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

tag_button

FMODB ID: R9728

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2732678.142657
FMO2-HF: Nuclear repulsion 2643592.422989
FMO2-HF: Total energy -89085.719668
FMO2-MP2: Total energy -89342.811259


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.
-8.584-1.6713.092-5.138-4.868-0.025
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 : 0.004 / q_NPA : 0.010
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].
3A92ARG10.8850.9323.803-3.0060.257-0.030-1.792-1.4420.008
4A93LEU0-0.025-0.0096.909-0.088-0.0880.0000.0000.0000.000
5A94ASN00.0240.0489.6940.1060.1060.0000.0000.0000.000
6A95ILE00.0290.01813.3850.0050.0050.0000.0000.0000.000
7A96ALA00.0360.01915.6740.0330.0330.0000.0000.0000.000
8A97VAL0-0.022-0.03119.121-0.020-0.0200.0000.0000.0000.000
9A98LEU00.0590.04821.7000.0180.0180.0000.0000.0000.000
10A99PRO00.0790.04525.338-0.004-0.0040.0000.0000.0000.000
11A100THR0-0.050-0.02027.4310.0010.0010.0000.0000.0000.000
12A101ILE0-0.0070.01323.7310.0040.0040.0000.0000.0000.000
13A102ALA00.0050.00222.933-0.003-0.0030.0000.0000.0000.000
14A103PRO00.0520.01923.544-0.009-0.0090.0000.0000.0000.000
15A104TYR00.0100.04926.1670.0040.0040.0000.0000.0000.000
16A105LEU0-0.0040.00221.016-0.001-0.0010.0000.0000.0000.000
17A106LEU00.0250.00818.344-0.015-0.0150.0000.0000.0000.000
18A107PRO00.0000.00320.007-0.013-0.0130.0000.0000.0000.000
19A108ARG10.9000.95221.6990.1590.1590.0000.0000.0000.000
20A109VAL00.0020.01716.746-0.005-0.0050.0000.0000.0000.000
21A110PHE0-0.0060.00315.807-0.037-0.0370.0000.0000.0000.000
22A111PRO0-0.020-0.01915.210-0.032-0.0320.0000.0000.0000.000
23A112ILE00.0320.01115.254-0.001-0.0010.0000.0000.0000.000
24A113TRP00.0650.02411.529-0.046-0.0460.0000.0000.0000.000
25A114LYS10.9120.98010.8520.2450.2450.0000.0000.0000.000
26A115LYS10.8950.94211.0080.1980.1980.0000.0000.0000.000
27A116GLU-1-0.879-0.94011.364-0.280-0.2800.0000.0000.0000.000
28A117LEU0-0.080-0.0437.763-0.065-0.0650.0000.0000.0000.000
29A118ALA0-0.0010.0076.519-0.310-0.3100.0000.0000.0000.000
30A119GLY0-0.008-0.0073.340-0.0600.3150.036-0.127-0.2840.000
31A120LEU0-0.039-0.0162.364-6.818-3.6113.087-3.199-3.094-0.033
32A121GLU-1-0.872-0.9204.3590.4980.566-0.001-0.020-0.0480.000
33A122ILE0-0.013-0.0167.229-0.042-0.0420.0000.0000.0000.000
34A123HIS0-0.079-0.06110.2460.1310.1310.0000.0000.0000.000
35A124VAL00.0040.00013.388-0.015-0.0150.0000.0000.0000.000
36A125SER0-0.022-0.00616.3820.0460.0460.0000.0000.0000.000
37A126GLU-1-0.865-0.93619.720-0.164-0.1640.0000.0000.0000.000
38A127MET0-0.090-0.04320.8400.0190.0190.0000.0000.0000.000
39A128GLN00.011-0.00325.168-0.004-0.0040.0000.0000.0000.000
40A129THR00.022-0.03127.008-0.009-0.0090.0000.0000.0000.000
41A130SER0-0.010-0.00827.277-0.008-0.0080.0000.0000.0000.000
42A131ARG10.9590.98625.5610.1130.1130.0000.0000.0000.000
43A132CYS00.0030.02323.107-0.009-0.0090.0000.0000.0000.000
44A133LEU00.0060.00223.191-0.015-0.0150.0000.0000.0000.000
45A134ALA00.0220.00925.156-0.002-0.0020.0000.0000.0000.000
46A135SER0-0.018-0.03121.0530.0050.0050.0000.0000.0000.000
47A136LEU0-0.047-0.00318.863-0.010-0.0100.0000.0000.0000.000
48A137LEU0-0.032-0.01720.813-0.008-0.0080.0000.0000.0000.000
49A138SER0-0.028-0.01522.726-0.001-0.0010.0000.0000.0000.000
50A139GLY00.0200.01618.6570.0120.0120.0000.0000.0000.000
51A140GLU-1-0.955-0.95117.456-0.148-0.1480.0000.0000.0000.000
52A141ILE0-0.076-0.05216.306-0.014-0.0140.0000.0000.0000.000
53A142ASP-1-0.881-0.94611.812-0.658-0.6580.0000.0000.0000.000
54A143MET0-0.071-0.04412.0800.0010.0010.0000.0000.0000.000
55A144ALA00.0270.01216.8240.0200.0200.0000.0000.0000.000
56A145ILE0-0.0220.01618.0440.0020.0020.0000.0000.0000.000
57A146ILE00.045-0.00921.4910.0200.0200.0000.0000.0000.000
58A147ALA0-0.026-0.01625.201-0.004-0.0040.0000.0000.0000.000
59A148SER0-0.003-0.00828.0380.0130.0130.0000.0000.0000.000
60A149LYS10.9290.96028.0040.1270.1270.0000.0000.0000.000
61A150ALA00.0230.01126.1030.0080.0080.0000.0000.0000.000
62A151GLU-1-0.985-0.97128.249-0.109-0.1090.0000.0000.0000.000
63A152THR0-0.028-0.04127.9560.0110.0110.0000.0000.0000.000
64A153GLU-1-0.927-0.95828.170-0.138-0.1380.0000.0000.0000.000
65A154GLY00.0570.02826.0400.0010.0010.0000.0000.0000.000
66A155LEU0-0.092-0.05222.672-0.024-0.0240.0000.0000.0000.000
67A156GLU-1-0.822-0.88121.451-0.260-0.2600.0000.0000.0000.000
68A157ASP-1-0.788-0.88922.514-0.215-0.2150.0000.0000.0000.000
69A158ASP-1-0.870-0.92320.842-0.281-0.2810.0000.0000.0000.000
70A159LEU0-0.055-0.03123.423-0.005-0.0050.0000.0000.0000.000
71A160LEU0-0.063-0.01920.225-0.017-0.0170.0000.0000.0000.000
72A161TYR00.006-0.02223.605-0.001-0.0010.0000.0000.0000.000
73A162TYR00.0290.02527.256-0.001-0.0010.0000.0000.0000.000
74A163GLU-1-0.770-0.91329.672-0.143-0.1430.0000.0000.0000.000
75A164GLU-1-0.803-0.87532.078-0.086-0.0860.0000.0000.0000.000
76A165PHE0-0.028-0.01634.777-0.002-0.0020.0000.0000.0000.000
77A166LEU00.0120.00637.3350.0050.0050.0000.0000.0000.000
78A167GLY00.0150.00439.640-0.001-0.0010.0000.0000.0000.000
79A168TYR0-0.065-0.04840.0790.0000.0000.0000.0000.0000.000
80A169VAL00.022-0.02042.4800.0010.0010.0000.0000.0000.000
81A170SER00.029-0.00646.1780.0010.0010.0000.0000.0000.000
82A171ARG10.8590.89846.2760.0450.0450.0000.0000.0000.000
83A172CYS0-0.053-0.00650.6450.0020.0020.0000.0000.0000.000
84A173GLU-1-0.762-0.80049.345-0.041-0.0410.0000.0000.0000.000
85A174PRO00.0640.02452.5830.0000.0000.0000.0000.0000.000
86A175LEU00.013-0.00849.8110.0000.0000.0000.0000.0000.000
87A176PHE0-0.039-0.00347.808-0.001-0.0010.0000.0000.0000.000
88A177GLU-1-0.970-0.97251.399-0.036-0.0360.0000.0000.0000.000
89A178GLN00.0310.03052.1420.0000.0000.0000.0000.0000.000
90A179ASP-1-0.877-0.93550.075-0.046-0.0460.0000.0000.0000.000
91A180VAL0-0.071-0.03947.429-0.003-0.0030.0000.0000.0000.000
92A181ILE0-0.021-0.00944.8920.0020.0020.0000.0000.0000.000
93A182ARG10.8490.94747.9700.0420.0420.0000.0000.0000.000
94A183THR00.0320.00248.8520.0000.0000.0000.0000.0000.000
95A184THR0-0.020-0.02350.0550.0000.0000.0000.0000.0000.000
96A185GLU-1-0.864-0.95352.631-0.040-0.0400.0000.0000.0000.000
97A186VAL0-0.034-0.00447.6200.0000.0000.0000.0000.0000.000
98A187ASN00.0290.00950.7260.0010.0010.0000.0000.0000.000
99A188PRO00.0730.05149.978-0.001-0.0010.0000.0000.0000.000
100A189HIS10.8700.93649.9040.0370.0370.0000.0000.0000.000
101A190ARG10.7560.84749.8300.0410.0410.0000.0000.0000.000
102A191LEU00.0040.02644.412-0.001-0.0010.0000.0000.0000.000
103A192TRP0-0.030-0.01842.2450.0010.0010.0000.0000.0000.000
104A193LEU00.003-0.01640.795-0.003-0.0030.0000.0000.0000.000
105A194LEU0-0.033-0.01834.2620.0000.0000.0000.0000.0000.000
106A195ASP-1-0.793-0.91536.965-0.071-0.0710.0000.0000.0000.000
107A196GLU-1-0.791-0.88030.076-0.125-0.1250.0000.0000.0000.000
108A197GLY0-0.047-0.04033.161-0.006-0.0060.0000.0000.0000.000
109A198HIS0-0.0170.00434.182-0.001-0.0010.0000.0000.0000.000
110A199CYS0-0.063-0.01537.4460.0030.0030.0000.0000.0000.000
111A200PHE00.0610.03431.9070.0030.0030.0000.0000.0000.000
112A201ARG10.9160.96232.3680.1120.1120.0000.0000.0000.000
113A202ASP-1-0.842-0.90838.250-0.068-0.0680.0000.0000.0000.000
114A203GLN00.0300.01433.8870.0000.0000.0000.0000.0000.000
115A204LEU00.0060.00338.8560.0030.0030.0000.0000.0000.000
116A205VAL00.0660.02641.2910.0050.0050.0000.0000.0000.000
117A206ARG10.8910.95643.6900.0700.0700.0000.0000.0000.000
118A207PHE0-0.005-0.03843.9820.0030.0030.0000.0000.0000.000
119A209GLN0-0.013-0.01544.4730.0050.0050.0000.0000.0000.000
120A210MET0-0.103-0.00647.6550.0030.0030.0000.0000.0000.000
121A211LYS10.9840.96150.2150.0430.0430.0000.0000.0000.000
122A212GLY00.0730.03653.4200.0000.0000.0000.0000.0000.000
123A213LEU0-0.024-0.00245.6830.0010.0010.0000.0000.0000.000
124A214HIS0-0.013-0.02045.9100.0010.0010.0000.0000.0000.000
125A215GLU-1-0.940-0.95650.568-0.035-0.0350.0000.0000.0000.000
126A216ARG10.8110.88247.2170.0470.0470.0000.0000.0000.000
127A217GLN0-0.0060.00452.892-0.001-0.0010.0000.0000.0000.000
128A218THR00.0110.00847.5390.0010.0010.0000.0000.0000.000
129A219ALA00.0090.01247.337-0.002-0.0020.0000.0000.0000.000
130A220TYR00.0130.00739.8630.0000.0000.0000.0000.0000.000
131A221SER0-0.0220.00041.148-0.002-0.0020.0000.0000.0000.000
132A222GLY00.0190.01137.0400.0020.0020.0000.0000.0000.000
133A223GLY0-0.010-0.01736.345-0.001-0.0010.0000.0000.0000.000
134A224SER00.0250.01733.412-0.004-0.0040.0000.0000.0000.000
135A225MET00.0440.01433.1570.0050.0050.0000.0000.0000.000
136A226GLU-1-0.948-0.96433.473-0.070-0.0700.0000.0000.0000.000
137A227ALA00.0150.00235.3560.0050.0050.0000.0000.0000.000
138A228PHE00.040-0.00338.3010.0040.0040.0000.0000.0000.000
139A229MET0-0.029-0.01036.0100.0010.0010.0000.0000.0000.000
140A230ARG10.8440.90935.5750.0690.0690.0000.0000.0000.000
141A231LEU00.0070.01740.9900.0030.0030.0000.0000.0000.000
142A232VAL0-0.0060.05142.6920.0030.0030.0000.0000.0000.000
143A233GLU-1-0.761-0.84639.681-0.059-0.0590.0000.0000.0000.000
144A234SER0-0.128-0.08744.3960.0020.0020.0000.0000.0000.000
145A235GLY00.000-0.02446.9890.0030.0030.0000.0000.0000.000
146A236GLN0-0.037-0.03547.5270.0010.0010.0000.0000.0000.000
147A237GLY00.0110.00546.801-0.002-0.0020.0000.0000.0000.000
148A238ILE00.0130.00844.9130.0000.0000.0000.0000.0000.000
149A239THR0-0.0060.00639.984-0.002-0.0020.0000.0000.0000.000
150A240PHE0-0.012-0.00339.1070.0010.0010.0000.0000.0000.000
151A241ILE00.0310.00935.700-0.003-0.0030.0000.0000.0000.000
152A242PRO00.0040.01031.4850.0020.0020.0000.0000.0000.000
153A243GLN00.0610.02132.7710.0050.0050.0000.0000.0000.000
154A244LEU0-0.034-0.01426.5340.0020.0020.0000.0000.0000.000
155A245THR0-0.041-0.07630.320-0.007-0.0070.0000.0000.0000.000
156A246VAL00.0250.01032.1240.0070.0070.0000.0000.0000.000
157A247GLU-1-0.932-0.98030.700-0.099-0.0990.0000.0000.0000.000
158A248GLN0-0.065-0.03427.6420.0060.0060.0000.0000.0000.000
159A249LEU0-0.0590.00132.5520.0050.0050.0000.0000.0000.000
160A250SER0-0.001-0.01436.2590.0030.0030.0000.0000.0000.000
161A251PRO00.012-0.02038.899-0.001-0.0010.0000.0000.0000.000
162A252SER00.0350.01542.0660.0000.0000.0000.0000.0000.000
163A253GLN00.0200.01037.140-0.001-0.0010.0000.0000.0000.000
164A254LYS10.9450.97236.8530.0710.0710.0000.0000.0000.000
165A255GLU-1-0.831-0.88541.390-0.045-0.0450.0000.0000.0000.000
166A256LEU0-0.0240.00843.0390.0020.0020.0000.0000.0000.000
167A257VAL0-0.045-0.00839.622-0.001-0.0010.0000.0000.0000.000
168A258ARG10.7790.87742.7230.0530.0530.0000.0000.0000.000
169A259PRO00.0580.02841.954-0.003-0.0030.0000.0000.0000.000
170A260PHE0-0.005-0.01341.4150.0040.0040.0000.0000.0000.000
171A261GLY00.0310.01944.5570.0000.0000.0000.0000.0000.000
172A262MET0-0.0650.00243.862-0.002-0.0020.0000.0000.0000.000
173A263PRO0-0.033-0.02843.5100.0030.0030.0000.0000.0000.000
174A264ARG00.010-0.00840.7740.0010.0010.0000.0000.0000.000
175A265PRO0-0.0330.00339.351-0.004-0.0040.0000.0000.0000.000
176A266VAL00.0310.02134.717-0.002-0.0020.0000.0000.0000.000
177A267ARG10.8620.91829.4670.1380.1380.0000.0000.0000.000
178A268GLU-1-0.803-0.89329.621-0.150-0.1500.0000.0000.0000.000
179A269VAL0-0.032-0.00924.093-0.002-0.0020.0000.0000.0000.000
180A270ARG10.7900.84224.2880.1820.1820.0000.0000.0000.000
181A271LEU0-0.016-0.01116.406-0.006-0.0060.0000.0000.0000.000
182A272ALA00.004-0.00221.0320.0020.0020.0000.0000.0000.000
183A273VAL00.024-0.01516.757-0.043-0.0430.0000.0000.0000.000
184A274ARG10.8610.93118.9550.2400.2400.0000.0000.0000.000
185A275GLN00.0010.00119.657-0.022-0.0220.0000.0000.0000.000
186A276ASP-1-0.874-0.92219.864-0.250-0.2500.0000.0000.0000.000
187A277TYR00.0350.02011.600-0.095-0.0950.0000.0000.0000.000
188A278SER0-0.012-0.01813.4130.0060.0060.0000.0000.0000.000
189A279ARG10.9050.9596.4551.3031.3030.0000.0000.0000.000
190A280ARG11.0321.00211.4560.3090.3090.0000.0000.0000.000
191A281LYS11.0051.0069.8090.6350.6350.0000.0000.0000.000
192A282LEU00.0430.0397.2880.0130.0130.0000.0000.0000.000
193A283ARG10.8170.8809.9380.4530.4530.0000.0000.0000.000
194A284GLU-1-0.945-0.96513.531-0.358-0.3580.0000.0000.0000.000
195A285GLN0-0.010-0.0098.929-0.103-0.1030.0000.0000.0000.000
196A286LEU0-0.013-0.02810.6990.0610.0610.0000.0000.0000.000
197A287ILE00.0150.01814.0020.0730.0730.0000.0000.0000.000
198A288GLY00.0000.00116.5260.0490.0490.0000.0000.0000.000
199A289LEU00.000-0.00912.1970.0360.0360.0000.0000.0000.000
200A290LEU00.0070.00416.6340.0430.0430.0000.0000.0000.000
201A291ARG10.9220.97718.8590.2660.2660.0000.0000.0000.000
202A292SER0-0.081-0.02519.0130.0300.0300.0000.0000.0000.000
203A293ALA00.0130.01419.8610.0160.0160.0000.0000.0000.000
204A294VAL0-0.046-0.02621.6960.0210.0210.0000.0000.0000.000
205A295PRO00.0210.00325.347-0.002-0.0020.0000.0000.0000.000
206A296SER00.0870.02427.823-0.002-0.0020.0000.0000.0000.000
207A297ASP-1-0.924-0.93528.733-0.107-0.1070.0000.0000.0000.000
208A298MET0-0.017-0.00128.8300.0010.0010.0000.0000.0000.000
209A299HIS0-0.091-0.06124.7640.0010.0010.0000.0000.0000.000
210A300LYS10.8970.94328.6660.1220.1220.0000.0000.0000.000
211A301LEU0-0.0030.01731.9910.0020.0020.0000.0000.0000.000
212A302GLN00.005-0.00234.0940.0080.0080.0000.0000.0000.000
213A303THR00.008-0.01237.6430.0010.0010.0000.0000.0000.000
214A304GLY00.0450.01941.3110.0020.0020.0000.0000.0000.000
215A305GLN0-0.081-0.05135.833-0.002-0.0020.0000.0000.0000.000
216A306HIS00.007-0.01439.7700.0000.0000.0000.0000.0000.000
217A307LEU0-0.035-0.01633.561-0.001-0.0010.0000.0000.0000.000
218A308ALA0-0.064-0.03037.2120.0050.0050.0000.0000.0000.000
219A309HIS00.0110.01437.454-0.004-0.0040.0000.0000.0000.000