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: 9G5V2

Calculation Name: 2HZS-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: F

ChEMBL ID:

UniProt ID: P32585

Base Structure: X-ray

Registration Date: 2023-06-21

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2724347.901517
FMO2-HF: Nuclear repulsion 2632480.170132
FMO2-HF: Total energy -91867.731385
FMO2-MP2: Total energy -92134.300191


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(F:2:VAL)


Summations of interaction energy for fragment #1(F:2:VAL)
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.
-18.579-11.1159.971-6.192-11.244-0.053
Interaction energy analysis for fragmet #1(F:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.024
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].
3F4GLN00.0290.0162.638-1.0921.4811.039-1.476-2.136-0.009
4F5LEU0-0.011-0.0014.5110.1900.269-0.001-0.016-0.0620.000
5F6SER0-0.012-0.0228.0040.0510.0510.0000.0000.0000.000
6F7LEU0-0.008-0.00210.6400.0550.0550.0000.0000.0000.000
7F8PHE00.028-0.00211.969-0.040-0.0400.0000.0000.0000.000
8F9GLY00.0390.01616.8170.0380.0380.0000.0000.0000.000
9F10SER0-0.050-0.01520.501-0.020-0.0200.0000.0000.0000.000
10F11ILE0-0.0140.00023.1000.0170.0170.0000.0000.0000.000
11F12GLY00.0750.04226.450-0.012-0.0120.0000.0000.0000.000
12F13ASP-1-0.776-0.89628.101-0.174-0.1740.0000.0000.0000.000
13F14ASP-1-0.936-0.96429.970-0.114-0.1140.0000.0000.0000.000
14F15GLY0-0.039-0.01829.9900.0080.0080.0000.0000.0000.000
15F16TYR0-0.007-0.00424.224-0.005-0.0050.0000.0000.0000.000
16F17ASP-1-0.827-0.92127.710-0.117-0.1170.0000.0000.0000.000
17F18LEU0-0.0080.01229.8060.0060.0060.0000.0000.0000.000
18F19LEU0-0.0120.01823.0920.0060.0060.0000.0000.0000.000
19F20ILE00.0720.03223.7030.0000.0000.0000.0000.0000.000
20F21SER0-0.022-0.00625.8870.0070.0070.0000.0000.0000.000
21F22THR0-0.052-0.03025.8200.0110.0110.0000.0000.0000.000
22F23LEU00.009-0.00720.4150.0080.0080.0000.0000.0000.000
23F24THR0-0.010-0.00422.8910.0030.0030.0000.0000.0000.000
24F25THR0-0.091-0.04425.0070.0120.0120.0000.0000.0000.000
25F26ILE0-0.056-0.01821.5270.0090.0090.0000.0000.0000.000
26F27SER0-0.060-0.04720.2480.0110.0110.0000.0000.0000.000
27F28GLY0-0.0270.00021.7060.0100.0100.0000.0000.0000.000
28F29ASN0-0.086-0.05121.5770.0060.0060.0000.0000.0000.000
29F30PRO00.0380.01923.431-0.007-0.0070.0000.0000.0000.000
30F31PRO0-0.0140.00521.778-0.005-0.0050.0000.0000.0000.000
31F32LEU0-0.025-0.01918.1040.0070.0070.0000.0000.0000.000
32F33LEU00.0200.01019.700-0.026-0.0260.0000.0000.0000.000
33F34TYR0-0.088-0.05114.3770.0190.0190.0000.0000.0000.000
34F35ASN00.016-0.01417.626-0.012-0.0120.0000.0000.0000.000
35F36SER0-0.035-0.01214.173-0.056-0.0560.0000.0000.0000.000
36F37LEU00.0580.04816.0960.0000.0000.0000.0000.0000.000
37F38CYS0-0.062-0.02113.787-0.129-0.1290.0000.0000.0000.000
38F39THR00.0520.03115.9310.0530.0530.0000.0000.0000.000
39F40VAL0-0.015-0.00515.664-0.083-0.0830.0000.0000.0000.000
40F41TRP00.007-0.00616.2480.1000.1000.0000.0000.0000.000
41F42LYS10.8750.92016.9740.2110.2110.0000.0000.0000.000
42F43PRO00.0480.01918.5300.0160.0160.0000.0000.0000.000
43F44ASN00.0480.02721.2200.0050.0050.0000.0000.0000.000
44F45PRO0-0.0100.00124.7580.0120.0120.0000.0000.0000.000
45F46SER0-0.040-0.02627.0310.0150.0150.0000.0000.0000.000
46F47TYR0-0.116-0.06025.4090.0130.0130.0000.0000.0000.000
47F48ASP-1-0.874-0.94127.087-0.110-0.1100.0000.0000.0000.000
48F49VAL0-0.051-0.02023.2900.0060.0060.0000.0000.0000.000
49F50GLU-1-0.884-0.94025.368-0.055-0.0550.0000.0000.0000.000
50F51ASN0-0.029-0.00621.846-0.017-0.0170.0000.0000.0000.000
51F52VAL0-0.021-0.01921.6380.0130.0130.0000.0000.0000.000
52F53ASN0-0.024-0.00517.5900.0030.0030.0000.0000.0000.000
53F54SER00.006-0.00421.3030.0040.0040.0000.0000.0000.000
54F55ARG10.8890.92917.340-0.120-0.1200.0000.0000.0000.000
55F56ASN0-0.009-0.00922.4760.0010.0010.0000.0000.0000.000
56F57GLN00.0420.03319.5560.0140.0140.0000.0000.0000.000
57F58LEU00.0320.01919.677-0.005-0.0050.0000.0000.0000.000
58F59VAL0-0.042-0.02416.1640.0220.0220.0000.0000.0000.000
59F60GLU-1-0.837-0.89615.650-0.200-0.2000.0000.0000.0000.000
60F61PRO00.0080.02116.418-0.028-0.0280.0000.0000.0000.000
61F62ASN00.0400.01211.228-0.013-0.0130.0000.0000.0000.000
62F63ARG10.8200.89214.5790.4490.4490.0000.0000.0000.000
63F64ILE0-0.023-0.00412.214-0.104-0.1040.0000.0000.0000.000
64F65LYS10.8860.9389.5371.2911.2910.0000.0000.0000.000
65F66LEU00.0020.00611.260-0.150-0.1500.0000.0000.0000.000
66F67SER0-0.081-0.05711.2670.0120.0120.0000.0000.0000.000
67F68LYS10.8660.93713.1650.3330.3330.0000.0000.0000.000
68F69GLU-1-0.850-0.91914.871-0.374-0.3740.0000.0000.0000.000
69F70VAL00.0290.01117.1000.0100.0100.0000.0000.0000.000
70F71PRO0-0.0100.00920.8890.0010.0010.0000.0000.0000.000
71F72PHE00.0880.00721.487-0.001-0.0010.0000.0000.0000.000
72F73SER00.0140.01525.5160.0020.0020.0000.0000.0000.000
73F74TYR0-0.042-0.01726.2000.0090.0090.0000.0000.0000.000
74F75LEU0-0.042-0.01821.805-0.018-0.0180.0000.0000.0000.000
75F76ILE0-0.016-0.00425.950-0.005-0.0050.0000.0000.0000.000
76F77ASP-1-0.892-0.92529.243-0.115-0.1150.0000.0000.0000.000
77F78GLU-1-1.074-1.02831.430-0.096-0.0960.0000.0000.0000.000
78F143ASP-1-0.803-0.89429.482-0.194-0.1940.0000.0000.0000.000
79F144ASP-1-0.977-0.99730.513-0.136-0.1360.0000.0000.0000.000
80F145ILE0-0.0090.00227.7340.0060.0060.0000.0000.0000.000
81F146ILE0-0.081-0.04025.543-0.005-0.0050.0000.0000.0000.000
82F147ASP-1-0.899-0.95728.603-0.142-0.1420.0000.0000.0000.000
83F148VAL0-0.071-0.04425.846-0.012-0.0120.0000.0000.0000.000
84F149ASP-1-0.921-0.95129.137-0.141-0.1410.0000.0000.0000.000
85F150MET0-0.075-0.02426.894-0.016-0.0160.0000.0000.0000.000
86F151ASP-1-0.837-0.90429.555-0.139-0.1390.0000.0000.0000.000
87F152ALA0-0.0090.00629.664-0.012-0.0120.0000.0000.0000.000
88F153SER0-0.147-0.08331.8640.0090.0090.0000.0000.0000.000
89F154PRO0-0.068-0.04330.289-0.009-0.0090.0000.0000.0000.000
90F155ALA00.0630.02627.3180.0060.0060.0000.0000.0000.000
91F156PRO00.0080.01529.2590.0050.0050.0000.0000.0000.000
92F157SER0-0.013-0.01029.132-0.008-0.0080.0000.0000.0000.000
93F158ASN0-0.098-0.04929.8570.0040.0040.0000.0000.0000.000
94F159GLU-1-0.907-0.95527.503-0.144-0.1440.0000.0000.0000.000
95F160SER0-0.0310.00023.086-0.006-0.0060.0000.0000.0000.000
96F161CYS0-0.061-0.02120.502-0.010-0.0100.0000.0000.0000.000
97F162SER00.0690.02418.7040.0200.0200.0000.0000.0000.000
98F163PRO00.003-0.01615.861-0.017-0.0170.0000.0000.0000.000
99F164TRP00.0030.00114.2150.0030.0030.0000.0000.0000.000
100F165SER0-0.049-0.0287.8620.0110.0110.0000.0000.0000.000
101F166LEU00.0110.0019.4070.1130.1130.0000.0000.0000.000
102F167GLN0-0.023-0.0285.2630.0900.0900.0000.0000.0000.000
103F168ILE00.0340.0116.9950.4010.4010.0000.0000.0000.000
104F169SER0-0.0140.0056.760-0.504-0.5040.0000.0000.0000.000
105F170ASP-1-0.834-0.8797.536-0.014-0.0140.0000.0000.0000.000
106F171ILE0-0.034-0.0129.455-0.129-0.1290.0000.0000.0000.000
107F172PRO0-0.031-0.01110.6400.0470.0470.0000.0000.0000.000
108F173ALA00.0280.01711.4090.1340.1340.0000.0000.0000.000
109F174ALA0-0.025-0.01813.059-0.007-0.0070.0000.0000.0000.000
110F175GLY00.014-0.00116.7520.0440.0440.0000.0000.0000.000
111F176ASN0-0.017-0.00918.785-0.038-0.0380.0000.0000.0000.000
112F177ASN0-0.039-0.02620.7610.0070.0070.0000.0000.0000.000
113F178ARG10.8550.93414.3000.3220.3220.0000.0000.0000.000
114F179SER0-0.007-0.02716.012-0.026-0.0260.0000.0000.0000.000
115F180VAL00.010-0.00611.491-0.019-0.0190.0000.0000.0000.000
116F181SER0-0.002-0.01012.0250.0400.0400.0000.0000.0000.000
117F182MET00.0050.0127.746-0.029-0.0290.0000.0000.0000.000
118F183GLN0-0.018-0.0227.0050.1880.1880.0000.0000.0000.000
119F184THR0-0.002-0.0183.997-0.866-0.6830.000-0.063-0.1200.000
120F185ILE0-0.018-0.0112.444-0.2391.2950.724-0.674-1.585-0.001
121F186ALA00.0080.0202.067-9.948-9.0825.344-2.995-3.215-0.041
122F187GLU-1-0.828-0.8923.802-2.830-2.5180.002-0.045-0.2700.000
123F188THR0-0.057-0.0235.3540.4200.473-0.0010.000-0.0510.000
124F189ILE00.0180.0037.887-0.084-0.0840.0000.0000.0000.000
125F190ILE00.0010.01311.1450.1160.1160.0000.0000.0000.000
126F191LEU0-0.011-0.01314.712-0.010-0.0100.0000.0000.0000.000
127F192SER00.0110.00717.2590.0150.0150.0000.0000.0000.000
128F193SER0-0.032-0.02820.221-0.010-0.0100.0000.0000.0000.000
129F194ALA00.0460.01822.9120.0120.0120.0000.0000.0000.000
130F195GLY00.0150.00626.605-0.002-0.0020.0000.0000.0000.000
131F196LYS10.9230.93429.3350.0880.0880.0000.0000.0000.000
132F197ASN00.006-0.00227.3670.0110.0110.0000.0000.0000.000
133F198SER00.0340.01725.102-0.008-0.0080.0000.0000.0000.000
134F199SER00.0980.07023.806-0.025-0.0250.0000.0000.0000.000
135F200VAL00.0770.01518.2820.0040.0040.0000.0000.0000.000
136F201SER00.0240.02520.792-0.009-0.0090.0000.0000.0000.000
137F202SER0-0.043-0.01822.9840.0050.0050.0000.0000.0000.000
138F203LEU0-0.022-0.00619.8170.0110.0110.0000.0000.0000.000
139F204MET00.0030.01316.095-0.003-0.0030.0000.0000.0000.000
140F205ASN00.0230.00720.194-0.002-0.0020.0000.0000.0000.000
141F206GLY0-0.058-0.01923.4590.0160.0160.0000.0000.0000.000
142F207LEU0-0.051-0.03116.4700.0160.0160.0000.0000.0000.000
143F208GLY0-0.0160.00620.199-0.002-0.0020.0000.0000.0000.000
144F209TYR0-0.081-0.05616.0690.0130.0130.0000.0000.0000.000
145F210VAL0-0.015-0.01120.9140.0140.0140.0000.0000.0000.000
146F211PHE00.0170.01621.011-0.029-0.0290.0000.0000.0000.000
147F212GLU-1-0.832-0.88220.535-0.309-0.3090.0000.0000.0000.000
148F213PHE00.0370.00617.8730.0150.0150.0000.0000.0000.000
149F214GLN0-0.019-0.01619.604-0.055-0.0550.0000.0000.0000.000
150F215TYR00.006-0.00313.5950.0000.0000.0000.0000.0000.000
151F216LEU00.0380.03018.650-0.039-0.0390.0000.0000.0000.000
152F217THR0-0.045-0.02715.0730.0340.0340.0000.0000.0000.000
153F218ILE00.0590.01618.506-0.005-0.0050.0000.0000.0000.000
154F219GLY00.0360.01619.5890.0040.0040.0000.0000.0000.000
155F220VAL0-0.0250.00120.1340.0110.0110.0000.0000.0000.000
156F221LYS10.8360.91311.6080.4490.4490.0000.0000.0000.000
157F222PHE00.0390.02416.8610.0250.0250.0000.0000.0000.000
158F223PHE0-0.002-0.00311.906-0.029-0.0290.0000.0000.0000.000
159F224MET00.0240.00914.8000.0160.0160.0000.0000.0000.000
160F225LYS10.9590.96914.930-0.008-0.0080.0000.0000.0000.000
161F226HIS00.015-0.00113.6370.0070.0070.0000.0000.0000.000
162F227GLY00.0190.02310.2850.0580.0580.0000.0000.0000.000
163F228LEU0-0.036-0.0099.996-0.048-0.0480.0000.0000.0000.000
164F229ILE0-0.041-0.0128.8740.0130.0130.0000.0000.0000.000
165F230LEU00.019-0.00312.444-0.039-0.0390.0000.0000.0000.000
166F231GLU-1-0.808-0.86512.322-0.598-0.5980.0000.0000.0000.000
167F232LEU00.0220.00916.513-0.001-0.0010.0000.0000.0000.000
168F233GLN0-0.018-0.00414.485-0.016-0.0160.0000.0000.0000.000
169F234LYS10.7880.87919.8610.2100.2100.0000.0000.0000.000
170F235ILE0-0.004-0.01717.252-0.024-0.0240.0000.0000.0000.000
171F236TRP00.002-0.02221.1770.0130.0130.0000.0000.0000.000
172F237GLN0-0.078-0.04522.316-0.052-0.0520.0000.0000.0000.000
173F238ILE0-0.009-0.00823.5360.0180.0180.0000.0000.0000.000
174F239GLU-1-0.887-0.92925.406-0.234-0.2340.0000.0000.0000.000
175F240GLU-1-0.838-0.93428.230-0.167-0.1670.0000.0000.0000.000
176F241ALA0-0.085-0.03731.5790.0100.0100.0000.0000.0000.000
177F242GLY00.0120.01531.4480.0080.0080.0000.0000.0000.000
178F243ASN00.0330.00727.631-0.022-0.0220.0000.0000.0000.000
179F244SER00.004-0.00427.0990.0090.0090.0000.0000.0000.000
180F245GLN00.0140.00325.345-0.027-0.0270.0000.0000.0000.000
181F246ILE0-0.002-0.00720.9970.0110.0110.0000.0000.0000.000
182F247THR0-0.048-0.02021.386-0.007-0.0070.0000.0000.0000.000
183F248SER0-0.0110.00324.4160.0150.0150.0000.0000.0000.000
184F249GLY00.0260.02228.2150.0040.0040.0000.0000.0000.000
185F250GLY00.007-0.00426.7990.0120.0120.0000.0000.0000.000
186F251PHE00.0010.02722.631-0.013-0.0130.0000.0000.0000.000
187F252LEU0-0.010-0.00416.5330.0080.0080.0000.0000.0000.000
188F253LEU0-0.016-0.00818.380-0.006-0.0060.0000.0000.0000.000
189F254LYS10.8540.9308.7440.9760.9760.0000.0000.0000.000
190F255ALA00.0350.02213.7080.0280.0280.0000.0000.0000.000
191F256TYR0-0.060-0.0827.072-0.106-0.1060.0000.0000.0000.000
192F257ILE00.0590.0436.9770.0950.0950.0000.0000.0000.000
193F258ASN00.0160.0202.567-1.834-1.1370.377-0.293-0.7810.002
194F259VAL00.010-0.0053.006-0.3490.5240.133-0.259-0.7470.000
195F260SER00.006-0.0022.381-1.272-0.1812.333-1.482-1.942-0.004
196F261ARG10.8930.9593.095-0.787-1.5840.0211.111-0.3350.000
197F262GLY00.1030.0595.7650.2320.2320.0000.0000.0000.000
198F263THR0-0.052-0.0426.815-0.449-0.4490.0000.0000.0000.000
199F264ASP-1-0.835-0.9169.5510.7740.7740.0000.0000.0000.000
200F265ILE00.0770.03711.209-0.031-0.0310.0000.0000.0000.000
201F266ASP-1-0.875-0.92513.7540.3080.3080.0000.0000.0000.000
202F267ARG10.8640.9178.678-0.865-0.8650.0000.0000.0000.000
203F268ILE0-0.0090.0167.587-0.029-0.0290.0000.0000.0000.000
204F269ASN00.0640.02410.876-0.110-0.1100.0000.0000.0000.000
205F270TYR0-0.047-0.01612.900-0.059-0.0590.0000.0000.0000.000
206F271THR0-0.009-0.0328.261-0.030-0.0300.0000.0000.0000.000
207F272GLU-1-0.851-0.90211.630-0.056-0.0560.0000.0000.0000.000
208F273THR0-0.042-0.02813.729-0.037-0.0370.0000.0000.0000.000
209F274VAL0-0.026-0.00513.512-0.020-0.0200.0000.0000.0000.000
210F275LEU00.0020.00210.805-0.021-0.0210.0000.0000.0000.000
211F276MET00.004-0.00214.862-0.022-0.0220.0000.0000.0000.000
212F277ASN0-0.075-0.03918.170-0.005-0.0050.0000.0000.0000.000
213F278LEU00.0420.03516.347-0.006-0.0060.0000.0000.0000.000
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