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: G5V21

Calculation Name: 3DSH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DSH

Chain ID: A

ChEMBL ID:

UniProt ID: Q13568

Base Structure: X-ray

Registration Date: 2023-09-23

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2810846.697923
FMO2-HF: Nuclear repulsion 2714711.836422
FMO2-HF: Total energy -96134.861502
FMO2-MP2: Total energy -96415.192708


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:222:GLU)


Summations of interaction energy for fragment #1(A:222:GLU)
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.
-14.083-17.55330.608-13.194-13.9460.139
Interaction energy analysis for fragmet #1(A:222:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.803 / q_NPA : -0.902
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].
3A224LEU00.0250.0153.765-6.855-4.571-0.009-1.059-1.2160.002
4A225LEU00.0030.0092.522-4.287-3.1210.994-0.669-1.492-0.002
5A226PRO00.024-0.0065.179-2.601-2.478-0.001-0.011-0.1110.000
6A227ASP-1-0.887-0.9408.43321.16521.1650.0000.0000.0000.000
7A228LEU0-0.076-0.0306.330-1.673-1.6730.0000.0000.0000.000
8A229LEU00.0020.0027.684-1.326-1.3260.0000.0000.0000.000
9A230ILE0-0.047-0.01610.698-1.368-1.3680.0000.0000.0000.000
10A231SER00.035-0.01813.114-1.052-1.0520.0000.0000.0000.000
11A232PRO00.000-0.00515.8520.0420.0420.0000.0000.0000.000
12A233HIS0-0.0310.00914.487-0.879-0.8790.0000.0000.0000.000
13A234MET0-0.038-0.01012.437-0.282-0.2820.0000.0000.0000.000
14A235LEU00.0020.00312.8590.1440.1440.0000.0000.0000.000
15A236PRO00.0260.01917.119-0.371-0.3710.0000.0000.0000.000
16A237LEU0-0.042-0.03215.949-0.044-0.0440.0000.0000.0000.000
17A238THR0-0.049-0.03619.5830.1620.1620.0000.0000.0000.000
18A239ASP-1-0.888-0.94222.59511.24711.2470.0000.0000.0000.000
19A240LEU0-0.049-0.02522.7780.6030.6030.0000.0000.0000.000
20A241GLU-1-0.791-0.85824.45011.79211.7920.0000.0000.0000.000
21A242ILE0-0.016-0.01626.7600.1830.1830.0000.0000.0000.000
22A243LYS10.8880.93929.696-10.444-10.4440.0000.0000.0000.000
23A244PHE00.0480.02431.9060.0910.0910.0000.0000.0000.000
24A245GLN0-0.042-0.04334.7470.1310.1310.0000.0000.0000.000
25A246TYR00.021-0.00436.5740.0350.0350.0000.0000.0000.000
26A247ARG10.9180.96240.142-7.217-7.2170.0000.0000.0000.000
27A248GLY00.0210.01641.606-0.183-0.1830.0000.0000.0000.000
28A249ARG10.8180.90241.309-7.274-7.2740.0000.0000.0000.000
29A250PRO00.0380.01839.2600.1760.1760.0000.0000.0000.000
30A251PRO00.0010.01134.466-0.070-0.0700.0000.0000.0000.000
31A252ARG10.8250.90036.192-7.629-7.6290.0000.0000.0000.000
32A253ALA0-0.014-0.01831.6220.0960.0960.0000.0000.0000.000
33A254LEU0-0.0190.00331.977-0.297-0.2970.0000.0000.0000.000
34A255THR00.0380.01626.6320.2090.2090.0000.0000.0000.000
35A256ILE0-0.034-0.00128.332-0.370-0.3700.0000.0000.0000.000
36A257SER00.0630.03226.6290.2550.2550.0000.0000.0000.000
37A258ASN0-0.010-0.00627.3580.3830.3830.0000.0000.0000.000
38A259PRO00.0330.00826.5290.1900.1900.0000.0000.0000.000
39A260HIS0-0.0050.01127.1870.2300.2300.0000.0000.0000.000
40A261GLY0-0.0130.00728.1790.1290.1290.0000.0000.0000.000
41A262CYS0-0.053-0.02329.016-0.304-0.3040.0000.0000.0000.000
42A263ARG10.8480.90531.838-7.786-7.7860.0000.0000.0000.000
43A264LEU0-0.0070.01931.711-0.200-0.2000.0000.0000.0000.000
44A265PHE0-0.025-0.01635.626-0.048-0.0480.0000.0000.0000.000
45A266TYR0-0.009-0.00839.435-0.028-0.0280.0000.0000.0000.000
46A267SER00.014-0.01842.936-0.083-0.0830.0000.0000.0000.000
47A268GLN0-0.0030.00846.0620.1000.1000.0000.0000.0000.000
48A269LEU0-0.023-0.00747.368-0.119-0.1190.0000.0000.0000.000
49A270GLU-1-0.779-0.87743.9827.1747.1740.0000.0000.0000.000
50A271ALA0-0.0010.00141.077-0.075-0.0750.0000.0000.0000.000
51A272THR0-0.006-0.01343.072-0.026-0.0260.0000.0000.0000.000
52A273GLN0-0.003-0.00241.5550.2050.2050.0000.0000.0000.000
53A274GLU-1-0.883-0.95544.5226.6066.6060.0000.0000.0000.000
54A275GLN0-0.023-0.01145.629-0.035-0.0350.0000.0000.0000.000
55A276VAL00.0140.01539.3130.1040.1040.0000.0000.0000.000
56A277GLU-1-0.906-0.95040.8017.7257.7250.0000.0000.0000.000
57A278LEU0-0.078-0.01942.3440.0660.0660.0000.0000.0000.000
58A279PHE0-0.010-0.01841.2370.0810.0810.0000.0000.0000.000
59A280GLY00.0530.03237.5520.1770.1770.0000.0000.0000.000
60A281PRO0-0.016-0.02434.631-0.193-0.1930.0000.0000.0000.000
61A282ILE00.0450.01737.1530.1180.1180.0000.0000.0000.000
62A283SER0-0.045-0.01734.149-0.099-0.0990.0000.0000.0000.000
63A284LEU0-0.0410.00431.9620.2290.2290.0000.0000.0000.000
64A285GLU-1-0.784-0.90432.4118.8788.8780.0000.0000.0000.000
65A286GLN00.0120.01334.444-0.019-0.0190.0000.0000.0000.000
66A287VAL0-0.010-0.00933.348-0.188-0.1880.0000.0000.0000.000
67A288ARG10.8070.87236.715-7.022-7.0220.0000.0000.0000.000
68A289PHE0-0.012-0.01336.5520.1460.1460.0000.0000.0000.000
69A290PRO0-0.022-0.01238.431-0.224-0.2240.0000.0000.0000.000
70A291SER00.006-0.02441.570-0.009-0.0090.0000.0000.0000.000
71A292PRO00.0060.00244.9510.0820.0820.0000.0000.0000.000
72A293GLU-1-0.866-0.90146.3866.2646.2640.0000.0000.0000.000
73A294ASP-1-0.809-0.88645.2466.8396.8390.0000.0000.0000.000
74A295ILE0-0.060-0.01744.6320.0540.0540.0000.0000.0000.000
75A296PRO00.0260.02048.041-0.122-0.1220.0000.0000.0000.000
76A297SER0-0.0020.00349.693-0.156-0.1560.0000.0000.0000.000
77A298ASP-1-0.751-0.86550.9785.9325.9320.0000.0000.0000.000
78A299LYS10.9170.96551.957-6.048-6.0480.0000.0000.0000.000
79A300GLN0-0.015-0.02744.8440.0420.0420.0000.0000.0000.000
80A301ARG10.8660.92448.075-5.954-5.9540.0000.0000.0000.000
81A302PHE0-0.0010.01549.5180.0580.0580.0000.0000.0000.000
82A303TYR00.0260.00347.480-0.020-0.0200.0000.0000.0000.000
83A304THR0-0.023-0.03143.8160.1490.1490.0000.0000.0000.000
84A305ASN00.004-0.02045.8030.0980.0980.0000.0000.0000.000
85A306GLN0-0.008-0.00448.0730.0700.0700.0000.0000.0000.000
86A307LEU0-0.036-0.00342.3660.0540.0540.0000.0000.0000.000
87A308LEU0-0.028-0.01942.2920.1380.1380.0000.0000.0000.000
88A309ASP-1-0.936-0.96044.9406.3576.3570.0000.0000.0000.000
89A310VAL0-0.0190.00344.365-0.034-0.0340.0000.0000.0000.000
90A311LEU0-0.014-0.02538.7100.2170.2170.0000.0000.0000.000
91A312ASP-1-0.783-0.84641.5037.0267.0260.0000.0000.0000.000
92A313ARG10.7540.84341.061-7.565-7.5650.0000.0000.0000.000
93A314GLY00.0320.02238.3150.1410.1410.0000.0000.0000.000
94A315LEU0-0.072-0.03231.571-0.021-0.0210.0000.0000.0000.000
95A316ILE00.0080.01131.2470.0550.0550.0000.0000.0000.000
96A317LEU0-0.026-0.01828.0170.2340.2340.0000.0000.0000.000
97A318GLN00.0670.03327.6710.1120.1120.0000.0000.0000.000
98A319LEU00.0630.03621.7270.3530.3530.0000.0000.0000.000
99A320GLN0-0.030-0.02822.491-0.590-0.5900.0000.0000.0000.000
100A321GLY00.0300.03419.9900.6180.6180.0000.0000.0000.000
101A322GLN00.0500.01615.540-0.941-0.9410.0000.0000.0000.000
102A323ASP-1-0.761-0.82817.64516.87616.8760.0000.0000.0000.000
103A324LEU0-0.025-0.01619.702-0.591-0.5910.0000.0000.0000.000
104A325TYR0-0.019-0.03521.4870.0510.0510.0000.0000.0000.000
105A326ALA00.0310.01625.913-0.305-0.3050.0000.0000.0000.000
106A327ILE0-0.017-0.00529.2550.0440.0440.0000.0000.0000.000
107A328ARG10.8280.92432.586-8.554-8.5540.0000.0000.0000.000
108A329LEU00.0740.04735.407-0.094-0.0940.0000.0000.0000.000
109A330CYS0-0.100-0.02938.574-0.202-0.2020.0000.0000.0000.000
110A331GLN00.0220.00240.5620.1150.1150.0000.0000.0000.000
111A332CYS0-0.022-0.01039.915-0.018-0.0180.0000.0000.0000.000
112A333LYS10.9780.98638.964-7.516-7.5160.0000.0000.0000.000
113A334VAL00.0440.02433.562-0.066-0.0660.0000.0000.0000.000
114A335PHE0-0.0090.00333.230-0.031-0.0310.0000.0000.0000.000
115A336TRP00.0350.02923.9800.0150.0150.0000.0000.0000.000
116A337SER0-0.021-0.01825.926-0.068-0.0680.0000.0000.0000.000
117A338GLY00.0580.03023.028-0.220-0.2200.0000.0000.0000.000
118A339PRO0-0.0100.00517.544-0.144-0.1440.0000.0000.0000.000
119A340CYS0-0.0370.01018.2600.8460.8460.0000.0000.0000.000
120A341ALA0-0.030-0.00220.582-0.504-0.5040.0000.0000.0000.000
121A342SER0-0.003-0.00622.6450.5740.5740.0000.0000.0000.000
122A343ALA00.0080.00222.233-0.249-0.2490.0000.0000.0000.000
123A344HIS0-0.046-0.01424.3530.5310.5310.0000.0000.0000.000
124A345ASP-1-0.827-0.92126.5539.5239.5230.0000.0000.0000.000
125A346SER0-0.070-0.04528.7410.2940.2940.0000.0000.0000.000
126A347CYS0-0.083-0.02431.344-0.197-0.1970.0000.0000.0000.000
127A348PRO0-0.025-0.01132.1590.2690.2690.0000.0000.0000.000
128A349ASN0-0.005-0.01327.724-0.066-0.0660.0000.0000.0000.000
129A350PRO0-0.019-0.01231.6390.0710.0710.0000.0000.0000.000
130A351ILE00.0120.00830.7960.2070.2070.0000.0000.0000.000
131A352GLN00.0170.00133.069-0.454-0.4540.0000.0000.0000.000
132A353ARG10.8220.91834.891-7.421-7.4210.0000.0000.0000.000
133A354GLU-1-0.737-0.88336.2977.9477.9470.0000.0000.0000.000
134A355VAL0-0.040-0.00431.0730.1370.1370.0000.0000.0000.000
135A356LYS10.8840.94425.845-11.477-11.4770.0000.0000.0000.000
136A357THR0-0.031-0.01327.4020.2540.2540.0000.0000.0000.000
137A358LYS10.8320.90917.753-16.340-16.3400.0000.0000.0000.000
138A359LEU0-0.044-0.02323.439-0.119-0.1190.0000.0000.0000.000
139A360PHE00.034-0.01015.7470.1910.1910.0000.0000.0000.000
140A361SER00.016-0.03115.699-0.163-0.1630.0000.0000.0000.000
141A362LEU00.0050.01013.1700.9840.9840.0000.0000.0000.000
142A363GLU-1-0.929-0.94510.51824.10924.1090.0000.0000.0000.000
143A364HIS0-0.047-0.04110.1012.0022.0020.0000.0000.0000.000
144A365PHE0-0.027-0.02110.6011.8441.8440.0000.0000.0000.000
145A366LEU00.0480.0296.4570.8280.8280.0000.0000.0000.000
146A367ASN0-0.004-0.0086.2406.0316.0310.0000.0000.0000.000
147A368GLU-1-0.839-0.9216.07534.08234.0820.0000.0000.0000.000
148A369LEU0-0.077-0.0198.2740.7010.7010.0000.0000.0000.000
149A370ILE00.0110.0072.387-1.193-0.0503.345-1.361-3.1270.011
150A371LEU0-0.049-0.0244.0326.6447.0580.001-0.063-0.3520.000
151A372PHE0-0.001-0.0016.260-2.251-2.2510.0000.0000.0000.000
152A373GLN0-0.032-0.0176.486-2.056-2.0560.0000.0000.0000.000
153A374LYS10.7680.8781.753-139.458-148.16326.279-10.031-7.5440.128
154A375GLY00.0150.0197.228-1.936-1.9360.0000.0000.0000.000
155A376GLN0-0.061-0.0265.5215.4505.555-0.0010.000-0.1040.000
156A377THR0-0.002-0.0139.271-1.782-1.7820.0000.0000.0000.000
157A378ASN00.0400.01111.5860.3430.3430.0000.0000.0000.000
158A379THR0-0.058-0.02114.129-1.349-1.3490.0000.0000.0000.000
159A380PRO00.0230.02513.6181.5031.5030.0000.0000.0000.000
160A381PRO00.0270.02111.556-1.194-1.1940.0000.0000.0000.000
161A382PRO0-0.010-0.00714.252-1.106-1.1060.0000.0000.0000.000
162A383PHE00.035-0.01217.0980.2470.2470.0000.0000.0000.000
163A384GLU-1-0.831-0.89418.97811.31411.3140.0000.0000.0000.000
164A385ILE00.004-0.00622.1370.2340.2340.0000.0000.0000.000
165A386PHE0-0.029-0.01524.871-0.493-0.4930.0000.0000.0000.000
166A387PHE00.0300.00027.8740.0030.0030.0000.0000.0000.000
167A388CYS0-0.066-0.03631.496-0.236-0.2360.0000.0000.0000.000
168A389PHE00.0650.01533.8660.0190.0190.0000.0000.0000.000
169A390GLY00.012-0.01238.022-0.157-0.1570.0000.0000.0000.000
170A391GLU-1-0.882-0.94139.3207.7187.7180.0000.0000.0000.000
171A392GLU-1-0.887-0.94137.1618.2338.2330.0000.0000.0000.000
172A393TRP00.0370.00529.232-0.245-0.2450.0000.0000.0000.000
173A394PRO00.0820.04529.3430.0220.0220.0000.0000.0000.000
174A395ASP-1-0.723-0.83832.1448.0468.0460.0000.0000.0000.000
175A396ARG10.9650.98134.615-7.937-7.9370.0000.0000.0000.000
176A397LYS10.7530.87437.125-8.039-8.0390.0000.0000.0000.000
177A398PRO00.0380.02135.7750.1550.1550.0000.0000.0000.000
178A399ARG10.9210.95128.163-11.036-11.0360.0000.0000.0000.000
179A400GLU-1-0.865-0.93434.7509.0689.0680.0000.0000.0000.000
180A401LYS10.8630.92638.066-7.751-7.7510.0000.0000.0000.000
181A402LYS10.7590.89236.360-8.654-8.6540.0000.0000.0000.000
182A403LEU0-0.030-0.01839.513-0.009-0.0090.0000.0000.0000.000
183A404ILE00.0170.00838.050-0.052-0.0520.0000.0000.0000.000
184A405THR0-0.042-0.01433.9590.1820.1820.0000.0000.0000.000
185A406VAL0-0.005-0.00631.045-0.188-0.1880.0000.0000.0000.000
186A407GLN0-0.022-0.00526.447-0.190-0.1900.0000.0000.0000.000
187A408VAL0-0.001-0.00525.332-0.279-0.2790.0000.0000.0000.000
188A409VAL00.0170.00521.2270.4060.4060.0000.0000.0000.000
189A410PRO00.0180.02218.976-0.440-0.4400.0000.0000.0000.000
190A411VAL00.0290.00619.4020.7230.7230.0000.0000.0000.000
191A412ALA00.0130.00816.3180.4270.4270.0000.0000.0000.000
192A413ALA00.0080.00814.8450.9820.9820.0000.0000.0000.000
193A414ARG10.7620.85015.039-12.618-12.6180.0000.0000.0000.000
194A415LEU00.0370.01316.6110.3600.3600.0000.0000.0000.000
195A416LEU00.0050.00910.0660.5170.5170.0000.0000.0000.000
196A417LEU00.0060.00012.1991.0671.0670.0000.0000.0000.000
197A418GLU-1-0.878-0.93613.79115.14615.1460.0000.0000.0000.000
198A419MET0-0.023-0.00811.5860.4620.4620.0000.0000.0000.000
199A420PHE00.016-0.0145.3950.5250.5250.0000.0000.0000.000
200A421SER0-0.064-0.04410.9590.6100.6100.0000.0000.0000.000
201A422GLY0-0.051-0.01314.061-0.945-0.9450.0000.0000.0000.000
202A423GLU-1-0.956-0.95910.26521.56921.5690.0000.0000.0000.000
203A424LEU0-0.003-0.00611.8120.8800.8800.0000.0000.0000.000
204A425SER00.0010.00410.565-0.149-0.1490.0000.0000.0000.000
205A426TRP00.004-0.00511.457-1.940-1.9400.0000.0000.0000.000
206A427SER0-0.025-0.00712.602-0.787-0.7870.0000.0000.0000.000
207A428ALA0-0.045-0.02211.472-0.848-0.8480.0000.0000.0000.000
208A429ASP-1-0.863-0.93313.41316.91416.9140.0000.0000.0000.000
209A430ASP-1-0.902-0.94915.30317.73117.7310.0000.0000.0000.000
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