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

tag_button

FMODB ID: P4J5N

Calculation Name: 2R8E-B-Xray19

Preferred Name:

Target Type:

Ligand Name: chloride ion

ligand 3-letter code: CL

PDB ID: 2R8E

Chain ID: B

ChEMBL ID:

UniProt ID: P67653

Base Structure: X-ray

Registration Date: 2018-06-04

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandCharge MG2=2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1794231.830004
FMO2-HF: Nuclear repulsion 1726650.000253
FMO2-HF: Total energy -67581.829751
FMO2-MP2: Total energy -67776.625097


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:7:ACE)


Summations of interaction energy for fragment #1(B:7:ACE)
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.
0.3670.0326.845-3.601-2.911-0.023
Interaction energy analysis for fragmet #1(B:7:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.024
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].
3B9ALA0-0.020-0.0013.8591.2732.008-0.011-0.336-0.3890.000
4B10THR00.037-0.0066.8910.1120.1120.0000.0000.0000.000
5B11CYS0-0.007-0.0139.6380.0890.0890.0000.0000.0000.000
6B12TYR0-0.052-0.03311.8220.0810.0810.0000.0000.0000.000
7B13GLY00.0110.0129.7240.0940.0940.0000.0000.0000.000
8B14PRO0-0.037-0.0124.473-0.171-0.156-0.001-0.006-0.0080.000
9B15VAL00.0370.0474.4480.3490.476-0.001-0.045-0.0810.000
10B16SER00.0480.0142.414-0.029-0.5853.938-2.121-1.261-0.017
11B17ALA00.0510.0112.437-1.128-1.7222.857-1.155-1.108-0.005
12B18ASP-1-0.888-0.9333.5040.2470.1850.0630.062-0.064-0.001
13B19VAL0-0.014-0.0085.834-0.165-0.1650.0000.0000.0000.000
14B20MET0-0.039-0.0125.2500.0300.0300.0000.0000.0000.000
15B21ALA00.0700.0316.9780.0930.0930.0000.0000.0000.000
16B22LYS10.8510.9359.1450.0020.0020.0000.0000.0000.000
17B23ALA0-0.002-0.00310.1580.0260.0260.0000.0000.0000.000
18B24GLU-1-0.941-0.9779.460-0.630-0.6300.0000.0000.0000.000
19B25ASN0-0.041-0.02312.8600.0490.0490.0000.0000.0000.000
20B26ILE0-0.0430.00514.7450.0360.0360.0000.0000.0000.000
21B27ARG10.8720.91317.3010.1580.1580.0000.0000.0000.000
22B28LEU0-0.0110.00520.6480.0070.0070.0000.0000.0000.000
23B29LEU0-0.0050.00018.4380.0000.0000.0000.0000.0000.000
24B30ILE0-0.030-0.02021.2350.0070.0070.0000.0000.0000.000
25B31LEU0-0.025-0.02821.2840.0000.0000.0000.0000.0000.000
26B32ASP-1-0.810-0.90724.047-0.010-0.0100.0000.0000.0000.000
27B33VAL0-0.065-0.04725.965-0.006-0.0060.0000.0000.0000.000
28B34ASP-1-0.842-0.91128.005-0.016-0.0160.0000.0000.0000.000
29B35GLY00.1130.06827.0750.0030.0030.0000.0000.0000.000
30B36VAL0-0.0320.00522.0610.0000.0000.0000.0000.0000.000
31B37LEU0-0.036-0.02724.209-0.008-0.0080.0000.0000.0000.000
32B38SER0-0.050-0.04226.299-0.003-0.0030.0000.0000.0000.000
33B39ASP-1-0.824-0.93227.328-0.017-0.0170.0000.0000.0000.000
34B40GLY00.0380.03129.1920.0050.0050.0000.0000.0000.000
35B41LEU0-0.065-0.01230.3730.0040.0040.0000.0000.0000.000
36B42ILE0-0.024-0.01434.012-0.003-0.0030.0000.0000.0000.000
37B43TYR0-0.092-0.01734.4170.0020.0020.0000.0000.0000.000
38B44MET00.008-0.00539.802-0.001-0.0010.0000.0000.0000.000
39B45GLY00.0180.01943.1930.0010.0010.0000.0000.0000.000
40B46ASN0-0.029-0.03346.6190.0010.0010.0000.0000.0000.000
41B47ASN0-0.071-0.02949.6230.0010.0010.0000.0000.0000.000
42B48GLY0-0.021-0.00247.920-0.001-0.0010.0000.0000.0000.000
43B49GLU-1-0.764-0.84544.984-0.012-0.0120.0000.0000.0000.000
44B50GLU-1-0.760-0.88738.717-0.012-0.0120.0000.0000.0000.000
45B51LEU0-0.065-0.03138.853-0.002-0.0020.0000.0000.0000.000
46B52LYS10.8440.89633.6180.0170.0170.0000.0000.0000.000
47B53ALA0-0.0030.01432.751-0.002-0.0020.0000.0000.0000.000
48B54PHE00.0510.02029.4000.0000.0000.0000.0000.0000.000
49B55ASN00.0050.00625.506-0.009-0.0090.0000.0000.0000.000
50B56VAL00.013-0.01227.534-0.006-0.0060.0000.0000.0000.000
51B57ARG10.9580.97122.6160.0890.0890.0000.0000.0000.000
52B58ASP-1-0.728-0.86622.731-0.095-0.0950.0000.0000.0000.000
53B59GLY0-0.026-0.01424.161-0.006-0.0060.0000.0000.0000.000
54B60TYR0-0.044-0.02523.4040.0030.0030.0000.0000.0000.000
55B61GLY00.0520.01521.681-0.009-0.0090.0000.0000.0000.000
56B62ILE00.0550.01922.215-0.009-0.0090.0000.0000.0000.000
57B63ARG10.8750.94724.1710.0790.0790.0000.0000.0000.000
58B64CYS0-0.025-0.01321.9740.0000.0000.0000.0000.0000.000
59B65ALA00.0200.02720.839-0.009-0.0090.0000.0000.0000.000
60B66LEU00.0150.00922.070-0.002-0.0020.0000.0000.0000.000
61B67THR0-0.109-0.04525.4640.0020.0020.0000.0000.0000.000
62B68SER0-0.026-0.02621.284-0.007-0.0070.0000.0000.0000.000
63B69ASP-1-0.930-0.96321.796-0.149-0.1490.0000.0000.0000.000
64B70ILE0-0.043-0.00218.214-0.005-0.0050.0000.0000.0000.000
65B71GLU-1-0.808-0.90722.391-0.074-0.0740.0000.0000.0000.000
66B72VAL0-0.022-0.01823.212-0.005-0.0050.0000.0000.0000.000
67B73ALA0-0.0010.00025.3120.0070.0070.0000.0000.0000.000
68B74ILE0-0.0070.00126.240-0.001-0.0010.0000.0000.0000.000
69B75ILE00.0140.01027.7210.0030.0030.0000.0000.0000.000
70B76THR0-0.0420.00730.1530.0030.0030.0000.0000.0000.000
71B77GLY00.0260.00032.9420.0010.0010.0000.0000.0000.000
72B78ARG10.7880.86435.5450.0120.0120.0000.0000.0000.000
73B79LYS10.9190.97437.6160.0180.0180.0000.0000.0000.000
74B80ALA00.0400.01237.7050.0020.0020.0000.0000.0000.000
75B81LYS10.9290.96838.5210.0260.0260.0000.0000.0000.000
76B82LEU00.0130.01635.529-0.003-0.0030.0000.0000.0000.000
77B83VAL00.0220.00332.930-0.003-0.0030.0000.0000.0000.000
78B84GLU-1-0.808-0.89734.649-0.029-0.0290.0000.0000.0000.000
79B85ASP-1-0.821-0.90636.614-0.034-0.0340.0000.0000.0000.000
80B86ARG10.8840.95329.0260.0540.0540.0000.0000.0000.000
81B87CYS00.0070.00331.924-0.005-0.0050.0000.0000.0000.000
82B88ALA00.0320.02332.996-0.004-0.0040.0000.0000.0000.000
83B89THR0-0.092-0.04633.181-0.003-0.0030.0000.0000.0000.000
84B90LEU0-0.086-0.05528.029-0.004-0.0040.0000.0000.0000.000
85B91GLY00.0200.03230.149-0.006-0.0060.0000.0000.0000.000
86B92ILE0-0.0140.00127.742-0.003-0.0030.0000.0000.0000.000
87B93THR00.004-0.01430.7880.0060.0060.0000.0000.0000.000
88B94HIS0-0.0150.02029.5520.0100.0100.0000.0000.0000.000
89B95LEU00.008-0.00530.596-0.001-0.0010.0000.0000.0000.000
90B96TYR0-0.052-0.03131.6010.0020.0020.0000.0000.0000.000
91B97GLN00.009-0.06133.7050.0010.0010.0000.0000.0000.000
92B98GLY0-0.040-0.02536.3810.0010.0010.0000.0000.0000.000
93B99GLN0-0.041-0.02433.9730.0020.0020.0000.0000.0000.000
94B100SER0-0.060-0.06333.1890.0010.0010.0000.0000.0000.000
95B101ASN00.1140.11333.1480.0000.0000.0000.0000.0000.000
96B102LYS10.9790.97428.0120.0070.0070.0000.0000.0000.000
97B103LEU00.0320.01427.728-0.003-0.0030.0000.0000.0000.000
98B104ILE0-0.0190.00130.424-0.002-0.0020.0000.0000.0000.000
99B105ALA00.0400.01931.450-0.002-0.0020.0000.0000.0000.000
100B106PHE00.0220.00823.927-0.002-0.0020.0000.0000.0000.000
101B107SER0-0.004-0.01728.910-0.003-0.0030.0000.0000.0000.000
102B108ASP-1-0.788-0.87330.726-0.027-0.0270.0000.0000.0000.000
103B109LEU0-0.043-0.01127.293-0.003-0.0030.0000.0000.0000.000
104B110LEU0-0.005-0.00624.782-0.005-0.0050.0000.0000.0000.000
105B111GLU-1-0.960-0.96428.659-0.021-0.0210.0000.0000.0000.000
106B112LYS10.7870.89232.0970.0300.0300.0000.0000.0000.000
107B113LEU0-0.035-0.03227.578-0.002-0.0020.0000.0000.0000.000
108B114ALA0-0.0210.00829.180-0.005-0.0050.0000.0000.0000.000
109B115ILE0-0.044-0.01223.393-0.006-0.0060.0000.0000.0000.000
110B116ALA00.0280.01722.7590.0080.0080.0000.0000.0000.000
111B117PRO00.032-0.00522.389-0.008-0.0080.0000.0000.0000.000
112B118GLU-1-0.857-0.94117.932-0.037-0.0370.0000.0000.0000.000
113B119ASN0-0.087-0.04117.461-0.001-0.0010.0000.0000.0000.000
114B120VAL00.0000.00419.425-0.013-0.0130.0000.0000.0000.000
115B121ALA00.0260.00816.5460.0040.0040.0000.0000.0000.000
116B122TYR0-0.059-0.06718.1550.0010.0010.0000.0000.0000.000
117B123VAL0-0.018-0.00717.9070.0050.0050.0000.0000.0000.000
118B124GLY00.0470.00520.042-0.002-0.0020.0000.0000.0000.000
119B125ASP-1-0.781-0.90421.3550.0080.0080.0000.0000.0000.000
120B126ASP-1-0.774-0.87423.8140.0330.0330.0000.0000.0000.000
121B127LEU0-0.046-0.04325.4000.0010.0010.0000.0000.0000.000
122B128ILE0-0.055-0.03227.0780.0010.0010.0000.0000.0000.000
123B129ASP-1-0.773-0.86623.956-0.002-0.0020.0000.0000.0000.000
124B130TRP00.0330.00318.873-0.004-0.0040.0000.0000.0000.000
125B131PRO0-0.015-0.00623.7780.0000.0000.0000.0000.0000.000
126B132VAL0-0.010-0.00723.5940.0000.0000.0000.0000.0000.000
127B133MET0-0.025-0.00218.837-0.003-0.0030.0000.0000.0000.000
128B134GLU-1-0.977-0.98219.8000.0570.0570.0000.0000.0000.000
129B135LYS10.8980.93920.959-0.013-0.0130.0000.0000.0000.000
130B136VAL0-0.081-0.01518.100-0.006-0.0060.0000.0000.0000.000
131B137GLY00.0320.03316.6860.0150.0150.0000.0000.0000.000
132B138LEU0-0.049-0.02811.2970.0060.0060.0000.0000.0000.000
133B139SER00.0020.01314.752-0.007-0.0070.0000.0000.0000.000
134B140VAL0-0.014-0.02214.0500.0100.0100.0000.0000.0000.000
135B141ALA00.0130.01616.089-0.003-0.0030.0000.0000.0000.000
136B142VAL00.003-0.00816.920-0.002-0.0020.0000.0000.0000.000
137B143ALA0-0.0030.00218.1100.0150.0150.0000.0000.0000.000
138B144ASP-1-0.833-0.89618.9810.0170.0170.0000.0000.0000.000
139B145ALA00.0190.02721.148-0.004-0.0040.0000.0000.0000.000
140B146HIS00.0600.03022.9680.0120.0120.0000.0000.0000.000
141B147PRO00.027-0.00523.1670.0070.0070.0000.0000.0000.000
142B148LEU0-0.063-0.03822.7460.0110.0110.0000.0000.0000.000
143B149LEU0-0.021-0.01220.6580.0070.0070.0000.0000.0000.000
144B150ILE0-0.0060.00417.3330.0100.0100.0000.0000.0000.000
145B151PRO0-0.041-0.02916.9480.0120.0120.0000.0000.0000.000
146B152ARG10.8670.94916.975-0.057-0.0570.0000.0000.0000.000
147B153ALA0-0.0250.01015.737-0.004-0.0040.0000.0000.0000.000
148B154ASP-1-0.820-0.90511.4130.1200.1200.0000.0000.0000.000
149B155TYR0-0.092-0.0769.2020.0220.0220.0000.0000.0000.000
150B156VAL00.0120.01211.783-0.020-0.0200.0000.0000.0000.000
151B157THR0-0.080-0.04412.9880.0010.0010.0000.0000.0000.000
152B158ARG10.8500.8988.4480.0560.0560.0000.0000.0000.000
153B159ILE0-0.102-0.03915.6040.0130.0130.0000.0000.0000.000
154B160ALA00.0580.03018.8580.0030.0030.0000.0000.0000.000
155B161GLY00.0690.03921.844-0.014-0.0140.0000.0000.0000.000
156B162GLY0-0.0070.00623.7230.0030.0030.0000.0000.0000.000
157B163ARG10.8090.88023.2930.0310.0310.0000.0000.0000.000
158B164GLY0-0.012-0.01121.600-0.004-0.0040.0000.0000.0000.000
159B165ALA00.0330.03418.504-0.018-0.0180.0000.0000.0000.000
160B166VAL00.0530.02718.072-0.016-0.0160.0000.0000.0000.000
161B167ARG10.8230.90719.1250.1520.1520.0000.0000.0000.000
162B168GLU-1-0.721-0.82113.646-0.127-0.1270.0000.0000.0000.000
163B169VAL00.0370.01214.572-0.049-0.0490.0000.0000.0000.000
164B170CYS0-0.054-0.02015.208-0.027-0.0270.0000.0000.0000.000
165B171ASP-1-0.806-0.89315.013-0.253-0.2530.0000.0000.0000.000
166B172LEU0-0.027-0.0088.547-0.071-0.0710.0000.0000.0000.000
167B173LEU00.0400.00711.916-0.085-0.0850.0000.0000.0000.000
168B174LEU00.0010.00114.202-0.024-0.0240.0000.0000.0000.000
169B175LEU0-0.045-0.0159.3360.0060.0060.0000.0000.0000.000
170B176ALA00.003-0.00410.465-0.060-0.0600.0000.0000.0000.000
171B177GLN0-0.0270.00611.3500.0350.0350.0000.0000.0000.000
172B178GLY0-0.029-0.00214.0930.0500.0500.0000.0000.0000.000
173B179LYS10.7950.87715.7000.2800.2800.0000.0000.0000.000
174B180LEU0-0.065-0.01414.3950.0340.0340.0000.0000.0000.000
175B181NME0-0.0030.00617.526-0.001-0.0010.0000.0000.0000.000
176B202MG221.5041.94646.159-0.017-0.0170.0000.0000.0000.000
177A202HOH0-0.049-0.03524.4060.0020.0020.0000.0000.0000.000
178A205HOH0-0.033-0.02949.2350.0000.0000.0000.0000.0000.000
179A215HOH0-0.0150.00032.1360.0000.0000.0000.0000.0000.000
180A226HOH0-0.061-0.04030.2220.0020.0020.0000.0000.0000.000
181A227HOH0-0.046-0.03128.467-0.001-0.0010.0000.0000.0000.000
182A238HOH0-0.079-0.05730.086-0.001-0.0010.0000.0000.0000.000
183A252HOH0-0.056-0.04425.6550.0010.0010.0000.0000.0000.000
184A260HOH0-0.009-0.00426.6990.0000.0000.0000.0000.0000.000
185A275HOH0-0.029-0.02053.5740.0000.0000.0000.0000.0000.000
186A289HOH00.0400.02135.379-0.001-0.0010.0000.0000.0000.000
187A305HOH0-0.056-0.04748.9430.0000.0000.0000.0000.0000.000
188A346HOH00.0200.02528.4270.0010.0010.0000.0000.0000.000
189A361HOH00.0190.01430.0070.0000.0000.0000.0000.0000.000
190A396HOH00.0160.01152.7370.0000.0000.0000.0000.0000.000
191A403HOH0-0.036-0.02346.776-0.001-0.0010.0000.0000.0000.000
192A434HOH00.0300.02538.497-0.001-0.0010.0000.0000.0000.000
193A449HOH0-0.020-0.02535.4330.0000.0000.0000.0000.0000.000
194A452HOH0-0.037-0.02423.9330.0020.0020.0000.0000.0000.000
195A455HOH00.0240.02753.2140.0000.0000.0000.0000.0000.000
196B215HOH0-0.017-0.01846.4850.0000.0000.0000.0000.0000.000
197B351HOH00.1640.01947.8410.0000.0000.0000.0000.0000.000
198B352HOH00.1690.02047.4440.0010.0010.0000.0000.0000.000
199B353HOH00.1630.01646.3000.0010.0010.0000.0000.0000.000
200B363HOH0-0.056-0.02628.5000.0000.0000.0000.0000.0000.000