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: MVQ5Z

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091215.552481
FMO2-HF: Nuclear repulsion 2016979.617233
FMO2-HF: Total energy -74235.935248
FMO2-MP2: Total energy -74457.929438


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.
-5.592-2.9644.323-3.872-3.08-0.027
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 : -0.009 / q_NPA : -0.010
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].
3A8VAL0-0.033-0.0203.812-1.580-0.577-0.009-0.511-0.4830.002
4A9VAL00.0160.0136.7250.5780.5780.0000.0000.0000.000
5A10ALA0-0.011-0.0109.848-0.064-0.0640.0000.0000.0000.000
6A11ILE00.006-0.00213.3390.0890.0890.0000.0000.0000.000
7A12VAL00.003-0.01116.416-0.009-0.0090.0000.0000.0000.000
8A13PRO0-0.036-0.00719.5900.0330.0330.0000.0000.0000.000
9A14ALA0-0.036-0.01922.3490.0020.0020.0000.0000.0000.000
10A15ALA00.0000.00425.7250.0140.0140.0000.0000.0000.000
11A26PRO00.0390.01533.4510.0000.0000.0000.0000.0000.000
12A27LYS10.8100.89029.9520.0950.0950.0000.0000.0000.000
13A28ALA00.0730.05427.7020.0000.0000.0000.0000.0000.000
14A29PHE00.0820.01528.841-0.002-0.0020.0000.0000.0000.000
15A30TYR0-0.039-0.00731.3990.0070.0070.0000.0000.0000.000
16A31GLN00.0270.00532.117-0.004-0.0040.0000.0000.0000.000
17A32LEU0-0.0340.00130.9040.0030.0030.0000.0000.0000.000
18A33ASP-1-0.819-0.91533.210-0.061-0.0610.0000.0000.0000.000
19A34GLY00.0170.01934.5600.0000.0000.0000.0000.0000.000
20A35GLN00.0250.02526.722-0.001-0.0010.0000.0000.0000.000
21A36THR0-0.029-0.02028.841-0.007-0.0070.0000.0000.0000.000
22A37LEU0-0.023-0.02328.034-0.003-0.0030.0000.0000.0000.000
23A38ILE00.0030.00022.824-0.013-0.0130.0000.0000.0000.000
24A39GLU-1-0.798-0.88023.627-0.065-0.0650.0000.0000.0000.000
25A40ARG10.8830.95023.8230.0740.0740.0000.0000.0000.000
26A41ALA0-0.034-0.01322.213-0.013-0.0130.0000.0000.0000.000
27A42VAL0-0.026-0.02218.968-0.028-0.0280.0000.0000.0000.000
28A43ASP-1-0.778-0.88318.956-0.102-0.1020.0000.0000.0000.000
29A44GLY00.0240.02319.538-0.009-0.0090.0000.0000.0000.000
30A45LEU0-0.056-0.04415.460-0.031-0.0310.0000.0000.0000.000
31A46LEU00.0160.02014.909-0.048-0.0480.0000.0000.0000.000
32A47ASP-1-0.917-0.96115.624-0.119-0.1190.0000.0000.0000.000
33A48SER0-0.157-0.09113.954-0.020-0.0200.0000.0000.0000.000
34A49GLY0-0.0080.00313.339-0.014-0.0140.0000.0000.0000.000
35A50VAL0-0.037-0.0169.1220.0360.0360.0000.0000.0000.000
36A51VAL0-0.019-0.0118.934-0.310-0.3100.0000.0000.0000.000
37A52ASP-1-0.828-0.8956.545-0.685-0.6850.0000.0000.0000.000
38A53THR0-0.025-0.0279.8440.2080.2080.0000.0000.0000.000
39A54VAL00.0100.00811.878-0.117-0.1170.0000.0000.0000.000
40A55VAL00.0070.00614.3040.0630.0630.0000.0000.0000.000
41A56VAL00.0060.00716.926-0.030-0.0300.0000.0000.0000.000
42A57ALA00.0020.00120.4970.0210.0210.0000.0000.0000.000
43A58VAL0-0.0090.00322.677-0.005-0.0050.0000.0000.0000.000
44A59PRO00.0380.00926.3690.0060.0060.0000.0000.0000.000
45A60ALA00.0430.00829.2610.0030.0030.0000.0000.0000.000
46A61ASP-1-0.945-0.97730.188-0.032-0.0320.0000.0000.0000.000
47A62ARG10.8090.87530.2690.0490.0490.0000.0000.0000.000
48A63THR0-0.0070.00426.1030.0030.0030.0000.0000.0000.000
49A64ASP-1-0.866-0.94327.5350.0000.0000.0000.0000.0000.000
50A65GLU-1-0.779-0.86329.584-0.038-0.0380.0000.0000.0000.000
51A66ALA00.007-0.00426.047-0.001-0.0010.0000.0000.0000.000
52A67ARG10.9180.96024.6120.0040.0040.0000.0000.0000.000
53A68GLN0-0.098-0.04926.3240.0030.0030.0000.0000.0000.000
54A69ILE0-0.035-0.00526.8550.0020.0020.0000.0000.0000.000
55A70LEU00.0160.00822.349-0.001-0.0010.0000.0000.0000.000
56A71GLY00.0290.01522.9720.0020.0020.0000.0000.0000.000
57A72HIS0-0.061-0.04720.035-0.006-0.0060.0000.0000.0000.000
58A73ARG10.7730.88518.6570.0600.0600.0000.0000.0000.000
59A74ALA00.0290.01517.671-0.032-0.0320.0000.0000.0000.000
60A75MET0-0.0150.02515.7420.0250.0250.0000.0000.0000.000
61A76ILE0-0.038-0.01918.900-0.026-0.0260.0000.0000.0000.000
62A77VAL0-0.001-0.00519.3500.0160.0160.0000.0000.0000.000
63A78ALA0-0.034-0.02922.320-0.007-0.0070.0000.0000.0000.000
64A79GLY0-0.031-0.02724.588-0.007-0.0070.0000.0000.0000.000
65A80GLY00.0490.02226.3120.0060.0060.0000.0000.0000.000
66A81SER0-0.116-0.04328.1690.0000.0000.0000.0000.0000.000
67A82ASN00.0290.01028.053-0.010-0.0100.0000.0000.0000.000
68A83ARG10.9270.95221.3780.2220.2220.0000.0000.0000.000
69A84THR00.020-0.01323.3770.0010.0010.0000.0000.0000.000
70A85ASP-1-0.866-0.93023.388-0.091-0.0910.0000.0000.0000.000
71A86THR00.0270.01522.3670.0060.0060.0000.0000.0000.000
72A87VAL0-0.0030.00818.2940.0020.0020.0000.0000.0000.000
73A88ASN00.0650.04018.832-0.018-0.0180.0000.0000.0000.000
74A89LEU0-0.0010.02219.3230.0050.0050.0000.0000.0000.000
75A90ALA0-0.010-0.03917.9990.0100.0100.0000.0000.0000.000
76A91LEU0-0.020-0.01514.761-0.003-0.0030.0000.0000.0000.000
77A92THR0-0.076-0.03115.1230.0100.0100.0000.0000.0000.000
78A93VAL0-0.090-0.04116.3350.0360.0360.0000.0000.0000.000
79A94LEU00.0280.03810.139-0.047-0.0470.0000.0000.0000.000
80A95SER0-0.049-0.03213.4690.0650.0650.0000.0000.0000.000
81A96GLY0-0.011-0.01111.221-0.052-0.0520.0000.0000.0000.000
82A97THR0-0.073-0.03111.6000.0380.0380.0000.0000.0000.000
83A98ALA00.0790.0507.4680.0050.0050.0000.0000.0000.000
84A99GLU-1-1.000-1.0246.9650.4880.4880.0000.0000.0000.000
85A100PRO00.0060.0175.0720.1660.1660.0000.0000.0000.000
86A101GLU-1-0.863-0.9252.327-8.582-7.6294.317-3.088-2.182-0.029
87A102PHE00.000-0.0094.7230.6130.719-0.001-0.016-0.0890.000
88A103VAL0-0.017-0.0117.0410.0870.0870.0000.0000.0000.000
89A104LEU0-0.0070.01610.4510.0730.0730.0000.0000.0000.000
90A105VAL0-0.0070.01313.1190.0660.0660.0000.0000.0000.000
91A106HIS00.1090.04016.692-0.022-0.0220.0000.0000.0000.000
92A107ASP-1-0.876-0.95119.164-0.144-0.1440.0000.0000.0000.000
93A108ALA00.0650.02422.9600.0020.0020.0000.0000.0000.000
94A109ALA0-0.066-0.03924.5380.0140.0140.0000.0000.0000.000
95A110ARG10.8370.93923.3360.2160.2160.0000.0000.0000.000
96A111ALA0-0.0010.00024.436-0.013-0.0130.0000.0000.0000.000
97A112LEU0-0.014-0.00625.4510.0020.0020.0000.0000.0000.000
98A113THR00.001-0.01020.736-0.002-0.0020.0000.0000.0000.000
99A114PRO0-0.0160.01022.5620.0030.0030.0000.0000.0000.000
100A115PRO00.1100.04218.310-0.029-0.0290.0000.0000.0000.000
101A116ALA00.0060.00017.387-0.044-0.0440.0000.0000.0000.000
102A117LEU0-0.045-0.00117.657-0.036-0.0360.0000.0000.0000.000
103A118VAL00.0430.00814.105-0.029-0.0290.0000.0000.0000.000
104A119ALA00.0460.03513.273-0.093-0.0930.0000.0000.0000.000
105A120ARG10.8380.91313.5350.2270.2270.0000.0000.0000.000
106A121VAL0-0.040-0.02513.353-0.021-0.0210.0000.0000.0000.000
107A122VAL0-0.008-0.0178.586-0.077-0.0770.0000.0000.0000.000
108A123GLU-1-0.892-0.9619.902-1.021-1.0210.0000.0000.0000.000
109A124ALA0-0.015-0.00711.587-0.026-0.0260.0000.0000.0000.000
110A125LEU0-0.056-0.0188.6880.0600.0600.0000.0000.0000.000
111A126ARG10.8410.9293.1805.0835.6490.016-0.257-0.3260.000
112A127ASP-1-0.936-0.9558.575-0.569-0.5690.0000.0000.0000.000
113A128GLY0-0.067-0.02610.5570.1450.1450.0000.0000.0000.000
114A129TYR0-0.069-0.03411.8920.0760.0760.0000.0000.0000.000
115A130ALA00.0430.01811.641-0.102-0.1020.0000.0000.0000.000
116A131ALA00.013-0.00412.641-0.035-0.0350.0000.0000.0000.000
117A132VAL00.0220.03013.6880.0660.0660.0000.0000.0000.000
118A133VAL00.011-0.00716.0120.0020.0020.0000.0000.0000.000
119A134PRO00.0150.03518.4640.0200.0200.0000.0000.0000.000
120A135VAL00.002-0.00620.9480.0240.0240.0000.0000.0000.000
121A136LEU00.0030.01224.5810.0020.0020.0000.0000.0000.000
122A137PRO0-0.018-0.00427.9930.0030.0030.0000.0000.0000.000
123A138LEU00.002-0.01631.4070.0000.0000.0000.0000.0000.000
124A139SER0-0.030-0.00534.1050.0020.0020.0000.0000.0000.000
125A140ASP-1-0.900-0.93937.023-0.085-0.0850.0000.0000.0000.000
126A141THR0-0.052-0.03738.192-0.003-0.0030.0000.0000.0000.000
127A142ILE00.0410.03135.6330.0020.0020.0000.0000.0000.000
128A143LYS10.8970.92739.1190.0770.0770.0000.0000.0000.000
129A144ALA00.0140.01940.565-0.002-0.0020.0000.0000.0000.000
130A145VAL0-0.016-0.00741.7330.0040.0040.0000.0000.0000.000
131A146ASP-1-0.770-0.88143.416-0.062-0.0620.0000.0000.0000.000
132A147ALA0-0.002-0.01145.7670.0000.0000.0000.0000.0000.000
133A148ASN0-0.076-0.04146.8230.0030.0030.0000.0000.0000.000
134A149GLY0-0.0140.00647.9140.0020.0020.0000.0000.0000.000
135A150VAL0-0.035-0.01648.9350.0010.0010.0000.0000.0000.000
136A151VAL0-0.034-0.02945.776-0.003-0.0030.0000.0000.0000.000
137A152LEU0-0.005-0.00443.6340.0020.0020.0000.0000.0000.000
138A153GLY00.022-0.00244.6950.0010.0010.0000.0000.0000.000
139A154THR0-0.028-0.00841.907-0.002-0.0020.0000.0000.0000.000
140A155PRO00.0110.03437.6390.0020.0020.0000.0000.0000.000
141A156GLU-1-0.902-0.95437.754-0.112-0.1120.0000.0000.0000.000
142A157ARG10.9210.92637.4320.0920.0920.0000.0000.0000.000
143A158ALA0-0.040-0.01834.604-0.002-0.0020.0000.0000.0000.000
144A159GLY00.0170.03231.986-0.007-0.0070.0000.0000.0000.000
145A160LEU00.0270.01030.761-0.009-0.0090.0000.0000.0000.000
146A161ARG10.9100.94927.6140.1670.1670.0000.0000.0000.000
147A162ALA0-0.0080.00428.9670.0020.0020.0000.0000.0000.000
148A163VAL00.0700.03022.990-0.007-0.0070.0000.0000.0000.000
149A164GLN0-0.086-0.06723.2070.0100.0100.0000.0000.0000.000
150A165THR0-0.046-0.02219.9030.0030.0030.0000.0000.0000.000
151A166PRO00.0300.00415.6920.0380.0380.0000.0000.0000.000
152A167GLN0-0.032-0.03616.976-0.017-0.0170.0000.0000.0000.000
153A168GLY00.0360.01012.902-0.010-0.0100.0000.0000.0000.000
154A169PHE00.025-0.00111.7730.0750.0750.0000.0000.0000.000
155A170THR00.1070.0618.000-0.143-0.1430.0000.0000.0000.000
156A171THR0-0.023-0.0128.0430.1910.1910.0000.0000.0000.000
157A172ASP-1-0.794-0.8779.923-0.232-0.2320.0000.0000.0000.000
158A173LEU0-0.0080.00311.9650.0810.0810.0000.0000.0000.000
159A174LEU0-0.0020.00113.1480.0640.0640.0000.0000.0000.000
160A175LEU0-0.010-0.01312.7870.0600.0600.0000.0000.0000.000
161A176ARG10.7970.87014.2860.3380.3380.0000.0000.0000.000
162A177SER0-0.006-0.01917.5790.0260.0260.0000.0000.0000.000
163A178TYR0-0.128-0.05718.8060.0300.0300.0000.0000.0000.000
164A179GLN0-0.057-0.01120.3430.0220.0220.0000.0000.0000.000
165A190TYR00.0290.00626.6190.0010.0010.0000.0000.0000.000
166A191THR0-0.026-0.03425.7900.0090.0090.0000.0000.0000.000
167A192ASP-1-0.869-0.90923.786-0.248-0.2480.0000.0000.0000.000
168A193ASP-1-0.786-0.87118.936-0.263-0.2630.0000.0000.0000.000
169A194ALA00.0550.01719.614-0.001-0.0010.0000.0000.0000.000
170A195SER0-0.001-0.01720.5510.0120.0120.0000.0000.0000.000
171A196LEU0-0.011-0.00921.2670.0130.0130.0000.0000.0000.000
172A197VAL0-0.0100.00517.4240.0060.0060.0000.0000.0000.000
173A198GLU-1-0.922-0.96020.263-0.221-0.2210.0000.0000.0000.000
174A199HIS0-0.098-0.03823.2490.0160.0160.0000.0000.0000.000
175A200ILE0-0.086-0.03818.7140.0160.0160.0000.0000.0000.000
176A201GLY0-0.038-0.01323.1110.0060.0060.0000.0000.0000.000
177A202GLY0-0.043-0.01419.349-0.004-0.0040.0000.0000.0000.000
178A203GLN0-0.012-0.01119.4120.0230.0230.0000.0000.0000.000
179A204VAL0-0.007-0.00818.301-0.040-0.0400.0000.0000.0000.000
180A205GLN0-0.064-0.00917.2740.0480.0480.0000.0000.0000.000
181A206VAL0-0.016-0.01518.691-0.022-0.0220.0000.0000.0000.000
182A207VAL00.0050.00417.2460.0000.0000.0000.0000.0000.000
183A208ASP-1-0.906-0.95520.422-0.222-0.2220.0000.0000.0000.000
184A209GLY00.0160.01021.774-0.027-0.0270.0000.0000.0000.000
185A210ASP-1-0.838-0.95123.616-0.171-0.1710.0000.0000.0000.000
186A211PRO0-0.0030.01326.045-0.003-0.0030.0000.0000.0000.000
187A212LEU00.0020.00626.6510.0100.0100.0000.0000.0000.000
188A213ALA0-0.0020.00123.9160.0030.0030.0000.0000.0000.000
189A214PHE0-0.056-0.02625.879-0.004-0.0040.0000.0000.0000.000
190A215LYS10.9270.95727.7900.1300.1300.0000.0000.0000.000
191A216ILE00.0400.02829.3440.0120.0120.0000.0000.0000.000
192A217THR0-0.096-0.06931.8470.0010.0010.0000.0000.0000.000
193A218THR0-0.025-0.03834.2820.0100.0100.0000.0000.0000.000
194A219LYS10.9960.96937.4130.0580.0580.0000.0000.0000.000
195A220LEU00.0390.02539.4410.0020.0020.0000.0000.0000.000
196A221ASP-1-0.688-0.79634.067-0.098-0.0980.0000.0000.0000.000
197A222LEU00.0140.01335.081-0.001-0.0010.0000.0000.0000.000
198A223LEU0-0.0190.00336.8740.0020.0020.0000.0000.0000.000
199A224LEU00.003-0.00134.2690.0020.0020.0000.0000.0000.000
200A225ALA0-0.016-0.00632.919-0.002-0.0020.0000.0000.0000.000
201A226GLN0-0.025-0.02734.2860.0030.0030.0000.0000.0000.000
202A227ALA0-0.023-0.01836.6240.0020.0020.0000.0000.0000.000
203A228ILE00.0050.00431.1660.0020.0020.0000.0000.0000.000
204A229VAL0-0.054-0.01630.9630.0010.0010.0000.0000.0000.000
205A230ARG10.8020.89033.1930.0570.0570.0000.0000.0000.000
206A231GLY0-0.032-0.00335.3890.0070.0070.0000.0000.0000.000