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: 3QKRL

Calculation Name: 1EL6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EL6

Chain ID: A

ChEMBL ID:

UniProt ID: P10929

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889301.049817
FMO2-HF: Nuclear repulsion 1811120.030114
FMO2-HF: Total energy -78181.019703
FMO2-MP2: Total energy -78413.080636


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:12:SER)


Summations of interaction energy for fragment #1(A:12:SER)
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.
-30.396-27.48916.97-9.147-10.731-0.009
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.050
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].
3A14LEU00.0780.0203.805-1.2701.037-0.022-1.290-0.9960.005
4A15ALA00.0480.0435.4420.5320.5320.0000.0000.0000.000
5A16ASP-1-0.801-0.9162.332-4.697-2.3114.357-3.145-3.598-0.038
6A17PHE0-0.083-0.0482.464-0.9930.5400.861-0.907-1.487-0.004
7A18LEU0-0.0130.0156.5500.1740.1740.0000.0000.0000.000
8A19GLY00.0480.0249.5340.1480.1480.0000.0000.0000.000
9A20PHE0-0.017-0.00512.548-0.061-0.0610.0000.0000.0000.000
10A21ARG10.9500.96914.6680.2050.2050.0000.0000.0000.000
11A22PRO00.0310.02417.599-0.007-0.0070.0000.0000.0000.000
12A23LYS10.8040.90819.589-0.056-0.0560.0000.0000.0000.000
13A24THR00.037-0.00123.0670.0170.0170.0000.0000.0000.000
14A25GLY0-0.014-0.01725.784-0.005-0.0050.0000.0000.0000.000
15A26ASP-1-0.807-0.88021.5980.0790.0790.0000.0000.0000.000
16A27ILE00.0060.01023.5040.0140.0140.0000.0000.0000.000
17A28ASP-1-0.851-0.94022.4120.0880.0880.0000.0000.0000.000
18A29VAL00.0060.02617.4800.0090.0090.0000.0000.0000.000
19A30MET00.013-0.00620.3980.0070.0070.0000.0000.0000.000
20A31ASN0-0.047-0.01822.814-0.011-0.0110.0000.0000.0000.000
21A32ARG10.8950.94422.541-0.274-0.2740.0000.0000.0000.000
22A33GLN0-0.025-0.00817.4280.0230.0230.0000.0000.0000.000
23A34SER0-0.025-0.01819.651-0.006-0.0060.0000.0000.0000.000
24A35VAL00.0130.02116.9440.0370.0370.0000.0000.0000.000
25A36GLY00.004-0.00813.820-0.060-0.0600.0000.0000.0000.000
26A37SER0-0.096-0.05413.698-0.015-0.0150.0000.0000.0000.000
27A38VAL0-0.0130.01210.7910.0570.0570.0000.0000.0000.000
28A39THR00.0160.0069.4520.1250.1250.0000.0000.0000.000
29A40ILE00.042-0.00310.3030.1050.1050.0000.0000.0000.000
30A41SER00.0220.0096.0370.2780.2780.0000.0000.0000.000
31A42GLN00.0410.0215.6191.0901.0900.0000.0000.0000.000
32A43LEU00.0130.0227.1110.1010.1010.0000.0000.0000.000
33A44ALA0-0.047-0.0207.911-0.131-0.1310.0000.0000.0000.000
34A45LYS10.8240.9161.860-24.379-27.69811.774-3.805-4.6500.028
35A46GLY00.0020.0086.020-0.785-0.7850.0000.0000.0000.000
36A47PHE0-0.030-0.0187.444-0.454-0.4540.0000.0000.0000.000
37A48TYR00.004-0.0269.3490.2030.2030.0000.0000.0000.000
38A49GLU-1-0.943-0.94911.820-0.141-0.1410.0000.0000.0000.000
39A50PRO0-0.007-0.00311.8180.0480.0480.0000.0000.0000.000
40A51ASN0-0.020-0.0298.906-0.118-0.1180.0000.0000.0000.000
41A52ILE00.020-0.0059.7410.1040.1040.0000.0000.0000.000
42A53GLU-1-0.882-0.9255.366-0.286-0.2860.0000.0000.0000.000
43A54SER0-0.024-0.0148.4220.2100.2100.0000.0000.0000.000
44A55ALA00.0450.01710.6280.0310.0310.0000.0000.0000.000
45A56ILE0-0.028-0.01610.6570.0320.0320.0000.0000.0000.000
46A57ASN0-0.055-0.0498.5520.1220.1220.0000.0000.0000.000
47A58ASP-1-0.810-0.90512.7140.3320.3320.0000.0000.0000.000
48A59VAL0-0.008-0.01115.776-0.005-0.0050.0000.0000.0000.000
49A60HIS0-0.038-0.00113.3990.0120.0120.0000.0000.0000.000
50A61ASN00.004-0.01215.1160.0050.0050.0000.0000.0000.000
51A62PHE0-0.027-0.00118.478-0.010-0.0100.0000.0000.0000.000
52A63SER0-0.061-0.04319.632-0.016-0.0160.0000.0000.0000.000
53A64ILE0-0.0360.00019.271-0.020-0.0200.0000.0000.0000.000
54A65LYS10.8850.93922.284-0.096-0.0960.0000.0000.0000.000
55A66ASP-1-0.837-0.90625.0610.2240.2240.0000.0000.0000.000
56A67VAL0-0.028-0.01425.746-0.022-0.0220.0000.0000.0000.000
57A68GLY00.0270.01728.1800.0080.0080.0000.0000.0000.000
58A69THR0-0.061-0.04029.141-0.010-0.0100.0000.0000.0000.000
59A70ILE0-0.009-0.01231.595-0.008-0.0080.0000.0000.0000.000
60A71ILE0-0.0010.01129.461-0.002-0.0020.0000.0000.0000.000
61A72THR0-0.018-0.01034.035-0.001-0.0010.0000.0000.0000.000
62A73ASN00.0000.01135.472-0.005-0.0050.0000.0000.0000.000
63A74LYS10.9760.97538.586-0.004-0.0040.0000.0000.0000.000
64A75THR0-0.011-0.00237.9250.0000.0000.0000.0000.0000.000
65A76GLY00.0380.02939.795-0.002-0.0020.0000.0000.0000.000
66A77VAL0-0.031-0.01534.6680.0000.0000.0000.0000.0000.000
67A78SER00.000-0.02532.7080.0050.0050.0000.0000.0000.000
68A79PRO0-0.022-0.02430.004-0.010-0.0100.0000.0000.0000.000
69A80GLU-1-0.801-0.86528.1250.0310.0310.0000.0000.0000.000
70A81GLY0-0.0120.01825.923-0.009-0.0090.0000.0000.0000.000
71A82VAL0-0.032-0.02227.0050.0080.0080.0000.0000.0000.000
72A83SER00.0370.01624.640-0.005-0.0050.0000.0000.0000.000
73A84GLN00.0020.00626.0970.0020.0020.0000.0000.0000.000
74A85THR0-0.041-0.02527.8230.0000.0000.0000.0000.0000.000
75A86ASP-1-0.732-0.82028.319-0.182-0.1820.0000.0000.0000.000
76A87TYR00.010-0.00831.3870.0090.0090.0000.0000.0000.000
77A88TRP0-0.047-0.02625.022-0.011-0.0110.0000.0000.0000.000
78A89ALA00.0210.00432.6030.0110.0110.0000.0000.0000.000
79A90PHE00.026-0.00130.794-0.014-0.0140.0000.0000.0000.000
80A91SER0-0.015-0.01436.4550.0110.0110.0000.0000.0000.000
81A92GLY00.0350.02738.563-0.008-0.0080.0000.0000.0000.000
82A93THR0-0.017-0.02640.5550.0050.0050.0000.0000.0000.000
83A94VAL0-0.0310.01335.172-0.006-0.0060.0000.0000.0000.000
84A95THR0-0.046-0.05537.5330.0110.0110.0000.0000.0000.000
85A96ASP-1-0.800-0.94535.404-0.210-0.2100.0000.0000.0000.000
86A97ASP-1-0.941-0.94438.233-0.150-0.1500.0000.0000.0000.000
87A98SER0-0.057-0.01337.6750.0040.0040.0000.0000.0000.000
88A99LEU0-0.076-0.04335.3250.0020.0020.0000.0000.0000.000
89A100PRO0-0.0020.00939.9780.0050.0050.0000.0000.0000.000
90A101PRO00.000-0.01441.413-0.005-0.0050.0000.0000.0000.000
91A102GLY00.0210.02540.9830.0050.0050.0000.0000.0000.000
92A103SER0-0.031-0.02537.5740.0010.0010.0000.0000.0000.000
93A104PRO0-0.040-0.02333.629-0.004-0.0040.0000.0000.0000.000
94A105ILE00.003-0.00131.975-0.007-0.0070.0000.0000.0000.000
95A106THR0-0.024-0.01325.5730.0030.0030.0000.0000.0000.000
96A107VAL0-0.010-0.00428.896-0.011-0.0110.0000.0000.0000.000
97A108LEU00.0110.01222.847-0.001-0.0010.0000.0000.0000.000
98A109VAL00.0200.01726.0330.0090.0090.0000.0000.0000.000
99A110PHE00.015-0.00324.531-0.007-0.0070.0000.0000.0000.000
100A111GLY0-0.0080.00021.223-0.022-0.0220.0000.0000.0000.000
101A112LEU0-0.016-0.00221.134-0.026-0.0260.0000.0000.0000.000
102A113PRO00.002-0.00921.4330.0180.0180.0000.0000.0000.000
103A114VAL00.0040.01324.4440.0220.0220.0000.0000.0000.000
104A115SER0-0.027-0.00128.1000.0000.0000.0000.0000.0000.000
105A116ALA00.014-0.00830.2620.0150.0150.0000.0000.0000.000
106A117THR00.0490.01833.552-0.003-0.0030.0000.0000.0000.000
107A118THR00.0120.00536.7580.0060.0060.0000.0000.0000.000
108A119GLY00.0070.00238.9360.0070.0070.0000.0000.0000.000
109A120MET0-0.078-0.01536.8730.0010.0010.0000.0000.0000.000
110A121THR0-0.001-0.03040.270-0.005-0.0050.0000.0000.0000.000
111A122ALA00.0430.01638.419-0.004-0.0040.0000.0000.0000.000
112A123ILE00.0100.00137.998-0.004-0.0040.0000.0000.0000.000
113A124GLU-1-0.820-0.88538.781-0.108-0.1080.0000.0000.0000.000
114A125PHE00.0200.00131.008-0.002-0.0020.0000.0000.0000.000
115A126VAL00.0300.02234.028-0.007-0.0070.0000.0000.0000.000
116A127ALA0-0.019-0.01733.9200.0000.0000.0000.0000.0000.000
117A128LYS10.9000.95431.9530.1320.1320.0000.0000.0000.000
118A129VAL00.0140.00729.101-0.010-0.0100.0000.0000.0000.000
119A130ARG10.8420.90629.1510.0980.0980.0000.0000.0000.000
120A131VAL0-0.041-0.01428.3040.0060.0060.0000.0000.0000.000
121A132ALA00.0550.03625.408-0.001-0.0010.0000.0000.0000.000
122A133LEU0-0.003-0.00124.597-0.011-0.0110.0000.0000.0000.000
123A134GLN0-0.010-0.00125.1090.0060.0060.0000.0000.0000.000
124A135GLU-1-0.919-0.95222.877-0.183-0.1830.0000.0000.0000.000
125A136ALA0-0.0120.00520.587-0.006-0.0060.0000.0000.0000.000
126A137ILE0-0.029-0.01320.5630.0060.0060.0000.0000.0000.000
127A138ALA0-0.032-0.01122.0340.0190.0190.0000.0000.0000.000
128A139SER0-0.087-0.04417.2740.0090.0090.0000.0000.0000.000
129A140PHE0-0.036-0.02016.914-0.005-0.0050.0000.0000.0000.000
130A141THR00.0110.01015.905-0.044-0.0440.0000.0000.0000.000
131A142ALA00.0060.00517.521-0.002-0.0020.0000.0000.0000.000
132A143ILE0-0.028-0.03019.2190.0230.0230.0000.0000.0000.000
133A144ASN0-0.014-0.00522.5380.0240.0240.0000.0000.0000.000
134A145SER0-0.002-0.01724.4570.0160.0160.0000.0000.0000.000
135A146TYR0-0.025-0.02127.839-0.013-0.0130.0000.0000.0000.000
136A147LYS10.8270.91130.4480.0850.0850.0000.0000.0000.000
137A148ASP-1-0.776-0.85734.241-0.101-0.1010.0000.0000.0000.000
138A149HIS00.0220.01736.8960.0080.0080.0000.0000.0000.000
139A150PRO0-0.031-0.01638.9870.0030.0030.0000.0000.0000.000
140A151THR0-0.016-0.02842.2850.0040.0040.0000.0000.0000.000
141A152ASP-1-0.836-0.88641.343-0.101-0.1010.0000.0000.0000.000
142A153GLY00.0170.00040.474-0.003-0.0030.0000.0000.0000.000
143A154SER0-0.106-0.07438.857-0.006-0.0060.0000.0000.0000.000
144A155LYS10.8230.88836.3170.1040.1040.0000.0000.0000.000
145A156LEU0-0.022-0.00331.9220.0070.0070.0000.0000.0000.000
146A157GLU-1-0.808-0.88333.315-0.088-0.0880.0000.0000.0000.000
147A158VAL0-0.003-0.01126.8210.0030.0030.0000.0000.0000.000
148A159THR00.0090.01427.0730.0040.0040.0000.0000.0000.000
149A160TYR0-0.026-0.03522.475-0.012-0.0120.0000.0000.0000.000
150A161LEU0-0.021-0.00818.9020.0220.0220.0000.0000.0000.000
151A162ASP-1-0.852-0.89818.722-0.208-0.2080.0000.0000.0000.000
152A163ASN0-0.058-0.04220.682-0.005-0.0050.0000.0000.0000.000
153A164GLN0-0.046-0.02616.585-0.020-0.0200.0000.0000.0000.000
154A165LYN0-0.0140.02722.4300.0090.0090.0000.0000.0000.000
155A166HIS10.7790.86720.1750.2340.2340.0000.0000.0000.000
156A167VAL00.0600.04424.8900.0190.0190.0000.0000.0000.000
157A168LEU0-0.029-0.01624.237-0.027-0.0270.0000.0000.0000.000
158A169SER0-0.027-0.01327.3470.0180.0180.0000.0000.0000.000
159A170THR00.019-0.00329.410-0.008-0.0080.0000.0000.0000.000
160A171TYR0-0.070-0.03327.581-0.010-0.0100.0000.0000.0000.000
161A172SER00.0380.01932.2900.0110.0110.0000.0000.0000.000
162A173THR0-0.038-0.01129.688-0.010-0.0100.0000.0000.0000.000
163A174TYR00.0540.02930.0930.0010.0010.0000.0000.0000.000
164A175GLY00.0150.02534.9560.0100.0100.0000.0000.0000.000
165A176ILE0-0.044-0.00534.1730.0100.0100.0000.0000.0000.000
166A177THR0-0.032-0.02834.466-0.011-0.0110.0000.0000.0000.000
167A178ILE0-0.022-0.00829.8500.0100.0100.0000.0000.0000.000
168A179SER00.003-0.01232.517-0.006-0.0060.0000.0000.0000.000
169A180GLN0-0.009-0.02527.894-0.001-0.0010.0000.0000.0000.000
170A181GLU-1-0.848-0.90031.999-0.118-0.1180.0000.0000.0000.000
171A182ILE0-0.013-0.00929.9270.0030.0030.0000.0000.0000.000
172A183ILE0-0.042-0.01032.8940.0090.0090.0000.0000.0000.000
173A184SER0-0.011-0.01432.7460.0120.0120.0000.0000.0000.000
174A185GLU-1-0.894-0.93730.724-0.139-0.1390.0000.0000.0000.000
175A186SER0-0.014-0.02626.1540.0090.0090.0000.0000.0000.000
176A187LYS10.8020.88927.5810.0260.0260.0000.0000.0000.000
177A188PRO00.0510.01625.4270.0050.0050.0000.0000.0000.000
178A189GLY00.0330.01324.7730.0090.0090.0000.0000.0000.000
179A190TYR00.0180.00722.334-0.002-0.0020.0000.0000.0000.000
180A191GLY00.0050.00123.5930.0050.0050.0000.0000.0000.000
181A192THR00.0170.01825.280-0.009-0.0090.0000.0000.0000.000
182A193TRP0-0.058-0.05127.3540.0160.0160.0000.0000.0000.000
183A194ASN00.0260.01831.668-0.012-0.0120.0000.0000.0000.000
184A195LEU0-0.043-0.00935.2720.0020.0020.0000.0000.0000.000
185A196LEU0-0.006-0.00637.8260.0000.0000.0000.0000.0000.000
186A197GLY00.0270.01540.337-0.001-0.0010.0000.0000.0000.000
187A198ALA0-0.040-0.02842.490-0.001-0.0010.0000.0000.0000.000
188A199GLN00.0190.02444.6250.0040.0040.0000.0000.0000.000
189A200THR00.004-0.00546.566-0.002-0.0020.0000.0000.0000.000
190A201VAL0-0.006-0.01046.9940.0020.0020.0000.0000.0000.000
191A202THR00.0100.00949.878-0.003-0.0030.0000.0000.0000.000
192A203LEU0-0.033-0.01147.0230.0020.0020.0000.0000.0000.000
193A204ASP-1-0.863-0.93950.9800.0260.0260.0000.0000.0000.000
194A205ASN0-0.047-0.01353.259-0.001-0.0010.0000.0000.0000.000
195A206GLN0-0.027-0.01250.387-0.002-0.0020.0000.0000.0000.000
196A207GLN00.0240.01055.4250.0020.0020.0000.0000.0000.000
197A208THR0-0.018-0.01353.6650.0010.0010.0000.0000.0000.000
198A209PRO00.0140.01352.7130.0010.0010.0000.0000.0000.000
199A210THR0-0.023-0.01646.292-0.004-0.0040.0000.0000.0000.000
200A211VAL0-0.0120.00346.1670.0030.0030.0000.0000.0000.000
201A212PHE0-0.024-0.01742.159-0.003-0.0030.0000.0000.0000.000
202A213TYR00.0300.01740.3300.0030.0030.0000.0000.0000.000
203A214HIS10.8380.88838.406-0.046-0.0460.0000.0000.0000.000
204A215PHE00.0560.02634.135-0.001-0.0010.0000.0000.0000.000
205A216GLU-1-0.880-0.94333.4580.0990.0990.0000.0000.0000.000
206A217ARG10.8430.92122.716-0.174-0.1740.0000.0000.0000.000
207A218THR00.0490.00130.4330.0100.0100.0000.0000.0000.000
208A219ALA0-0.0020.03224.8900.0240.0240.0000.0000.0000.000