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: MNR6Z

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 OptAll
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 -1592574.523098
FMO2-HF: Nuclear repulsion 1521616.861567
FMO2-HF: Total energy -70957.661531
FMO2-MP2: Total energy -71169.248766


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.
-11.968-10.5412.85-7.574-6.702-0.013
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 : 0.029 / q_NPA : 0.026
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].
3B115ARG10.7590.8543.8560.5282.468-0.019-1.094-0.8270.004
4B116GLY00.0470.0466.931-0.015-0.0150.0000.0000.0000.000
5B117HIS0-0.006-0.0039.133-0.039-0.0390.0000.0000.0000.000
6B118ASP-1-0.752-0.85512.524-0.478-0.4780.0000.0000.0000.000
7B119LEU0-0.0300.00115.7900.0210.0210.0000.0000.0000.000
8B120GLU-1-0.761-0.84218.764-0.268-0.2680.0000.0000.0000.000
9B121ILE0-0.007-0.00522.4620.0160.0160.0000.0000.0000.000
10B122GLU-1-0.815-0.91125.622-0.159-0.1590.0000.0000.0000.000
11B123VAL0-0.056-0.02428.4290.0120.0120.0000.0000.0000.000
12B124ALA00.0360.02631.0730.0000.0000.0000.0000.0000.000
13B125VAL0-0.050-0.01634.1960.0030.0030.0000.0000.0000.000
14B126PHE00.0170.01236.9060.0000.0000.0000.0000.0000.000
15B127LEU00.0410.02440.650-0.002-0.0020.0000.0000.0000.000
16B128GLU-1-0.846-0.93642.590-0.055-0.0550.0000.0000.0000.000
17B129GLU-1-0.830-0.91338.608-0.067-0.0670.0000.0000.0000.000
18B130THR0-0.0240.01439.104-0.002-0.0020.0000.0000.0000.000
19B131LEU0-0.042-0.03039.379-0.003-0.0030.0000.0000.0000.000
20B132ALA0-0.018-0.01240.3340.0030.0030.0000.0000.0000.000
21B133GLU-1-0.849-0.90034.584-0.078-0.0780.0000.0000.0000.000
22B134GLN00.0130.01534.8330.0040.0040.0000.0000.0000.000
23B135THR0-0.017-0.02732.571-0.006-0.0060.0000.0000.0000.000
24B136ARG10.8230.90631.2020.0800.0800.0000.0000.0000.000
25B137THR00.009-0.00230.070-0.005-0.0050.0000.0000.0000.000
26B138ILE0-0.0080.01125.0450.0020.0020.0000.0000.0000.000
27B139SER0-0.015-0.02326.3430.0060.0060.0000.0000.0000.000
28B140TYR0-0.079-0.06118.7170.0050.0050.0000.0000.0000.000
29B141ASN00.006-0.01321.5300.0120.0120.0000.0000.0000.000
30B142LEU0-0.024-0.01315.564-0.033-0.0330.0000.0000.0000.000
31B143PRO0-0.0040.00516.1900.0290.0290.0000.0000.0000.000
32B144VAL0-0.0090.00515.4130.0020.0020.0000.0000.0000.000
33B145TYR00.003-0.01513.751-0.029-0.0290.0000.0000.0000.000
34B146ASN00.0210.01215.9100.0480.0480.0000.0000.0000.000
35B147VAL00.0100.00315.6030.0250.0250.0000.0000.0000.000
36B148PHE0-0.042-0.02916.2050.0290.0290.0000.0000.0000.000
37B149GLY00.0220.01414.726-0.028-0.0280.0000.0000.0000.000
38B150MET0-0.024-0.00315.691-0.051-0.0510.0000.0000.0000.000
39B151ILE00.0010.01117.7320.0270.0270.0000.0000.0000.000
40B152GLU-1-0.961-0.98218.8810.1720.1720.0000.0000.0000.000
41B153SER0-0.027-0.01420.272-0.011-0.0110.0000.0000.0000.000
42B154GLU-1-0.832-0.91819.717-0.063-0.0630.0000.0000.0000.000
43B155THR0-0.037-0.00618.5630.0110.0110.0000.0000.0000.000
44B156PRO00.0030.00820.610-0.021-0.0210.0000.0000.0000.000
45B157LYS10.9150.95616.9600.1310.1310.0000.0000.0000.000
46B158THR0-0.010-0.01023.152-0.005-0.0050.0000.0000.0000.000
47B159LEU00.0030.00221.4780.0000.0000.0000.0000.0000.000
48B160ASN0-0.0010.00926.070-0.004-0.0040.0000.0000.0000.000
49B161VAL00.0000.00825.7800.0000.0000.0000.0000.0000.000
50B162LYS10.7900.87228.5060.0780.0780.0000.0000.0000.000
51B163ILE00.0150.00829.946-0.011-0.0110.0000.0000.0000.000
52B164PRO00.0150.00731.2160.0070.0070.0000.0000.0000.000
53B165ALA00.0220.01134.2370.0000.0000.0000.0000.0000.000
54B166GLY0-0.052-0.04436.869-0.004-0.0040.0000.0000.0000.000
55B167VAL0-0.050-0.00832.914-0.004-0.0040.0000.0000.0000.000
56B168VAL0-0.002-0.00534.9130.0060.0060.0000.0000.0000.000
57B169ASP-1-0.792-0.91734.716-0.110-0.1100.0000.0000.0000.000
58B170GLY00.0220.02632.599-0.003-0.0030.0000.0000.0000.000
59B171GLN0-0.093-0.03430.036-0.005-0.0050.0000.0000.0000.000
60B172ARG10.7940.85322.9440.2360.2360.0000.0000.0000.000
61B173ILE00.0000.00225.6520.0070.0070.0000.0000.0000.000
62B174ARG10.8130.89716.4480.3580.3580.0000.0000.0000.000
63B175LEU00.0130.01420.5850.0140.0140.0000.0000.0000.000
64B176LYS10.9550.96513.8830.3780.3780.0000.0000.0000.000
65B177GLY00.001-0.00813.3520.0390.0390.0000.0000.0000.000
66B178GLN0-0.053-0.01514.2790.0490.0490.0000.0000.0000.000
67B179GLY00.0560.04815.4250.0400.0400.0000.0000.0000.000
68B180THR0-0.005-0.01011.6340.0520.0520.0000.0000.0000.000
69B181PRO00.041-0.00110.196-0.120-0.1200.0000.0000.0000.000
70B182GLY00.0250.0196.637-0.087-0.0870.0000.0000.0000.000
71B183GLU-1-0.891-0.9313.4900.4330.8420.011-0.134-0.2850.000
72B184ASN0-0.054-0.0602.014-12.049-13.80412.802-6.060-4.986-0.015
73B185GLY00.0060.0153.907-0.1020.0340.000-0.012-0.1240.000
74B186GLY0-0.0200.0023.328-0.940-0.3850.048-0.261-0.342-0.002
75B187PRO0-0.051-0.0373.7450.3980.5410.008-0.013-0.1380.000
76B188ASN00.0410.0157.536-0.210-0.2100.0000.0000.0000.000
77B189GLY0-0.0090.01210.231-0.095-0.0950.0000.0000.0000.000
78B190ASP-1-0.827-0.90412.577-0.373-0.3730.0000.0000.0000.000
79B191LEU0-0.0030.00016.010-0.005-0.0050.0000.0000.0000.000
80B192TRP0-0.027-0.04018.6110.0380.0380.0000.0000.0000.000
81B193LEU0-0.021-0.00722.2290.0130.0130.0000.0000.0000.000
82B194VAL0-0.004-0.01425.808-0.007-0.0070.0000.0000.0000.000
83B195ILE0-0.008-0.00528.3530.0090.0090.0000.0000.0000.000
84B196HIS0-0.029-0.01430.4040.0040.0040.0000.0000.0000.000
85B197ILE0-0.044-0.03534.7710.0060.0060.0000.0000.0000.000
86B198ALA0-0.014-0.00638.2970.0010.0010.0000.0000.0000.000
87B199PRO0-0.008-0.00240.2360.0010.0010.0000.0000.0000.000
88B200HIS0-0.005-0.00343.4930.0030.0030.0000.0000.0000.000
89B201PRO0-0.019-0.01146.5270.0010.0010.0000.0000.0000.000
90B202LEU0-0.074-0.03349.6720.0030.0030.0000.0000.0000.000
91B203PHE0-0.054-0.04048.6790.0010.0010.0000.0000.0000.000
92B204ASP-1-0.836-0.90846.009-0.066-0.0660.0000.0000.0000.000
93B205ILE0-0.024-0.02642.0810.0010.0010.0000.0000.0000.000
94B206VAL00.0250.02344.736-0.003-0.0030.0000.0000.0000.000
95B207GLY00.0040.00143.8820.0020.0020.0000.0000.0000.000
96B208HIS0-0.029-0.01642.917-0.005-0.0050.0000.0000.0000.000
97B209ASN0-0.018-0.01345.1320.0010.0010.0000.0000.0000.000
98B210LEU00.0430.03746.489-0.002-0.0020.0000.0000.0000.000
99B211GLU-1-0.829-0.87949.394-0.055-0.0550.0000.0000.0000.000
100B212ILE00.0390.01051.6900.0000.0000.0000.0000.0000.000
101B213VAL00.0050.00454.1350.0010.0010.0000.0000.0000.000
102B214LEU0-0.0010.00456.5570.0010.0010.0000.0000.0000.000
103B215PRO0-0.036-0.01559.5700.0010.0010.0000.0000.0000.000
104B216LEU00.0310.01362.3680.0000.0000.0000.0000.0000.000
105B217ALA00.0380.02166.0520.0000.0000.0000.0000.0000.000
106B218PRO0-0.004-0.01569.2720.0000.0000.0000.0000.0000.000
107B219TRP00.0490.01271.0330.0000.0000.0000.0000.0000.000
108B220GLU-1-0.887-0.93368.811-0.028-0.0280.0000.0000.0000.000
109B221ALA0-0.040-0.01368.1730.0000.0000.0000.0000.0000.000
110B222ALA00.0060.00669.7800.0000.0000.0000.0000.0000.000
111B223LEU00.006-0.00573.3120.0000.0000.0000.0000.0000.000
112B224GLY00.0160.03171.1140.0000.0000.0000.0000.0000.000
113B225ALA0-0.007-0.01269.1620.0010.0010.0000.0000.0000.000
114B226LYS10.9010.94168.3760.0260.0260.0000.0000.0000.000
115B227VAL00.0570.03464.2940.0010.0010.0000.0000.0000.000
116B228THR0-0.018-0.01262.869-0.001-0.0010.0000.0000.0000.000
117B229VAL0-0.0040.00457.7710.0000.0000.0000.0000.0000.000
118B230PRO00.0330.02055.4130.0000.0000.0000.0000.0000.000
119B231THR0-0.025-0.05353.803-0.002-0.0020.0000.0000.0000.000
120B232LEU00.0170.00748.0630.0000.0000.0000.0000.0000.000
121B233LYS10.9270.97148.6480.0470.0470.0000.0000.0000.000
122B234GLU-1-0.773-0.86853.113-0.039-0.0390.0000.0000.0000.000
123B235SER0-0.0080.00756.585-0.002-0.0020.0000.0000.0000.000
124B236ILE0-0.0150.00058.7020.0010.0010.0000.0000.0000.000
125B237LEU0-0.009-0.00961.5660.0000.0000.0000.0000.0000.000
126B238LEU00.0110.01961.0620.0000.0000.0000.0000.0000.000
127B239THR0-0.027-0.02364.1720.0010.0010.0000.0000.0000.000
128B240VAL00.0030.00165.319-0.001-0.0010.0000.0000.0000.000
129B241PRO00.007-0.00366.6950.0010.0010.0000.0000.0000.000
130B242PRO00.0410.03069.7380.0000.0000.0000.0000.0000.000
131B243GLY0-0.0030.00771.845-0.001-0.0010.0000.0000.0000.000
132B244SER0-0.039-0.02066.789-0.001-0.0010.0000.0000.0000.000
133B245GLN0-0.022-0.01866.0640.0010.0010.0000.0000.0000.000
134B246ALA0-0.007-0.01663.372-0.001-0.0010.0000.0000.0000.000
135B247GLY00.0190.01259.9280.0000.0000.0000.0000.0000.000
136B248GLN0-0.055-0.02460.276-0.002-0.0020.0000.0000.0000.000
137B249ARG10.8090.88152.1080.0550.0550.0000.0000.0000.000
138B250LEU00.0130.01759.5660.0000.0000.0000.0000.0000.000
139B251ARG10.8590.90755.0450.0490.0490.0000.0000.0000.000
140B252ILE00.0010.00756.9640.0020.0020.0000.0000.0000.000
141B253LYS10.9570.96555.4930.0410.0410.0000.0000.0000.000
142B254GLY00.0030.00052.9820.0020.0020.0000.0000.0000.000
143B255LYS10.7880.88252.4950.0440.0440.0000.0000.0000.000
144B256GLY00.0390.03049.4860.0000.0000.0000.0000.0000.000
145B257LEU00.0160.00342.1690.0010.0010.0000.0000.0000.000
146B258VAL0-0.008-0.01044.9800.0000.0000.0000.0000.0000.000
147B259SER00.0170.00240.766-0.002-0.0020.0000.0000.0000.000
148B260LYS10.9710.99136.3210.1050.1050.0000.0000.0000.000
149B261THR0-0.016-0.00541.902-0.002-0.0020.0000.0000.0000.000
150B262HIS10.8520.92743.3590.0790.0790.0000.0000.0000.000
151B263THR00.0320.01246.042-0.003-0.0030.0000.0000.0000.000
152B264GLY00.0250.03748.1820.0000.0000.0000.0000.0000.000
153B265ASP-1-0.876-0.93249.277-0.051-0.0510.0000.0000.0000.000
154B266LEU00.0340.02351.191-0.002-0.0020.0000.0000.0000.000
155B267PHE00.001-0.02751.6220.0020.0020.0000.0000.0000.000
156B268ALA00.0200.01355.1980.0000.0000.0000.0000.0000.000
157B269VAL00.0050.00355.0440.0010.0010.0000.0000.0000.000
158B270ILE00.0160.01058.1590.0010.0010.0000.0000.0000.000
159B271LYS10.9490.97558.1370.0380.0380.0000.0000.0000.000
160B272ILE00.0250.01361.8380.0010.0010.0000.0000.0000.000
161B273VAL0-0.057-0.02962.808-0.001-0.0010.0000.0000.0000.000
162B274MET00.008-0.00265.8590.0010.0010.0000.0000.0000.000
163B275PRO0-0.0010.01268.0130.0000.0000.0000.0000.0000.000
164B276THR00.0430.01169.6050.0000.0000.0000.0000.0000.000
165B277LYS10.9030.94371.3530.0190.0190.0000.0000.0000.000
166B278PRO00.0210.02174.4970.0000.0000.0000.0000.0000.000
167B279ASP-1-0.767-0.88377.445-0.018-0.0180.0000.0000.0000.000
168B280GLU-1-0.840-0.91180.692-0.016-0.0160.0000.0000.0000.000
169B281LYS10.8590.91883.9380.0170.0170.0000.0000.0000.000
170B282ALA00.0440.00578.8500.0000.0000.0000.0000.0000.000
171B283ARG10.7600.88280.2770.0170.0170.0000.0000.0000.000
172B284GLU-1-0.796-0.87081.221-0.018-0.0180.0000.0000.0000.000
173B285LEU00.0260.00981.8360.0000.0000.0000.0000.0000.000
174B286TRP00.024-0.00274.138-0.001-0.0010.0000.0000.0000.000
175B287GLN0-0.028-0.01580.2540.0000.0000.0000.0000.0000.000
176B288GLN0-0.040-0.03283.0250.0000.0000.0000.0000.0000.000
177B289LEU0-0.012-0.00977.7680.0000.0000.0000.0000.0000.000
178B290ALA0-0.041-0.01779.8430.0000.0000.0000.0000.0000.000
179B291ALA0-0.021-0.01180.8600.0000.0000.0000.0000.0000.000
180B292ALA0-0.034-0.01382.6270.0000.0000.0000.0000.0000.000
181B293GLU-1-0.913-0.95978.252-0.025-0.0250.0000.0000.0000.000
182B294ALA0-0.032-0.00679.500-0.001-0.0010.0000.0000.0000.000
183B295SER0-0.042-0.01780.7230.0000.0000.0000.0000.0000.000
184B296PHE0-0.004-0.00271.242-0.001-0.0010.0000.0000.0000.000
185B297ASP-1-0.787-0.89973.551-0.029-0.0290.0000.0000.0000.000
186B298PRO0-0.075-0.03470.197-0.001-0.0010.0000.0000.0000.000
187B299ARG10.9190.95068.9080.0270.0270.0000.0000.0000.000
188B300LYS10.9190.96470.1380.0300.0300.0000.0000.0000.000
189B301THR0-0.029-0.00865.3510.0000.0000.0000.0000.0000.000
190B302TRP0-0.035-0.00964.7900.0000.0000.0000.0000.0000.000