24ALA00.0210.02629.187-0.009-0.0090.0000.0000.0000.000
23A25GLU-1-0.900-0.94429.3910.1150.1150.0000.0000.0000.000
24A26ASN0-0.050-0.02332.347-0.003-0.0030.0000.0000.0000.000
25A27ASN00.0500.03430.741-0.004-0.0040.0000.0000.0000.000
26A28SER00.0440.00430.9500.0080.0080.0000.0000.0000.000
27A29GLY00.003-0.00131.1920.0060.0060.0000.0000.0000.000
28A30LYS10.9770.99726.091-0.146-0.1460.0000.0000.0000.000
29A31ALA00.011-0.00726.9290.0150.0150.0000.0000.0000.000
30A32ARG10.8340.92526.770-0.097-0.0970.0000.0000.0000.000
31A33ARG10.7820.85326.192-0.140-0.1400.0000.0000.0000.000
32A34PHE0-0.005-0.01121.1260.0170.0170.0000.0000.0000.000
33A35GLY00.0640.04222.0090.0230.0230.0000.0000.0000.000
34A36ARG10.6870.82022.988-0.149-0.1490.0000.0000.0000.000
35A37ILE00.0220.02518.3200.0140.0140.0000.0000.0000.000
36A38VAL00.010-0.00117.8010.0490.0490.0000.0000.0000.000
37A39LYS10.9540.98918.207-0.148-0.1480.0000.0000.0000.000
38A40GLN00.0260.02818.279-0.005-0.0050.0000.0000.0000.000
39A41TYR00.003-0.01211.5280.0620.0620.0000.0000.0000.000
40A42GLU-1-0.950-0.97514.4220.3080.3080.0000.0000.0000.000
41A43ASP-1-0.938-0.97116.5240.2260.2260.0000.0000.0000.000
42A44ALA0-0.014-0.01812.759-0.011-0.0110.0000.0000.0000.000
43A45ILE0-0.018-0.00911.2550.0370.0370.0000.0000.0000.000
44A46LYS10.8850.93812.576-0.241-0.2410.0000.0000.0000.000
45A47LEU0-0.039-0.01814.110-0.054-0.0540.0000.0000.0000.000
46A48TYR00.0460.0234.326-0.0230.123-0.001-0.007-0.1380.000
47A49LYS10.9160.95810.244-0.359-0.3590.0000.0000.0000.000
48A50ALA0-0.046-0.00911.671-0.087-0.0870.0000.0000.0000.000
49A51GLY00.0010.00811.682-0.035-0.0350.0000.0000.0000.000
50A52LYS10.8970.95512.732-0.149-0.1490.0000.0000.0000.000
51A53PRO00.000-0.00213.1840.0420.0420.0000.0000.0000.000
52A54VAL00.0360.01310.539-0.005-0.0050.0000.0000.0000.000
53A55PRO00.0190.01413.370-0.001-0.0010.0000.0000.0000.000
54A56TYR00.022-0.0177.988-0.026-0.0260.0000.0000.0000.000
55A57ASP-1-0.908-0.94713.6840.2800.2800.0000.0000.0000.000
56A58GLU-1-1.003-1.00216.7760.2230.2230.0000.0000.0000.000
57A59LEU0-0.064-0.01912.9200.0000.0000.0000.0000.0000.000
58A60PRO00.0450.05016.0350.0000.0000.0000.0000.0000.000
59A61VAL0-0.008-0.00612.8350.0770.0770.0000.0000.0000.000
60A62PRO0-0.0060.01014.127-0.048-0.0480.0000.0000.0000.000
61A63PRO00.043-0.00115.6940.0190.0190.0000.0000.0000.000
62A64GLY00.0250.01615.855-0.004-0.0040.0000.0000.0000.000
63A65PHE0-0.026-0.00610.918-0.003-0.0030.0000.0000.0000.000
64A66GLY00.0000.00010.1350.0610.0610.0000.0000.0000.000
65A76GLY00.0380.00639.0910.0000.0000.0000.0000.0000.000
66A77THR00.0510.01735.6710.0010.0010.0000.0000.0000.000
67A78THR00.0060.01033.1990.0060.0060.0000.0000.0000.000
68A79GLY00.0540.02334.2400.0040.0040.0000.0000.0000.000
69A80GLU-1-0.916-0.96936.8790.0670.0670.0000.0000.0000.000
70A81ALA0-0.039-0.01531.8790.0020.0020.0000.0000.0000.000
71A82ILE00.0350.02031.8920.0050.0050.0000.0000.0000.000
72A83GLN0-0.013-0.01133.5220.0030.0030.0000.0000.0000.000
73A84LYS10.9930.99234.357-0.080-0.0800.0000.0000.0000.000
74A85LEU00.0010.01428.4370.0020.0020.0000.0000.0000.000
75A86ARG10.9670.98932.122-0.081-0.0810.0000.0000.0000.000
76A87GLU-1-0.965-0.97434.2650.0770.0770.0000.0000.0000.000
77A88THR0-0.026-0.03331.078-0.001-0.0010.0000.0000.0000.000
78A89GLU-1-0.813-0.91530.0070.1300.1300.0000.0000.0000.000
79A90ASN00.0020.00232.3760.0030.0030.0000.0000.0000.000
80A91MET0-0.055-0.01835.355-0.003-0.0030.0000.0000.0000.000
81A92LEU00.0060.00828.8750.0000.0000.0000.0000.0000.000
82A93ILE00.0150.00832.1910.0030.0030.0000.0000.0000.000
83A94LYS10.9770.98833.728-0.079-0.0790.0000.0000.0000.000
84A95LYS10.8900.96333.745-0.098-0.0980.0000.0000.0000.000
85A96GLN0-0.0060.00230.6510.0040.0040.0000.0000.0000.000
86A97GLU-1-0.919-0.96033.1320.0870.0870.0000.0000.0000.000
87A98PHE0-0.021-0.01536.236-0.004-0.0040.0000.0000.0000.000
88A99LEU0-0.030-0.02132.095-0.004-0.0040.0000.0000.0000.000
89A100GLU-1-0.757-0.88632.0540.1140.1140.0000.0000.0000.000
90A101ALA00.0410.02735.135-0.003-0.0030.0000.0000.0000.000
91A102LYS10.9590.99038.010-0.078-0.0780.0000.0000.0000.000
92A103ILE0-0.021-0.01832.309-0.003-0.0030.0000.0000.0000.000
93A104GLU-1-0.945-0.96936.6080.0690.0690.0000.0000.0000.000
94A105ASP-1-0.895-0.94338.6750.0610.0610.0000.0000.0000.000
95A106GLU-1-0.910-0.97938.4840.0650.0650.0000.0000.0000.000
96A107LEU0-0.048-0.01836.608-0.003-0.0030.0000.0000.0000.000
97A108ASN0-0.006-0.01539.456-0.004-0.0040.0000.0000.0000.000
98A109ILE0-0.041-0.01843.068-0.005-0.0050.0000.0000.0000.000
99A110ALA0-0.014-0.01640.367-0.003-0.0030.0000.0000.0000.000
100A111ARG10.9530.97638.532-0.065-0.0650.0000.0000.0000.000
101A112LYS10.9290.97543.542-0.049-0.0490.0000.0000.0000.000
102A113ASN0-0.095-0.05146.125-0.005-0.0050.0000.0000.0000.000
103A114ALA00.0340.02943.8670.0000.0000.0000.0000.0000.000
104A115SER0-0.007-0.00745.2760.0000.0000.0000.0000.0000.000
105A116LYS10.9370.98348.393-0.039-0.0390.0000.0000.0000.000
106A117ASN00.0390.01348.9070.0000.0000.0000.0000.0000.000
107A118LYS11.0471.02543.128-0.045-0.0450.0000.0000.0000.000
108A119GLU-1-0.864-0.95844.7790.0510.0510.0000.0000.0000.000
109A120VAL0-0.032-0.00144.7060.0030.0030.0000.0000.0000.000
110A121ALA00.0180.01343.0390.0030.0030.0000.0000.0000.000
111A122LEU0-0.004-0.00338.7000.0040.0040.0000.0000.0000.000
112A123GLN00.008-0.00639.6470.0060.0060.0000.0000.0000.000
113A124ALA00.0330.02040.1040.0040.0040.0000.0000.0000.000
114A125LEU0-0.0010.00036.3970.0050.0050.0000.0000.0000.000
115A126LYS10.8860.94533.585-0.077-0.0770.0000.0000.0000.000
116A127LYS10.9690.99335.248-0.059-0.0590.0000.0000.0000.000
117A128LYS10.9761.00133.236-0.089-0.0890.0000.0000.0000.000
118A129LYS10.9370.97128.864-0.104-0.1040.0000.0000.0000.000
119A130GLU-1-0.927-0.96430.6960.1220.1220.0000.0000.0000.000
120A131LEU00.010-0.00431.7590.0050.0050.0000.0000.0000.000
121A132GLU-1-0.892-0.95228.9270.1220.1220.0000.0000.0000.000
122A133LYS10.9390.97627.055-0.115-0.1150.0000.0000.0000.000
123A134GLN0-0.027-0.02027.3690.0070.0070.0000.0000.0000.000
124A135LEU0-0.019-0.01328.6430.0030.0030.0000.0000.0000.000
125A136GLN00.0090.01721.8700.0000.0000.0000.0000.0000.000
126A137GLN0-0.004-0.00924.2920.0120.0120.0000.0000.0000.000
127A138ILE0-0.043-0.02325.4800.0030.0030.0000.0000.0000.000
128A139ASP-1-0.744-0.85524.0810.1780.1780.0000.0000.0000.000
129A140GLY00.0280.01321.7730.0090.0090.0000.0000.0000.000
130A141THR0-0.013-0.00222.4160.0070.0070.0000.0000.0000.000
131A142LEU0-0.025-0.01224.485-0.004-0.0040.0000.0000.0000.000
132A143SER0-0.0040.00321.9690.0040.0040.0000.0000.0000.000
133A144THR0-0.018-0.02120.6360.0110.0110.0000.0000.0000.000
134A145ILE00.001-0.00322.431-0.007-0.0070.0000.0000.0000.000
135A146GLU-1-0.748-0.84125.8090.1520.1520.0000.0000.0000.000
136A147MET0-0.027-0.00919.3950.0030.0030.0000.0000.0000.000
137A148GLN0-0.015-0.00223.439-0.002-0.0020.0000.0000.0000.000
138A149ARG10.8100.89424.568-0.133-0.1330.0000.0000.0000.000
139A150GLU-1-0.939-0.96726.0190.1410.1410.0000.0000.0000.000
140A151ALA0-0.010-0.00523.783-0.009-0.0090.0000.0000.0000.000
141A152LEU0-0.004-0.00525.893-0.010-0.0100.0000.0000.0000.000
142A153GLU-1-0.839-0.92728.6470.0920.0920.0000.0000.0000.000
143A154SER0-0.011-0.00127.691-0.010-0.0100.0000.0000.0000.000
144A155ALA0-0.022-0.00727.452-0.008-0.0080.0000.0000.0000.000
145A156ASN0-0.013-0.01429.409-0.008-0.0080.0000.0000.0000.000
146A157THR0-0.005-0.00332.799-0.008-0.0080.0000.0000.0000.000
147A158ASN00.014-0.00228.750-0.009-0.0090.0000.0000.0000.000
148A159THR00.0100.01632.096-0.006-0.0060.0000.0000.0000.000
149A160ALA00.0080.02334.236-0.005-0.0050.0000.0000.0000.000
150A161VAL0-0.006-0.01235.597-0.005-0.0050.0000.0000.0000.000
151A162LEU00.004-0.00931.969-0.005-0.0050.0000.0000.0000.000
152A163THR0-0.043-0.02736.591-0.004-0.0040.0000.0000.0000.000
153A164THR0-0.014-0.01439.510-0.003-0.0030.0000.0000.0000.000
154A165MET00.0090.00837.727-0.002-0.0020.0000.0000.0000.000
155A166LYS10.8670.94939.773-0.029-0.0290.0000.0000.0000.000
156A167ASN00.0270.00341.497-0.003-0.0030.0000.0000.0000.000
157A168ALA0-0.0010.00643.924-0.002-0.0020.0000.0000.0000.000
158A169ALA00.0130.00542.537-0.002-0.0020.0000.0000.0000.000
159A170ASP-1-0.849-0.93344.6270.0210.0210.0000.0000.0000.000
160A171ALA0-0.022-0.00746.869-0.002-0.0020.0000.0000.0000.000
161A172LEU0-0.013-0.01645.881-0.002-0.0020.0000.0000.0000.000
162A173LYS10.9300.96845.722-0.014-0.0140.0000.0000.0000.000
163A174ARG10.9130.96549.581-0.014-0.0140.0000.0000.0000.000
164A175ALA0-0.039-0.01552.450-0.001-0.0010.0000.0000.0000.000
165A176HIS0-0.035-0.01250.255-0.001-0.0010.0000.0000.0000.000
166A177GLN0-0.019-0.01153.8100.0010.0010.0000.0000.0000.000
167A178ASN00.0390.02354.3300.0000.0000.0000.0000.0000.000
168A179MET00.028-0.00158.1210.0000.0000.0000.0000.0000.000
169A180ASP-1-0.875-0.92260.1940.0020.0020.0000.0000.0000.000
170A181VAL0-0.036-0.03758.077-0.001-0.0010.0000.0000.0000.000
171A182ASP-1-0.896-0.95061.1070.0050.0050.0000.0000.0000.000
172A183LYS10.9030.96463.220-0.002-0.0020.0000.0000.0000.000
173A184VAL0-0.035-0.03064.2970.0000.0000.0000.0000.0000.000
174A185HIS00.032-0.00660.283-0.001-0.0010.0000.0000.0000.000
175A186ASP-1-0.947-0.96265.7520.0030.0030.0000.0000.0000.000
176A187MET0-0.069-0.03768.6130.0000.0000.0000.0000.0000.000
177A188MET0-0.114-0.04665.5010.0000.0000.0000.0000.0000.000
178A189ASP-1-0.943-0.95967.7310.0020.0020.0000.0000.0000.000
179A190ASP-1-1.057-1.01070.9040.0020.0020.0000.0000.0000.000