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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: 5JN5Z

Calculation Name: 2P2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q75TD0

Base Structure: X-ray

Registration Date: 2023-09-22

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1935416.113561
FMO2-HF: Nuclear repulsion 1864085.340431
FMO2-HF: Total energy -71330.773131
FMO2-MP2: Total energy -71540.565024


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:2:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-157.226-144.69616.263-12.544-16.251-0.118
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.882 / q_NPA : 0.951
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].
3A4GLU-1-0.740-0.8742.986-46.071-42.8830.203-1.731-1.661-0.001
4A5LYS10.8660.9255.67623.96223.9620.0000.0000.0000.000
5A6GLU-1-0.804-0.8772.027-65.384-61.5014.804-3.989-4.698-0.036
6A7LYS10.7610.8672.57523.59128.1761.742-2.477-3.850-0.021
7A8MET0-0.0120.0163.2172.5382.4410.0410.323-0.267-0.001
8A9LEU0-0.004-0.0015.7042.0872.0870.0000.0000.0000.000
9A10ALA0-0.072-0.0282.056-1.528-1.6533.025-1.453-1.447-0.012
10A11GLY00.0150.0213.9183.5243.769-0.001-0.132-0.112-0.001
11A12HIS0-0.113-0.0532.106-26.569-25.7186.449-3.085-4.216-0.046
12A13LEU00.0200.0035.8662.3802.3800.0000.0000.0000.000
13A14TYR0-0.027-0.0276.903-4.830-4.8300.0000.0000.0000.000
14A15ASN00.0570.0188.4464.1264.1260.0000.0000.0000.000
15A16PRO00.0490.03110.884-0.611-0.6110.0000.0000.0000.000
16A17ALA0-0.014-0.00713.0291.0031.0030.0000.0000.0000.000
17A18ASP-1-0.848-0.9279.502-26.053-26.0530.0000.0000.0000.000
18A19LEU00.022-0.01011.9000.7340.7340.0000.0000.0000.000
19A20GLU-1-0.899-0.9269.356-25.904-25.9040.0000.0000.0000.000
20A21LEU00.002-0.0068.9000.9370.9370.0000.0000.0000.000
21A22VAL0-0.0140.00212.6471.2221.2220.0000.0000.0000.000
22A23LYS10.9790.99515.82916.29016.2900.0000.0000.0000.000
23A24GLU-1-0.871-0.91712.767-22.028-22.0280.0000.0000.0000.000
24A25ARG10.8810.93414.13220.31620.3160.0000.0000.0000.000
25A26GLU-1-0.936-0.96818.145-13.535-13.5350.0000.0000.0000.000
26A27ARG10.8880.94516.27717.92617.9260.0000.0000.0000.000
27A28ALA00.0420.03019.4830.6690.6690.0000.0000.0000.000
28A29ARG10.8140.88219.36116.05416.0540.0000.0000.0000.000
29A30ARG10.9160.97324.12712.27112.2710.0000.0000.0000.000
30A31LEU00.0120.00123.1970.5760.5760.0000.0000.0000.000
31A32VAL00.0020.01524.2340.4720.4720.0000.0000.0000.000
32A33ARG10.8190.89727.10210.54110.5410.0000.0000.0000.000
33A34LEU0-0.015-0.01228.9980.3860.3860.0000.0000.0000.000
34A35TYR0-0.037-0.03929.2060.3180.3180.0000.0000.0000.000
35A36ASN0-0.026-0.02629.0960.3850.3850.0000.0000.0000.000
36A37GLU-1-0.873-0.91732.709-9.212-9.2120.0000.0000.0000.000
37A38THR0-0.086-0.02633.9340.3090.3090.0000.0000.0000.000
38A39LEU00.0280.00436.6090.0410.0410.0000.0000.0000.000
39A40GLU-1-0.881-0.93638.845-7.731-7.7310.0000.0000.0000.000
40A41THR0-0.004-0.02540.421-0.036-0.0360.0000.0000.0000.000
41A42GLU-1-0.825-0.88637.939-8.411-8.4110.0000.0000.0000.000
42A43TYR00.008-0.00736.831-0.242-0.2420.0000.0000.0000.000
43A44ASP-1-0.887-0.94435.448-8.657-8.6570.0000.0000.0000.000
44A45LYS10.7860.88934.4558.4658.4650.0000.0000.0000.000
45A46ARG10.8600.92532.4738.6588.6580.0000.0000.0000.000
46A47THR00.0070.00130.783-0.423-0.4230.0000.0000.0000.000
47A48GLY0-0.011-0.00729.616-0.382-0.3820.0000.0000.0000.000
48A49LEU0-0.0010.00228.545-0.355-0.3550.0000.0000.0000.000
49A50LEU00.000-0.00426.154-0.539-0.5390.0000.0000.0000.000
50A51LYS10.8320.92424.83110.27910.2790.0000.0000.0000.000
51A52GLU-1-0.986-0.97224.178-12.604-12.6040.0000.0000.0000.000
52A53LEU0-0.061-0.03721.605-0.635-0.6350.0000.0000.0000.000
53A54PHE0-0.022-0.03220.448-0.685-0.6850.0000.0000.0000.000
54A55GLY00.0170.02617.739-0.021-0.0210.0000.0000.0000.000
55A56SER0-0.098-0.06218.6200.3690.3690.0000.0000.0000.000
56A57THR00.012-0.01421.393-0.047-0.0470.0000.0000.0000.000
57A58GLY00.0360.03724.807-0.035-0.0350.0000.0000.0000.000
58A59GLU-1-0.936-0.99527.944-10.075-10.0750.0000.0000.0000.000
59A60ARG10.8850.95531.2698.7338.7330.0000.0000.0000.000
60A61LEU00.0160.00926.833-0.217-0.2170.0000.0000.0000.000
61A62PHE0-0.025-0.01230.8640.1900.1900.0000.0000.0000.000
62A63ILE00.0220.01626.842-0.150-0.1500.0000.0000.0000.000
63A64GLU-1-0.827-0.89531.304-8.548-8.5480.0000.0000.0000.000
64A65PRO0-0.0520.00732.295-0.273-0.2730.0000.0000.0000.000
65A66ASN0-0.055-0.04531.0100.1590.1590.0000.0000.0000.000
66A67PHE00.0580.02223.221-0.024-0.0240.0000.0000.0000.000
67A68ARG10.8580.92325.04210.96810.9680.0000.0000.0000.000
68A69CYS0-0.0020.01320.3360.1090.1090.0000.0000.0000.000
69A70ASP-1-0.842-0.90916.656-16.972-16.9720.0000.0000.0000.000
70A71TYR0-0.009-0.03012.7310.0780.0780.0000.0000.0000.000
71A72GLY0-0.009-0.00217.0810.4310.4310.0000.0000.0000.000
72A73TYR00.020-0.02711.749-0.292-0.2920.0000.0000.0000.000
73A74ASN0-0.080-0.03811.324-1.022-1.0220.0000.0000.0000.000
74A75ILE0-0.0250.00314.925-0.043-0.0430.0000.0000.0000.000
75A76HIS0-0.0120.00314.5891.2931.2930.0000.0000.0000.000
76A77VAL0-0.025-0.01219.8620.1050.1050.0000.0000.0000.000
77A78GLY00.0650.03823.4490.0350.0350.0000.0000.0000.000
78A79GLU-1-0.875-0.94526.032-10.338-10.3380.0000.0000.0000.000
79A80ASN0-0.101-0.05529.6470.1710.1710.0000.0000.0000.000
80A81PHE00.0510.03925.8880.0990.0990.0000.0000.0000.000
81A82PHE00.0230.00629.5420.2460.2460.0000.0000.0000.000
82A83MET0-0.035-0.00526.086-0.342-0.3420.0000.0000.0000.000
83A84ASN00.0280.01030.4880.2130.2130.0000.0000.0000.000
84A85PHE00.0210.00731.870-0.252-0.2520.0000.0000.0000.000
85A86ASP-1-0.839-0.90831.413-9.497-9.4970.0000.0000.0000.000
86A87GLY0-0.0070.00528.159-0.102-0.1020.0000.0000.0000.000
87A88VAL0-0.052-0.04323.176-0.056-0.0560.0000.0000.0000.000
88A89ILE00.0210.00819.380-0.017-0.0170.0000.0000.0000.000
89A90LEU00.0090.01718.226-0.138-0.1380.0000.0000.0000.000
90A91ASP-1-0.670-0.83015.778-18.620-18.6200.0000.0000.0000.000
91A92VAL00.0430.01810.823-0.739-0.7390.0000.0000.0000.000
92A93CYS0-0.035-0.0088.838-2.305-2.3050.0000.0000.0000.000
93A94GLU-1-0.795-0.87111.172-21.141-21.1410.0000.0000.0000.000
94A95VAL0-0.004-0.00513.4510.4020.4020.0000.0000.0000.000
95A96ARG10.7880.87214.22920.08020.0800.0000.0000.0000.000
96A97ILE0-0.004-0.01118.7770.2790.2790.0000.0000.0000.000
97A98GLY00.0050.01522.5640.0000.0000.0000.0000.0000.000
98A99ASP-1-0.831-0.93625.123-11.142-11.1420.0000.0000.0000.000
99A100HIS0-0.064-0.04428.5640.2110.2110.0000.0000.0000.000
100A101CYS0-0.0430.00727.7080.0790.0790.0000.0000.0000.000
101A102PHE00.0320.02129.7690.1920.1920.0000.0000.0000.000
102A103ILE00.013-0.00426.239-0.063-0.0630.0000.0000.0000.000
103A104GLY00.002-0.00230.6010.2290.2290.0000.0000.0000.000
104A105PRO00.004-0.00131.676-0.246-0.2460.0000.0000.0000.000
105A106GLY00.035-0.00331.3470.0570.0570.0000.0000.0000.000
106A107VAL0-0.081-0.02526.603-0.084-0.0840.0000.0000.0000.000
107A108HIS00.0090.01924.746-0.545-0.5450.0000.0000.0000.000
108A109ILE00.0100.00119.8910.1290.1290.0000.0000.0000.000
109A110TYR0-0.035-0.04019.277-0.212-0.2120.0000.0000.0000.000
110A111THR00.001-0.01313.828-0.594-0.5940.0000.0000.0000.000
111A112ALA00.0170.01614.294-1.345-1.3450.0000.0000.0000.000
112A113THR0-0.057-0.03614.3821.5851.5850.0000.0000.0000.000
113A114HIS00.0160.00015.165-0.762-0.7620.0000.0000.0000.000
114A115PRO00.0260.02414.9110.3690.3690.0000.0000.0000.000
115A116LEU00.003-0.01617.2390.8760.8760.0000.0000.0000.000
116A117ASP-1-0.782-0.88020.090-13.148-13.1480.0000.0000.0000.000
117A118PRO0-0.027-0.02021.009-0.478-0.4780.0000.0000.0000.000
118A119HIS00.0070.01020.6050.1210.1210.0000.0000.0000.000
119A120GLU-1-0.902-0.96617.141-18.073-18.0730.0000.0000.0000.000
120A121ARG10.8110.92417.39813.53813.5380.0000.0000.0000.000
121A122ASN0-0.039-0.03418.961-0.370-0.3700.0000.0000.0000.000
122A123SER0-0.061-0.02815.634-0.237-0.2370.0000.0000.0000.000
123A124GLY0-0.0090.00016.193-0.267-0.2670.0000.0000.0000.000
124A125LEU0-0.070-0.03210.357-1.038-1.0380.0000.0000.0000.000
125A126GLU-1-0.825-0.88912.081-18.812-18.8120.0000.0000.0000.000
126A127TYR0-0.015-0.0399.875-2.584-2.5840.0000.0000.0000.000
127A128GLY00.0410.0129.9292.4172.4170.0000.0000.0000.000
128A129LYS10.9140.95410.39017.97017.9700.0000.0000.0000.000
129A130PRO00.0510.02410.8561.3681.3680.0000.0000.0000.000
130A131VAL0-0.0170.01213.6110.8340.8340.0000.0000.0000.000
131A132VAL0-0.024-0.00716.688-0.228-0.2280.0000.0000.0000.000
132A133ILE0-0.003-0.01319.2070.6130.6130.0000.0000.0000.000
133A134GLY00.0280.02222.926-0.150-0.1500.0000.0000.0000.000
134A135HIS00.0580.03125.2660.2320.2320.0000.0000.0000.000
135A136ASN0-0.065-0.04628.2700.2950.2950.0000.0000.0000.000
136A137VAL0-0.0060.01627.1470.2310.2310.0000.0000.0000.000
137A138TRP0-0.023-0.00730.1890.2210.2210.0000.0000.0000.000
138A139ILE00.0180.00226.014-0.003-0.0030.0000.0000.0000.000
139A140GLY00.0180.00530.4610.1540.1540.0000.0000.0000.000
140A141GLY00.041-0.00432.035-0.248-0.2480.0000.0000.0000.000
141A142ARG10.9270.95131.7599.5639.5630.0000.0000.0000.000
142A143ALA0-0.0400.00829.119-0.024-0.0240.0000.0000.0000.000
143A144VAL00.0200.00624.834-0.139-0.1390.0000.0000.0000.000
144A145ILE0-0.0110.00221.7160.2300.2300.0000.0000.0000.000
145A146ASN0-0.023-0.03121.085-0.559-0.5590.0000.0000.0000.000
146A147PRO00.0450.01115.612-0.051-0.0510.0000.0000.0000.000
147A148GLY0-0.057-0.03015.6400.3340.3340.0000.0000.0000.000
148A149VAL0-0.0610.00516.5150.4670.4670.0000.0000.0000.000
149A150THR00.0230.00719.199-0.554-0.5540.0000.0000.0000.000
150A151ILE0-0.047-0.03121.0600.7040.7040.0000.0000.0000.000
151A152GLY00.0290.00524.566-0.164-0.1640.0000.0000.0000.000
152A153ASP-1-0.799-0.91026.534-11.277-11.2770.0000.0000.0000.000
153A154ASN0-0.056-0.03728.8020.5330.5330.0000.0000.0000.000
154A155ALA0-0.0160.01829.0430.3280.3280.0000.0000.0000.000
155A156VAL0-0.020-0.01331.1430.0520.0520.0000.0000.0000.000
156A157ILE0-0.028-0.00328.0560.0320.0320.0000.0000.0000.000
157A158ALA00.0440.01931.5710.1490.1490.0000.0000.0000.000
158A159SER00.0410.00533.318-0.174-0.1740.0000.0000.0000.000
159A160GLY0-0.073-0.03333.3460.1710.1710.0000.0000.0000.000
160A161ALA0-0.083-0.02430.939-0.053-0.0530.0000.0000.0000.000
161A162VAL00.0260.01827.293-0.269-0.2690.0000.0000.0000.000
162A163VAL00.007-0.01324.9670.1660.1660.0000.0000.0000.000
163A164THR00.0050.00523.806-0.451-0.4510.0000.0000.0000.000
164A165LYS10.9510.98022.99010.49810.4980.0000.0000.0000.000
165A166ASP-1-0.784-0.88021.212-14.534-14.5340.0000.0000.0000.000
166A167VAL0-0.075-0.03923.9200.6550.6550.0000.0000.0000.000
167A168PRO0-0.011-0.00426.582-0.196-0.1960.0000.0000.0000.000
168A169ALA00.0820.03828.6590.1160.1160.0000.0000.0000.000
169A170ASN0-0.067-0.04629.8350.0710.0710.0000.0000.0000.000
170A171ALA00.0150.02731.3870.3730.3730.0000.0000.0000.000
171A172VAL00.0060.00332.693-0.105-0.1050.0000.0000.0000.000
172A173VAL00.0070.00129.5620.1190.1190.0000.0000.0000.000
173A174GLY00.0450.01133.0240.0410.0410.0000.0000.0000.000
174A175GLY0-0.0120.00034.4100.0470.0470.0000.0000.0000.000
175A176ASN00.0170.01130.857-0.546-0.5460.0000.0000.0000.000
176A177PRO00.0400.01328.8490.1940.1940.0000.0000.0000.000
177A178ALA0-0.048-0.00429.4500.3320.3320.0000.0000.0000.000
178A179LYS10.9060.94630.7008.2458.2450.0000.0000.0000.000
179A180VAL00.0710.02532.0390.0590.0590.0000.0000.0000.000
180A181ILE0-0.080-0.04434.2260.2280.2280.0000.0000.0000.000
181A182LYS10.9450.97636.8788.0468.0460.0000.0000.0000.000
182A183TRP00.0410.02232.584-0.291-0.2910.0000.0000.0000.000
183A184LEU0-0.032-0.00635.4870.3090.3090.0000.0000.0000.000
184A185LYS10.9420.97935.4528.6788.6780.0000.0000.0000.000