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: JQN99

Calculation Name: 1K7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K7K

Chain ID: A

ChEMBL ID:

UniProt ID: P52061

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 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 209
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2202373.168101
FMO2-HF: Nuclear repulsion 2124220.249108
FMO2-HF: Total energy -78152.918993
FMO2-MP2: Total energy -78383.192849


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:-11:SER)


Summations of interaction energy for fragment #1(A:-11: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.
-6.311-17.47626.898-8.509-7.224-0.039
Interaction energy analysis for fragmet #1(A:-11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.007
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].
3A-9GLY00.0600.0303.821-2.931-1.4150.007-0.798-0.7250.003
4A-8ARG10.8170.8636.3940.7740.7740.0000.0000.0000.000
5A-7DGL-1-0.783-0.8639.328-0.626-0.6260.0000.0000.0000.000
6A-6ASN00.0050.0126.9670.3140.3140.0000.0000.0000.000
7A-5LEU00.0390.0358.1790.0680.0680.0000.0000.0000.000
8A-4TYR00.0090.01211.657-0.012-0.0120.0000.0000.0000.000
9A-3PHE00.008-0.0029.227-0.022-0.0220.0000.0000.0000.000
10A-2GLN0-0.027-0.01815.0330.0170.0170.0000.0000.0000.000
11A-1GLY0-0.003-0.01618.0810.0310.0310.0000.0000.0000.000
12A0HIS0-0.0170.01720.4570.0120.0120.0000.0000.0000.000
13A1MET0-0.005-0.00818.984-0.019-0.0190.0000.0000.0000.000
14A2GLN0-0.061-0.02416.0920.0060.0060.0000.0000.0000.000
15A3LYS10.8680.92018.4480.1390.1390.0000.0000.0000.000
16A4VAL0-0.021-0.00715.686-0.012-0.0120.0000.0000.0000.000
17A5VAL00.0070.02418.9390.0160.0160.0000.0000.0000.000
18A6LEU0-0.003-0.00918.521-0.003-0.0030.0000.0000.0000.000
19A7ALA00.0110.00420.5410.0090.0090.0000.0000.0000.000
20A8THR0-0.060-0.04822.5510.0150.0150.0000.0000.0000.000
21A9GLY00.1310.06125.206-0.007-0.0070.0000.0000.0000.000
22A10ASN0-0.095-0.04126.093-0.005-0.0050.0000.0000.0000.000
23A11VAL00.1290.05226.469-0.006-0.0060.0000.0000.0000.000
24A12GLY00.0010.00626.972-0.007-0.0070.0000.0000.0000.000
25A13LYS10.8660.91621.8460.0050.0050.0000.0000.0000.000
26A14VAL00.0430.03122.115-0.011-0.0110.0000.0000.0000.000
27A15ARG10.9370.96222.7720.0470.0470.0000.0000.0000.000
28A16GLU-1-0.856-0.90220.467-0.054-0.0540.0000.0000.0000.000
29A17LEU00.0260.00015.497-0.008-0.0080.0000.0000.0000.000
30A18ALA00.009-0.00218.524-0.026-0.0260.0000.0000.0000.000
31A19SER0-0.017-0.02020.188-0.011-0.0110.0000.0000.0000.000
32A20LEU0-0.060-0.02816.555-0.007-0.0070.0000.0000.0000.000
33A21LEU00.013-0.00513.009-0.027-0.0270.0000.0000.0000.000
34A22SER0-0.034-0.00116.091-0.030-0.0300.0000.0000.0000.000
35A23ASP-1-0.960-0.96615.303-0.261-0.2610.0000.0000.0000.000
36A24PHE0-0.009-0.00710.035-0.023-0.0230.0000.0000.0000.000
37A25GLY0-0.001-0.00214.281-0.046-0.0460.0000.0000.0000.000
38A26LEU0-0.057-0.02212.5350.0090.0090.0000.0000.0000.000
39A27ASP-1-0.839-0.90617.033-0.129-0.1290.0000.0000.0000.000
40A28ILE0-0.012-0.00316.7200.0050.0050.0000.0000.0000.000
41A29VAL00.002-0.00720.7600.0150.0150.0000.0000.0000.000
42A30ALA00.0180.02423.343-0.001-0.0010.0000.0000.0000.000
43A31GLN0-0.012-0.02424.558-0.002-0.0020.0000.0000.0000.000
44A32THR00.0380.01926.1130.0020.0020.0000.0000.0000.000
45A33ASP-1-0.933-0.96228.209-0.067-0.0670.0000.0000.0000.000
46A34LEU0-0.093-0.05225.110-0.001-0.0010.0000.0000.0000.000
47A35GLY00.0010.01329.4180.0010.0010.0000.0000.0000.000
48A36VAL0-0.038-0.01526.3370.0030.0030.0000.0000.0000.000
49A37ASP-1-0.864-0.92329.549-0.023-0.0230.0000.0000.0000.000
50A38SER0-0.067-0.06028.508-0.003-0.0030.0000.0000.0000.000
51A39ALA0-0.0060.00926.1340.0010.0010.0000.0000.0000.000
52A40GLU-1-0.879-0.94128.1450.0240.0240.0000.0000.0000.000
53A41GLU-1-0.923-0.95325.9290.0320.0320.0000.0000.0000.000
54A42THR0-0.005-0.01526.7200.0030.0030.0000.0000.0000.000
55A43GLY0-0.0120.00223.6240.0050.0050.0000.0000.0000.000
56A44LEU0-0.011-0.01024.036-0.006-0.0060.0000.0000.0000.000
57A45THR0-0.047-0.05920.0800.0140.0140.0000.0000.0000.000
58A46PHE00.0160.01219.118-0.004-0.0040.0000.0000.0000.000
59A47ILE00.0140.00313.241-0.013-0.0130.0000.0000.0000.000
60A48GLU-1-0.838-0.89417.2510.1250.1250.0000.0000.0000.000
61A49ASN00.012-0.00919.638-0.020-0.0200.0000.0000.0000.000
62A50ALA0-0.0060.00917.134-0.018-0.0180.0000.0000.0000.000
63A51ILE00.005-0.01414.341-0.024-0.0240.0000.0000.0000.000
64A52LEU0-0.027-0.00617.866-0.025-0.0250.0000.0000.0000.000
65A53LYS10.8110.90521.213-0.049-0.0490.0000.0000.0000.000
66A54ALA0-0.004-0.00317.463-0.017-0.0170.0000.0000.0000.000
67A55ARG10.9090.94517.599-0.060-0.0600.0000.0000.0000.000
68A56HIS0-0.039-0.01820.743-0.011-0.0110.0000.0000.0000.000
69A57ALA00.0490.02121.678-0.007-0.0070.0000.0000.0000.000
70A58ALA00.0040.01419.564-0.009-0.0090.0000.0000.0000.000
71A59LYS10.8250.90121.6700.0380.0380.0000.0000.0000.000
72A60VAL0-0.034-0.01524.571-0.003-0.0030.0000.0000.0000.000
73A61THR0-0.028-0.03623.785-0.007-0.0070.0000.0000.0000.000
74A62ALA0-0.049-0.00823.591-0.006-0.0060.0000.0000.0000.000
75A63LEU0-0.039-0.00320.811-0.019-0.0190.0000.0000.0000.000
76A64PRO00.0110.00915.4780.0170.0170.0000.0000.0000.000
77A65ALA0-0.0010.00116.6340.0130.0130.0000.0000.0000.000
78A66ILE0-0.0030.00513.9640.0020.0020.0000.0000.0000.000
79A67ALA00.0040.00816.3140.0080.0080.0000.0000.0000.000
80A68ASP-1-0.811-0.89116.7710.0080.0080.0000.0000.0000.000
81A69ASP-1-0.752-0.87318.7860.0580.0580.0000.0000.0000.000
82A70SER0-0.048-0.02719.9710.0120.0120.0000.0000.0000.000
83A71GLY0-0.009-0.00322.364-0.006-0.0060.0000.0000.0000.000
84A72LEU0-0.030-0.00324.1680.0050.0050.0000.0000.0000.000
85A73ALA0-0.033-0.01124.2690.0000.0000.0000.0000.0000.000
86A74VAL00.035-0.00326.2620.0020.0020.0000.0000.0000.000
87A75ASP-1-0.884-0.94026.1960.1070.1070.0000.0000.0000.000
88A76VAL0-0.001-0.00528.8010.0010.0010.0000.0000.0000.000
89A77LEU0-0.048-0.02131.397-0.003-0.0030.0000.0000.0000.000
90A78GLY0-0.007-0.00329.1270.0000.0000.0000.0000.0000.000
91A79GLY0-0.009-0.00226.4470.0070.0070.0000.0000.0000.000
92A80ALA0-0.0120.01327.197-0.001-0.0010.0000.0000.0000.000
93A81PRO00.040-0.01029.8260.0010.0010.0000.0000.0000.000
94A82GLY00.0630.04425.9000.0000.0000.0000.0000.0000.000
95A83ILE00.0090.02223.986-0.007-0.0070.0000.0000.0000.000
96A84TYR00.002-0.00626.561-0.010-0.0100.0000.0000.0000.000
97A85SER0-0.019-0.03027.536-0.005-0.0050.0000.0000.0000.000
98A86ALA00.0470.02829.615-0.004-0.0040.0000.0000.0000.000
99A87ARG10.9610.99329.447-0.047-0.0470.0000.0000.0000.000
100A88TYR00.0330.02933.2030.0010.0010.0000.0000.0000.000
101A89SER0-0.085-0.07334.7340.0000.0000.0000.0000.0000.000
102A90GLY0-0.021-0.00537.306-0.002-0.0020.0000.0000.0000.000
103A91GLU-1-0.911-0.95538.5800.0150.0150.0000.0000.0000.000
104A92ASP-1-0.864-0.93740.6260.0120.0120.0000.0000.0000.000
105A93ALA0-0.079-0.00336.8530.0000.0000.0000.0000.0000.000
106A94THR00.0430.00738.036-0.002-0.0020.0000.0000.0000.000
107A95ASP-1-0.780-0.90634.1540.0200.0200.0000.0000.0000.000
108A96GLN00.0360.01836.5170.0030.0030.0000.0000.0000.000
109A97LYS10.8550.91639.550-0.017-0.0170.0000.0000.0000.000
110A98ASN00.0140.02034.4260.0020.0020.0000.0000.0000.000
111A99LEU00.0210.00735.8580.0030.0030.0000.0000.0000.000
112A100GLN00.004-0.00236.9730.0010.0010.0000.0000.0000.000
113A101LYS10.8820.95837.369-0.037-0.0370.0000.0000.0000.000
114A102LEU0-0.0230.00332.6260.0020.0020.0000.0000.0000.000
115A103LEU00.0170.00436.8850.0020.0020.0000.0000.0000.000
116A104GLU-1-0.845-0.89939.3770.0310.0310.0000.0000.0000.000
117A105THR0-0.082-0.06036.7580.0010.0010.0000.0000.0000.000
118A106MET0-0.0020.00533.7060.0020.0020.0000.0000.0000.000
119A107LYS10.8380.92838.593-0.031-0.0310.0000.0000.0000.000
120A108ASP-1-0.898-0.95341.9720.0350.0350.0000.0000.0000.000
121A109VAL0-0.061-0.01535.8820.0010.0010.0000.0000.0000.000
122A110PRO00.0310.01138.753-0.002-0.0020.0000.0000.0000.000
123A111ASP-1-0.782-0.89737.8150.0430.0430.0000.0000.0000.000
124A112ASP-1-0.934-0.94835.8520.0570.0570.0000.0000.0000.000
125A113GLN0-0.063-0.03733.8790.0050.0050.0000.0000.0000.000
126A114ARG10.7950.88333.692-0.044-0.0440.0000.0000.0000.000
127A115GLN0-0.017-0.00428.170-0.003-0.0030.0000.0000.0000.000
128A116ALA00.0350.01527.4940.0010.0010.0000.0000.0000.000
129A117ARG10.9150.95218.943-0.142-0.1420.0000.0000.0000.000
130A118PHE00.0080.02323.580-0.001-0.0010.0000.0000.0000.000
131A119HIS00.0480.01219.3680.0200.0200.0000.0000.0000.000
132A120CYS0-0.088-0.03718.152-0.021-0.0210.0000.0000.0000.000
133A121VAL00.0160.01414.2110.0150.0150.0000.0000.0000.000
134A122LEU00.0220.01612.394-0.021-0.0210.0000.0000.0000.000
135A123VAL0-0.026-0.02612.3950.0540.0540.0000.0000.0000.000
136A124TYR00.003-0.02810.472-0.034-0.0340.0000.0000.0000.000
137A125LEU0-0.0200.00311.6490.0220.0220.0000.0000.0000.000
138A126ARG10.8400.8917.8440.5260.5260.0000.0000.0000.000
139A127HIS00.0460.01214.6840.0140.0140.0000.0000.0000.000
140A128ALA00.0180.01217.6660.0200.0200.0000.0000.0000.000
141A129GLU-1-0.844-0.91819.229-0.006-0.0060.0000.0000.0000.000
142A130ASP-1-0.836-0.88412.576-0.125-0.1250.0000.0000.0000.000
143A131PRO00.005-0.00612.8960.0360.0360.0000.0000.0000.000
144A132THR0-0.081-0.0348.7690.0550.0550.0000.0000.0000.000
145A133PRO00.0320.0299.462-0.041-0.0410.0000.0000.0000.000
146A134LEU0-0.0040.0055.3040.3200.3200.0000.0000.0000.000
147A135VAL00.008-0.0017.994-0.178-0.1780.0000.0000.0000.000
148A136CYS0-0.052-0.0078.4860.0290.0290.0000.0000.0000.000
149A137HIS0-0.020-0.02310.722-0.020-0.0200.0000.0000.0000.000
150A138GLY00.0230.02513.3690.0100.0100.0000.0000.0000.000
151A139SER0-0.060-0.04015.7190.0010.0010.0000.0000.0000.000
152A140TRP00.0480.00918.730-0.006-0.0060.0000.0000.0000.000
153A141PRO0-0.003-0.00321.669-0.002-0.0020.0000.0000.0000.000
154A142GLY00.0390.01424.492-0.006-0.0060.0000.0000.0000.000
155A143VAL0-0.039-0.01328.1900.0050.0050.0000.0000.0000.000
156A144ILE0-0.037-0.01730.702-0.004-0.0040.0000.0000.0000.000
157A145THR0-0.006-0.00533.7670.0010.0010.0000.0000.0000.000
158A146ARG10.8220.88437.101-0.037-0.0370.0000.0000.0000.000
159A147GLU-1-0.876-0.93940.3490.0300.0300.0000.0000.0000.000
160A148PRO0-0.016-0.00338.8440.0010.0010.0000.0000.0000.000
161A149ALA00.0160.02038.376-0.002-0.0020.0000.0000.0000.000
162A150GLY00.0540.02537.5280.0010.0010.0000.0000.0000.000
163A151THR0-0.041-0.03638.3900.0010.0010.0000.0000.0000.000
164A152GLY0-0.0090.00634.894-0.002-0.0020.0000.0000.0000.000
165A153GLY0-0.058-0.03431.4170.0020.0020.0000.0000.0000.000
166A154PHE0-0.029-0.02127.043-0.003-0.0030.0000.0000.0000.000
167A155GLY00.0090.00731.5900.0040.0040.0000.0000.0000.000
168A156TYR0-0.056-0.06530.2620.0000.0000.0000.0000.0000.000
169A157ASP-1-0.716-0.83929.5330.0280.0280.0000.0000.0000.000
170A158PRO00.022-0.00432.1110.0020.0020.0000.0000.0000.000
171A159ILE00.0040.01733.9730.0000.0000.0000.0000.0000.000
172A160PHE0-0.0340.00626.0980.0030.0030.0000.0000.0000.000
173A161PHE00.0700.02931.683-0.003-0.0030.0000.0000.0000.000
174A162VAL00.0380.00927.5130.0060.0060.0000.0000.0000.000
175A163PRO0-0.005-0.00929.305-0.003-0.0030.0000.0000.0000.000
176A164SER0-0.085-0.06627.8480.0000.0000.0000.0000.0000.000
177A165GLU-1-0.891-0.92528.2940.0380.0380.0000.0000.0000.000
178A166GLY0-0.054-0.01631.781-0.003-0.0030.0000.0000.0000.000
179A167LYS10.8540.92833.556-0.024-0.0240.0000.0000.0000.000
180A168THR0-0.009-0.01632.9760.0030.0030.0000.0000.0000.000
181A169ALA00.0010.00029.497-0.003-0.0030.0000.0000.0000.000
182A170ALA0-0.060-0.01331.139-0.004-0.0040.0000.0000.0000.000
183A171GLU-1-0.854-0.93434.0930.0210.0210.0000.0000.0000.000
184A172LEU0-0.0560.01128.779-0.002-0.0020.0000.0000.0000.000
185A173THR0-0.008-0.03432.053-0.004-0.0040.0000.0000.0000.000
186A174ARG10.8600.90329.359-0.003-0.0030.0000.0000.0000.000
187A175GLU-1-0.893-0.93527.514-0.014-0.0140.0000.0000.0000.000
188A176GLU-1-0.745-0.83626.7180.0150.0150.0000.0000.0000.000
189A177LYS10.8010.88526.195-0.021-0.0210.0000.0000.0000.000
190A178SER0-0.035-0.05023.7530.0070.0070.0000.0000.0000.000
191A179ALA0-0.0280.00522.153-0.003-0.0030.0000.0000.0000.000
192A180ILE00.0050.00821.8140.0050.0050.0000.0000.0000.000
193A181SER0-0.0280.00522.1810.0100.0100.0000.0000.0000.000
194A182HIS00.0290.00719.4620.0000.0000.0000.0000.0000.000
195A183ARG10.8320.86618.1960.0340.0340.0000.0000.0000.000
196A184GLY00.0660.04317.708-0.013-0.0130.0000.0000.0000.000
197A185GLN0-0.098-0.06115.9810.0030.0030.0000.0000.0000.000
198A186ALA00.0110.00213.7700.0000.0000.0000.0000.0000.000
199A187LEU00.001-0.00112.813-0.028-0.0280.0000.0000.0000.000
200A188LYS10.9630.99212.908-0.104-0.1040.0000.0000.0000.000
201A189LEU0-0.031-0.0129.232-0.028-0.0280.0000.0000.0000.000
202A190LEU00.0180.0028.436-0.100-0.1000.0000.0000.0000.000
203A191LEU0-0.018-0.0168.847-0.176-0.1760.0000.0000.0000.000
204A192ASP-1-0.903-0.9436.7830.0690.0690.0000.0000.0000.000
205A193ALA00.001-0.0073.971-0.1150.040-0.001-0.018-0.1360.000
206A194LEU0-0.043-0.0163.758-1.753-1.5250.002-0.112-0.118-0.001
207A195ARG10.8840.9536.1680.0040.0040.0000.0000.0000.000
208A196ASN0-0.067-0.0394.557-0.0270.088-0.001-0.073-0.0400.000
209A197GLY00.0380.0232.091-1.953-15.13226.891-7.508-6.205-0.041