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

tag_button

FMODB ID: 9GKM2

Calculation Name: 1K4N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K4N

Chain ID: A

ChEMBL ID:

UniProt ID: P52007

Base Structure: X-ray

Registration Date: 2023-06-19

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015273.973887
FMO2-HF: Nuclear repulsion 1942588.559051
FMO2-HF: Total energy -72685.414836
FMO2-MP2: Total energy -72898.061449


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-1.342-0.046-0.003-0.664-0.6290.003
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / 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].
3A3MET0-0.005-0.0073.856-0.4160.880-0.003-0.664-0.6290.003
4A4ILE0-0.010-0.0105.8060.6930.6930.0000.0000.0000.000
5A5MET0-0.0030.0138.0340.1270.1270.0000.0000.0000.000
6A6ALA00.0070.01611.6690.0280.0280.0000.0000.0000.000
7A7ASN00.025-0.00114.5680.0750.0750.0000.0000.0000.000
8A8TRP00.0950.01516.9980.0670.0670.0000.0000.0000.000
9A9GLN0-0.088-0.04620.5320.0250.0250.0000.0000.0000.000
10A10SER0-0.081-0.04617.3800.0110.0110.0000.0000.0000.000
11A11ILE00.0060.02618.0560.0040.0040.0000.0000.0000.000
12A12ASP-1-0.832-0.91121.111-0.133-0.1330.0000.0000.0000.000
13A13GLU-1-0.923-0.97323.997-0.183-0.1830.0000.0000.0000.000
14A14LEU0-0.029-0.01222.8710.0110.0110.0000.0000.0000.000
15A15GLN0-0.008-0.00924.8420.0070.0070.0000.0000.0000.000
16A16ASP-1-0.778-0.83627.004-0.140-0.1400.0000.0000.0000.000
17A17ILE00.0290.00026.5710.0040.0040.0000.0000.0000.000
18A18ALA00.0050.00925.254-0.004-0.0040.0000.0000.0000.000
19A19SER0-0.036-0.03127.1510.0060.0060.0000.0000.0000.000
20A20ASP-1-0.764-0.84730.239-0.119-0.1190.0000.0000.0000.000
21A21LEU0-0.0140.00727.1090.0060.0060.0000.0000.0000.000
22A22PRO00.012-0.00829.8490.0030.0030.0000.0000.0000.000
23A23ARG10.8050.87032.5030.1230.1230.0000.0000.0000.000
24A24PHE0-0.012-0.00832.4350.0050.0050.0000.0000.0000.000
25A25ILE00.0120.00930.0700.0000.0000.0000.0000.0000.000
26A26HIS00.0010.01134.1340.0030.0030.0000.0000.0000.000
27A27ALA00.0010.00337.6220.0040.0040.0000.0000.0000.000
28A28LEU00.000-0.00434.2040.0040.0040.0000.0000.0000.000
29A29ASP-1-0.830-0.87337.054-0.104-0.1040.0000.0000.0000.000
30A30GLU-1-0.826-0.91238.798-0.078-0.0780.0000.0000.0000.000
31A31LEU0-0.044-0.01541.1830.0050.0050.0000.0000.0000.000
32A32SER0-0.020-0.03539.6260.0020.0020.0000.0000.0000.000
33A33ARG10.7500.84340.2450.0960.0960.0000.0000.0000.000
34A34ARG10.9110.95944.1710.0810.0810.0000.0000.0000.000
35A35LEU00.0000.00243.9770.0030.0030.0000.0000.0000.000
36A36GLY00.0230.03846.4730.0020.0020.0000.0000.0000.000
37A37LEU0-0.044-0.01240.927-0.001-0.0010.0000.0000.0000.000
38A38ASN00.000-0.01939.876-0.008-0.0080.0000.0000.0000.000
39A39ILE00.0710.02535.263-0.003-0.0030.0000.0000.0000.000
40A40THR0-0.0030.00134.562-0.008-0.0080.0000.0000.0000.000
41A41PRO0-0.032-0.01234.684-0.010-0.0100.0000.0000.0000.000
42A42LEU0-0.0250.00936.064-0.003-0.0030.0000.0000.0000.000
43A43THR00.0380.01631.811-0.011-0.0110.0000.0000.0000.000
44A44ALA00.0000.00630.0400.0070.0070.0000.0000.0000.000
45A45ASP-1-0.764-0.85330.669-0.210-0.2100.0000.0000.0000.000
46A46HIS10.7520.85729.6760.1690.1690.0000.0000.0000.000
47A47ILE00.0140.02128.4180.0170.0170.0000.0000.0000.000
48A48SER0-0.029-0.04631.330-0.009-0.0090.0000.0000.0000.000
49A49LEU00.0320.03629.6100.0090.0090.0000.0000.0000.000
50A50ARG10.7500.85933.9910.1360.1360.0000.0000.0000.000
51A51CYS00.0180.01536.019-0.001-0.0010.0000.0000.0000.000
52A52HIS0-0.062-0.04938.0980.0020.0020.0000.0000.0000.000
53A53GLN00.0010.01238.3010.0060.0060.0000.0000.0000.000
54A54ASN00.050-0.00537.482-0.008-0.0080.0000.0000.0000.000
55A55ALA0-0.0120.00135.520-0.006-0.0060.0000.0000.0000.000
56A56THR0-0.014-0.02033.421-0.005-0.0050.0000.0000.0000.000
57A57ALA00.0480.02832.379-0.009-0.0090.0000.0000.0000.000
58A58GLU-1-0.819-0.91531.568-0.154-0.1540.0000.0000.0000.000
59A59ARG10.7750.88129.3500.1250.1250.0000.0000.0000.000
60A60TRP00.013-0.03727.866-0.011-0.0110.0000.0000.0000.000
61A61ARG10.7390.85526.8980.1620.1620.0000.0000.0000.000
62A62ARG10.7890.86525.6330.1600.1600.0000.0000.0000.000
63A63GLY00.0480.03423.452-0.018-0.0180.0000.0000.0000.000
64A64PHE00.042-0.01922.129-0.027-0.0270.0000.0000.0000.000
65A65GLU-1-0.837-0.90021.888-0.246-0.2460.0000.0000.0000.000
66A66GLN0-0.072-0.03618.719-0.019-0.0190.0000.0000.0000.000
67A67CYS0-0.095-0.01917.400-0.031-0.0310.0000.0000.0000.000
68A68GLY00.0460.01918.635-0.021-0.0210.0000.0000.0000.000
69A69GLU-1-0.906-0.92018.148-0.539-0.5390.0000.0000.0000.000
70A70LEU0-0.067-0.03422.0810.0150.0150.0000.0000.0000.000
71A71LEU00.0000.00424.8450.0010.0010.0000.0000.0000.000
72A72SER00.013-0.00127.3280.0140.0140.0000.0000.0000.000
73A73GLU-1-0.821-0.88930.703-0.168-0.1680.0000.0000.0000.000
74A74ASN00.0240.01232.9670.0120.0120.0000.0000.0000.000
75A75MET0-0.0200.00636.6690.0020.0020.0000.0000.0000.000
76A76ILE00.0090.00639.3880.0050.0050.0000.0000.0000.000
77A77ASN0-0.051-0.04341.994-0.001-0.0010.0000.0000.0000.000
78A78GLY00.0220.01544.7440.0020.0020.0000.0000.0000.000
79A79ARG10.8420.92539.5730.1150.1150.0000.0000.0000.000
80A80PRO00.0490.02935.7840.0000.0000.0000.0000.0000.000
81A81ILE0-0.054-0.03734.6170.0030.0030.0000.0000.0000.000
82A82CYS0-0.0020.02329.930-0.003-0.0030.0000.0000.0000.000
83A83LEU0-0.018-0.00929.9830.0050.0050.0000.0000.0000.000
84A84PHE00.0510.02224.173-0.003-0.0030.0000.0000.0000.000
85A85LYS10.8770.92622.0560.3990.3990.0000.0000.0000.000
86A86LEU0-0.027-0.01720.645-0.017-0.0170.0000.0000.0000.000
87A87HIS0-0.045-0.04815.260-0.026-0.0260.0000.0000.0000.000
88A88GLU-1-0.881-0.92814.339-0.787-0.7870.0000.0000.0000.000
89A89PRO0-0.034-0.01218.1330.0480.0480.0000.0000.0000.000
90A90VAL00.0060.01121.8600.0070.0070.0000.0000.0000.000
91A91GLN0-0.021-0.01123.894-0.016-0.0160.0000.0000.0000.000
92A92VAL0-0.018-0.02425.6740.0190.0190.0000.0000.0000.000
93A93ALA00.0170.00629.5470.0030.0030.0000.0000.0000.000
94A94HIS0-0.006-0.00328.771-0.014-0.0140.0000.0000.0000.000
95A95TRP0-0.004-0.00727.765-0.015-0.0150.0000.0000.0000.000
96A96GLN0-0.003-0.01121.682-0.019-0.0190.0000.0000.0000.000
97A97PHE00.0130.00425.418-0.012-0.0120.0000.0000.0000.000
98A98SER00.0270.01622.901-0.022-0.0220.0000.0000.0000.000
99A99ILE0-0.0190.00423.930-0.017-0.0170.0000.0000.0000.000
100A100VAL00.0230.00726.0080.0200.0200.0000.0000.0000.000
101A101GLU-1-0.770-0.84628.622-0.151-0.1510.0000.0000.0000.000
102A102LEU00.0180.00629.5680.0060.0060.0000.0000.0000.000
103A103PRO0-0.051-0.01932.4060.0020.0020.0000.0000.0000.000
104A104TRP00.0460.00231.4640.0010.0010.0000.0000.0000.000
105A105PRO00.0000.01237.5790.0020.0020.0000.0000.0000.000
106A106GLY00.0190.00040.7900.0000.0000.0000.0000.0000.000
107A107GLU-1-0.858-0.89543.747-0.070-0.0700.0000.0000.0000.000
108A108LYS10.8640.94444.6050.0950.0950.0000.0000.0000.000
109A109ARG10.8790.91444.3850.0670.0670.0000.0000.0000.000
110A110TYR0-0.045-0.07041.5380.0050.0050.0000.0000.0000.000
111A111PRO0-0.009-0.01042.368-0.002-0.0020.0000.0000.0000.000
112A112HIS0-0.069-0.01236.0620.0090.0090.0000.0000.0000.000
113A113GLU-1-0.747-0.84936.150-0.109-0.1090.0000.0000.0000.000
114A114GLY00.0550.02333.733-0.001-0.0010.0000.0000.0000.000
115A115TRP0-0.030-0.01927.488-0.001-0.0010.0000.0000.0000.000
116A116GLU-1-0.807-0.85134.315-0.108-0.1080.0000.0000.0000.000
117A117HIS10.7220.82135.9690.1490.1490.0000.0000.0000.000
118A118ILE00.0380.04032.587-0.009-0.0090.0000.0000.0000.000
119A119GLU-1-0.832-0.90134.215-0.136-0.1360.0000.0000.0000.000
120A120ILE00.0290.01734.179-0.012-0.0120.0000.0000.0000.000
121A121VAL00.0290.01533.7940.0080.0080.0000.0000.0000.000
122A122LEU0-0.023-0.01236.6630.0020.0020.0000.0000.0000.000
123A123PRO00.0470.02536.9150.0070.0070.0000.0000.0000.000
124A124GLY00.0090.00239.7180.0060.0060.0000.0000.0000.000
125A125ASP-1-0.778-0.86643.157-0.097-0.0970.0000.0000.0000.000
126A126PRO00.0030.00743.6380.0000.0000.0000.0000.0000.000
127A127GLU-1-0.926-0.96045.698-0.091-0.0910.0000.0000.0000.000
128A128THR0-0.058-0.06748.7200.0010.0010.0000.0000.0000.000
129A129LEU0-0.061-0.00242.3960.0010.0010.0000.0000.0000.000
130A130ASN00.035-0.00846.326-0.003-0.0030.0000.0000.0000.000
131A131ALA00.0200.01248.3230.0010.0010.0000.0000.0000.000
132A132ARG10.7860.87442.7890.1130.1130.0000.0000.0000.000
133A133ALA00.0190.00444.389-0.002-0.0020.0000.0000.0000.000
134A134LEU0-0.022-0.02045.6120.0000.0000.0000.0000.0000.000
135A135ALA0-0.021-0.00548.4040.0020.0020.0000.0000.0000.000
136A136LEU0-0.060-0.01742.2280.0000.0000.0000.0000.0000.000
137A137LEU0-0.046-0.02245.092-0.002-0.0020.0000.0000.0000.000
138A138SER00.014-0.00148.1210.0040.0040.0000.0000.0000.000
139A139ASP-1-0.874-0.94950.805-0.066-0.0660.0000.0000.0000.000
140A140GLU-1-0.948-0.95652.881-0.062-0.0620.0000.0000.0000.000
141A141GLY00.0550.02849.9650.0000.0000.0000.0000.0000.000
142A142LEU0-0.081-0.05550.421-0.001-0.0010.0000.0000.0000.000
143A143SER0-0.089-0.05952.4470.0020.0020.0000.0000.0000.000
144A144LEU0-0.0060.01750.3650.0030.0030.0000.0000.0000.000
145A145PRO00.0090.00153.423-0.001-0.0010.0000.0000.0000.000
146A146GLY0-0.050-0.03851.658-0.001-0.0010.0000.0000.0000.000
147A147ILE0-0.0210.01047.528-0.004-0.0040.0000.0000.0000.000
148A148SER0-0.063-0.02849.0870.0030.0030.0000.0000.0000.000
149A149VAL00.0590.01548.157-0.005-0.0050.0000.0000.0000.000
150A150LYS10.9080.95647.5750.0870.0870.0000.0000.0000.000
151A151THR00.0540.03347.489-0.003-0.0030.0000.0000.0000.000
152A152SER0-0.030-0.00444.8260.0020.0020.0000.0000.0000.000
153A160ARG10.9980.99740.7180.1100.1100.0000.0000.0000.000
154A161LEU00.0040.00738.3600.0070.0070.0000.0000.0000.000
155A162PRO0-0.016-0.00642.1410.0010.0010.0000.0000.0000.000
156A163ASN00.0990.05239.942-0.009-0.0090.0000.0000.0000.000
157A164PRO0-0.0060.01742.8330.0000.0000.0000.0000.0000.000
158A165THR0-0.007-0.02841.153-0.007-0.0070.0000.0000.0000.000
159A166LEU00.0020.02243.7310.0050.0050.0000.0000.0000.000
160A167ALA0-0.026-0.02743.375-0.007-0.0070.0000.0000.0000.000
161A168VAL00.0480.02443.7040.0060.0060.0000.0000.0000.000
162A169THR0-0.010-0.02443.626-0.004-0.0040.0000.0000.0000.000
163A170ASP-1-0.686-0.84044.573-0.083-0.0830.0000.0000.0000.000
164A171GLY0-0.033-0.00746.1950.0050.0050.0000.0000.0000.000
165A172LYS10.7040.82343.2030.0800.0800.0000.0000.0000.000
166A173THR00.0230.03339.056-0.006-0.0060.0000.0000.0000.000
167A174THR0-0.073-0.03440.0240.0080.0080.0000.0000.0000.000
168A175ILE00.0450.03138.473-0.008-0.0080.0000.0000.0000.000
169A176LYS10.8040.88938.8940.1400.1400.0000.0000.0000.000
170A177PHE00.0650.03038.947-0.007-0.0070.0000.0000.0000.000
171A178HIS10.8230.88735.5200.1670.1670.0000.0000.0000.000
172A179PRO0-0.0030.00039.395-0.004-0.0040.0000.0000.0000.000
173A180TRP0-0.023-0.00936.7200.0000.0000.0000.0000.0000.000
174A181SER0-0.010-0.03531.303-0.001-0.0010.0000.0000.0000.000
175A182ILE0-0.017-0.02330.2300.0100.0100.0000.0000.0000.000
176A183GLU-1-0.791-0.88926.450-0.294-0.2940.0000.0000.0000.000
177A184GLU-1-0.835-0.88930.354-0.187-0.1870.0000.0000.0000.000
178A185ILE0-0.034-0.01533.7300.0110.0110.0000.0000.0000.000
179A186VAL00.0350.02730.0640.0090.0090.0000.0000.0000.000
180A187ALA0-0.001-0.00431.9380.0050.0050.0000.0000.0000.000
181A188SER0-0.109-0.07033.3460.0110.0110.0000.0000.0000.000
182A189GLU-1-0.986-0.99535.879-0.136-0.1360.0000.0000.0000.000
183A190GLN0-0.085-0.02231.012-0.008-0.0080.0000.0000.0000.000