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: 493NN

Calculation Name: 2HZS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: A

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238560.61667
FMO2-HF: Nuclear repulsion 2159402.501287
FMO2-HF: Total energy -79158.115383
FMO2-MP2: Total energy -79390.288433


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-8.767-3.5382.603-3.967-3.862-0.032
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.008
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].
3A4SER0-0.044-0.0613.821-0.0381.201-0.015-0.661-0.5630.001
4A5ALA00.0150.0057.0600.1290.1290.0000.0000.0000.000
5A6VAL0-0.0340.00010.8240.0420.0420.0000.0000.0000.000
6A7ILE00.0020.00013.8120.0330.0330.0000.0000.0000.000
7A8PHE0-0.029-0.00917.1810.0060.0060.0000.0000.0000.000
8A9VAL0-0.017-0.02720.2940.0140.0140.0000.0000.0000.000
9A10GLU-1-0.797-0.89523.456-0.119-0.1190.0000.0000.0000.000
10A11ARG10.7830.87126.2840.0780.0780.0000.0000.0000.000
11A12ALA00.0330.01226.9240.0030.0030.0000.0000.0000.000
12A13THR0-0.022-0.01428.9540.0010.0010.0000.0000.0000.000
13A14PRO00.000-0.01528.509-0.002-0.0020.0000.0000.0000.000
14A15ALA0-0.0020.01228.405-0.002-0.0020.0000.0000.0000.000
15A16THR00.0490.02225.4560.0010.0010.0000.0000.0000.000
16A17LEU0-0.0050.01022.5630.0010.0010.0000.0000.0000.000
17A18THR00.022-0.00724.0020.0000.0000.0000.0000.0000.000
18A19GLU-1-0.883-0.93926.082-0.043-0.0430.0000.0000.0000.000
19A20LEU0-0.009-0.00919.6630.0070.0070.0000.0000.0000.000
20A21LYS10.8110.89521.9810.0510.0510.0000.0000.0000.000
21A22ASP-1-0.884-0.95123.063-0.012-0.0120.0000.0000.0000.000
22A23ALA0-0.083-0.02123.4790.0090.0090.0000.0000.0000.000
23A24LEU00.018-0.00318.0090.0080.0080.0000.0000.0000.000
24A25SER00.0280.00321.4870.0130.0130.0000.0000.0000.000
25A26ASN0-0.074-0.03323.9460.0070.0070.0000.0000.0000.000
26A27SER0-0.080-0.04418.5890.0080.0080.0000.0000.0000.000
27A28ILE0-0.032-0.00618.4300.0110.0110.0000.0000.0000.000
28A29LEU00.0080.02716.4360.0100.0100.0000.0000.0000.000
29A30SER0-0.050-0.02917.515-0.007-0.0070.0000.0000.0000.000
30A31VAL00.003-0.00818.183-0.005-0.0050.0000.0000.0000.000
31A32ARG10.8940.96114.0410.1120.1120.0000.0000.0000.000
32A33ASP-1-0.861-0.94118.259-0.074-0.0740.0000.0000.0000.000
33A34PRO0-0.022-0.00417.976-0.014-0.0140.0000.0000.0000.000
34A35TRP0-0.051-0.00615.763-0.012-0.0120.0000.0000.0000.000
35A36SER0-0.012-0.02318.0200.0120.0120.0000.0000.0000.000
36A37ILE0-0.017-0.00315.708-0.027-0.0270.0000.0000.0000.000
37A38ASP-1-0.803-0.87619.183-0.154-0.1540.0000.0000.0000.000
38A39PHE00.0280.00718.607-0.022-0.0220.0000.0000.0000.000
39A40ARG10.7940.89421.6510.2030.2030.0000.0000.0000.000
40A41THR00.0370.02023.544-0.019-0.0190.0000.0000.0000.000
41A42TYR0-0.030-0.04025.1330.0240.0240.0000.0000.0000.000
42A43ARG10.8750.91828.3240.0970.0970.0000.0000.0000.000
43A44CYS0-0.052-0.00430.9480.0070.0070.0000.0000.0000.000
44A45SER0-0.016-0.01932.5120.0040.0040.0000.0000.0000.000
45A46ILE0-0.017-0.00735.0450.0070.0070.0000.0000.0000.000
46A47LYS10.9470.96037.0850.0660.0660.0000.0000.0000.000
47A48ASN00.0030.00339.1260.0020.0020.0000.0000.0000.000
48A49LEU0-0.030-0.02332.7210.0010.0010.0000.0000.0000.000
49A50PRO00.0110.01633.8050.0030.0030.0000.0000.0000.000
50A51ALA0-0.006-0.01233.930-0.005-0.0050.0000.0000.0000.000
51A52ASP-1-0.930-0.96430.597-0.097-0.0970.0000.0000.0000.000
52A53VAL00.0420.04529.048-0.007-0.0070.0000.0000.0000.000
53A54SER0-0.026-0.03526.5820.0080.0080.0000.0000.0000.000
54A55LYS10.9010.93028.9440.1010.1010.0000.0000.0000.000
55A56LEU0-0.011-0.00226.5030.0070.0070.0000.0000.0000.000
56A57MET00.0050.02023.531-0.007-0.0070.0000.0000.0000.000
57A58TYR0-0.036-0.04120.5010.0220.0220.0000.0000.0000.000
58A59SER0-0.064-0.04520.640-0.022-0.0220.0000.0000.0000.000
59A60ILE00.0190.02015.6150.0220.0220.0000.0000.0000.000
60A61THR00.0120.01417.289-0.022-0.0220.0000.0000.0000.000
61A62PHE00.0520.02012.8710.0100.0100.0000.0000.0000.000
62A63HIS0-0.051-0.03716.2840.0150.0150.0000.0000.0000.000
63A64HIS0-0.038-0.03216.872-0.012-0.0120.0000.0000.0000.000
64A65HIS00.0400.03212.2330.0350.0350.0000.0000.0000.000
65A66GLY00.0750.02713.617-0.047-0.0470.0000.0000.0000.000
66A67ARG10.8680.93916.2760.1860.1860.0000.0000.0000.000
67A68GLN0-0.047-0.01013.825-0.035-0.0350.0000.0000.0000.000
68A69THR0-0.023-0.02417.340-0.001-0.0010.0000.0000.0000.000
69A70VAL00.0050.01513.4870.0050.0050.0000.0000.0000.000
70A71LEU0-0.024-0.01516.9690.0270.0270.0000.0000.0000.000
71A72ILE00.0170.01415.051-0.018-0.0180.0000.0000.0000.000
72A73LYS10.8370.89519.5210.1950.1950.0000.0000.0000.000
73A74ASP-1-0.779-0.85321.867-0.173-0.1730.0000.0000.0000.000
74A75ASN00.0050.01018.666-0.015-0.0150.0000.0000.0000.000
75A76SER00.0500.04917.903-0.014-0.0140.0000.0000.0000.000
76A77ALA00.027-0.00615.0570.0090.0090.0000.0000.0000.000
77A78MET0-0.0230.00017.1970.0110.0110.0000.0000.0000.000
78A79VAL00.0300.02413.2770.0090.0090.0000.0000.0000.000
79A80THR0-0.054-0.03316.5680.0440.0440.0000.0000.0000.000
80A81THR00.035-0.01118.330-0.013-0.0130.0000.0000.0000.000
81A82ALA00.0130.02420.0820.0180.0180.0000.0000.0000.000
82A83ALA0-0.030-0.01620.6490.0220.0220.0000.0000.0000.000
83A84ALA00.0450.00722.655-0.005-0.0050.0000.0000.0000.000
84A85ALA0-0.054-0.03222.0310.0030.0030.0000.0000.0000.000
85A86ASP-1-0.794-0.87917.894-0.255-0.2550.0000.0000.0000.000
86A87ILE0-0.089-0.02120.036-0.015-0.0150.0000.0000.0000.000
87A88PRO00.0260.01520.2600.0120.0120.0000.0000.0000.000
88A89PRO00.0690.01722.3820.0110.0110.0000.0000.0000.000
89A90ALA0-0.008-0.00624.9620.0080.0080.0000.0000.0000.000
90A91LEU0-0.008-0.00423.8440.0060.0060.0000.0000.0000.000
91A92VAL0-0.002-0.00426.7280.0040.0040.0000.0000.0000.000
92A93PHE0-0.045-0.01729.3120.0070.0070.0000.0000.0000.000
93A94ASN0-0.005-0.01330.2770.0020.0020.0000.0000.0000.000
94A95GLY00.0180.01932.2680.0030.0030.0000.0000.0000.000
95A96SER0-0.043-0.00829.1730.0000.0000.0000.0000.0000.000
96A97SER00.0060.00727.174-0.003-0.0030.0000.0000.0000.000
97A98THR00.0230.00529.7780.0040.0040.0000.0000.0000.000
98A99GLY0-0.002-0.00328.8290.0060.0060.0000.0000.0000.000
99A100VAL0-0.053-0.03729.139-0.001-0.0010.0000.0000.0000.000
100A101PRO0-0.0250.00725.0960.0030.0030.0000.0000.0000.000
101A102GLU-1-0.885-0.95727.184-0.116-0.1160.0000.0000.0000.000
102A103SER00.0190.00024.218-0.015-0.0150.0000.0000.0000.000
103A104ILE00.0830.03722.0460.0160.0160.0000.0000.0000.000
104A105ASP-1-0.705-0.81423.917-0.193-0.1930.0000.0000.0000.000
105A106THR0-0.0040.01026.4790.0080.0080.0000.0000.0000.000
106A107ILE00.0380.03727.4430.0100.0100.0000.0000.0000.000
107A108LEU0-0.034-0.01625.7600.0100.0100.0000.0000.0000.000
108A109SER0-0.038-0.03329.9260.0110.0110.0000.0000.0000.000
109A110SER0-0.042-0.03332.3190.0100.0100.0000.0000.0000.000
110A111LYS10.9040.94933.3150.0980.0980.0000.0000.0000.000
111A112LEU00.0040.01030.1930.0030.0030.0000.0000.0000.000
112A113SER00.0520.02833.831-0.001-0.0010.0000.0000.0000.000
113A114ASN0-0.057-0.01735.021-0.002-0.0020.0000.0000.0000.000
114A115ILE0-0.039-0.02232.7620.0030.0030.0000.0000.0000.000
115A116TRP00.0340.00128.418-0.004-0.0040.0000.0000.0000.000
116A117MET00.0020.00932.2500.0050.0050.0000.0000.0000.000
117A118GLN00.0420.01228.542-0.012-0.0120.0000.0000.0000.000
118A119ARG10.8700.93229.9840.1100.1100.0000.0000.0000.000
119A120GLN0-0.003-0.01027.9680.0030.0030.0000.0000.0000.000
120A121LEU0-0.007-0.01225.592-0.009-0.0090.0000.0000.0000.000
121A122ILE0-0.0310.00023.7370.0120.0120.0000.0000.0000.000
122A123LYS10.8520.91823.5590.1260.1260.0000.0000.0000.000
123A124GLY00.0640.03821.5920.0100.0100.0000.0000.0000.000
124A125ASP-1-0.876-0.93421.673-0.146-0.1460.0000.0000.0000.000
125A126ALA0-0.015-0.01923.2970.0030.0030.0000.0000.0000.000
126A127GLY00.0560.04019.5780.0070.0070.0000.0000.0000.000
127A128GLU-1-0.832-0.92419.513-0.053-0.0530.0000.0000.0000.000
128A129THR0-0.027-0.02813.903-0.032-0.0320.0000.0000.0000.000
129A130LEU0-0.013-0.00716.0060.0270.0270.0000.0000.0000.000
130A131ILE00.0040.01013.043-0.013-0.0130.0000.0000.0000.000
131A132LEU00.0140.00013.5510.0030.0030.0000.0000.0000.000
132A133ASP-1-0.918-0.95513.6230.2880.2880.0000.0000.0000.000
133A134GLY00.0180.0129.9270.0240.0240.0000.0000.0000.000
134A135LEU0-0.045-0.0308.4100.0680.0680.0000.0000.0000.000
135A136THR0-0.0090.0009.021-0.010-0.0100.0000.0000.0000.000
136A137VAL00.004-0.01210.605-0.084-0.0840.0000.0000.0000.000
137A138ARG10.8160.89510.0950.3560.3560.0000.0000.0000.000
138A139LEU00.0130.02814.987-0.018-0.0180.0000.0000.0000.000
139A140VAL00.0080.01418.4360.0090.0090.0000.0000.0000.000
140A141ASN00.0290.01320.712-0.008-0.0080.0000.0000.0000.000
141A142LEU00.0060.01320.311-0.001-0.0010.0000.0000.0000.000
142A143PHE00.008-0.00824.1980.0150.0150.0000.0000.0000.000
143A144SER00.0480.03127.311-0.011-0.0110.0000.0000.0000.000
144A145SER0-0.040-0.02029.5540.0050.0050.0000.0000.0000.000
145A146THR0-0.026-0.03232.4620.0040.0040.0000.0000.0000.000
146A147GLY00.0240.02433.2080.0030.0030.0000.0000.0000.000
147A148PHE0-0.016-0.01926.916-0.006-0.0060.0000.0000.0000.000
148A149LYS10.8050.90525.4320.1340.1340.0000.0000.0000.000
149A150GLY00.0700.02925.412-0.002-0.0020.0000.0000.0000.000
150A151LEU0-0.029-0.00121.5430.0000.0000.0000.0000.0000.000
151A152LEU0-0.0290.00215.720-0.004-0.0040.0000.0000.0000.000
152A153ILE0-0.005-0.01015.1210.0160.0160.0000.0000.0000.000
153A154GLU-1-0.802-0.89410.862-0.512-0.5120.0000.0000.0000.000
154A155LEU0-0.016-0.00310.3530.0710.0710.0000.0000.0000.000
155A156GLN00.0370.0326.395-0.104-0.1040.0000.0000.0000.000
156A157ALA00.016-0.0074.9340.2640.2640.0000.0000.0000.000
157A158ASP-1-0.912-0.9462.710-0.5810.4260.305-0.721-0.590-0.005
158A159GLU-1-0.963-0.9923.4722.3982.8960.020-0.236-0.281-0.002
159A160ALA0-0.009-0.0024.553-0.518-0.439-0.001-0.026-0.0520.000
160A161GLY0-0.043-0.0115.388-0.743-0.765-0.0010.0000.0240.000
161A162GLU-1-0.891-0.9578.9300.1630.1630.0000.0000.0000.000
162A163PHE00.0340.0207.075-0.063-0.0630.0000.0000.0000.000
163A164GLU-1-0.794-0.9249.680-0.131-0.1310.0000.0000.0000.000
164A165THR0-0.021-0.00412.749-0.037-0.0370.0000.0000.0000.000
165A166LYS10.8700.9528.774-0.544-0.5440.0000.0000.0000.000
166A167ILE0-0.0050.00312.115-0.032-0.0320.0000.0000.0000.000
167A168ALA00.0260.01313.726-0.009-0.0090.0000.0000.0000.000
168A169GLY00.0040.00016.325-0.002-0.0020.0000.0000.0000.000
169A170ILE0-0.024-0.02014.519-0.002-0.0020.0000.0000.0000.000
170A171GLU-1-0.777-0.85417.546-0.121-0.1210.0000.0000.0000.000
171A172GLY0-0.0020.01319.6540.0030.0030.0000.0000.0000.000
172A173HIS10.8450.89819.599-0.008-0.0080.0000.0000.0000.000
173A174LEU00.0700.03920.067-0.001-0.0010.0000.0000.0000.000
174A175ALA0-0.032-0.01923.4790.0000.0000.0000.0000.0000.000
175A176GLU-1-0.849-0.90825.2350.0030.0030.0000.0000.0000.000
176A177ILE0-0.035-0.01024.8960.0030.0030.0000.0000.0000.000
177A178ARG10.8040.88828.1440.0160.0160.0000.0000.0000.000
178A179ALA00.0610.04225.258-0.002-0.0020.0000.0000.0000.000
179A180LYS10.8430.93325.9230.0360.0360.0000.0000.0000.000
180A181GLU-1-0.839-0.89227.456-0.081-0.0810.0000.0000.0000.000
181A182TYR0-0.065-0.04620.5130.0020.0020.0000.0000.0000.000
182A183LYS10.8790.94520.1490.1990.1990.0000.0000.0000.000
183A184THR0-0.001-0.03015.609-0.018-0.0180.0000.0000.0000.000
184A185SER0-0.065-0.05215.183-0.004-0.0040.0000.0000.0000.000
185A186SER00.0540.01510.839-0.039-0.0390.0000.0000.0000.000
186A187ASP-1-0.866-0.88311.217-0.355-0.3550.0000.0000.0000.000
187A188SER0-0.025-0.0409.554-0.080-0.0800.0000.0000.0000.000
188A189LEU0-0.044-0.02311.6120.1430.1430.0000.0000.0000.000
189A190GLY00.0020.00112.341-0.033-0.0330.0000.0000.0000.000
190A191PRO0-0.064-0.01911.7120.0590.0590.0000.0000.0000.000
191A192ASP-1-0.918-0.97314.560-0.358-0.3580.0000.0000.0000.000
192A193THR0-0.046-0.02510.6900.0480.0480.0000.0000.0000.000
193A194SER00.0100.0114.9290.1380.1380.0000.0000.0000.000
194A195ASN00.016-0.0097.454-0.051-0.0510.0000.0000.0000.000
195A196GLU-1-0.780-0.9032.375-9.518-7.0902.295-2.323-2.400-0.026
196A197ILE0-0.048-0.0196.1540.2900.2900.0000.0000.0000.000
197A198CYS0-0.024-0.0129.2140.2290.2290.0000.0000.0000.000
198A199ASP-1-0.727-0.8288.002-0.940-0.9400.0000.0000.0000.000
199A200LEU0-0.0140.0148.0690.1850.1850.0000.0000.0000.000
200A201ALA0-0.008-0.0169.8050.1720.1720.0000.0000.0000.000
201A202TYR00.010-0.02112.7610.1220.1220.0000.0000.0000.000
202A203GLN00.0060.0088.7630.0810.0810.0000.0000.0000.000
203A204TYR0-0.033-0.05112.5780.1140.1140.0000.0000.0000.000
204A205VAL0-0.021-0.01115.9690.0540.0540.0000.0000.0000.000
205A206ARG10.8170.91516.6670.3290.3290.0000.0000.0000.000
206A207ALA0-0.036-0.02317.1550.0430.0430.0000.0000.0000.000
207A208LEU0-0.042-0.01319.0470.0300.0300.0000.0000.0000.000
208A209GLU-1-0.952-0.94621.507-0.200-0.2000.0000.0000.0000.000