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: K3113

Calculation Name: 3C9B-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C9B

Chain ID: B

ChEMBL ID:

UniProt ID: P53853

Base Structure: X-ray

Registration Date: 2023-06-21

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456754.542147
FMO2-HF: Nuclear repulsion 2372556.185455
FMO2-HF: Total energy -84198.356693
FMO2-MP2: Total energy -84446.730982


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(B:17:GLY)


Summations of interaction energy for fragment #1(B:17: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.
-4.487-1.2730.942-1.506-2.6490.008
Interaction energy analysis for fragmet #1(B:17:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.016
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].
3B19ALA00.0300.0163.195-0.1161.6280.017-0.777-0.9830.001
4B20LYS10.7560.8552.804-4.729-3.5780.924-0.621-1.4540.007
5B21CYS00.0120.0084.513-1.153-0.8340.001-0.108-0.2120.000
6B22GLU-1-0.912-0.9566.364-0.220-0.2200.0000.0000.0000.000
7B23GLU-1-0.810-0.8787.9691.8151.8150.0000.0000.0000.000
8B24GLU-1-0.943-0.9737.364-0.174-0.1740.0000.0000.0000.000
9B25VAL0-0.0030.00610.613-0.018-0.0180.0000.0000.0000.000
10B26ASP-1-0.875-0.92912.6510.0800.0800.0000.0000.0000.000
11B27ALA0-0.082-0.04313.710-0.003-0.0030.0000.0000.0000.000
12B28ILE0-0.006-0.01613.030-0.015-0.0150.0000.0000.0000.000
13B29GLU-1-0.899-0.95516.380-0.068-0.0680.0000.0000.0000.000
14B30ARG10.8470.92618.525-0.079-0.0790.0000.0000.0000.000
15B31GLU-1-0.953-0.97118.6070.0330.0330.0000.0000.0000.000
16B32VAL00.001-0.00720.261-0.004-0.0040.0000.0000.0000.000
17B33GLU-1-0.838-0.88322.587-0.007-0.0070.0000.0000.0000.000
18B34LEU00.001-0.00624.017-0.001-0.0010.0000.0000.0000.000
19B35TYR00.0220.02224.691-0.003-0.0030.0000.0000.0000.000
20B36ARG10.8110.86725.7120.0110.0110.0000.0000.0000.000
21B37LEU00.0050.00528.212-0.001-0.0010.0000.0000.0000.000
22B38ASN0-0.018-0.02628.3070.0000.0000.0000.0000.0000.000
23B39LYS10.8550.94229.9800.0040.0040.0000.0000.0000.000
24B40MET0-0.007-0.00832.683-0.002-0.0020.0000.0000.0000.000
25B41LYS10.9310.97934.421-0.021-0.0210.0000.0000.0000.000
26B42PRO0-0.015-0.00935.878-0.001-0.0010.0000.0000.0000.000
27B43VAL00.0370.00637.414-0.001-0.0010.0000.0000.0000.000
28B44TYR00.0370.00635.654-0.002-0.0020.0000.0000.0000.000
29B45GLU-1-0.840-0.90140.0290.0140.0140.0000.0000.0000.000
30B46LYS10.8010.90141.507-0.008-0.0080.0000.0000.0000.000
31B47ARG10.7700.87141.366-0.002-0.0020.0000.0000.0000.000
32B48ASP-1-0.737-0.86043.4140.0050.0050.0000.0000.0000.000
33B49ALA00.0180.02646.1050.0000.0000.0000.0000.0000.000
34B50TYR0-0.025-0.01047.3420.0000.0000.0000.0000.0000.000
35B51ILE0-0.069-0.03045.9290.0000.0000.0000.0000.0000.000
36B52ASP-1-0.939-0.95949.9720.0070.0070.0000.0000.0000.000
37B53GLU-1-0.978-0.98451.9970.0020.0020.0000.0000.0000.000
38B54ILE0-0.098-0.04351.596-0.001-0.0010.0000.0000.0000.000
39B55ALA00.003-0.00254.7050.0000.0000.0000.0000.0000.000
40B56GLU-1-0.901-0.95756.3100.0010.0010.0000.0000.0000.000
41B57PHE00.0270.00847.426-0.001-0.0010.0000.0000.0000.000
42B58TRP00.0830.00844.473-0.001-0.0010.0000.0000.0000.000
43B59LYS10.8450.94950.995-0.001-0.0010.0000.0000.0000.000
44B60ILE0-0.002-0.00752.901-0.001-0.0010.0000.0000.0000.000
45B61VAL0-0.009-0.00746.935-0.001-0.0010.0000.0000.0000.000
46B62LEU0-0.046-0.02747.002-0.001-0.0010.0000.0000.0000.000
47B63SER0-0.081-0.04049.8740.0000.0000.0000.0000.0000.000
48B64GLN0-0.066-0.03349.7190.0000.0000.0000.0000.0000.000
49B65HIS0-0.053-0.02242.6260.0000.0000.0000.0000.0000.000
50B66VAL00.0150.00445.0500.0000.0000.0000.0000.0000.000
51B67SER0-0.015-0.01243.0620.0010.0010.0000.0000.0000.000
52B68PHE00.0570.01445.5390.0010.0010.0000.0000.0000.000
53B69ALA00.0330.00346.7790.0010.0010.0000.0000.0000.000
54B70ASN0-0.062-0.01946.8870.0010.0010.0000.0000.0000.000
55B71TYR0-0.032-0.00441.4540.0010.0010.0000.0000.0000.000
56B72ILE0-0.0360.00747.4210.0010.0010.0000.0000.0000.000
57B73ARG10.9110.95250.422-0.005-0.0050.0000.0000.0000.000
58B74ALA00.0540.01454.0820.0000.0000.0000.0000.0000.000
59B75SER0-0.065-0.04857.0100.0000.0000.0000.0000.0000.000
60B76ASP-1-0.712-0.84652.8860.0060.0060.0000.0000.0000.000
61B77PHE00.0440.02552.5960.0010.0010.0000.0000.0000.000
62B78LYS10.9050.96456.309-0.004-0.0040.0000.0000.0000.000
63B79TYR0-0.042-0.04655.7170.0000.0000.0000.0000.0000.000
64B80ILE00.007-0.00150.8200.0010.0010.0000.0000.0000.000
65B81ASP-1-0.832-0.90953.4570.0010.0010.0000.0000.0000.000
66B82THR0-0.098-0.05656.0200.0000.0000.0000.0000.0000.000
67B83ILE0-0.052-0.01549.4700.0010.0010.0000.0000.0000.000
68B84ASP-1-0.790-0.86352.8990.0070.0070.0000.0000.0000.000
69B85LYS10.9270.95247.530-0.012-0.0120.0000.0000.0000.000
70B86ILE0-0.011-0.00543.6240.0010.0010.0000.0000.0000.000
71B87LYS10.8370.91039.769-0.015-0.0150.0000.0000.0000.000
72B88VAL0-0.0120.01436.7440.0010.0010.0000.0000.0000.000
73B89GLU-1-0.862-0.90836.8630.0180.0180.0000.0000.0000.000
74B90TRP00.0310.00031.0340.0000.0000.0000.0000.0000.000
75B91LEU00.0160.00031.7060.0010.0010.0000.0000.0000.000
76B92ALA0-0.0040.01526.8420.0040.0040.0000.0000.0000.000
77B93LEU0-0.063-0.03728.1690.0040.0040.0000.0000.0000.000
78B94GLU-1-0.980-0.98430.5940.0400.0400.0000.0000.0000.000
79B95SER0-0.041-0.02828.3160.0040.0040.0000.0000.0000.000
80B96GLU-1-0.865-0.94523.3370.0950.0950.0000.0000.0000.000
81B97MET0-0.083-0.03424.1560.0120.0120.0000.0000.0000.000
82B98TYR0-0.0510.00226.369-0.004-0.0040.0000.0000.0000.000
83B99ASP-1-0.726-0.83924.5790.0530.0530.0000.0000.0000.000
84B100THR00.015-0.01024.193-0.001-0.0010.0000.0000.0000.000
85B101ARG10.7710.85624.646-0.038-0.0380.0000.0000.0000.000
86B102ASP-1-0.782-0.87828.8740.0450.0450.0000.0000.0000.000
87B103PHE00.007-0.00331.077-0.001-0.0010.0000.0000.0000.000
88B104SER0-0.018-0.00234.5590.0010.0010.0000.0000.0000.000
89B105ILE0-0.024-0.01538.163-0.002-0.0020.0000.0000.0000.000
90B106THR0-0.041-0.03041.2120.0010.0010.0000.0000.0000.000
91B107PHE00.0120.00044.189-0.001-0.0010.0000.0000.0000.000
92B108HIS10.7350.81247.771-0.008-0.0080.0000.0000.0000.000
93B109PHE00.003-0.00350.002-0.001-0.0010.0000.0000.0000.000
94B110HIS00.0760.03254.1000.0010.0010.0000.0000.0000.000
95B111GLY00.0150.01157.3990.0000.0000.0000.0000.0000.000
96B112ILE0-0.072-0.04959.032-0.001-0.0010.0000.0000.0000.000
97B113GLU-1-0.890-0.94262.3290.0060.0060.0000.0000.0000.000
98B114GLY0-0.011-0.00965.2940.0000.0000.0000.0000.0000.000
99B115ASP-1-0.794-0.85962.8230.0060.0060.0000.0000.0000.000
100B116PHE0-0.045-0.03554.2620.0000.0000.0000.0000.0000.000
101B117LYS10.9040.95757.492-0.013-0.0130.0000.0000.0000.000
102B118GLU-1-0.837-0.87856.2490.0110.0110.0000.0000.0000.000
103B119GLN0-0.006-0.00453.0960.0020.0020.0000.0000.0000.000
104B120GLN00.0270.01048.495-0.002-0.0020.0000.0000.0000.000
105B121VAL0-0.025-0.00846.6870.0010.0010.0000.0000.0000.000
106B122THR00.0360.02141.704-0.002-0.0020.0000.0000.0000.000
107B123LYS10.7800.91040.860-0.019-0.0190.0000.0000.0000.000
108B124VAL00.0540.02636.134-0.001-0.0010.0000.0000.0000.000
109B125PHE0-0.020-0.01035.2680.0000.0000.0000.0000.0000.000
110B126GLN00.0450.01331.1930.0040.0040.0000.0000.0000.000
111B127ILE00.0170.01226.116-0.002-0.0020.0000.0000.0000.000
112B128LYS10.8200.92528.318-0.044-0.0440.0000.0000.0000.000
113B129LYS10.9310.95320.632-0.078-0.0780.0000.0000.0000.000
114B130GLY0-0.0010.00026.2340.0050.0050.0000.0000.0000.000
115B131LYS10.7110.84627.347-0.031-0.0310.0000.0000.0000.000
116B132ASP-1-0.779-0.87825.9870.0390.0390.0000.0000.0000.000
117B133ASP-1-0.869-0.92624.6430.0050.0050.0000.0000.0000.000
118B134GLN0-0.137-0.10017.9160.0050.0050.0000.0000.0000.000
119B135GLU-1-0.790-0.85918.0620.0590.0590.0000.0000.0000.000
120B136ASP-1-0.908-0.94421.2140.0140.0140.0000.0000.0000.000
121B137GLY0-0.012-0.01223.7060.0050.0050.0000.0000.0000.000
122B138ILE0-0.037-0.02126.425-0.008-0.0080.0000.0000.0000.000
123B139LEU00.0300.01930.1350.0050.0050.0000.0000.0000.000
124B140THR0-0.099-0.05832.612-0.001-0.0010.0000.0000.0000.000
125B141SER0-0.017-0.03934.974-0.001-0.0010.0000.0000.0000.000
126B142GLU-1-0.936-0.96237.6620.0380.0380.0000.0000.0000.000
127B143PRO0-0.085-0.04940.625-0.002-0.0020.0000.0000.0000.000
128B144VAL00.0190.02244.2630.0010.0010.0000.0000.0000.000
129B145PRO0-0.055-0.03445.995-0.001-0.0010.0000.0000.0000.000
130B146ILE00.0160.02249.8060.0000.0000.0000.0000.0000.000
131B147GLU-1-0.883-0.94051.7980.0120.0120.0000.0000.0000.000
132B148TRP0-0.034-0.03551.892-0.001-0.0010.0000.0000.0000.000
133B149PRO00.0200.01856.4240.0000.0000.0000.0000.0000.000
134B150GLN00.0430.02759.6260.0000.0000.0000.0000.0000.000
135B151SER0-0.052-0.03862.2070.0000.0000.0000.0000.0000.000
136B152TYR0-0.110-0.09255.771-0.001-0.0010.0000.0000.0000.000
137B153ASP-1-0.780-0.89059.8890.0090.0090.0000.0000.0000.000
138B154SER0-0.085-0.04261.6450.0000.0000.0000.0000.0000.000
139B155ILE0-0.080-0.05957.1940.0000.0000.0000.0000.0000.000
140B156ASN00.1210.07456.7800.0010.0010.0000.0000.0000.000
141B157PRO0-0.0180.00152.7390.0000.0000.0000.0000.0000.000
142B158ASP-1-0.786-0.85153.8940.0150.0150.0000.0000.0000.000
143B159LEU0-0.039-0.01256.6040.0000.0000.0000.0000.0000.000
144B160ILE0-0.083-0.03357.6480.0000.0000.0000.0000.0000.000
145B161LYS10.9780.99160.002-0.010-0.0100.0000.0000.0000.000
146B162ASP-1-0.890-0.93861.6230.0090.0090.0000.0000.0000.000
147B163LYS10.9100.93954.651-0.013-0.0130.0000.0000.0000.000
148B164ARG10.9680.97756.955-0.011-0.0110.0000.0000.0000.000
149B165SER00.0620.04759.592-0.001-0.0010.0000.0000.0000.000
150B166PRO00.0230.00261.9330.0000.0000.0000.0000.0000.000
151B167GLU-1-0.874-0.93661.9320.0040.0040.0000.0000.0000.000
152B168GLY00.0790.03161.2420.0000.0000.0000.0000.0000.000
153B169LYS10.8700.92757.121-0.007-0.0070.0000.0000.0000.000
154B170LYS10.8420.92456.757-0.004-0.0040.0000.0000.0000.000
155B171LYS10.9310.96757.982-0.006-0.0060.0000.0000.0000.000
156B172TYR00.0600.02350.5730.0000.0000.0000.0000.0000.000
157B173ARG10.9410.96452.311-0.005-0.0050.0000.0000.0000.000
158B174GLN0-0.039-0.02353.1490.0000.0000.0000.0000.0000.000
159B175GLY00.0790.05154.5810.0000.0000.0000.0000.0000.000
160B176MET0-0.031-0.01048.6830.0010.0010.0000.0000.0000.000
161B177LYS10.9170.94749.333-0.004-0.0040.0000.0000.0000.000
162B178THR0-0.053-0.00450.890-0.001-0.0010.0000.0000.0000.000
163B179ILE00.0710.02647.4690.0010.0010.0000.0000.0000.000
164B180PHE00.0260.00748.9280.0010.0010.0000.0000.0000.000
165B181GLY0-0.045-0.01649.4820.0010.0010.0000.0000.0000.000
166B182TRP0-0.038-0.01641.4480.0010.0010.0000.0000.0000.000
167B183PHE00.0630.02344.5030.0010.0010.0000.0000.0000.000
168B184ARG10.7820.84545.455-0.013-0.0130.0000.0000.0000.000
169B185TRP0-0.0380.01236.4600.0020.0020.0000.0000.0000.000
170B186THR0-0.029-0.03139.3050.0020.0020.0000.0000.0000.000
171B187GLY00.1390.07237.0480.0020.0020.0000.0000.0000.000
172B188LEU0-0.054-0.03134.8180.0010.0010.0000.0000.0000.000
173B189LYS10.8860.95037.992-0.026-0.0260.0000.0000.0000.000
174B190PRO00.1030.04138.035-0.002-0.0020.0000.0000.0000.000
175B191GLY00.0030.00440.8280.0000.0000.0000.0000.0000.000
176B192LYS10.8280.91044.135-0.013-0.0130.0000.0000.0000.000
177B193GLU-1-0.790-0.87441.1500.0190.0190.0000.0000.0000.000
178B194PHE00.0080.00944.139-0.001-0.0010.0000.0000.0000.000
179B195PRO0-0.069-0.05343.8490.0010.0010.0000.0000.0000.000
180B196HIS00.0600.03640.4470.0000.0000.0000.0000.0000.000
181B197GLY00.0340.00941.377-0.001-0.0010.0000.0000.0000.000
182B198ASP-1-0.824-0.90835.7370.0080.0080.0000.0000.0000.000
183B199SER00.016-0.00137.172-0.001-0.0010.0000.0000.0000.000
184B200LEU0-0.041-0.00638.497-0.001-0.0010.0000.0000.0000.000
185B201ALA0-0.010-0.01037.6830.0000.0000.0000.0000.0000.000
186B202SER00.033-0.01133.8750.0020.0020.0000.0000.0000.000
187B203LEU0-0.0380.00736.650-0.002-0.0020.0000.0000.0000.000
188B204PHE00.001-0.01139.656-0.001-0.0010.0000.0000.0000.000
189B205SER00.0350.01035.121-0.002-0.0020.0000.0000.0000.000
190B206GLU-1-0.901-0.92733.179-0.003-0.0030.0000.0000.0000.000
191B207GLU-1-0.920-0.95936.000-0.011-0.0110.0000.0000.0000.000
192B208ILE0-0.043-0.02639.3590.0000.0000.0000.0000.0000.000
193B209TYR0-0.037-0.05738.7940.0000.0000.0000.0000.0000.000
194B210PRO00.0290.02936.7380.0000.0000.0000.0000.0000.000
195B211PHE0-0.054-0.03936.052-0.001-0.0010.0000.0000.0000.000
196B212CYS00.0060.03941.769-0.001-0.0010.0000.0000.0000.000
197B213VAL00.0590.00844.7930.0000.0000.0000.0000.0000.000
198B214LYS10.8900.95140.3800.0130.0130.0000.0000.0000.000
199B215TYR00.0690.03442.7790.0000.0000.0000.0000.0000.000
200B216TYR00.0270.02347.8000.0000.0000.0000.0000.0000.000
201B217ALA0-0.018-0.01849.2900.0000.0000.0000.0000.0000.000
202B218GLU-1-0.960-0.96948.270-0.011-0.0110.0000.0000.0000.000
203B219ALA00.0150.01251.2330.0000.0000.0000.0000.0000.000
204B220GLN0-0.064-0.01253.7200.0010.0010.0000.0000.0000.000
205B221ARG10.9090.96151.6710.0110.0110.0000.0000.0000.000