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: LNRV9

Calculation Name: 4PZ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PZ9

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIC7

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2424105.774875
FMO2-HF: Nuclear repulsion 2343500.946603
FMO2-HF: Total energy -80604.828272
FMO2-MP2: Total energy -80844.200864


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:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-44.711-37.8732.761-2.943-6.657-0.011
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.965 / q_NPA : 0.973
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].
3A4ARG10.9861.0153.81832.84134.684-0.031-0.894-0.919-0.001
4A5ARG10.8750.9376.53119.16119.1610.0000.0000.0000.000
5A6LEU00.0020.0149.8970.5560.5560.0000.0000.0000.000
6A7VAL0-0.012-0.01413.0490.2930.2930.0000.0000.0000.000
7A8MET0-0.017-0.00116.4150.4980.4980.0000.0000.0000.000
8A9LEU00.0180.00719.6320.1670.1670.0000.0000.0000.000
9A10ARG10.8580.94122.9099.3549.3540.0000.0000.0000.000
10A11HIS00.0150.00226.2810.0320.0320.0000.0000.0000.000
11A12GLY00.0450.01629.246-0.009-0.0090.0000.0000.0000.000
12A13GLN0-0.0020.01432.1330.0860.0860.0000.0000.0000.000
13A14THR00.0190.01235.287-0.015-0.0150.0000.0000.0000.000
14A15ASP-1-0.951-0.96437.744-6.583-6.5830.0000.0000.0000.000
15A16TYR00.012-0.01739.7960.1290.1290.0000.0000.0000.000
16A17ASN0-0.029-0.00240.815-0.223-0.2230.0000.0000.0000.000
17A18VAL00.0510.00336.3400.0280.0280.0000.0000.0000.000
18A19GLY0-0.0050.00839.319-0.066-0.0660.0000.0000.0000.000
19A20SER0-0.047-0.02140.3910.1060.1060.0000.0000.0000.000
20A21ARG10.8790.93541.8226.6616.6610.0000.0000.0000.000
21A22MET0-0.0050.03438.374-0.231-0.2310.0000.0000.0000.000
22A23GLN00.0500.04735.3730.2340.2340.0000.0000.0000.000
23A24GLY00.0680.03535.0300.0840.0840.0000.0000.0000.000
24A25GLN0-0.038-0.05732.2360.0430.0430.0000.0000.0000.000
25A26LEU0-0.0070.02135.6030.0850.0850.0000.0000.0000.000
26A27ASP-1-0.799-0.90235.870-8.182-8.1820.0000.0000.0000.000
27A28THR0-0.074-0.06137.5550.0620.0620.0000.0000.0000.000
28A29GLU-1-0.780-0.89336.908-7.586-7.5860.0000.0000.0000.000
29A30LEU0-0.040-0.01832.8000.0280.0280.0000.0000.0000.000
30A31SER0-0.009-0.01736.9710.1280.1280.0000.0000.0000.000
31A32GLU-1-0.838-0.93938.377-7.263-7.2630.0000.0000.0000.000
32A33LEU0-0.0030.00936.861-0.126-0.1260.0000.0000.0000.000
33A34GLY00.0360.02134.898-0.219-0.2190.0000.0000.0000.000
34A35ARG10.9180.96133.7946.9706.9700.0000.0000.0000.000
35A36THR0-0.030-0.02434.090-0.182-0.1820.0000.0000.0000.000
36A37GLN00.028-0.00431.815-0.253-0.2530.0000.0000.0000.000
37A38ALA00.0200.02229.705-0.296-0.2960.0000.0000.0000.000
38A39VAL0-0.0070.00529.179-0.264-0.2640.0000.0000.0000.000
39A40ALA00.0200.00729.605-0.210-0.2100.0000.0000.0000.000
40A41ALA00.010-0.00526.093-0.270-0.2700.0000.0000.0000.000
41A42ALA00.0180.01325.006-0.474-0.4740.0000.0000.0000.000
42A43GLU-1-0.895-0.93724.908-9.753-9.7530.0000.0000.0000.000
43A44VAL0-0.078-0.03222.316-0.247-0.2470.0000.0000.0000.000
44A45LEU0-0.054-0.04219.497-0.552-0.5520.0000.0000.0000.000
45A46GLY00.0340.00420.150-0.513-0.5130.0000.0000.0000.000
46A47LYS10.8630.94421.23610.63510.6350.0000.0000.0000.000
47A48ARG10.9270.99215.13514.24214.2420.0000.0000.0000.000
48A49GLN00.0710.01418.112-0.343-0.3430.0000.0000.0000.000
49A50PRO0-0.020-0.00815.837-0.801-0.8010.0000.0000.0000.000
50A51LEU00.0360.02510.7990.2480.2480.0000.0000.0000.000
51A52LEU00.0090.00514.9960.6170.6170.0000.0000.0000.000
52A53ILE0-0.0170.00217.505-0.181-0.1810.0000.0000.0000.000
53A54VAL0-0.026-0.01018.9270.3120.3120.0000.0000.0000.000
54A55SER0-0.027-0.02921.522-0.104-0.1040.0000.0000.0000.000
55A56SER0-0.009-0.02724.6810.1190.1190.0000.0000.0000.000
56A57ASP-1-0.761-0.85927.138-9.055-9.0550.0000.0000.0000.000
57A58LEU0-0.035-0.00930.2800.2740.2740.0000.0000.0000.000
58A59ARG10.9040.94531.4647.2787.2780.0000.0000.0000.000
59A60ARG10.8520.94631.9548.2998.2990.0000.0000.0000.000
60A61ALA0-0.037-0.01727.555-0.129-0.1290.0000.0000.0000.000
61A62TYR00.0320.01828.568-0.278-0.2780.0000.0000.0000.000
62A63ASP-1-0.866-0.94329.648-8.344-8.3440.0000.0000.0000.000
63A64THR0-0.090-0.06527.1240.0430.0430.0000.0000.0000.000
64A65ALA0-0.014-0.02125.292-0.179-0.1790.0000.0000.0000.000
65A66VAL00.0210.01226.376-0.223-0.2230.0000.0000.0000.000
66A67LYS10.9420.98028.8758.3118.3110.0000.0000.0000.000
67A68LEU00.0070.00521.182-0.026-0.0260.0000.0000.0000.000
68A69GLY00.0360.02624.749-0.277-0.2770.0000.0000.0000.000
69A70GLU-1-0.950-0.97225.769-8.618-8.6180.0000.0000.0000.000
70A71ARG10.8260.92825.20010.26110.2610.0000.0000.0000.000
71A72THR0-0.067-0.05421.716-0.168-0.1680.0000.0000.0000.000
72A73GLY0-0.0010.01123.657-0.227-0.2270.0000.0000.0000.000
73A74LEU0-0.053-0.00919.532-0.134-0.1340.0000.0000.0000.000
74A75VAL0-0.002-0.00623.7760.3790.3790.0000.0000.0000.000
75A76VAL00.0220.00623.745-0.390-0.3900.0000.0000.0000.000
76A77ARG10.9410.97921.44112.21512.2150.0000.0000.0000.000
77A78VAL00.0210.01924.563-0.086-0.0860.0000.0000.0000.000
78A79ASP-1-0.762-0.89223.526-11.700-11.7000.0000.0000.0000.000
79A80THR00.0070.01225.900-0.106-0.1060.0000.0000.0000.000
80A81ARG10.7430.84722.11612.41112.4110.0000.0000.0000.000
81A82LEU0-0.030-0.01321.152-0.248-0.2480.0000.0000.0000.000
82A83ARG10.8060.87025.2298.9458.9450.0000.0000.0000.000
83A84GLU-1-0.879-0.93128.416-9.653-9.6530.0000.0000.0000.000
84A85THR0-0.027-0.01829.955-0.020-0.0200.0000.0000.0000.000
85A86HIS00.0260.01831.5070.2140.2140.0000.0000.0000.000
86A87LEU0-0.020-0.02534.787-0.027-0.0270.0000.0000.0000.000
87A88GLY00.005-0.00337.5510.1620.1620.0000.0000.0000.000
88A89ASP-1-0.832-0.91140.263-6.728-6.7280.0000.0000.0000.000
89A90TRP0-0.014-0.01539.2210.0530.0530.0000.0000.0000.000
90A91GLN00.0130.02037.458-0.226-0.2260.0000.0000.0000.000
91A92GLY00.0350.01141.5480.1450.1450.0000.0000.0000.000
92A93LEU0-0.0150.02343.8390.1810.1810.0000.0000.0000.000
93A94THR0-0.008-0.02244.058-0.170-0.1700.0000.0000.0000.000
94A95HIS00.024-0.01840.348-0.078-0.0780.0000.0000.0000.000
95A96ALA00.0150.02345.0630.0200.0200.0000.0000.0000.000
96A97GLN00.0250.01448.131-0.011-0.0110.0000.0000.0000.000
97A98ILE00.0590.03142.7090.0350.0350.0000.0000.0000.000
98A99ASP-1-0.835-0.88945.230-6.765-6.7650.0000.0000.0000.000
99A100ALA0-0.058-0.02847.7370.0680.0680.0000.0000.0000.000
100A101ASP-1-0.926-0.95048.814-5.993-5.9930.0000.0000.0000.000
101A102ALA0-0.054-0.02946.2010.0290.0290.0000.0000.0000.000
102A103PRO00.0430.02246.449-0.160-0.1600.0000.0000.0000.000
103A104GLY0-0.031-0.01544.889-0.028-0.0280.0000.0000.0000.000
104A105ALA00.0170.00842.625-0.190-0.1900.0000.0000.0000.000
105A106ARG10.8180.86640.3196.8666.8660.0000.0000.0000.000
106A107LEU0-0.012-0.02838.944-0.199-0.1990.0000.0000.0000.000
107A108ALA00.0250.02638.173-0.189-0.1890.0000.0000.0000.000
108A109TRP0-0.0040.00434.487-0.148-0.1480.0000.0000.0000.000
109A110ARG10.7550.87130.4468.8698.8690.0000.0000.0000.000
110A111GLU-1-0.831-0.91532.621-9.082-9.0820.0000.0000.0000.000
111A112ASP-1-0.789-0.88732.980-8.949-8.9490.0000.0000.0000.000
112A113ALA0-0.058-0.03328.4560.0340.0340.0000.0000.0000.000
113A114THR0-0.060-0.04530.417-0.158-0.1580.0000.0000.0000.000
114A115TRP00.0120.02632.4050.1610.1610.0000.0000.0000.000
115A116ALA00.001-0.01934.718-0.208-0.2080.0000.0000.0000.000
116A117PRO0-0.0100.01036.6590.1750.1750.0000.0000.0000.000
117A118HIS0-0.023-0.03439.510-0.136-0.1360.0000.0000.0000.000
118A119GLY00.0330.01940.8190.0700.0700.0000.0000.0000.000
119A120GLY0-0.048-0.02837.174-0.056-0.0560.0000.0000.0000.000
120A121GLU-1-0.801-0.86431.451-9.468-9.4680.0000.0000.0000.000
121A122SER00.0080.00631.415-0.075-0.0750.0000.0000.0000.000
122A123ARG10.8700.92027.3849.8159.8150.0000.0000.0000.000
123A124VAL00.0320.00026.709-0.462-0.4620.0000.0000.0000.000
124A125ASP-1-0.803-0.88227.034-9.703-9.7030.0000.0000.0000.000
125A126VAL0-0.024-0.01125.687-0.221-0.2210.0000.0000.0000.000
126A127ALA0-0.027-0.00822.874-0.396-0.3960.0000.0000.0000.000
127A128ALA0-0.019-0.00223.054-0.529-0.5290.0000.0000.0000.000
128A129ARG10.7280.84024.5729.8859.8850.0000.0000.0000.000
129A130SER0-0.008-0.02321.876-0.363-0.3630.0000.0000.0000.000
130A131ARG10.8410.89515.84915.88115.8810.0000.0000.0000.000
131A132PRO0-0.010-0.01617.978-0.877-0.8770.0000.0000.0000.000
132A133LEU00.0380.03918.799-0.334-0.3340.0000.0000.0000.000
133A134VAL00.007-0.00613.486-0.535-0.5350.0000.0000.0000.000
134A135ALA0-0.031-0.01514.135-1.050-1.0500.0000.0000.0000.000
135A136GLU-1-0.809-0.89914.654-13.968-13.9680.0000.0000.0000.000
136A137LEU0-0.008-0.00314.166-0.218-0.2180.0000.0000.0000.000
137A138VAL0-0.071-0.0329.318-1.063-1.0630.0000.0000.0000.000
138A139ALA0-0.064-0.02211.076-1.215-1.2150.0000.0000.0000.000
139A140SER0-0.060-0.03513.6900.1130.1130.0000.0000.0000.000
140A141GLU-1-0.877-0.93011.988-15.972-15.9720.0000.0000.0000.000
141A142PRO0-0.027-0.01710.145-1.728-1.7280.0000.0000.0000.000
142A143GLU-1-0.908-0.9578.795-19.583-19.5830.0000.0000.0000.000
143A144TRP0-0.022-0.0138.415-1.341-1.3410.0000.0000.0000.000
144A145GLY0-0.049-0.0254.574-2.264-2.215-0.001-0.003-0.0450.000
145A146GLY0-0.044-0.0243.623-5.176-4.6190.009-0.230-0.337-0.001
146A147ALA0-0.059-0.0525.6150.0810.0810.0000.0000.0000.000
147A148ASP-1-0.893-0.9286.581-20.409-20.4090.0000.0000.0000.000
148A149GLU-1-0.876-0.9599.350-16.073-16.0730.0000.0000.0000.000
149A150PRO0-0.058-0.0054.7290.4310.534-0.001-0.007-0.0950.000
150A151ASP-1-0.852-0.9336.495-20.115-20.1150.0000.0000.0000.000
151A152ARG10.8350.9229.00017.01917.0190.0000.0000.0000.000
152A153PRO0-0.043-0.01210.706-0.805-0.8050.0000.0000.0000.000
153A154VAL00.0600.04212.1740.7680.7680.0000.0000.0000.000
154A155VAL0-0.023-0.01714.189-0.062-0.0620.0000.0000.0000.000
155A156LEU00.0060.01017.5170.3190.3190.0000.0000.0000.000
156A157VAL0-0.031-0.02019.9500.1060.1060.0000.0000.0000.000
157A158ALA00.0410.00923.4570.2330.2330.0000.0000.0000.000
158A159HIS00.0640.04125.2450.3280.3280.0000.0000.0000.000
159A160GLY0-0.008-0.00226.105-0.312-0.3120.0000.0000.0000.000
160A161GLY00.0560.02726.605-0.251-0.2510.0000.0000.0000.000
161A162LEU00.0270.01922.477-0.221-0.2210.0000.0000.0000.000
162A163ILE00.008-0.00221.241-0.512-0.5120.0000.0000.0000.000
163A164ALA00.0090.00821.897-0.566-0.5660.0000.0000.0000.000
164A165ALA00.0030.01223.143-0.308-0.3080.0000.0000.0000.000
165A166LEU00.0210.00818.265-0.414-0.4140.0000.0000.0000.000
166A167SER0-0.007-0.02418.250-0.928-0.9280.0000.0000.0000.000
167A168ALA00.0150.00218.277-0.667-0.6670.0000.0000.0000.000
168A169ALA00.0060.00819.691-0.355-0.3550.0000.0000.0000.000
169A170LEU0-0.077-0.03514.255-0.572-0.5720.0000.0000.0000.000
170A171LEU0-0.065-0.03314.651-1.109-1.1090.0000.0000.0000.000
171A172LYS10.8320.92612.94620.33720.3370.0000.0000.0000.000
172A173LEU0-0.0050.00818.1130.2030.2030.0000.0000.0000.000
173A174PRO00.0400.02020.9070.1770.1770.0000.0000.0000.000
174A175VAL00.0810.03724.0410.1240.1240.0000.0000.0000.000
175A176ALA00.003-0.00126.4310.2220.2220.0000.0000.0000.000
176A177ASN0-0.032-0.02824.7340.0760.0760.0000.0000.0000.000
177A178TRP00.010-0.00622.7440.0070.0070.0000.0000.0000.000
178A179PRO0-0.019-0.00125.917-0.157-0.1570.0000.0000.0000.000
179A180ALA0-0.0150.00225.5070.2540.2540.0000.0000.0000.000
180A181LEU0-0.051-0.00121.569-0.099-0.0990.0000.0000.0000.000
181A182GLY00.0160.00325.7110.3420.3420.0000.0000.0000.000
182A183GLY0-0.001-0.00327.707-0.127-0.1270.0000.0000.0000.000
183A184MET0-0.052-0.01722.767-0.260-0.2600.0000.0000.0000.000
184A185GLY00.0380.01227.8600.3270.3270.0000.0000.0000.000
185A186ASN0-0.058-0.05429.197-0.216-0.2160.0000.0000.0000.000
186A187ALA00.0030.00828.2000.0320.0320.0000.0000.0000.000
187A188SER0-0.0170.01325.8880.0130.0130.0000.0000.0000.000
188A189TRP00.014-0.01319.6000.0290.0290.0000.0000.0000.000
189A190THR0-0.0080.00018.4210.2170.2170.0000.0000.0000.000
190A191GLN0-0.064-0.03212.5230.6880.6880.0000.0000.0000.000
191A192LEU0-0.009-0.00113.0150.1140.1140.0000.0000.0000.000
192A193SER00.005-0.0578.207-0.294-0.2940.0000.0000.0000.000
193A194GLY0-0.005-0.0098.1740.3830.3830.0000.0000.0000.000
194A195HIS0-0.041-0.0374.392-0.465-0.300-0.001-0.028-0.1360.000
195A196TRP0-0.029-0.0112.321-9.325-5.3702.787-1.781-4.960-0.009
196A197ALA00.001-0.0224.0810.0510.217-0.0010.000-0.1650.000
197A198PRO0-0.0410.0006.779-3.543-3.5430.0000.0000.0000.000
198A199GLY00.0550.0316.9952.1192.1190.0000.0000.0000.000
199A200SER0-0.047-0.0396.571-4.951-4.9510.0000.0000.0000.000
200A201ASP-1-0.802-0.8588.837-23.509-23.5090.0000.0000.0000.000
201A202PHE00.0450.00610.984-1.498-1.4980.0000.0000.0000.000
202A203GLU-1-0.790-0.88611.900-17.986-17.9860.0000.0000.0000.000
203A204SER0-0.018-0.02110.4100.8560.8560.0000.0000.0000.000
204A205ILE0-0.081-0.0127.266-2.686-2.6860.0000.0000.0000.000
205A206ARG10.9050.9397.68228.64528.6450.0000.0000.0000.000
206A207TRP00.0350.0208.680-1.968-1.9680.0000.0000.0000.000
207A208ARG10.9150.9718.41526.55226.5520.0000.0000.0000.000
208A209LEU00.0240.00512.724-0.117-0.1170.0000.0000.0000.000
209A210ASP-1-0.805-0.82511.960-20.073-20.0730.0000.0000.0000.000
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