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: G6KM1

Calculation Name: 4AO6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AO6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2648927.35566
FMO2-HF: Nuclear repulsion 2563703.002541
FMO2-HF: Total energy -85224.353118
FMO2-MP2: Total energy -85471.682361


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:5:MET)


Summations of interaction energy for fragment #1(A:5:MET)
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.
-10.231-21.71231.793-10.7-9.614-0.061
Interaction energy analysis for fragmet #1(A:5:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.012
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].
3A7TRP0-0.040-0.0313.814-0.9781.359-0.028-1.294-1.0160.003
4A8ASN0-0.143-0.0896.8700.2380.2380.0000.0000.0000.000
5A9GLY00.0310.0117.160-0.274-0.2740.0000.0000.0000.000
6A10LYS10.9090.9689.3880.7330.7330.0000.0000.0000.000
7A11ASP-1-0.892-0.93112.456-0.736-0.7360.0000.0000.0000.000
8A12GLU-1-0.912-0.93214.586-0.242-0.2420.0000.0000.0000.000
9A13ARG10.9040.93318.1190.2220.2220.0000.0000.0000.000
10A14LYS10.9650.99620.8410.2050.2050.0000.0000.0000.000
11A15LEU00.009-0.00323.4000.0040.0040.0000.0000.0000.000
12A16SER0-0.002-0.00825.043-0.010-0.0100.0000.0000.0000.000
13A17VAL00.0060.00919.825-0.003-0.0030.0000.0000.0000.000
14A18GLN0-0.035-0.01916.3690.0380.0380.0000.0000.0000.000
15A19GLU-1-0.926-0.96315.284-0.309-0.3090.0000.0000.0000.000
16A20ARG10.8900.92411.2880.7190.7190.0000.0000.0000.000
17A21GLY00.0630.03710.2030.0340.0340.0000.0000.0000.000
18A22PHE0-0.029-0.0214.770-0.324-0.241-0.001-0.004-0.0780.000
19A23SER00.0160.0144.0240.2701.114-0.001-0.501-0.343-0.001
20A24LEU00.0380.0061.782-7.141-18.63131.395-14.013-5.892-0.061
21A25GLU-1-0.891-0.9292.7751.043-3.7120.1845.647-1.0760.002
22A26VAL0-0.030-0.0164.7130.0920.273-0.001-0.009-0.1720.000
23A27ASP-1-0.968-0.9787.3570.3370.3370.0000.0000.0000.000
24A28GLY0-0.041-0.0249.410-0.171-0.1710.0000.0000.0000.000
25A29ARG10.8880.9459.997-0.885-0.8850.0000.0000.0000.000
26A30THR00.0270.0337.0100.4210.4210.0000.0000.0000.000
27A31VAL0-0.042-0.0306.034-0.331-0.3310.0000.0000.0000.000
28A32PRO00.0010.0075.814-0.034-0.0340.0000.0000.0000.000
29A33GLY00.0470.0137.7990.1490.1490.0000.0000.0000.000
30A34VAL0-0.029-0.0049.023-0.196-0.1960.0000.0000.0000.000
31A35TYR00.0250.01110.5190.0840.0840.0000.0000.0000.000
32A36TRP00.0340.00812.517-0.021-0.0210.0000.0000.0000.000
33A37SER00.006-0.00715.860-0.006-0.0060.0000.0000.0000.000
34A38PRO00.0390.00317.7100.0040.0040.0000.0000.0000.000
35A39ALA0-0.059-0.02420.002-0.021-0.0210.0000.0000.0000.000
36A40GLU-1-0.926-0.94821.676-0.197-0.1970.0000.0000.0000.000
37A41GLY0-0.075-0.01922.8330.0190.0190.0000.0000.0000.000
38A42SER00.043-0.01319.687-0.030-0.0300.0000.0000.0000.000
39A43SER0-0.047-0.02918.5940.0120.0120.0000.0000.0000.000
40A44ASP-1-0.871-0.93619.071-0.157-0.1570.0000.0000.0000.000
41A45ARG10.7840.89019.6860.1220.1220.0000.0000.0000.000
42A46LEU00.0060.01712.774-0.022-0.0220.0000.0000.0000.000
43A47VAL0-0.026-0.01617.3060.0290.0290.0000.0000.0000.000
44A48LEU00.0040.01312.934-0.023-0.0230.0000.0000.0000.000
45A49LEU0-0.057-0.03215.6720.0170.0170.0000.0000.0000.000
46A50GLY00.0390.01416.4640.0120.0120.0000.0000.0000.000
47A51HIS00.010-0.01615.5740.0010.0010.0000.0000.0000.000
48A60GLU-1-0.910-0.95322.361-0.085-0.0850.0000.0000.0000.000
49A61TYR00.043-0.00723.400-0.009-0.0090.0000.0000.0000.000
50A62ILE00.0010.00718.096-0.004-0.0040.0000.0000.0000.000
51A63GLU-1-0.831-0.91820.267-0.195-0.1950.0000.0000.0000.000
52A64GLN0-0.030-0.02421.411-0.003-0.0030.0000.0000.0000.000
53A65VAL00.011-0.00622.366-0.004-0.0040.0000.0000.0000.000
54A66ALA00.0420.02919.165-0.003-0.0030.0000.0000.0000.000
55A67LYS10.9110.96320.9800.1360.1360.0000.0000.0000.000
56A68LEU0-0.046-0.02323.5410.0000.0000.0000.0000.0000.000
57A69LEU0-0.008-0.00420.6690.0040.0040.0000.0000.0000.000
58A70VAL00.0590.04119.743-0.001-0.0010.0000.0000.0000.000
59A71GLY0-0.032-0.00722.3960.0000.0000.0000.0000.0000.000
60A72ARG10.7270.85225.3220.0910.0910.0000.0000.0000.000
61A73GLY00.0220.01023.5700.0060.0060.0000.0000.0000.000
62A74ILE0-0.111-0.03120.117-0.006-0.0060.0000.0000.0000.000
63A75SER00.0450.01015.750-0.014-0.0140.0000.0000.0000.000
64A76ALA0-0.025-0.01516.3330.0310.0310.0000.0000.0000.000
65A77MET0-0.0270.0139.100-0.023-0.0230.0000.0000.0000.000
66A78ALA0-0.018-0.00512.6080.0590.0590.0000.0000.0000.000
67A79ILE00.0340.0218.440-0.065-0.0650.0000.0000.0000.000
68A80ASP-1-0.912-0.94511.185-0.013-0.0130.0000.0000.0000.000
69A81GLY00.007-0.00612.5110.0840.0840.0000.0000.0000.000
70A82PRO0-0.076-0.01915.236-0.019-0.0190.0000.0000.0000.000
71A83GLY00.010-0.00117.497-0.027-0.0270.0000.0000.0000.000
72A97THR0-0.009-0.01029.5780.0010.0010.0000.0000.0000.000
73A98ASP-1-0.789-0.89826.3260.0170.0170.0000.0000.0000.000
74A99VAL00.0640.03622.5790.0020.0020.0000.0000.0000.000
75A100VAL0-0.022-0.01825.1530.0060.0060.0000.0000.0000.000
76A101GLY0-0.020-0.00127.2700.0020.0020.0000.0000.0000.000
77A102LEU0-0.056-0.02026.433-0.003-0.0030.0000.0000.0000.000
78A103ASP-1-0.840-0.93229.5880.0520.0520.0000.0000.0000.000
79A104ALA0-0.079-0.06027.2550.0060.0060.0000.0000.0000.000
80A105PHE00.0330.01022.1720.0100.0100.0000.0000.0000.000
81A106PRO00.0310.00124.7550.0130.0130.0000.0000.0000.000
82A107ARG10.9240.97025.308-0.056-0.0560.0000.0000.0000.000
83A108MET00.0150.02121.6450.0110.0110.0000.0000.0000.000
84A109TRP00.0170.01619.9430.0260.0260.0000.0000.0000.000
85A110HIS00.006-0.01520.3550.0350.0350.0000.0000.0000.000
86A111GLU-1-0.970-0.97720.9240.1770.1770.0000.0000.0000.000
87A112GLY0-0.027-0.00317.0520.0240.0240.0000.0000.0000.000
88A113GLY00.000-0.00816.1700.0530.0530.0000.0000.0000.000
89A114GLY00.0070.00118.047-0.004-0.0040.0000.0000.0000.000
90A115THR0-0.019-0.05218.1730.0240.0240.0000.0000.0000.000
91A116ALA0-0.002-0.00416.6630.0060.0060.0000.0000.0000.000
92A117ALA00.0130.02713.9920.0250.0250.0000.0000.0000.000
93A118VAL00.0290.02313.2360.0630.0630.0000.0000.0000.000
94A119ILE0-0.053-0.03013.7810.0110.0110.0000.0000.0000.000
95A120ALA00.0270.0149.969-0.032-0.0320.0000.0000.0000.000
96A121ASP-1-0.822-0.9159.1780.9700.9700.0000.0000.0000.000
97A122TRP0-0.009-0.0458.8750.0670.0670.0000.0000.0000.000
98A123ALA0-0.0210.0029.904-0.093-0.0930.0000.0000.0000.000
99A124ALA00.0420.0265.003-0.169-0.1690.0000.0000.0000.000
100A125ALA00.011-0.0105.562-0.227-0.2270.0000.0000.0000.000
101A126LEU0-0.063-0.0326.878-0.339-0.3390.0000.0000.0000.000
102A127ASP-1-0.837-0.9225.346-0.463-0.4630.0000.0000.0000.000
103A128PHE0-0.036-0.0203.103-1.755-0.4500.246-0.525-1.025-0.004
104A129ILE0-0.006-0.0065.285-0.047-0.033-0.001-0.001-0.0120.000
105A130GLU-1-0.897-0.9588.372-0.199-0.1990.0000.0000.0000.000
106A131ALA0-0.048-0.0176.4750.1010.1010.0000.0000.0000.000
107A132GLU-1-0.918-0.9466.613-1.267-1.2670.0000.0000.0000.000
108A133GLU-1-0.944-0.9789.281-0.537-0.5370.0000.0000.0000.000
109A134GLY0-0.0260.00611.9300.0850.0850.0000.0000.0000.000
110A135PRO0-0.017-0.01212.9280.0020.0020.0000.0000.0000.000
111A136ARG10.8830.93913.6050.3500.3500.0000.0000.0000.000
112A137PRO0-0.098-0.04817.5220.0140.0140.0000.0000.0000.000
113A138THR00.0850.03715.119-0.020-0.0200.0000.0000.0000.000
114A139GLY0-0.024-0.01118.2610.0210.0210.0000.0000.0000.000
115A140TRP00.0010.04615.396-0.013-0.0130.0000.0000.0000.000
116A141TRP00.006-0.01719.6080.0010.0010.0000.0000.0000.000
117A142GLY00.0600.01420.3700.0010.0010.0000.0000.0000.000
118A143LEU0-0.0280.01922.2720.0070.0070.0000.0000.0000.000
119A144SER00.0320.00124.1820.0060.0060.0000.0000.0000.000
120A145MET00.0590.03018.2720.0030.0030.0000.0000.0000.000
121A146GLY00.0300.01120.3630.0150.0150.0000.0000.0000.000
122A147THR0-0.019-0.03021.194-0.003-0.0030.0000.0000.0000.000
123A148MET0-0.033-0.00122.5070.0000.0000.0000.0000.0000.000
124A149MET00.0080.02816.9110.0260.0260.0000.0000.0000.000
125A150GLY00.0720.00919.0760.0070.0070.0000.0000.0000.000
126A151LEU0-0.055-0.00620.246-0.008-0.0080.0000.0000.0000.000
127A152PRO00.009-0.01819.610-0.006-0.0060.0000.0000.0000.000
128A153VAL00.0450.04415.5100.0000.0000.0000.0000.0000.000
129A154THR00.005-0.00817.904-0.018-0.0180.0000.0000.0000.000
130A155ALA0-0.094-0.03820.362-0.008-0.0080.0000.0000.0000.000
131A156SER0-0.041-0.03416.653-0.001-0.0010.0000.0000.0000.000
132A157ASP-1-0.776-0.86413.381-0.025-0.0250.0000.0000.0000.000
133A158LYS10.8290.91216.527-0.041-0.0410.0000.0000.0000.000
134A159ARG10.7710.8779.6540.1480.1480.0000.0000.0000.000
135A160ILE0-0.045-0.00916.129-0.016-0.0160.0000.0000.0000.000
136A161LYS10.8720.91419.3580.0810.0810.0000.0000.0000.000
137A162VAL0-0.050-0.03322.3220.0030.0030.0000.0000.0000.000
138A163ALA00.0140.01822.479-0.004-0.0040.0000.0000.0000.000
139A164LEU0-0.055-0.01723.7040.0010.0010.0000.0000.0000.000
140A165LEU00.007-0.00622.9150.0030.0030.0000.0000.0000.000
141A166GLY00.047-0.00726.192-0.006-0.0060.0000.0000.0000.000
142A167LEU0-0.062-0.02127.8210.0050.0050.0000.0000.0000.000
143A168MET00.0410.02626.5700.0050.0050.0000.0000.0000.000
144A169GLY00.0590.00429.701-0.005-0.0050.0000.0000.0000.000
145A170VAL0-0.028-0.02430.6340.0060.0060.0000.0000.0000.000
146A171GLU-1-0.791-0.78532.7050.0390.0390.0000.0000.0000.000
147A172GLY0-0.012-0.00329.0470.0010.0010.0000.0000.0000.000
148A173VAL00.0220.00725.7980.0020.0020.0000.0000.0000.000
149A174ASN0-0.048-0.02822.880-0.006-0.0060.0000.0000.0000.000
150A175GLY00.0410.02126.3590.0000.0000.0000.0000.0000.000
151A176GLU-1-0.911-0.96928.5560.0810.0810.0000.0000.0000.000
152A177ASP-1-0.798-0.87423.5860.1270.1270.0000.0000.0000.000
153A178LEU0-0.029-0.00724.539-0.005-0.0050.0000.0000.0000.000
154A179VAL0-0.009-0.01326.866-0.008-0.0080.0000.0000.0000.000
155A180ARG10.8630.92622.276-0.116-0.1160.0000.0000.0000.000
156A181LEU0-0.007-0.01221.516-0.002-0.0020.0000.0000.0000.000
157A182ALA00.0280.03325.379-0.006-0.0060.0000.0000.0000.000
158A183PRO00.0130.00427.812-0.007-0.0070.0000.0000.0000.000
159A184GLN0-0.033-0.02023.210-0.003-0.0030.0000.0000.0000.000
160A185VAL00.0160.01324.066-0.003-0.0030.0000.0000.0000.000
161A186THR0-0.029-0.03225.256-0.002-0.0020.0000.0000.0000.000
162A187CYS0-0.0340.01524.338-0.002-0.0020.0000.0000.0000.000
163A188PRO0-0.031-0.02926.4380.0050.0050.0000.0000.0000.000
164A189VAL00.0270.02326.616-0.001-0.0010.0000.0000.0000.000
165A190ARG10.9110.97828.2660.0290.0290.0000.0000.0000.000
166A191TYR00.005-0.02328.4180.0000.0000.0000.0000.0000.000
167A192LEU00.0090.00629.866-0.002-0.0020.0000.0000.0000.000
168A193LEU0-0.020-0.00531.7940.0050.0050.0000.0000.0000.000
169A194GLN00.0170.00434.323-0.005-0.0050.0000.0000.0000.000
170A195TRP0-0.038-0.02936.5390.0030.0030.0000.0000.0000.000
171A196ASP-1-0.863-0.93539.8000.0000.0000.0000.0000.0000.000
172A197ASP-1-0.794-0.88333.4870.0100.0100.0000.0000.0000.000
173A198GLU-1-0.819-0.93135.5420.0050.0050.0000.0000.0000.000
174A199LEU0-0.077-0.03630.8170.0020.0020.0000.0000.0000.000
175A200VAL0-0.0320.01031.0470.0050.0050.0000.0000.0000.000
176A201SER0-0.016-0.02934.306-0.004-0.0040.0000.0000.0000.000
177A202LEU00.0750.02336.8850.0010.0010.0000.0000.0000.000
178A203GLN0-0.006-0.01738.1580.0010.0010.0000.0000.0000.000
179A204SER00.045-0.01634.9530.0010.0010.0000.0000.0000.000
180A205GLY00.0190.00133.7020.0030.0030.0000.0000.0000.000
181A206LEU0-0.055-0.04134.4180.0000.0000.0000.0000.0000.000
182A207GLU-1-0.942-0.96235.9450.0330.0330.0000.0000.0000.000
183A208LEU0-0.010-0.00628.5760.0010.0010.0000.0000.0000.000
184A209PHE00.0300.00932.3210.0000.0000.0000.0000.0000.000
185A210GLY0-0.011-0.01433.378-0.002-0.0020.0000.0000.0000.000
186A211LYS10.8970.94732.099-0.038-0.0380.0000.0000.0000.000
187A212LEU0-0.0330.00528.1670.0020.0020.0000.0000.0000.000
188A213GLY00.0490.02629.558-0.003-0.0030.0000.0000.0000.000
189A214THR0-0.079-0.02729.155-0.003-0.0030.0000.0000.0000.000
190A215LYS10.9610.96531.088-0.009-0.0090.0000.0000.0000.000
191A216GLN0-0.051-0.01031.538-0.001-0.0010.0000.0000.0000.000
192A217LYS10.8560.94231.619-0.016-0.0160.0000.0000.0000.000
193A218THR0-0.052-0.02832.797-0.001-0.0010.0000.0000.0000.000
194A219LEU00.0110.01533.312-0.001-0.0010.0000.0000.0000.000
195A220HIS0-0.111-0.06634.594-0.001-0.0010.0000.0000.0000.000
196A221VAL00.011-0.00835.4850.0010.0010.0000.0000.0000.000
197A222ASN0-0.050-0.02036.218-0.002-0.0020.0000.0000.0000.000
198A223PRO00.0330.01339.1330.0020.0020.0000.0000.0000.000
199A224GLY00.0060.00939.545-0.002-0.0020.0000.0000.0000.000
200A225LYS10.9280.96937.0770.0030.0030.0000.0000.0000.000
201A226HIS10.7820.85628.678-0.014-0.0140.0000.0000.0000.000
202A227SER0-0.038-0.02531.8180.0000.0000.0000.0000.0000.000
203A228ALA0-0.080-0.03332.857-0.004-0.0040.0000.0000.0000.000
204A229VAL00.0440.03831.4000.0000.0000.0000.0000.0000.000
205A230PRO0-0.0120.00334.229-0.004-0.0040.0000.0000.0000.000
206A231THR00.0700.02233.296-0.001-0.0010.0000.0000.0000.000
207A232TRP00.0190.01233.124-0.005-0.0050.0000.0000.0000.000
208A233GLU-1-0.816-0.88732.976-0.027-0.0270.0000.0000.0000.000
209A234MET00.003-0.01228.414-0.003-0.0030.0000.0000.0000.000
210A235PHE0-0.0090.01627.174-0.003-0.0030.0000.0000.0000.000
211A236ALA00.0140.00929.664-0.002-0.0020.0000.0000.0000.000
212A237GLY00.0560.03131.586-0.001-0.0010.0000.0000.0000.000
213A238THR0-0.064-0.04927.061-0.002-0.0020.0000.0000.0000.000
214A239VAL00.0510.03025.912-0.002-0.0020.0000.0000.0000.000
215A240ASP-1-0.832-0.91327.741-0.064-0.0640.0000.0000.0000.000
216A241TYR0-0.085-0.04427.3460.0010.0010.0000.0000.0000.000
217A242LEU00.0420.00322.7750.0020.0020.0000.0000.0000.000
218A243ASP-1-0.804-0.87826.066-0.091-0.0910.0000.0000.0000.000
219A244GLN0-0.054-0.03927.4100.0030.0030.0000.0000.0000.000
220A245ARG10.8880.94528.0480.0370.0370.0000.0000.0000.000
221A246LEU0-0.0310.02220.6890.0060.0060.0000.0000.0000.000
222A247LYS10.9951.00624.5050.0710.0710.0000.0000.0000.000