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: YYGY2

Calculation Name: 3P5J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P5J

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CWY8

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1811196.891373
FMO2-HF: Nuclear repulsion 1740339.141574
FMO2-HF: Total energy -70857.749799
FMO2-MP2: Total energy -71067.747664


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:11:ALA)


Summations of interaction energy for fragment #1(B:11:ALA)
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.
1.5233.437-0.004-0.987-0.9220.004
Interaction energy analysis for fragmet #1(B:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.034
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].
3B13ARG10.9360.9643.8820.5722.407-0.003-0.983-0.8490.004
4B14GLN00.001-0.0014.8420.6480.6480.0000.0000.0000.000
5B15LEU0-0.072-0.0377.5450.0030.0030.0000.0000.0000.000
6B16VAL00.0540.03411.2690.0690.0690.0000.0000.0000.000
7B17PHE00.003-0.00713.6540.0010.0010.0000.0000.0000.000
8B18LEU00.0120.02916.9910.0270.0270.0000.0000.0000.000
9B19LEU0-0.002-0.02019.061-0.008-0.0080.0000.0000.0000.000
10B20PRO0-0.015-0.00722.3900.0130.0130.0000.0000.0000.000
11B21GLU-1-0.901-0.95625.571-0.074-0.0740.0000.0000.0000.000
12B22HIS00.0360.01626.8290.0050.0050.0000.0000.0000.000
13B23LEU0-0.090-0.04323.7990.0030.0030.0000.0000.0000.000
14B24LYS10.9731.00322.0550.0450.0450.0000.0000.0000.000
15B25ASP-1-0.890-0.94124.596-0.059-0.0590.0000.0000.0000.000
16B26ALA00.007-0.01727.988-0.006-0.0060.0000.0000.0000.000
17B27SER0-0.032-0.00729.347-0.003-0.0030.0000.0000.0000.000
18B28LYS10.8980.95427.6970.0970.0970.0000.0000.0000.000
19B29LYS10.8900.95033.3020.0580.0580.0000.0000.0000.000
20B30LYS11.0311.02132.6480.0540.0540.0000.0000.0000.000
21B31LYS10.9010.94630.2120.0730.0730.0000.0000.0000.000
22B32LYS10.9790.99525.4550.0650.0650.0000.0000.0000.000
23B33SER00.0210.02024.001-0.004-0.0040.0000.0000.0000.000
24B34SER0-0.010-0.02324.9360.0000.0000.0000.0000.0000.000
25B35LEU00.0310.02920.4260.0040.0040.0000.0000.0000.000
26B36LEU00.0200.00422.947-0.010-0.0100.0000.0000.0000.000
27B37PHE00.0040.00818.6590.0020.0020.0000.0000.0000.000
28B38VAL00.0280.01222.477-0.009-0.0090.0000.0000.0000.000
29B39LYS10.8960.94221.7260.3140.3140.0000.0000.0000.000
30B40LEU0-0.0160.00125.6320.0160.0160.0000.0000.0000.000
31B41ALA00.027-0.00228.605-0.011-0.0110.0000.0000.0000.000
32B42ASN0-0.023-0.01128.2260.0120.0120.0000.0000.0000.000
33B43PRO0-0.016-0.00431.1860.0060.0060.0000.0000.0000.000
34B44HIS0-0.0340.01032.6610.0020.0020.0000.0000.0000.000
35B45SER00.021-0.00733.1930.0060.0060.0000.0000.0000.000
36B46GLY00.0340.02230.392-0.010-0.0100.0000.0000.0000.000
37B47GLU-1-0.918-0.95529.188-0.184-0.1840.0000.0000.0000.000
38B48GLY0-0.051-0.03827.6020.0040.0040.0000.0000.0000.000
39B49ALA00.0030.00624.797-0.011-0.0110.0000.0000.0000.000
40B50THR0-0.043-0.02720.3930.0030.0030.0000.0000.0000.000
41B51TYR00.0770.04623.5110.0090.0090.0000.0000.0000.000
42B52LEU0-0.0170.00521.761-0.009-0.0090.0000.0000.0000.000
43B53ILE00.003-0.01124.6060.0150.0150.0000.0000.0000.000
44B54ASP-1-0.759-0.87826.815-0.107-0.1070.0000.0000.0000.000
45B55MET00.0480.02128.2920.0070.0070.0000.0000.0000.000
46B56CYS0-0.162-0.07429.5660.0080.0080.0000.0000.0000.000
47B57LEU0-0.012-0.03131.1840.0070.0070.0000.0000.0000.000
48B58GLN0-0.092-0.03132.2680.0070.0070.0000.0000.0000.000
49B59GLN00.0460.01731.2040.0000.0000.0000.0000.0000.000
50B60LEU00.0200.01228.968-0.008-0.0080.0000.0000.0000.000
51B61PHE00.0210.01726.1290.0080.0080.0000.0000.0000.000
52B62GLU-1-0.811-0.88926.609-0.174-0.1740.0000.0000.0000.000
53B63ILE0-0.051-0.03219.786-0.005-0.0050.0000.0000.0000.000
54B64LYS10.9300.99023.1340.1800.1800.0000.0000.0000.000
55B65VAL0-0.003-0.03017.414-0.020-0.0200.0000.0000.0000.000
56B66PHE0-0.0130.01818.7400.0130.0130.0000.0000.0000.000
57B67LYS10.8180.88816.1680.3480.3480.0000.0000.0000.000
58B68GLU-1-0.821-0.91518.995-0.150-0.1500.0000.0000.0000.000
59B69LYS10.8880.94119.0410.1810.1810.0000.0000.0000.000
60B70HIS00.002-0.00617.577-0.004-0.0040.0000.0000.0000.000
61B71HIS00.0940.07016.2850.0260.0260.0000.0000.0000.000
62B72SER0-0.110-0.06411.120-0.060-0.0600.0000.0000.0000.000
63B73TRP00.009-0.00910.1110.0730.0730.0000.0000.0000.000
64B74PHE00.0610.0369.617-0.045-0.0450.0000.0000.0000.000
65B75ILE0-0.023-0.0097.984-0.018-0.0180.0000.0000.0000.000
66B76ASN00.0060.0068.4930.0770.0770.0000.0000.0000.000
67B77GLN00.0050.0089.172-0.093-0.0930.0000.0000.0000.000
68B78SER0-0.014-0.0224.6070.1240.203-0.001-0.004-0.0730.000
69B79VAL00.0430.0265.942-0.141-0.1410.0000.0000.0000.000
70B80GLN00.0330.0335.447-0.834-0.8340.0000.0000.0000.000
71B81SER00.0160.0047.2050.2210.2210.0000.0000.0000.000
72B82GLY0-0.020-0.0159.941-0.079-0.0790.0000.0000.0000.000
73B83GLY00.0940.03812.2420.0800.0800.0000.0000.0000.000
74B84LEU0-0.048-0.02013.1150.0390.0390.0000.0000.0000.000
75B85LEU00.0320.03214.455-0.018-0.0180.0000.0000.0000.000
76B86HIS0-0.016-0.01113.9860.0460.0460.0000.0000.0000.000
77B87PHE00.0360.01118.2960.0210.0210.0000.0000.0000.000
78B88ALA0-0.0190.00121.725-0.008-0.0080.0000.0000.0000.000
79B89THR00.0390.00923.6470.0120.0120.0000.0000.0000.000
80B90PRO0-0.018-0.02027.237-0.005-0.0050.0000.0000.0000.000
81B91MET00.0150.02630.120-0.001-0.0010.0000.0000.0000.000
82B92ASP-1-0.811-0.90131.932-0.084-0.0840.0000.0000.0000.000
83B93PRO00.005-0.02434.467-0.003-0.0030.0000.0000.0000.000
84B94LEU00.0070.02835.990-0.001-0.0010.0000.0000.0000.000
85B95PHE00.0530.00935.4260.0030.0030.0000.0000.0000.000
86B96LEU00.009-0.00230.672-0.001-0.0010.0000.0000.0000.000
87B97LEU0-0.067-0.03735.256-0.001-0.0010.0000.0000.0000.000
88B98LEU00.0110.02338.4730.0050.0050.0000.0000.0000.000
89B99HIS00.0330.01334.4580.0100.0100.0000.0000.0000.000
90B100TYR00.0280.02539.2710.0000.0000.0000.0000.0000.000
91B101LEU0-0.023-0.01640.9140.0040.0040.0000.0000.0000.000
92B102LEU0-0.026-0.01340.3840.0030.0030.0000.0000.0000.000
93B103LYS10.9170.95338.6350.1110.1110.0000.0000.0000.000
94B104ALA00.0110.02044.6540.0030.0030.0000.0000.0000.000
95B105GLY00.0430.02347.8040.0030.0030.0000.0000.0000.000
96B106LYS10.9010.95649.4280.0670.0670.0000.0000.0000.000
97B123PRO00.020-0.00929.7520.0040.0040.0000.0000.0000.000
98B124ASP-1-0.854-0.92127.544-0.184-0.1840.0000.0000.0000.000
99B125CYS0-0.062-0.05430.8990.0050.0050.0000.0000.0000.000
100B126THR00.0160.00834.1020.0040.0040.0000.0000.0000.000
101B127LEU0-0.032-0.01729.4560.0090.0090.0000.0000.0000.000
102B128LEU0-0.0140.00532.2250.0030.0030.0000.0000.0000.000
103B129LEU00.0240.01733.5080.0030.0030.0000.0000.0000.000
104B130ARG10.9310.96634.5390.0960.0960.0000.0000.0000.000
105B131PHE00.0310.00131.887-0.001-0.0010.0000.0000.0000.000
106B132PRO00.0030.00237.4970.0030.0030.0000.0000.0000.000
107B133GLU-1-0.848-0.95939.941-0.061-0.0610.0000.0000.0000.000
108B134LEU0-0.0100.02340.526-0.001-0.0010.0000.0000.0000.000
109B135GLU-1-0.805-0.90441.994-0.055-0.0550.0000.0000.0000.000
110B136LYS10.8870.96044.8880.0570.0570.0000.0000.0000.000
111B137SER0-0.037-0.00440.9690.0020.0020.0000.0000.0000.000
112B138LEU00.0390.00242.755-0.001-0.0010.0000.0000.0000.000
113B139ARG10.8240.91645.0780.0540.0540.0000.0000.0000.000
114B140HIS00.0030.00045.2550.0020.0020.0000.0000.0000.000
115B141VAL00.0270.02143.6860.0010.0010.0000.0000.0000.000
116B142THR0-0.056-0.00945.5190.0010.0010.0000.0000.0000.000
117B143GLU-1-0.826-0.92148.040-0.053-0.0530.0000.0000.0000.000
118B151LYS10.9960.98350.6070.0490.0490.0000.0000.0000.000
119B152TYR0-0.030-0.01050.126-0.002-0.0020.0000.0000.0000.000
120B153TYR00.0460.02847.3350.0000.0000.0000.0000.0000.000
121B154LYS10.8780.93149.8910.0560.0560.0000.0000.0000.000
122B155TYR00.0480.01445.6680.0010.0010.0000.0000.0000.000
123B156SER0-0.022-0.02649.3570.0040.0040.0000.0000.0000.000
124B157SER00.0780.03549.690-0.002-0.0020.0000.0000.0000.000
125B158GLU-1-0.776-0.87150.605-0.052-0.0520.0000.0000.0000.000
126B159LYS10.8710.94150.2160.0560.0560.0000.0000.0000.000
127B160THR0-0.011-0.02045.095-0.002-0.0020.0000.0000.0000.000
128B161LEU00.0470.04046.824-0.002-0.0020.0000.0000.0000.000
129B162LYS10.8350.91348.8780.0500.0500.0000.0000.0000.000
130B163TRP0-0.091-0.04940.2110.0010.0010.0000.0000.0000.000
131B164LEU00.040-0.00442.066-0.001-0.0010.0000.0000.0000.000
132B165GLU-1-0.717-0.82544.574-0.059-0.0590.0000.0000.0000.000
133B166LYS10.9140.96945.4550.0630.0630.0000.0000.0000.000
134B167LYS10.8220.91838.9330.0870.0870.0000.0000.0000.000
135B168VAL00.0790.04742.186-0.001-0.0010.0000.0000.0000.000
136B169ASN0-0.046-0.04243.5330.0020.0020.0000.0000.0000.000
137B170GLN0-0.034-0.01941.125-0.002-0.0020.0000.0000.0000.000
138B171THR0-0.050-0.03738.365-0.001-0.0010.0000.0000.0000.000
139B172VAL00.0610.02940.341-0.001-0.0010.0000.0000.0000.000
140B173VAL0-0.038-0.01242.6500.0020.0020.0000.0000.0000.000
141B174ALA00.000-0.00237.5750.0010.0010.0000.0000.0000.000
142B175LEU0-0.0040.00437.4890.0000.0000.0000.0000.0000.000
143B176LYS10.8220.91239.6500.0540.0540.0000.0000.0000.000
144B177ALA0-0.047-0.01639.6080.0020.0020.0000.0000.0000.000
145B178ASN0-0.038-0.03934.9780.0040.0040.0000.0000.0000.000
146B179ASN0-0.0260.00136.548-0.002-0.0020.0000.0000.0000.000
147B180VAL0-0.016-0.00535.242-0.002-0.0020.0000.0000.0000.000
148B181ASN0-0.0230.00237.3400.0040.0040.0000.0000.0000.000
149B203GLU-1-0.817-0.90548.652-0.050-0.0500.0000.0000.0000.000
150B204ASP-1-0.895-0.95345.071-0.058-0.0580.0000.0000.0000.000
151B205TYR00.0650.01542.580-0.002-0.0020.0000.0000.0000.000
152B206VAL0-0.061-0.01744.039-0.003-0.0030.0000.0000.0000.000
153B207ARG10.8870.94744.7990.0540.0540.0000.0000.0000.000
154B208TYR00.0430.02535.360-0.003-0.0030.0000.0000.0000.000
155B209ALA00.014-0.00539.969-0.005-0.0050.0000.0000.0000.000
156B210HIS0-0.016-0.01140.817-0.002-0.0020.0000.0000.0000.000
157B211GLY00.0480.02139.525-0.003-0.0030.0000.0000.0000.000
158B212LEU0-0.0020.01834.493-0.005-0.0050.0000.0000.0000.000
159B213ILE0-0.040-0.01935.813-0.006-0.0060.0000.0000.0000.000
160B214SER00.0390.00637.528-0.004-0.0040.0000.0000.0000.000
161B215ASP-1-0.908-0.94532.511-0.133-0.1330.0000.0000.0000.000
162B216TYR0-0.148-0.10930.242-0.010-0.0100.0000.0000.0000.000
163B217ILE0-0.067-0.04635.0810.0010.0010.0000.0000.0000.000
164B218PRO00.0500.03738.2340.0020.0020.0000.0000.0000.000
165B219LYS10.7250.85139.7910.0810.0810.0000.0000.0000.000
166B220GLU-1-0.791-0.91440.787-0.083-0.0830.0000.0000.0000.000
167B221LEU0-0.008-0.00440.5060.0030.0030.0000.0000.0000.000
168B222SER0-0.064-0.03344.1040.0040.0040.0000.0000.0000.000
169B223ASP-1-0.797-0.88444.507-0.074-0.0740.0000.0000.0000.000
170B224ASP-1-0.860-0.92945.934-0.072-0.0720.0000.0000.0000.000
171B225LEU00.000-0.00447.1980.0030.0030.0000.0000.0000.000
172B226SER00.009-0.00947.5540.0030.0030.0000.0000.0000.000
173B227LYS10.8480.95344.1970.0760.0760.0000.0000.0000.000
174B228PHE00.004-0.01248.4200.0020.0020.0000.0000.0000.000
175B229LEU0-0.010-0.01151.5140.0020.0020.0000.0000.0000.000
176B230LYS10.8330.92549.8280.0570.0570.0000.0000.0000.000
177B231LEU0-0.041-0.01050.796-0.002-0.0020.0000.0000.0000.000