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: 98QR2

Calculation Name: 4PZ9-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4PZ9

Chain ID: A

ChEMBL ID:
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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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2425289.82947
FMO2-HF: Nuclear repulsion 2344684.424404
FMO2-HF: Total energy -80605.405066
FMO2-MP2: Total energy -80844.739187


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.
-51.921-44.3227.31-4.559-10.352-0.026
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 : 0.992 / q_NPA : 1.001
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].
3A4ARG10.9581.0033.81831.56333.719-0.032-1.122-1.0020.000
4A5ARG10.8350.8946.49221.14421.1440.0000.0000.0000.000
5A6LEU00.0050.0149.5730.7400.7400.0000.0000.0000.000
6A7VAL0-0.004-0.01313.0090.3270.3270.0000.0000.0000.000
7A8MET0-0.0150.00116.1330.5780.5780.0000.0000.0000.000
8A9LEU00.0100.00419.5760.1790.1790.0000.0000.0000.000
9A10ARG10.8540.92722.6539.6159.6150.0000.0000.0000.000
10A11HIS00.0500.02026.1170.0230.0230.0000.0000.0000.000
11A12GLY00.0270.01229.038-0.009-0.0090.0000.0000.0000.000
12A13GLN0-0.0020.01831.7350.0880.0880.0000.0000.0000.000
13A14THR00.0230.00935.219-0.035-0.0350.0000.0000.0000.000
14A15ASP-1-0.958-0.96837.574-6.712-6.7120.0000.0000.0000.000
15A16TYR0-0.004-0.03939.7030.1330.1330.0000.0000.0000.000
16A17ASN0-0.027-0.00340.702-0.237-0.2370.0000.0000.0000.000
17A18VAL00.0470.00136.4690.0260.0260.0000.0000.0000.000
18A19GLY00.0000.01739.286-0.073-0.0730.0000.0000.0000.000
19A20SER0-0.060-0.04140.3910.0850.0850.0000.0000.0000.000
20A21ARG10.9020.95441.7966.7426.7420.0000.0000.0000.000
21A22MET00.0270.05137.742-0.248-0.2480.0000.0000.0000.000
22A23GLN00.0410.05835.0570.2540.2540.0000.0000.0000.000
23A24GLY00.0800.03835.0100.0880.0880.0000.0000.0000.000
24A25GLN0-0.025-0.02832.2130.0160.0160.0000.0000.0000.000
25A26LEU0-0.0010.02435.5820.0890.0890.0000.0000.0000.000
26A27ASP-1-0.788-0.87435.776-8.283-8.2830.0000.0000.0000.000
27A28THR0-0.052-0.04537.4410.0690.0690.0000.0000.0000.000
28A29GLU-1-0.770-0.87536.871-7.703-7.7030.0000.0000.0000.000
29A30LEU0-0.041-0.01832.5370.0250.0250.0000.0000.0000.000
30A31SER0-0.010-0.02936.7720.1400.1400.0000.0000.0000.000
31A32GLU-1-0.821-0.91637.949-7.312-7.3120.0000.0000.0000.000
32A33LEU0-0.0070.00736.288-0.130-0.1300.0000.0000.0000.000
33A34GLY00.0400.01934.403-0.229-0.2290.0000.0000.0000.000
34A35ARG10.8980.93833.2737.1527.1520.0000.0000.0000.000
35A36THR0-0.035-0.02233.430-0.177-0.1770.0000.0000.0000.000
36A37GLN00.017-0.01031.150-0.228-0.2280.0000.0000.0000.000
37A38ALA00.0260.02529.103-0.319-0.3190.0000.0000.0000.000
38A39VAL0-0.0030.00428.460-0.285-0.2850.0000.0000.0000.000
39A40ALA00.0010.00028.724-0.222-0.2220.0000.0000.0000.000
40A41ALA00.012-0.00325.388-0.286-0.2860.0000.0000.0000.000
41A42ALA00.0180.01424.170-0.504-0.5040.0000.0000.0000.000
42A43GLU-1-0.794-0.86723.996-10.294-10.2940.0000.0000.0000.000
43A44VAL0-0.060-0.02421.522-0.236-0.2360.0000.0000.0000.000
44A45LEU0-0.049-0.03418.685-0.592-0.5920.0000.0000.0000.000
45A46GLY00.0420.00319.241-0.549-0.5490.0000.0000.0000.000
46A47LYS10.7970.91320.54510.63010.6300.0000.0000.0000.000
47A48ARG10.9180.98714.43514.80914.8090.0000.0000.0000.000
48A49GLN00.0470.00017.126-0.408-0.4080.0000.0000.0000.000
49A50PRO0-0.006-0.00215.154-0.836-0.8360.0000.0000.0000.000
50A51LEU00.0090.01210.9840.2930.2930.0000.0000.0000.000
51A52LEU00.0120.00514.7890.6950.6950.0000.0000.0000.000
52A53ILE0-0.0060.00417.461-0.237-0.2370.0000.0000.0000.000
53A54VAL0-0.027-0.01118.8630.3560.3560.0000.0000.0000.000
54A55SER0-0.021-0.02021.488-0.139-0.1390.0000.0000.0000.000
55A56SER00.004-0.02524.6470.1400.1400.0000.0000.0000.000
56A57ASP-1-0.761-0.87027.110-9.229-9.2290.0000.0000.0000.000
57A58LEU0-0.032-0.00430.2530.2800.2800.0000.0000.0000.000
58A59ARG10.8810.90731.4297.3497.3490.0000.0000.0000.000
59A60ARG10.8240.91231.9688.5268.5260.0000.0000.0000.000
60A61ALA0-0.037-0.01927.586-0.137-0.1370.0000.0000.0000.000
61A62TYR00.0340.02028.525-0.283-0.2830.0000.0000.0000.000
62A63ASP-1-0.871-0.94329.603-8.455-8.4550.0000.0000.0000.000
63A64THR0-0.088-0.06526.8340.0290.0290.0000.0000.0000.000
64A65ALA0-0.013-0.01725.301-0.192-0.1920.0000.0000.0000.000
65A66VAL00.0110.00826.116-0.229-0.2290.0000.0000.0000.000
66A67LYS10.8060.89528.4818.5148.5140.0000.0000.0000.000
67A68LEU00.0120.00720.722-0.025-0.0250.0000.0000.0000.000
68A69GLY00.0390.03424.222-0.287-0.2870.0000.0000.0000.000
69A70GLU-1-0.820-0.89425.373-8.726-8.7260.0000.0000.0000.000
70A71ARG10.7680.87423.88010.46210.4620.0000.0000.0000.000
71A72THR0-0.052-0.05120.915-0.173-0.1730.0000.0000.0000.000
72A73GLY00.0080.01922.936-0.236-0.2360.0000.0000.0000.000
73A74LEU0-0.047-0.00619.033-0.118-0.1180.0000.0000.0000.000
74A75VAL0-0.009-0.01123.4970.3860.3860.0000.0000.0000.000
75A76VAL00.0190.00723.700-0.412-0.4120.0000.0000.0000.000
76A77ARG10.9460.98420.61612.80712.8070.0000.0000.0000.000
77A78VAL00.0190.01624.530-0.103-0.1030.0000.0000.0000.000
78A79ASP-1-0.767-0.87823.586-11.863-11.8630.0000.0000.0000.000
79A80THR00.0160.01525.882-0.116-0.1160.0000.0000.0000.000
80A81ARG10.7250.80922.15712.62012.6200.0000.0000.0000.000
81A82LEU0-0.033-0.01721.064-0.270-0.2700.0000.0000.0000.000
82A83ARG10.8020.87625.2129.0529.0520.0000.0000.0000.000
83A84GLU-1-0.865-0.93528.401-9.939-9.9390.0000.0000.0000.000
84A85THR0-0.035-0.01930.208-0.013-0.0130.0000.0000.0000.000
85A86HIS00.0250.01231.4950.2380.2380.0000.0000.0000.000
86A87LEU0-0.024-0.02334.650-0.033-0.0330.0000.0000.0000.000
87A88GLY00.0070.00537.5400.1650.1650.0000.0000.0000.000
88A89ASP-1-0.837-0.91740.255-6.832-6.8320.0000.0000.0000.000
89A90TRP0-0.010-0.01739.5710.0550.0550.0000.0000.0000.000
90A91GLN00.0100.01337.600-0.223-0.2230.0000.0000.0000.000
91A92GLY00.0410.01641.5310.1520.1520.0000.0000.0000.000
92A93LEU0-0.0360.00743.8160.1940.1940.0000.0000.0000.000
93A94THR0-0.025-0.04944.036-0.150-0.1500.0000.0000.0000.000
94A95HIS0-0.003-0.02640.266-0.080-0.0800.0000.0000.0000.000
95A96ALA00.0340.03345.0630.0180.0180.0000.0000.0000.000
96A97GLN00.0490.03848.2130.0000.0000.0000.0000.0000.000
97A98ILE00.0550.03242.6530.0340.0340.0000.0000.0000.000
98A99ASP-1-0.843-0.90045.256-6.881-6.8810.0000.0000.0000.000
99A100ALA0-0.054-0.02447.8040.0710.0710.0000.0000.0000.000
100A101ASP-1-0.933-0.95548.825-6.093-6.0930.0000.0000.0000.000
101A102ALA0-0.046-0.02746.3400.0300.0300.0000.0000.0000.000
102A103PRO00.0390.01946.591-0.168-0.1680.0000.0000.0000.000
103A104GLY0-0.029-0.01145.115-0.027-0.0270.0000.0000.0000.000
104A105ALA00.0120.00642.773-0.197-0.1970.0000.0000.0000.000
105A106ARG10.8180.87040.5126.9676.9670.0000.0000.0000.000
106A107LEU0-0.015-0.02739.131-0.205-0.2050.0000.0000.0000.000
107A108ALA00.0210.02538.419-0.198-0.1980.0000.0000.0000.000
108A109TRP00.0070.00934.489-0.153-0.1530.0000.0000.0000.000
109A110ARG10.7300.83530.5469.1069.1060.0000.0000.0000.000
110A111GLU-1-0.801-0.87732.850-9.388-9.3880.0000.0000.0000.000
111A112ASP-1-0.779-0.86533.158-9.124-9.1240.0000.0000.0000.000
112A113ALA0-0.063-0.03628.5260.0360.0360.0000.0000.0000.000
113A114THR0-0.064-0.06530.463-0.188-0.1880.0000.0000.0000.000
114A115TRP00.0070.02232.4450.1940.1940.0000.0000.0000.000
115A116ALA00.002-0.01734.756-0.216-0.2160.0000.0000.0000.000
116A117PRO0-0.0090.00936.6510.1790.1790.0000.0000.0000.000
117A118HIS0-0.019-0.03039.450-0.149-0.1490.0000.0000.0000.000
118A119GLY00.0400.02540.8180.0690.0690.0000.0000.0000.000
119A120GLY0-0.057-0.03137.171-0.060-0.0600.0000.0000.0000.000
120A121GLU-1-0.800-0.85031.357-9.688-9.6880.0000.0000.0000.000
121A122SER0-0.009-0.02931.536-0.063-0.0630.0000.0000.0000.000
122A123ARG10.8750.91927.44310.05710.0570.0000.0000.0000.000
123A124VAL00.0330.00226.674-0.477-0.4770.0000.0000.0000.000
124A125ASP-1-0.793-0.85226.923-9.900-9.9000.0000.0000.0000.000
125A126VAL0-0.020-0.00525.716-0.212-0.2120.0000.0000.0000.000
126A127ALA0-0.026-0.00322.828-0.415-0.4150.0000.0000.0000.000
127A128ALA0-0.021-0.00322.945-0.545-0.5450.0000.0000.0000.000
128A129ARG10.7260.82024.49410.10010.1000.0000.0000.0000.000
129A130SER0-0.005-0.02321.839-0.369-0.3690.0000.0000.0000.000
130A131ARG10.7750.83516.37716.12816.1280.0000.0000.0000.000
131A132PRO0-0.006-0.01017.987-0.903-0.9030.0000.0000.0000.000
132A133LEU00.0310.03718.810-0.330-0.3300.0000.0000.0000.000
133A134VAL0-0.001-0.01013.437-0.560-0.5600.0000.0000.0000.000
134A135ALA0-0.033-0.02114.137-1.081-1.0810.0000.0000.0000.000
135A136GLU-1-0.811-0.88214.670-14.098-14.0980.0000.0000.0000.000
136A137LEU00.0160.01414.217-0.193-0.1930.0000.0000.0000.000
137A138VAL0-0.075-0.0399.350-1.139-1.1390.0000.0000.0000.000
138A139ALA0-0.072-0.02411.087-1.155-1.1550.0000.0000.0000.000
139A140SER0-0.039-0.03513.7070.0520.0520.0000.0000.0000.000
140A141GLU-1-0.900-0.93311.844-15.814-15.8140.0000.0000.0000.000
141A142PRO0-0.009-0.01310.135-1.785-1.7850.0000.0000.0000.000
142A143GLU-1-0.888-0.9468.782-19.598-19.5980.0000.0000.0000.000
143A144TRP0-0.003-0.0078.378-1.660-1.6600.0000.0000.0000.000
144A145GLY0-0.033-0.0184.525-2.212-2.158-0.001-0.005-0.0490.000
145A146GLY0-0.042-0.0233.573-6.074-5.3290.013-0.367-0.392-0.002
146A147ALA0-0.045-0.0445.560-0.440-0.4400.0000.0000.0000.000
147A148ASP-1-0.915-0.9426.838-20.747-20.7470.0000.0000.0000.000
148A149GLU-1-0.848-0.9298.904-16.489-16.4890.0000.0000.0000.000
149A150PRO0-0.058-0.0163.845-0.0080.1510.000-0.033-0.1260.000
150A151ASP-1-0.827-0.8975.556-22.020-22.0200.0000.0000.0000.000
151A152ARG10.8290.9228.04117.77717.7770.0000.0000.0000.000
152A153PRO0-0.060-0.02010.145-0.914-0.9140.0000.0000.0000.000
153A154VAL00.0460.03612.0760.9540.9540.0000.0000.0000.000
154A155VAL0-0.019-0.01714.144-0.104-0.1040.0000.0000.0000.000
155A156LEU00.0140.01517.4510.3800.3800.0000.0000.0000.000
156A157VAL0-0.037-0.02219.9130.0980.0980.0000.0000.0000.000
157A158ALA00.0480.00623.4880.2540.2540.0000.0000.0000.000
158A159HIS00.0350.03025.2120.3630.3630.0000.0000.0000.000
159A160GLY0-0.009-0.00226.078-0.328-0.3280.0000.0000.0000.000
160A161GLY00.0550.02626.601-0.266-0.2660.0000.0000.0000.000
161A162LEU00.0170.01922.584-0.247-0.2470.0000.0000.0000.000
162A163ILE00.000-0.00421.144-0.526-0.5260.0000.0000.0000.000
163A164ALA00.0060.01621.897-0.609-0.6090.0000.0000.0000.000
164A165ALA00.0100.01023.289-0.327-0.3270.0000.0000.0000.000
165A166LEU00.0280.01118.322-0.424-0.4240.0000.0000.0000.000
166A167SER0-0.001-0.02118.283-0.973-0.9730.0000.0000.0000.000
167A168ALA00.002-0.00418.447-0.708-0.7080.0000.0000.0000.000
168A169ALA00.0220.01319.846-0.374-0.3740.0000.0000.0000.000
169A170LEU0-0.065-0.02414.142-0.560-0.5600.0000.0000.0000.000
170A171LEU0-0.064-0.03414.780-1.170-1.1700.0000.0000.0000.000
171A172LYS10.8250.92713.06120.64620.6460.0000.0000.0000.000
172A173LEU00.0020.01518.2650.2410.2410.0000.0000.0000.000
173A174PRO00.0470.02621.1620.1760.1760.0000.0000.0000.000
174A175VAL00.0690.02824.2570.1190.1190.0000.0000.0000.000
175A176ALA00.0030.00126.5870.2260.2260.0000.0000.0000.000
176A177ASN0-0.030-0.02825.0750.1130.1130.0000.0000.0000.000
177A178TRP00.006-0.01122.858-0.009-0.0090.0000.0000.0000.000
178A179PRO0-0.017-0.00126.160-0.172-0.1720.0000.0000.0000.000
179A180ALA0-0.0120.00625.8280.2680.2680.0000.0000.0000.000
180A181LEU0-0.053-0.00221.771-0.107-0.1070.0000.0000.0000.000
181A182GLY00.0160.00425.9290.3590.3590.0000.0000.0000.000
182A183GLY0-0.002-0.00327.707-0.130-0.1300.0000.0000.0000.000
183A184MET0-0.054-0.01122.928-0.287-0.2870.0000.0000.0000.000
184A185GLY00.0300.00427.7730.3510.3510.0000.0000.0000.000
185A186ASN0-0.053-0.04428.870-0.250-0.2500.0000.0000.0000.000
186A187ALA00.0080.00727.6590.0410.0410.0000.0000.0000.000
187A188SER0-0.0100.01925.4830.0320.0320.0000.0000.0000.000
188A189TRP00.021-0.01219.2000.0270.0270.0000.0000.0000.000
189A190THR0-0.008-0.00118.5030.2060.2060.0000.0000.0000.000
190A191GLN0-0.071-0.03412.3320.6320.6320.0000.0000.0000.000
191A192LEU00.0020.00513.1280.1540.1540.0000.0000.0000.000
192A193SER00.027-0.0188.155-0.789-0.7890.0000.0000.0000.000
193A194GLY0-0.003-0.0058.2630.6070.6070.0000.0000.0000.000
194A195HIS0-0.017-0.0124.642-0.259-0.071-0.001-0.034-0.1520.000
195A196TRP0-0.008-0.0032.214-13.331-9.3447.331-2.930-8.389-0.024
196A197ALA00.018-0.0114.030-0.735-0.4250.000-0.068-0.2420.000
197A198PRO0-0.037-0.0106.127-4.197-4.1970.0000.0000.0000.000
198A199GLY00.0640.0396.6603.0643.0640.0000.0000.0000.000
199A200SER0-0.060-0.0436.467-4.619-4.6190.0000.0000.0000.000
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