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: K93R3

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238055.379119
FMO2-HF: Nuclear repulsion 2158898.871513
FMO2-HF: Total energy -79156.507606
FMO2-MP2: Total energy -79388.765668


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.
-11.009-4.9443.131-4.909-4.286-0.04
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 : 0.049 / q_NPA : 0.026
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].
3A4SER0-0.032-0.0583.8210.2291.900-0.015-0.930-0.7260.003
4A5ALA00.0250.0097.064-0.003-0.0030.0000.0000.0000.000
5A6VAL0-0.0340.00210.8290.1250.1250.0000.0000.0000.000
6A7ILE00.0050.00213.8160.0150.0150.0000.0000.0000.000
7A8PHE0-0.024-0.01317.1840.0310.0310.0000.0000.0000.000
8A9VAL0-0.015-0.02920.2970.0080.0080.0000.0000.0000.000
9A10GLU-1-0.918-0.95123.458-0.178-0.1780.0000.0000.0000.000
10A11ARG10.8820.94726.2880.1430.1430.0000.0000.0000.000
11A12ALA00.0270.00526.9030.0030.0030.0000.0000.0000.000
12A13THR0-0.044-0.02128.9550.0040.0040.0000.0000.0000.000
13A14PRO0-0.002-0.01428.520-0.001-0.0010.0000.0000.0000.000
14A15ALA00.0160.01628.4020.0030.0030.0000.0000.0000.000
15A16THR00.0560.02825.3000.0040.0040.0000.0000.0000.000
16A17LEU00.0060.01322.618-0.001-0.0010.0000.0000.0000.000
17A18THR00.016-0.01324.0070.0030.0030.0000.0000.0000.000
18A19GLU-1-0.909-0.94226.087-0.053-0.0530.0000.0000.0000.000
19A20LEU0-0.014-0.01619.6200.0060.0060.0000.0000.0000.000
20A21LYS10.8480.94021.989-0.007-0.0070.0000.0000.0000.000
21A22ASP-1-0.890-0.95523.0670.0190.0190.0000.0000.0000.000
22A23ALA0-0.059-0.01223.4260.0130.0130.0000.0000.0000.000
23A24LEU00.010-0.00717.9750.0050.0050.0000.0000.0000.000
24A25SER00.027-0.00721.4900.0290.0290.0000.0000.0000.000
25A26ASN0-0.067-0.03223.9490.0240.0240.0000.0000.0000.000
26A27SER0-0.070-0.03418.619-0.004-0.0040.0000.0000.0000.000
27A28ILE0-0.044-0.00618.4320.0290.0290.0000.0000.0000.000
28A29LEU00.0070.03116.2020.0080.0080.0000.0000.0000.000
29A30SER0-0.046-0.03117.459-0.006-0.0060.0000.0000.0000.000
30A31VAL00.004-0.00718.187-0.005-0.0050.0000.0000.0000.000
31A32ARG10.9220.98013.691-0.163-0.1630.0000.0000.0000.000
32A33ASP-1-0.906-0.97018.2480.0860.0860.0000.0000.0000.000
33A34PRO0-0.016-0.00317.969-0.006-0.0060.0000.0000.0000.000
34A35TRP0-0.0270.00615.7180.0050.0050.0000.0000.0000.000
35A36SER0-0.023-0.02318.0040.0020.0020.0000.0000.0000.000
36A37ILE0-0.007-0.01116.729-0.024-0.0240.0000.0000.0000.000
37A38ASP-1-0.861-0.90219.185-0.155-0.1550.0000.0000.0000.000
38A39PHE00.0330.01218.742-0.025-0.0250.0000.0000.0000.000
39A40ARG10.8940.95321.6570.2170.2170.0000.0000.0000.000
40A41THR00.0310.02223.553-0.028-0.0280.0000.0000.0000.000
41A42TYR0-0.052-0.06125.1420.0340.0340.0000.0000.0000.000
42A43ARG10.9340.95628.3340.1430.1430.0000.0000.0000.000
43A44CYS0-0.057-0.00730.9970.0120.0120.0000.0000.0000.000
44A45SER0-0.024-0.02932.5240.0030.0030.0000.0000.0000.000
45A46ILE0-0.036-0.01334.7550.0100.0100.0000.0000.0000.000
46A47LYS10.9500.95137.0970.0970.0970.0000.0000.0000.000
47A48ASN00.0270.01639.1730.0040.0040.0000.0000.0000.000
48A49LEU0-0.058-0.02933.1550.0000.0000.0000.0000.0000.000
49A50PRO00.0070.01434.0710.0040.0040.0000.0000.0000.000
50A51ALA00.007-0.01234.237-0.007-0.0070.0000.0000.0000.000
51A52ASP-1-0.931-0.96430.804-0.203-0.2030.0000.0000.0000.000
52A53VAL00.0560.06029.357-0.011-0.0110.0000.0000.0000.000
53A54SER0-0.062-0.06726.5640.0120.0120.0000.0000.0000.000
54A55LYS10.8930.92528.9570.1720.1720.0000.0000.0000.000
55A56LEU0-0.013-0.00426.5530.0160.0160.0000.0000.0000.000
56A57MET0-0.0020.02423.429-0.016-0.0160.0000.0000.0000.000
57A58TYR00.0140.00720.5560.0360.0360.0000.0000.0000.000
58A59SER0-0.057-0.04520.704-0.028-0.0280.0000.0000.0000.000
59A60ILE00.0220.01915.4460.0290.0290.0000.0000.0000.000
60A61THR0-0.003-0.01617.295-0.023-0.0230.0000.0000.0000.000
61A62PHE00.0560.02212.6960.0160.0160.0000.0000.0000.000
62A63HIS0-0.057-0.04916.2870.0350.0350.0000.0000.0000.000
63A64HIS0-0.030-0.03016.870-0.009-0.0090.0000.0000.0000.000
64A65HIS00.0190.02712.5580.0930.0930.0000.0000.0000.000
65A66GLY00.056-0.00713.618-0.057-0.0570.0000.0000.0000.000
66A67ARG10.9020.95016.2770.1070.1070.0000.0000.0000.000
67A68GLN0-0.0140.03013.512-0.063-0.0630.0000.0000.0000.000
68A69THR0-0.022-0.00217.344-0.002-0.0020.0000.0000.0000.000
69A70VAL00.0140.02213.5190.0080.0080.0000.0000.0000.000
70A71LEU0-0.001-0.01416.9780.0250.0250.0000.0000.0000.000
71A72ILE00.0210.02015.102-0.031-0.0310.0000.0000.0000.000
72A73LYS10.8610.92519.5330.3100.3100.0000.0000.0000.000
73A74ASP-1-0.804-0.87122.035-0.299-0.2990.0000.0000.0000.000
74A75ASN0-0.018-0.01419.019-0.044-0.0440.0000.0000.0000.000
75A76SER00.0500.04818.231-0.039-0.0390.0000.0000.0000.000
76A77ALA00.027-0.00715.2140.0220.0220.0000.0000.0000.000
77A78MET0-0.0240.00217.3060.0150.0150.0000.0000.0000.000
78A79VAL00.0300.02413.3350.0090.0090.0000.0000.0000.000
79A80THR0-0.054-0.02516.5780.0600.0600.0000.0000.0000.000
80A81THR00.0440.00718.336-0.011-0.0110.0000.0000.0000.000
81A82ALA00.0200.02620.0870.0120.0120.0000.0000.0000.000
82A83ALA0-0.047-0.02620.6900.0220.0220.0000.0000.0000.000
83A84ALA00.0480.00622.657-0.001-0.0010.0000.0000.0000.000
84A85ALA0-0.060-0.03422.0130.0030.0030.0000.0000.0000.000
85A86ASP-1-0.837-0.91518.266-0.089-0.0890.0000.0000.0000.000
86A87ILE0-0.104-0.02620.039-0.022-0.0220.0000.0000.0000.000
87A88PRO00.0180.01119.9100.0210.0210.0000.0000.0000.000
88A89PRO00.0740.02021.938-0.001-0.0010.0000.0000.0000.000
89A90ALA0-0.007-0.00824.5950.0000.0000.0000.0000.0000.000
90A91LEU0-0.0010.00223.781-0.001-0.0010.0000.0000.0000.000
91A92VAL0-0.004-0.00426.701-0.002-0.0020.0000.0000.0000.000
92A93PHE0-0.044-0.01829.0220.0030.0030.0000.0000.0000.000
93A94ASN0-0.003-0.01229.7380.0040.0040.0000.0000.0000.000
94A95GLY00.0160.01531.971-0.002-0.0020.0000.0000.0000.000
95A96SER0-0.050-0.01028.844-0.003-0.0030.0000.0000.0000.000
96A97SER00.0160.01227.278-0.008-0.0080.0000.0000.0000.000
97A98THR00.0260.00729.6480.0070.0070.0000.0000.0000.000
98A99GLY0-0.003-0.00428.8270.0080.0080.0000.0000.0000.000
99A100VAL0-0.058-0.03629.1410.0050.0050.0000.0000.0000.000
100A101PRO0-0.0260.00525.053-0.003-0.0030.0000.0000.0000.000
101A102GLU-1-0.894-0.95627.192-0.100-0.1000.0000.0000.0000.000
102A103SER00.001-0.00924.387-0.017-0.0170.0000.0000.0000.000
103A104ILE00.0910.03922.1110.0140.0140.0000.0000.0000.000
104A105ASP-1-0.725-0.82823.701-0.227-0.2270.0000.0000.0000.000
105A106THR00.0050.00526.4860.0060.0060.0000.0000.0000.000
106A107ILE00.0450.05727.6970.0080.0080.0000.0000.0000.000
107A108LEU0-0.032-0.01725.7960.0080.0080.0000.0000.0000.000
108A109SER0-0.060-0.03129.9340.0110.0110.0000.0000.0000.000
109A110SER0-0.021-0.04932.3270.0090.0090.0000.0000.0000.000
110A111LYS10.9000.94233.3000.1010.1010.0000.0000.0000.000
111A112LEU0-0.0050.00830.0530.0010.0010.0000.0000.0000.000
112A113SER00.0510.04033.841-0.005-0.0050.0000.0000.0000.000
113A114ASN0-0.034-0.01335.030-0.003-0.0030.0000.0000.0000.000
114A115ILE0-0.049-0.02632.8750.0010.0010.0000.0000.0000.000
115A116TRP00.0290.00228.508-0.012-0.0120.0000.0000.0000.000
116A117MET00.0010.00732.2600.0100.0100.0000.0000.0000.000
117A118GLN00.0660.03128.652-0.017-0.0170.0000.0000.0000.000
118A119ARG10.8640.92929.9970.1600.1600.0000.0000.0000.000
119A120GLN00.0160.00127.438-0.001-0.0010.0000.0000.0000.000
120A121LEU0-0.020-0.02025.694-0.010-0.0100.0000.0000.0000.000
121A122ILE0-0.0140.00623.5620.0170.0170.0000.0000.0000.000
122A123LYS10.9350.96923.5720.1070.1070.0000.0000.0000.000
123A124GLY00.0700.04121.5950.0060.0060.0000.0000.0000.000
124A125ASP-1-0.951-0.98021.673-0.115-0.1150.0000.0000.0000.000
125A126ALA0-0.033-0.02723.3400.0010.0010.0000.0000.0000.000
126A127GLY00.0430.03419.5730.0030.0030.0000.0000.0000.000
127A128GLU-1-0.880-0.96619.5070.0140.0140.0000.0000.0000.000
128A129THR0-0.030-0.02713.926-0.041-0.0410.0000.0000.0000.000
129A130LEU0-0.018-0.00816.0040.0420.0420.0000.0000.0000.000
130A131ILE00.0060.00813.120-0.003-0.0030.0000.0000.0000.000
131A132LEU00.0110.00013.557-0.021-0.0210.0000.0000.0000.000
132A133ASP-1-0.906-0.95013.6250.5340.5340.0000.0000.0000.000
133A134GLY00.0430.0259.930-0.002-0.0020.0000.0000.0000.000
134A135LEU0-0.040-0.0218.4110.1020.1020.0000.0000.0000.000
135A136THR0-0.0130.0039.031-0.028-0.0280.0000.0000.0000.000
136A137VAL00.005-0.00610.610-0.136-0.1360.0000.0000.0000.000
137A138ARG10.8970.94310.1910.1500.1500.0000.0000.0000.000
138A139LEU00.0030.01814.982-0.052-0.0520.0000.0000.0000.000
139A140VAL00.0210.02918.4330.0240.0240.0000.0000.0000.000
140A141ASN00.0180.01720.710-0.024-0.0240.0000.0000.0000.000
141A142LEU00.0110.01320.2720.0040.0040.0000.0000.0000.000
142A143PHE00.0140.00924.2000.0110.0110.0000.0000.0000.000
143A144SER00.0430.03227.314-0.011-0.0110.0000.0000.0000.000
144A145SER0-0.053-0.03029.5570.0080.0080.0000.0000.0000.000
145A146THR0-0.037-0.03932.4650.0050.0050.0000.0000.0000.000
146A147GLY00.0260.02533.2100.0020.0020.0000.0000.0000.000
147A148PHE0-0.002-0.03026.662-0.006-0.0060.0000.0000.0000.000
148A149LYS10.8960.95525.5400.1930.1930.0000.0000.0000.000
149A150GLY00.0980.04525.426-0.010-0.0100.0000.0000.0000.000
150A151LEU0-0.027-0.00121.3690.0080.0080.0000.0000.0000.000
151A152LEU0-0.017-0.00115.969-0.017-0.0170.0000.0000.0000.000
152A153ILE00.001-0.00815.0580.0400.0400.0000.0000.0000.000
153A154GLU-1-0.825-0.88810.846-0.532-0.5320.0000.0000.0000.000
154A155LEU0-0.021-0.00110.4090.1280.1280.0000.0000.0000.000
155A156GLN00.0550.0296.301-0.078-0.0780.0000.0000.0000.000
156A157ALA00.003-0.0154.9420.3290.3290.0000.0000.0000.000
157A158ASP-1-0.909-0.9422.7211.6772.7000.296-0.720-0.600-0.005
158A159GLU-1-0.951-0.9853.4683.4083.8830.021-0.233-0.262-0.002
159A160ALA0-0.022-0.0114.369-1.074-0.998-0.001-0.018-0.0570.000
160A161GLY0-0.049-0.0155.382-0.879-0.892-0.001-0.0010.0160.000
161A162GLU-1-0.931-0.9708.926-0.013-0.0130.0000.0000.0000.000
162A163PHE00.0130.0047.495-0.070-0.0700.0000.0000.0000.000
163A164GLU-1-0.868-0.9629.678-0.539-0.5390.0000.0000.0000.000
164A165THR0-0.0100.00512.7480.0010.0010.0000.0000.0000.000
165A166LYS10.8540.9318.074-0.599-0.5990.0000.0000.0000.000
166A167ILE0-0.0040.01112.2770.0110.0110.0000.0000.0000.000
167A168ALA00.0440.02413.7270.0260.0260.0000.0000.0000.000
168A169GLY0-0.004-0.00516.3290.0230.0230.0000.0000.0000.000
169A170ILE0-0.041-0.02914.4480.0230.0230.0000.0000.0000.000
170A171GLU-1-0.854-0.93917.338-0.293-0.2930.0000.0000.0000.000
171A172GLY00.0150.02019.6570.0120.0120.0000.0000.0000.000
172A173HIS10.9060.94919.2840.0230.0230.0000.0000.0000.000
173A174LEU00.0560.03620.0220.0080.0080.0000.0000.0000.000
174A175ALA0-0.023-0.01423.4830.0030.0030.0000.0000.0000.000
175A176GLU-1-0.945-0.97625.688-0.016-0.0160.0000.0000.0000.000
176A177ILE0-0.040-0.01424.4780.0050.0050.0000.0000.0000.000
177A178ARG10.8300.88428.1480.0420.0420.0000.0000.0000.000
178A179ALA00.0680.04025.228-0.001-0.0010.0000.0000.0000.000
179A180LYS10.8190.94925.9270.0860.0860.0000.0000.0000.000
180A181GLU-1-0.949-0.98327.446-0.172-0.1720.0000.0000.0000.000
181A182TYR00.0090.01620.8100.0140.0140.0000.0000.0000.000
182A183LYS10.9090.96819.9800.3810.3810.0000.0000.0000.000
183A184THR00.0510.01115.572-0.002-0.0020.0000.0000.0000.000
184A185SER0-0.061-0.03815.366-0.019-0.0190.0000.0000.0000.000
185A186SER00.0650.02210.7980.0200.0200.0000.0000.0000.000
186A187ASP-1-0.934-0.94111.217-0.846-0.8460.0000.0000.0000.000
187A188SER0-0.019-0.0229.853-0.169-0.1690.0000.0000.0000.000
188A189LEU0-0.044-0.02211.7800.2430.2430.0000.0000.0000.000
189A190GLY00.0080.00412.508-0.103-0.1030.0000.0000.0000.000
190A191PRO0-0.067-0.01711.6580.1240.1240.0000.0000.0000.000
191A192ASP-1-0.912-0.96914.776-0.547-0.5470.0000.0000.0000.000
192A193THR0-0.042-0.02410.8690.0210.0210.0000.0000.0000.000
193A194SER00.0160.0095.339-0.007-0.0070.0000.0000.0000.000
194A195ASN00.009-0.0107.7380.0770.0770.0000.0000.0000.000
195A196GLU-1-0.768-0.9012.281-13.296-10.4632.831-3.007-2.657-0.036
196A197ILE0-0.062-0.0206.1650.2780.2780.0000.0000.0000.000
197A198CYS0-0.026-0.0159.2220.2710.2710.0000.0000.0000.000
198A199ASP-1-0.765-0.8697.963-1.921-1.9210.0000.0000.0000.000
199A200LEU0-0.0100.0198.1360.2320.2320.0000.0000.0000.000
200A201ALA00.005-0.0139.8140.2140.2140.0000.0000.0000.000
201A202TYR00.018-0.01312.7740.1820.1820.0000.0000.0000.000
202A203GLN00.0270.0198.4970.2430.2430.0000.0000.0000.000
203A204TYR0-0.062-0.08512.4350.1450.1450.0000.0000.0000.000
204A205VAL0-0.036-0.02115.9760.0760.0760.0000.0000.0000.000
205A206ARG10.8900.97016.6790.6140.6140.0000.0000.0000.000
206A207ALA0-0.063-0.03917.1980.0520.0520.0000.0000.0000.000
207A208LEU0-0.038-0.01319.0550.0490.0490.0000.0000.0000.000
208A209GLU-1-1.019-0.99921.520-0.350-0.3500.0000.0000.0000.000