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: 94132

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2092198.177543
FMO2-HF: Nuclear repulsion 2017963.389286
FMO2-HF: Total energy -74234.788256
FMO2-MP2: Total energy -74456.944109


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.
-6.707-4.0345.262-4.4-3.537-0.035
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 : -0.006 / q_NPA : -0.011
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].
3A8VAL0-0.046-0.0213.812-1.585-0.626-0.009-0.481-0.4700.002
4A9VAL00.0390.0236.7250.6020.6020.0000.0000.0000.000
5A10ALA0-0.031-0.0159.848-0.063-0.0630.0000.0000.0000.000
6A11ILE00.006-0.00213.3390.0950.0950.0000.0000.0000.000
7A12VAL0-0.008-0.01516.413-0.008-0.0080.0000.0000.0000.000
8A13PRO0-0.033-0.00619.5330.0370.0370.0000.0000.0000.000
9A14ALA0-0.033-0.01622.3380.0030.0030.0000.0000.0000.000
10A15ALA0-0.009-0.00225.7250.0150.0150.0000.0000.0000.000
11A26PRO00.0350.01733.4450.0000.0000.0000.0000.0000.000
12A27LYS10.8430.91429.6930.1080.1080.0000.0000.0000.000
13A28ALA00.0760.05227.7700.0000.0000.0000.0000.0000.000
14A29PHE00.0690.00928.841-0.002-0.0020.0000.0000.0000.000
15A30TYR0-0.046-0.00631.3990.0080.0080.0000.0000.0000.000
16A31GLN00.0220.00332.117-0.005-0.0050.0000.0000.0000.000
17A32LEU0-0.052-0.01131.0670.0040.0040.0000.0000.0000.000
18A33ASP-1-0.899-0.99033.210-0.072-0.0720.0000.0000.0000.000
19A34GLY00.0310.03334.5600.0000.0000.0000.0000.0000.000
20A35GLN00.0400.03527.0860.0030.0030.0000.0000.0000.000
21A36THR0-0.007-0.01328.756-0.008-0.0080.0000.0000.0000.000
22A37LEU0-0.029-0.02527.987-0.004-0.0040.0000.0000.0000.000
23A38ILE00.0100.00222.990-0.015-0.0150.0000.0000.0000.000
24A39GLU-1-0.866-0.93223.627-0.081-0.0810.0000.0000.0000.000
25A40ARG10.8970.96323.8230.0890.0890.0000.0000.0000.000
26A41ALA0-0.038-0.01622.161-0.014-0.0140.0000.0000.0000.000
27A42VAL0-0.025-0.02818.764-0.031-0.0310.0000.0000.0000.000
28A43ASP-1-0.800-0.89918.956-0.126-0.1260.0000.0000.0000.000
29A44GLY00.0150.01919.456-0.012-0.0120.0000.0000.0000.000
30A45LEU0-0.060-0.04515.529-0.034-0.0340.0000.0000.0000.000
31A46LEU00.0130.02515.009-0.055-0.0550.0000.0000.0000.000
32A47ASP-1-0.909-0.96115.536-0.151-0.1510.0000.0000.0000.000
33A48SER0-0.157-0.09813.925-0.019-0.0190.0000.0000.0000.000
34A49GLY0-0.0090.00213.259-0.013-0.0130.0000.0000.0000.000
35A50VAL0-0.048-0.0198.9720.0220.0220.0000.0000.0000.000
36A51VAL0-0.026-0.0178.869-0.334-0.3340.0000.0000.0000.000
37A52ASP-1-0.841-0.9026.465-0.893-0.8930.0000.0000.0000.000
38A53THR0-0.013-0.0119.8440.2380.2380.0000.0000.0000.000
39A54VAL00.0080.00411.878-0.124-0.1240.0000.0000.0000.000
40A55VAL0-0.0040.00014.3270.0690.0690.0000.0000.0000.000
41A56VAL00.0120.00716.931-0.031-0.0310.0000.0000.0000.000
42A57ALA0-0.0070.00020.5020.0230.0230.0000.0000.0000.000
43A58VAL0-0.0130.00622.679-0.005-0.0050.0000.0000.0000.000
44A59PRO00.0340.00726.3720.0060.0060.0000.0000.0000.000
45A60ALA00.0530.01029.2640.0030.0030.0000.0000.0000.000
46A61ASP-1-0.943-0.97330.192-0.038-0.0380.0000.0000.0000.000
47A62ARG10.8640.93830.0970.0590.0590.0000.0000.0000.000
48A63THR0-0.024-0.00426.2270.0020.0020.0000.0000.0000.000
49A64ASP-1-0.921-0.97527.543-0.009-0.0090.0000.0000.0000.000
50A65GLU-1-0.812-0.92029.594-0.046-0.0460.0000.0000.0000.000
51A66ALA0-0.008-0.01026.046-0.001-0.0010.0000.0000.0000.000
52A67ARG10.9650.98424.3340.0090.0090.0000.0000.0000.000
53A68GLN0-0.084-0.03126.3340.0020.0020.0000.0000.0000.000
54A69ILE0-0.0310.00026.5810.0020.0020.0000.0000.0000.000
55A70LEU00.0150.00722.147-0.001-0.0010.0000.0000.0000.000
56A71GLY00.0230.01422.9720.0010.0010.0000.0000.0000.000
57A72HIS0-0.064-0.04720.003-0.006-0.0060.0000.0000.0000.000
58A73ARG10.8560.94918.6720.0740.0740.0000.0000.0000.000
59A74ALA00.0320.01617.681-0.036-0.0360.0000.0000.0000.000
60A75MET0-0.0190.02116.0720.0300.0300.0000.0000.0000.000
61A76ILE0-0.021-0.01418.910-0.028-0.0280.0000.0000.0000.000
62A77VAL0-0.020-0.01319.2430.0180.0180.0000.0000.0000.000
63A78ALA0-0.024-0.02622.324-0.007-0.0070.0000.0000.0000.000
64A79GLY0-0.037-0.03424.589-0.008-0.0080.0000.0000.0000.000
65A80GLY00.0500.02326.3120.0070.0070.0000.0000.0000.000
66A81SER0-0.107-0.04128.1660.0000.0000.0000.0000.0000.000
67A82ASN00.0120.00128.190-0.011-0.0110.0000.0000.0000.000
68A83ARG10.9120.94121.2920.2460.2460.0000.0000.0000.000
69A84THR00.024-0.01123.3780.0010.0010.0000.0000.0000.000
70A85ASP-1-0.866-0.92123.390-0.103-0.1030.0000.0000.0000.000
71A86THR00.0350.01622.4160.0070.0070.0000.0000.0000.000
72A87VAL0-0.0010.01618.2220.0020.0020.0000.0000.0000.000
73A88ASN00.0780.03918.827-0.023-0.0230.0000.0000.0000.000
74A89LEU0-0.0040.02119.3180.0050.0050.0000.0000.0000.000
75A90ALA0-0.016-0.04217.8830.0110.0110.0000.0000.0000.000
76A91LEU0-0.026-0.01814.462-0.005-0.0050.0000.0000.0000.000
77A92THR0-0.060-0.02515.1200.0090.0090.0000.0000.0000.000
78A93VAL0-0.084-0.03316.1480.0390.0390.0000.0000.0000.000
79A94LEU00.0030.03610.041-0.049-0.0490.0000.0000.0000.000
80A95SER0-0.037-0.03713.4730.0700.0700.0000.0000.0000.000
81A96GLY0-0.014-0.01511.288-0.056-0.0560.0000.0000.0000.000
82A97THR0-0.086-0.03811.9450.0370.0370.0000.0000.0000.000
83A98ALA00.0740.0437.8480.0100.0100.0000.0000.0000.000
84A99GLU-1-0.991-1.0176.5350.6040.6040.0000.0000.0000.000
85A100PRO00.0050.0305.1010.1690.1690.0000.0000.0000.000
86A101GLU-1-0.868-0.9402.150-8.689-7.4505.264-3.780-2.724-0.037
87A102PHE0-0.020-0.0224.0620.7000.835-0.001-0.025-0.1100.000
88A103VAL0-0.016-0.0127.0370.0890.0890.0000.0000.0000.000
89A104LEU0-0.0030.02410.4440.0760.0760.0000.0000.0000.000
90A105VAL0-0.0040.01613.1060.0670.0670.0000.0000.0000.000
91A106HIS00.1000.04216.680-0.016-0.0160.0000.0000.0000.000
92A107ASP-1-0.900-0.94219.148-0.158-0.1580.0000.0000.0000.000
93A108ALA00.0800.02722.9440.0020.0020.0000.0000.0000.000
94A109ALA0-0.069-0.04824.5370.0140.0140.0000.0000.0000.000
95A110ARG10.8430.93223.6810.2320.2320.0000.0000.0000.000
96A111ALA00.0060.00724.412-0.014-0.0140.0000.0000.0000.000
97A112LEU0-0.024-0.00825.4510.0020.0020.0000.0000.0000.000
98A113THR00.001-0.01320.751-0.001-0.0010.0000.0000.0000.000
99A114PRO0-0.0200.00122.3120.0030.0030.0000.0000.0000.000
100A115PRO00.0950.04218.232-0.030-0.0300.0000.0000.0000.000
101A116ALA00.0120.00417.347-0.047-0.0470.0000.0000.0000.000
102A117LEU0-0.052-0.00617.639-0.037-0.0370.0000.0000.0000.000
103A118VAL00.0560.01314.183-0.031-0.0310.0000.0000.0000.000
104A119ALA00.0340.03613.249-0.100-0.1000.0000.0000.0000.000
105A120ARG10.8620.92913.5340.2560.2560.0000.0000.0000.000
106A121VAL0-0.042-0.02213.157-0.020-0.0200.0000.0000.0000.000
107A122VAL0-0.002-0.0228.712-0.084-0.0840.0000.0000.0000.000
108A123GLU-1-0.888-0.9599.923-1.032-1.0320.0000.0000.0000.000
109A124ALA0-0.020-0.00611.639-0.024-0.0240.0000.0000.0000.000
110A125LEU0-0.055-0.0228.6710.0590.0590.0000.0000.0000.000
111A126ARG10.8820.9593.0944.1034.4430.008-0.114-0.2330.000
112A127ASP-1-0.935-0.9558.565-0.626-0.6260.0000.0000.0000.000
113A128GLY0-0.058-0.02410.5550.1530.1530.0000.0000.0000.000
114A129TYR0-0.067-0.03511.8970.0690.0690.0000.0000.0000.000
115A130ALA00.0400.01611.647-0.108-0.1080.0000.0000.0000.000
116A131ALA00.012-0.00212.645-0.039-0.0390.0000.0000.0000.000
117A132VAL00.0180.02813.4960.0710.0710.0000.0000.0000.000
118A133VAL00.005-0.00616.0050.0010.0010.0000.0000.0000.000
119A134PRO00.0190.03218.4930.0210.0210.0000.0000.0000.000
120A135VAL0-0.016-0.01120.9320.0260.0260.0000.0000.0000.000
121A136LEU00.0030.00524.5670.0020.0020.0000.0000.0000.000
122A137PRO0-0.010-0.00127.9770.0040.0040.0000.0000.0000.000
123A138LEU0-0.001-0.01231.392-0.001-0.0010.0000.0000.0000.000
124A139SER0-0.024-0.00834.0900.0020.0020.0000.0000.0000.000
125A140ASP-1-0.890-0.92937.006-0.091-0.0910.0000.0000.0000.000
126A141THR0-0.056-0.03938.179-0.003-0.0030.0000.0000.0000.000
127A142ILE00.0400.02935.6920.0020.0020.0000.0000.0000.000
128A143LYS10.8830.91239.1090.0820.0820.0000.0000.0000.000
129A144ALA00.0120.01940.566-0.003-0.0030.0000.0000.0000.000
130A145VAL0-0.023-0.00841.7280.0050.0050.0000.0000.0000.000
131A146ASP-1-0.780-0.88143.412-0.069-0.0690.0000.0000.0000.000
132A147ALA00.004-0.02545.7640.0000.0000.0000.0000.0000.000
133A148ASN0-0.054-0.02646.8200.0030.0030.0000.0000.0000.000
134A149GLY0-0.0160.00747.9050.0020.0020.0000.0000.0000.000
135A150VAL0-0.037-0.01648.9290.0010.0010.0000.0000.0000.000
136A151VAL0-0.043-0.03046.012-0.003-0.0030.0000.0000.0000.000
137A152LEU0-0.001-0.00443.6920.0020.0020.0000.0000.0000.000
138A153GLY00.022-0.00144.6960.0020.0020.0000.0000.0000.000
139A154THR0-0.023-0.00341.923-0.002-0.0020.0000.0000.0000.000
140A155PRO00.0140.04137.5730.0020.0020.0000.0000.0000.000
141A156GLU-1-0.906-0.95037.758-0.119-0.1190.0000.0000.0000.000
142A157ARG10.9220.91637.4250.0990.0990.0000.0000.0000.000
143A158ALA0-0.027-0.00734.536-0.002-0.0020.0000.0000.0000.000
144A159GLY00.0150.02931.980-0.007-0.0070.0000.0000.0000.000
145A160LEU00.0110.00430.754-0.010-0.0100.0000.0000.0000.000
146A161ARG10.9020.95027.4490.1820.1820.0000.0000.0000.000
147A162ALA00.0010.00328.9540.0020.0020.0000.0000.0000.000
148A163VAL00.0760.03423.041-0.007-0.0070.0000.0000.0000.000
149A164GLN0-0.102-0.07023.1510.0080.0080.0000.0000.0000.000
150A165THR0-0.045-0.02819.9150.0030.0030.0000.0000.0000.000
151A166PRO00.011-0.00315.6930.0410.0410.0000.0000.0000.000
152A167GLN00.017-0.00916.965-0.020-0.0200.0000.0000.0000.000
153A168GLY00.0360.00012.876-0.014-0.0140.0000.0000.0000.000
154A169PHE00.015-0.00411.7700.0800.0800.0000.0000.0000.000
155A170THR00.1080.0637.873-0.143-0.1430.0000.0000.0000.000
156A171THR0-0.018-0.0027.5210.2390.2390.0000.0000.0000.000
157A172ASP-1-0.813-0.8999.945-0.228-0.2280.0000.0000.0000.000
158A173LEU0-0.021-0.00711.9850.0900.0900.0000.0000.0000.000
159A174LEU00.0140.00513.1580.0700.0700.0000.0000.0000.000
160A175LEU0-0.010-0.01312.8990.0670.0670.0000.0000.0000.000
161A176ARG10.8260.90514.2410.3730.3730.0000.0000.0000.000
162A177SER0-0.005-0.01917.6030.0290.0290.0000.0000.0000.000
163A178TYR0-0.113-0.03518.6510.0280.0280.0000.0000.0000.000
164A179GLN0-0.055-0.01420.7060.0240.0240.0000.0000.0000.000
165A190TYR00.0300.00926.6460.0010.0010.0000.0000.0000.000
166A191THR0-0.031-0.04025.7840.0100.0100.0000.0000.0000.000
167A192ASP-1-0.867-0.91023.790-0.268-0.2680.0000.0000.0000.000
168A193ASP-1-0.789-0.88118.951-0.300-0.3000.0000.0000.0000.000
169A194ALA00.0360.00719.621-0.001-0.0010.0000.0000.0000.000
170A195SER00.006-0.01920.5500.0140.0140.0000.0000.0000.000
171A196LEU0-0.021-0.01621.2250.0160.0160.0000.0000.0000.000
172A197VAL0-0.0170.00417.4040.0070.0070.0000.0000.0000.000
173A198GLU-1-0.919-0.96120.272-0.242-0.2420.0000.0000.0000.000
174A199HIS0-0.100-0.04123.2570.0170.0170.0000.0000.0000.000
175A200ILE0-0.083-0.03618.8200.0170.0170.0000.0000.0000.000
176A201GLY0-0.037-0.01223.1280.0060.0060.0000.0000.0000.000
177A202GLY0-0.045-0.01419.361-0.004-0.0040.0000.0000.0000.000
178A203GLN00.001-0.00619.4370.0350.0350.0000.0000.0000.000
179A204VAL0-0.009-0.01118.308-0.042-0.0420.0000.0000.0000.000
180A205GLN0-0.043-0.00217.3670.0430.0430.0000.0000.0000.000
181A206VAL0-0.020-0.01618.685-0.024-0.0240.0000.0000.0000.000
182A207VAL0-0.0130.00317.2800.0020.0020.0000.0000.0000.000
183A208ASP-1-0.898-0.95420.408-0.230-0.2300.0000.0000.0000.000
184A209GLY00.0090.00021.754-0.029-0.0290.0000.0000.0000.000
185A210ASP-1-0.823-0.94523.596-0.186-0.1860.0000.0000.0000.000
186A211PRO0-0.0010.02126.035-0.004-0.0040.0000.0000.0000.000
187A212LEU00.0180.00626.5990.0110.0110.0000.0000.0000.000
188A213ALA0-0.020-0.00324.0140.0030.0030.0000.0000.0000.000
189A214PHE0-0.047-0.01525.856-0.005-0.0050.0000.0000.0000.000
190A215LYS10.9560.96927.6610.1470.1470.0000.0000.0000.000
191A216ILE00.0290.02329.3250.0120.0120.0000.0000.0000.000
192A217THR0-0.090-0.08231.8260.0020.0020.0000.0000.0000.000
193A218THR0-0.023-0.01634.2640.0100.0100.0000.0000.0000.000
194A219LYS10.9970.97037.3930.0660.0660.0000.0000.0000.000
195A220LEU00.0450.02039.2100.0020.0020.0000.0000.0000.000
196A221ASP-1-0.734-0.82434.019-0.112-0.1120.0000.0000.0000.000
197A222LEU00.0240.00835.190-0.001-0.0010.0000.0000.0000.000
198A223LEU0-0.0320.00236.8500.0010.0010.0000.0000.0000.000
199A224LEU00.008-0.00233.7960.0030.0030.0000.0000.0000.000
200A225ALA0-0.012-0.00432.866-0.002-0.0020.0000.0000.0000.000
201A226GLN0-0.004-0.02034.2670.0030.0030.0000.0000.0000.000
202A227ALA0-0.023-0.01936.5640.0020.0020.0000.0000.0000.000
203A228ILE0-0.0030.00431.1480.0020.0020.0000.0000.0000.000
204A229VAL0-0.056-0.01730.8790.0010.0010.0000.0000.0000.000
205A230ARG10.8770.95233.1290.0660.0660.0000.0000.0000.000
206A231GLY0-0.042-0.00735.3270.0070.0070.0000.0000.0000.000