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: YVK62

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1820197.382738
FMO2-HF: Nuclear repulsion 1747591.820348
FMO2-HF: Total energy -72605.562389
FMO2-MP2: Total energy -72818.335622


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.
-1.1532.7190.434-2.12-2.1890.002
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 : 0.030 / q_NPA : 0.016
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].
3A74VAL00.0400.0393.810-2.1691.064-0.027-1.719-1.4880.003
4A75ALA00.0280.0066.254-0.195-0.1950.0000.0000.0000.000
5A76SER0-0.0110.0129.9240.1190.1190.0000.0000.0000.000
6A77SER00.032-0.00413.188-0.056-0.0560.0000.0000.0000.000
7A78THR00.0000.00916.7020.0190.0190.0000.0000.0000.000
8A79THR00.0050.00119.9330.0200.0200.0000.0000.0000.000
9A80GLU-1-0.867-0.92619.944-0.012-0.0120.0000.0000.0000.000
10A81ASP-1-0.845-0.90021.034-0.035-0.0350.0000.0000.0000.000
11A82LEU0-0.053-0.01618.753-0.002-0.0020.0000.0000.0000.000
12A83LYS10.9240.95716.6970.0140.0140.0000.0000.0000.000
13A84VAL00.0320.01512.138-0.014-0.0140.0000.0000.0000.000
14A85SER0-0.0140.00210.3370.0100.0100.0000.0000.0000.000
15A86THR00.0390.0106.451-0.015-0.0150.0000.0000.0000.000
16A87THR0-0.028-0.0056.346-0.039-0.0390.0000.0000.0000.000
17A88ALA00.039-0.0022.654-0.953-0.3890.460-0.441-0.5840.000
18A89GLY00.013-0.0013.481-1.638-1.7370.0020.0890.008-0.001
19A90ALA00.0000.0236.3510.0840.0840.0000.0000.0000.000
20A91ALA00.0340.0347.592-0.460-0.4600.0000.0000.0000.000
21A92ALA00.0200.0038.8400.0370.0370.0000.0000.0000.000
22A93GLY00.0150.00810.2530.1190.1190.0000.0000.0000.000
23A94THR0-0.0100.00713.800-0.006-0.0060.0000.0000.0000.000
24A95TYR0-0.034-0.03212.6210.0370.0370.0000.0000.0000.000
25A96LYS10.8640.93718.0680.1620.1620.0000.0000.0000.000
26A97ILE00.008-0.01017.950-0.001-0.0010.0000.0000.0000.000
27A98ASN0-0.022-0.00422.4230.0230.0230.0000.0000.0000.000
28A99VAL00.0060.00524.030-0.004-0.0040.0000.0000.0000.000
29A100THR0-0.006-0.02026.6370.0080.0080.0000.0000.0000.000
30A101GLN0-0.063-0.04129.2300.0090.0090.0000.0000.0000.000
31A102LEU0-0.0050.01726.892-0.007-0.0070.0000.0000.0000.000
32A103ALA0-0.017-0.01227.8520.0030.0030.0000.0000.0000.000
33A104ALA0-0.004-0.00829.5380.0040.0040.0000.0000.0000.000
34A105ALA00.0270.01032.371-0.002-0.0020.0000.0000.0000.000
35A106GLN0-0.004-0.01133.9000.0020.0020.0000.0000.0000.000
36A107SER0-0.040-0.02237.5100.0030.0030.0000.0000.0000.000
37A108LEU00.0180.00939.406-0.001-0.0010.0000.0000.0000.000
38A109ALA00.0240.00542.9900.0020.0020.0000.0000.0000.000
39A110THR00.0210.00345.652-0.001-0.0010.0000.0000.0000.000
40A111LYS10.8780.94649.1610.0080.0080.0000.0000.0000.000
41A112THR0-0.0120.01051.9350.0000.0000.0000.0000.0000.000
42A113THR0-0.049-0.01850.8650.0000.0000.0000.0000.0000.000
43A114PHE00.0420.00551.9640.0000.0000.0000.0000.0000.000
44A115ALA00.0420.03353.6370.0000.0000.0000.0000.0000.000
45A116THR0-0.084-0.06653.4480.0010.0010.0000.0000.0000.000
46A117THR0-0.023-0.03748.167-0.001-0.0010.0000.0000.0000.000
47A118LYS10.8790.91049.820-0.015-0.0150.0000.0000.0000.000
48A119GLU-1-0.849-0.90353.5000.0060.0060.0000.0000.0000.000
49A120GLN0-0.003-0.00954.5720.0000.0000.0000.0000.0000.000
50A121LEU00.0280.00651.206-0.001-0.0010.0000.0000.0000.000
51A122GLY00.0350.03055.198-0.001-0.0010.0000.0000.0000.000
52A123ASP-1-0.841-0.91656.0670.0030.0030.0000.0000.0000.000
53A124THR0-0.008-0.01159.0900.0000.0000.0000.0000.0000.000
54A125SER0-0.079-0.04560.7540.0010.0010.0000.0000.0000.000
55A126VAL0-0.053-0.01657.2280.0000.0000.0000.0000.0000.000
56A127THR00.004-0.00258.2270.0000.0000.0000.0000.0000.000
57A128SER0-0.071-0.05353.4600.0010.0010.0000.0000.0000.000
58A129ARG10.7760.90851.725-0.006-0.0060.0000.0000.0000.000
59A130THR00.0100.00947.6600.0020.0020.0000.0000.0000.000
60A131ILE00.0030.00445.563-0.001-0.0010.0000.0000.0000.000
61A132LYS10.7940.87745.5320.0040.0040.0000.0000.0000.000
62A133ILE00.0210.00040.633-0.001-0.0010.0000.0000.0000.000
63A134GLU-1-0.847-0.91641.347-0.011-0.0110.0000.0000.0000.000
64A135GLN00.0450.01035.6020.0020.0020.0000.0000.0000.000
65A136PRO0-0.0030.01536.7000.0000.0000.0000.0000.0000.000
66A137GLY00.0050.00733.774-0.001-0.0010.0000.0000.0000.000
67A138ARG10.7430.86833.8920.0070.0070.0000.0000.0000.000
68A139LYS10.8520.91135.9460.0080.0080.0000.0000.0000.000
69A140GLU-1-0.894-0.93637.815-0.002-0.0020.0000.0000.0000.000
70A141PRO00.008-0.00639.4980.0000.0000.0000.0000.0000.000
71A142LEU00.0110.02338.1680.0020.0020.0000.0000.0000.000
72A143GLU-1-0.843-0.92341.229-0.001-0.0010.0000.0000.0000.000
73A144ILE00.0180.01640.9240.0010.0010.0000.0000.0000.000
74A145LYS10.8460.92644.862-0.005-0.0050.0000.0000.0000.000
75A146LEU00.0090.00647.8610.0010.0010.0000.0000.0000.000
76A147ASP-1-0.814-0.91150.2510.0090.0090.0000.0000.0000.000
77A148LYS10.8710.91949.714-0.013-0.0130.0000.0000.0000.000
78A149GLY0-0.0050.01153.2240.0010.0010.0000.0000.0000.000
79A150ASP-1-0.767-0.87352.1260.0120.0120.0000.0000.0000.000
80A151THR0-0.058-0.02951.870-0.001-0.0010.0000.0000.0000.000
81A152SER00.011-0.00151.410-0.001-0.0010.0000.0000.0000.000
82A153MET0-0.0040.00247.1320.0000.0000.0000.0000.0000.000
83A154GLU-1-0.832-0.88546.4790.0150.0150.0000.0000.0000.000
84A155ALA00.0270.03746.1050.0010.0010.0000.0000.0000.000
85A156ILE0-0.013-0.01445.9750.0000.0000.0000.0000.0000.000
86A157ARG10.7960.85941.729-0.016-0.0160.0000.0000.0000.000
87A158ASP-1-0.802-0.87541.9820.0180.0180.0000.0000.0000.000
88A159ALA00.0220.02241.9730.0010.0010.0000.0000.0000.000
89A160ILE0-0.048-0.04039.7280.0000.0000.0000.0000.0000.000
90A161ASN0-0.012-0.01637.892-0.002-0.0020.0000.0000.0000.000
91A162ASP-1-0.912-0.94337.2600.0220.0220.0000.0000.0000.000
92A163ALA0-0.104-0.05138.1880.0010.0010.0000.0000.0000.000
93A164ASP-1-0.948-0.95832.2640.0210.0210.0000.0000.0000.000
94A165SER00.0080.00933.628-0.002-0.0020.0000.0000.0000.000
95A166GLY0-0.014-0.00332.272-0.004-0.0040.0000.0000.0000.000
96A167ILE0-0.041-0.02833.083-0.004-0.0040.0000.0000.0000.000
97A168ALA00.0210.03134.7420.0030.0030.0000.0000.0000.000
98A169ALA00.0030.00136.782-0.003-0.0030.0000.0000.0000.000
99A170SER0-0.042-0.02838.7670.0020.0020.0000.0000.0000.000
100A171ILE00.002-0.00740.864-0.001-0.0010.0000.0000.0000.000
101A172VAL00.0200.01842.0670.0010.0010.0000.0000.0000.000
102A173LYS10.8080.89744.547-0.012-0.0120.0000.0000.0000.000
103A174VAL0-0.008-0.00746.7630.0000.0000.0000.0000.0000.000
104A175LYS10.8020.88348.541-0.002-0.0020.0000.0000.0000.000
105A176GLU-1-0.829-0.91151.1130.0110.0110.0000.0000.0000.000
106A177ASN0-0.051-0.02453.5620.0000.0000.0000.0000.0000.000
107A178GLU-1-0.776-0.85952.4950.0010.0010.0000.0000.0000.000
108A179PHE0-0.043-0.02748.1240.0010.0010.0000.0000.0000.000
109A180GLN00.0180.00047.0270.0000.0000.0000.0000.0000.000
110A181LEU0-0.010-0.00944.4570.0010.0010.0000.0000.0000.000
111A182VAL0-0.007-0.00640.532-0.002-0.0020.0000.0000.0000.000
112A183LEU00.0170.01140.5650.0020.0020.0000.0000.0000.000
113A184THR0-0.0020.00334.986-0.003-0.0030.0000.0000.0000.000
114A185ALA00.0170.03335.2670.0020.0020.0000.0000.0000.000
115A186ASN00.0440.01129.7580.0020.0020.0000.0000.0000.000
116A187SER0-0.055-0.05928.497-0.001-0.0010.0000.0000.0000.000
117A188GLY00.0460.03130.447-0.002-0.0020.0000.0000.0000.000
118A189THR0-0.015-0.02631.7150.0030.0030.0000.0000.0000.000
119A190ASP-1-0.874-0.94331.576-0.044-0.0440.0000.0000.0000.000
120A191ASN0-0.071-0.03630.8850.0060.0060.0000.0000.0000.000
121A192THR00.0030.00535.1310.0030.0030.0000.0000.0000.000
122A193MET0-0.029-0.01338.5030.0010.0010.0000.0000.0000.000
123A194LYS10.8090.91641.0610.0110.0110.0000.0000.0000.000
124A195ILE00.0140.01442.9630.0010.0010.0000.0000.0000.000
125A196THR00.0190.01346.123-0.001-0.0010.0000.0000.0000.000
126A197VAL0-0.025-0.01848.7820.0010.0010.0000.0000.0000.000
127A198GLU-1-0.862-0.91250.521-0.003-0.0030.0000.0000.0000.000
128A199GLY00.028-0.00653.1820.0010.0010.0000.0000.0000.000
129A200ASP-1-0.736-0.86454.8430.0030.0030.0000.0000.0000.000
130A201THR00.0420.01455.6150.0000.0000.0000.0000.0000.000
131A202LYS10.8480.92957.324-0.003-0.0030.0000.0000.0000.000
132A203LEU00.0250.00950.7050.0000.0000.0000.0000.0000.000
133A204ASN00.0170.01152.516-0.001-0.0010.0000.0000.0000.000
134A205ASP-1-0.918-0.96753.078-0.004-0.0040.0000.0000.0000.000
135A206LEU0-0.072-0.02151.2430.0000.0000.0000.0000.0000.000
136A207LEU0-0.019-0.04747.6090.0000.0000.0000.0000.0000.000
137A208ALA0-0.0140.01448.136-0.001-0.0010.0000.0000.0000.000
138A209TYR0-0.024-0.02144.2490.0000.0000.0000.0000.0000.000
139A210ASP-1-0.721-0.83746.869-0.016-0.0160.0000.0000.0000.000
140A211SER00.037-0.01242.504-0.001-0.0010.0000.0000.0000.000
141A212THR0-0.119-0.06144.541-0.002-0.0020.0000.0000.0000.000
142A213THR0-0.069-0.06445.948-0.001-0.0010.0000.0000.0000.000
143A214ASN0-0.056-0.01944.3340.0010.0010.0000.0000.0000.000
144A215THR0-0.039-0.00447.4960.0010.0010.0000.0000.0000.000
145A216GLY00.0520.02349.4140.0000.0000.0000.0000.0000.000
146A217ASN0-0.045-0.02251.094-0.001-0.0010.0000.0000.0000.000
147A218MET0-0.0230.02245.0190.0010.0010.0000.0000.0000.000
148A219GLN0-0.036-0.03447.1020.0000.0000.0000.0000.0000.000
149A220GLU-1-0.826-0.91241.733-0.020-0.0200.0000.0000.0000.000
150A221LEU0-0.059-0.03042.3630.0000.0000.0000.0000.0000.000
151A222VAL0-0.038-0.01636.363-0.001-0.0010.0000.0000.0000.000
152A223LYS10.9140.95838.3520.0360.0360.0000.0000.0000.000
153A224ALA0-0.022-0.00435.452-0.001-0.0010.0000.0000.0000.000
154A225GLU-1-0.857-0.92833.102-0.042-0.0420.0000.0000.0000.000
155A226ASN00.0160.01929.9080.0040.0040.0000.0000.0000.000
156A227ALA0-0.0010.00825.7630.0000.0000.0000.0000.0000.000
157A228LYS10.8420.90527.8140.0660.0660.0000.0000.0000.000
158A229LEU0-0.014-0.01221.3900.0040.0040.0000.0000.0000.000
159A230ASN0-0.035-0.01225.223-0.013-0.0130.0000.0000.0000.000
160A231VAL00.0280.00518.600-0.004-0.0040.0000.0000.0000.000
161A232ASN0-0.062-0.04218.6760.0110.0110.0000.0000.0000.000
162A233GLY00.0370.01622.6530.0000.0000.0000.0000.0000.000
163A234ILE0-0.042-0.00822.0810.0120.0120.0000.0000.0000.000
164A235ASP-1-0.849-0.90924.699-0.119-0.1190.0000.0000.0000.000
165A236ILE0-0.064-0.03622.069-0.005-0.0050.0000.0000.0000.000
166A237GLU-1-0.782-0.88725.345-0.065-0.0650.0000.0000.0000.000
167A238ARG10.8180.90020.2900.1380.1380.0000.0000.0000.000
168A239GLN00.0720.04326.0360.0070.0070.0000.0000.0000.000
169A240SER00.0410.03023.4000.0090.0090.0000.0000.0000.000
170A241ASN00.0460.01824.091-0.017-0.0170.0000.0000.0000.000
171A242THR0-0.0020.02318.434-0.002-0.0020.0000.0000.0000.000
172A243VAL0-0.007-0.00719.2030.0030.0030.0000.0000.0000.000
173A244THR00.030-0.00516.115-0.015-0.0150.0000.0000.0000.000
174A245ASP-1-0.837-0.91115.894-0.174-0.1740.0000.0000.0000.000
175A246ALA0-0.0370.01216.7530.0140.0140.0000.0000.0000.000
176A247PRO00.0260.00913.8130.0090.0090.0000.0000.0000.000
177A248GLN00.017-0.02614.019-0.024-0.0240.0000.0000.0000.000
178A249GLY0-0.047-0.01210.244-0.083-0.0830.0000.0000.0000.000
179A250ILE00.0110.0059.646-0.115-0.1150.0000.0000.0000.000
180A251THR0-0.026-0.00412.1090.0760.0760.0000.0000.0000.000
181A252LEU0-0.007-0.00514.339-0.010-0.0100.0000.0000.0000.000
182A253THR0-0.012-0.01217.0900.0240.0240.0000.0000.0000.000
183A254LEU0-0.043-0.02719.7000.0000.0000.0000.0000.0000.000
184A255THR0-0.031-0.03522.4740.0130.0130.0000.0000.0000.000
185A256LYS10.8800.92425.0540.0440.0440.0000.0000.0000.000
186A257LYS10.9470.98226.3760.0450.0450.0000.0000.0000.000
187A258VAL0-0.019-0.00323.4410.0050.0050.0000.0000.0000.000
188A259THR00.0260.00026.903-0.003-0.0030.0000.0000.0000.000
189A260ASP-1-0.828-0.91625.596-0.119-0.1190.0000.0000.0000.000
190A261ALA00.0050.02621.3700.0040.0040.0000.0000.0000.000
191A262THR0-0.018-0.02118.145-0.016-0.0160.0000.0000.0000.000
192A263VAL00.0020.01113.9960.0160.0160.0000.0000.0000.000
193A264THR00.010-0.00713.128-0.024-0.0240.0000.0000.0000.000
194A265VAL0-0.0210.0068.4630.0170.0170.0000.0000.0000.000
195A266THR00.005-0.0017.8830.0680.0680.0000.0000.0000.000
196A267LYS10.8460.9074.2474.0154.189-0.001-0.049-0.1250.000