Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 89G8Y

Calculation Name: 3NAS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NAS

Chain ID: A

ChEMBL ID:

UniProt ID: O06995

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287301.313169
FMO2-HF: Nuclear repulsion 2205834.417477
FMO2-HF: Total energy -81466.895692
FMO2-MP2: Total energy -81704.462763


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-21.973-5.44616.369-10.469-22.431-0.089
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : 0.022
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].
3A3ALA00.002-0.0062.740-2.6480.2200.059-1.446-1.4810.002
4A4VAL0-0.0040.0082.521-2.229-0.6471.072-0.726-1.929-0.006
5A5ILE0-0.032-0.0144.6070.2370.291-0.001-0.011-0.0420.000
6A6PHE00.0250.0107.904-0.098-0.0980.0000.0000.0000.000
7A7ASP-1-0.712-0.83010.763-0.134-0.1340.0000.0000.0000.000
8A8LEU0-0.032-0.05114.366-0.022-0.0220.0000.0000.0000.000
9A9ASP-1-0.825-0.90217.236-0.183-0.1830.0000.0000.0000.000
10A10GLY00.0410.04617.705-0.019-0.0190.0000.0000.0000.000
11A11VAL0-0.072-0.02912.331-0.029-0.0290.0000.0000.0000.000
12A12ILE0-0.035-0.02813.087-0.027-0.0270.0000.0000.0000.000
13A13THR00.0220.00616.5990.0230.0230.0000.0000.0000.000
14A14ASP-1-0.798-0.89620.438-0.210-0.2100.0000.0000.0000.000
15A15THR0-0.064-0.07422.3170.0140.0140.0000.0000.0000.000
16A16ALA00.0310.02524.0170.0170.0170.0000.0000.0000.000
17A17GLU-1-0.762-0.84925.711-0.128-0.1280.0000.0000.0000.000
18A18TYR0-0.066-0.07524.3670.0130.0130.0000.0000.0000.000
19A19HIS00.0210.00226.4870.0200.0200.0000.0000.0000.000
20A20PHE0-0.0160.00529.9520.0120.0120.0000.0000.0000.000
21A21LEU0-0.026-0.01230.7820.0110.0110.0000.0000.0000.000
22A22ALA00.0050.01032.7820.0070.0070.0000.0000.0000.000
23A23TRP0-0.035-0.02333.0680.0100.0100.0000.0000.0000.000
24A24LYS10.8780.93835.8950.0960.0960.0000.0000.0000.000
25A25HIS10.8240.89635.9500.0920.0920.0000.0000.0000.000
26A26ILE0-0.040-0.01738.2350.0050.0050.0000.0000.0000.000
27A27ALA00.0090.01240.2140.0040.0040.0000.0000.0000.000
28A28GLU-1-0.766-0.86340.354-0.078-0.0780.0000.0000.0000.000
29A29GLN0-0.063-0.02541.1850.0060.0060.0000.0000.0000.000
30A30ILE0-0.052-0.02044.6300.0030.0030.0000.0000.0000.000
31A31ASP-1-0.933-0.95046.858-0.052-0.0520.0000.0000.0000.000
32A32ILE0-0.055-0.01843.6470.0010.0010.0000.0000.0000.000
33A33PRO0-0.045-0.02743.301-0.003-0.0030.0000.0000.0000.000
34A34PHE00.012-0.01435.0240.0000.0000.0000.0000.0000.000
35A35ASP-1-0.853-0.94637.452-0.098-0.0980.0000.0000.0000.000
36A36ARG10.8580.88529.8770.1380.1380.0000.0000.0000.000
37A37ASP-1-0.800-0.86133.687-0.108-0.1080.0000.0000.0000.000
38A38MET0-0.0180.00235.8920.0010.0010.0000.0000.0000.000
39A39ASN00.026-0.00130.4960.0040.0040.0000.0000.0000.000
40A40GLU-1-0.881-0.92430.594-0.148-0.1480.0000.0000.0000.000
41A41ARG10.8330.89531.7730.0940.0940.0000.0000.0000.000
42A42LEU0-0.015-0.00533.7690.0030.0030.0000.0000.0000.000
43A43LYS10.8020.88426.9910.1500.1500.0000.0000.0000.000
44A44GLY0-0.0010.00828.9930.0000.0000.0000.0000.0000.000
45A45ILE0-0.0270.00829.6080.0070.0070.0000.0000.0000.000
46A46SER00.0140.00932.794-0.002-0.0020.0000.0000.0000.000
47A47ARG10.8150.86934.1030.0610.0610.0000.0000.0000.000
48A48GLU-1-0.722-0.87135.429-0.059-0.0590.0000.0000.0000.000
49A49GLU-1-0.868-0.92336.513-0.074-0.0740.0000.0000.0000.000
50A50SER00.0100.01535.079-0.002-0.0020.0000.0000.0000.000
51A51LEU0-0.012-0.00637.5470.0000.0000.0000.0000.0000.000
52A52GLU-1-0.801-0.89240.226-0.050-0.0500.0000.0000.0000.000
53A53SER0-0.028-0.02639.6370.0010.0010.0000.0000.0000.000
54A54ILE0-0.049-0.02437.7860.0000.0000.0000.0000.0000.000
55A55LEU0-0.007-0.01542.0460.0020.0020.0000.0000.0000.000
56A56ILE00.0100.00744.5620.0020.0020.0000.0000.0000.000
57A57PHE0-0.057-0.01543.9140.0020.0020.0000.0000.0000.000
58A58GLY00.0380.02846.1480.0000.0000.0000.0000.0000.000
59A59GLY0-0.031-0.01648.6110.0030.0030.0000.0000.0000.000
60A60ALA0-0.043-0.02448.1890.0030.0030.0000.0000.0000.000
61A61GLU-1-0.759-0.84747.586-0.048-0.0480.0000.0000.0000.000
62A62THR0-0.064-0.06548.7410.0020.0020.0000.0000.0000.000
63A63LYS10.7780.89451.1650.0490.0490.0000.0000.0000.000
64A64TYR00.0090.01848.3560.0000.0000.0000.0000.0000.000
65A65THR0-0.030-0.05250.1860.0000.0000.0000.0000.0000.000
66A66ASN00.036-0.00345.287-0.004-0.0040.0000.0000.0000.000
67A67ALA00.0050.00646.059-0.002-0.0020.0000.0000.0000.000
68A68GLU-1-0.768-0.85646.517-0.040-0.0400.0000.0000.0000.000
69A69LYS10.8180.88143.8050.0460.0460.0000.0000.0000.000
70A70GLN0-0.028-0.02141.177-0.004-0.0040.0000.0000.0000.000
71A71GLU-1-0.850-0.92741.511-0.050-0.0500.0000.0000.0000.000
72A72LEU00.005-0.00142.080-0.003-0.0030.0000.0000.0000.000
73A73MET0-0.0250.00837.906-0.005-0.0050.0000.0000.0000.000
74A74HIS0-0.057-0.01437.254-0.003-0.0030.0000.0000.0000.000
75A75ARG10.8630.91837.7840.0540.0540.0000.0000.0000.000
76A76LYS10.8590.95132.2640.0960.0960.0000.0000.0000.000
77A77ASN00.0160.00032.161-0.010-0.0100.0000.0000.0000.000
78A78ARG10.9300.95633.3170.0500.0500.0000.0000.0000.000
79A79ASP-1-0.864-0.93734.955-0.086-0.0860.0000.0000.0000.000
80A80TYR00.0350.01825.422-0.003-0.0030.0000.0000.0000.000
81A81GLN0-0.042-0.02728.959-0.006-0.0060.0000.0000.0000.000
82A82MET0-0.027-0.01131.0220.0000.0000.0000.0000.0000.000
83A83LEU0-0.032-0.00830.0550.0000.0000.0000.0000.0000.000
84A84ILE00.0570.03325.063-0.003-0.0030.0000.0000.0000.000
85A85SER0-0.136-0.09127.7330.0010.0010.0000.0000.0000.000
86A86LYS10.8910.93330.3590.0930.0930.0000.0000.0000.000
87A87LEU0-0.0130.03424.0720.0010.0010.0000.0000.0000.000
88A88THR0-0.053-0.05326.6020.0080.0080.0000.0000.0000.000
89A89PRO00.024-0.00322.851-0.010-0.0100.0000.0000.0000.000
90A90GLU-1-0.899-0.92422.425-0.164-0.1640.0000.0000.0000.000
91A91ASP-1-0.833-0.88523.737-0.160-0.1600.0000.0000.0000.000
92A92LEU0-0.070-0.02316.297-0.013-0.0130.0000.0000.0000.000
93A93LEU00.0010.01517.008-0.001-0.0010.0000.0000.0000.000
94A94PRO00.014-0.00416.984-0.029-0.0290.0000.0000.0000.000
95A95GLY00.0220.02214.712-0.027-0.0270.0000.0000.0000.000
96A96ILE00.0460.02812.143-0.047-0.0470.0000.0000.0000.000
97A97GLY00.0460.02312.579-0.028-0.0280.0000.0000.0000.000
98A98ARG10.7370.84411.2890.6390.6390.0000.0000.0000.000
99A99LEU00.0250.0226.117-0.017-0.0170.0000.0000.0000.000
100A100LEU00.0180.0098.936-0.089-0.0890.0000.0000.0000.000
101A101CYS0-0.021-0.00510.9190.0110.0110.0000.0000.0000.000
102A102GLN00.013-0.0128.5510.0510.0510.0000.0000.0000.000
103A103LEU00.0280.0164.296-0.138-0.036-0.001-0.009-0.0920.000
104A104LYS10.7700.8967.8860.2740.2740.0000.0000.0000.000
105A105ASN0-0.070-0.02810.9090.1460.1460.0000.0000.0000.000
106A106GLU-1-0.898-0.9556.240-1.304-1.3040.0000.0000.0000.000
107A107ASN0-0.118-0.0587.9130.1380.1380.0000.0000.0000.000
108A108ILE0-0.0110.0222.700-0.8680.1410.292-0.206-1.0950.000
109A109LYS10.8160.9055.810-0.689-0.6890.0000.0000.0000.000
110A110ILE00.0410.0246.766-0.210-0.2100.0000.0000.0000.000
111A111GLY00.0280.0028.9840.1350.1350.0000.0000.0000.000
112A112LEU0-0.073-0.03010.502-0.074-0.0740.0000.0000.0000.000
113A113ALA00.0350.00512.6600.0540.0540.0000.0000.0000.000
114A114SER0-0.009-0.01114.3390.0200.0200.0000.0000.0000.000
115A115SER00.0300.00917.1900.0270.0270.0000.0000.0000.000
116A116SER0-0.0110.00320.3610.0220.0220.0000.0000.0000.000
117A117ARG10.9920.98121.9320.0560.0560.0000.0000.0000.000
118A118ASN0-0.036-0.02324.0710.0160.0160.0000.0000.0000.000
119A119ALA00.0990.05918.921-0.001-0.0010.0000.0000.0000.000
120A120PRO00.0640.03420.539-0.011-0.0110.0000.0000.0000.000
121A121LYS10.8640.91921.4650.0590.0590.0000.0000.0000.000
122A122ILE0-0.0170.01721.3820.0060.0060.0000.0000.0000.000
123A123LEU00.1020.04516.1470.0000.0000.0000.0000.0000.000
124A124ARG10.8250.90520.0730.0760.0760.0000.0000.0000.000
125A125ARG10.7770.88823.0650.1020.1020.0000.0000.0000.000
126A126LEU00.0040.00419.2920.0030.0030.0000.0000.0000.000
127A127ALA0-0.051-0.02421.010-0.013-0.0130.0000.0000.0000.000
128A128ILE00.0740.03915.806-0.002-0.0020.0000.0000.0000.000
129A129ILE0-0.064-0.03416.930-0.012-0.0120.0000.0000.0000.000
130A130ASP-1-0.841-0.90917.369-0.090-0.0900.0000.0000.0000.000
131A131ASP-1-0.818-0.92813.383-0.275-0.2750.0000.0000.0000.000
132A132PHE0-0.062-0.02112.188-0.020-0.0200.0000.0000.0000.000
133A133HIS0-0.014-0.01312.2890.0170.0170.0000.0000.0000.000
134A134ALA00.0110.01312.8970.0500.0500.0000.0000.0000.000
135A135ILE0-0.039-0.03213.938-0.055-0.0550.0000.0000.0000.000
136A136VAL0-0.0080.00714.8700.0270.0270.0000.0000.0000.000
137A137ASP-1-0.951-0.96117.564-0.010-0.0100.0000.0000.0000.000
138A138PRO0-0.078-0.03521.0810.0120.0120.0000.0000.0000.000
139A148PRO0-0.017-0.03218.1890.0020.0020.0000.0000.0000.000
140A149ASP-1-0.881-0.94516.5090.0210.0210.0000.0000.0000.000
141A150ILE00.0290.02415.4290.0240.0240.0000.0000.0000.000
142A151PHE00.0710.01910.5780.0080.0080.0000.0000.0000.000
143A152LEU00.0100.01411.5800.0330.0330.0000.0000.0000.000
144A153THR0-0.005-0.00413.4840.0440.0440.0000.0000.0000.000
145A154ALA00.0300.00611.4240.0290.0290.0000.0000.0000.000
146A155ALA00.0100.0059.4520.0050.0050.0000.0000.0000.000
147A156ALA0-0.021-0.01410.3920.1000.1000.0000.0000.0000.000
148A157MET0-0.078-0.04113.7260.0220.0220.0000.0000.0000.000
149A158LEU00.0020.0148.531-0.036-0.0360.0000.0000.0000.000
150A159ASP-1-0.941-0.96610.7080.7920.7920.0000.0000.0000.000
151A160VAL0-0.0050.0016.7200.2300.2300.0000.0000.0000.000
152A161SER0-0.025-0.0387.201-0.472-0.4720.0000.0000.0000.000
153A162PRO00.0830.0217.0070.1010.1010.0000.0000.0000.000
154A163ALA00.0480.0336.746-0.213-0.2130.0000.0000.0000.000
155A164ASP-1-0.845-0.8823.4317.8638.3430.013-0.099-0.3940.000
156A165CYS0-0.053-0.0182.582-4.452-1.7451.702-2.036-2.373-0.025
157A166ALA00.0140.0112.676-1.169-0.2930.917-0.391-1.4020.000
158A167ALA0-0.021-0.0183.9010.1260.1500.0030.024-0.0510.000
159A168ILE0-0.019-0.0036.558-0.021-0.0210.0000.0000.0000.000
160A169GLU-1-0.808-0.9239.592-0.217-0.2170.0000.0000.0000.000
161A170ASP-1-0.899-0.96613.248-0.285-0.2850.0000.0000.0000.000
162A171ALA00.0050.01416.8520.0250.0250.0000.0000.0000.000
163A172GLU-1-0.920-0.96417.581-0.215-0.2150.0000.0000.0000.000
164A173ALA0-0.039-0.03218.7330.0020.0020.0000.0000.0000.000
165A174GLY00.0360.02816.2910.0180.0180.0000.0000.0000.000
166A175ILE00.0220.01013.998-0.013-0.0130.0000.0000.0000.000
167A176SER00.0030.00314.5690.0010.0010.0000.0000.0000.000
168A177ALA0-0.054-0.01115.8510.0250.0250.0000.0000.0000.000
169A178ILE00.0160.0139.6750.0320.0320.0000.0000.0000.000
170A179LYS10.8290.89410.4510.3810.3810.0000.0000.0000.000
171A180SER0-0.077-0.04813.3300.0520.0520.0000.0000.0000.000
172A181ALA0-0.056-0.02912.1700.0500.0500.0000.0000.0000.000
173A182GLY0-0.037-0.01411.6570.0720.0720.0000.0000.0000.000
174A183MET0-0.082-0.0217.1670.0640.0640.0000.0000.0000.000
175A184PHE00.0100.0014.131-0.310-0.099-0.001-0.021-0.1900.000
176A185ALA00.006-0.0076.654-0.061-0.0610.0000.0000.0000.000
177A186VAL0-0.019-0.0136.926-0.041-0.0410.0000.0000.0000.000
178A187GLY00.0280.0169.9830.0600.0600.0000.0000.0000.000
179A188VAL0-0.063-0.04813.4600.0010.0010.0000.0000.0000.000
180A196GLY00.007-0.00717.662-0.005-0.0050.0000.0000.0000.000
181A197ALA0-0.015-0.00912.3900.0150.0150.0000.0000.0000.000
182A198ASP-1-0.841-0.8909.620-0.486-0.4860.0000.0000.0000.000
183A199LEU00.0040.0069.114-0.018-0.0180.0000.0000.0000.000
184A200VAL0-0.018-0.00811.4860.0230.0230.0000.0000.0000.000
185A201VAL0-0.033-0.00611.989-0.003-0.0030.0000.0000.0000.000
186A202ARG10.9030.96614.8090.3500.3500.0000.0000.0000.000
187A203GLN0-0.037-0.04116.7690.0550.0550.0000.0000.0000.000
188A204THR00.055-0.00513.910-0.031-0.0310.0000.0000.0000.000
189A205SER0-0.059-0.02713.439-0.033-0.0330.0000.0000.0000.000
190A206ASP-1-0.804-0.89713.777-0.447-0.4470.0000.0000.0000.000
191A207LEU0-0.0110.0169.145-0.074-0.0740.0000.0000.0000.000
192A208THR0-0.019-0.0159.443-0.046-0.0460.0000.0000.0000.000
193A209LEU00.0290.0133.463-0.366-0.0520.025-0.059-0.2810.000
194A210GLU-1-0.760-0.8565.204-1.206-1.2060.0000.0000.0000.000
195A211LEU00.0080.0097.382-0.091-0.0910.0000.0000.0000.000
196A212LEU0-0.012-0.0132.981-0.566-0.0650.060-0.094-0.4680.000
197A213HIS0-0.028-0.0262.752-4.854-2.2491.237-1.210-2.632-0.014
198A214GLU-1-0.941-0.9633.970-1.101-1.0180.0010.033-0.1170.000
199A215GLU-1-0.815-0.9056.886-0.682-0.6820.0000.0000.0000.000
200A216TRP00.0040.0222.298-8.249-5.26510.992-4.212-9.765-0.046
201A217GLU-1-0.908-0.9664.870-1.025-0.898-0.001-0.006-0.1190.000
202A218GLN0-0.062-0.0346.5060.6230.6230.0000.0000.0000.000
203A219TYR0-0.083-0.0756.2610.2270.2270.0000.0000.0000.000
204A220ARG10.8920.9345.184-0.064-0.0640.0000.0000.0000.000
205A221ILE0-0.0290.0008.4580.2930.2930.0000.0000.0000.000
206A222ARG10.7320.85310.8430.7520.7520.0000.0000.0000.000
207A223GLU-1-0.917-0.90710.3010.0000.0000.0000.0000.0000.000