Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VQ181

Calculation Name: 5H5T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H5T

Chain ID: A

ChEMBL ID:

UniProt ID: P16328

Base Structure: X-ray

Registration Date: 2023-09-24

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1819264.663082
FMO2-HF: Nuclear repulsion 1746658.890601
FMO2-HF: Total energy -72605.772481
FMO2-MP2: Total energy -72818.649463


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:72:SER)


Summations of interaction energy for fragment #1(A:72:SER)
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.
-0.5612.9690.541-1.951-2.1190.002
Interaction energy analysis for fragmet #1(A:72:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.032
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].
3A74VAL00.0350.0403.893-1.8030.916-0.014-1.474-1.2300.003
4A75ALA00.0140.0106.299-0.242-0.2420.0000.0000.0000.000
5A76SER0-0.0130.0049.9850.1040.1040.0000.0000.0000.000
6A77SER00.043-0.00213.442-0.059-0.0590.0000.0000.0000.000
7A78THR00.0010.01617.1460.0180.0180.0000.0000.0000.000
8A79THR0-0.006-0.00820.4030.0100.0100.0000.0000.0000.000
9A80GLU-1-0.868-0.92620.1420.0330.0330.0000.0000.0000.000
10A81ASP-1-0.815-0.88121.222-0.007-0.0070.0000.0000.0000.000
11A82LEU0-0.057-0.00719.112-0.005-0.0050.0000.0000.0000.000
12A83LYS10.9340.95917.306-0.016-0.0160.0000.0000.0000.000
13A84VAL00.019-0.00412.294-0.024-0.0240.0000.0000.0000.000
14A85SER0-0.019-0.00310.6920.0300.0300.0000.0000.0000.000
15A86THR00.0140.0007.0600.0190.0190.0000.0000.0000.000
16A87THR0-0.007-0.0036.573-0.131-0.1310.0000.0000.0000.000
17A88ALA00.0360.0012.706-0.667-0.1400.554-0.417-0.664-0.001
18A89GLY00.0080.0123.844-1.160-1.1440.002-0.009-0.0090.000
19A90ALA0-0.0220.0086.8920.1620.1620.0000.0000.0000.000
20A91ALA00.0420.0288.206-0.346-0.3460.0000.0000.0000.000
21A92ALA00.0070.0089.0130.0640.0640.0000.0000.0000.000
22A93GLY00.0180.00710.7480.0670.0670.0000.0000.0000.000
23A94THR0-0.0130.00214.2360.0120.0120.0000.0000.0000.000
24A95TYR0-0.021-0.03413.1040.0110.0110.0000.0000.0000.000
25A96LYS10.8230.91118.5110.1120.1120.0000.0000.0000.000
26A97ILE00.003-0.00718.761-0.008-0.0080.0000.0000.0000.000
27A98ASN0-0.0200.00423.1670.0220.0220.0000.0000.0000.000
28A99VAL00.0010.00224.654-0.006-0.0060.0000.0000.0000.000
29A100THR00.010-0.00327.3930.0080.0080.0000.0000.0000.000
30A101GLN0-0.064-0.04229.8260.0070.0070.0000.0000.0000.000
31A102LEU0-0.013-0.00127.194-0.005-0.0050.0000.0000.0000.000
32A103ALA0-0.017-0.00428.1680.0010.0010.0000.0000.0000.000
33A104ALA0-0.008-0.00729.9250.0040.0040.0000.0000.0000.000
34A105ALA00.0380.02832.695-0.003-0.0030.0000.0000.0000.000
35A106GLN0-0.002-0.01234.2730.0010.0010.0000.0000.0000.000
36A107SER0-0.036-0.02737.8690.0020.0020.0000.0000.0000.000
37A108LEU00.0270.01239.743-0.001-0.0010.0000.0000.0000.000
38A109ALA00.0210.00443.3850.0020.0020.0000.0000.0000.000
39A110THR00.0260.00446.078-0.001-0.0010.0000.0000.0000.000
40A111LYS10.8400.92149.6720.0060.0060.0000.0000.0000.000
41A112THR0-0.0140.00552.3780.0000.0000.0000.0000.0000.000
42A113THR0-0.036-0.00851.3020.0000.0000.0000.0000.0000.000
43A114PHE00.0270.00452.1870.0000.0000.0000.0000.0000.000
44A115ALA00.0180.01554.2090.0010.0010.0000.0000.0000.000
45A116THR0-0.079-0.08153.7070.0010.0010.0000.0000.0000.000
46A117THR0-0.022-0.03348.332-0.001-0.0010.0000.0000.0000.000
47A118LYS10.8820.91149.911-0.015-0.0150.0000.0000.0000.000
48A119GLU-1-0.780-0.86153.8120.0070.0070.0000.0000.0000.000
49A120GLN0-0.006-0.01254.9510.0000.0000.0000.0000.0000.000
50A121LEU00.0320.01651.197-0.001-0.0010.0000.0000.0000.000
51A122GLY00.0540.03255.171-0.001-0.0010.0000.0000.0000.000
52A123ASP-1-0.827-0.89955.9800.0030.0030.0000.0000.0000.000
53A124THR00.0080.00058.9300.0000.0000.0000.0000.0000.000
54A125SER0-0.108-0.06760.8400.0000.0000.0000.0000.0000.000
55A126VAL0-0.037-0.00357.7080.0000.0000.0000.0000.0000.000
56A127THR00.0060.00258.3230.0000.0000.0000.0000.0000.000
57A128SER0-0.078-0.07053.3030.0000.0000.0000.0000.0000.000
58A129ARG10.7580.86152.100-0.005-0.0050.0000.0000.0000.000
59A130THR00.013-0.00147.7890.0010.0010.0000.0000.0000.000
60A131ILE00.0160.01745.847-0.001-0.0010.0000.0000.0000.000
61A132LYS10.7930.88145.8870.0050.0050.0000.0000.0000.000
62A133ILE00.0210.00240.9880.0000.0000.0000.0000.0000.000
63A134GLU-1-0.829-0.89641.740-0.012-0.0120.0000.0000.0000.000
64A135GLN00.0510.01035.6850.0020.0020.0000.0000.0000.000
65A136PRO0-0.0120.00537.0560.0000.0000.0000.0000.0000.000
66A137GLY00.0040.00934.037-0.002-0.0020.0000.0000.0000.000
67A138ARG10.7490.86434.1180.0090.0090.0000.0000.0000.000
68A139LYS10.8460.91036.2850.0140.0140.0000.0000.0000.000
69A140GLU-1-0.888-0.93138.132-0.009-0.0090.0000.0000.0000.000
70A141PRO00.011-0.00440.0020.0000.0000.0000.0000.0000.000
71A142LEU00.0090.02138.2170.0010.0010.0000.0000.0000.000
72A143GLU-1-0.852-0.92541.422-0.003-0.0030.0000.0000.0000.000
73A144ILE00.0300.03640.9910.0010.0010.0000.0000.0000.000
74A145LYS10.8470.91544.903-0.002-0.0020.0000.0000.0000.000
75A146LEU0-0.009-0.00248.0060.0010.0010.0000.0000.0000.000
76A147ASP-1-0.809-0.87050.4540.0060.0060.0000.0000.0000.000
77A148LYS10.8730.91449.817-0.010-0.0100.0000.0000.0000.000
78A149GLY00.0160.01253.5430.0010.0010.0000.0000.0000.000
79A150ASP-1-0.772-0.84152.1550.0100.0100.0000.0000.0000.000
80A151THR0-0.057-0.03352.344-0.001-0.0010.0000.0000.0000.000
81A152SER0-0.026-0.03251.311-0.001-0.0010.0000.0000.0000.000
82A153MET0-0.0030.01047.8920.0000.0000.0000.0000.0000.000
83A154GLU-1-0.788-0.85646.7240.0150.0150.0000.0000.0000.000
84A155ALA00.0320.03046.2920.0000.0000.0000.0000.0000.000
85A156ILE0-0.017-0.01646.2620.0000.0000.0000.0000.0000.000
86A157ARG10.7240.81242.227-0.016-0.0160.0000.0000.0000.000
87A158ASP-1-0.781-0.86042.0690.0160.0160.0000.0000.0000.000
88A159ALA00.0240.01541.9460.0000.0000.0000.0000.0000.000
89A160ILE0-0.045-0.03339.756-0.001-0.0010.0000.0000.0000.000
90A161ASN0-0.016-0.01437.953-0.002-0.0020.0000.0000.0000.000
91A162ASP-1-0.905-0.95337.2680.0190.0190.0000.0000.0000.000
92A163ALA0-0.105-0.04438.5920.0000.0000.0000.0000.0000.000
93A164ASP-1-0.958-0.97331.9970.0130.0130.0000.0000.0000.000
94A165SER00.0310.02133.762-0.002-0.0020.0000.0000.0000.000
95A166GLY0-0.020-0.00632.093-0.003-0.0030.0000.0000.0000.000
96A167ILE0-0.041-0.03432.891-0.003-0.0030.0000.0000.0000.000
97A168ALA00.0150.03234.9660.0020.0020.0000.0000.0000.000
98A169ALA0-0.011-0.00736.999-0.002-0.0020.0000.0000.0000.000
99A170SER0-0.043-0.02239.2640.0020.0020.0000.0000.0000.000
100A171ILE0-0.001-0.01341.342-0.001-0.0010.0000.0000.0000.000
101A172VAL0-0.0010.00542.5980.0010.0010.0000.0000.0000.000
102A173LYS10.8100.89645.113-0.015-0.0150.0000.0000.0000.000
103A174VAL00.0030.00647.4560.0010.0010.0000.0000.0000.000
104A175LYS10.7940.88248.955-0.005-0.0050.0000.0000.0000.000
105A176GLU-1-0.817-0.89851.6910.0130.0130.0000.0000.0000.000
106A177ASN0-0.056-0.03053.8810.0000.0000.0000.0000.0000.000
107A178GLU-1-0.792-0.87052.9850.0050.0050.0000.0000.0000.000
108A179PHE0-0.016-0.01548.6210.0010.0010.0000.0000.0000.000
109A180GLN0-0.008-0.01147.4630.0000.0000.0000.0000.0000.000
110A181LEU00.0180.00144.9990.0010.0010.0000.0000.0000.000
111A182VAL0-0.011-0.01440.941-0.001-0.0010.0000.0000.0000.000
112A183LEU00.0170.01740.8300.0020.0020.0000.0000.0000.000
113A184THR0-0.0010.00435.288-0.002-0.0020.0000.0000.0000.000
114A185ALA00.0160.02935.3760.0020.0020.0000.0000.0000.000
115A186ASN00.0350.01330.1380.0040.0040.0000.0000.0000.000
116A187SER0-0.058-0.05928.5730.0000.0000.0000.0000.0000.000
117A188GLY00.0540.02130.767-0.002-0.0020.0000.0000.0000.000
118A189THR0-0.021-0.02632.0010.0030.0030.0000.0000.0000.000
119A190ASP-1-0.855-0.91732.371-0.041-0.0410.0000.0000.0000.000
120A191ASN0-0.053-0.03131.1200.0050.0050.0000.0000.0000.000
121A192THR0-0.016-0.01435.2160.0030.0030.0000.0000.0000.000
122A193MET0-0.026-0.00738.6780.0000.0000.0000.0000.0000.000
123A194LYS10.8040.91141.3080.0110.0110.0000.0000.0000.000
124A195ILE00.0030.00143.1270.0000.0000.0000.0000.0000.000
125A196THR00.0140.01346.493-0.001-0.0010.0000.0000.0000.000
126A197VAL0-0.028-0.01949.2500.0010.0010.0000.0000.0000.000
127A198GLU-1-0.846-0.90350.281-0.004-0.0040.0000.0000.0000.000
128A199GLY00.020-0.00553.5050.0010.0010.0000.0000.0000.000
129A200ASP-1-0.760-0.86554.9000.0030.0030.0000.0000.0000.000
130A201THR00.0540.02055.6680.0000.0000.0000.0000.0000.000
131A202LYS10.8140.90657.251-0.004-0.0040.0000.0000.0000.000
132A203LEU00.0240.00950.8120.0000.0000.0000.0000.0000.000
133A204ASN00.013-0.00352.761-0.001-0.0010.0000.0000.0000.000
134A205ASP-1-0.903-0.96153.219-0.003-0.0030.0000.0000.0000.000
135A206LEU0-0.068-0.02651.7050.0000.0000.0000.0000.0000.000
136A207LEU0-0.008-0.03447.9070.0000.0000.0000.0000.0000.000
137A208ALA00.0110.02148.413-0.001-0.0010.0000.0000.0000.000
138A209TYR0-0.046-0.03444.6110.0010.0010.0000.0000.0000.000
139A210ASP-1-0.713-0.82646.748-0.015-0.0150.0000.0000.0000.000
140A211SER00.040-0.00242.7830.0000.0000.0000.0000.0000.000
141A212THR0-0.125-0.06744.769-0.002-0.0020.0000.0000.0000.000
142A213THR0-0.072-0.05446.5140.0000.0000.0000.0000.0000.000
143A214ASN0-0.040-0.01544.7610.0010.0010.0000.0000.0000.000
144A215THR0-0.052-0.01647.8620.0010.0010.0000.0000.0000.000
145A216GLY00.0430.01549.8120.0000.0000.0000.0000.0000.000
146A217ASN0-0.057-0.01851.744-0.001-0.0010.0000.0000.0000.000
147A218MET00.0090.03545.1580.0010.0010.0000.0000.0000.000
148A219GLN0-0.052-0.03647.5050.0000.0000.0000.0000.0000.000
149A220GLU-1-0.811-0.90341.913-0.015-0.0150.0000.0000.0000.000
150A221LEU0-0.065-0.03442.7100.0000.0000.0000.0000.0000.000
151A222VAL0-0.046-0.02136.4950.0000.0000.0000.0000.0000.000
152A223LYS10.8740.93438.2110.0270.0270.0000.0000.0000.000
153A224ALA00.0080.01436.0120.0000.0000.0000.0000.0000.000
154A225GLU-1-0.864-0.91933.641-0.033-0.0330.0000.0000.0000.000
155A226ASN00.0230.01130.2910.0030.0030.0000.0000.0000.000
156A227ALA00.0090.01326.1550.0010.0010.0000.0000.0000.000
157A228LYS10.8130.88628.0830.0500.0500.0000.0000.0000.000
158A229LEU0-0.018-0.01421.9610.0060.0060.0000.0000.0000.000
159A230ASN0-0.049-0.03025.936-0.011-0.0110.0000.0000.0000.000
160A231VAL00.0300.00019.3960.0020.0020.0000.0000.0000.000
161A232ASN0-0.068-0.04419.0380.0100.0100.0000.0000.0000.000
162A233GLY00.0360.02723.103-0.002-0.0020.0000.0000.0000.000
163A234ILE0-0.030-0.00222.5520.0100.0100.0000.0000.0000.000
164A235ASP-1-0.845-0.90625.247-0.094-0.0940.0000.0000.0000.000
165A236ILE0-0.057-0.03422.518-0.008-0.0080.0000.0000.0000.000
166A237GLU-1-0.767-0.87025.762-0.052-0.0520.0000.0000.0000.000
167A238ARG10.8020.89120.7480.1220.1220.0000.0000.0000.000
168A239GLN00.0430.03626.3830.0080.0080.0000.0000.0000.000
169A240SER00.0180.00623.2600.0110.0110.0000.0000.0000.000
170A241ASN00.0480.01824.604-0.013-0.0130.0000.0000.0000.000
171A242THR0-0.0120.01418.800-0.001-0.0010.0000.0000.0000.000
172A243VAL00.0010.00519.6370.0010.0010.0000.0000.0000.000
173A244THR00.035-0.00116.283-0.007-0.0070.0000.0000.0000.000
174A245ASP-1-0.827-0.89616.451-0.184-0.1840.0000.0000.0000.000
175A246ALA0-0.0120.01117.3310.0170.0170.0000.0000.0000.000
176A247PRO00.0220.01514.4790.0120.0120.0000.0000.0000.000
177A248GLN00.010-0.02914.796-0.013-0.0130.0000.0000.0000.000
178A249GLY0-0.0180.00410.850-0.075-0.0750.0000.0000.0000.000
179A250ILE0-0.011-0.00210.132-0.103-0.1030.0000.0000.0000.000
180A251THR0-0.016-0.00612.5040.0620.0620.0000.0000.0000.000
181A252LEU00.0150.00914.5350.0010.0010.0000.0000.0000.000
182A253THR0-0.015-0.02317.3800.0150.0150.0000.0000.0000.000
183A254LEU0-0.0230.00119.9930.0080.0080.0000.0000.0000.000
184A255THR0-0.038-0.04522.6630.0100.0100.0000.0000.0000.000
185A256LYS10.8780.93025.1090.0130.0130.0000.0000.0000.000
186A257LYS10.9610.99126.6630.0270.0270.0000.0000.0000.000
187A258VAL0-0.018-0.01123.9640.0050.0050.0000.0000.0000.000
188A259THR00.004-0.00727.408-0.004-0.0040.0000.0000.0000.000
189A260ASP-1-0.803-0.90826.494-0.074-0.0740.0000.0000.0000.000
190A261ALA00.0220.03822.0380.0020.0020.0000.0000.0000.000
191A262THR0-0.017-0.02418.758-0.017-0.0170.0000.0000.0000.000
192A263VAL00.0100.01714.6030.0200.0200.0000.0000.0000.000
193A264THR0-0.007-0.01613.552-0.034-0.0340.0000.0000.0000.000
194A265VAL0-0.0180.0038.9370.0610.0610.0000.0000.0000.000
195A266THR0-0.023-0.0178.4480.0740.0740.0000.0000.0000.000
196A267LYS10.8710.9164.4683.3913.659-0.001-0.051-0.2160.000