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: K38M3

Calculation Name: 2D2S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D2S

Chain ID: A

ChEMBL ID:

UniProt ID: P38261

Base Structure: X-ray

Registration Date: 2023-03-13

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2478617.550217
FMO2-HF: Nuclear repulsion 2390473.000902
FMO2-HF: Total energy -88144.549316
FMO2-MP2: Total energy -88404.423141


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:525:ASP)


Summations of interaction energy for fragment #1(A:525:ASP)
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.
55.43758.523-0.022-1.686-1.3780.005
Interaction energy analysis for fragmet #1(A:525:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.892 / q_NPA : -0.943
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].
3A527SER0-0.0020.0063.658-0.7362.350-0.022-1.686-1.3780.005
4A528SER00.037-0.0045.875-1.227-1.2270.0000.0000.0000.000
5A529THR00.0740.0299.443-0.400-0.4000.0000.0000.0000.000
6A530ALA00.0160.0207.731-1.301-1.3010.0000.0000.0000.000
7A531GLN0-0.0140.0069.716-1.161-1.1610.0000.0000.0000.000
8A532ARG10.9450.96110.799-17.561-17.5610.0000.0000.0000.000
9A533LEU00.021-0.00112.389-0.678-0.6780.0000.0000.0000.000
10A534LYS10.9950.9968.627-24.970-24.9700.0000.0000.0000.000
11A535PHE00.0220.00113.270-0.487-0.4870.0000.0000.0000.000
12A536LEU0-0.0220.01016.449-0.812-0.8120.0000.0000.0000.000
13A537ASP-1-0.887-0.92315.59714.91514.9150.0000.0000.0000.000
14A538GLU-1-0.941-0.95615.72316.67816.6780.0000.0000.0000.000
15A539GLY00.029-0.00118.822-0.701-0.7010.0000.0000.0000.000
16A540VAL00.021-0.01720.859-0.655-0.6550.0000.0000.0000.000
17A541GLU-1-0.847-0.91619.28713.45013.4500.0000.0000.0000.000
18A542GLU-1-0.944-0.96423.01911.05711.0570.0000.0000.0000.000
19A543ILE0-0.0060.00325.015-0.571-0.5710.0000.0000.0000.000
20A544ASP-1-0.854-0.91926.11110.32610.3260.0000.0000.0000.000
21A545ILE0-0.083-0.05025.912-0.439-0.4390.0000.0000.0000.000
22A546GLU-1-0.811-0.93829.2759.1779.1770.0000.0000.0000.000
23A547LEU00.0020.01031.194-0.420-0.4200.0000.0000.0000.000
24A548ALA0-0.078-0.02131.826-0.328-0.3280.0000.0000.0000.000
25A549ARG10.7990.90729.758-9.965-9.9650.0000.0000.0000.000
26A550LEU0-0.031-0.02035.593-0.174-0.1740.0000.0000.0000.000
27A551ARG10.8970.97532.659-9.232-9.2320.0000.0000.0000.000
28A552PHE00.031-0.01234.3720.2200.2200.0000.0000.0000.000
29A553GLU-1-0.907-0.94035.2998.2778.2770.0000.0000.0000.000
30A554SER00.0010.00531.1240.2190.2190.0000.0000.0000.000
31A555ALA0-0.0140.00130.7230.2910.2910.0000.0000.0000.000
32A556VAL00.0150.00030.4660.2670.2670.0000.0000.0000.000
33A557GLU-1-0.950-0.97831.2379.2849.2840.0000.0000.0000.000
34A558THR00.007-0.00325.5740.3520.3520.0000.0000.0000.000
35A559LEU0-0.040-0.01226.8990.3420.3420.0000.0000.0000.000
36A560LEU00.0140.00727.2970.1610.1610.0000.0000.0000.000
37A561ASP-1-0.912-0.93024.70912.05312.0530.0000.0000.0000.000
38A562ILE0-0.041-0.03821.4600.4770.4770.0000.0000.0000.000
39A563GLU-1-0.833-0.94323.01410.78910.7890.0000.0000.0000.000
40A564SER0-0.026-0.01125.612-0.107-0.1070.0000.0000.0000.000
41A565GLN0-0.057-0.03020.2010.9950.9950.0000.0000.0000.000
42A566LEU0-0.074-0.03519.5550.6130.6130.0000.0000.0000.000
43A567GLU-1-0.942-0.96121.68810.78910.7890.0000.0000.0000.000
44A568ASP-1-0.893-0.92721.33212.47412.4740.0000.0000.0000.000
45A569LEU0-0.163-0.08516.0650.6420.6420.0000.0000.0000.000
46A570SER0-0.088-0.04017.9700.4360.4360.0000.0000.0000.000
47A578LEU00.0250.00913.6460.3570.3570.0000.0000.0000.000
48A579MET00.0140.00312.896-0.494-0.4940.0000.0000.0000.000
49A580LEU00.0230.00910.562-0.515-0.5150.0000.0000.0000.000
50A581LEU00.0710.04413.972-0.410-0.4100.0000.0000.0000.000
51A582ASN00.008-0.01116.909-0.169-0.1690.0000.0000.0000.000
52A583LEU0-0.012-0.00814.792-0.547-0.5470.0000.0000.0000.000
53A584ILE00.0430.01615.077-0.401-0.4010.0000.0000.0000.000
54A585SER0-0.001-0.00818.905-0.682-0.6820.0000.0000.0000.000
55A586LEU0-0.0050.00121.649-0.517-0.5170.0000.0000.0000.000
56A587LYS10.6990.82717.995-14.858-14.8580.0000.0000.0000.000
57A588ILE00.0730.02721.923-0.321-0.3210.0000.0000.0000.000
58A589GLU-1-0.867-0.92324.9679.4329.4320.0000.0000.0000.000
59A590GLN0-0.084-0.04025.662-0.674-0.6740.0000.0000.0000.000
60A591ARG10.8500.92223.014-11.809-11.8090.0000.0000.0000.000
61A592ARG10.8900.96628.426-9.652-9.6520.0000.0000.0000.000
62A593GLU-1-0.970-0.99730.5168.0528.0520.0000.0000.0000.000
63A594ALA00.010-0.00331.166-0.286-0.2860.0000.0000.0000.000
64A595ILE0-0.005-0.00730.325-0.297-0.2970.0000.0000.0000.000
65A596SER00.0450.02834.121-0.324-0.3240.0000.0000.0000.000
66A597SER0-0.0390.00336.459-0.347-0.3470.0000.0000.0000.000
67A598LYS10.9580.97435.380-8.455-8.4550.0000.0000.0000.000
68A599LEU00.0540.03337.039-0.235-0.2350.0000.0000.0000.000
69A600SER00.000-0.01540.180-0.252-0.2520.0000.0000.0000.000
70A601GLN0-0.042-0.01540.525-0.176-0.1760.0000.0000.0000.000
71A602SER0-0.038-0.01241.881-0.212-0.2120.0000.0000.0000.000
72A603ILE00.0110.01143.596-0.168-0.1680.0000.0000.0000.000
73A604LEU0-0.046-0.04845.957-0.170-0.1700.0000.0000.0000.000
74A605SER0-0.109-0.04746.722-0.122-0.1220.0000.0000.0000.000
75A606SER0-0.0300.00648.062-0.052-0.0520.0000.0000.0000.000
76A607ASN0-0.019-0.00649.588-0.132-0.1320.0000.0000.0000.000
77A608GLU-1-0.937-0.97450.3116.0116.0110.0000.0000.0000.000
78A609ILE00.0300.00451.1940.1030.1030.0000.0000.0000.000
79A610VAL00.0590.02147.7880.1100.1100.0000.0000.0000.000
80A611HIS00.0190.00845.6720.0530.0530.0000.0000.0000.000
81A612LEU00.0140.01446.2210.1320.1320.0000.0000.0000.000
82A613LYS10.8370.95647.113-6.296-6.2960.0000.0000.0000.000
83A614SER00.0540.03042.7040.1180.1180.0000.0000.0000.000
84A615GLY0-0.0090.01442.0570.1620.1620.0000.0000.0000.000
85A616THR00.010-0.04842.2140.1100.1100.0000.0000.0000.000
86A617GLU-1-0.854-0.94542.6737.0557.0550.0000.0000.0000.000
87A618ASN0-0.035-0.01537.9690.3130.3130.0000.0000.0000.000
88A619MET00.0100.00938.1620.2450.2450.0000.0000.0000.000
89A620ILE0-0.002-0.01039.5820.0680.0680.0000.0000.0000.000
90A621LYS10.9100.96535.876-8.149-8.1490.0000.0000.0000.000
91A622LEU00.0180.00733.4260.2020.2020.0000.0000.0000.000
92A623GLY0-0.007-0.00635.4180.1810.1810.0000.0000.0000.000
93A624LEU0-0.060-0.02536.495-0.043-0.0430.0000.0000.0000.000
94A625PRO00.0420.00740.342-0.154-0.1540.0000.0000.0000.000
95A626GLU-1-0.914-0.96443.6916.4266.4260.0000.0000.0000.000
96A627GLN00.0450.03540.522-0.070-0.0700.0000.0000.0000.000
97A628ALA00.0190.00643.261-0.081-0.0810.0000.0000.0000.000
98A629LEU0-0.033-0.02544.923-0.123-0.1230.0000.0000.0000.000
99A630ASP-1-0.967-0.99147.4516.0846.0840.0000.0000.0000.000
100A631LEU0-0.0200.00043.749-0.110-0.1100.0000.0000.0000.000
101A632PHE00.003-0.00848.135-0.149-0.1490.0000.0000.0000.000
102A633LEU00.015-0.00349.721-0.127-0.1270.0000.0000.0000.000
103A634GLN00.0330.03649.685-0.188-0.1880.0000.0000.0000.000
104A635ASN0-0.0120.01450.543-0.171-0.1710.0000.0000.0000.000
105A636ARG10.8850.94652.725-5.749-5.7490.0000.0000.0000.000
106A637SER00.020-0.00355.699-0.132-0.1320.0000.0000.0000.000
107A638ASN00.0230.00553.209-0.175-0.1750.0000.0000.0000.000
108A639PHE0-0.0060.00156.517-0.102-0.1020.0000.0000.0000.000
109A640ILE0-0.047-0.03858.107-0.113-0.1130.0000.0000.0000.000
110A641GLN0-0.027-0.01359.695-0.140-0.1400.0000.0000.0000.000
111A642ASP-1-0.871-0.93557.8155.2195.2190.0000.0000.0000.000
112A643LEU0-0.058-0.03861.079-0.092-0.0920.0000.0000.0000.000
113A644ILE0-0.049-0.03563.716-0.101-0.1010.0000.0000.0000.000
114A645LEU0-0.010-0.00562.788-0.090-0.0900.0000.0000.0000.000
115A646GLN0-0.0650.00263.733-0.112-0.1120.0000.0000.0000.000
116A647ILE0-0.093-0.04866.909-0.042-0.0420.0000.0000.0000.000
117A648GLY0-0.018-0.00970.553-0.025-0.0250.0000.0000.0000.000
118A649SER0-0.030-0.03673.7000.0060.0060.0000.0000.0000.000
119A650VAL0-0.032-0.00674.544-0.002-0.0020.0000.0000.0000.000
120A651ASP-1-0.916-0.92976.1994.1064.1060.0000.0000.0000.000
121A652ASN00.030-0.02278.565-0.074-0.0740.0000.0000.0000.000
122A653PRO00.0840.04479.3110.0570.0570.0000.0000.0000.000
123A654THR00.0140.00079.1250.0520.0520.0000.0000.0000.000
124A655ASN0-0.056-0.03677.886-0.003-0.0030.0000.0000.0000.000
125A656TYR00.0560.04671.2140.0480.0480.0000.0000.0000.000
126A657LEU00.0640.02773.9590.0640.0640.0000.0000.0000.000
127A658THR0-0.025-0.01473.8430.0490.0490.0000.0000.0000.000
128A659GLN00.0110.02069.314-0.012-0.0120.0000.0000.0000.000
129A660LEU00.013-0.00869.7340.0720.0720.0000.0000.0000.000
130A661ALA0-0.004-0.00268.9480.0730.0730.0000.0000.0000.000
131A662VAL0-0.001-0.01468.1420.0620.0620.0000.0000.0000.000
132A663ILE00.0210.02964.5610.0660.0660.0000.0000.0000.000
133A664ARG10.9140.96163.324-4.761-4.7610.0000.0000.0000.000
134A665PHE00.0300.00764.1680.0680.0680.0000.0000.0000.000
135A666GLN0-0.0020.00864.8790.0490.0490.0000.0000.0000.000
136A667THR0-0.080-0.04759.0870.0870.0870.0000.0000.0000.000
137A668ILE0-0.0090.00459.9920.0940.0940.0000.0000.0000.000
138A669LYS10.9170.96360.724-4.774-4.7740.0000.0000.0000.000
139A670LYS10.9740.99558.124-5.220-5.2200.0000.0000.0000.000
140A671THR0-0.042-0.02355.1470.1180.1180.0000.0000.0000.000
141A672VAL00.0020.01155.8620.1010.1010.0000.0000.0000.000
142A673GLU-1-0.878-0.97156.9455.1725.1720.0000.0000.0000.000
143A674ASP-1-0.889-0.94853.2895.7795.7790.0000.0000.0000.000
144A675PHE0-0.030-0.01551.6190.1290.1290.0000.0000.0000.000
145A676GLN0-0.046-0.02452.5120.0490.0490.0000.0000.0000.000
146A677ASP-1-0.936-0.97551.8986.1686.1680.0000.0000.0000.000
147A678ILE0-0.028-0.00447.1780.1290.1290.0000.0000.0000.000
148A679PHE0-0.0040.01046.9170.1370.1370.0000.0000.0000.000
149A680LYS10.9470.97848.229-6.337-6.3370.0000.0000.0000.000
150A681GLU-1-0.977-1.00146.8356.6906.6900.0000.0000.0000.000
151A682LEU00.0050.02245.1830.1070.1070.0000.0000.0000.000
152A683GLY00.0030.01047.5320.0790.0790.0000.0000.0000.000
153A684ALA0-0.040-0.02949.924-0.085-0.0850.0000.0000.0000.000
154A685LYS11.0070.99548.920-6.223-6.2230.0000.0000.0000.000
155A686ILE00.0930.04846.620-0.099-0.0990.0000.0000.0000.000
156A687SER00.015-0.00750.675-0.049-0.0490.0000.0000.0000.000
157A688SER0-0.086-0.03053.976-0.118-0.1180.0000.0000.0000.000
158A689ILE00.0490.01951.139-0.063-0.0630.0000.0000.0000.000
159A690LEU0-0.0060.00754.305-0.076-0.0760.0000.0000.0000.000
160A691VAL0-0.014-0.02455.482-0.086-0.0860.0000.0000.0000.000
161A692ASP-1-0.872-0.92856.9205.3075.3070.0000.0000.0000.000
162A693TRP00.0420.02656.079-0.079-0.0790.0000.0000.0000.000
163A694CYS0-0.067-0.03258.200-0.101-0.1010.0000.0000.0000.000
164A695SER0-0.034-0.02260.975-0.142-0.1420.0000.0000.0000.000
165A696ASP-1-0.853-0.92659.8045.0375.0370.0000.0000.0000.000
166A697GLU-1-0.838-0.91159.8495.0295.0290.0000.0000.0000.000
167A698VAL0-0.070-0.03363.075-0.098-0.0980.0000.0000.0000.000
168A699ASP-1-0.862-0.94065.3174.6264.6260.0000.0000.0000.000
169A700ASN0-0.102-0.06761.993-0.126-0.1260.0000.0000.0000.000
170A701HIS0-0.017-0.00166.353-0.037-0.0370.0000.0000.0000.000
171A702PHE00.0440.01268.887-0.078-0.0780.0000.0000.0000.000
172A703LYS10.9590.99365.001-4.798-4.7980.0000.0000.0000.000
173A704LEU0-0.038-0.02867.094-0.030-0.0300.0000.0000.0000.000
174A705ILE0-0.049-0.01471.140-0.061-0.0610.0000.0000.0000.000
175A706ASP-1-0.876-0.95873.4644.1624.1620.0000.0000.0000.000
176A707LYS10.8540.93670.636-4.417-4.4170.0000.0000.0000.000
177A708GLN00.1020.04373.997-0.101-0.1010.0000.0000.0000.000
178A709LEU0-0.114-0.04377.220-0.062-0.0620.0000.0000.0000.000
179A710LEU0-0.055-0.03176.507-0.043-0.0430.0000.0000.0000.000
180A711ASN0-0.072-0.05179.919-0.006-0.0060.0000.0000.0000.000
181A712ASP-1-0.873-0.94582.3073.6233.6230.0000.0000.0000.000
182A713GLU-1-0.946-0.96683.7183.7283.7280.0000.0000.0000.000
183A714MET0-0.0470.01781.9530.0130.0130.0000.0000.0000.000
184A715LEU00.0040.01879.2630.0630.0630.0000.0000.0000.000
185A716SER00.0190.00282.112-0.069-0.0690.0000.0000.0000.000
186A717PRO00.0470.00282.6790.0540.0540.0000.0000.0000.000
187A718GLY0-0.049-0.01883.6260.0030.0030.0000.0000.0000.000
188A719SER0-0.001-0.00279.0460.0220.0220.0000.0000.0000.000
189A720ILE00.0170.02078.3670.0600.0600.0000.0000.0000.000
190A721LYS10.9670.97778.595-3.717-3.7170.0000.0000.0000.000
191A722SER0-0.0400.00276.4570.0540.0540.0000.0000.0000.000
192A723SER00.0890.01974.2560.0660.0660.0000.0000.0000.000
193A724ARG10.8800.90173.943-4.010-4.0100.0000.0000.0000.000
194A725LYS10.9861.00574.424-4.137-4.1370.0000.0000.0000.000
195A726GLN0-0.074-0.04169.9150.1020.1020.0000.0000.0000.000
196A727ILE00.0170.01070.2200.0620.0620.0000.0000.0000.000
197A728ASP-1-0.924-0.96770.5124.2654.2650.0000.0000.0000.000
198A729GLY0-0.046-0.03070.4900.0390.0390.0000.0000.0000.000
199A730LEU00.0260.01365.0000.0630.0630.0000.0000.0000.000
200A731LYS10.8710.94966.050-4.343-4.3430.0000.0000.0000.000
201A732ALA0-0.089-0.03366.7910.0290.0290.0000.0000.0000.000
202A733VAL0-0.030-0.00661.3390.0430.0430.0000.0000.0000.000
203A734GLY00.0080.00662.1750.0700.0700.0000.0000.0000.000
204A735LEU0-0.011-0.01261.3970.0110.0110.0000.0000.0000.000
205A736ASP-1-0.884-0.95565.4574.3754.3750.0000.0000.0000.000
206A737PHE00.0630.01563.663-0.004-0.0040.0000.0000.0000.000
207A738VAL0-0.013-0.01369.443-0.039-0.0390.0000.0000.0000.000
208A739TYR00.0340.01266.948-0.046-0.0460.0000.0000.0000.000
209A740LYS10.9280.98566.058-4.768-4.7680.0000.0000.0000.000
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