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: 17JZZ

Calculation Name: 2A6T-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A6T

Chain ID: B

ChEMBL ID:

UniProt ID: O13828

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130195.470174
FMO2-HF: Nuclear repulsion 2051108.376141
FMO2-HF: Total energy -79087.094033
FMO2-MP2: Total energy -79313.893278


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:35:CYS)


Summations of interaction energy for fragment #1(B:35:CYS)
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.
-8.54-2.1179.37-5.207-10.588-0.03
Interaction energy analysis for fragmet #1(B:35:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.014
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].
3B37GLN00.0460.0073.553-2.242-0.5620.000-0.764-0.9150.002
4B38ILE0-0.0010.0122.047-0.666-0.2052.342-0.961-1.8430.001
5B39GLU-1-0.796-0.8874.402-1.842-1.497-0.001-0.060-0.2850.000
6B40GLN0-0.042-0.0126.5390.5670.5670.0000.0000.0000.000
7B41ALA00.0250.0088.0510.2290.2290.0000.0000.0000.000
8B42HIS0-0.038-0.0108.7400.0770.0770.0000.0000.0000.000
9B43TRP00.014-0.0059.2820.2500.2500.0000.0000.0000.000
10B44PHE00.0310.02612.2430.1200.1200.0000.0000.0000.000
11B45TYR00.009-0.00313.3460.0810.0810.0000.0000.0000.000
12B46GLU-1-0.763-0.86314.164-0.327-0.3270.0000.0000.0000.000
13B47ASP-1-0.876-0.94015.990-0.351-0.3510.0000.0000.0000.000
14B48PHE0-0.0230.00417.5900.0410.0410.0000.0000.0000.000
15B49ILE0-0.0100.00216.2550.0320.0320.0000.0000.0000.000
16B50ARG10.8010.87418.5690.2950.2950.0000.0000.0000.000
17B51ALA0-0.025-0.00720.9430.0240.0240.0000.0000.0000.000
18B52GLN0-0.083-0.04922.1080.0350.0350.0000.0000.0000.000
19B53ASN0-0.022-0.02523.0250.0190.0190.0000.0000.0000.000
20B54ASP-1-0.864-0.91323.323-0.189-0.1890.0000.0000.0000.000
21B55GLN0-0.0410.01124.4950.0020.0020.0000.0000.0000.000
22B56LEU0-0.024-0.00722.587-0.018-0.0180.0000.0000.0000.000
23B57PRO0-0.029-0.01919.067-0.011-0.0110.0000.0000.0000.000
24B58SER0-0.045-0.04117.6930.0110.0110.0000.0000.0000.000
25B59LEU0-0.030-0.04014.3630.0320.0320.0000.0000.0000.000
26B60GLY00.0530.02513.896-0.046-0.0460.0000.0000.0000.000
27B61LEU00.0490.0236.3850.0400.0400.0000.0000.0000.000
28B62ARG10.8510.9199.2090.0060.0060.0000.0000.0000.000
29B63VAL0-0.033-0.01310.6190.0510.0510.0000.0000.0000.000
30B64PHE00.0270.0088.9670.0490.0490.0000.0000.0000.000
31B65SER00.012-0.0227.0850.0750.0750.0000.0000.0000.000
32B66ALA00.0000.0109.0070.0520.0520.0000.0000.0000.000
33B67LYS10.8660.93912.0170.3320.3320.0000.0000.0000.000
34B68LEU0-0.0310.0088.1420.0340.0340.0000.0000.0000.000
35B83GLU-1-0.885-0.9547.9040.0930.0930.0000.0000.0000.000
36B84GLU-1-0.903-0.9527.9280.4340.4340.0000.0000.0000.000
37B85ALA0-0.005-0.0136.2070.0300.0300.0000.0000.0000.000
38B86PHE0-0.018-0.0152.650-1.150-0.1442.026-0.907-2.1250.000
39B87ASP-1-0.725-0.8424.705-0.225-0.257-0.0010.0300.0020.000
40B88ASP-1-0.823-0.9327.8200.1870.1870.0000.0000.0000.000
41B89PHE0-0.060-0.0222.603-6.285-3.3225.004-2.545-5.422-0.033
42B90LEU0-0.033-0.0045.546-0.756-0.7560.0000.0000.0000.000
43B91ARG10.8070.9067.371-0.221-0.2210.0000.0000.0000.000
44B92TYR00.0080.0068.579-0.131-0.1310.0000.0000.0000.000
45B93LYS10.8310.8995.0011.4811.4810.0000.0000.0000.000
46B94THR0-0.090-0.0538.415-0.029-0.0290.0000.0000.0000.000
47B95ARG10.8120.90311.0010.3810.3810.0000.0000.0000.000
48B96ILE00.0050.01413.8290.0370.0370.0000.0000.0000.000
49B97PRO0-0.0090.00116.546-0.008-0.0080.0000.0000.0000.000
50B98VAL0-0.003-0.00119.4380.0140.0140.0000.0000.0000.000
51B99ARG10.8040.90022.6120.1170.1170.0000.0000.0000.000
52B100GLY00.0860.03426.2320.0030.0030.0000.0000.0000.000
53B101ALA0-0.020-0.00129.8400.0000.0000.0000.0000.0000.000
54B102ILE0-0.051-0.03032.323-0.001-0.0010.0000.0000.0000.000
55B103MET00.0280.02735.5740.0030.0030.0000.0000.0000.000
56B104LEU0-0.041-0.03938.878-0.001-0.0010.0000.0000.0000.000
57B105ASP-1-0.686-0.82341.796-0.039-0.0390.0000.0000.0000.000
58B106MET0-0.044-0.01445.6250.0000.0000.0000.0000.0000.000
59B107SER00.039-0.00147.812-0.001-0.0010.0000.0000.0000.000
60B108MET0-0.088-0.04543.248-0.002-0.0020.0000.0000.0000.000
61B109GLN00.0200.00843.859-0.002-0.0020.0000.0000.0000.000
62B110GLN0-0.040-0.02543.951-0.002-0.0020.0000.0000.0000.000
63B111CYS0-0.049-0.01538.827-0.002-0.0020.0000.0000.0000.000
64B112VAL00.0690.04638.9140.0010.0010.0000.0000.0000.000
65B113LEU0-0.098-0.04735.393-0.005-0.0050.0000.0000.0000.000
66B114VAL00.0630.02134.1340.0050.0050.0000.0000.0000.000
67B115LYS10.9570.98734.2250.0480.0480.0000.0000.0000.000
68B123TRP0-0.066-0.03934.451-0.001-0.0010.0000.0000.0000.000
69B124GLY0-0.002-0.01731.612-0.007-0.0070.0000.0000.0000.000
70B125PHE00.0400.01131.5360.0060.0060.0000.0000.0000.000
71B126PRO00.0230.03131.335-0.006-0.0060.0000.0000.0000.000
72B127LYS10.8130.88226.8640.1000.1000.0000.0000.0000.000
73B128GLY00.0520.03825.5580.0000.0000.0000.0000.0000.000
74B129LYS10.8970.94617.7030.1680.1680.0000.0000.0000.000
75B130ILE0-0.011-0.01920.5040.0050.0050.0000.0000.0000.000
76B131ASP-1-0.846-0.91421.108-0.051-0.0510.0000.0000.0000.000
77B132LYS10.7450.82820.062-0.015-0.0150.0000.0000.0000.000
78B133ASP-1-0.852-0.90722.0620.0060.0060.0000.0000.0000.000
79B134GLU-1-0.730-0.83424.221-0.062-0.0620.0000.0000.0000.000
80B135SER0-0.004-0.02724.766-0.006-0.0060.0000.0000.0000.000
81B136ASP-1-0.853-0.93224.684-0.102-0.1020.0000.0000.0000.000
82B137VAL0-0.003-0.01426.734-0.003-0.0030.0000.0000.0000.000
83B138ASP-1-0.794-0.87929.110-0.042-0.0420.0000.0000.0000.000
84B139CYS0-0.0290.02725.837-0.002-0.0020.0000.0000.0000.000
85B140ALA0-0.043-0.02428.1770.0000.0000.0000.0000.0000.000
86B141ILE0-0.020-0.02130.3960.0010.0010.0000.0000.0000.000
87B142ARG10.7610.85126.6980.0620.0620.0000.0000.0000.000
88B143GLU-1-0.800-0.89126.651-0.078-0.0780.0000.0000.0000.000
89B144VAL0-0.015-0.01430.7990.0020.0020.0000.0000.0000.000
90B145TYR0-0.0300.00934.0880.0030.0030.0000.0000.0000.000
91B146GLU-1-0.845-0.90630.575-0.046-0.0460.0000.0000.0000.000
92B147GLU-1-0.877-0.93631.557-0.075-0.0750.0000.0000.0000.000
93B148THR0-0.120-0.11234.7220.0020.0020.0000.0000.0000.000
94B149GLY00.0120.01438.0990.0020.0020.0000.0000.0000.000
95B150PHE0-0.045-0.03439.1260.0030.0030.0000.0000.0000.000
96B151ASP-1-0.772-0.86438.631-0.038-0.0380.0000.0000.0000.000
97B152CYS0-0.048-0.01936.470-0.001-0.0010.0000.0000.0000.000
98B153SER00.046-0.01837.529-0.002-0.0020.0000.0000.0000.000
99B154SER0-0.052-0.02038.4910.0000.0000.0000.0000.0000.000
100B155ARG10.8200.91140.3220.0400.0400.0000.0000.0000.000
101B156ILE0-0.0120.01533.091-0.002-0.0020.0000.0000.0000.000
102B157ASN00.0460.01736.3760.0010.0010.0000.0000.0000.000
103B158PRO00.0390.01332.498-0.004-0.0040.0000.0000.0000.000
104B159ASN0-0.026-0.02431.947-0.006-0.0060.0000.0000.0000.000
105B160GLU-1-0.790-0.87134.210-0.062-0.0620.0000.0000.0000.000
106B161PHE00.000-0.00227.7590.0000.0000.0000.0000.0000.000
107B162ILE0-0.059-0.01929.1910.0000.0000.0000.0000.0000.000
108B163ASP-1-0.815-0.88723.666-0.154-0.1540.0000.0000.0000.000
109B164MET0-0.0150.00223.9030.0020.0020.0000.0000.0000.000
110B165THR0-0.0050.00717.259-0.004-0.0040.0000.0000.0000.000
111B166ILE0-0.014-0.00920.0830.0040.0040.0000.0000.0000.000
112B167ARG10.8970.93516.8130.2880.2880.0000.0000.0000.000
113B168GLY00.0940.05314.277-0.032-0.0320.0000.0000.0000.000
114B169GLN0-0.018-0.00914.717-0.024-0.0240.0000.0000.0000.000
115B170ASN0-0.007-0.00617.4520.0310.0310.0000.0000.0000.000
116B171VAL00.001-0.00319.9790.0080.0080.0000.0000.0000.000
117B172ARG10.8050.88723.5510.1200.1200.0000.0000.0000.000
118B173LEU0-0.027-0.01126.2890.0060.0060.0000.0000.0000.000
119B174TYR00.0590.02629.0550.0000.0000.0000.0000.0000.000
120B175ILE0-0.062-0.02232.8380.0010.0010.0000.0000.0000.000
121B176ILE00.0030.00435.8440.0030.0030.0000.0000.0000.000
122B177PRO0-0.012-0.00739.1230.0010.0010.0000.0000.0000.000
123B178GLY00.0320.00042.5360.0010.0010.0000.0000.0000.000
124B179ILE0-0.072-0.01441.5600.0020.0020.0000.0000.0000.000
125B180SER00.028-0.00645.0530.0000.0000.0000.0000.0000.000
126B181LEU00.0160.00847.111-0.001-0.0010.0000.0000.0000.000
127B182ASP-1-0.841-0.90248.120-0.031-0.0310.0000.0000.0000.000
128B183THR0-0.091-0.05443.7190.0010.0010.0000.0000.0000.000
129B184ARG10.8880.92545.3660.0270.0270.0000.0000.0000.000
130B185PHE00.0970.06040.8230.0000.0000.0000.0000.0000.000
131B186GLU-1-0.795-0.88742.804-0.029-0.0290.0000.0000.0000.000
132B187SER00.0130.03241.3470.0000.0000.0000.0000.0000.000
133B188ARG10.8490.89643.4780.0280.0280.0000.0000.0000.000
134B189THR0-0.057-0.02241.643-0.001-0.0010.0000.0000.0000.000
135B190ARG10.8890.95037.9040.0440.0440.0000.0000.0000.000
136B191LYS10.9260.96235.6250.0290.0290.0000.0000.0000.000
137B192GLU-1-0.833-0.91533.197-0.044-0.0440.0000.0000.0000.000
138B193ILE00.0410.01232.618-0.005-0.0050.0000.0000.0000.000
139B194SER0-0.0360.00435.9850.0040.0040.0000.0000.0000.000
140B195LYS10.8640.90538.1660.0420.0420.0000.0000.0000.000
141B196ILE00.0480.03738.178-0.004-0.0040.0000.0000.0000.000
142B197GLU-1-0.917-0.96940.122-0.045-0.0450.0000.0000.0000.000
143B198TRP00.0030.01841.222-0.005-0.0050.0000.0000.0000.000
144B199HIS10.8540.92440.3240.0540.0540.0000.0000.0000.000
145B200ASN00.0630.02742.894-0.001-0.0010.0000.0000.0000.000
146B201LEU00.0370.00439.438-0.003-0.0030.0000.0000.0000.000
147B202MET0-0.048-0.03541.834-0.003-0.0030.0000.0000.0000.000
148B203ASP-1-0.796-0.89244.232-0.048-0.0480.0000.0000.0000.000
149B204LEU0-0.0210.00437.933-0.002-0.0020.0000.0000.0000.000
150B205PRO00.002-0.01537.2090.0000.0000.0000.0000.0000.000
151B206THR0-0.021-0.02535.2550.0000.0000.0000.0000.0000.000
152B207PHE00.0300.06038.658-0.001-0.0010.0000.0000.0000.000
153B208LYS10.9620.95940.1580.0550.0550.0000.0000.0000.000
154B209LYS10.7980.92642.5130.0520.0520.0000.0000.0000.000
155B210ASN00.0720.02143.893-0.002-0.0020.0000.0000.0000.000
156B211LYS10.9580.99037.6630.0780.0780.0000.0000.0000.000
157B212PRO00.0760.04639.829-0.005-0.0050.0000.0000.0000.000
158B213GLN00.0990.05433.950-0.001-0.0010.0000.0000.0000.000
159B214THR00.0220.01636.9730.0050.0050.0000.0000.0000.000
160B215MET00.0370.01237.821-0.001-0.0010.0000.0000.0000.000
161B216LYS10.8540.92135.6170.0810.0810.0000.0000.0000.000
162B217ASN00.038-0.00533.232-0.002-0.0020.0000.0000.0000.000
163B218LYS10.9290.97333.2710.0570.0570.0000.0000.0000.000
164B219PHE00.0400.02334.4670.0010.0010.0000.0000.0000.000
165B220TYR00.011-0.00126.146-0.004-0.0040.0000.0000.0000.000
166B221MET00.0220.01927.690-0.008-0.0080.0000.0000.0000.000
167B222VAL0-0.0190.00229.595-0.001-0.0010.0000.0000.0000.000
168B223ILE0-0.032-0.03232.1760.0010.0010.0000.0000.0000.000
169B224PRO00.0290.01627.8390.0050.0050.0000.0000.0000.000
170B225PHE00.0940.04526.5870.0030.0030.0000.0000.0000.000
171B226LEU0-0.038-0.00831.5850.0060.0060.0000.0000.0000.000
172B227ALA0-0.0030.00433.7860.0050.0050.0000.0000.0000.000
173B228PRO00.0400.00830.7680.0060.0060.0000.0000.0000.000
174B229LEU00.0600.02933.8880.0050.0050.0000.0000.0000.000
175B230LYS10.8620.93136.2280.0700.0700.0000.0000.0000.000
176B231LYS10.9380.97235.3650.0810.0810.0000.0000.0000.000
177B232TRP00.005-0.01535.7350.0040.0040.0000.0000.0000.000
178B233ILE00.0440.02138.3390.0030.0030.0000.0000.0000.000
179B234LYS10.9340.96641.6340.0540.0540.0000.0000.0000.000
180B235LYS10.8700.95437.6640.0630.0630.0000.0000.0000.000
181B236ARG10.8610.93140.5830.0510.0510.0000.0000.0000.000
182B237ASN00.006-0.01643.4490.0040.0040.0000.0000.0000.000
183B238ILE00.0090.01644.9780.0020.0020.0000.0000.0000.000
184B239ALA0-0.0040.00844.6170.0020.0020.0000.0000.0000.000
185B240ASN0-0.038-0.02846.7030.0010.0010.0000.0000.0000.000
186B241ASN0-0.071-0.03449.0060.0030.0030.0000.0000.0000.000
187B242THR0-0.024-0.01749.3740.0000.0000.0000.0000.0000.000
188B243THR00.0110.01851.9740.0010.0010.0000.0000.0000.000