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: 5239Z

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2240030.998323
FMO2-HF: Nuclear repulsion 2160872.09107
FMO2-HF: Total energy -79158.907253
FMO2-MP2: Total energy -79391.012831


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.
-10.12-5.282.912-3.928-3.824-0.038
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 : 0.003 / q_NPA : 0.001
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].
3A4SER0-0.036-0.0413.8770.2641.263-0.010-0.491-0.4980.000
4A5ALA00.0040.0016.8580.1360.1360.0000.0000.0000.000
5A6VAL0-0.036-0.00110.6480.0290.0290.0000.0000.0000.000
6A7ILE00.005-0.00213.8250.0340.0340.0000.0000.0000.000
7A8PHE0-0.0200.00917.2260.0130.0130.0000.0000.0000.000
8A9VAL0-0.001-0.02020.3420.0140.0140.0000.0000.0000.000
9A10GLU-1-0.755-0.86823.538-0.132-0.1320.0000.0000.0000.000
10A11ARG10.7690.85326.6640.0980.0980.0000.0000.0000.000
11A12ALA00.0190.01626.3800.0020.0020.0000.0000.0000.000
12A13THR0-0.001-0.00828.4960.0050.0050.0000.0000.0000.000
13A14PRO00.010-0.01128.186-0.005-0.0050.0000.0000.0000.000
14A15ALA00.0040.02228.047-0.003-0.0030.0000.0000.0000.000
15A16THR00.008-0.00725.4590.0000.0000.0000.0000.0000.000
16A17LEU0-0.0080.00622.414-0.005-0.0050.0000.0000.0000.000
17A18THR00.003-0.00923.963-0.003-0.0030.0000.0000.0000.000
18A19GLU-1-0.850-0.92126.416-0.077-0.0770.0000.0000.0000.000
19A20LEU00.000-0.00419.6350.0050.0050.0000.0000.0000.000
20A21LYS10.8300.89922.0090.0880.0880.0000.0000.0000.000
21A22ASP-1-0.904-0.95923.064-0.052-0.0520.0000.0000.0000.000
22A23ALA0-0.063-0.02924.0470.0090.0090.0000.0000.0000.000
23A24LEU0-0.023-0.00618.2710.0020.0020.0000.0000.0000.000
24A25SER00.0220.01121.6520.0090.0090.0000.0000.0000.000
25A26ASN0-0.042-0.02123.8110.0070.0070.0000.0000.0000.000
26A27SER0-0.067-0.05418.8720.0050.0050.0000.0000.0000.000
27A28ILE0-0.043-0.00118.6640.0040.0040.0000.0000.0000.000
28A29LEU0-0.0240.00816.3730.0120.0120.0000.0000.0000.000
29A30SER0-0.047-0.03217.4570.0010.0010.0000.0000.0000.000
30A31VAL00.006-0.00818.301-0.012-0.0120.0000.0000.0000.000
31A32ARG10.8940.96113.8250.1790.1790.0000.0000.0000.000
32A33ASP-1-0.844-0.93517.787-0.110-0.1100.0000.0000.0000.000
33A34PRO0-0.022-0.00918.014-0.019-0.0190.0000.0000.0000.000
34A35TRP0-0.065-0.01516.413-0.017-0.0170.0000.0000.0000.000
35A36SER0-0.041-0.05418.6050.0150.0150.0000.0000.0000.000
36A37ILE0-0.010-0.00115.988-0.022-0.0220.0000.0000.0000.000
37A38ASP-1-0.793-0.86619.576-0.159-0.1590.0000.0000.0000.000
38A39PHE00.0390.01419.001-0.024-0.0240.0000.0000.0000.000
39A40ARG10.7660.86521.8850.2030.2030.0000.0000.0000.000
40A41THR00.0430.02223.913-0.018-0.0180.0000.0000.0000.000
41A42TYR0-0.044-0.05125.6530.0220.0220.0000.0000.0000.000
42A43ARG10.8520.91028.7340.0900.0900.0000.0000.0000.000
43A44CYS0-0.0180.02931.2810.0070.0070.0000.0000.0000.000
44A45SER0-0.020-0.02632.8640.0030.0030.0000.0000.0000.000
45A46ILE0-0.035-0.02535.1010.0060.0060.0000.0000.0000.000
46A47LYS10.9680.97736.9440.0580.0580.0000.0000.0000.000
47A48ASN0-0.003-0.01039.356-0.001-0.0010.0000.0000.0000.000
48A49LEU0-0.0090.00831.7340.0020.0020.0000.0000.0000.000
49A50PRO00.0240.00433.6960.0000.0000.0000.0000.0000.000
50A51ALA00.0090.00534.190-0.004-0.0040.0000.0000.0000.000
51A52ASP-1-0.913-0.95430.425-0.081-0.0810.0000.0000.0000.000
52A53VAL0-0.0070.01428.058-0.005-0.0050.0000.0000.0000.000
53A54SER0-0.035-0.04726.0990.0030.0030.0000.0000.0000.000
54A55LYS10.8760.92728.3640.0860.0860.0000.0000.0000.000
55A56LEU0-0.015-0.00727.0680.0060.0060.0000.0000.0000.000
56A57MET0-0.0060.00023.712-0.001-0.0010.0000.0000.0000.000
57A58TYR0-0.047-0.04521.0200.0190.0190.0000.0000.0000.000
58A59SER0-0.042-0.03821.089-0.013-0.0130.0000.0000.0000.000
59A60ILE00.0160.01816.2560.0170.0170.0000.0000.0000.000
60A61THR00.0170.02917.826-0.027-0.0270.0000.0000.0000.000
61A62PHE00.0710.03113.3640.0110.0110.0000.0000.0000.000
62A63HIS0-0.059-0.04516.7240.0080.0080.0000.0000.0000.000
63A64HIS0-0.030-0.02617.504-0.013-0.0130.0000.0000.0000.000
64A65HIS00.0290.03612.2530.0330.0330.0000.0000.0000.000
65A66GLY00.0730.02614.504-0.025-0.0250.0000.0000.0000.000
66A67ARG10.8260.90516.8470.1790.1790.0000.0000.0000.000
67A68GLN0-0.023-0.00714.295-0.031-0.0310.0000.0000.0000.000
68A69THR0-0.023-0.03317.682-0.007-0.0070.0000.0000.0000.000
69A70VAL0-0.0090.00514.0440.0110.0110.0000.0000.0000.000
70A71LEU0-0.0010.00017.4380.0170.0170.0000.0000.0000.000
71A72ILE00.0130.00915.350-0.018-0.0180.0000.0000.0000.000
72A73LYS10.8290.89119.6280.1690.1690.0000.0000.0000.000
73A74ASP-1-0.751-0.83721.364-0.150-0.1500.0000.0000.0000.000
74A75ASN00.0040.01318.518-0.012-0.0120.0000.0000.0000.000
75A76SER00.0400.04017.664-0.006-0.0060.0000.0000.0000.000
76A77ALA00.014-0.01014.938-0.002-0.0020.0000.0000.0000.000
77A78MET0-0.023-0.00717.0830.0220.0220.0000.0000.0000.000
78A79VAL00.0310.02513.1260.0080.0080.0000.0000.0000.000
79A80THR0-0.063-0.03516.4970.0480.0480.0000.0000.0000.000
80A81THR00.036-0.01918.564-0.018-0.0180.0000.0000.0000.000
81A82ALA00.0240.03120.5490.0190.0190.0000.0000.0000.000
82A83ALA0-0.021-0.00421.0640.0190.0190.0000.0000.0000.000
83A84ALA00.028-0.00623.040-0.004-0.0040.0000.0000.0000.000
84A85ALA0-0.040-0.02322.0350.0050.0050.0000.0000.0000.000
85A86ASP-1-0.778-0.85618.227-0.242-0.2420.0000.0000.0000.000
86A87ILE0-0.073-0.01819.905-0.008-0.0080.0000.0000.0000.000
87A88PRO00.0430.01719.7760.0130.0130.0000.0000.0000.000
88A89PRO00.0470.01722.1470.0090.0090.0000.0000.0000.000
89A90ALA0-0.004-0.00325.0900.0060.0060.0000.0000.0000.000
90A91LEU00.000-0.00223.5140.0050.0050.0000.0000.0000.000
91A92VAL00.0020.00026.9140.0010.0010.0000.0000.0000.000
92A93PHE0-0.044-0.01929.3340.0060.0060.0000.0000.0000.000
93A94ASN0-0.014-0.00729.8570.0010.0010.0000.0000.0000.000
94A95GLY00.0180.01632.2350.0020.0020.0000.0000.0000.000
95A96SER0-0.042-0.02328.9350.0000.0000.0000.0000.0000.000
96A97SER0-0.007-0.00527.033-0.006-0.0060.0000.0000.0000.000
97A98THR00.0150.00529.7040.0040.0040.0000.0000.0000.000
98A99GLY0-0.0020.00928.7730.0050.0050.0000.0000.0000.000
99A100VAL0-0.048-0.03529.147-0.003-0.0030.0000.0000.0000.000
100A101PRO0-0.0040.01625.2730.0040.0040.0000.0000.0000.000
101A102GLU-1-0.902-0.96627.801-0.107-0.1070.0000.0000.0000.000
102A103SER00.0170.00624.517-0.012-0.0120.0000.0000.0000.000
103A104ILE00.0900.04022.3550.0160.0160.0000.0000.0000.000
104A105ASP-1-0.704-0.81924.205-0.187-0.1870.0000.0000.0000.000
105A106THR0-0.0110.01926.9760.0080.0080.0000.0000.0000.000
106A107ILE00.0550.05127.3430.0100.0100.0000.0000.0000.000
107A108LEU0-0.026-0.01825.9720.0100.0100.0000.0000.0000.000
108A109SER0-0.032-0.04930.2320.0110.0110.0000.0000.0000.000
109A110SER0-0.041-0.02932.6540.0100.0100.0000.0000.0000.000
110A111LYS10.8630.92433.1720.0950.0950.0000.0000.0000.000
111A112LEU00.0190.02430.2140.0030.0030.0000.0000.0000.000
112A113SER00.0370.02533.9840.0000.0000.0000.0000.0000.000
113A114ASN0-0.039-0.01435.157-0.002-0.0020.0000.0000.0000.000
114A115ILE0-0.047-0.02332.8580.0030.0030.0000.0000.0000.000
115A116TRP00.0540.01228.422-0.004-0.0040.0000.0000.0000.000
116A117MET00.0090.01332.4510.0020.0020.0000.0000.0000.000
117A118GLN00.0500.01528.701-0.011-0.0110.0000.0000.0000.000
118A119ARG10.8730.93630.6530.1060.1060.0000.0000.0000.000
119A120GLN0-0.005-0.00828.5180.0040.0040.0000.0000.0000.000
120A121LEU0-0.022-0.00525.713-0.008-0.0080.0000.0000.0000.000
121A122ILE0-0.031-0.00224.1920.0120.0120.0000.0000.0000.000
122A123LYS10.8300.89823.5300.1450.1450.0000.0000.0000.000
123A124GLY00.0640.03621.8240.0080.0080.0000.0000.0000.000
124A125ASP-1-0.837-0.88622.027-0.165-0.1650.0000.0000.0000.000
125A126ALA00.000-0.01123.4000.0050.0050.0000.0000.0000.000
126A127GLY00.0450.04519.9220.0090.0090.0000.0000.0000.000
127A128GLU-1-0.791-0.89019.658-0.098-0.0980.0000.0000.0000.000
128A129THR0-0.028-0.04013.843-0.043-0.0430.0000.0000.0000.000
129A130LEU00.0050.01216.4130.0280.0280.0000.0000.0000.000
130A131ILE0-0.0140.00413.127-0.029-0.0290.0000.0000.0000.000
131A132LEU00.0410.01013.9810.0130.0130.0000.0000.0000.000
132A133ASP-1-0.899-0.95413.5830.1590.1590.0000.0000.0000.000
133A134GLY00.0010.00510.111-0.011-0.0110.0000.0000.0000.000
134A135LEU0-0.020-0.0139.000-0.015-0.0150.0000.0000.0000.000
135A136THR00.0020.0149.4220.0380.0380.0000.0000.0000.000
136A137VAL0-0.010-0.01810.798-0.090-0.0900.0000.0000.0000.000
137A138ARG10.8190.89310.3020.4610.4610.0000.0000.0000.000
138A139LEU0-0.0120.00214.999-0.014-0.0140.0000.0000.0000.000
139A140VAL0-0.017-0.00918.4810.0120.0120.0000.0000.0000.000
140A141ASN00.0110.00620.829-0.006-0.0060.0000.0000.0000.000
141A142LEU00.0250.01420.721-0.002-0.0020.0000.0000.0000.000
142A143PHE0-0.011-0.01124.5930.0170.0170.0000.0000.0000.000
143A144SER00.0540.02327.305-0.012-0.0120.0000.0000.0000.000
144A145SER0-0.025-0.01429.9520.0050.0050.0000.0000.0000.000
145A146THR0-0.030-0.01932.9020.0040.0040.0000.0000.0000.000
146A147GLY00.0340.02833.1310.0050.0050.0000.0000.0000.000
147A148PHE0-0.018-0.01326.777-0.006-0.0060.0000.0000.0000.000
148A149LYS10.7680.87325.4740.1520.1520.0000.0000.0000.000
149A150GLY00.0790.03325.831-0.001-0.0010.0000.0000.0000.000
150A151LEU0-0.031-0.00321.722-0.003-0.0030.0000.0000.0000.000
151A152LEU0-0.039-0.01216.093-0.002-0.0020.0000.0000.0000.000
152A153ILE0-0.0070.00115.1100.0160.0160.0000.0000.0000.000
153A154GLU-1-0.761-0.86311.104-0.562-0.5620.0000.0000.0000.000
154A155LEU0-0.024-0.00610.6090.0700.0700.0000.0000.0000.000
155A156GLN00.0130.0036.503-0.112-0.1120.0000.0000.0000.000
156A157ALA00.014-0.0015.0880.3330.3330.0000.0000.0000.000
157A158ASP-1-0.878-0.9332.695-1.214-0.1370.509-0.941-0.645-0.006
158A159GLU-1-0.968-0.9823.3250.9171.5790.045-0.355-0.352-0.004
159A160ALA0-0.020-0.0153.446-0.892-0.6710.010-0.085-0.1460.000
160A161GLY0-0.030-0.0044.485-0.431-0.435-0.001-0.0080.0130.000
161A162GLU-1-0.864-0.9248.326-0.061-0.0610.0000.0000.0000.000
162A163PHE00.0220.0087.136-0.126-0.1260.0000.0000.0000.000
163A164GLU-1-0.788-0.9079.389-0.270-0.2700.0000.0000.0000.000
164A165THR0-0.034-0.04012.650-0.018-0.0180.0000.0000.0000.000
165A166LYS10.8200.9318.920-0.175-0.1750.0000.0000.0000.000
166A167ILE00.0190.01012.416-0.008-0.0080.0000.0000.0000.000
167A168ALA00.0220.01214.0520.0110.0110.0000.0000.0000.000
168A169GLY00.0180.01316.6430.0110.0110.0000.0000.0000.000
169A170ILE0-0.024-0.01414.8870.0090.0090.0000.0000.0000.000
170A171GLU-1-0.785-0.85517.900-0.171-0.1710.0000.0000.0000.000
171A172GLY0-0.0080.00420.1260.0120.0120.0000.0000.0000.000
172A173HIS10.8630.90819.7510.0660.0660.0000.0000.0000.000
173A174LEU00.0400.01520.0540.0040.0040.0000.0000.0000.000
174A175ALA0-0.040-0.02323.6320.0070.0070.0000.0000.0000.000
175A176GLU-1-0.834-0.89724.955-0.045-0.0450.0000.0000.0000.000
176A177ILE0-0.032-0.00924.8820.0070.0070.0000.0000.0000.000
177A178ARG10.8230.89828.4110.0480.0480.0000.0000.0000.000
178A179ALA00.0850.06925.5410.0000.0000.0000.0000.0000.000
179A180LYS10.7830.87927.1290.0790.0790.0000.0000.0000.000
180A181GLU-1-0.848-0.88727.368-0.097-0.0970.0000.0000.0000.000
181A182TYR0-0.059-0.04520.8760.0070.0070.0000.0000.0000.000
182A183LYS10.8490.93220.3690.2160.2160.0000.0000.0000.000
183A184THR0-0.001-0.03115.707-0.024-0.0240.0000.0000.0000.000
184A185SER0-0.062-0.04915.1760.0050.0050.0000.0000.0000.000
185A186SER00.0380.00610.956-0.042-0.0420.0000.0000.0000.000
186A187ASP-1-0.843-0.87010.999-0.384-0.3840.0000.0000.0000.000
187A188SER0-0.030-0.0369.271-0.090-0.0900.0000.0000.0000.000
188A189LEU0-0.046-0.02711.4270.1280.1280.0000.0000.0000.000
189A190GLY0-0.0020.00112.6970.0170.0170.0000.0000.0000.000
190A191PRO0-0.063-0.02210.9340.0390.0390.0000.0000.0000.000
191A192ASP-1-0.910-0.96614.000-0.231-0.2310.0000.0000.0000.000
192A193THR0-0.048-0.02710.1910.0850.0850.0000.0000.0000.000
193A194SER0-0.022-0.0134.4770.2860.297-0.0010.000-0.0090.000
194A195ASN00.0440.0097.047-0.078-0.0780.0000.0000.0000.000
195A196GLU-1-0.755-0.8752.272-9.197-7.3232.360-2.048-2.187-0.028
196A197ILE0-0.030-0.0036.1290.2610.2610.0000.0000.0000.000
197A198CYS0-0.044-0.0339.6400.2060.2060.0000.0000.0000.000
198A199ASP-1-0.753-0.8477.953-0.794-0.7940.0000.0000.0000.000
199A200LEU0-0.0030.0128.5060.1400.1400.0000.0000.0000.000
200A201ALA0-0.007-0.01110.1920.1550.1550.0000.0000.0000.000
201A202TYR00.003-0.01613.0330.1070.1070.0000.0000.0000.000
202A203GLN00.0090.0138.8820.0480.0480.0000.0000.0000.000
203A204TYR0-0.025-0.05612.9420.1110.1110.0000.0000.0000.000
204A205VAL0-0.040-0.02416.0710.0530.0530.0000.0000.0000.000
205A206ARG10.8320.91716.7380.3280.3280.0000.0000.0000.000
206A207ALA0-0.027-0.01217.0300.0400.0400.0000.0000.0000.000
207A208LEU0-0.046-0.02118.9570.0330.0330.0000.0000.0000.000
208A209GLU-1-0.939-0.94621.406-0.199-0.1990.0000.0000.0000.000