FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4LJ5N

Calculation Name: 2O0Y-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O0Y

Chain ID: B

ChEMBL ID:

UniProt ID: Q0S167

Base Structure: X-ray

Registration Date: 2023-09-27

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 244
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2659323.487918
FMO2-HF: Nuclear repulsion 2567715.656428
FMO2-HF: Total energy -91607.83149
FMO2-MP2: Total energy -91876.778446


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:ALA)


Summations of interaction energy for fragment #1(B:17:ALA)
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.
-12.634-8.8463.282-2.683-4.3890.019
Interaction energy analysis for fragmet #1(B:17:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.012
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].
3B19VAL00.0910.0302.795-0.7111.5900.601-1.172-1.7310.006
4B20ARG10.9190.9732.448-9.404-8.2292.671-1.401-2.4460.012
5B21SER00.002-0.0234.208-2.079-1.7670.010-0.110-0.2120.001
6B22VAL00.0300.0246.194-0.417-0.4170.0000.0000.0000.000
7B23THR00.0180.0127.243-0.379-0.3790.0000.0000.0000.000
8B24ARG10.8970.9706.707-0.819-0.8190.0000.0000.0000.000
9B25VAL0-0.007-0.01010.088-0.177-0.1770.0000.0000.0000.000
10B26ILE00.0220.00711.363-0.076-0.0760.0000.0000.0000.000
11B27ASP-1-0.843-0.93312.1220.7080.7080.0000.0000.0000.000
12B28LEU0-0.101-0.05613.500-0.094-0.0940.0000.0000.0000.000
13B29LEU0-0.026-0.02916.142-0.052-0.0520.0000.0000.0000.000
14B30GLU-1-0.889-0.94216.9580.3420.3420.0000.0000.0000.000
15B31LEU0-0.077-0.00918.634-0.033-0.0330.0000.0000.0000.000
16B32PHE0-0.099-0.04719.866-0.034-0.0340.0000.0000.0000.000
17B33ASP-1-0.786-0.89523.5760.1800.1800.0000.0000.0000.000
18B34ALA00.017-0.00226.473-0.010-0.0100.0000.0000.0000.000
19B35ALA00.0030.00729.811-0.010-0.0100.0000.0000.0000.000
20B36HIS0-0.121-0.05326.589-0.017-0.0170.0000.0000.0000.000
21B37PRO00.0610.03726.6450.0130.0130.0000.0000.0000.000
22B38THR0-0.069-0.05726.4590.0040.0040.0000.0000.0000.000
23B39ARG10.9000.96222.773-0.156-0.1560.0000.0000.0000.000
24B40SER00.0210.00224.440-0.004-0.0040.0000.0000.0000.000
25B41LEU00.031-0.00118.9930.0090.0090.0000.0000.0000.000
26B42LYS10.8280.88920.941-0.062-0.0620.0000.0000.0000.000
27B43GLU-1-0.725-0.86322.3940.1200.1200.0000.0000.0000.000
28B44LEU00.0340.03118.0650.0160.0160.0000.0000.0000.000
29B45VAL0-0.085-0.04017.5180.0250.0250.0000.0000.0000.000
30B46GLU-1-0.877-0.92618.3110.1070.1070.0000.0000.0000.000
31B47GLY00.0020.01320.0330.0030.0030.0000.0000.0000.000
32B48THR0-0.006-0.02114.2640.0220.0220.0000.0000.0000.000
33B49LYS10.9200.96515.055-0.135-0.1350.0000.0000.0000.000
34B50LEU0-0.0180.00210.404-0.003-0.0030.0000.0000.0000.000
35B51PRO00.011-0.00111.925-0.032-0.0320.0000.0000.0000.000
36B52LYS11.0541.02314.474-0.026-0.0260.0000.0000.0000.000
37B53THR00.0110.00114.7800.0130.0130.0000.0000.0000.000
38B54THR0-0.049-0.0209.680-0.040-0.0400.0000.0000.0000.000
39B55VAL00.0700.03012.2990.0150.0150.0000.0000.0000.000
40B56VAL00.000-0.00114.5850.0040.0040.0000.0000.0000.000
41B57ARG10.9530.9839.0820.1270.1270.0000.0000.0000.000
42B58LEU0-0.028-0.0199.114-0.012-0.0120.0000.0000.0000.000
43B59VAL00.0810.03813.2160.0130.0130.0000.0000.0000.000
44B60ALA00.0010.00816.675-0.004-0.0040.0000.0000.0000.000
45B61THR0-0.032-0.01013.565-0.018-0.0180.0000.0000.0000.000
46B62MET0-0.011-0.00514.9710.0140.0140.0000.0000.0000.000
47B63CYS0-0.0230.00017.427-0.003-0.0030.0000.0000.0000.000
48B64ALA0-0.028-0.00819.072-0.005-0.0050.0000.0000.0000.000
49B65ARG10.9250.96417.058-0.123-0.1230.0000.0000.0000.000
50B66SER00.0070.00420.4030.0070.0070.0000.0000.0000.000
51B67VAL00.0110.01117.6130.0030.0030.0000.0000.0000.000
52B68LEU00.0100.02018.7530.0090.0090.0000.0000.0000.000
53B69THR0-0.008-0.01822.032-0.016-0.0160.0000.0000.0000.000
54B70SER00.0050.00924.9560.0050.0050.0000.0000.0000.000
55B71ARG10.8750.93026.095-0.084-0.0840.0000.0000.0000.000
56B72ALA00.0250.00529.566-0.002-0.0020.0000.0000.0000.000
57B73ASP-1-0.829-0.88830.7580.0660.0660.0000.0000.0000.000
58B74GLY0-0.007-0.00528.7120.0010.0010.0000.0000.0000.000
59B75SER0-0.104-0.06126.4700.0080.0080.0000.0000.0000.000
60B76TYR0-0.010-0.01322.653-0.008-0.0080.0000.0000.0000.000
61B77SER00.0430.02925.0540.0010.0010.0000.0000.0000.000
62B78LEU00.0410.01922.0590.0020.0020.0000.0000.0000.000
63B79GLY0-0.019-0.01123.517-0.015-0.0150.0000.0000.0000.000
64B80PRO00.037-0.00825.2590.0090.0090.0000.0000.0000.000
65B81GLU-1-0.873-0.92821.0730.1410.1410.0000.0000.0000.000
66B82MET0-0.003-0.00720.4330.0070.0070.0000.0000.0000.000
67B83LEU00.0100.00124.5870.0010.0010.0000.0000.0000.000
68B84ARG10.8190.92623.510-0.124-0.1240.0000.0000.0000.000
69B85TRP0-0.020-0.01620.7750.0000.0000.0000.0000.0000.000
70B86VAL00.0420.03627.0040.0010.0010.0000.0000.0000.000
71B87ARG10.9500.97330.171-0.076-0.0760.0000.0000.0000.000
72B88LEU0-0.005-0.01426.192-0.005-0.0050.0000.0000.0000.000
73B89ALA00.0510.02428.312-0.001-0.0010.0000.0000.0000.000
74B90GLY00.0180.01129.882-0.002-0.0020.0000.0000.0000.000
75B91ARG10.8750.92333.429-0.084-0.0840.0000.0000.0000.000
76B92THR0-0.070-0.04130.219-0.001-0.0010.0000.0000.0000.000
77B93TRP00.0040.02632.0040.0010.0010.0000.0000.0000.000
78B94ALA00.012-0.00333.161-0.008-0.0080.0000.0000.0000.000
79B95PRO0-0.0150.00433.8150.0060.0060.0000.0000.0000.000
80B96PRO00.0330.02133.0270.0020.0020.0000.0000.0000.000
81B97GLU-1-0.881-0.94834.2890.0820.0820.0000.0000.0000.000
82B98GLU-1-0.915-0.96235.9890.0930.0930.0000.0000.0000.000
83B99VAL0-0.0010.00537.282-0.005-0.0050.0000.0000.0000.000
84B100VAL0-0.014-0.01838.318-0.006-0.0060.0000.0000.0000.000
85B101ASP-1-0.853-0.92340.1260.0720.0720.0000.0000.0000.000
86B102ILE00.0040.01841.072-0.005-0.0050.0000.0000.0000.000
87B103MET0-0.020-0.01442.644-0.003-0.0030.0000.0000.0000.000
88B104ARG10.8490.90941.359-0.072-0.0720.0000.0000.0000.000
89B105GLN0-0.049-0.03646.396-0.002-0.0020.0000.0000.0000.000
90B106LEU00.0480.04248.020-0.003-0.0030.0000.0000.0000.000
91B107SER0-0.028-0.02249.293-0.003-0.0030.0000.0000.0000.000
92B108ALA0-0.070-0.03550.829-0.003-0.0030.0000.0000.0000.000
93B109ASP-1-0.876-0.91952.0340.0450.0450.0000.0000.0000.000
94B110THR0-0.056-0.04453.350-0.002-0.0020.0000.0000.0000.000
95B111GLY0-0.017-0.01155.041-0.002-0.0020.0000.0000.0000.000
96B112GLU-1-0.773-0.85054.6740.0360.0360.0000.0000.0000.000
97B113THR0-0.028-0.02350.2450.0010.0010.0000.0000.0000.000
98B114VAL00.0160.02346.841-0.001-0.0010.0000.0000.0000.000
99B115ASN0-0.026-0.00846.9020.0020.0020.0000.0000.0000.000
100B116LEU00.0620.03440.456-0.001-0.0010.0000.0000.0000.000
101B117TYR0-0.021-0.03043.6800.0000.0000.0000.0000.0000.000
102B118ILE00.0730.04138.9450.0010.0010.0000.0000.0000.000
103B119ARG10.9640.96442.626-0.066-0.0660.0000.0000.0000.000
104B120GLN0-0.051-0.02938.6510.0010.0010.0000.0000.0000.000
105B121GLY00.0090.00942.797-0.003-0.0030.0000.0000.0000.000
106B122LEU00.0530.02844.6890.0010.0010.0000.0000.0000.000
107B123SER00.0000.00746.516-0.002-0.0020.0000.0000.0000.000
108B124ARG10.8910.95146.379-0.043-0.0430.0000.0000.0000.000
109B125VAL0-0.0170.00442.687-0.002-0.0020.0000.0000.0000.000
110B126VAL00.0080.01644.2000.0020.0020.0000.0000.0000.000
111B127VAL00.006-0.00839.3700.0000.0000.0000.0000.0000.000
112B128ALA00.0290.01940.0210.0040.0040.0000.0000.0000.000
113B129GLN0-0.081-0.06942.046-0.003-0.0030.0000.0000.0000.000
114B130CYS0-0.0320.00745.0170.0020.0020.0000.0000.0000.000
115B131GLU-1-0.833-0.90447.1000.0440.0440.0000.0000.0000.000
116B132SER00.0210.02050.5230.0000.0000.0000.0000.0000.000
117B133THR0-0.016-0.02153.4020.0000.0000.0000.0000.0000.000
118B134ALA0-0.0180.00755.672-0.002-0.0020.0000.0000.0000.000
119B135THR0-0.004-0.02058.1210.0010.0010.0000.0000.0000.000
120B136VAL00.0070.02460.4360.0000.0000.0000.0000.0000.000
121B137ARG10.8370.90253.244-0.041-0.0410.0000.0000.0000.000
122B138SER00.0160.02052.807-0.001-0.0010.0000.0000.0000.000
123B139VAL00.0300.01052.2730.0010.0010.0000.0000.0000.000
124B140ILE0-0.035-0.01049.6080.0000.0000.0000.0000.0000.000
125B141PRO00.0430.03648.5520.0020.0020.0000.0000.0000.000
126B142LEU00.0360.01342.5780.0010.0010.0000.0000.0000.000
127B143GLY0-0.054-0.03742.974-0.001-0.0010.0000.0000.0000.000
128B144VAL0-0.040-0.01543.625-0.001-0.0010.0000.0000.0000.000
129B145PRO0-0.024-0.00245.9410.0000.0000.0000.0000.0000.000
130B146TYR00.008-0.00747.712-0.003-0.0030.0000.0000.0000.000
131B147PRO00.0490.03550.1700.0020.0020.0000.0000.0000.000
132B148LEU0-0.016-0.01948.0480.0010.0010.0000.0000.0000.000
133B149TRP00.0370.02752.1100.0000.0000.0000.0000.0000.000
134B150ALA0-0.0070.01255.531-0.001-0.0010.0000.0000.0000.000
135B151GLY0-0.046-0.04455.1700.0020.0020.0000.0000.0000.000
136B152ALA0-0.013-0.00454.2400.0010.0010.0000.0000.0000.000
137B153ALA00.0380.01249.1430.0010.0010.0000.0000.0000.000
138B154GLY0-0.0090.00049.8840.0020.0020.0000.0000.0000.000
139B155LYS10.8770.90850.884-0.037-0.0370.0000.0000.0000.000
140B156ILE00.0050.01847.5990.0000.0000.0000.0000.0000.000
141B157LEU0-0.015-0.02044.5510.0020.0020.0000.0000.0000.000
142B158LEU0-0.026-0.01146.8910.0020.0020.0000.0000.0000.000
143B159LEU0-0.022-0.00147.983-0.001-0.0010.0000.0000.0000.000
144B160ALA0-0.040-0.02443.5740.0000.0000.0000.0000.0000.000
145B161ALA0-0.039-0.00945.1830.0020.0020.0000.0000.0000.000
146B162PRO00.0370.02147.206-0.002-0.0020.0000.0000.0000.000
147B163GLU-1-0.902-0.97245.9400.0530.0530.0000.0000.0000.000
148B164LEU0-0.033-0.01945.962-0.001-0.0010.0000.0000.0000.000
149B165ILE0-0.026-0.00350.320-0.001-0.0010.0000.0000.0000.000
150B166ASP-1-0.800-0.89553.5810.0340.0340.0000.0000.0000.000
151B167ASP-1-0.929-0.96051.6030.0390.0390.0000.0000.0000.000
152B168VAL0-0.067-0.04151.3460.0000.0000.0000.0000.0000.000
153B169ALA0-0.005-0.00453.935-0.001-0.0010.0000.0000.0000.000
154B170ALA0-0.035-0.02156.985-0.001-0.0010.0000.0000.0000.000
155B171ASP-1-0.950-0.96854.5650.0370.0370.0000.0000.0000.000
156B172SER0-0.0360.00156.848-0.001-0.0010.0000.0000.0000.000
157B173PRO0-0.038-0.02659.251-0.001-0.0010.0000.0000.0000.000
158B174HIS0-0.078-0.04561.301-0.002-0.0020.0000.0000.0000.000
159B175GLY00.0350.02664.1780.0000.0000.0000.0000.0000.000
160B176PRO0-0.005-0.02264.4370.0010.0010.0000.0000.0000.000
161B177GLU-1-0.898-0.94664.4160.0260.0260.0000.0000.0000.000
162B178PHE00.000-0.00559.0380.0010.0010.0000.0000.0000.000
163B179ALA00.0070.00459.4400.0010.0010.0000.0000.0000.000
164B180ASP-1-0.909-0.96959.5620.0310.0310.0000.0000.0000.000
165B181GLN00.0040.00761.4400.0010.0010.0000.0000.0000.000
166B182LEU0-0.023-0.00955.3540.0010.0010.0000.0000.0000.000
167B183ARG10.8750.91456.132-0.034-0.0340.0000.0000.0000.000
168B184GLU-1-0.949-0.96257.4450.0310.0310.0000.0000.0000.000
169B185LYN00.0700.05258.7780.0010.0010.0000.0000.0000.000
170B186VAL0-0.086-0.04952.4860.0010.0010.0000.0000.0000.000
171B187GLU-1-0.829-0.90454.6260.0440.0440.0000.0000.0000.000
172B188ASP-1-0.822-0.90856.3510.0350.0350.0000.0000.0000.000
173B189GLY0-0.111-0.06954.7690.0000.0000.0000.0000.0000.000
174B190ARG10.7810.88049.175-0.047-0.0470.0000.0000.0000.000
175B191GLU-1-0.971-0.97053.3930.0380.0380.0000.0000.0000.000
176B192ARG10.8190.92556.001-0.039-0.0390.0000.0000.0000.000
177B193GLY00.0040.00652.3120.0000.0000.0000.0000.0000.000
178B194TYR0-0.007-0.02051.7740.0020.0020.0000.0000.0000.000
179B195GLN0-0.0200.00253.678-0.003-0.0030.0000.0000.0000.000
180B196LEU00.0120.00355.5390.0010.0010.0000.0000.0000.000
181B197VAL0-0.0050.01757.742-0.001-0.0010.0000.0000.0000.000
182B198HIS00.0590.01560.0970.0010.0010.0000.0000.0000.000
183B199GLY0-0.035-0.01462.398-0.001-0.0010.0000.0000.0000.000
184B200GLU-1-0.815-0.88459.0240.0360.0360.0000.0000.0000.000
185B201ARG10.8970.95054.899-0.040-0.0400.0000.0000.0000.000
186B202GLU-1-0.901-0.94759.2100.0340.0340.0000.0000.0000.000
187B203LEU00.0220.01362.0830.0000.0000.0000.0000.0000.000
188B204GLY00.0230.01364.4250.0000.0000.0000.0000.0000.000
189B205SER0-0.054-0.01859.1430.0010.0010.0000.0000.0000.000
190B206SER00.0350.00059.735-0.001-0.0010.0000.0000.0000.000
191B207GLY0-0.054-0.02555.9800.0010.0010.0000.0000.0000.000
192B208LEU00.0230.02453.850-0.001-0.0010.0000.0000.0000.000
193B209SER0-0.067-0.04749.8450.0020.0020.0000.0000.0000.000
194B210PHE00.1120.03848.647-0.002-0.0020.0000.0000.0000.000
195B211PRO0-0.0060.00346.0550.0020.0020.0000.0000.0000.000
196B212LEU0-0.035-0.00241.5540.0000.0000.0000.0000.0000.000
197B213VAL00.001-0.00941.074-0.001-0.0010.0000.0000.0000.000
198B214ASP-1-0.801-0.89835.8730.0950.0950.0000.0000.0000.000
199B215SER00.006-0.03034.154-0.004-0.0040.0000.0000.0000.000
200B216HIS0-0.108-0.03436.844-0.003-0.0030.0000.0000.0000.000
201B217GLY00.0230.01638.701-0.005-0.0050.0000.0000.0000.000
202B218THR0-0.070-0.03539.498-0.007-0.0070.0000.0000.0000.000
203B219VAL0-0.027-0.00841.0290.0030.0030.0000.0000.0000.000
204B220VAL00.0120.00737.526-0.001-0.0010.0000.0000.0000.000
205B221ALA0-0.033-0.02140.6300.0010.0010.0000.0000.0000.000
206B222ALA00.0080.00442.679-0.002-0.0020.0000.0000.0000.000
207B223LEU00.0290.02844.7080.0000.0000.0000.0000.0000.000
208B224THR0-0.050-0.03046.763-0.003-0.0030.0000.0000.0000.000
209B225LEU00.0380.05049.9810.0010.0010.0000.0000.0000.000
210B226GLY0-0.023-0.02052.874-0.001-0.0010.0000.0000.0000.000
211B227GLY0-0.012-0.01455.1370.0010.0010.0000.0000.0000.000
212B228PRO0-0.014-0.00358.146-0.001-0.0010.0000.0000.0000.000
213B229THR00.046-0.00161.9120.0000.0000.0000.0000.0000.000
214B230GLY0-0.037-0.02063.8420.0000.0000.0000.0000.0000.000
215B231ARG10.7550.84958.718-0.036-0.0360.0000.0000.0000.000
216B232PHE0-0.028-0.00856.7410.0010.0010.0000.0000.0000.000
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