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: 3QV9L

Calculation Name: 3PUF-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: B

ChEMBL ID:

UniProt ID: O75792

Base Structure: X-ray

Registration Date: 2023-06-19

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2060054.164436
FMO2-HF: Nuclear repulsion 1983344.874589
FMO2-HF: Total energy -76709.289847
FMO2-MP2: Total energy -76934.69612


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(B:13:MET)


Summations of interaction energy for fragment #1(B:13: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.
-3.358-0.0770.38-1.334-2.327-0.006
Interaction energy analysis for fragmet #1(B:13:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.008
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].
3B15GLN00.0340.0072.850-3.592-0.6360.380-1.296-2.040-0.006
4B16HIS0-0.046-0.0483.7931.3331.6580.000-0.038-0.2870.000
5B17VAL00.0420.0326.361-0.125-0.1250.0000.0000.0000.000
6B18PHE00.016-0.0128.5990.1960.1960.0000.0000.0000.000
7B19LEU00.0000.02211.660-0.036-0.0360.0000.0000.0000.000
8B20VAL00.000-0.00913.7520.0390.0390.0000.0000.0000.000
9B21SER00.0260.00816.7470.0200.0200.0000.0000.0000.000
10B22GLU-1-0.930-0.96519.403-0.255-0.2550.0000.0000.0000.000
11B23TYR0-0.045-0.03320.675-0.017-0.0170.0000.0000.0000.000
12B24LEU0-0.061-0.01816.612-0.003-0.0030.0000.0000.0000.000
13B35LEU00.0000.00814.0420.0110.0110.0000.0000.0000.000
14B36MET0-0.040-0.01712.842-0.038-0.0380.0000.0000.0000.000
15B37PHE00.0240.0098.9590.0110.0110.0000.0000.0000.000
16B38VAL0-0.011-0.00512.9940.0590.0590.0000.0000.0000.000
17B39LYS10.9460.97815.704-0.440-0.4400.0000.0000.0000.000
18B40LEU0-0.008-0.01217.201-0.004-0.0040.0000.0000.0000.000
19B41VAL00.0370.03720.8350.0150.0150.0000.0000.0000.000
20B42ASN00.0330.01923.297-0.035-0.0350.0000.0000.0000.000
21B43PRO0-0.017-0.02024.6180.0040.0040.0000.0000.0000.000
22B44CYS0-0.031-0.00427.7020.0040.0040.0000.0000.0000.000
23B45SER00.0220.00526.055-0.005-0.0050.0000.0000.0000.000
24B46GLY0-0.051-0.01327.8210.0080.0080.0000.0000.0000.000
25B47GLU-1-0.903-0.96123.7150.2280.2280.0000.0000.0000.000
26B48GLY0-0.035-0.03020.788-0.013-0.0130.0000.0000.0000.000
27B49ALA0-0.010-0.00318.8330.0160.0160.0000.0000.0000.000
28B50ILE0-0.031-0.02712.6740.0260.0260.0000.0000.0000.000
29B51TYR0-0.001-0.01116.067-0.046-0.0460.0000.0000.0000.000
30B52LEU0-0.021-0.00912.9950.0100.0100.0000.0000.0000.000
31B53PHE00.0260.00415.8140.0010.0010.0000.0000.0000.000
32B54ASN00.0530.01517.569-0.013-0.0130.0000.0000.0000.000
33B55MET00.0520.00918.3770.0190.0190.0000.0000.0000.000
34B56CYS0-0.015-0.00420.9960.0150.0150.0000.0000.0000.000
35B57LEU00.0030.00822.8980.0040.0040.0000.0000.0000.000
36B58GLN0-0.064-0.03423.8680.0190.0190.0000.0000.0000.000
37B59GLN00.0640.05022.794-0.005-0.0050.0000.0000.0000.000
38B60LEU0-0.014-0.00820.093-0.009-0.0090.0000.0000.0000.000
39B61PHE0-0.010-0.01018.027-0.010-0.0100.0000.0000.0000.000
40B62GLU-1-0.746-0.84618.7050.0270.0270.0000.0000.0000.000
41B63VAL0-0.041-0.03412.813-0.049-0.0490.0000.0000.0000.000
42B64LYS10.8850.94816.2280.0370.0370.0000.0000.0000.000
43B65VAL0-0.047-0.03713.975-0.037-0.0370.0000.0000.0000.000
44B66PHE00.0200.03116.3080.0300.0300.0000.0000.0000.000
45B67LYS10.8160.87415.537-0.071-0.0710.0000.0000.0000.000
46B68GLU-1-0.816-0.87017.940-0.004-0.0040.0000.0000.0000.000
47B69LYS10.9290.94019.382-0.159-0.1590.0000.0000.0000.000
48B70HIS00.009-0.00320.123-0.013-0.0130.0000.0000.0000.000
49B71HIS00.0280.02517.261-0.059-0.0590.0000.0000.0000.000
50B72SER0-0.081-0.06314.0980.0660.0660.0000.0000.0000.000
51B73TRP0-0.021-0.01411.211-0.032-0.0320.0000.0000.0000.000
52B74PHE00.0160.00212.444-0.019-0.0190.0000.0000.0000.000
53B75ILE0-0.002-0.0018.5110.0740.0740.0000.0000.0000.000
54B76ASN00.0240.02210.560-0.096-0.0960.0000.0000.0000.000
55B77GLN00.0010.00812.2960.0680.0680.0000.0000.0000.000
56B78SER0-0.020-0.0088.036-0.207-0.2070.0000.0000.0000.000
57B79VAL00.0510.0209.1870.1560.1560.0000.0000.0000.000
58B80GLN0-0.018-0.0066.291-0.751-0.7510.0000.0000.0000.000
59B81SER00.0400.0069.4810.0580.0580.0000.0000.0000.000
60B82GLY00.0150.02410.6920.0780.0780.0000.0000.0000.000
61B83GLY00.0680.03312.2390.0340.0340.0000.0000.0000.000
62B84LEU0-0.067-0.01510.9450.0710.0710.0000.0000.0000.000
63B85LEU00.0090.02212.106-0.138-0.1380.0000.0000.0000.000
64B86HIS00.0330.02410.0510.0960.0960.0000.0000.0000.000
65B87PHE00.0350.00913.358-0.076-0.0760.0000.0000.0000.000
66B88ALA0-0.0040.00414.5660.0470.0470.0000.0000.0000.000
67B89THR00.0200.00616.555-0.020-0.0200.0000.0000.0000.000
68B90PRO0-0.013-0.00820.4010.0210.0210.0000.0000.0000.000
69B91VAL00.0150.01622.3950.0080.0080.0000.0000.0000.000
70B92ASP-1-0.811-0.90124.897-0.014-0.0140.0000.0000.0000.000
71B93PRO00.025-0.00526.8200.0100.0100.0000.0000.0000.000
72B94LEU00.0060.00428.1910.0120.0120.0000.0000.0000.000
73B95PHE00.0320.02028.3520.0050.0050.0000.0000.0000.000
74B96LEU00.0050.00723.6140.0090.0090.0000.0000.0000.000
75B97LEU0-0.006-0.01028.3090.0090.0090.0000.0000.0000.000
76B98LEU00.0030.00331.3590.0050.0050.0000.0000.0000.000
77B99HIS00.0070.01829.6780.0110.0110.0000.0000.0000.000
78B100TYR0-0.037-0.05127.1100.0050.0050.0000.0000.0000.000
79B101LEU00.0030.00132.6200.0000.0000.0000.0000.0000.000
80B102ILE0-0.021-0.01535.293-0.001-0.0010.0000.0000.0000.000
81B103LYS10.8740.95329.569-0.118-0.1180.0000.0000.0000.000
82B104ALA00.0670.03535.7970.0010.0010.0000.0000.0000.000
83B105ASP-1-0.886-0.93038.1440.0490.0490.0000.0000.0000.000
84B106LYS10.7860.86639.356-0.068-0.0680.0000.0000.0000.000
85B107GLU-1-0.902-0.91240.7250.0700.0700.0000.0000.0000.000
86B108GLY00.0890.04142.643-0.002-0.0020.0000.0000.0000.000
87B109LYS10.8330.89544.641-0.041-0.0410.0000.0000.0000.000
88B110PHE0-0.054-0.03843.8930.0000.0000.0000.0000.0000.000
89B111GLN00.0760.05439.4570.0000.0000.0000.0000.0000.000
90B112PRO00.0310.03139.152-0.004-0.0040.0000.0000.0000.000
91B113LEU00.0250.00232.5160.0050.0050.0000.0000.0000.000
92B114ASP-1-0.858-0.93533.4670.0580.0580.0000.0000.0000.000
93B115GLN0-0.073-0.05334.1080.0070.0070.0000.0000.0000.000
94B116VAL0-0.0120.00734.5590.0050.0050.0000.0000.0000.000
95B117VAL0-0.082-0.04429.1950.0060.0060.0000.0000.0000.000
96B118VAL00.0560.03830.3970.0030.0030.0000.0000.0000.000
97B119ASP-1-0.789-0.91326.6310.1590.1590.0000.0000.0000.000
98B120ASN0-0.013-0.00527.157-0.001-0.0010.0000.0000.0000.000
99B121VAL0-0.0220.00923.8370.0190.0190.0000.0000.0000.000
100B122PHE0-0.043-0.01721.0810.0330.0330.0000.0000.0000.000
101B123PRO00.0910.03422.451-0.022-0.0220.0000.0000.0000.000
102B124ASN0-0.012-0.00918.369-0.032-0.0320.0000.0000.0000.000
103B125CYS0-0.0340.00122.148-0.021-0.0210.0000.0000.0000.000
104B126ILE00.0720.02925.180-0.016-0.0160.0000.0000.0000.000
105B127LEU0-0.031-0.01320.045-0.013-0.0130.0000.0000.0000.000
106B128LEU0-0.012-0.01024.734-0.015-0.0150.0000.0000.0000.000
107B129LEU00.0130.01327.360-0.009-0.0090.0000.0000.0000.000
108B130LYS10.8330.91626.948-0.011-0.0110.0000.0000.0000.000
109B131LEU00.0240.03125.481-0.011-0.0110.0000.0000.0000.000
110B132PRO00.0150.01427.9510.0030.0030.0000.0000.0000.000
111B133GLY0-0.002-0.01431.0320.0000.0000.0000.0000.0000.000
112B134LEU00.0180.01130.9850.0000.0000.0000.0000.0000.000
113B135GLU-1-0.739-0.83234.2520.0120.0120.0000.0000.0000.000
114B136LYS10.9650.97237.2750.0230.0230.0000.0000.0000.000
115B137LEU0-0.0110.01031.350-0.002-0.0020.0000.0000.0000.000
116B138LEU00.0730.02534.6840.0020.0020.0000.0000.0000.000
117B139HIS0-0.054-0.00737.4110.0000.0000.0000.0000.0000.000
118B140HIS0-0.053-0.02738.0540.0010.0010.0000.0000.0000.000
119B141VAL00.0070.00235.9950.0010.0010.0000.0000.0000.000
120B142THR0-0.045-0.03138.4080.0050.0050.0000.0000.0000.000
121B143GLU-1-0.821-0.87841.2410.0140.0140.0000.0000.0000.000
122B144GLU-1-0.837-0.91542.3680.0150.0150.0000.0000.0000.000
123B145LYS10.8720.93144.406-0.023-0.0230.0000.0000.0000.000
124B146GLY00.0520.02045.4250.0020.0020.0000.0000.0000.000
125B147ASN0-0.040-0.04047.339-0.003-0.0030.0000.0000.0000.000
126B148PRO00.0420.00146.4580.0010.0010.0000.0000.0000.000
127B149GLU-1-0.919-0.93847.3750.0070.0070.0000.0000.0000.000
128B150ILE0-0.041-0.01646.1840.0000.0000.0000.0000.0000.000
129B151ASP-1-0.898-0.96042.1830.0180.0180.0000.0000.0000.000
130B152ASN0-0.098-0.05441.015-0.001-0.0010.0000.0000.0000.000
131B153LYN0-0.0440.00741.8710.0010.0010.0000.0000.0000.000
132B154LYS10.8120.92240.440-0.010-0.0100.0000.0000.0000.000
133B155TYR00.003-0.01340.7640.0040.0040.0000.0000.0000.000
134B156TYR0-0.005-0.04638.517-0.003-0.0030.0000.0000.0000.000
135B157LYS10.7960.90241.523-0.042-0.0420.0000.0000.0000.000
136B158TYR00.0520.02338.511-0.003-0.0030.0000.0000.0000.000
137B159SER0-0.014-0.01841.0170.0000.0000.0000.0000.0000.000
138B160LYS10.8970.93842.097-0.042-0.0420.0000.0000.0000.000
139B161GLU-1-0.785-0.88443.3140.0120.0120.0000.0000.0000.000
140B162LYS10.8350.91142.748-0.016-0.0160.0000.0000.0000.000
141B163THR00.017-0.00637.953-0.002-0.0020.0000.0000.0000.000
142B164LEU0-0.0140.00639.863-0.001-0.0010.0000.0000.0000.000
143B165LYS10.8580.91442.054-0.013-0.0130.0000.0000.0000.000
144B166TRP0-0.052-0.02632.493-0.004-0.0040.0000.0000.0000.000
145B167LEU00.027-0.00335.483-0.004-0.0040.0000.0000.0000.000
146B168GLU-1-0.871-0.92838.5350.0010.0010.0000.0000.0000.000
147B169LYS10.8570.94439.0260.0020.0020.0000.0000.0000.000
148B170LYS10.8370.93132.2710.0130.0130.0000.0000.0000.000
149B171VAL00.0570.04536.070-0.004-0.0040.0000.0000.0000.000
150B172ASN0-0.017-0.01738.299-0.005-0.0050.0000.0000.0000.000
151B173GLN0-0.017-0.01234.2930.0000.0000.0000.0000.0000.000
152B174THR0-0.008-0.02632.524-0.005-0.0050.0000.0000.0000.000
153B175VAL00.0340.01835.151-0.005-0.0050.0000.0000.0000.000
154B176ALA0-0.012-0.00337.972-0.003-0.0030.0000.0000.0000.000
155B177ALA00.0040.01332.810-0.005-0.0050.0000.0000.0000.000
156B178LEU00.0210.00732.963-0.006-0.0060.0000.0000.0000.000
157B179LYS10.8400.90035.2560.0230.0230.0000.0000.0000.000
158B180THR0-0.067-0.04135.299-0.002-0.0020.0000.0000.0000.000
159B181ASN0-0.093-0.05231.162-0.013-0.0130.0000.0000.0000.000
160B182ASN0-0.073-0.03333.788-0.005-0.0050.0000.0000.0000.000
161B183VAL00.0200.02132.3030.0010.0010.0000.0000.0000.000
162B184ASN0-0.063-0.03234.6310.0060.0060.0000.0000.0000.000
163B205GLU-1-0.832-0.90444.150-0.018-0.0180.0000.0000.0000.000
164B206GLU-1-0.818-0.90443.8260.0080.0080.0000.0000.0000.000
165B207ASP-1-0.816-0.89841.831-0.013-0.0130.0000.0000.0000.000
166B208TYR00.0220.00737.2670.0000.0000.0000.0000.0000.000
167B209ILE00.0040.00739.0200.0010.0010.0000.0000.0000.000
168B210ARG10.8260.89439.902-0.010-0.0100.0000.0000.0000.000
169B211TYR00.0070.01031.4550.0050.0050.0000.0000.0000.000
170B212ALA0-0.014-0.01035.3910.0020.0020.0000.0000.0000.000
171B213HIS0-0.066-0.03835.4310.0010.0010.0000.0000.0000.000
172B214GLY00.0450.02735.0590.0050.0050.0000.0000.0000.000
173B215LEU00.0040.01429.1690.0050.0050.0000.0000.0000.000
174B216ILE0-0.020-0.02330.7290.0010.0010.0000.0000.0000.000
175B217SER0-0.077-0.05432.1550.0080.0080.0000.0000.0000.000
176B218ASP-1-0.862-0.92127.5280.0550.0550.0000.0000.0000.000
177B219TYR0-0.120-0.07024.5230.0060.0060.0000.0000.0000.000
178B220ILE0-0.056-0.03629.281-0.001-0.0010.0000.0000.0000.000
179B221PRO00.0280.03032.3280.0030.0030.0000.0000.0000.000
180B222LYS10.8920.92533.671-0.069-0.0690.0000.0000.0000.000
181B223GLU-1-0.861-0.94936.1140.0730.0730.0000.0000.0000.000
182B224LEU0-0.029-0.02136.029-0.006-0.0060.0000.0000.0000.000
183B225SER00.0320.02035.843-0.008-0.0080.0000.0000.0000.000
184B226ASP-1-0.798-0.87337.9080.0490.0490.0000.0000.0000.000
185B227ASP-1-0.820-0.88541.2600.0370.0370.0000.0000.0000.000
186B228LEU0-0.027-0.00937.611-0.004-0.0040.0000.0000.0000.000
187B229SER0-0.077-0.04341.545-0.003-0.0030.0000.0000.0000.000
188B230LYS10.8430.90843.004-0.043-0.0430.0000.0000.0000.000
189B231TYR0-0.0140.00744.319-0.001-0.0010.0000.0000.0000.000