Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 5NJ7Z

Calculation Name: 2ZYZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZYZ

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZVI1

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1949258.324498
FMO2-HF: Nuclear repulsion 1877535.746426
FMO2-HF: Total energy -71722.578072
FMO2-MP2: Total energy -71935.123478


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:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-11.855-6.90315.851-4.598-16.21-0.042
Interaction energy analysis for fragmet #1(B:1:MET)
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 : 0.001
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].
3B3GLY0-0.023-0.0143.879-2.249-1.036-0.012-0.568-0.6330.001
4B4TYR00.0080.0026.8580.5080.5080.0000.0000.0000.000
5B5LEU0-0.016-0.00610.468-0.094-0.0940.0000.0000.0000.000
6B6ARG10.8330.88012.2460.1380.1380.0000.0000.0000.000
7B7GLY00.0320.01716.216-0.032-0.0320.0000.0000.0000.000
8B8LEU0-0.049-0.03417.6520.0240.0240.0000.0000.0000.000
9B9ALA0-0.041-0.00914.643-0.011-0.0110.0000.0000.0000.000
10B10VAL00.0260.0148.2450.0360.0360.0000.0000.0000.000
11B11ILE0-0.021-0.00511.070-0.125-0.1250.0000.0000.0000.000
12B12VAL00.0090.0105.3510.0430.0430.0000.0000.0000.000
13B13GLU-1-0.788-0.8827.249-0.060-0.0600.0000.0000.0000.000
14B14ASP-1-0.797-0.8893.014-5.150-3.4700.098-0.881-0.897-0.009
15B15VAL00.035-0.0035.845-0.397-0.3970.0000.0000.0000.000
16B16GLU-1-0.812-0.8706.835-1.025-1.0250.0000.0000.0000.000
17B17PHE0-0.034-0.0232.759-3.458-1.6385.456-2.248-5.030-0.019
18B18ALA00.0140.0105.1680.1330.162-0.001-0.001-0.0280.000
19B19ARG10.8200.8937.7380.8280.8280.0000.0000.0000.000
20B20ARG10.8070.8854.9322.2582.2580.0000.0000.0000.000
21B21LEU00.0380.0185.0950.3460.3460.0000.0000.0000.000
22B22TYR0-0.068-0.0288.3160.2560.2560.0000.0000.0000.000
23B23LYS10.8400.89611.7560.7870.7870.0000.0000.0000.000
24B24GLU-1-0.848-0.9037.597-1.141-1.1410.0000.0000.0000.000
25B25GLY00.0750.03310.685-0.005-0.0050.0000.0000.0000.000
26B26PHE0-0.008-0.00613.2630.0660.0660.0000.0000.0000.000
27B27TYR0-0.0040.0059.9750.0750.0750.0000.0000.0000.000
28B28GLY00.0430.01411.773-0.101-0.1010.0000.0000.0000.000
29B29ARG10.8430.89612.9100.3350.3350.0000.0000.0000.000
30B30PHE00.0490.03311.4120.0050.0050.0000.0000.0000.000
31B31LEU0-0.0020.01115.1250.0710.0710.0000.0000.0000.000
32B32GLY0-0.007-0.01017.594-0.014-0.0140.0000.0000.0000.000
33B33TYR00.0160.00018.1170.0200.0200.0000.0000.0000.000
34B34ASP-1-0.806-0.90620.021-0.211-0.2110.0000.0000.0000.000
35B35LYS10.7970.87821.5570.1860.1860.0000.0000.0000.000
36B36VAL00.0140.04117.0350.0050.0050.0000.0000.0000.000
37B37LYS10.8890.93319.3580.2420.2420.0000.0000.0000.000
38B38ARG10.8730.91015.0250.4650.4650.0000.0000.0000.000
39B39ASP-1-0.862-0.92317.459-0.335-0.3350.0000.0000.0000.000
40B40GLU-1-0.783-0.87519.874-0.282-0.2820.0000.0000.0000.000
41B41VAL0-0.0170.00313.234-0.003-0.0030.0000.0000.0000.000
42B42GLU-1-0.804-0.89013.880-0.718-0.7180.0000.0000.0000.000
43B43LYS10.8830.93316.3720.3430.3430.0000.0000.0000.000
44B44ILE0-0.0110.02414.8980.0370.0370.0000.0000.0000.000
45B45ASN0-0.021-0.02114.139-0.092-0.0920.0000.0000.0000.000
46B46ALA00.0200.02113.8150.0590.0590.0000.0000.0000.000
47B47PRO00.0610.02811.229-0.100-0.1000.0000.0000.0000.000
48B48LEU0-0.071-0.0198.9610.0880.0880.0000.0000.0000.000
49B49ILE0-0.0190.00310.630-0.084-0.0840.0000.0000.0000.000
50B50LEU00.0050.0117.3980.0100.0100.0000.0000.0000.000
51B51GLY00.015-0.00412.0190.0710.0710.0000.0000.0000.000
52B52LEU00.0350.01813.142-0.027-0.0270.0000.0000.0000.000
53B53TYR00.0170.00313.4670.0300.0300.0000.0000.0000.000
54B54GLU-1-0.800-0.88611.630-0.372-0.3720.0000.0000.0000.000
55B55ALA00.011-0.0028.789-0.002-0.0020.0000.0000.0000.000
56B56LEU00.0290.0288.8400.1740.1740.0000.0000.0000.000
57B57TYR00.003-0.02910.7780.1030.1030.0000.0000.0000.000
58B58LEU0-0.032-0.0245.8550.0160.0160.0000.0000.0000.000
59B59ALA00.0200.0136.3970.6720.6720.0000.0000.0000.000
60B60GLU-1-0.858-0.9217.4280.4200.4200.0000.0000.0000.000
61B61LYS10.7990.9087.816-0.118-0.1180.0000.0000.0000.000
62B62GLY0-0.0080.0215.156-0.459-0.4590.0000.0000.0000.000
63B63ARG10.7670.8552.767-1.528-0.1911.571-0.511-2.397-0.006
64B64LEU0-0.024-0.0262.164-3.030-4.1036.132-1.214-3.845-0.010
65B65LYS10.8230.9002.738-1.664-1.7602.6060.858-3.3690.001
66B66VAL0-0.001-0.0014.685-1.060-1.0180.001-0.033-0.0110.000
67B67MET0-0.0030.0177.5620.4300.4300.0000.0000.0000.000
68B68GLY00.0440.01110.113-0.188-0.1880.0000.0000.0000.000
69B69GLU-1-0.912-0.97113.9330.0980.0980.0000.0000.0000.000
70B70ASP-1-0.836-0.88716.3520.3460.3460.0000.0000.0000.000
71B71GLY0-0.020-0.00613.6780.0150.0150.0000.0000.0000.000
72B72ARG10.8210.90113.154-0.259-0.2590.0000.0000.0000.000
73B73GLU-1-0.808-0.8977.9232.1422.1420.0000.0000.0000.000
74B74VAL0-0.054-0.04110.488-0.132-0.1320.0000.0000.0000.000
75B75ALA00.0310.02010.6160.0960.0960.0000.0000.0000.000
76B76PRO00.019-0.01810.092-0.127-0.1270.0000.0000.0000.000
77B77GLU-1-0.748-0.85312.6280.1280.1280.0000.0000.0000.000
78B78GLU-1-0.834-0.90914.7970.4520.4520.0000.0000.0000.000
79B79LEU0-0.045-0.02010.099-0.071-0.0710.0000.0000.0000.000
80B80ALA00.016-0.00114.806-0.059-0.0590.0000.0000.0000.000
81B81ALA0-0.015-0.00217.455-0.037-0.0370.0000.0000.0000.000
82B82LEU0-0.0030.00016.306-0.026-0.0260.0000.0000.0000.000
83B83GLY00.026-0.01518.592-0.027-0.0270.0000.0000.0000.000
84B84ARG10.6830.77019.905-0.164-0.1640.0000.0000.0000.000
85B85GLU-1-0.893-0.92222.5380.0900.0900.0000.0000.0000.000
86B86ARG10.8360.91021.289-0.069-0.0690.0000.0000.0000.000
87B87MET0-0.083-0.02118.774-0.017-0.0170.0000.0000.0000.000
88B88ARG10.9750.98024.2040.0000.0000.0000.0000.0000.000
89B89ASN0-0.029-0.03526.372-0.012-0.0120.0000.0000.0000.000
90B90PHE00.0270.04716.695-0.010-0.0100.0000.0000.0000.000
91B91ASP-1-0.757-0.86021.4130.0960.0960.0000.0000.0000.000
92B92GLU-1-0.842-0.92522.4180.0240.0240.0000.0000.0000.000
93B93ILE0-0.0100.00121.283-0.010-0.0100.0000.0000.0000.000
94B94TYR0-0.048-0.06214.201-0.042-0.0420.0000.0000.0000.000
95B95LYS10.8670.94419.088-0.042-0.0420.0000.0000.0000.000
96B96ILE00.0000.00021.300-0.011-0.0110.0000.0000.0000.000
97B97TYR0-0.015-0.01014.014-0.023-0.0230.0000.0000.0000.000
98B98LYS10.8700.92614.871-0.095-0.0950.0000.0000.0000.000
99B99TYR00.0180.01517.799-0.015-0.0150.0000.0000.0000.000
100B100PHE00.017-0.00720.649-0.011-0.0110.0000.0000.0000.000
101B101ARG10.8090.90713.8360.2920.2920.0000.0000.0000.000
102B102ASP-1-0.783-0.85415.262-0.043-0.0430.0000.0000.0000.000
103B103LEU0-0.051-0.01117.265-0.008-0.0080.0000.0000.0000.000
104B104GLY0-0.0020.00517.222-0.005-0.0050.0000.0000.0000.000
105B105TYR0-0.032-0.00518.299-0.024-0.0240.0000.0000.0000.000
106B106VAL0-0.009-0.00617.113-0.020-0.0200.0000.0000.0000.000
107B107VAL0-0.004-0.00117.5570.0290.0290.0000.0000.0000.000
108B108LYS10.7680.87414.7760.3690.3690.0000.0000.0000.000
109B109SER00.0650.02419.6480.0300.0300.0000.0000.0000.000
110B110GLY00.0610.04521.857-0.008-0.0080.0000.0000.0000.000
111B111LEU00.0530.03724.9560.0050.0050.0000.0000.0000.000
112B112LYS10.8470.91725.6900.1340.1340.0000.0000.0000.000
113B113PHE0-0.008-0.01225.448-0.003-0.0030.0000.0000.0000.000
114B114GLY00.0170.01930.0330.0050.0050.0000.0000.0000.000
115B115ALA0-0.037-0.02028.4770.0070.0070.0000.0000.0000.000
116B116LEU0-0.0120.00724.165-0.003-0.0030.0000.0000.0000.000
117B117PHE0-0.017-0.03020.165-0.010-0.0100.0000.0000.0000.000
118B118SER0-0.045-0.01423.0800.0010.0010.0000.0000.0000.000
119B119VAL00.0220.01022.327-0.016-0.0160.0000.0000.0000.000
120B120TYR0-0.017-0.02121.6720.0080.0080.0000.0000.0000.000
121B121GLU-1-0.843-0.91621.936-0.154-0.1540.0000.0000.0000.000
122B122LYS10.8230.90221.5880.1700.1700.0000.0000.0000.000
123B123GLY00.0550.01720.100-0.035-0.0350.0000.0000.0000.000
124B124PRO0-0.056-0.02720.0400.0200.0200.0000.0000.0000.000
125B125GLY00.0090.00922.5090.0240.0240.0000.0000.0000.000
126B126ILE0-0.047-0.01122.493-0.023-0.0230.0000.0000.0000.000
127B127ASP-1-0.839-0.93424.665-0.166-0.1660.0000.0000.0000.000
128B128HIS0-0.057-0.01126.766-0.010-0.0100.0000.0000.0000.000
129B129ALA00.051-0.00726.671-0.009-0.0090.0000.0000.0000.000
130B130PRO0-0.0640.00026.467-0.001-0.0010.0000.0000.0000.000
131B131MET00.0010.01127.0720.0120.0120.0000.0000.0000.000
132B132VAL0-0.013-0.01427.141-0.003-0.0030.0000.0000.0000.000
133B133VAL00.0040.00325.7710.0080.0080.0000.0000.0000.000
134B134VAL0-0.013-0.01527.735-0.001-0.0010.0000.0000.0000.000
135B135PHE00.0330.01127.5190.0010.0010.0000.0000.0000.000
136B136LEU0-0.007-0.00229.754-0.002-0.0020.0000.0000.0000.000
137B137GLU-1-0.860-0.92331.177-0.014-0.0140.0000.0000.0000.000
138B138PRO00.0270.00330.491-0.001-0.0010.0000.0000.0000.000
139B139ASP-1-0.812-0.85933.5420.0140.0140.0000.0000.0000.000
140B140LYS10.7950.92535.5600.0180.0180.0000.0000.0000.000
141B141GLY00.0560.03137.536-0.002-0.0020.0000.0000.0000.000
142B142ILE0-0.024-0.01737.581-0.002-0.0020.0000.0000.0000.000
143B143SER00.015-0.01140.5620.0010.0010.0000.0000.0000.000
144B144ALA00.0680.01342.182-0.002-0.0020.0000.0000.0000.000
145B145THR00.0270.00642.761-0.003-0.0030.0000.0000.0000.000
146B146ASP-1-0.787-0.87038.163-0.027-0.0270.0000.0000.0000.000
147B147ILE00.0180.02338.429-0.004-0.0040.0000.0000.0000.000
148B148THR0-0.036-0.02239.717-0.004-0.0040.0000.0000.0000.000
149B149ARG10.8860.94836.0210.0320.0320.0000.0000.0000.000
150B150GLY00.0530.01935.488-0.004-0.0040.0000.0000.0000.000
151B151GLY0-0.006-0.00635.938-0.005-0.0050.0000.0000.0000.000
152B152ARG10.8690.92838.4200.0540.0540.0000.0000.0000.000
153B153LEU0-0.0090.00232.672-0.002-0.0020.0000.0000.0000.000
154B154SER0-0.044-0.02133.672-0.008-0.0080.0000.0000.0000.000
155B155HIS0-0.022-0.02331.611-0.006-0.0060.0000.0000.0000.000
156B156SER00.0160.01634.686-0.003-0.0030.0000.0000.0000.000
157B157VAL00.0620.02436.8940.0040.0040.0000.0000.0000.000
158B158ARG10.9290.95837.9770.0790.0790.0000.0000.0000.000
159B159LYS10.8940.95838.4510.0540.0540.0000.0000.0000.000
160B160THR00.0340.02134.8760.0030.0030.0000.0000.0000.000
161B161TRP0-0.0130.02432.733-0.006-0.0060.0000.0000.0000.000
162B162THR00.0160.00529.2460.0020.0020.0000.0000.0000.000
163B163LEU0-0.0230.00231.086-0.002-0.0020.0000.0000.0000.000
164B164ALA00.0270.00527.173-0.001-0.0010.0000.0000.0000.000
165B165THR0-0.015-0.02829.2970.0040.0040.0000.0000.0000.000
166B166VAL00.006-0.00925.9460.0000.0000.0000.0000.0000.000
167B167LEU00.0180.02429.2880.0030.0030.0000.0000.0000.000
168B168ARG10.7930.84331.520-0.017-0.0170.0000.0000.0000.000
169B169GLN0-0.0170.00032.7000.0020.0020.0000.0000.0000.000
170B170THR00.0360.01131.9890.0040.0040.0000.0000.0000.000
171B171GLY0-0.0330.00028.1600.0030.0030.0000.0000.0000.000
172B172GLU-1-0.860-0.93527.040-0.007-0.0070.0000.0000.0000.000
173B173VAL0-0.028-0.01324.0630.0010.0010.0000.0000.0000.000
174B174VAL00.0020.01227.505-0.005-0.0050.0000.0000.0000.000
175B175LEU0-0.005-0.00526.476-0.002-0.0020.0000.0000.0000.000
176B176LEU00.0100.00430.6950.0020.0020.0000.0000.0000.000
177B177GLY00.0140.01933.608-0.004-0.0040.0000.0000.0000.000
178B178PHE00.0150.00434.6730.0050.0050.0000.0000.0000.000
179B179GLY00.048-0.00437.013-0.006-0.0060.0000.0000.0000.000
180B180TRP0-0.032-0.02139.7260.0030.0030.0000.0000.0000.000
181B181ALA00.0620.02543.211-0.001-0.0010.0000.0000.0000.000
182B182ARG10.8840.95745.8320.0510.0510.0000.0000.0000.000
183B183LEU00.0380.02648.6630.0000.0000.0000.0000.0000.000