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: QY26Y

Calculation Name: 3HO7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HO7

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXD3

Base Structure: X-ray

Registration Date: 2023-09-20

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2732070.061633
FMO2-HF: Nuclear repulsion 2642982.768115
FMO2-HF: Total energy -89087.293518
FMO2-MP2: Total energy -89344.228731


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:90:THR)


Summations of interaction energy for fragment #1(A:90:THR)
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.
-8.117-1.1753.033-5.028-4.95-0.025
Interaction energy analysis for fragmet #1(A:90:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : 0.006
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].
3A92ARG10.7920.8823.803-2.7610.513-0.030-1.805-1.4390.008
4A93LEU0-0.020-0.0076.962-0.098-0.0980.0000.0000.0000.000
5A94ASN00.0070.0179.6870.1960.1960.0000.0000.0000.000
6A95ILE00.0200.01513.3830.0030.0030.0000.0000.0000.000
7A96ALA00.0490.02515.6650.0360.0360.0000.0000.0000.000
8A97VAL0-0.028-0.03119.127-0.019-0.0190.0000.0000.0000.000
9A98LEU00.0550.03321.6910.0190.0190.0000.0000.0000.000
10A99PRO00.0630.03825.332-0.003-0.0030.0000.0000.0000.000
11A100THR0-0.052-0.02027.4290.0020.0020.0000.0000.0000.000
12A101ILE0-0.009-0.00223.7840.0040.0040.0000.0000.0000.000
13A102ALA00.0100.01022.954-0.002-0.0020.0000.0000.0000.000
14A103PRO00.0470.01723.541-0.007-0.0070.0000.0000.0000.000
15A104TYR00.0020.00826.1670.0050.0050.0000.0000.0000.000
16A105LEU00.0060.00821.0710.0000.0000.0000.0000.0000.000
17A106LEU00.0320.01318.200-0.013-0.0130.0000.0000.0000.000
18A107PRO0-0.017-0.00220.004-0.010-0.0100.0000.0000.0000.000
19A108ARG10.8390.90921.6970.1520.1520.0000.0000.0000.000
20A109VAL00.0100.00916.475-0.003-0.0030.0000.0000.0000.000
21A110PHE0-0.0090.00215.811-0.032-0.0320.0000.0000.0000.000
22A111PRO0-0.005-0.01215.211-0.025-0.0250.0000.0000.0000.000
23A112ILE00.0270.01015.2560.0030.0030.0000.0000.0000.000
24A113TRP00.0520.01211.552-0.045-0.0450.0000.0000.0000.000
25A114LYS10.9170.98410.8430.1820.1820.0000.0000.0000.000
26A115LYS10.7950.87710.9370.1950.1950.0000.0000.0000.000
27A116GLU-1-0.786-0.87511.338-0.194-0.1940.0000.0000.0000.000
28A117LEU0-0.068-0.0387.731-0.060-0.0600.0000.0000.0000.000
29A118ALA00.0000.0086.512-0.298-0.2980.0000.0000.0000.000
30A119GLY0-0.007-0.0073.184-0.0580.3380.065-0.144-0.3180.000
31A120LEU0-0.036-0.0132.405-6.458-3.2632.999-3.061-3.134-0.033
32A121GLU-1-0.845-0.9014.3720.5330.610-0.001-0.018-0.0590.000
33A122ILE0-0.008-0.0167.194-0.075-0.0750.0000.0000.0000.000
34A123HIS0-0.041-0.03210.2580.1460.1460.0000.0000.0000.000
35A124VAL0-0.005-0.00213.388-0.021-0.0210.0000.0000.0000.000
36A125SER0-0.0070.00116.3900.0470.0470.0000.0000.0000.000
37A126GLU-1-0.865-0.93619.728-0.162-0.1620.0000.0000.0000.000
38A127MET0-0.079-0.03621.1440.0160.0160.0000.0000.0000.000
39A128GLN00.0620.02925.167-0.004-0.0040.0000.0000.0000.000
40A129THR00.041-0.01626.999-0.011-0.0110.0000.0000.0000.000
41A130SER0-0.006-0.00227.262-0.009-0.0090.0000.0000.0000.000
42A131ARG10.9090.95125.6580.1150.1150.0000.0000.0000.000
43A132CYS00.0040.02123.100-0.012-0.0120.0000.0000.0000.000
44A133LEU00.005-0.00223.175-0.018-0.0180.0000.0000.0000.000
45A134ALA00.0260.00925.137-0.004-0.0040.0000.0000.0000.000
46A135SER00.003-0.03621.0770.0030.0030.0000.0000.0000.000
47A136LEU0-0.059-0.00818.864-0.014-0.0140.0000.0000.0000.000
48A137LEU0-0.032-0.01020.813-0.012-0.0120.0000.0000.0000.000
49A138SER0-0.039-0.02322.726-0.003-0.0030.0000.0000.0000.000
50A139GLY00.0040.00718.6590.0100.0100.0000.0000.0000.000
51A140GLU-1-0.943-0.92717.463-0.168-0.1680.0000.0000.0000.000
52A141ILE0-0.055-0.03816.297-0.014-0.0140.0000.0000.0000.000
53A142ASP-1-0.823-0.88912.080-0.803-0.8030.0000.0000.0000.000
54A143MET0-0.038-0.03512.0760.0110.0110.0000.0000.0000.000
55A144ALA00.0260.01816.7980.0220.0220.0000.0000.0000.000
56A145ILE0-0.0170.01618.0340.0020.0020.0000.0000.0000.000
57A146ILE00.0260.00221.4680.0200.0200.0000.0000.0000.000
58A147ALA00.006-0.00325.177-0.004-0.0040.0000.0000.0000.000
59A148SER00.008-0.00728.0080.0140.0140.0000.0000.0000.000
60A149LYS10.8760.92827.9730.1270.1270.0000.0000.0000.000
61A150ALA00.0320.00426.0390.0090.0090.0000.0000.0000.000
62A151GLU-1-0.932-0.94828.200-0.118-0.1180.0000.0000.0000.000
63A152THR0-0.022-0.02527.9810.0120.0120.0000.0000.0000.000
64A153GLU-1-0.931-0.95928.102-0.155-0.1550.0000.0000.0000.000
65A154GLY00.0680.03225.9580.0010.0010.0000.0000.0000.000
66A155LEU0-0.087-0.04922.658-0.027-0.0270.0000.0000.0000.000
67A156GLU-1-0.829-0.89821.662-0.275-0.2750.0000.0000.0000.000
68A157ASP-1-0.789-0.88122.482-0.224-0.2240.0000.0000.0000.000
69A158ASP-1-0.826-0.88820.422-0.309-0.3090.0000.0000.0000.000
70A159LEU0-0.046-0.02623.398-0.005-0.0050.0000.0000.0000.000
71A160LEU0-0.045-0.01919.988-0.017-0.0170.0000.0000.0000.000
72A161TYR00.006-0.01723.5110.0010.0010.0000.0000.0000.000
73A162TYR00.0240.02027.219-0.002-0.0020.0000.0000.0000.000
74A163GLU-1-0.764-0.89229.621-0.139-0.1390.0000.0000.0000.000
75A164GLU-1-0.816-0.89332.050-0.084-0.0840.0000.0000.0000.000
76A165PHE0-0.042-0.02134.942-0.001-0.0010.0000.0000.0000.000
77A166LEU0-0.009-0.00437.1310.0050.0050.0000.0000.0000.000
78A167GLY00.0210.00539.621-0.001-0.0010.0000.0000.0000.000
79A168TYR0-0.066-0.05539.7810.0000.0000.0000.0000.0000.000
80A169VAL00.018-0.01742.4700.0010.0010.0000.0000.0000.000
81A170SER00.0380.01746.1690.0020.0020.0000.0000.0000.000
82A171ARG10.8290.88246.0700.0410.0410.0000.0000.0000.000
83A172CYS0-0.049-0.00750.6410.0020.0020.0000.0000.0000.000
84A173GLU-1-0.765-0.81249.397-0.040-0.0400.0000.0000.0000.000
85A174PRO00.0530.01652.5760.0000.0000.0000.0000.0000.000
86A175LEU00.014-0.00749.5980.0000.0000.0000.0000.0000.000
87A176PHE0-0.028-0.00247.790-0.001-0.0010.0000.0000.0000.000
88A177GLU-1-0.915-0.93751.388-0.035-0.0350.0000.0000.0000.000
89A178GLN0-0.040-0.01052.259-0.001-0.0010.0000.0000.0000.000
90A179ASP-1-0.859-0.92350.064-0.044-0.0440.0000.0000.0000.000
91A180VAL0-0.064-0.04147.168-0.003-0.0030.0000.0000.0000.000
92A181ILE0-0.044-0.01044.7520.0020.0020.0000.0000.0000.000
93A182ARG10.8530.91347.9500.0400.0400.0000.0000.0000.000
94A183THR00.023-0.00148.7400.0000.0000.0000.0000.0000.000
95A184THR0-0.004-0.01450.0330.0000.0000.0000.0000.0000.000
96A185GLU-1-0.859-0.92252.621-0.039-0.0390.0000.0000.0000.000
97A186VAL0-0.037-0.00347.5170.0010.0010.0000.0000.0000.000
98A187ASN00.0300.00850.7110.0000.0000.0000.0000.0000.000
99A188PRO00.0510.03149.953-0.001-0.0010.0000.0000.0000.000
100A189HIS10.8220.89049.8950.0370.0370.0000.0000.0000.000
101A190ARG10.7680.85349.8170.0390.0390.0000.0000.0000.000
102A191LEU00.0170.03444.746-0.001-0.0010.0000.0000.0000.000
103A192TRP0-0.030-0.01442.3010.0010.0010.0000.0000.0000.000
104A193LEU00.0280.01240.780-0.003-0.0030.0000.0000.0000.000
105A194LEU0-0.027-0.00834.3010.0000.0000.0000.0000.0000.000
106A195ASP-1-0.785-0.90836.941-0.074-0.0740.0000.0000.0000.000
107A196GLU-1-0.809-0.89830.229-0.130-0.1300.0000.0000.0000.000
108A197GLY0-0.028-0.02633.147-0.006-0.0060.0000.0000.0000.000
109A198HIS0-0.023-0.01234.1690.0000.0000.0000.0000.0000.000
110A199CYS0-0.061-0.01737.4300.0030.0030.0000.0000.0000.000
111A200PHE00.0610.03631.5820.0030.0030.0000.0000.0000.000
112A201ARG10.8420.91432.2070.1210.1210.0000.0000.0000.000
113A202ASP-1-0.854-0.91738.227-0.070-0.0700.0000.0000.0000.000
114A203GLN00.0380.01633.5190.0020.0020.0000.0000.0000.000
115A204LEU00.0150.01138.8310.0030.0030.0000.0000.0000.000
116A205VAL00.0600.02541.2680.0050.0050.0000.0000.0000.000
117A206ARG10.8720.94243.9500.0700.0700.0000.0000.0000.000
118A207PHE00.010-0.02743.5990.0030.0030.0000.0000.0000.000
119A209GLN0-0.023-0.01744.4550.0050.0050.0000.0000.0000.000
120A210MET0-0.0990.00347.6370.0020.0020.0000.0000.0000.000
121A211LYS10.9630.95450.1970.0470.0470.0000.0000.0000.000
122A212GLY00.0940.04353.4050.0000.0000.0000.0000.0000.000
123A213LEU0-0.051-0.00645.6360.0010.0010.0000.0000.0000.000
124A214HIS00.005-0.01545.9720.0010.0010.0000.0000.0000.000
125A215GLU-1-0.907-0.92750.561-0.036-0.0360.0000.0000.0000.000
126A216ARG10.8230.89546.5580.0480.0480.0000.0000.0000.000
127A217GLN0-0.025-0.00252.953-0.001-0.0010.0000.0000.0000.000
128A218THR00.0240.00847.5680.0010.0010.0000.0000.0000.000
129A219ALA00.0100.01347.401-0.002-0.0020.0000.0000.0000.000
130A220TYR00.010-0.00940.0390.0000.0000.0000.0000.0000.000
131A221SER0-0.037-0.00841.032-0.002-0.0020.0000.0000.0000.000
132A222GLY00.0160.01037.0420.0020.0020.0000.0000.0000.000
133A223GLY0-0.019-0.00736.349-0.001-0.0010.0000.0000.0000.000
134A224SER00.0320.01533.400-0.005-0.0050.0000.0000.0000.000
135A225MET00.0400.01533.1440.0050.0050.0000.0000.0000.000
136A226GLU-1-0.941-0.96133.439-0.064-0.0640.0000.0000.0000.000
137A227ALA00.0170.00935.3610.0050.0050.0000.0000.0000.000
138A228PHE00.032-0.00938.3000.0040.0040.0000.0000.0000.000
139A229MET0-0.029-0.00635.7140.0010.0010.0000.0000.0000.000
140A230ARG10.8560.90835.6920.0640.0640.0000.0000.0000.000
141A231LEU0-0.0220.00040.9960.0030.0030.0000.0000.0000.000
142A232VAL00.0040.02542.6870.0030.0030.0000.0000.0000.000
143A233GLU-1-0.750-0.82639.618-0.056-0.0560.0000.0000.0000.000
144A234SER0-0.101-0.04544.3990.0030.0030.0000.0000.0000.000
145A235GLY00.007-0.01646.9950.0020.0020.0000.0000.0000.000
146A236GLN0-0.068-0.05247.4790.0020.0020.0000.0000.0000.000
147A237GLY00.0260.01246.800-0.002-0.0020.0000.0000.0000.000
148A238ILE0-0.004-0.00144.8340.0000.0000.0000.0000.0000.000
149A239THR0-0.003-0.01639.669-0.002-0.0020.0000.0000.0000.000
150A240PHE00.0000.00239.1240.0010.0010.0000.0000.0000.000
151A241ILE00.0300.00735.671-0.003-0.0030.0000.0000.0000.000
152A242PRO0-0.0070.00531.4710.0010.0010.0000.0000.0000.000
153A243GLN00.0630.02932.8150.0050.0050.0000.0000.0000.000
154A244LEU0-0.021-0.01326.4390.0030.0030.0000.0000.0000.000
155A245THR0-0.029-0.02730.3080.0000.0000.0000.0000.0000.000
156A246VAL00.0250.01532.1140.0070.0070.0000.0000.0000.000
157A247GLU-1-0.861-0.93530.251-0.101-0.1010.0000.0000.0000.000
158A248GLN0-0.054-0.03427.4960.0070.0070.0000.0000.0000.000
159A249LEU0-0.0560.00232.5490.0050.0050.0000.0000.0000.000
160A250SER00.009-0.01636.2560.0020.0020.0000.0000.0000.000
161A251PRO00.021-0.01438.900-0.001-0.0010.0000.0000.0000.000
162A252SER00.0360.01842.0640.0000.0000.0000.0000.0000.000
163A253GLN00.0330.01137.3650.0000.0000.0000.0000.0000.000
164A254LYS10.8820.93836.0930.0660.0660.0000.0000.0000.000
165A255GLU-1-0.821-0.87741.383-0.041-0.0410.0000.0000.0000.000
166A256LEU0-0.0300.00342.8720.0010.0010.0000.0000.0000.000
167A257VAL0-0.053-0.01339.672-0.001-0.0010.0000.0000.0000.000
168A258ARG10.7920.88742.7110.0510.0510.0000.0000.0000.000
169A259PRO00.0510.03341.893-0.003-0.0030.0000.0000.0000.000
170A260PHE00.008-0.01241.2240.0040.0040.0000.0000.0000.000
171A261GLY00.0320.01944.5330.0000.0000.0000.0000.0000.000
172A262MET0-0.0520.00544.099-0.002-0.0020.0000.0000.0000.000
173A263PRO0-0.032-0.03043.4510.0030.0030.0000.0000.0000.000
174A264ARG00.003-0.00840.7250.0010.0010.0000.0000.0000.000
175A265PRO0-0.0290.00339.370-0.004-0.0040.0000.0000.0000.000
176A266VAL00.0270.01334.586-0.002-0.0020.0000.0000.0000.000
177A267ARG10.8300.89929.2450.1370.1370.0000.0000.0000.000
178A268GLU-1-0.796-0.88429.632-0.151-0.1510.0000.0000.0000.000
179A269VAL0-0.021-0.00624.096-0.002-0.0020.0000.0000.0000.000
180A270ARG10.7790.85124.2800.1870.1870.0000.0000.0000.000
181A271LEU0-0.011-0.00816.582-0.007-0.0070.0000.0000.0000.000
182A272ALA00.009-0.00121.0010.0020.0020.0000.0000.0000.000
183A273VAL0-0.003-0.02116.475-0.046-0.0460.0000.0000.0000.000
184A274ARG10.8710.89218.8950.2740.2740.0000.0000.0000.000
185A275GLN00.0000.00319.585-0.025-0.0250.0000.0000.0000.000
186A276ASP-1-0.863-0.89519.778-0.291-0.2910.0000.0000.0000.000
187A277TYR0-0.035-0.03311.636-0.101-0.1010.0000.0000.0000.000
188A278SER0-0.003-0.01513.4350.0140.0140.0000.0000.0000.000
189A279ARG10.8960.9587.7991.2131.2130.0000.0000.0000.000
190A280ARG10.9840.98611.3840.3510.3510.0000.0000.0000.000
191A281LYS11.0161.0159.8340.6180.6180.0000.0000.0000.000
192A282LEU00.0340.0327.1610.0380.0380.0000.0000.0000.000
193A283ARG10.7960.8649.9150.4780.4780.0000.0000.0000.000
194A284GLU-1-0.944-0.96913.501-0.386-0.3860.0000.0000.0000.000
195A285GLN0-0.012-0.0108.988-0.107-0.1070.0000.0000.0000.000
196A286LEU0-0.003-0.02210.5980.0680.0680.0000.0000.0000.000
197A287ILE00.0230.01914.0090.0760.0760.0000.0000.0000.000
198A288GLY00.0000.00416.5410.0500.0500.0000.0000.0000.000
199A289LEU0-0.016-0.01412.0810.0400.0400.0000.0000.0000.000
200A290LEU00.0070.00716.5970.0440.0440.0000.0000.0000.000
201A291ARG10.8920.95318.8270.2610.2610.0000.0000.0000.000
202A292SER0-0.101-0.04418.9830.0270.0270.0000.0000.0000.000
203A293ALA00.0100.01019.7910.0170.0170.0000.0000.0000.000
204A294VAL0-0.039-0.01621.6700.0210.0210.0000.0000.0000.000
205A295PRO00.0320.00625.319-0.002-0.0020.0000.0000.0000.000
206A296SER00.0620.02327.819-0.003-0.0030.0000.0000.0000.000
207A297ASP-1-0.915-0.93928.724-0.106-0.1060.0000.0000.0000.000
208A298MET00.0100.01028.8330.0020.0020.0000.0000.0000.000
209A299HIS0-0.050-0.02224.552-0.005-0.0050.0000.0000.0000.000
210A300LYS10.8940.94428.6860.1190.1190.0000.0000.0000.000
211A301LEU0-0.0040.01532.0060.0020.0020.0000.0000.0000.000
212A302GLN0-0.003-0.00434.0960.0080.0080.0000.0000.0000.000
213A303THR00.017-0.01037.6610.0010.0010.0000.0000.0000.000
214A304GLY00.0400.02041.3280.0020.0020.0000.0000.0000.000
215A305GLN0-0.054-0.02935.855-0.003-0.0030.0000.0000.0000.000
216A306HIS00.005-0.01439.7430.0000.0000.0000.0000.0000.000
217A307LEU0-0.036-0.01333.701-0.001-0.0010.0000.0000.0000.000
218A308ALA0-0.053-0.02537.2040.0050.0050.0000.0000.0000.000
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