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: LJG69

Calculation Name: 2D13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D13

Chain ID: A

ChEMBL ID:

UniProt ID: O58996

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2619851.6619
FMO2-HF: Nuclear repulsion 2535560.636212
FMO2-HF: Total energy -84291.025688
FMO2-MP2: Total energy -84542.503432


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-24.072-24.39813.137-5.741-7.0710.033
Interaction energy analysis for fragmet #1(A:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.008
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].
3A4LEU0-0.024-0.0103.361-1.4001.2800.031-1.430-1.2810.000
4A5ALA00.0070.0066.0920.4110.4110.0000.0000.0000.000
5A6ASP-1-0.808-0.8824.2243.6793.889-0.001-0.054-0.1550.000
6A7VAL0-0.030-0.0126.567-0.250-0.2500.0000.0000.0000.000
7A8ALA00.0400.0199.8330.2490.2490.0000.0000.0000.000
8A9VAL0-0.019-0.01812.505-0.136-0.1360.0000.0000.0000.000
9A10LEU00.0340.02315.1400.0430.0430.0000.0000.0000.000
10A11TYR0-0.060-0.05617.298-0.038-0.0380.0000.0000.0000.000
11A12SER00.0460.00919.5900.0160.0160.0000.0000.0000.000
12A13GLY00.0450.02821.557-0.001-0.0010.0000.0000.0000.000
13A14GLY00.0530.02922.740-0.017-0.0170.0000.0000.0000.000
14A15LYS10.8000.86122.7580.0330.0330.0000.0000.0000.000
15A16ASP-1-0.736-0.83322.257-0.050-0.0500.0000.0000.0000.000
16A17SER0-0.018-0.00519.700-0.014-0.0140.0000.0000.0000.000
17A18ASN00.0040.02018.0170.0050.0050.0000.0000.0000.000
18A19TYR0-0.066-0.05617.727-0.040-0.0400.0000.0000.0000.000
19A20ALA00.002-0.00517.372-0.049-0.0490.0000.0000.0000.000
20A21LEU00.0150.01012.038-0.048-0.0480.0000.0000.0000.000
21A22TYR00.024-0.00413.013-0.098-0.0980.0000.0000.0000.000
22A23TRP00.0260.00214.020-0.113-0.1130.0000.0000.0000.000
23A24ALA00.0250.02911.081-0.098-0.0980.0000.0000.0000.000
24A25LEU00.0150.0088.637-0.195-0.1950.0000.0000.0000.000
25A26LYS10.8830.9539.8370.2000.2000.0000.0000.0000.000
26A27SER0-0.054-0.04411.727-0.009-0.0090.0000.0000.0000.000
27A28GLY00.0210.0157.708-0.057-0.0570.0000.0000.0000.000
28A29LEU0-0.034-0.0066.799-0.711-0.7110.0000.0000.0000.000
29A30ARG10.8200.8922.012-23.537-26.84613.108-4.254-5.5460.033
30A31VAL0-0.009-0.0195.3200.7970.890-0.001-0.003-0.0890.000
31A32ARG10.8660.9596.049-2.915-2.9150.0000.0000.0000.000
32A33TYR00.0130.0028.5110.1470.1470.0000.0000.0000.000
33A34LEU0-0.0030.00712.145-0.142-0.1420.0000.0000.0000.000
34A35VAL00.0180.00114.9340.0500.0500.0000.0000.0000.000
35A36SER0-0.067-0.03517.999-0.057-0.0570.0000.0000.0000.000
36A37MET00.0170.01421.2740.0180.0180.0000.0000.0000.000
37A38VAL0-0.047-0.02324.377-0.018-0.0180.0000.0000.0000.000
38A39SER00.0060.00427.8180.0070.0070.0000.0000.0000.000
39A40GLU-1-0.901-0.94031.2660.1030.1030.0000.0000.0000.000
40A41ASN0-0.071-0.02632.767-0.012-0.0120.0000.0000.0000.000
41A51ASN0-0.001-0.01129.5820.0060.0060.0000.0000.0000.000
42A52VAL00.0560.02026.1680.0000.0000.0000.0000.0000.000
43A53GLU-1-0.913-0.93825.2620.1540.1540.0000.0000.0000.000
44A54LEU00.0270.01425.4510.0160.0160.0000.0000.0000.000
45A55THR00.004-0.01521.1090.0130.0130.0000.0000.0000.000
46A56SER00.0070.00120.4950.0290.0290.0000.0000.0000.000
47A57LEU0-0.057-0.02021.1600.0210.0210.0000.0000.0000.000
48A58GLN00.015-0.00119.3220.0210.0210.0000.0000.0000.000
49A59ALA00.0390.02316.233-0.010-0.0100.0000.0000.0000.000
50A60ARG10.9230.97015.652-0.166-0.1660.0000.0000.0000.000
51A61ALA00.0240.01916.9730.0080.0080.0000.0000.0000.000
52A62LEU00.0110.00313.498-0.039-0.0390.0000.0000.0000.000
53A63GLY0-0.0500.00012.433-0.026-0.0260.0000.0000.0000.000
54A64ILE0-0.013-0.0059.8420.1380.1380.0000.0000.0000.000
55A65PRO00.002-0.00110.883-0.117-0.1170.0000.0000.0000.000
56A66ILE0-0.016-0.00913.875-0.016-0.0160.0000.0000.0000.000
57A67ILE00.0230.02415.570-0.013-0.0130.0000.0000.0000.000
58A68LYS10.8700.93318.642-0.271-0.2710.0000.0000.0000.000
59A69GLY00.0350.01622.3180.0200.0200.0000.0000.0000.000
60A70PHE0-0.010-0.01524.870-0.014-0.0140.0000.0000.0000.000
61A71THR0-0.025-0.03628.589-0.001-0.0010.0000.0000.0000.000
62A72LYS10.8630.93231.016-0.126-0.1260.0000.0000.0000.000
63A73GLY00.016-0.00233.8530.0020.0020.0000.0000.0000.000
64A74GLU-1-0.836-0.91135.8670.1020.1020.0000.0000.0000.000
65A75LYS10.8330.89233.287-0.072-0.0720.0000.0000.0000.000
66A76GLU-1-0.821-0.89934.0690.0730.0730.0000.0000.0000.000
67A77LYS10.8340.89930.575-0.162-0.1620.0000.0000.0000.000
68A78GLU-1-0.790-0.88129.5590.1050.1050.0000.0000.0000.000
69A79VAL0-0.023-0.01427.4400.0130.0130.0000.0000.0000.000
70A80GLU-1-0.797-0.87726.5160.1620.1620.0000.0000.0000.000
71A81ASP-1-0.793-0.84426.2720.1980.1980.0000.0000.0000.000
72A82LEU0-0.038-0.02721.7380.0270.0270.0000.0000.0000.000
73A83LYS10.8620.92822.097-0.155-0.1550.0000.0000.0000.000
74A84ASN0-0.011-0.02721.7110.0400.0400.0000.0000.0000.000
75A85VAL0-0.034-0.01719.5920.0410.0410.0000.0000.0000.000
76A86LEU0-0.037-0.02816.8700.0640.0640.0000.0000.0000.000
77A87GLU-1-0.891-0.95317.1490.3230.3230.0000.0000.0000.000
78A88GLY0-0.0050.01318.2330.0140.0140.0000.0000.0000.000
79A89LEU0-0.112-0.05213.3910.1290.1290.0000.0000.0000.000
80A90LYS10.9520.96610.749-1.084-1.0840.0000.0000.0000.000
81A91VAL0-0.054-0.0289.3400.3580.3580.0000.0000.0000.000
82A92ASP-1-0.812-0.8998.4660.1500.1500.0000.0000.0000.000
83A93GLY0-0.002-0.01911.519-0.116-0.1160.0000.0000.0000.000
84A94ILE0-0.0230.00212.8970.0940.0940.0000.0000.0000.000
85A95VAL0-0.016-0.00713.268-0.075-0.0750.0000.0000.0000.000
86A96ALA00.0300.01016.1850.0490.0490.0000.0000.0000.000
87A97GLY00.002-0.00719.756-0.035-0.0350.0000.0000.0000.000
88A98ALA0-0.022-0.00921.9910.0020.0020.0000.0000.0000.000
89A99LEU00.0240.02124.798-0.014-0.0140.0000.0000.0000.000
90A100ALA00.0740.02127.268-0.008-0.0080.0000.0000.0000.000
91A101SER0-0.015-0.01529.9140.0030.0030.0000.0000.0000.000
92A102ARG10.8980.91629.6170.0460.0460.0000.0000.0000.000
93A103TYR00.0630.04030.2760.0060.0060.0000.0000.0000.000
94A104GLN00.0440.02227.8640.0000.0000.0000.0000.0000.000
95A105LYS10.8070.91723.6240.0570.0570.0000.0000.0000.000
96A106GLU-1-0.816-0.91525.8870.0220.0220.0000.0000.0000.000
97A107ARG10.7810.88227.507-0.070-0.0700.0000.0000.0000.000
98A108ILE0-0.013-0.00321.7360.0160.0160.0000.0000.0000.000
99A109GLU-1-0.843-0.92923.034-0.004-0.0040.0000.0000.0000.000
100A110ASN0-0.063-0.04224.0960.0010.0010.0000.0000.0000.000
101A111VAL00.0440.02822.2710.0070.0070.0000.0000.0000.000
102A112ALA0-0.011-0.01119.7490.0200.0200.0000.0000.0000.000
103A113ARG10.8950.94120.902-0.030-0.0300.0000.0000.0000.000
104A114GLU-1-0.908-0.93623.3580.1340.1340.0000.0000.0000.000
105A115LEU0-0.043-0.01719.0800.0180.0180.0000.0000.0000.000
106A116GLY0-0.0210.00218.7810.0270.0270.0000.0000.0000.000
107A117LEU0-0.048-0.00114.504-0.015-0.0150.0000.0000.0000.000
108A118LYS10.9480.96312.2230.1600.1600.0000.0000.0000.000
109A119VAL00.0230.01415.6960.0160.0160.0000.0000.0000.000
110A120TYR0-0.008-0.00211.537-0.086-0.0860.0000.0000.0000.000
111A121THR00.002-0.01217.6120.0350.0350.0000.0000.0000.000
112A122PRO0-0.0030.01117.475-0.002-0.0020.0000.0000.0000.000
113A123ALA0-0.010-0.01220.390-0.012-0.0120.0000.0000.0000.000
114A124TRP0-0.059-0.04623.4510.0160.0160.0000.0000.0000.000
115A125GLU-1-0.818-0.88625.631-0.079-0.0790.0000.0000.0000.000
116A126LYS10.8390.94323.6180.1720.1720.0000.0000.0000.000
117A127ASP-1-0.768-0.89828.989-0.077-0.0770.0000.0000.0000.000
118A128PRO00.0350.00930.507-0.008-0.0080.0000.0000.0000.000
119A129TYR0-0.049-0.04531.240-0.003-0.0030.0000.0000.0000.000
120A130GLN00.019-0.01930.299-0.010-0.0100.0000.0000.0000.000
121A131TYR0-0.051-0.03623.501-0.017-0.0170.0000.0000.0000.000
122A132MET00.0000.01327.023-0.005-0.0050.0000.0000.0000.000
123A133LEU0-0.013-0.00928.996-0.003-0.0030.0000.0000.0000.000
124A134GLU-1-0.805-0.85822.584-0.225-0.2250.0000.0000.0000.000
125A135ILE0-0.001-0.00823.871-0.012-0.0120.0000.0000.0000.000
126A136ILE0-0.023-0.00924.960-0.003-0.0030.0000.0000.0000.000
127A137LYS10.8760.93626.5010.1340.1340.0000.0000.0000.000
128A138LEU0-0.053-0.01320.250-0.017-0.0170.0000.0000.0000.000
129A139GLY00.0150.00421.866-0.009-0.0090.0000.0000.0000.000
130A140PHE0-0.035-0.01919.2390.0170.0170.0000.0000.0000.000
131A141LYS10.7540.87923.9610.0780.0780.0000.0000.0000.000
132A142VAL00.002-0.01325.3350.0110.0110.0000.0000.0000.000
133A143VAL00.0300.03127.789-0.005-0.0050.0000.0000.0000.000
134A144PHE00.0250.00930.4230.0040.0040.0000.0000.0000.000
135A145VAL0-0.003-0.00630.1240.0020.0020.0000.0000.0000.000
136A146ALA00.0080.00133.1180.0070.0070.0000.0000.0000.000
137A147VAL0-0.063-0.03135.368-0.006-0.0060.0000.0000.0000.000
138A148SER00.0180.02438.0340.0050.0050.0000.0000.0000.000
139A149ALA00.0570.04239.9730.0000.0000.0000.0000.0000.000
140A150TYR00.0120.00341.695-0.001-0.0010.0000.0000.0000.000
141A151GLY00.0600.02644.399-0.003-0.0030.0000.0000.0000.000
142A152LEU0-0.082-0.03538.065-0.002-0.0020.0000.0000.0000.000
143A153ASN00.0570.04842.0970.0040.0040.0000.0000.0000.000
144A154GLU-1-0.794-0.91542.4250.0140.0140.0000.0000.0000.000
145A155SER0-0.074-0.05241.9880.0000.0000.0000.0000.0000.000
146A156TRP0-0.009-0.00536.985-0.004-0.0040.0000.0000.0000.000
147A157LEU0-0.0460.01037.310-0.001-0.0010.0000.0000.0000.000
148A158GLY00.026-0.01135.145-0.001-0.0010.0000.0000.0000.000
149A159ARG10.7520.87235.5170.0160.0160.0000.0000.0000.000
150A160GLU-1-0.816-0.90829.759-0.045-0.0450.0000.0000.0000.000
151A161LEU0-0.026-0.00528.402-0.003-0.0030.0000.0000.0000.000
152A162ASN00.0290.00730.865-0.008-0.0080.0000.0000.0000.000
153A163TYR00.0910.02830.7140.0000.0000.0000.0000.0000.000
154A164LYS10.8840.94735.0450.0340.0340.0000.0000.0000.000
155A165ASN00.0310.00135.6530.0050.0050.0000.0000.0000.000
156A166LEU00.0190.01932.1900.0030.0030.0000.0000.0000.000
157A167GLU-1-0.754-0.88435.831-0.063-0.0630.0000.0000.0000.000
158A168GLU-1-0.820-0.88339.139-0.025-0.0250.0000.0000.0000.000
159A169LEU00.0200.01434.6560.0020.0020.0000.0000.0000.000
160A170LYS10.8040.91838.2470.0640.0640.0000.0000.0000.000
161A171LYS10.7920.88739.6140.0520.0520.0000.0000.0000.000
162A172LEU00.011-0.00541.6960.0020.0020.0000.0000.0000.000
163A173SER00.004-0.00139.5830.0020.0020.0000.0000.0000.000
164A174GLU-1-0.813-0.89141.715-0.048-0.0480.0000.0000.0000.000
165A175LYS10.7820.86844.4510.0290.0290.0000.0000.0000.000
166A176TYR0-0.019-0.00244.4830.0010.0010.0000.0000.0000.000
167A177GLY00.0040.01843.2930.0030.0030.0000.0000.0000.000
168A178ILE0-0.0010.02239.2520.0000.0000.0000.0000.0000.000
169A179HIS0-0.043-0.01935.101-0.003-0.0030.0000.0000.0000.000
170A180ILE0-0.008-0.01033.9550.0010.0010.0000.0000.0000.000
171A181ALA0-0.028-0.03029.784-0.002-0.0020.0000.0000.0000.000
172A182GLY00.0330.02830.6920.0030.0030.0000.0000.0000.000
173A183GLU-1-0.845-0.94231.283-0.030-0.0300.0000.0000.0000.000
174A184GLY00.0160.00433.021-0.001-0.0010.0000.0000.0000.000
175A185GLY00.0070.00434.1160.0060.0060.0000.0000.0000.000
176A186GLU-1-0.859-0.91635.095-0.003-0.0030.0000.0000.0000.000
177A187PHE0-0.008-0.01931.1740.0000.0000.0000.0000.0000.000
178A188GLU-1-0.817-0.87530.8430.0500.0500.0000.0000.0000.000
179A189THR0-0.024-0.02927.690-0.007-0.0070.0000.0000.0000.000
180A190PHE00.0150.01024.4120.0100.0100.0000.0000.0000.000
181A191VAL0-0.048-0.01221.491-0.013-0.0130.0000.0000.0000.000
182A192LEU00.0410.02723.4390.0170.0170.0000.0000.0000.000
183A193ASP-1-0.756-0.87421.351-0.068-0.0680.0000.0000.0000.000
184A194MET0-0.0020.03215.244-0.026-0.0260.0000.0000.0000.000
185A195PRO00.0110.00216.7930.0100.0100.0000.0000.0000.000
186A196PHE00.019-0.00212.167-0.005-0.0050.0000.0000.0000.000
187A197PHE0-0.0450.00114.4960.0540.0540.0000.0000.0000.000
188A198LYS10.8970.92711.471-0.149-0.1490.0000.0000.0000.000
189A199ALA0-0.0030.00117.4360.0030.0030.0000.0000.0000.000
190A200LYS10.8760.93520.9720.0550.0550.0000.0000.0000.000
191A201ILE00.009-0.00122.3510.0170.0170.0000.0000.0000.000
192A202VAL0-0.021-0.01325.458-0.013-0.0130.0000.0000.0000.000
193A203ILE00.004-0.00529.1820.0100.0100.0000.0000.0000.000
194A204ASP-1-0.866-0.91731.9730.0490.0490.0000.0000.0000.000
195A205ASP-1-0.848-0.94334.7920.0440.0440.0000.0000.0000.000
196A206ALA0-0.015-0.00735.1420.0060.0060.0000.0000.0000.000
197A207GLU-1-0.886-0.92637.0820.0380.0380.0000.0000.0000.000
198A208LYS10.8260.91538.817-0.008-0.0080.0000.0000.0000.000
199A209PHE00.0030.01139.5910.0010.0010.0000.0000.0000.000
200A210TRP00.0430.00941.653-0.001-0.0010.0000.0000.0000.000
201A211ASP-1-0.819-0.90844.1210.0260.0260.0000.0000.0000.000
202A212GLY0-0.007-0.00346.4750.0000.0000.0000.0000.0000.000
203A213LEU0-0.113-0.06046.170-0.003-0.0030.0000.0000.0000.000
204A214SER0-0.027-0.01240.431-0.002-0.0020.0000.0000.0000.000
205A215GLY00.0680.01840.3480.0010.0010.0000.0000.0000.000
206A216LYS10.8300.89834.003-0.053-0.0530.0000.0000.0000.000
207A217PHE0-0.010-0.00134.054-0.002-0.0020.0000.0000.0000.000
208A218ILE00.0250.01834.4030.0030.0030.0000.0000.0000.000
209A219ILE0-0.016-0.02530.199-0.003-0.0030.0000.0000.0000.000
210A220LYS10.8650.95132.820-0.040-0.0400.0000.0000.0000.000
211A221ARG10.8840.94632.577-0.052-0.0520.0000.0000.0000.000
212A222ALA00.0240.01628.842-0.009-0.0090.0000.0000.0000.000
213A223HIS10.7630.85228.069-0.031-0.0310.0000.0000.0000.000
214A224LEU0-0.011-0.01321.477-0.003-0.0030.0000.0000.0000.000
215A225GLU-1-0.843-0.90924.9500.0130.0130.0000.0000.0000.000
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