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: VQYG1

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2806622.220474
FMO2-HF: Nuclear repulsion 2710489.691474
FMO2-HF: Total energy -96132.529
FMO2-MP2: Total energy -96412.940124


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.
31.72737.38912.185-7.261-10.5880.063
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 : -0.855 / q_NPA : -0.961
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].
3A224LEU00.0160.0113.571-8.416-5.642-0.012-1.305-1.4570.003
4A225LEU00.0230.0182.536-4.925-3.6801.150-0.793-1.602-0.001
5A226PRO00.0220.0024.795-3.179-3.034-0.001-0.018-0.1270.000
6A227ASP-1-0.875-0.9347.90820.63120.6310.0000.0000.0000.000
7A228LEU0-0.104-0.0386.143-1.735-1.7350.0000.0000.0000.000
8A229LEU00.000-0.0067.684-1.740-1.7400.0000.0000.0000.000
9A230ILE0-0.042-0.02010.225-1.639-1.6390.0000.0000.0000.000
10A231SER00.023-0.02812.631-0.981-0.9810.0000.0000.0000.000
11A232PRO00.0030.00515.322-0.028-0.0280.0000.0000.0000.000
12A233HIS0-0.0190.01514.533-0.816-0.8160.0000.0000.0000.000
13A234MET0-0.042-0.01311.815-0.358-0.3580.0000.0000.0000.000
14A235LEU0-0.016-0.00912.7940.0850.0850.0000.0000.0000.000
15A236PRO00.0440.02716.962-0.437-0.4370.0000.0000.0000.000
16A237LEU0-0.046-0.03115.730-0.059-0.0590.0000.0000.0000.000
17A238THR0-0.056-0.03919.6620.0720.0720.0000.0000.0000.000
18A239ASP-1-0.885-0.93222.67811.42111.4210.0000.0000.0000.000
19A240LEU0-0.066-0.03323.0250.5540.5540.0000.0000.0000.000
20A241GLU-1-0.849-0.89925.13111.51911.5190.0000.0000.0000.000
21A242ILE00.0050.00127.0880.2200.2200.0000.0000.0000.000
22A243LYS10.9510.96929.937-10.485-10.4850.0000.0000.0000.000
23A244PHE00.0450.00931.8740.0380.0380.0000.0000.0000.000
24A245GLN0-0.039-0.02535.2540.1890.1890.0000.0000.0000.000
25A246TYR00.004-0.02436.9750.0090.0090.0000.0000.0000.000
26A247ARG10.8940.94440.602-7.270-7.2700.0000.0000.0000.000
27A248GLY00.0060.00441.257-0.191-0.1910.0000.0000.0000.000
28A249ARG10.9340.98041.391-7.235-7.2350.0000.0000.0000.000
29A250PRO00.010-0.00139.1140.1950.1950.0000.0000.0000.000
30A251PRO0-0.0050.01134.462-0.081-0.0810.0000.0000.0000.000
31A252ARG10.9510.97036.277-7.896-7.8960.0000.0000.0000.000
32A253ALA0-0.024-0.01731.3170.1040.1040.0000.0000.0000.000
33A254LEU0-0.0120.00832.071-0.287-0.2870.0000.0000.0000.000
34A255THR00.0420.01527.0140.2050.2050.0000.0000.0000.000
35A256ILE0-0.041-0.00828.673-0.369-0.3690.0000.0000.0000.000
36A257SER00.0880.03926.7560.2460.2460.0000.0000.0000.000
37A258ASN0-0.0230.00127.6970.3220.3220.0000.0000.0000.000
38A259PRO00.0350.00326.4390.2240.2240.0000.0000.0000.000
39A260HIS0-0.018-0.00827.0780.3070.3070.0000.0000.0000.000
40A261GLY0-0.0040.01028.5440.1440.1440.0000.0000.0000.000
41A262CYS0-0.045-0.01529.321-0.237-0.2370.0000.0000.0000.000
42A263ARG10.8630.92232.209-7.783-7.7830.0000.0000.0000.000
43A264LEU0-0.0090.01032.086-0.161-0.1610.0000.0000.0000.000
44A265PHE0-0.022-0.02036.043-0.045-0.0450.0000.0000.0000.000
45A266TYR0-0.002-0.00239.7470.0270.0270.0000.0000.0000.000
46A267SER00.027-0.00143.201-0.096-0.0960.0000.0000.0000.000
47A268GLN00.0160.01546.1270.1130.1130.0000.0000.0000.000
48A269LEU0-0.050-0.01947.355-0.099-0.0990.0000.0000.0000.000
49A270GLU-1-0.856-0.92744.4897.1787.1780.0000.0000.0000.000
50A271ALA0-0.016-0.00441.335-0.066-0.0660.0000.0000.0000.000
51A272THR0-0.002-0.03443.320-0.066-0.0660.0000.0000.0000.000
52A273GLN00.0250.00441.0960.1310.1310.0000.0000.0000.000
53A274GLU-1-0.893-0.96244.5356.6136.6130.0000.0000.0000.000
54A275GLN0-0.0110.02545.7300.0220.0220.0000.0000.0000.000
55A276VAL00.0030.01039.3460.1060.1060.0000.0000.0000.000
56A277GLU-1-0.930-0.96340.6587.7287.7280.0000.0000.0000.000
57A278LEU0-0.054-0.01341.9440.0760.0760.0000.0000.0000.000
58A279PHE00.004-0.01341.3320.1090.1090.0000.0000.0000.000
59A280GLY00.0290.02637.8180.1680.1680.0000.0000.0000.000
60A281PRO0-0.010-0.01934.785-0.190-0.1900.0000.0000.0000.000
61A282ILE00.0360.01537.5760.1110.1110.0000.0000.0000.000
62A283SER0-0.037-0.00334.024-0.059-0.0590.0000.0000.0000.000
63A284LEU0-0.0410.00132.0270.2240.2240.0000.0000.0000.000
64A285GLU-1-0.808-0.92732.8158.6518.6510.0000.0000.0000.000
65A286GLN0-0.0060.00034.672-0.011-0.0110.0000.0000.0000.000
66A287VAL00.0060.00533.594-0.111-0.1110.0000.0000.0000.000
67A288ARG10.8270.90837.007-7.084-7.0840.0000.0000.0000.000
68A289PHE0-0.044-0.02836.9050.1410.1410.0000.0000.0000.000
69A290PRO00.006-0.00138.751-0.200-0.2000.0000.0000.0000.000
70A291SER00.0830.07441.886-0.035-0.0350.0000.0000.0000.000
71A292PRO0-0.003-0.00945.0940.1020.1020.0000.0000.0000.000
72A293GLU-1-0.935-0.97946.5486.2056.2050.0000.0000.0000.000
73A294ASP-1-0.904-0.93846.9796.5326.5320.0000.0000.0000.000
74A295ILE0-0.107-0.05844.9820.0810.0810.0000.0000.0000.000
75A296PRO00.0100.01447.961-0.125-0.1250.0000.0000.0000.000
76A297SER0-0.0190.00449.928-0.149-0.1490.0000.0000.0000.000
77A298ASP-1-0.727-0.86251.2735.8845.8840.0000.0000.0000.000
78A299LYS10.9090.96251.910-6.002-6.0020.0000.0000.0000.000
79A300GLN0-0.022-0.03144.687-0.052-0.0520.0000.0000.0000.000
80A301ARG10.8760.92948.189-5.972-5.9720.0000.0000.0000.000
81A302PHE0-0.029-0.00949.6630.0340.0340.0000.0000.0000.000
82A303TYR00.0210.00247.480-0.017-0.0170.0000.0000.0000.000
83A304THR0-0.027-0.03744.1410.1520.1520.0000.0000.0000.000
84A305ASN00.0500.01046.0480.1770.1770.0000.0000.0000.000
85A306GLN0-0.0210.00648.6800.0700.0700.0000.0000.0000.000
86A307LEU0-0.036-0.00942.3790.0490.0490.0000.0000.0000.000
87A308LEU0-0.036-0.02742.7190.1000.1000.0000.0000.0000.000
88A309ASP-1-0.902-0.94945.1746.3826.3820.0000.0000.0000.000
89A310VAL0-0.0420.01344.524-0.010-0.0100.0000.0000.0000.000
90A311LEU0-0.011-0.04539.3380.2300.2300.0000.0000.0000.000
91A312ASP-1-0.794-0.87041.9446.9586.9580.0000.0000.0000.000
92A313ARG10.8510.90941.427-7.409-7.4090.0000.0000.0000.000
93A314GLY00.0310.02038.5640.1370.1370.0000.0000.0000.000
94A315LEU0-0.050-0.02831.652-0.029-0.0290.0000.0000.0000.000
95A316ILE0-0.0060.00731.1940.0350.0350.0000.0000.0000.000
96A317LEU0-0.021-0.01227.9620.2180.2180.0000.0000.0000.000
97A318GLN00.0360.00627.0720.0450.0450.0000.0000.0000.000
98A319LEU00.0390.02221.3020.2950.2950.0000.0000.0000.000
99A320GLN0-0.016-0.00322.741-0.448-0.4480.0000.0000.0000.000
100A321GLY00.0210.00919.7900.5350.5350.0000.0000.0000.000
101A322GLN00.0520.01215.704-0.794-0.7940.0000.0000.0000.000
102A323ASP-1-0.849-0.92217.49717.17117.1710.0000.0000.0000.000
103A324LEU0-0.0090.00319.704-0.703-0.7030.0000.0000.0000.000
104A325TYR0-0.006-0.00922.0850.0690.0690.0000.0000.0000.000
105A326ALA00.0350.01225.784-0.261-0.2610.0000.0000.0000.000
106A327ILE00.0070.00829.1710.0220.0220.0000.0000.0000.000
107A328ARG10.8700.95232.515-8.453-8.4530.0000.0000.0000.000
108A329LEU00.0870.03935.368-0.067-0.0670.0000.0000.0000.000
109A330CYS0-0.108-0.01738.659-0.191-0.1910.0000.0000.0000.000
110A331GLN00.007-0.00740.5760.0820.0820.0000.0000.0000.000
111A332CYS0-0.0120.00540.244-0.010-0.0100.0000.0000.0000.000
112A333LYS10.9560.96939.174-7.475-7.4750.0000.0000.0000.000
113A334VAL00.0510.02733.642-0.066-0.0660.0000.0000.0000.000
114A335PHE00.0090.01433.8340.0060.0060.0000.0000.0000.000
115A336TRP00.0280.01324.3580.0570.0570.0000.0000.0000.000
116A337SER00.0160.02926.991-0.183-0.1830.0000.0000.0000.000
117A338GLY00.0320.00223.893-0.202-0.2020.0000.0000.0000.000
118A339PRO00.0000.02018.403-0.083-0.0830.0000.0000.0000.000
119A340CYS0-0.047-0.00819.0830.5520.5520.0000.0000.0000.000
120A341ALA0-0.053-0.00821.348-0.441-0.4410.0000.0000.0000.000
121A342SER00.021-0.00423.4210.5490.5490.0000.0000.0000.000
122A343ALA0-0.020-0.00323.101-0.247-0.2470.0000.0000.0000.000
123A344HIS0-0.015-0.00925.1430.5410.5410.0000.0000.0000.000
124A345ASP-1-0.890-0.92627.6279.6069.6060.0000.0000.0000.000
125A346SER0-0.011-0.04029.7240.3690.3690.0000.0000.0000.000
126A347CYS0-0.101-0.02632.129-0.094-0.0940.0000.0000.0000.000
127A348PRO00.0180.00232.9940.2580.2580.0000.0000.0000.000
128A349ASN0-0.009-0.00528.263-0.088-0.0880.0000.0000.0000.000
129A350PRO0-0.050-0.02032.4320.0670.0670.0000.0000.0000.000
130A351ILE00.0260.01231.0030.1690.1690.0000.0000.0000.000
131A352GLN0-0.012-0.02333.406-0.318-0.3180.0000.0000.0000.000
132A353ARG10.8330.91134.753-7.478-7.4780.0000.0000.0000.000
133A354GLU-1-0.882-0.95236.0567.7977.7970.0000.0000.0000.000
134A355VAL0-0.0170.01231.2000.0390.0390.0000.0000.0000.000
135A356LYS10.8900.95426.234-11.236-11.2360.0000.0000.0000.000
136A357THR0-0.021-0.01827.2800.1370.1370.0000.0000.0000.000
137A358LYS10.9310.97317.973-16.149-16.1490.0000.0000.0000.000
138A359LEU0-0.028-0.02423.436-0.085-0.0850.0000.0000.0000.000
139A360PHE00.019-0.00815.7540.1650.1650.0000.0000.0000.000
140A361SER00.0180.01815.188-0.063-0.0630.0000.0000.0000.000
141A362LEU00.0260.01313.1600.7840.7840.0000.0000.0000.000
142A363GLU-1-0.912-0.94910.62523.57723.5770.0000.0000.0000.000
143A364HIS0-0.005-0.01110.0432.8422.8420.0000.0000.0000.000
144A365PHE0-0.010-0.01010.9971.7021.7020.0000.0000.0000.000
145A366LEU00.0170.0186.8110.8990.8990.0000.0000.0000.000
146A367ASN00.014-0.0056.2715.9245.9240.0000.0000.0000.000
147A368GLU-1-0.906-0.9666.69334.21334.2130.0000.0000.0000.000
148A369LEU0-0.093-0.0218.5190.5120.5120.0000.0000.0000.000
149A370ILE00.0350.0092.683-2.654-0.4811.301-1.157-2.3180.010
150A371LEU0-0.063-0.0254.6406.3426.635-0.001-0.010-0.2820.000
151A372PHE00.0030.0026.437-2.400-2.4000.0000.0000.0000.000
152A373GLN00.0250.0196.421-2.888-2.8880.0000.0000.0000.000
153A374LYS10.8230.9282.257-92.697-93.6659.748-3.978-4.8020.051
154A375GLY00.0170.0216.380-2.129-2.1290.0000.0000.0000.000
155A376GLN0-0.074-0.0346.7052.5482.5480.0000.0000.0000.000
156A377THR0-0.013-0.0089.160-2.419-2.4190.0000.0000.0000.000
157A378ASN00.0490.00911.8040.7320.7320.0000.0000.0000.000
158A379THR0-0.070-0.03614.311-1.419-1.4190.0000.0000.0000.000
159A380PRO00.0210.02713.8291.3571.3570.0000.0000.0000.000
160A381PRO00.0370.03311.656-1.260-1.2600.0000.0000.0000.000
161A382PRO0-0.024-0.01114.747-1.027-1.0270.0000.0000.0000.000
162A383PHE00.047-0.01317.0030.2300.2300.0000.0000.0000.000
163A384GLU-1-0.971-0.97118.95411.72511.7250.0000.0000.0000.000
164A385ILE0-0.031-0.02222.6240.0960.0960.0000.0000.0000.000
165A386PHE0-0.008-0.01025.248-0.433-0.4330.0000.0000.0000.000
166A387PHE00.0280.00428.352-0.024-0.0240.0000.0000.0000.000
167A388CYS0-0.075-0.04131.835-0.214-0.2140.0000.0000.0000.000
168A389PHE00.027-0.00934.274-0.017-0.0170.0000.0000.0000.000
169A390GLY00.028-0.00838.111-0.156-0.1560.0000.0000.0000.000
170A391GLU-1-0.933-0.96939.4297.5237.5230.0000.0000.0000.000
171A392GLU-1-0.924-0.94937.9208.2358.2350.0000.0000.0000.000
172A393TRP00.007-0.00830.051-0.295-0.2950.0000.0000.0000.000
173A394PRO00.0750.03730.2220.0250.0250.0000.0000.0000.000
174A395ASP-1-0.800-0.89433.0278.0618.0610.0000.0000.0000.000
175A396ARG10.9770.98835.509-7.808-7.8080.0000.0000.0000.000
176A397LYS10.8470.91137.729-7.778-7.7780.0000.0000.0000.000
177A398PRO00.0350.02836.7390.1670.1670.0000.0000.0000.000
178A399ARG11.0651.00729.063-10.806-10.8060.0000.0000.0000.000
179A400GLU-1-0.887-0.93136.0208.8778.8770.0000.0000.0000.000
180A401LYS10.8660.91838.646-7.573-7.5730.0000.0000.0000.000
181A402LYS10.8280.93936.883-8.674-8.6740.0000.0000.0000.000
182A403LEU0-0.018-0.00839.879-0.005-0.0050.0000.0000.0000.000
183A404ILE00.0240.00938.000-0.037-0.0370.0000.0000.0000.000
184A405THR0-0.043-0.01233.8740.1850.1850.0000.0000.0000.000
185A406VAL00.0100.00131.038-0.175-0.1750.0000.0000.0000.000
186A407GLN0-0.0170.00626.469-0.174-0.1740.0000.0000.0000.000
187A408VAL0-0.013-0.01125.149-0.256-0.2560.0000.0000.0000.000
188A409VAL00.0140.00221.3620.4020.4020.0000.0000.0000.000
189A410PRO00.0510.02419.068-0.453-0.4530.0000.0000.0000.000
190A411VAL00.0320.02019.4530.7170.7170.0000.0000.0000.000
191A412ALA00.0130.01216.3600.4180.4180.0000.0000.0000.000
192A413ALA00.0050.00114.9560.9760.9760.0000.0000.0000.000
193A414ARG10.8450.90715.220-12.547-12.5470.0000.0000.0000.000
194A415LEU00.0340.00716.5270.2820.2820.0000.0000.0000.000
195A416LEU0-0.0010.00910.2460.5440.5440.0000.0000.0000.000
196A417LEU00.0140.00612.0701.1871.1870.0000.0000.0000.000
197A418GLU-1-0.949-0.98313.63315.63715.6370.0000.0000.0000.000
198A419MET0-0.027-0.01011.4960.3270.3270.0000.0000.0000.000
199A420PHE00.011-0.0205.2210.7560.7560.0000.0000.0000.000
200A421SER0-0.041-0.01610.6380.5380.5380.0000.0000.0000.000
201A422GLY0-0.070-0.02213.592-0.639-0.6390.0000.0000.0000.000
202A423GLU-1-0.978-0.97210.37123.58923.5890.0000.0000.0000.000
203A424LEU0-0.009-0.00711.4591.3041.3040.0000.0000.0000.000
204A425SER00.0020.00910.1130.3550.3550.0000.0000.0000.000
205A426TRP00.001-0.01011.823-1.867-1.8670.0000.0000.0000.000
206A427SER0-0.0060.00511.954-0.390-0.3900.0000.0000.0000.000
207A428ALA0-0.061-0.03511.279-1.081-1.0810.0000.0000.0000.000
208A429ASP-1-0.891-0.95013.22618.32218.3220.0000.0000.0000.000
209A430ASP-1-0.968-0.98414.52618.86418.8640.0000.0000.0000.000
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211A432ARG10.9020.95119.723-15.014-15.0140.0000.0000.0000.000
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