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: 4343N

Calculation Name: 4OK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZKK2

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2835378.797886
FMO2-HF: Nuclear repulsion 2744098.408971
FMO2-HF: Total energy -91280.388915
FMO2-MP2: Total energy -91545.440839


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:LEU)


Summations of interaction energy for fragment #1(A:12:LEU)
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.
-8.82-2.7027.178-3.805-9.494-0.013
Interaction energy analysis for fragmet #1(A:12:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.015
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].
3A14GLU-1-0.867-0.9483.304-3.382-1.2160.036-1.096-1.1070.002
4A15GLN0-0.082-0.0455.9170.0120.0120.0000.0000.0000.000
5A16ALA00.0700.0322.399-0.422-0.5652.219-0.587-1.489-0.001
6A17LEU00.0120.0252.276-2.186-1.1872.826-0.824-3.001-0.002
7A18ASN0-0.033-0.0363.469-0.0580.0910.0310.094-0.2750.000
8A19HIS00.0190.0395.8240.0730.0730.0000.0000.0000.000
9A20GLU-1-0.786-0.8743.106-4.020-2.8000.122-0.519-0.824-0.005
10A21LYS10.8440.9115.8160.7480.7480.0000.0000.0000.000
11A22LEU0-0.0060.0017.9260.1100.1100.0000.0000.0000.000
12A23MET0-0.013-0.0016.4570.1150.1150.0000.0000.0000.000
13A24ARG10.9120.9436.4501.1371.1370.0000.0000.0000.000
14A25ALA0-0.029-0.00110.6090.0670.0670.0000.0000.0000.000
15A26ILE00.003-0.00313.3450.0560.0560.0000.0000.0000.000
16A27VAL00.003-0.01113.1950.0380.0380.0000.0000.0000.000
17A28LYS10.8950.94413.0350.4390.4390.0000.0000.0000.000
18A29ASN0-0.0270.00116.2270.0440.0440.0000.0000.0000.000
19A30LEU00.0160.00518.3370.0250.0250.0000.0000.0000.000
20A31ALA00.0300.03519.1620.0170.0170.0000.0000.0000.000
21A32ASP-1-0.837-0.87820.943-0.152-0.1520.0000.0000.0000.000
22A33THR0-0.079-0.05323.0050.0190.0190.0000.0000.0000.000
23A34PRO00.000-0.03024.735-0.005-0.0050.0000.0000.0000.000
24A35MET0-0.0480.00621.1230.0060.0060.0000.0000.0000.000
25A36VAL00.0120.01221.117-0.013-0.0130.0000.0000.0000.000
26A37LEU0-0.0190.00213.1870.0130.0130.0000.0000.0000.000
27A38LYS10.8730.91517.4400.0860.0860.0000.0000.0000.000
28A39GLY00.0750.03116.040-0.015-0.0150.0000.0000.0000.000
29A40GLU-1-0.778-0.89412.197-0.062-0.0620.0000.0000.0000.000
30A41THR00.039-0.0119.367-0.048-0.0480.0000.0000.0000.000
31A42ALA0-0.0180.01711.349-0.084-0.0840.0000.0000.0000.000
32A43LEU00.0160.01512.862-0.039-0.0390.0000.0000.0000.000
33A44TYR0-0.069-0.0493.274-0.8720.0070.077-0.289-0.667-0.001
34A45LEU0-0.059-0.0437.678-0.124-0.1240.0000.0000.0000.000
35A46GLY0-0.045-0.01910.219-0.003-0.0030.0000.0000.0000.000
36A47TYR0-0.028-0.04312.6590.0330.0330.0000.0000.0000.000
37A48GLY00.0440.03910.0960.0510.0510.0000.0000.0000.000
38A49LEU0-0.044-0.0069.4700.0080.0080.0000.0000.0000.000
39A50ASN0-0.001-0.0088.119-0.189-0.1890.0000.0000.0000.000
40A51ARG10.8250.8886.8780.1220.1220.0000.0000.0000.000
41A52PHE0-0.0040.0102.538-1.255-0.4131.868-0.583-2.127-0.006
42A53SER00.006-0.0245.3750.2120.218-0.001-0.001-0.0040.000
43A54GLU-1-0.833-0.9166.9320.1720.1720.0000.0000.0000.000
44A55ASP-1-0.769-0.8599.078-0.015-0.0150.0000.0000.0000.000
45A56LEU0-0.0210.00012.102-0.060-0.0600.0000.0000.0000.000
46A57ASP-1-0.841-0.91414.335-0.056-0.0560.0000.0000.0000.000
47A58PHE0-0.006-0.03716.612-0.025-0.0250.0000.0000.0000.000
48A59ASP-1-0.788-0.87320.138-0.072-0.0720.0000.0000.0000.000
49A60CYS0-0.042-0.04123.678-0.015-0.0150.0000.0000.0000.000
50A61HIS00.0570.02426.1260.0110.0110.0000.0000.0000.000
51A62LYS10.9390.98129.2360.0920.0920.0000.0000.0000.000
52A63LYS10.8670.92328.8310.0500.0500.0000.0000.0000.000
53A64ILE00.0300.01224.017-0.001-0.0010.0000.0000.0000.000
54A65ASN00.0060.00228.0170.0040.0040.0000.0000.0000.000
55A66LEU00.0520.03221.072-0.008-0.0080.0000.0000.0000.000
56A67LEU00.0470.01223.073-0.011-0.0110.0000.0000.0000.000
57A68GLY00.0000.00523.843-0.006-0.0060.0000.0000.0000.000
58A69ARG10.7900.87421.7860.1520.1520.0000.0000.0000.000
59A70VAL00.0220.00818.044-0.016-0.0160.0000.0000.0000.000
60A71LYS10.9370.96119.3670.0720.0720.0000.0000.0000.000
61A72SER0-0.045-0.03221.026-0.003-0.0030.0000.0000.0000.000
62A73ALA0-0.0220.00116.903-0.008-0.0080.0000.0000.0000.000
63A74ILE0-0.0280.00216.006-0.036-0.0360.0000.0000.0000.000
64A75PRO00.0040.02412.2180.0100.0100.0000.0000.0000.000
65A76ASN00.042-0.00515.2960.0280.0280.0000.0000.0000.000
66A77GLY0-0.021-0.01813.628-0.057-0.0570.0000.0000.0000.000
67A78ILE0-0.0210.01010.641-0.001-0.0010.0000.0000.0000.000
68A79ILE0-0.018-0.00714.6480.0160.0160.0000.0000.0000.000
69A80LEU00.0020.00517.4200.0070.0070.0000.0000.0000.000
70A81ASN0-0.064-0.04219.226-0.005-0.0050.0000.0000.0000.000
71A82ASP-1-0.870-0.95320.501-0.028-0.0280.0000.0000.0000.000
72A83ILE0-0.086-0.03320.426-0.012-0.0120.0000.0000.0000.000
73A84HIS00.0490.03722.1560.0060.0060.0000.0000.0000.000
74A85ILE00.008-0.01323.339-0.005-0.0050.0000.0000.0000.000
75A86LYS10.8800.94022.576-0.016-0.0160.0000.0000.0000.000
76A87LYS10.9160.94825.9760.0180.0180.0000.0000.0000.000
77A88ASP-1-0.796-0.86326.751-0.064-0.0640.0000.0000.0000.000
78A89THR0-0.033-0.02029.2190.0060.0060.0000.0000.0000.000
79A90ASP-1-0.861-0.92630.965-0.041-0.0410.0000.0000.0000.000
80A91SER0-0.035-0.02130.948-0.002-0.0020.0000.0000.0000.000
81A92VAL0-0.030-0.01125.370-0.002-0.0020.0000.0000.0000.000
82A93GLY00.0300.02525.0020.0030.0030.0000.0000.0000.000
83A94ARG10.8090.86521.8460.0130.0130.0000.0000.0000.000
84A95TYR0-0.029-0.04120.4240.0050.0050.0000.0000.0000.000
85A96MET0-0.0060.01118.7120.0110.0110.0000.0000.0000.000
86A97VAL00.0280.02716.1710.0020.0020.0000.0000.0000.000
87A98ARG10.8950.94616.305-0.014-0.0140.0000.0000.0000.000
88A99TYR0-0.022-0.0509.673-0.022-0.0220.0000.0000.0000.000
89A100ALA00.0950.04914.8590.0320.0320.0000.0000.0000.000
90A101THR0-0.018-0.01110.407-0.064-0.0640.0000.0000.0000.000
91A102LYS10.8280.89111.5670.3940.3940.0000.0000.0000.000
92A103ASP-1-0.784-0.86310.905-0.323-0.3230.0000.0000.0000.000
93A104ASN00.013-0.00512.6530.0360.0360.0000.0000.0000.000
94A105LYS10.9890.99214.350-0.092-0.0920.0000.0000.0000.000
95A106GLU-1-0.962-0.96814.4040.2360.2360.0000.0000.0000.000
96A107GLU-1-0.848-0.90315.1820.0010.0010.0000.0000.0000.000
97A108GLN0-0.0250.00011.4060.0720.0720.0000.0000.0000.000
98A109THR0-0.030-0.03513.520-0.016-0.0160.0000.0000.0000.000
99A110LEU0-0.0030.00211.2590.0090.0090.0000.0000.0000.000
100A111LYS10.8010.90013.757-0.037-0.0370.0000.0000.0000.000
101A112LEU00.0110.01115.232-0.024-0.0240.0000.0000.0000.000
102A113GLU-1-0.801-0.86817.562-0.009-0.0090.0000.0000.0000.000
103A114ILE0-0.006-0.01120.032-0.016-0.0160.0000.0000.0000.000
104A115SER00.0000.01022.7070.0170.0170.0000.0000.0000.000
105A116TYR00.003-0.03525.552-0.011-0.0110.0000.0000.0000.000
106A117ARG10.9370.97028.6470.0330.0330.0000.0000.0000.000
107A118ASP-1-0.878-0.93228.689-0.048-0.0480.0000.0000.0000.000
108A119ALA0-0.019-0.00227.291-0.005-0.0050.0000.0000.0000.000
109A120PRO0-0.0150.00224.7010.0040.0040.0000.0000.0000.000
110A121LYS10.9120.95427.8950.0820.0820.0000.0000.0000.000
111A122GLU-1-0.797-0.89727.754-0.127-0.1270.0000.0000.0000.000
112A123SER0-0.013-0.00428.346-0.005-0.0050.0000.0000.0000.000
113A124GLU-1-0.816-0.90627.243-0.087-0.0870.0000.0000.0000.000
114A125VAL0-0.044-0.01722.832-0.006-0.0060.0000.0000.0000.000
115A126ASN0-0.0040.00620.8010.0190.0190.0000.0000.0000.000
116A127VAL0-0.002-0.01119.889-0.005-0.0050.0000.0000.0000.000
117A128ILE00.0200.02114.9150.0080.0080.0000.0000.0000.000
118A129GLU-1-0.889-0.94613.293-0.428-0.4280.0000.0000.0000.000
119A130GLY0-0.049-0.02915.295-0.022-0.0220.0000.0000.0000.000
120A131MET0-0.053-0.01511.6280.0010.0010.0000.0000.0000.000
121A132ARG10.8210.88916.9620.1620.1620.0000.0000.0000.000
122A133ILE0-0.027-0.01314.610-0.007-0.0070.0000.0000.0000.000
123A134ALA00.0270.01518.9030.0170.0170.0000.0000.0000.000
124A135LYS10.8780.95720.0580.1150.1150.0000.0000.0000.000
125A136ILE00.0570.03218.0060.0050.0050.0000.0000.0000.000
126A137GLU-1-0.796-0.88521.332-0.101-0.1010.0000.0000.0000.000
127A138ARG10.8330.91923.4850.0970.0970.0000.0000.0000.000
128A139ILE0-0.024-0.00917.2800.0090.0090.0000.0000.0000.000
129A140ILE00.0230.01020.9710.0120.0120.0000.0000.0000.000
130A141ASP-1-0.835-0.91122.582-0.026-0.0260.0000.0000.0000.000
131A142ASN0-0.052-0.04122.0730.0110.0110.0000.0000.0000.000
132A143LYS10.7380.84915.8600.0100.0100.0000.0000.0000.000
133A144LEU00.0290.01221.8250.0150.0150.0000.0000.0000.000
134A145CYS0-0.0150.00425.1380.0080.0080.0000.0000.0000.000
135A146ALA0-0.043-0.02722.2530.0080.0080.0000.0000.0000.000
136A147CYS0-0.062-0.03222.4400.0080.0080.0000.0000.0000.000
137A148PHE0-0.089-0.04024.5130.0100.0100.0000.0000.0000.000
138A149ASP-1-0.783-0.88027.9350.0010.0010.0000.0000.0000.000
139A150GLY00.0480.03728.932-0.005-0.0050.0000.0000.0000.000
140A151GLU-1-0.992-0.99429.9190.0040.0040.0000.0000.0000.000
141A152HIS0-0.088-0.05126.3570.0050.0050.0000.0000.0000.000
142A153THR0-0.0390.01026.7800.0020.0020.0000.0000.0000.000
143A154ARG10.7450.84117.990-0.031-0.0310.0000.0000.0000.000
144A155THR00.0380.01523.719-0.005-0.0050.0000.0000.0000.000
145A156LYS10.7990.89215.507-0.224-0.2240.0000.0000.0000.000
146A157ALA00.0570.02117.406-0.015-0.0150.0000.0000.0000.000
147A158ARG10.7450.83411.400-0.312-0.3120.0000.0000.0000.000
148A159ASP-1-0.745-0.82515.6200.0220.0220.0000.0000.0000.000
149A160LEU00.0360.03218.482-0.020-0.0200.0000.0000.0000.000
150A161PHE00.014-0.00911.172-0.009-0.0090.0000.0000.0000.000
151A162ASP-1-0.724-0.85313.370-0.023-0.0230.0000.0000.0000.000
152A163LEU00.0040.00615.830-0.033-0.0330.0000.0000.0000.000
153A164HIS0-0.045-0.02018.020-0.023-0.0230.0000.0000.0000.000
154A165PHE00.0390.01713.005-0.019-0.0190.0000.0000.0000.000
155A166LEU0-0.046-0.03316.612-0.026-0.0260.0000.0000.0000.000
156A167ALA0-0.031-0.01618.982-0.009-0.0090.0000.0000.0000.000
157A168LYS10.8210.88918.551-0.034-0.0340.0000.0000.0000.000
158A169HIS0-0.046-0.02115.648-0.015-0.0150.0000.0000.0000.000
159A170TYR0-0.065-0.04615.375-0.017-0.0170.0000.0000.0000.000
160A171GLU-1-0.898-0.95121.417-0.042-0.0420.0000.0000.0000.000
161A172GLU-1-0.828-0.91223.652-0.112-0.1120.0000.0000.0000.000
162A173HIS10.6860.81922.9510.1210.1210.0000.0000.0000.000
163A174PHE00.0090.01122.5970.0050.0050.0000.0000.0000.000
164A175ASN00.0280.01627.3630.0060.0060.0000.0000.0000.000
165A176LEU00.026-0.00630.8580.0040.0040.0000.0000.0000.000
166A177ASP-1-0.832-0.91431.642-0.018-0.0180.0000.0000.0000.000
167A178LEU00.0260.01126.2900.0040.0040.0000.0000.0000.000
168A179ALA00.0160.00828.5310.0060.0060.0000.0000.0000.000
169A180SER0-0.039-0.01729.7410.0070.0070.0000.0000.0000.000
170A181ARG10.7240.83328.7950.0230.0230.0000.0000.0000.000
171A182LEU00.0100.02223.6570.0070.0070.0000.0000.0000.000
172A183LYS10.8970.95127.6890.0030.0030.0000.0000.0000.000
173A184ASP-1-0.856-0.91830.3000.0310.0310.0000.0000.0000.000
174A185PHE00.0040.00323.0780.0070.0070.0000.0000.0000.000
175A186SER0-0.048-0.04826.0450.0090.0090.0000.0000.0000.000
176A187LYS10.7830.88427.991-0.031-0.0310.0000.0000.0000.000
177A188ASP-1-0.908-0.95630.8530.0700.0700.0000.0000.0000.000
178A189PRO00.0330.00127.6980.0060.0060.0000.0000.0000.000
179A190ASP-1-0.851-0.92527.7590.1060.1060.0000.0000.0000.000
180A191LYS10.8210.90629.464-0.069-0.0690.0000.0000.0000.000
181A192LEU0-0.0170.00724.6210.0080.0080.0000.0000.0000.000
182A193VAL00.004-0.00324.6220.0140.0140.0000.0000.0000.000
183A194SER0-0.059-0.04725.6070.0150.0150.0000.0000.0000.000
184A195ASP-1-0.878-0.91826.4380.0990.0990.0000.0000.0000.000
185A196TYR0-0.014-0.01921.3770.0070.0070.0000.0000.0000.000
186A197LEU00.0020.01921.6820.0320.0320.0000.0000.0000.000
187A198VAL0-0.014-0.02621.7810.0290.0290.0000.0000.0000.000
188A199ASP-1-0.784-0.89918.7130.2560.2560.0000.0000.0000.000
189A200VAL00.0370.01616.8600.0370.0370.0000.0000.0000.000
190A201LYS10.9020.95616.680-0.282-0.2820.0000.0000.0000.000
191A202LEU00.003-0.00817.3670.0490.0490.0000.0000.0000.000
192A203ASP-1-0.762-0.82812.5860.4530.4530.0000.0000.0000.000
193A204ALA00.0110.01110.6440.0450.0450.0000.0000.0000.000
194A205LEU0-0.057-0.0306.7010.2540.2540.0000.0000.0000.000
195A206LEU00.006-0.0099.533-0.023-0.0230.0000.0000.0000.000
196A207ASN0-0.086-0.04112.3870.1490.1490.0000.0000.0000.000
197A208GLN0-0.0080.0029.694-0.207-0.2070.0000.0000.0000.000
198A209ILE0-0.050-0.0307.971-0.016-0.0160.0000.0000.0000.000
199A210MET0-0.0370.00511.266-0.114-0.1140.0000.0000.0000.000
200A211ASP-1-0.825-0.89114.6910.2640.2640.0000.0000.0000.000
201A212LEU0-0.055-0.01018.078-0.034-0.0340.0000.0000.0000.000
202A213GLU-1-0.855-0.94920.4820.2030.2030.0000.0000.0000.000
203A214GLU-1-0.932-0.96619.3470.1350.1350.0000.0000.0000.000
204A215THR0-0.050-0.04618.378-0.023-0.0230.0000.0000.0000.000
205A216ALA0-0.010-0.01220.824-0.026-0.0260.0000.0000.0000.000
206A217LEU0-0.0190.00523.906-0.018-0.0180.0000.0000.0000.000
207A218GLU-1-0.766-0.87120.8600.0460.0460.0000.0000.0000.000
208A219LEU00.0020.00021.996-0.016-0.0160.0000.0000.0000.000
209A220GLY00.0610.04324.071-0.012-0.0120.0000.0000.0000.000
210A221VAL0-0.064-0.03527.526-0.010-0.0100.0000.0000.0000.000
211A222MET0-0.016-0.00621.128-0.013-0.0130.0000.0000.0000.000
212A223ALA00.0410.03126.740-0.010-0.0100.0000.0000.0000.000
213A224GLN00.0110.00628.078-0.010-0.0100.0000.0000.0000.000
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