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: LNQM9

Calculation Name: 3LZ8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LZ8

Chain ID: B

ChEMBL ID:

UniProt ID: A6TH30

Base Structure: X-ray

Registration Date: 2023-09-22

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1593267.19313
FMO2-HF: Nuclear repulsion 1522312.184368
FMO2-HF: Total energy -70955.008762
FMO2-MP2: Total energy -71166.794102


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:113:ALA)


Summations of interaction energy for fragment #1(B:113: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.
-11.361-7.1698.314-7.073-5.435-0.011
Interaction energy analysis for fragmet #1(B:113:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.008
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].
3B115ARG10.8530.9283.8400.6452.402-0.021-0.932-0.8050.005
4B116GLY00.0410.0516.7850.0650.0650.0000.0000.0000.000
5B117HIS0-0.029-0.0309.341-0.085-0.0850.0000.0000.0000.000
6B118ASP-1-0.785-0.91012.629-0.533-0.5330.0000.0000.0000.000
7B119LEU0-0.025-0.00515.9560.0250.0250.0000.0000.0000.000
8B120GLU-1-0.861-0.94318.877-0.292-0.2920.0000.0000.0000.000
9B121ILE00.0020.00522.4600.0180.0180.0000.0000.0000.000
10B122GLU-1-0.909-0.96225.492-0.173-0.1730.0000.0000.0000.000
11B123VAL0-0.059-0.01828.5900.0120.0120.0000.0000.0000.000
12B124ALA00.0360.02131.1560.0000.0000.0000.0000.0000.000
13B125VAL0-0.013-0.00734.2990.0030.0030.0000.0000.0000.000
14B126PHE00.0590.03536.992-0.001-0.0010.0000.0000.0000.000
15B127LEU00.0530.03440.745-0.001-0.0010.0000.0000.0000.000
16B128GLU-1-0.916-0.97142.063-0.058-0.0580.0000.0000.0000.000
17B129GLU-1-0.948-0.98939.766-0.067-0.0670.0000.0000.0000.000
18B130THR0-0.0320.00739.416-0.003-0.0030.0000.0000.0000.000
19B131LEU0-0.039-0.02639.382-0.003-0.0030.0000.0000.0000.000
20B132ALA0-0.017-0.00540.3000.0020.0020.0000.0000.0000.000
21B133GLU-1-0.966-0.96735.491-0.090-0.0900.0000.0000.0000.000
22B134GLN00.0420.01635.1930.0070.0070.0000.0000.0000.000
23B135THR00.016-0.01532.696-0.005-0.0050.0000.0000.0000.000
24B136ARG10.8810.95731.2490.0930.0930.0000.0000.0000.000
25B137THR00.001-0.02929.781-0.002-0.0020.0000.0000.0000.000
26B138ILE0-0.068-0.03525.4550.0010.0010.0000.0000.0000.000
27B139SER00.045-0.00226.2950.0090.0090.0000.0000.0000.000
28B140TYR0-0.062-0.01918.9410.0030.0030.0000.0000.0000.000
29B141ASN00.0370.01621.7660.0110.0110.0000.0000.0000.000
30B142LEU0-0.032-0.00915.375-0.028-0.0280.0000.0000.0000.000
31B143PRO00.0360.02116.0440.0320.0320.0000.0000.0000.000
32B144VAL0-0.020-0.01315.8560.0020.0020.0000.0000.0000.000
33B145TYR00.000-0.00713.706-0.026-0.0260.0000.0000.0000.000
34B146ASN00.0300.04316.1790.0450.0450.0000.0000.0000.000
35B147VAL00.0470.01916.0840.0300.0300.0000.0000.0000.000
36B148PHE0-0.063-0.05216.5640.0350.0350.0000.0000.0000.000
37B149GLY00.0090.00915.377-0.025-0.0250.0000.0000.0000.000
38B150MET0-0.005-0.01416.249-0.048-0.0480.0000.0000.0000.000
39B151ILE0-0.035-0.00618.0270.0220.0220.0000.0000.0000.000
40B152GLU-1-0.944-0.97219.4720.1550.1550.0000.0000.0000.000
41B153SER0-0.053-0.02420.822-0.009-0.0090.0000.0000.0000.000
42B154GLU-1-0.856-0.93220.258-0.061-0.0610.0000.0000.0000.000
43B155THR0-0.077-0.03718.5580.0030.0030.0000.0000.0000.000
44B156PRO00.0440.03321.335-0.020-0.0200.0000.0000.0000.000
45B157LYS10.9360.96217.7650.0850.0850.0000.0000.0000.000
46B158THR00.025-0.00623.386-0.002-0.0020.0000.0000.0000.000
47B159LEU0-0.0300.00121.8780.0000.0000.0000.0000.0000.000
48B160ASN00.0290.04326.1440.0000.0000.0000.0000.0000.000
49B161VAL0-0.007-0.00126.027-0.002-0.0020.0000.0000.0000.000
50B162LYS10.9230.96028.6380.0800.0800.0000.0000.0000.000
51B163ILE0-0.016-0.00630.612-0.010-0.0100.0000.0000.0000.000
52B164PRO00.0200.00030.7200.0060.0060.0000.0000.0000.000
53B165ALA00.0250.02533.945-0.001-0.0010.0000.0000.0000.000
54B166GLY0-0.077-0.05636.839-0.004-0.0040.0000.0000.0000.000
55B167VAL0-0.061-0.00532.789-0.005-0.0050.0000.0000.0000.000
56B168VAL0-0.010-0.00934.3930.0050.0050.0000.0000.0000.000
57B169ASP-1-0.762-0.91034.462-0.120-0.1200.0000.0000.0000.000
58B170GLY00.0380.02332.266-0.003-0.0030.0000.0000.0000.000
59B171GLN0-0.118-0.03429.497-0.009-0.0090.0000.0000.0000.000
60B172ARG10.8460.91422.5490.2620.2620.0000.0000.0000.000
61B173ILE0-0.005-0.00125.3320.0000.0000.0000.0000.0000.000
62B174ARG10.9320.97917.4720.3540.3540.0000.0000.0000.000
63B175LEU00.0020.01120.6960.0140.0140.0000.0000.0000.000
64B176LYS10.9220.94214.0700.4640.4640.0000.0000.0000.000
65B177GLY0-0.001-0.00913.5620.0380.0380.0000.0000.0000.000
66B178GLN0-0.068-0.03014.5330.0460.0460.0000.0000.0000.000
67B179GLY00.0020.01215.4940.0360.0360.0000.0000.0000.000
68B180THR00.0210.00511.1580.0630.0630.0000.0000.0000.000
69B181PRO00.0050.00210.640-0.134-0.1340.0000.0000.0000.000
70B182GLY00.0400.0236.852-0.071-0.0710.0000.0000.0000.000
71B183GLU-1-0.910-0.9493.7950.3740.5660.002-0.047-0.1470.000
72B184ASN0-0.027-0.0281.839-11.071-9.8808.239-5.677-3.754-0.012
73B185GLY00.002-0.0114.429-0.121-0.010-0.001-0.019-0.0900.000
74B186GLY0-0.030-0.0013.323-1.609-0.8100.089-0.391-0.498-0.004
75B187PRO0-0.065-0.0223.7950.6360.7780.006-0.007-0.1410.000
76B188ASN00.027-0.0047.498-0.157-0.1570.0000.0000.0000.000
77B189GLY00.0060.00610.450-0.088-0.0880.0000.0000.0000.000
78B190ASP-1-0.914-0.95812.451-0.437-0.4370.0000.0000.0000.000
79B191LEU00.0140.01215.9150.0020.0020.0000.0000.0000.000
80B192TRP0-0.042-0.03018.3900.0300.0300.0000.0000.0000.000
81B193LEU00.0110.01022.3110.0140.0140.0000.0000.0000.000
82B194VAL00.0330.00425.937-0.006-0.0060.0000.0000.0000.000
83B195ILE0-0.021-0.02328.2310.0110.0110.0000.0000.0000.000
84B196HIS00.0070.01930.1140.0010.0010.0000.0000.0000.000
85B197ILE0-0.061-0.03134.6730.0060.0060.0000.0000.0000.000
86B198ALA0-0.023-0.02038.1240.0010.0010.0000.0000.0000.000
87B199PRO0-0.027-0.00740.3460.0010.0010.0000.0000.0000.000
88B200HIS00.0320.02043.4770.0030.0030.0000.0000.0000.000
89B201PRO00.0060.00646.4670.0010.0010.0000.0000.0000.000
90B202LEU0-0.078-0.03549.7050.0020.0020.0000.0000.0000.000
91B203PHE0-0.037-0.04048.6010.0000.0000.0000.0000.0000.000
92B204ASP-1-0.864-0.92046.908-0.069-0.0690.0000.0000.0000.000
93B205ILE0-0.007-0.02041.6400.0010.0010.0000.0000.0000.000
94B206VAL00.0810.05644.711-0.003-0.0030.0000.0000.0000.000
95B207GLY0-0.018-0.00843.8710.0020.0020.0000.0000.0000.000
96B208HIS0-0.037-0.03942.798-0.005-0.0050.0000.0000.0000.000
97B209ASN00.007-0.00844.9870.0010.0010.0000.0000.0000.000
98B210LEU00.0190.02946.240-0.002-0.0020.0000.0000.0000.000
99B211GLU-1-0.842-0.91049.283-0.059-0.0590.0000.0000.0000.000
100B212ILE00.0650.03251.5570.0000.0000.0000.0000.0000.000
101B213VAL00.0150.00254.3250.0010.0010.0000.0000.0000.000
102B214LEU0-0.036-0.03056.6960.0010.0010.0000.0000.0000.000
103B215PRO0-0.036-0.02759.4020.0010.0010.0000.0000.0000.000
104B216LEU00.0220.02062.4010.0000.0000.0000.0000.0000.000
105B217ALA00.0140.02065.9530.0000.0000.0000.0000.0000.000
106B218PRO00.0280.00969.1700.0000.0000.0000.0000.0000.000
107B219TRP00.0400.00970.9980.0000.0000.0000.0000.0000.000
108B220GLU-1-0.884-0.95368.248-0.031-0.0310.0000.0000.0000.000
109B221ALA0-0.045-0.01168.3210.0000.0000.0000.0000.0000.000
110B222ALA0-0.003-0.00469.9820.0000.0000.0000.0000.0000.000
111B223LEU0-0.020-0.01573.4180.0000.0000.0000.0000.0000.000
112B224GLY00.0330.04071.2060.0000.0000.0000.0000.0000.000
113B225ALA0-0.009-0.01869.8670.0010.0010.0000.0000.0000.000
114B226LYS10.9020.95068.3080.0280.0280.0000.0000.0000.000
115B227VAL00.0480.02364.7320.0010.0010.0000.0000.0000.000
116B228THR0-0.006-0.00463.272-0.001-0.0010.0000.0000.0000.000
117B229VAL0-0.020-0.00357.8090.0000.0000.0000.0000.0000.000
118B230PRO00.0250.01855.4670.0000.0000.0000.0000.0000.000
119B231THR0-0.033-0.04554.123-0.002-0.0020.0000.0000.0000.000
120B232LEU00.0000.00347.8510.0000.0000.0000.0000.0000.000
121B233LYS10.9460.96749.3210.0520.0520.0000.0000.0000.000
122B234GLU-1-0.842-0.89353.293-0.044-0.0440.0000.0000.0000.000
123B235SER00.006-0.00756.739-0.001-0.0010.0000.0000.0000.000
124B236ILE0-0.0060.02158.6290.0010.0010.0000.0000.0000.000
125B237LEU00.023-0.00861.1620.0010.0010.0000.0000.0000.000
126B238LEU0-0.0060.01760.8410.0000.0000.0000.0000.0000.000
127B239THR0-0.034-0.02763.9010.0010.0010.0000.0000.0000.000
128B240VAL0-0.010-0.00765.284-0.001-0.0010.0000.0000.0000.000
129B241PRO0-0.010-0.00666.7660.0010.0010.0000.0000.0000.000
130B242PRO00.0670.02969.9550.0000.0000.0000.0000.0000.000
131B243GLY0-0.0110.00272.108-0.001-0.0010.0000.0000.0000.000
132B244SER0-0.079-0.04266.643-0.001-0.0010.0000.0000.0000.000
133B245GLN00.0420.01966.1250.0010.0010.0000.0000.0000.000
134B246ALA00.004-0.00163.683-0.001-0.0010.0000.0000.0000.000
135B247GLY00.0080.00759.9820.0000.0000.0000.0000.0000.000
136B248GLN0-0.030-0.00659.842-0.002-0.0020.0000.0000.0000.000
137B249ARG10.8570.91451.7890.0590.0590.0000.0000.0000.000
138B250LEU00.0030.01259.3690.0000.0000.0000.0000.0000.000
139B251ARG10.8690.93255.2820.0530.0530.0000.0000.0000.000
140B252ILE00.0060.00556.8280.0020.0020.0000.0000.0000.000
141B253LYS10.9540.98055.3160.0450.0450.0000.0000.0000.000
142B254GLY0-0.019-0.01253.7370.0020.0020.0000.0000.0000.000
143B255LYS10.8460.91652.3600.0480.0480.0000.0000.0000.000
144B256GLY00.0960.03649.6060.0010.0010.0000.0000.0000.000
145B257LEU00.0080.02542.6370.0010.0010.0000.0000.0000.000
146B258VAL00.0200.00244.7250.0010.0010.0000.0000.0000.000
147B259SER00.0550.05241.173-0.005-0.0050.0000.0000.0000.000
148B260LYS10.9990.96936.2290.1140.1140.0000.0000.0000.000
149B261THR0-0.048-0.02442.045-0.001-0.0010.0000.0000.0000.000
150B262HIS10.8540.95443.5340.0850.0850.0000.0000.0000.000
151B263THR00.001-0.01745.857-0.003-0.0030.0000.0000.0000.000
152B264GLY0-0.0440.00348.1510.0000.0000.0000.0000.0000.000
153B265ASP-1-0.863-0.95249.066-0.055-0.0550.0000.0000.0000.000
154B266LEU00.0240.02751.330-0.002-0.0020.0000.0000.0000.000
155B267PHE0-0.041-0.03952.3660.0020.0020.0000.0000.0000.000
156B268ALA00.0210.01355.2130.0000.0000.0000.0000.0000.000
157B269VAL0-0.006-0.00755.2890.0010.0010.0000.0000.0000.000
158B270ILE00.0220.02358.1490.0010.0010.0000.0000.0000.000
159B271LYS10.9710.98958.1960.0400.0400.0000.0000.0000.000
160B272ILE00.0090.00761.7920.0010.0010.0000.0000.0000.000
161B273VAL0-0.047-0.02862.8730.0000.0000.0000.0000.0000.000
162B274MET0-0.001-0.00265.8840.0010.0010.0000.0000.0000.000
163B275PRO00.0040.01968.1820.0000.0000.0000.0000.0000.000
164B276THR00.0230.00269.1050.0000.0000.0000.0000.0000.000
165B277LYS10.9710.97671.3310.0200.0200.0000.0000.0000.000
166B278PRO00.0130.01974.5280.0000.0000.0000.0000.0000.000
167B279ASP-1-0.868-0.95177.415-0.019-0.0190.0000.0000.0000.000
168B280GLU-1-0.960-0.98980.700-0.017-0.0170.0000.0000.0000.000
169B281LYS10.9560.99083.9950.0180.0180.0000.0000.0000.000
170B282ALA00.0740.02078.9720.0000.0000.0000.0000.0000.000
171B283ARG10.8780.95580.5540.0180.0180.0000.0000.0000.000
172B284GLU-1-0.847-0.94781.545-0.019-0.0190.0000.0000.0000.000
173B285LEU00.0100.02181.7940.0000.0000.0000.0000.0000.000
174B286TRP00.0480.00473.926-0.001-0.0010.0000.0000.0000.000
175B287GLN0-0.041-0.01780.2600.0000.0000.0000.0000.0000.000
176B288GLN0-0.018-0.00782.9150.0000.0000.0000.0000.0000.000
177B289LEU0-0.0190.01177.7440.0000.0000.0000.0000.0000.000
178B290ALA0-0.026-0.00479.9450.0000.0000.0000.0000.0000.000
179B291ALA0-0.026-0.02280.8910.0000.0000.0000.0000.0000.000
180B292ALA0-0.056-0.02982.3240.0000.0000.0000.0000.0000.000
181B293GLU-1-0.935-0.97378.153-0.026-0.0260.0000.0000.0000.000
182B294ALA0-0.038-0.01479.558-0.001-0.0010.0000.0000.0000.000
183B295SER0-0.053-0.02480.8440.0000.0000.0000.0000.0000.000
184B296PHE0-0.013-0.00771.283-0.001-0.0010.0000.0000.0000.000
185B297ASP-1-0.829-0.91773.761-0.029-0.0290.0000.0000.0000.000
186B298PRO0-0.101-0.04970.527-0.001-0.0010.0000.0000.0000.000
187B299ARG10.8820.93168.7490.0290.0290.0000.0000.0000.000
188B300LYS11.0461.03669.8300.0330.0330.0000.0000.0000.000
189B301THR0-0.051-0.03065.2590.0000.0000.0000.0000.0000.000
190B302TRP00.0030.01764.7580.0000.0000.0000.0000.0000.000