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: 98LN2

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1593695.64075
FMO2-HF: Nuclear repulsion 1522739.165238
FMO2-HF: Total energy -70956.475512
FMO2-MP2: Total energy -71168.142968


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.
-9.299-3.5824.905-5.659-4.962-0.011
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 : 0.002 / q_NPA : 0.011
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].
3B115ARG10.8400.9073.8400.6362.380-0.020-0.924-0.8000.005
4B116GLY00.0490.0536.8590.0420.0420.0000.0000.0000.000
5B117HIS0-0.030-0.0299.369-0.049-0.0490.0000.0000.0000.000
6B118ASP-1-0.737-0.86312.656-0.513-0.5130.0000.0000.0000.000
7B119LEU0-0.0290.00115.9850.0220.0220.0000.0000.0000.000
8B120GLU-1-0.809-0.89018.905-0.279-0.2790.0000.0000.0000.000
9B121ILE0-0.013-0.00522.4880.0160.0160.0000.0000.0000.000
10B122GLU-1-0.844-0.92625.520-0.171-0.1710.0000.0000.0000.000
11B123VAL0-0.051-0.02128.6230.0110.0110.0000.0000.0000.000
12B124ALA00.0330.02631.1850.0000.0000.0000.0000.0000.000
13B125VAL0-0.027-0.01534.3520.0030.0030.0000.0000.0000.000
14B126PHE00.0360.02437.0920.0000.0000.0000.0000.0000.000
15B127LEU00.0570.04040.845-0.001-0.0010.0000.0000.0000.000
16B128GLU-1-0.807-0.92242.163-0.059-0.0590.0000.0000.0000.000
17B129GLU-1-0.894-0.96839.180-0.070-0.0700.0000.0000.0000.000
18B130THR0-0.0050.01239.501-0.003-0.0030.0000.0000.0000.000
19B131LEU0-0.040-0.02139.481-0.003-0.0030.0000.0000.0000.000
20B132ALA0-0.015-0.00740.5410.0020.0020.0000.0000.0000.000
21B133GLU-1-0.850-0.90234.940-0.083-0.0830.0000.0000.0000.000
22B134GLN00.0150.01735.0760.0040.0040.0000.0000.0000.000
23B135THR00.016-0.00532.637-0.006-0.0060.0000.0000.0000.000
24B136ARG10.8390.93831.3850.0860.0860.0000.0000.0000.000
25B137THR00.016-0.00430.298-0.003-0.0030.0000.0000.0000.000
26B138ILE0-0.040-0.01625.3370.0000.0000.0000.0000.0000.000
27B139SER00.002-0.02626.2820.0090.0090.0000.0000.0000.000
28B140TYR0-0.075-0.04518.7220.0050.0050.0000.0000.0000.000
29B141ASN00.025-0.00421.7850.0100.0100.0000.0000.0000.000
30B142LEU0-0.031-0.00815.660-0.029-0.0290.0000.0000.0000.000
31B143PRO00.0030.00616.5260.0290.0290.0000.0000.0000.000
32B144VAL0-0.0080.00015.868-0.002-0.0020.0000.0000.0000.000
33B145TYR0-0.007-0.01713.964-0.013-0.0130.0000.0000.0000.000
34B146ASN0-0.0130.01116.1750.0420.0420.0000.0000.0000.000
35B147VAL00.0400.02516.0740.0250.0250.0000.0000.0000.000
36B148PHE0-0.053-0.04716.5480.0320.0320.0000.0000.0000.000
37B149GLY00.0110.00915.369-0.023-0.0230.0000.0000.0000.000
38B150MET0-0.010-0.00216.240-0.045-0.0450.0000.0000.0000.000
39B151ILE0-0.0130.00818.0320.0230.0230.0000.0000.0000.000
40B152GLU-1-0.929-0.97319.4030.1360.1360.0000.0000.0000.000
41B153SER0-0.031-0.02020.846-0.005-0.0050.0000.0000.0000.000
42B154GLU-1-0.847-0.91420.266-0.077-0.0770.0000.0000.0000.000
43B155THR0-0.045-0.01918.9160.0070.0070.0000.0000.0000.000
44B156PRO00.0170.01621.349-0.019-0.0190.0000.0000.0000.000
45B157LYS10.9530.97317.3920.1270.1270.0000.0000.0000.000
46B158THR0-0.009-0.02023.409-0.003-0.0030.0000.0000.0000.000
47B159LEU0-0.0120.01021.7390.0000.0000.0000.0000.0000.000
48B160ASN00.0250.02426.2300.0000.0000.0000.0000.0000.000
49B161VAL0-0.010-0.00525.978-0.001-0.0010.0000.0000.0000.000
50B162LYS10.7860.86628.7310.0810.0810.0000.0000.0000.000
51B163ILE0-0.0070.00130.492-0.009-0.0090.0000.0000.0000.000
52B164PRO00.0200.00731.1100.0070.0070.0000.0000.0000.000
53B165ALA00.0080.00734.041-0.001-0.0010.0000.0000.0000.000
54B166GLY0-0.068-0.05436.937-0.003-0.0030.0000.0000.0000.000
55B167VAL0-0.062-0.00432.761-0.004-0.0040.0000.0000.0000.000
56B168VAL0-0.030-0.02234.7200.0050.0050.0000.0000.0000.000
57B169ASP-1-0.756-0.90234.563-0.115-0.1150.0000.0000.0000.000
58B170GLY00.0180.01732.343-0.003-0.0030.0000.0000.0000.000
59B171GLN0-0.112-0.03429.676-0.006-0.0060.0000.0000.0000.000
60B172ARG10.8330.87322.8750.2480.2480.0000.0000.0000.000
61B173ILE0-0.015-0.00425.4930.0020.0020.0000.0000.0000.000
62B174ARG10.8210.91016.4290.3690.3690.0000.0000.0000.000
63B175LEU00.0240.02320.8370.0150.0150.0000.0000.0000.000
64B176LYS10.9380.95313.8960.4170.4170.0000.0000.0000.000
65B177GLY00.005-0.00713.6550.0370.0370.0000.0000.0000.000
66B178GLN0-0.094-0.03714.6260.0480.0480.0000.0000.0000.000
67B179GLY00.0380.03915.5760.0360.0360.0000.0000.0000.000
68B180THR00.002-0.00411.7990.0580.0580.0000.0000.0000.000
69B181PRO00.0330.01310.621-0.123-0.1230.0000.0000.0000.000
70B182GLY00.0220.0156.934-0.072-0.0720.0000.0000.0000.000
71B183GLU-1-0.921-0.9533.8640.3540.5580.001-0.046-0.1590.000
72B184ASN0-0.025-0.0301.971-9.309-6.5174.852-4.306-3.337-0.013
73B185GLY00.008-0.0054.428-0.0390.068-0.001-0.018-0.0870.000
74B186GLY0-0.0200.0033.327-1.324-0.5900.069-0.354-0.449-0.003
75B187PRO0-0.067-0.0313.8850.5250.6610.004-0.011-0.1300.000
76B188ASN00.006-0.0117.589-0.148-0.1480.0000.0000.0000.000
77B189GLY00.0020.01010.544-0.076-0.0760.0000.0000.0000.000
78B190ASP-1-0.831-0.91512.551-0.391-0.3910.0000.0000.0000.000
79B191LEU0-0.0080.00716.015-0.001-0.0010.0000.0000.0000.000
80B192TRP0-0.022-0.03418.4860.0290.0290.0000.0000.0000.000
81B193LEU00.0030.00722.4120.0120.0120.0000.0000.0000.000
82B194VAL0-0.005-0.00225.865-0.004-0.0040.0000.0000.0000.000
83B195ILE0-0.006-0.02228.3320.0100.0100.0000.0000.0000.000
84B196HIS0-0.0140.00130.2340.0030.0030.0000.0000.0000.000
85B197ILE0-0.068-0.04034.7030.0060.0060.0000.0000.0000.000
86B198ALA0-0.023-0.00938.2250.0010.0010.0000.0000.0000.000
87B199PRO0-0.015-0.01340.3760.0010.0010.0000.0000.0000.000
88B200HIS0-0.019-0.00143.5060.0030.0030.0000.0000.0000.000
89B201PRO00.0000.00046.4960.0010.0010.0000.0000.0000.000
90B202LEU0-0.092-0.03649.7340.0020.0020.0000.0000.0000.000
91B203PHE0-0.050-0.03848.6600.0000.0000.0000.0000.0000.000
92B204ASP-1-0.843-0.92346.346-0.068-0.0680.0000.0000.0000.000
93B205ILE0-0.012-0.01341.7850.0010.0010.0000.0000.0000.000
94B206VAL00.0530.04244.741-0.003-0.0030.0000.0000.0000.000
95B207GLY0-0.006-0.00243.9680.0020.0020.0000.0000.0000.000
96B208HIS0-0.044-0.03842.913-0.005-0.0050.0000.0000.0000.000
97B209ASN0-0.015-0.01945.0860.0010.0010.0000.0000.0000.000
98B210LEU00.0340.03746.358-0.002-0.0020.0000.0000.0000.000
99B211GLU-1-0.814-0.87749.383-0.057-0.0570.0000.0000.0000.000
100B212ILE00.0720.03551.6310.0000.0000.0000.0000.0000.000
101B213VAL0-0.006-0.00354.3710.0010.0010.0000.0000.0000.000
102B214LEU0-0.024-0.03156.7250.0010.0010.0000.0000.0000.000
103B215PRO0-0.032-0.01359.6480.0010.0010.0000.0000.0000.000
104B216LEU00.0290.01262.4300.0000.0000.0000.0000.0000.000
105B217ALA00.0170.01465.9820.0000.0000.0000.0000.0000.000
106B218PRO00.017-0.00569.1990.0000.0000.0000.0000.0000.000
107B219TRP00.0510.01571.0260.0000.0000.0000.0000.0000.000
108B220GLU-1-0.881-0.93768.525-0.030-0.0300.0000.0000.0000.000
109B221ALA0-0.051-0.01568.3470.0000.0000.0000.0000.0000.000
110B222ALA0-0.003-0.00370.0120.0000.0000.0000.0000.0000.000
111B223LEU0-0.010-0.01273.4470.0000.0000.0000.0000.0000.000
112B224GLY00.0330.03971.3060.0000.0000.0000.0000.0000.000
113B225ALA0-0.008-0.01469.8000.0010.0010.0000.0000.0000.000
114B226LYS10.9030.94968.4080.0270.0270.0000.0000.0000.000
115B227VAL00.0470.02264.6350.0010.0010.0000.0000.0000.000
116B228THR00.001-0.00363.206-0.001-0.0010.0000.0000.0000.000
117B229VAL0-0.031-0.01057.9880.0000.0000.0000.0000.0000.000
118B230PRO00.0340.02455.5710.0000.0000.0000.0000.0000.000
119B231THR0-0.042-0.05554.198-0.002-0.0020.0000.0000.0000.000
120B232LEU00.0120.01148.1210.0000.0000.0000.0000.0000.000
121B233LYS10.9400.96849.0740.0490.0490.0000.0000.0000.000
122B234GLU-1-0.783-0.86753.393-0.042-0.0420.0000.0000.0000.000
123B235SER0-0.006-0.00356.839-0.001-0.0010.0000.0000.0000.000
124B236ILE0-0.0090.01358.7050.0010.0010.0000.0000.0000.000
125B237LEU00.015-0.00861.2620.0010.0010.0000.0000.0000.000
126B238LEU00.0040.02360.8730.0000.0000.0000.0000.0000.000
127B239THR0-0.024-0.02564.0020.0010.0010.0000.0000.0000.000
128B240VAL0-0.013-0.01065.369-0.001-0.0010.0000.0000.0000.000
129B241PRO0-0.006-0.00766.9630.0010.0010.0000.0000.0000.000
130B242PRO00.0710.03370.0550.0000.0000.0000.0000.0000.000
131B243GLY00.0000.01072.2080.0000.0000.0000.0000.0000.000
132B244SER0-0.055-0.02566.714-0.001-0.0010.0000.0000.0000.000
133B245GLN0-0.013-0.00966.1890.0000.0000.0000.0000.0000.000
134B246ALA00.009-0.00363.781-0.001-0.0010.0000.0000.0000.000
135B247GLY00.0140.01160.0100.0000.0000.0000.0000.0000.000
136B248GLN0-0.051-0.01659.871-0.002-0.0020.0000.0000.0000.000
137B249ARG10.8170.87851.8870.0560.0560.0000.0000.0000.000
138B250LEU0-0.0010.01359.4620.0000.0000.0000.0000.0000.000
139B251ARG10.8580.92355.2630.0500.0500.0000.0000.0000.000
140B252ILE00.0000.00156.9290.0020.0020.0000.0000.0000.000
141B253LYS10.9500.97255.4200.0430.0430.0000.0000.0000.000
142B254GLY0-0.015-0.00853.8360.0020.0020.0000.0000.0000.000
143B255LYS10.7970.89052.4900.0450.0450.0000.0000.0000.000
144B256GLY00.0910.03349.7060.0000.0000.0000.0000.0000.000
145B257LEU00.0340.02842.2960.0010.0010.0000.0000.0000.000
146B258VAL0-0.015-0.01344.9130.0010.0010.0000.0000.0000.000
147B259SER00.0440.03641.108-0.003-0.0030.0000.0000.0000.000
148B260LYS11.0460.99636.3020.1070.1070.0000.0000.0000.000
149B261THR0-0.074-0.02942.092-0.001-0.0010.0000.0000.0000.000
150B262HIS10.8540.95243.4840.0810.0810.0000.0000.0000.000
151B263THR00.019-0.00845.954-0.002-0.0020.0000.0000.0000.000
152B264GLY0-0.0290.00648.2450.0000.0000.0000.0000.0000.000
153B265ASP-1-0.872-0.93849.165-0.052-0.0520.0000.0000.0000.000
154B266LEU00.0280.02951.430-0.002-0.0020.0000.0000.0000.000
155B267PHE0-0.020-0.03452.0380.0020.0020.0000.0000.0000.000
156B268ALA00.0200.00955.3130.0000.0000.0000.0000.0000.000
157B269VAL00.001-0.00555.1460.0010.0010.0000.0000.0000.000
158B270ILE00.0220.02558.1790.0010.0010.0000.0000.0000.000
159B271LYS10.9700.98858.0100.0400.0400.0000.0000.0000.000
160B272ILE00.0020.00361.8200.0010.0010.0000.0000.0000.000
161B273VAL0-0.043-0.02162.9460.0000.0000.0000.0000.0000.000
162B274MET0-0.003-0.00465.9110.0010.0010.0000.0000.0000.000
163B275PRO00.0040.01968.2090.0000.0000.0000.0000.0000.000
164B276THR00.0220.00269.2510.0000.0000.0000.0000.0000.000
165B277LYS10.9690.97471.3570.0200.0200.0000.0000.0000.000
166B278PRO00.0140.01574.5530.0000.0000.0000.0000.0000.000
167B279ASP-1-0.871-0.94977.440-0.019-0.0190.0000.0000.0000.000
168B280GLU-1-0.830-0.92380.726-0.017-0.0170.0000.0000.0000.000
169B281LYS10.8650.92584.0900.0180.0180.0000.0000.0000.000
170B282ALA00.0470.01278.9890.0000.0000.0000.0000.0000.000
171B283ARG10.7930.90780.5770.0180.0180.0000.0000.0000.000
172B284GLU-1-0.766-0.87181.570-0.019-0.0190.0000.0000.0000.000
173B285LEU00.0160.02581.6410.0000.0000.0000.0000.0000.000
174B286TRP00.0530.01473.9370.0000.0000.0000.0000.0000.000
175B287GLN0-0.046-0.02080.2860.0000.0000.0000.0000.0000.000
176B288GLN0-0.026-0.02482.9400.0000.0000.0000.0000.0000.000
177B289LEU0-0.0170.00278.0790.0000.0000.0000.0000.0000.000
178B290ALA0-0.026-0.00479.9950.0000.0000.0000.0000.0000.000
179B291ALA0-0.024-0.02280.9170.0000.0000.0000.0000.0000.000
180B292ALA0-0.047-0.02782.4530.0000.0000.0000.0000.0000.000
181B293GLU-1-0.946-0.98278.159-0.026-0.0260.0000.0000.0000.000
182B294ALA0-0.033-0.00879.584-0.001-0.0010.0000.0000.0000.000
183B295SER0-0.061-0.02780.8700.0000.0000.0000.0000.0000.000
184B296PHE0-0.001-0.00371.279-0.001-0.0010.0000.0000.0000.000
185B297ASP-1-0.812-0.91373.803-0.029-0.0290.0000.0000.0000.000
186B298PRO0-0.092-0.05470.531-0.001-0.0010.0000.0000.0000.000
187B299ARG10.8810.93568.7080.0280.0280.0000.0000.0000.000
188B300LYS11.0271.03370.1260.0310.0310.0000.0000.0000.000
189B301THR0-0.067-0.03665.3700.0000.0000.0000.0000.0000.000
190B302TRP00.0070.01864.7560.0000.0000.0000.0000.0000.000