Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7219K

Calculation Name: 3OKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OKR

Chain ID: A

ChEMBL ID:

UniProt ID: P9WKG9

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2092643.480683
FMO2-HF: Nuclear repulsion 2018406.701153
FMO2-HF: Total energy -74236.77953
FMO2-MP2: Total energy -74458.629603


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:6:GLY)


Summations of interaction energy for fragment #1(A:6: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.
-12.249-12.71711.811-5.98-5.362-0.054
Interaction energy analysis for fragmet #1(A:6:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.028
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].
3A8VAL0-0.029-0.0203.858-0.791-0.016-0.005-0.387-0.3830.000
4A9VAL00.0240.0156.8770.5750.5750.0000.0000.0000.000
5A10ALA0-0.0060.0029.827-0.021-0.0210.0000.0000.0000.000
6A11ILE00.0220.01213.3240.0740.0740.0000.0000.0000.000
7A12VAL0-0.008-0.01616.3500.0130.0130.0000.0000.0000.000
8A13PRO0-0.0330.00119.7550.0280.0280.0000.0000.0000.000
9A14ALA0-0.018-0.02322.4010.0100.0100.0000.0000.0000.000
10A15ALA0-0.022-0.00125.8290.0140.0140.0000.0000.0000.000
11A26PRO00.0520.02333.2750.0000.0000.0000.0000.0000.000
12A27LYS10.7890.86730.5060.0990.0990.0000.0000.0000.000
13A28ALA00.0750.04527.3700.0030.0030.0000.0000.0000.000
14A29PHE00.0680.02428.760-0.001-0.0010.0000.0000.0000.000
15A30TYR0-0.045-0.01531.3690.0090.0090.0000.0000.0000.000
16A31GLN00.0260.00332.146-0.004-0.0040.0000.0000.0000.000
17A32LEU0-0.025-0.00730.9720.0050.0050.0000.0000.0000.000
18A33ASP-1-0.817-0.91233.077-0.053-0.0530.0000.0000.0000.000
19A34GLY00.0240.02234.0490.0040.0040.0000.0000.0000.000
20A35GLN0-0.0250.00226.3700.0020.0020.0000.0000.0000.000
21A36THR0-0.031-0.01128.531-0.005-0.0050.0000.0000.0000.000
22A37LEU0-0.069-0.03728.084-0.003-0.0030.0000.0000.0000.000
23A38ILE00.007-0.00922.628-0.011-0.0110.0000.0000.0000.000
24A39GLU-1-0.764-0.86623.473-0.084-0.0840.0000.0000.0000.000
25A40ARG10.8830.93923.6050.0640.0640.0000.0000.0000.000
26A41ALA0-0.022-0.00822.274-0.004-0.0040.0000.0000.0000.000
27A42VAL0-0.024-0.01118.664-0.025-0.0250.0000.0000.0000.000
28A43ASP-1-0.770-0.87618.841-0.101-0.1010.0000.0000.0000.000
29A44GLY00.0080.00519.7350.0040.0040.0000.0000.0000.000
30A45LEU0-0.043-0.02915.407-0.015-0.0150.0000.0000.0000.000
31A46LEU00.0050.02114.726-0.027-0.0270.0000.0000.0000.000
32A47ASP-1-0.902-0.95815.705-0.032-0.0320.0000.0000.0000.000
33A48SER0-0.125-0.07413.7930.0160.0160.0000.0000.0000.000
34A49GLY0-0.024-0.00913.7330.0240.0240.0000.0000.0000.000
35A50VAL0-0.043-0.0169.2100.1200.1200.0000.0000.0000.000
36A51VAL00.002-0.0139.202-0.287-0.2870.0000.0000.0000.000
37A52ASP-1-0.824-0.8906.326-0.862-0.8620.0000.0000.0000.000
38A53THR0-0.025-0.0239.3060.1910.1910.0000.0000.0000.000
39A54VAL00.0010.00711.757-0.102-0.1020.0000.0000.0000.000
40A55VAL00.0250.01814.1980.0620.0620.0000.0000.0000.000
41A56VAL0-0.004-0.00916.826-0.006-0.0060.0000.0000.0000.000
42A57ALA00.0220.02020.5280.0150.0150.0000.0000.0000.000
43A58VAL00.0000.00822.6810.0020.0020.0000.0000.0000.000
44A59PRO00.0320.00026.4640.0030.0030.0000.0000.0000.000
45A60ALA00.0260.00629.6220.0030.0030.0000.0000.0000.000
46A61ASP-1-0.931-0.97530.526-0.071-0.0710.0000.0000.0000.000
47A62ARG10.8030.87430.4800.0820.0820.0000.0000.0000.000
48A63THR0-0.0050.01026.1380.0000.0000.0000.0000.0000.000
49A64ASP-1-0.814-0.90427.338-0.062-0.0620.0000.0000.0000.000
50A65GLU-1-0.799-0.85929.492-0.070-0.0700.0000.0000.0000.000
51A66ALA00.026-0.00125.7170.0020.0020.0000.0000.0000.000
52A67ARG10.8430.91524.3710.0890.0890.0000.0000.0000.000
53A68GLN0-0.072-0.05025.9660.0070.0070.0000.0000.0000.000
54A69ILE0-0.036-0.00426.9420.0050.0050.0000.0000.0000.000
55A70LEU00.0020.00522.0930.0030.0030.0000.0000.0000.000
56A71GLY00.0320.01823.1520.0060.0060.0000.0000.0000.000
57A72HIS0-0.044-0.04119.424-0.022-0.0220.0000.0000.0000.000
58A73ARG10.7470.86118.2440.0690.0690.0000.0000.0000.000
59A74ALA00.0180.00417.397-0.035-0.0350.0000.0000.0000.000
60A75MET0-0.0110.02015.5140.0250.0250.0000.0000.0000.000
61A76ILE0-0.053-0.02018.759-0.025-0.0250.0000.0000.0000.000
62A77VAL00.0150.00419.5840.0190.0190.0000.0000.0000.000
63A78ALA0-0.016-0.02122.5610.0050.0050.0000.0000.0000.000
64A79GLY00.004-0.00524.057-0.017-0.0170.0000.0000.0000.000
65A80GLY00.0090.00025.8400.0110.0110.0000.0000.0000.000
66A81SER0-0.098-0.03927.8980.0040.0040.0000.0000.0000.000
67A82ASN00.0220.00427.994-0.005-0.0050.0000.0000.0000.000
68A83ARG10.8540.93421.0810.2710.2710.0000.0000.0000.000
69A84THR00.0440.00623.459-0.010-0.0100.0000.0000.0000.000
70A85ASP-1-0.863-0.92923.121-0.170-0.1700.0000.0000.0000.000
71A86THR0-0.007-0.00722.559-0.001-0.0010.0000.0000.0000.000
72A87VAL0-0.0050.00618.107-0.009-0.0090.0000.0000.0000.000
73A88ASN00.0130.00318.841-0.025-0.0250.0000.0000.0000.000
74A89LEU0-0.035-0.00419.826-0.004-0.0040.0000.0000.0000.000
75A90ALA0-0.003-0.02817.858-0.002-0.0020.0000.0000.0000.000
76A91LEU0-0.020-0.01414.812-0.028-0.0280.0000.0000.0000.000
77A92THR0-0.0210.00314.913-0.017-0.0170.0000.0000.0000.000
78A93VAL0-0.092-0.04217.0880.0300.0300.0000.0000.0000.000
79A94LEU00.0180.01910.456-0.036-0.0360.0000.0000.0000.000
80A95SER0-0.061-0.02213.6200.0580.0580.0000.0000.0000.000
81A96GLY00.014-0.00410.981-0.053-0.0530.0000.0000.0000.000
82A97THR0-0.083-0.03611.9670.0570.0570.0000.0000.0000.000
83A98ALA00.0930.0617.5320.0670.0670.0000.0000.0000.000
84A99GLU-1-1.004-1.0166.998-0.010-0.0100.0000.0000.0000.000
85A100PRO00.0180.0134.745-0.0080.097-0.001-0.006-0.0980.000
86A101GLU-1-0.851-0.9061.885-15.643-18.10411.586-5.006-4.119-0.055
87A102PHE0-0.014-0.0264.2400.8041.0100.001-0.048-0.1590.000
88A103VAL0-0.009-0.0067.2630.0660.0660.0000.0000.0000.000
89A104LEU00.0020.00910.5660.1170.1170.0000.0000.0000.000
90A105VAL0-0.012-0.00513.3360.0430.0430.0000.0000.0000.000
91A106HIS00.0890.04616.8510.0070.0070.0000.0000.0000.000
92A107ASP-1-0.834-0.94219.672-0.165-0.1650.0000.0000.0000.000
93A108ALA00.0650.03323.4050.0070.0070.0000.0000.0000.000
94A109ALA0-0.058-0.03424.9500.0150.0150.0000.0000.0000.000
95A110ARG10.8160.93023.2460.2130.2130.0000.0000.0000.000
96A111ALA00.0050.00924.661-0.007-0.0070.0000.0000.0000.000
97A112LEU0-0.0110.00225.9140.0060.0060.0000.0000.0000.000
98A113THR0-0.014-0.02720.4540.0020.0020.0000.0000.0000.000
99A114PRO00.0040.02322.2950.0010.0010.0000.0000.0000.000
100A115PRO00.0940.03118.405-0.021-0.0210.0000.0000.0000.000
101A116ALA0-0.008-0.00517.254-0.022-0.0220.0000.0000.0000.000
102A117LEU0-0.058-0.01717.833-0.009-0.0090.0000.0000.0000.000
103A118VAL00.004-0.00313.845-0.035-0.0350.0000.0000.0000.000
104A119ALA00.0590.03412.952-0.081-0.0810.0000.0000.0000.000
105A120ARG10.8150.90213.1220.1260.1260.0000.0000.0000.000
106A121VAL0-0.023-0.01113.153-0.006-0.0060.0000.0000.0000.000
107A122VAL0-0.0030.0007.979-0.105-0.1050.0000.0000.0000.000
108A123GLU-1-0.851-0.9489.144-0.413-0.4130.0000.0000.0000.000
109A124ALA00.0100.00910.762-0.022-0.0220.0000.0000.0000.000
110A125LEU0-0.053-0.0208.4950.0320.0320.0000.0000.0000.000
111A126ARG10.8130.9032.3123.9004.8070.230-0.533-0.6030.001
112A127ASP-1-0.959-0.9657.721-0.175-0.1750.0000.0000.0000.000
113A128GLY0-0.045-0.01910.0620.0820.0820.0000.0000.0000.000
114A129TYR0-0.075-0.03811.0130.0430.0430.0000.0000.0000.000
115A130ALA00.0270.00411.502-0.073-0.0730.0000.0000.0000.000
116A131ALA00.0180.00612.590-0.049-0.0490.0000.0000.0000.000
117A132VAL0-0.0060.01613.2840.0730.0730.0000.0000.0000.000
118A133VAL00.018-0.00415.831-0.012-0.0120.0000.0000.0000.000
119A134PRO00.0250.03718.1020.0280.0280.0000.0000.0000.000
120A135VAL0-0.021-0.01720.5310.0120.0120.0000.0000.0000.000
121A136LEU0-0.0050.01124.1800.0110.0110.0000.0000.0000.000
122A137PRO0-0.003-0.00827.569-0.001-0.0010.0000.0000.0000.000
123A138LEU0-0.004-0.01431.069-0.002-0.0020.0000.0000.0000.000
124A139SER0-0.022-0.00833.8460.0030.0030.0000.0000.0000.000
125A140ASP-1-0.894-0.93136.843-0.070-0.0700.0000.0000.0000.000
126A141THR0-0.061-0.04238.108-0.003-0.0030.0000.0000.0000.000
127A142ILE00.0490.02435.5610.0030.0030.0000.0000.0000.000
128A143LYS10.8840.92539.0400.0670.0670.0000.0000.0000.000
129A144ALA00.0160.02740.791-0.003-0.0030.0000.0000.0000.000
130A145VAL0-0.036-0.02941.9210.0050.0050.0000.0000.0000.000
131A146ASP-1-0.773-0.87843.766-0.064-0.0640.0000.0000.0000.000
132A147ALA0-0.004-0.00246.3680.0000.0000.0000.0000.0000.000
133A148ASN0-0.089-0.05547.2730.0030.0030.0000.0000.0000.000
134A149GLY0-0.0010.01148.1220.0020.0020.0000.0000.0000.000
135A150VAL0-0.033-0.01849.1530.0010.0010.0000.0000.0000.000
136A151VAL0-0.022-0.02345.824-0.003-0.0030.0000.0000.0000.000
137A152LEU00.0140.00844.1330.0020.0020.0000.0000.0000.000
138A153GLY00.0150.00844.6330.0010.0010.0000.0000.0000.000
139A154THR0-0.027-0.01641.987-0.001-0.0010.0000.0000.0000.000
140A155PRO0-0.0020.01237.6920.0030.0030.0000.0000.0000.000
141A156GLU-1-0.848-0.91536.874-0.091-0.0910.0000.0000.0000.000
142A157ARG10.8620.90937.2930.0760.0760.0000.0000.0000.000
143A158ALA0-0.016-0.00534.755-0.002-0.0020.0000.0000.0000.000
144A159GLY00.0120.01731.983-0.007-0.0070.0000.0000.0000.000
145A160LEU00.0160.00630.718-0.008-0.0080.0000.0000.0000.000
146A161ARG10.9050.94927.4460.1290.1290.0000.0000.0000.000
147A162ALA0-0.0030.00929.029-0.002-0.0020.0000.0000.0000.000
148A163VAL00.0520.02723.338-0.003-0.0030.0000.0000.0000.000
149A164GLN0-0.063-0.05123.0180.0100.0100.0000.0000.0000.000
150A165THR0-0.029-0.02120.027-0.007-0.0070.0000.0000.0000.000
151A166PRO00.0230.00015.8280.0410.0410.0000.0000.0000.000
152A167GLN0-0.023-0.03117.151-0.004-0.0040.0000.0000.0000.000
153A168GLY00.0350.00312.974-0.026-0.0260.0000.0000.0000.000
154A169PHE00.0220.01012.0330.1020.1020.0000.0000.0000.000
155A170THR00.0880.0468.507-0.148-0.1480.0000.0000.0000.000
156A171THR0-0.015-0.0107.5080.2670.2670.0000.0000.0000.000
157A172ASP-1-0.792-0.86610.082-0.377-0.3770.0000.0000.0000.000
158A173LEU00.0060.01112.1490.1060.1060.0000.0000.0000.000
159A174LEU00.0190.02913.4480.0910.0910.0000.0000.0000.000
160A175LEU0-0.003-0.01712.4010.0810.0810.0000.0000.0000.000
161A176ARG10.7920.85614.8280.4850.4850.0000.0000.0000.000
162A177SER0-0.008-0.02017.7960.0410.0410.0000.0000.0000.000
163A178TYR0-0.111-0.06318.4530.0480.0480.0000.0000.0000.000
164A179GLN0-0.087-0.02518.9180.0400.0400.0000.0000.0000.000
165A190TYR00.0160.00026.4890.0040.0040.0000.0000.0000.000
166A191THR0-0.028-0.03526.3560.0020.0020.0000.0000.0000.000
167A192ASP-1-0.840-0.88023.878-0.264-0.2640.0000.0000.0000.000
168A193ASP-1-0.736-0.85319.150-0.316-0.3160.0000.0000.0000.000
169A194ALA00.0450.01719.857-0.013-0.0130.0000.0000.0000.000
170A195SER0-0.009-0.03120.7770.0100.0100.0000.0000.0000.000
171A196LEU0-0.051-0.02221.3660.0180.0180.0000.0000.0000.000
172A197VAL00.0070.01117.6750.0010.0010.0000.0000.0000.000
173A198GLU-1-0.934-0.96520.539-0.220-0.2200.0000.0000.0000.000
174A199HIS0-0.070-0.02823.6030.0180.0180.0000.0000.0000.000
175A200ILE0-0.076-0.02619.0850.0170.0170.0000.0000.0000.000
176A201GLY0-0.045-0.01823.3000.0010.0010.0000.0000.0000.000
177A202GLY0-0.034-0.01619.814-0.001-0.0010.0000.0000.0000.000
178A203GLN0-0.031-0.02119.6120.0180.0180.0000.0000.0000.000
179A204VAL00.0040.00518.146-0.046-0.0460.0000.0000.0000.000
180A205GLN0-0.058-0.02816.7210.0450.0450.0000.0000.0000.000
181A206VAL0-0.028-0.01418.466-0.018-0.0180.0000.0000.0000.000
182A207VAL00.0310.02516.4780.0080.0080.0000.0000.0000.000
183A208ASP-1-0.886-0.94719.795-0.146-0.1460.0000.0000.0000.000
184A209GLY00.0230.01621.059-0.020-0.0200.0000.0000.0000.000
185A210ASP-1-0.859-0.95423.264-0.099-0.0990.0000.0000.0000.000
186A211PRO00.0020.00625.405-0.007-0.0070.0000.0000.0000.000
187A212LEU00.0140.00626.4560.0020.0020.0000.0000.0000.000
188A213ALA00.0000.01923.504-0.001-0.0010.0000.0000.0000.000
189A214PHE0-0.050-0.02925.448-0.010-0.0100.0000.0000.0000.000
190A215LYS10.9170.96427.6650.1350.1350.0000.0000.0000.000
191A216ILE00.0480.03629.2780.0090.0090.0000.0000.0000.000
192A217THR0-0.045-0.03132.030-0.003-0.0030.0000.0000.0000.000
193A218THR0-0.042-0.06334.4280.0070.0070.0000.0000.0000.000
194A219LYS10.9770.96537.6550.0600.0600.0000.0000.0000.000
195A220LEU00.0390.03339.3740.0020.0020.0000.0000.0000.000
196A221ASP-1-0.703-0.81034.186-0.090-0.0900.0000.0000.0000.000
197A222LEU00.0020.00435.174-0.001-0.0010.0000.0000.0000.000
198A223LEU0-0.0240.00036.8260.0030.0030.0000.0000.0000.000
199A224LEU0-0.008-0.00433.8970.0030.0030.0000.0000.0000.000
200A225ALA00.0260.00932.7230.0010.0010.0000.0000.0000.000
201A226GLN00.001-0.01033.9280.0060.0060.0000.0000.0000.000
202A227ALA0-0.034-0.02036.5420.0030.0030.0000.0000.0000.000
203A228ILE00.0000.00230.7860.0030.0030.0000.0000.0000.000
204A229VAL0-0.027-0.00430.7280.0040.0040.0000.0000.0000.000
205A230ARG10.7810.88133.0640.0490.0490.0000.0000.0000.000
206A231GLY0-0.034-0.00535.5270.0060.0060.0000.0000.0000.000