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: 3Q2VL

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2727153.070069
FMO2-HF: Nuclear repulsion 2635288.21601
FMO2-HF: Total energy -91864.854059
FMO2-MP2: Total energy -92131.765619


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.
-16.806-9.63111.728-6.417-12.484-0.055
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 : -0.046 / q_NPA : -0.023
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].
3F4GLN00.0570.0353.108-1.2881.4020.141-1.185-1.646-0.003
4F5LEU0-0.011-0.0024.7620.1920.283-0.001-0.010-0.0800.000
5F6SER0-0.016-0.0288.0700.0420.0420.0000.0000.0000.000
6F7LEU0-0.001-0.00510.8760.0600.0600.0000.0000.0000.000
7F8PHE00.014-0.00411.777-0.032-0.0320.0000.0000.0000.000
8F9GLY00.0760.04116.8970.0420.0420.0000.0000.0000.000
9F10SER0-0.068-0.02020.327-0.023-0.0230.0000.0000.0000.000
10F11ILE00.0060.01422.9950.0180.0180.0000.0000.0000.000
11F12GLY00.0600.04026.237-0.012-0.0120.0000.0000.0000.000
12F13ASP-1-0.804-0.92628.653-0.164-0.1640.0000.0000.0000.000
13F14ASP-1-0.937-0.95929.930-0.106-0.1060.0000.0000.0000.000
14F15GLY0-0.086-0.04329.9610.0070.0070.0000.0000.0000.000
15F16TYR0-0.001-0.00924.3340.0030.0030.0000.0000.0000.000
16F17ASP-1-0.816-0.91928.041-0.111-0.1110.0000.0000.0000.000
17F18LEU0-0.062-0.01830.0970.0060.0060.0000.0000.0000.000
18F19LEU00.0480.01623.1200.0040.0040.0000.0000.0000.000
19F20ILE00.0250.01824.1180.0000.0000.0000.0000.0000.000
20F21SER0-0.001-0.00925.9080.0050.0050.0000.0000.0000.000
21F22THR0-0.041-0.00825.4480.0120.0120.0000.0000.0000.000
22F23LEU00.007-0.00620.7770.0100.0100.0000.0000.0000.000
23F24THR0-0.0090.01123.3430.0050.0050.0000.0000.0000.000
24F25THR0-0.074-0.02725.4450.0110.0110.0000.0000.0000.000
25F26ILE0-0.057-0.01621.7830.0090.0090.0000.0000.0000.000
26F27SER0-0.083-0.06120.2500.0100.0100.0000.0000.0000.000
27F28GLY0-0.032-0.00921.8830.0110.0110.0000.0000.0000.000
28F29ASN0-0.067-0.02921.0680.0110.0110.0000.0000.0000.000
29F30PRO00.0250.01123.515-0.006-0.0060.0000.0000.0000.000
30F31PRO00.0030.00721.648-0.003-0.0030.0000.0000.0000.000
31F32LEU0-0.033-0.01718.3070.0080.0080.0000.0000.0000.000
32F33LEU00.0250.01819.915-0.025-0.0250.0000.0000.0000.000
33F34TYR0-0.061-0.02515.1520.0200.0200.0000.0000.0000.000
34F35ASN00.030-0.00418.206-0.019-0.0190.0000.0000.0000.000
35F36SER0-0.030-0.01614.464-0.051-0.0510.0000.0000.0000.000
36F37LEU00.0560.03916.5240.0050.0050.0000.0000.0000.000
37F38CYS0-0.066-0.03413.742-0.113-0.1130.0000.0000.0000.000
38F39THR00.0460.03215.7800.0560.0560.0000.0000.0000.000
39F40VAL0-0.005-0.01415.453-0.081-0.0810.0000.0000.0000.000
40F41TRP0-0.005-0.01216.3700.0980.0980.0000.0000.0000.000
41F42LYS10.9390.97517.1130.2150.2150.0000.0000.0000.000
42F43PRO00.0290.01318.4790.0210.0210.0000.0000.0000.000
43F44ASN00.042-0.00221.1320.0180.0180.0000.0000.0000.000
44F45PRO0-0.038-0.02924.6210.0080.0080.0000.0000.0000.000
45F46SER0-0.0260.00326.7880.0160.0160.0000.0000.0000.000
46F47TYR0-0.108-0.04725.4810.0090.0090.0000.0000.0000.000
47F48ASP-1-0.846-0.93527.173-0.138-0.1380.0000.0000.0000.000
48F49VAL0-0.084-0.02323.2870.0090.0090.0000.0000.0000.000
49F50GLU-1-0.917-0.96125.394-0.085-0.0850.0000.0000.0000.000
50F51ASN00.0080.00521.375-0.027-0.0270.0000.0000.0000.000
51F52VAL00.0020.01021.6850.0180.0180.0000.0000.0000.000
52F53ASN00.0200.02917.977-0.028-0.0280.0000.0000.0000.000
53F54SER0-0.014-0.00721.7350.0060.0060.0000.0000.0000.000
54F55ARG10.9230.93416.768-0.110-0.1100.0000.0000.0000.000
55F56ASN0-0.004-0.03922.2760.0050.0050.0000.0000.0000.000
56F57GLN0-0.0070.01118.0650.0100.0100.0000.0000.0000.000
57F58LEU00.0280.02419.919-0.013-0.0130.0000.0000.0000.000
58F59VAL0-0.014-0.00216.0180.0140.0140.0000.0000.0000.000
59F60GLU-1-0.875-0.91815.175-0.219-0.2190.0000.0000.0000.000
60F61PRO00.0140.01816.093-0.044-0.0440.0000.0000.0000.000
61F62ASN00.0660.03011.8520.0120.0120.0000.0000.0000.000
62F63ARG10.7850.85714.6770.4640.4640.0000.0000.0000.000
63F64ILE0-0.0230.00112.304-0.113-0.1130.0000.0000.0000.000
64F65LYS10.9280.9649.3191.3401.3400.0000.0000.0000.000
65F66LEU00.0110.00011.467-0.144-0.1440.0000.0000.0000.000
66F67SER0-0.086-0.04911.1650.0430.0430.0000.0000.0000.000
67F68LYS10.9490.95813.1070.3130.3130.0000.0000.0000.000
68F69GLU-1-0.880-0.91815.017-0.374-0.3740.0000.0000.0000.000
69F70VAL0-0.0020.00317.4710.0150.0150.0000.0000.0000.000
70F71PRO0-0.019-0.00121.1520.0040.0040.0000.0000.0000.000
71F72PHE00.1020.01621.828-0.001-0.0010.0000.0000.0000.000
72F73SER0-0.0020.01025.4890.0010.0010.0000.0000.0000.000
73F74TYR0-0.038-0.01526.1430.0100.0100.0000.0000.0000.000
74F75LEU0-0.058-0.04322.090-0.015-0.0150.0000.0000.0000.000
75F76ILE0-0.049-0.02126.404-0.004-0.0040.0000.0000.0000.000
76F77ASP-1-0.864-0.91029.529-0.119-0.1190.0000.0000.0000.000
77F78GLU-1-1.056-1.01531.463-0.101-0.1010.0000.0000.0000.000
78F143ASP-1-0.788-0.89729.442-0.194-0.1940.0000.0000.0000.000
79F144ASP-1-0.982-1.00430.474-0.136-0.1360.0000.0000.0000.000
80F145ILE0-0.0280.00127.0950.0050.0050.0000.0000.0000.000
81F146ILE0-0.077-0.05426.200-0.004-0.0040.0000.0000.0000.000
82F147ASP-1-0.912-0.95328.956-0.140-0.1400.0000.0000.0000.000
83F148VAL0-0.063-0.03425.780-0.008-0.0080.0000.0000.0000.000
84F149ASP-1-0.904-0.94229.057-0.145-0.1450.0000.0000.0000.000
85F150MET0-0.103-0.05026.922-0.019-0.0190.0000.0000.0000.000
86F151ASP-1-0.868-0.92929.513-0.153-0.1530.0000.0000.0000.000
87F152ALA0-0.0120.00129.921-0.011-0.0110.0000.0000.0000.000
88F153SER0-0.130-0.06232.1200.0110.0110.0000.0000.0000.000
89F154PRO0-0.060-0.03430.276-0.009-0.0090.0000.0000.0000.000
90F155ALA00.0550.02327.5280.0050.0050.0000.0000.0000.000
91F156PRO00.0220.01829.5380.0070.0070.0000.0000.0000.000
92F157SER00.0280.01129.753-0.008-0.0080.0000.0000.0000.000
93F158ASN0-0.115-0.05330.4830.0050.0050.0000.0000.0000.000
94F159GLU-1-0.924-0.95927.604-0.157-0.1570.0000.0000.0000.000
95F160SER00.0070.03323.398-0.009-0.0090.0000.0000.0000.000
96F161CYS0-0.0420.00219.849-0.003-0.0030.0000.0000.0000.000
97F162SER00.0300.00719.8430.0040.0040.0000.0000.0000.000
98F163PRO00.014-0.01116.164-0.021-0.0210.0000.0000.0000.000
99F164TRP00.0170.01914.3530.0000.0000.0000.0000.0000.000
100F165SER0-0.0180.0128.162-0.076-0.0760.0000.0000.0000.000
101F166LEU00.0190.01010.0380.0670.0670.0000.0000.0000.000
102F167GLN0-0.022-0.0305.824-0.319-0.3190.0000.0000.0000.000
103F168ILE00.0360.0247.0760.3930.3930.0000.0000.0000.000
104F169SER0-0.0070.0076.736-0.560-0.5600.0000.0000.0000.000
105F170ASP-1-0.892-0.9307.688-0.236-0.2360.0000.0000.0000.000
106F171ILE0-0.039-0.0039.534-0.147-0.1470.0000.0000.0000.000
107F172PRO0-0.038-0.01810.3470.0700.0700.0000.0000.0000.000
108F173ALA00.0550.02610.9340.1240.1240.0000.0000.0000.000
109F174ALA0-0.022-0.01612.713-0.019-0.0190.0000.0000.0000.000
110F175GLY00.006-0.01716.4170.0380.0380.0000.0000.0000.000
111F176ASN0-0.031-0.00718.253-0.040-0.0400.0000.0000.0000.000
112F177ASN0-0.001-0.00121.2600.0070.0070.0000.0000.0000.000
113F178ARG10.9080.97814.6600.2610.2610.0000.0000.0000.000
114F179SER0-0.010-0.00416.534-0.029-0.0290.0000.0000.0000.000
115F180VAL00.0670.00111.604-0.023-0.0230.0000.0000.0000.000
116F181SER0-0.058-0.01511.4540.0160.0160.0000.0000.0000.000
117F182MET00.0450.0257.975-0.027-0.0270.0000.0000.0000.000
118F183GLN0-0.017-0.0236.4240.1350.1350.0000.0000.0000.000
119F184THR00.0380.0383.631-0.972-0.6910.004-0.107-0.1780.000
120F185ILE0-0.001-0.0022.433-0.1861.0961.595-0.820-2.0560.000
121F186ALA0-0.016-0.0022.279-9.969-8.1344.203-2.795-3.243-0.043
122F187GLU-1-0.877-0.9734.361-2.052-1.863-0.001-0.015-0.1730.000
123F188THR0-0.064-0.0215.8520.3730.3730.0000.0000.0000.000
124F189ILE00.0120.0098.743-0.048-0.0480.0000.0000.0000.000
125F190ILE0-0.0310.00211.4510.1060.1060.0000.0000.0000.000
126F191LEU00.015-0.00814.9790.0040.0040.0000.0000.0000.000
127F192SER0-0.057-0.02517.4280.0250.0250.0000.0000.0000.000
128F193SER0-0.016-0.04120.664-0.007-0.0070.0000.0000.0000.000
129F194ALA00.0510.01623.2800.0130.0130.0000.0000.0000.000
130F195GLY0-0.0010.00226.958-0.004-0.0040.0000.0000.0000.000
131F196LYS10.9390.95929.6850.1030.1030.0000.0000.0000.000
132F197ASN00.0270.00327.7850.0060.0060.0000.0000.0000.000
133F198SER0-0.005-0.01925.609-0.005-0.0050.0000.0000.0000.000
134F199SER00.1340.10024.282-0.022-0.0220.0000.0000.0000.000
135F200VAL00.0690.01518.4100.0060.0060.0000.0000.0000.000
136F201SER00.0230.01021.068-0.020-0.0200.0000.0000.0000.000
137F202SER0-0.024-0.01323.3570.0100.0100.0000.0000.0000.000
138F203LEU0-0.018-0.01220.5340.0070.0070.0000.0000.0000.000
139F204MET00.0090.01915.974-0.007-0.0070.0000.0000.0000.000
140F205ASN00.0420.02720.329-0.012-0.0120.0000.0000.0000.000
141F206GLY0-0.074-0.02823.4650.0160.0160.0000.0000.0000.000
142F207LEU0-0.067-0.03916.7480.0160.0160.0000.0000.0000.000
143F208GLY0-0.0100.01020.6880.0010.0010.0000.0000.0000.000
144F209TYR0-0.110-0.06716.0840.0010.0010.0000.0000.0000.000
145F210VAL0-0.0030.00521.0610.0240.0240.0000.0000.0000.000
146F211PHE00.0120.01221.243-0.035-0.0350.0000.0000.0000.000
147F212GLU-1-0.858-0.90520.148-0.343-0.3430.0000.0000.0000.000
148F213PHE00.0400.00617.6980.0170.0170.0000.0000.0000.000
149F214GLN00.0490.02019.331-0.071-0.0710.0000.0000.0000.000
150F215TYR0-0.018-0.00413.8970.0010.0010.0000.0000.0000.000
151F216LEU00.0350.02818.544-0.044-0.0440.0000.0000.0000.000
152F217THR0-0.082-0.03015.5310.0210.0210.0000.0000.0000.000
153F218ILE00.0700.03118.644-0.007-0.0070.0000.0000.0000.000
154F219GLY00.0330.00619.6550.0010.0010.0000.0000.0000.000
155F220VAL0-0.0220.00520.2690.0130.0130.0000.0000.0000.000
156F221LYS10.9290.96211.9020.3760.3760.0000.0000.0000.000
157F222PHE00.0310.01316.8640.0270.0270.0000.0000.0000.000
158F223PHE00.003-0.00312.542-0.022-0.0220.0000.0000.0000.000
159F224MET00.0300.01615.1040.0180.0180.0000.0000.0000.000
160F225LYS10.9520.95915.274-0.036-0.0360.0000.0000.0000.000
161F226HIS00.0020.01513.5780.0170.0170.0000.0000.0000.000
162F227GLY00.0200.02310.3690.0500.0500.0000.0000.0000.000
163F228LEU0-0.0150.00610.241-0.053-0.0530.0000.0000.0000.000
164F229ILE0-0.038-0.0089.6260.0150.0150.0000.0000.0000.000
165F230LEU00.018-0.01512.829-0.037-0.0370.0000.0000.0000.000
166F231GLU-1-0.925-0.96912.922-0.591-0.5910.0000.0000.0000.000
167F232LEU00.0020.00716.580-0.002-0.0020.0000.0000.0000.000
168F233GLN0-0.031-0.03513.949-0.002-0.0020.0000.0000.0000.000
169F234LYS10.8600.95419.6330.2170.2170.0000.0000.0000.000
170F235ILE0-0.017-0.02217.505-0.029-0.0290.0000.0000.0000.000
171F236TRP0-0.004-0.01821.1520.0160.0160.0000.0000.0000.000
172F237GLN0-0.041-0.01622.298-0.047-0.0470.0000.0000.0000.000
173F238ILE0-0.017-0.02623.1030.0170.0170.0000.0000.0000.000
174F239GLU-1-0.945-0.97925.224-0.239-0.2390.0000.0000.0000.000
175F240GLU-1-0.848-0.93228.018-0.168-0.1680.0000.0000.0000.000
176F241ALA0-0.083-0.02931.3150.0110.0110.0000.0000.0000.000
177F242GLY00.0100.00531.9850.0030.0030.0000.0000.0000.000
178F243ASN00.0340.00727.273-0.017-0.0170.0000.0000.0000.000
179F244SER00.0350.02227.4240.0070.0070.0000.0000.0000.000
180F245GLN00.0150.00925.307-0.027-0.0270.0000.0000.0000.000
181F246ILE0-0.0020.00421.4410.0100.0100.0000.0000.0000.000
182F247THR0-0.065-0.03721.377-0.003-0.0030.0000.0000.0000.000
183F248SER0-0.034-0.00924.3020.0150.0150.0000.0000.0000.000
184F249GLY00.0240.01928.0690.0020.0020.0000.0000.0000.000
185F250GLY00.0550.01326.7640.0140.0140.0000.0000.0000.000
186F251PHE0-0.032-0.00622.360-0.014-0.0140.0000.0000.0000.000
187F252LEU0-0.0110.00316.3760.0100.0100.0000.0000.0000.000
188F253LEU0-0.029-0.02418.451-0.008-0.0080.0000.0000.0000.000
189F254LYS10.8730.9438.6601.0051.0050.0000.0000.0000.000
190F255ALA00.0300.02913.6530.0220.0220.0000.0000.0000.000
191F256TYR0-0.044-0.0427.113-0.090-0.0900.0000.0000.0000.000
192F257ILE00.0470.0296.9570.1080.1080.0000.0000.0000.000
193F258ASN00.0330.0232.471-1.498-1.0210.683-0.289-0.8700.003
194F259VAL0-0.017-0.0103.008-0.1520.7530.108-0.265-0.749-0.001
195F260SER00.033-0.0052.102-0.973-0.3524.976-2.794-2.803-0.008
196F261ARG10.8570.9342.9150.280-1.0080.0211.870-0.603-0.003
197F262GLY00.1080.0634.7850.8420.934-0.001-0.007-0.0830.000
198F263THR0-0.037-0.0366.215-0.429-0.4290.0000.0000.0000.000
199F264ASP-1-0.890-0.9499.3450.6500.6500.0000.0000.0000.000
200F265ILE00.0590.01711.193-0.030-0.0300.0000.0000.0000.000
201F266ASP-1-0.866-0.90813.4870.3580.3580.0000.0000.0000.000
202F267ARG10.9230.9578.553-0.985-0.9850.0000.0000.0000.000
203F268ILE00.0050.0237.1920.0000.0000.0000.0000.0000.000
204F269ASN00.0870.03310.705-0.118-0.1180.0000.0000.0000.000
205F270TYR0-0.089-0.06512.825-0.073-0.0730.0000.0000.0000.000
206F271THR0-0.004-0.0388.263-0.036-0.0360.0000.0000.0000.000
207F272GLU-1-0.904-0.94611.5150.0140.0140.0000.0000.0000.000
208F273THR0-0.044-0.01513.419-0.050-0.0500.0000.0000.0000.000
209F274VAL0-0.030-0.00813.370-0.029-0.0290.0000.0000.0000.000
210F275LEU00.0240.01510.453-0.026-0.0260.0000.0000.0000.000
211F276MET0-0.024-0.00414.780-0.029-0.0290.0000.0000.0000.000
212F277ASN0-0.034-0.02817.982-0.011-0.0110.0000.0000.0000.000
213F278LEU00.0560.04816.139-0.005-0.0050.0000.0000.0000.000
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