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: XRY68

Calculation Name: 3RWV-B-Xray34

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RWV

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NZD2

Base Structure: X-ray

Registration Date: 2018-09-07

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 214
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2517634.919827
FMO2-HF: Nuclear repulsion 2433558.636424
FMO2-HF: Total energy -84076.283403
FMO2-MP2: Total energy -84320.826829


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:ACE)


Summations of interaction energy for fragment #1(B:1: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.
1.0622.071-0.007-0.389-0.6120
Interaction energy analysis for fragmet #1(B:1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.008
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].
3B3LEU00.0050.0143.8491.1371.799-0.011-0.292-0.3590.000
4B4LEU00.0310.0126.861-0.016-0.0160.0000.0000.0000.000
5B5ALA0-0.029-0.0218.8170.0270.0270.0000.0000.0000.000
6B6GLU-1-0.876-0.9447.229-1.962-1.9620.0000.0000.0000.000
7B7HIS0-0.042-0.0207.1490.1500.1500.0000.0000.0000.000
8B8LEU00.0020.01611.1260.0810.0810.0000.0000.0000.000
9B9LEU00.0200.01614.2670.0110.0110.0000.0000.0000.000
10B10LYS10.9580.98316.7090.1120.1120.0000.0000.0000.000
11B11PRO00.0340.02220.1330.0080.0080.0000.0000.0000.000
12B12LEU0-0.027-0.01922.9960.0030.0030.0000.0000.0000.000
13B13PRO00.0330.03125.651-0.002-0.0020.0000.0000.0000.000
14B14ALA00.014-0.00528.8120.0040.0040.0000.0000.0000.000
15B15ASP-1-0.874-0.94431.163-0.040-0.0400.0000.0000.0000.000
16B16LYS10.8890.94128.8070.0400.0400.0000.0000.0000.000
17B17GLN0-0.0020.01728.6120.0050.0050.0000.0000.0000.000
18B18ILE0-0.002-0.00322.353-0.008-0.0080.0000.0000.0000.000
19B19GLU-1-0.946-0.98023.538-0.072-0.0720.0000.0000.0000.000
20B20THR00.024-0.01122.238-0.006-0.0060.0000.0000.0000.000
21B21GLY00.0080.01720.6660.0000.0000.0000.0000.0000.000
22B22PRO00.013-0.01618.555-0.008-0.0080.0000.0000.0000.000
23B23PHE00.0190.02617.209-0.017-0.0170.0000.0000.0000.000
24B24LEU00.002-0.01116.3670.0000.0000.0000.0000.0000.000
25B25GLU-1-0.878-0.91412.953-0.272-0.2720.0000.0000.0000.000
26B26ALA00.0520.02612.681-0.028-0.0280.0000.0000.0000.000
27B27VAL0-0.009-0.02511.566-0.020-0.0200.0000.0000.0000.000
28B28SER0-0.069-0.02311.3720.0530.0530.0000.0000.0000.000
29B29HIS10.8440.9057.1790.5400.5400.0000.0000.0000.000
30B30LEU00.0070.0106.5660.0350.0350.0000.0000.0000.000
31B31PRO0-0.0260.0038.4960.1380.1380.0000.0000.0000.000
32B32PRO00.034-0.0023.558-0.0940.0410.005-0.039-0.1000.000
33B33PHE00.0380.0215.6650.3290.3290.0000.0000.0000.000
34B34PHE0-0.013-0.0327.806-0.020-0.0200.0000.0000.0000.000
35B35ASP-1-0.811-0.8825.8631.4571.4570.0000.0000.0000.000
36B36CYS0-0.068-0.0235.452-0.086-0.0860.0000.0000.0000.000
37B37LEU0-0.041-0.0247.567-0.200-0.2000.0000.0000.0000.000
38B38GLY00.0120.01310.178-0.091-0.0910.0000.0000.0000.000
39B39SER00.0410.02211.677-0.073-0.0730.0000.0000.0000.000
40B40PRO00.0380.00514.3980.0300.0300.0000.0000.0000.000
41B41VAL0-0.026-0.01216.089-0.012-0.0120.0000.0000.0000.000
42B42PHE00.0180.00813.612-0.033-0.0330.0000.0000.0000.000
43B43THR0-0.005-0.00513.5340.0360.0360.0000.0000.0000.000
44B44PRO0-0.015-0.00514.563-0.010-0.0100.0000.0000.0000.000
45B45ILE00.0400.02914.733-0.018-0.0180.0000.0000.0000.000
46B46LYS10.8630.9377.951-0.998-0.9980.0000.0000.0000.000
47B47ALA0-0.004-0.01513.133-0.024-0.0240.0000.0000.0000.000
48B48ASP-1-0.928-0.95415.3780.1090.1090.0000.0000.0000.000
49B49ILE00.0110.00113.753-0.029-0.0290.0000.0000.0000.000
50B50SER00.006-0.00512.217-0.025-0.0250.0000.0000.0000.000
51B51GLY0-0.0050.00314.385-0.032-0.0320.0000.0000.0000.000
52B52ASN0-0.001-0.02418.033-0.032-0.0320.0000.0000.0000.000
53B53ILE00.0320.02113.507-0.018-0.0180.0000.0000.0000.000
54B54THR0-0.030-0.01116.555-0.020-0.0200.0000.0000.0000.000
55B55LYS10.8930.94918.642-0.099-0.0990.0000.0000.0000.000
56B56ILE00.0170.01720.023-0.008-0.0080.0000.0000.0000.000
57B57LYS10.8410.90917.5760.0120.0120.0000.0000.0000.000
58B58ALA0-0.0080.00321.107-0.007-0.0070.0000.0000.0000.000
59B59VAL00.0230.02423.716-0.004-0.0040.0000.0000.0000.000
60B60TYR00.0030.00822.518-0.007-0.0070.0000.0000.0000.000
61B61ASP-1-0.760-0.89522.150-0.022-0.0220.0000.0000.0000.000
62B62THR0-0.104-0.05025.313-0.002-0.0020.0000.0000.0000.000
63B63ASN0-0.030-0.03028.462-0.004-0.0040.0000.0000.0000.000
64B64PRO00.0660.03426.2310.0000.0000.0000.0000.0000.000
65B65ALA0-0.011-0.00127.900-0.003-0.0030.0000.0000.0000.000
66B66LYS10.9220.97231.0550.0060.0060.0000.0000.0000.000
67B67PHE00.0190.00727.4240.0020.0020.0000.0000.0000.000
68B68ARG11.0031.01826.9540.0400.0400.0000.0000.0000.000
69B69THR0-0.016-0.00126.404-0.006-0.0060.0000.0000.0000.000
70B70LEU00.024-0.01022.3190.0060.0060.0000.0000.0000.000
71B71GLN00.036-0.01926.5080.0060.0060.0000.0000.0000.000
72B72ASN0-0.059-0.02229.913-0.001-0.0010.0000.0000.0000.000
73B73ILE0-0.018-0.00325.0760.0030.0030.0000.0000.0000.000
74B74LEU0-0.017-0.00728.2700.0030.0030.0000.0000.0000.000
75B75GLU-1-0.852-0.92031.494-0.011-0.0110.0000.0000.0000.000
76B76VAL0-0.008-0.01032.7090.0010.0010.0000.0000.0000.000
77B77GLU-1-0.741-0.86229.5340.0200.0200.0000.0000.0000.000
78B78LYS10.9290.97733.739-0.004-0.0040.0000.0000.0000.000
79B79GLU-1-0.966-0.98436.4670.0030.0030.0000.0000.0000.000
80B80MET0-0.108-0.04233.1010.0000.0000.0000.0000.0000.000
81B81TYR00.008-0.00631.9120.0010.0010.0000.0000.0000.000
82B82GLY00.0270.02937.7530.0010.0010.0000.0000.0000.000
83B83ALA0-0.037-0.04339.1950.0010.0010.0000.0000.0000.000
84B84GLU-1-0.943-0.95535.2080.0290.0290.0000.0000.0000.000
85B85TRP0-0.0260.00232.1970.0030.0030.0000.0000.0000.000
86B86PRO00.026-0.00132.329-0.001-0.0010.0000.0000.0000.000
87B87LYS10.8610.93231.572-0.040-0.0400.0000.0000.0000.000
88B88VAL00.0580.03031.3350.0020.0020.0000.0000.0000.000
89B89GLY00.0210.01828.767-0.001-0.0010.0000.0000.0000.000
90B90ALA0-0.002-0.01925.3400.0060.0060.0000.0000.0000.000
91B91THR00.0180.00325.5410.0000.0000.0000.0000.0000.000
92B92LEU0-0.0010.02127.1380.0030.0030.0000.0000.0000.000
93B93ALA0-0.030-0.01622.3340.0060.0060.0000.0000.0000.000
94B94LEU00.0270.00821.7460.0090.0090.0000.0000.0000.000
95B95MET0-0.0180.01723.2540.0000.0000.0000.0000.0000.000
96B96TRP00.005-0.02022.5640.0040.0040.0000.0000.0000.000
97B97LEU0-0.0100.00016.2340.0100.0100.0000.0000.0000.000
98B98LYS10.8080.90519.060-0.029-0.0290.0000.0000.0000.000
99B99ARG10.8140.91820.816-0.055-0.0550.0000.0000.0000.000
100B100GLY00.0380.01917.7580.0070.0070.0000.0000.0000.000
101B101LEU00.008-0.00514.9290.0140.0140.0000.0000.0000.000
102B102ARG10.8790.93517.022-0.022-0.0220.0000.0000.0000.000
103B103PHE0-0.012-0.00515.625-0.001-0.0010.0000.0000.0000.000
104B104ILE0-0.0030.00311.7230.0000.0000.0000.0000.0000.000
105B105GLN00.0400.01815.238-0.005-0.0050.0000.0000.0000.000
106B106VAL00.0040.00217.399-0.010-0.0100.0000.0000.0000.000
107B107PHE0-0.008-0.00115.5710.0000.0000.0000.0000.0000.000
108B108LEU00.004-0.00711.469-0.004-0.0040.0000.0000.0000.000
109B109GLN0-0.004-0.00515.651-0.020-0.0200.0000.0000.0000.000
110B110SER0-0.035-0.01119.090-0.002-0.0020.0000.0000.0000.000
111B111ILE0-0.025-0.01515.1210.0000.0000.0000.0000.0000.000
112B112CYS0-0.063-0.02616.465-0.017-0.0170.0000.0000.0000.000
113B113ASP-1-0.854-0.91818.942-0.021-0.0210.0000.0000.0000.000
114B114GLY0-0.034-0.00521.4010.0000.0000.0000.0000.0000.000
115B115GLU-1-0.875-0.92322.7180.0370.0370.0000.0000.0000.000
116B116ARG10.9140.94322.305-0.019-0.0190.0000.0000.0000.000
117B117ASP-1-0.812-0.90224.2270.0550.0550.0000.0000.0000.000
118B118GLU-1-0.917-0.97626.0550.0280.0280.0000.0000.0000.000
119B119ASN0-0.048-0.02028.293-0.003-0.0030.0000.0000.0000.000
120B120HIS0-0.093-0.04924.2180.0070.0070.0000.0000.0000.000
121B121PRO00.0140.01923.4140.0070.0070.0000.0000.0000.000
122B122ASN00.0310.01018.503-0.001-0.0010.0000.0000.0000.000
123B123LEU0-0.0180.00319.2480.0210.0210.0000.0000.0000.000
124B124ILE00.0820.03914.484-0.012-0.0120.0000.0000.0000.000
125B125ARG10.9340.96818.794-0.126-0.1260.0000.0000.0000.000
126B126VAL00.0450.02221.2350.0000.0000.0000.0000.0000.000
127B127ASN0-0.001-0.00718.6950.0060.0060.0000.0000.0000.000
128B128ALA00.0220.02118.116-0.003-0.0030.0000.0000.0000.000
129B129THR0-0.007-0.01019.453-0.001-0.0010.0000.0000.0000.000
130B130LYS10.9030.95222.913-0.041-0.0410.0000.0000.0000.000
131B131ALA00.0060.00119.399-0.008-0.0080.0000.0000.0000.000
132B132TYR0-0.045-0.06121.351-0.005-0.0050.0000.0000.0000.000
133B133GLU-1-0.976-1.00022.7600.0600.0600.0000.0000.0000.000
134B134MET0-0.049-0.02324.173-0.006-0.0060.0000.0000.0000.000
135B135ALA0-0.0400.00321.732-0.006-0.0060.0000.0000.0000.000
136B136LEU00.005-0.01619.889-0.002-0.0020.0000.0000.0000.000
137B137LYS10.9931.02024.340-0.075-0.0750.0000.0000.0000.000
138B138LYS10.9090.96027.023-0.040-0.0400.0000.0000.0000.000
139B139TYR00.005-0.00126.558-0.005-0.0050.0000.0000.0000.000
140B140HIS00.0690.07723.3170.0010.0010.0000.0000.0000.000
141B141GLY00.0190.00328.950-0.006-0.0060.0000.0000.0000.000
142B142TRP00.0330.00530.8630.0070.0070.0000.0000.0000.000
143B143ILE00.015-0.00831.0290.0030.0030.0000.0000.0000.000
144B144VAL00.0820.04125.9440.0060.0060.0000.0000.0000.000
145B145GLN0-0.048-0.02527.0350.0060.0060.0000.0000.0000.000
146B146LYS10.8880.95527.711-0.066-0.0660.0000.0000.0000.000
147B147ILE00.0040.00625.5890.0030.0030.0000.0000.0000.000
148B148PHE00.0250.01319.4870.0140.0140.0000.0000.0000.000
149B149GLN00.011-0.01122.8390.0070.0070.0000.0000.0000.000
150B150ALA0-0.028-0.01524.1150.0040.0040.0000.0000.0000.000
151B151ALA00.0130.00620.3760.0060.0060.0000.0000.0000.000
152B152LEU0-0.0010.00318.9400.0220.0220.0000.0000.0000.000
153B153TYR0-0.063-0.03419.9750.0030.0030.0000.0000.0000.000
154B154ALA0-0.030-0.01518.941-0.008-0.0080.0000.0000.0000.000
155B155ALA0-0.033-0.01116.1920.0300.0300.0000.0000.0000.000
156B156PRO0-0.0200.02212.403-0.025-0.0250.0000.0000.0000.000
157B157TYR0-0.003-0.01315.438-0.038-0.0380.0000.0000.0000.000
158B158LYS10.9050.95114.600-0.016-0.0160.0000.0000.0000.000
159B159SER00.0390.00614.0020.0040.0040.0000.0000.0000.000
160B160ASP-1-0.910-0.95412.2990.2200.2200.0000.0000.0000.000
161B161PHE0-0.033-0.01710.2330.0470.0470.0000.0000.0000.000
162B162LEU00.031-0.0029.1630.0380.0380.0000.0000.0000.000
163B163LYS10.9581.0009.455-0.177-0.1770.0000.0000.0000.000
164B164ALA0-0.027-0.0175.967-0.087-0.0870.0000.0000.0000.000
165B165LEU00.007-0.0044.557-0.0180.038-0.001-0.005-0.0490.000
166B166SER0-0.041-0.0146.465-0.362-0.3620.0000.0000.0000.000
167B167LYS10.8790.9573.8701.3391.4600.001-0.051-0.0720.000
168B168GLY0-0.004-0.0044.9090.0900.125-0.001-0.002-0.0320.000
169B169GLN0-0.071-0.0297.5780.0940.0940.0000.0000.0000.000
170B170ASN0-0.045-0.03710.3190.0750.0750.0000.0000.0000.000
171B171VAL00.0310.02812.195-0.028-0.0280.0000.0000.0000.000
172B172THR0-0.016-0.00714.6770.0380.0380.0000.0000.0000.000
173B173GLU-1-0.841-0.93415.7460.0020.0020.0000.0000.0000.000
174B174GLU-1-0.760-0.88416.254-0.071-0.0710.0000.0000.0000.000
175B175GLU-1-0.849-0.91315.644-0.161-0.1610.0000.0000.0000.000
176B176CYS0-0.068-0.01510.635-0.020-0.0200.0000.0000.0000.000
177B177LEU00.006-0.02113.393-0.024-0.0240.0000.0000.0000.000
178B178GLU-1-0.940-0.95315.662-0.174-0.1740.0000.0000.0000.000
179B179LYS10.9410.96012.5010.3150.3150.0000.0000.0000.000
180B180ILE0-0.012-0.00611.445-0.018-0.0180.0000.0000.0000.000
181B181ARG10.8440.88113.7450.0770.0770.0000.0000.0000.000
182B182LEU0-0.033-0.00415.6440.0060.0060.0000.0000.0000.000
183B183PHE0-0.021-0.01912.3760.0110.0110.0000.0000.0000.000
184B184LEU0-0.001-0.01215.0160.0210.0210.0000.0000.0000.000
185B185VAL00.0200.04317.3840.0200.0200.0000.0000.0000.000
186B186ASN0-0.008-0.03018.5610.0270.0270.0000.0000.0000.000
187B187TYR0-0.0210.00614.9480.0170.0170.0000.0000.0000.000
188B188THR00.018-0.01817.8800.0220.0220.0000.0000.0000.000
189B189ALA00.0180.02320.7550.0090.0090.0000.0000.0000.000
190B190THR0-0.017-0.02819.9700.0050.0050.0000.0000.0000.000
191B191ILE0-0.036-0.01817.7120.0100.0100.0000.0000.0000.000
192B192ASP-1-0.849-0.91621.921-0.003-0.0030.0000.0000.0000.000
193B193VAL0-0.028-0.00925.2190.0040.0040.0000.0000.0000.000
194B194ILE0-0.0060.00521.5660.0040.0040.0000.0000.0000.000
195B195TYR0-0.035-0.04022.8880.0080.0080.0000.0000.0000.000
196B196GLU-1-0.871-0.92627.321-0.002-0.0020.0000.0000.0000.000
197B197MET0-0.0030.01826.9960.0000.0000.0000.0000.0000.000
198B198TYR0-0.038-0.06926.3260.0010.0010.0000.0000.0000.000
199B199THR0-0.034-0.01230.6280.0030.0030.0000.0000.0000.000
200B200GLN0-0.065-0.03333.4730.0010.0010.0000.0000.0000.000
201B201MET0-0.0350.01132.920-0.001-0.0010.0000.0000.0000.000
202B202ASN0-0.070-0.03035.2560.0020.0020.0000.0000.0000.000
203B203ALA00.0240.01331.5710.0020.0020.0000.0000.0000.000
204B204GLU-1-0.802-0.88229.2160.0370.0370.0000.0000.0000.000
205B205LEU0-0.010-0.00731.0530.0000.0000.0000.0000.0000.000
206B206ASN00.005-0.02031.1650.0040.0040.0000.0000.0000.000
207B207TYR0-0.041-0.00728.9620.0000.0000.0000.0000.0000.000
208B208LYS10.9320.95930.717-0.049-0.0490.0000.0000.0000.000
209B209VAL-1-0.852-0.91526.3250.0780.0780.0000.0000.0000.000
210B301SO4-2-1.940-1.96945.549-0.026-0.0260.0000.0000.0000.000
211A318HOH0-0.034-0.01920.686-0.002-0.0020.0000.0000.0000.000
212B445HOH0-0.019-0.00825.590-0.001-0.0010.0000.0000.0000.000
213B540HOH0-0.060-0.03144.4810.0000.0000.0000.0000.0000.000
214B593HOH00.0220.00727.3160.0030.0030.0000.0000.0000.000