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: 2N7KR

Calculation Name: 1UDD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UDD

Chain ID: A

ChEMBL ID:

UniProt ID: O58873

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2804359.223105
FMO2-HF: Nuclear repulsion 2716836.045087
FMO2-HF: Total energy -87523.178017
FMO2-MP2: Total energy -87780.938486


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.942-1.791-0.023-1.019-1.1080
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / 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].
3A3VAL00.0190.0473.806-2.836-0.685-0.023-1.019-1.1080.000
4A4MET0-0.020-0.0246.1710.0150.0150.0000.0000.0000.000
5A5ILE0-0.027-0.0179.8080.1480.1480.0000.0000.0000.000
6A6THR0-0.031-0.09112.6290.0340.0340.0000.0000.0000.000
7A7ASP-1-0.780-0.8729.3650.6740.6740.0000.0000.0000.000
8A8LYS10.8300.9199.060-1.225-1.2250.0000.0000.0000.000
9A9LEU00.0040.02011.830-0.039-0.0390.0000.0000.0000.000
10A10ARG10.9861.02014.546-0.333-0.3330.0000.0000.0000.000
11A11ARG10.8820.9258.061-1.228-1.2280.0000.0000.0000.000
12A12ASP-1-0.808-0.88213.8090.7370.7370.0000.0000.0000.000
13A13SER0-0.067-0.04215.902-0.054-0.0540.0000.0000.0000.000
14A14GLU-1-0.910-0.95515.0390.3870.3870.0000.0000.0000.000
15A15GLN0-0.031-0.02219.188-0.054-0.0540.0000.0000.0000.000
16A16ILE0-0.017-0.01622.213-0.021-0.0210.0000.0000.0000.000
17A17TRP00.0500.01221.384-0.017-0.0170.0000.0000.0000.000
18A18LYS10.9380.99623.195-0.182-0.1820.0000.0000.0000.000
19A19LYS10.9240.95424.712-0.192-0.1920.0000.0000.0000.000
20A20ILE00.0040.00825.558-0.012-0.0120.0000.0000.0000.000
21A21PHE0-0.039-0.01722.052-0.007-0.0070.0000.0000.0000.000
22A22GLU-1-0.924-0.97027.8510.1200.1200.0000.0000.0000.000
23A23HIS0-0.008-0.00730.412-0.009-0.0090.0000.0000.0000.000
24A24PRO00.0070.00232.867-0.005-0.0050.0000.0000.0000.000
25A25PHE00.0530.02336.113-0.005-0.0050.0000.0000.0000.000
26A26VAL00.0440.03430.668-0.005-0.0050.0000.0000.0000.000
27A27VAL0-0.016-0.01632.468-0.006-0.0060.0000.0000.0000.000
28A28GLN0-0.002-0.02734.536-0.008-0.0080.0000.0000.0000.000
29A29LEU0-0.0330.01036.030-0.006-0.0060.0000.0000.0000.000
30A30TYR00.035-0.00231.950-0.005-0.0050.0000.0000.0000.000
31A31SER0-0.012-0.00535.851-0.004-0.0040.0000.0000.0000.000
32A32GLY00.008-0.01337.891-0.005-0.0050.0000.0000.0000.000
33A33THR0-0.077-0.03840.595-0.003-0.0030.0000.0000.0000.000
34A34LEU0-0.0240.00839.708-0.001-0.0010.0000.0000.0000.000
35A35PRO00.013-0.00142.266-0.003-0.0030.0000.0000.0000.000
36A36LEU00.0600.02445.2600.0020.0020.0000.0000.0000.000
37A37GLU-1-0.854-0.93646.6000.0480.0480.0000.0000.0000.000
38A38LYS10.8550.93642.678-0.066-0.0660.0000.0000.0000.000
39A39PHE00.0300.01339.1110.0030.0030.0000.0000.0000.000
40A40LYS10.9651.00042.890-0.043-0.0430.0000.0000.0000.000
41A41PHE00.0110.02142.5780.0010.0010.0000.0000.0000.000
42A42TYR0-0.005-0.02635.0850.0000.0000.0000.0000.0000.000
43A43VAL00.0810.03240.9290.0020.0020.0000.0000.0000.000
44A44LEU0-0.0180.00542.0940.0010.0010.0000.0000.0000.000
45A45GLN0-0.033-0.00840.6760.0050.0050.0000.0000.0000.000
46A46ASP-1-0.808-0.91437.9190.0880.0880.0000.0000.0000.000
47A47PHE00.0020.02339.6690.0020.0020.0000.0000.0000.000
48A48ASN0-0.016-0.03839.868-0.002-0.0020.0000.0000.0000.000
49A49TYR00.026-0.01131.1510.0050.0050.0000.0000.0000.000
50A50LEU00.0590.03836.6270.0040.0040.0000.0000.0000.000
51A51VAL0-0.008-0.00438.0740.0010.0010.0000.0000.0000.000
52A52GLY0-0.013-0.02337.3170.0010.0010.0000.0000.0000.000
53A53LEU00.044-0.02230.9120.0070.0070.0000.0000.0000.000
54A54THR00.0100.00534.2880.0020.0020.0000.0000.0000.000
55A55ARG10.9020.95136.719-0.078-0.0780.0000.0000.0000.000
56A56ALA00.0000.00032.2240.0000.0000.0000.0000.0000.000
57A57LEU00.0330.01730.2860.0050.0050.0000.0000.0000.000
58A58ALA00.0290.03133.261-0.002-0.0020.0000.0000.0000.000
59A59VAL00.0050.01833.524-0.002-0.0020.0000.0000.0000.000
60A60ILE0-0.0150.01128.1980.0020.0020.0000.0000.0000.000
61A61SER0-0.063-0.04531.525-0.003-0.0030.0000.0000.0000.000
62A62SER0-0.090-0.07333.167-0.004-0.0040.0000.0000.0000.000
63A63LYS10.8260.91131.102-0.131-0.1310.0000.0000.0000.000
64A64ALA0-0.053-0.00929.5900.0030.0030.0000.0000.0000.000
65A65GLU-1-0.860-0.91628.8780.0610.0610.0000.0000.0000.000
66A66TYR0-0.0070.01330.6470.0020.0020.0000.0000.0000.000
67A67PRO00.003-0.02529.112-0.001-0.0010.0000.0000.0000.000
68A68LEU00.0220.01425.5470.0020.0020.0000.0000.0000.000
69A69MET00.002-0.01429.2120.0010.0010.0000.0000.0000.000
70A70ALA0-0.014-0.01232.4180.0000.0000.0000.0000.0000.000
71A71GLU-1-0.944-0.96926.8860.0780.0780.0000.0000.0000.000
72A72LEU0-0.012-0.03028.0460.0040.0040.0000.0000.0000.000
73A73ILE0-0.013-0.00331.8780.0020.0020.0000.0000.0000.000
74A74GLU-1-0.930-0.95533.8850.0450.0450.0000.0000.0000.000
75A75LEU00.0110.01029.3330.0000.0000.0000.0000.0000.000
76A76ALA0-0.024-0.01833.6350.0010.0010.0000.0000.0000.000
77A77ARG10.9150.96135.972-0.046-0.0460.0000.0000.0000.000
78A78ASP-1-0.857-0.94035.7070.0520.0520.0000.0000.0000.000
79A79GLU-1-0.908-0.95534.8110.0830.0830.0000.0000.0000.000
80A80VAL0-0.079-0.04537.563-0.002-0.0020.0000.0000.0000.000
81A81THR0-0.059-0.02940.736-0.005-0.0050.0000.0000.0000.000
82A82VAL00.0290.00838.873-0.001-0.0010.0000.0000.0000.000
83A83GLU-1-0.881-0.94836.4440.0610.0610.0000.0000.0000.000
84A84VAL0-0.0050.01739.7720.0000.0000.0000.0000.0000.000
85A85GLU-1-0.970-0.98443.0070.0360.0360.0000.0000.0000.000
86A86ASN0-0.065-0.03539.042-0.006-0.0060.0000.0000.0000.000
87A87TYR0-0.014-0.02441.422-0.002-0.0020.0000.0000.0000.000
88A88VAL00.005-0.00142.879-0.001-0.0010.0000.0000.0000.000
89A89LYS10.8970.94744.881-0.037-0.0370.0000.0000.0000.000
90A90LEU0-0.0020.00740.950-0.002-0.0020.0000.0000.0000.000
91A91LEU0-0.004-0.01044.882-0.001-0.0010.0000.0000.0000.000
92A92LYS10.9801.00247.217-0.033-0.0330.0000.0000.0000.000
93A93GLH0-0.126-0.07545.0590.0000.0000.0000.0000.0000.000
94A94LEU0-0.057-0.02744.6170.0000.0000.0000.0000.0000.000
95A95ASP-1-0.977-0.98149.1940.0360.0360.0000.0000.0000.000
96A96LEU0-0.051-0.02147.9130.0010.0010.0000.0000.0000.000
97A97THR0-0.016-0.04251.164-0.001-0.0010.0000.0000.0000.000
98A98LEU00.018-0.00847.4090.0020.0020.0000.0000.0000.000
99A99GLU-1-0.933-0.96349.6200.0400.0400.0000.0000.0000.000
100A100ASP-1-0.816-0.87850.6450.0450.0450.0000.0000.0000.000
101A101ALA0-0.0030.00845.9390.0020.0020.0000.0000.0000.000
102A102ILE0-0.059-0.03447.5660.0020.0020.0000.0000.0000.000
103A103LYS10.8900.93948.865-0.043-0.0430.0000.0000.0000.000
104A104THR0-0.046-0.01746.2180.0000.0000.0000.0000.0000.000
105A105GLU-1-0.963-0.97047.0320.0670.0670.0000.0000.0000.000
106A106PRO0-0.031-0.01542.4100.0020.0020.0000.0000.0000.000
107A107THR00.046-0.01740.7940.0020.0020.0000.0000.0000.000
108A108LEU00.0260.00439.4550.0030.0030.0000.0000.0000.000
109A109VAL0-0.018-0.02335.5730.0040.0040.0000.0000.0000.000
110A110ASN00.0020.01436.6690.0100.0100.0000.0000.0000.000
111A111SER00.0410.01837.5270.0020.0020.0000.0000.0000.000
112A112ALA00.0160.01036.1120.0030.0030.0000.0000.0000.000
113A113TYR0-0.088-0.07729.3950.0120.0120.0000.0000.0000.000
114A114MET00.0110.03533.3390.0060.0060.0000.0000.0000.000
115A115ASP-1-0.893-0.94435.1530.1060.1060.0000.0000.0000.000
116A116PHE0-0.063-0.03326.5430.0070.0070.0000.0000.0000.000
117A117MET0-0.0260.04030.6000.0110.0110.0000.0000.0000.000
118A118LEU00.0330.01931.6660.0030.0030.0000.0000.0000.000
119A119ALA0-0.003-0.00833.3100.0010.0010.0000.0000.0000.000
120A120THR0-0.111-0.08926.9710.0080.0080.0000.0000.0000.000
121A121ALA00.0100.01129.4650.0060.0060.0000.0000.0000.000
122A122TYR0-0.028-0.00530.912-0.001-0.0010.0000.0000.0000.000
123A123LYS10.9260.95529.995-0.172-0.1720.0000.0000.0000.000
124A124GLY00.0050.02227.4160.0040.0040.0000.0000.0000.000
125A125ASN0-0.008-0.02622.982-0.007-0.0070.0000.0000.0000.000
126A126ILE00.1550.03924.3340.0080.0080.0000.0000.0000.000
127A127ILE0-0.0110.02419.3560.0030.0030.0000.0000.0000.000
128A128GLU-1-0.872-0.93022.6920.2600.2600.0000.0000.0000.000
129A129GLY00.0420.02723.9460.0020.0020.0000.0000.0000.000
130A130LEU00.0610.01523.7910.0010.0010.0000.0000.0000.000
131A131THR0-0.057-0.04820.3610.0150.0150.0000.0000.0000.000
132A132ALA0-0.048-0.04322.7870.0100.0100.0000.0000.0000.000
133A133LEU00.0250.01025.863-0.008-0.0080.0000.0000.0000.000
134A134LEU0-0.0370.00719.121-0.004-0.0040.0000.0000.0000.000
135A135PRO0-0.027-0.01222.839-0.005-0.0050.0000.0000.0000.000
136A136CYS00.0450.05524.378-0.007-0.0070.0000.0000.0000.000
137A137PHE00.0740.02025.550-0.004-0.0040.0000.0000.0000.000
138A138TRP0-0.067-0.04515.8730.0050.0050.0000.0000.0000.000
139A139SER0-0.019-0.02723.583-0.008-0.0080.0000.0000.0000.000
140A140TYR00.0580.04124.976-0.011-0.0110.0000.0000.0000.000
141A141ALA00.0140.01124.652-0.010-0.0100.0000.0000.0000.000
142A142GLU-1-0.933-0.97020.3540.1910.1910.0000.0000.0000.000
143A143ILE0-0.033-0.00724.111-0.006-0.0060.0000.0000.0000.000
144A144ALA00.0130.00927.333-0.008-0.0080.0000.0000.0000.000
145A145GLU-1-0.896-0.95822.7790.0770.0770.0000.0000.0000.000
146A146TYR0-0.049-0.03124.210-0.010-0.0100.0000.0000.0000.000
147A147HIS0-0.043-0.02326.494-0.013-0.0130.0000.0000.0000.000
148A148LYS10.9130.96425.695-0.071-0.0710.0000.0000.0000.000
149A149ASP-1-0.972-0.99730.3530.0560.0560.0000.0000.0000.000
150A150LYS10.9520.96531.792-0.080-0.0800.0000.0000.0000.000
151A151LEU00.0090.03433.065-0.003-0.0030.0000.0000.0000.000
152A152ARG10.8240.91830.492-0.042-0.0420.0000.0000.0000.000
153A153ASP-1-0.927-0.97136.3110.0280.0280.0000.0000.0000.000
154A154ASN00.0000.04838.374-0.004-0.0040.0000.0000.0000.000
155A155PRO00.0410.01740.172-0.002-0.0020.0000.0000.0000.000
156A156ILE00.0050.01043.195-0.003-0.0030.0000.0000.0000.000
157A157LYS10.9420.96142.580-0.027-0.0270.0000.0000.0000.000
158A158ILE00.0780.04742.5450.0010.0010.0000.0000.0000.000
159A159TYR0-0.011-0.00539.5260.0030.0030.0000.0000.0000.000
160A160ARG10.8680.93238.266-0.033-0.0330.0000.0000.0000.000
161A161GLU-1-0.957-0.97837.7330.0400.0400.0000.0000.0000.000
162A162TRP00.0390.01333.8650.0010.0010.0000.0000.0000.000
163A163GLY00.0620.02234.4660.0040.0040.0000.0000.0000.000
164A164LYS10.8780.92133.089-0.039-0.0390.0000.0000.0000.000
165A165VAL00.0400.03932.911-0.001-0.0010.0000.0000.0000.000
166A166TYR00.0300.02029.2210.0020.0020.0000.0000.0000.000
167A167LEU0-0.055-0.02027.8850.0050.0050.0000.0000.0000.000
168A168SER0-0.038-0.01228.603-0.005-0.0050.0000.0000.0000.000
169A169ASN00.0510.00627.0480.0100.0100.0000.0000.0000.000
170A170GLU-1-0.900-0.95226.9890.0440.0440.0000.0000.0000.000
171A171TYR00.002-0.00427.1820.0040.0040.0000.0000.0000.000
172A172LEU00.0330.01023.5250.0130.0130.0000.0000.0000.000
173A173ASN0-0.018-0.02023.3190.0170.0170.0000.0000.0000.000
174A174LEU0-0.041-0.00124.0070.0040.0040.0000.0000.0000.000
175A175VAL00.0380.02121.6470.0110.0110.0000.0000.0000.000
176A176GLY0-0.030-0.01319.9570.0200.0200.0000.0000.0000.000
177A177ARG10.9480.96219.937-0.059-0.0590.0000.0000.0000.000
178A178LEU00.0250.02621.9230.0080.0080.0000.0000.0000.000
179A179ARG10.9310.96616.922-0.212-0.2120.0000.0000.0000.000
180A180LYS10.9650.99817.266-0.025-0.0250.0000.0000.0000.000
181A181ILE0-0.0020.00518.1630.0060.0060.0000.0000.0000.000
182A182ILE00.012-0.00217.0750.0100.0100.0000.0000.0000.000
183A183ASP-1-0.740-0.82513.9210.4350.4350.0000.0000.0000.000
184A184SER0-0.130-0.03214.227-0.003-0.0030.0000.0000.0000.000
185A185SER0-0.025-0.03316.386-0.015-0.0150.0000.0000.0000.000
186A186GLY00.010-0.00415.0170.0120.0120.0000.0000.0000.000
187A187HIS00.007-0.0049.0540.2190.2190.0000.0000.0000.000
188A188SER0-0.015-0.00512.6810.1060.1060.0000.0000.0000.000
189A189GLY00.0650.01815.165-0.028-0.0280.0000.0000.0000.000
190A190TYR00.012-0.03113.801-0.005-0.0050.0000.0000.0000.000
191A191ASP-1-0.824-0.92015.8720.5900.5900.0000.0000.0000.000
192A192ARG10.7470.91017.949-0.352-0.3520.0000.0000.0000.000
193A193LEU00.0730.02816.934-0.024-0.0240.0000.0000.0000.000
194A194ARG10.9140.97315.960-0.553-0.5530.0000.0000.0000.000
195A195ARG10.9220.95018.571-0.348-0.3480.0000.0000.0000.000
196A196ILE00.0090.03622.154-0.022-0.0220.0000.0000.0000.000
197A197PHE00.0870.03619.819-0.018-0.0180.0000.0000.0000.000
198A198ILE0-0.018-0.01119.238-0.021-0.0210.0000.0000.0000.000
199A199THR0-0.085-0.04322.643-0.023-0.0230.0000.0000.0000.000
200A200GLY00.0590.02525.397-0.016-0.0160.0000.0000.0000.000
201A201SER00.0200.00522.940-0.011-0.0110.0000.0000.0000.000
202A202LYS10.9090.94325.431-0.234-0.2340.0000.0000.0000.000
203A203PHE00.0110.01327.973-0.012-0.0120.0000.0000.0000.000
204A204GLU-1-0.716-0.81327.4760.1340.1340.0000.0000.0000.000
205A205LEU0-0.045-0.01628.299-0.009-0.0090.0000.0000.0000.000
206A206ALA0-0.042-0.02730.546-0.010-0.0100.0000.0000.0000.000
207A207PHE00.0280.01633.036-0.008-0.0080.0000.0000.0000.000
208A208TRP00.0480.02830.448-0.012-0.0120.0000.0000.0000.000
209A209GLU-1-0.895-0.93734.7390.0950.0950.0000.0000.0000.000
210A210MET0-0.0500.01236.539-0.009-0.0090.0000.0000.0000.000
211A211ALA00.0520.03138.168-0.006-0.0060.0000.0000.0000.000
212A212TRP0-0.085-0.04738.529-0.007-0.0070.0000.0000.0000.000
213A213ARG10.8330.90839.648-0.094-0.0940.0000.0000.0000.000
214A214GLY00.0060.02942.541-0.004-0.0040.0000.0000.0000.000
215A215GLY0-0.025-0.01342.245-0.001-0.0010.0000.0000.0000.000