FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: XMNQZ

Calculation Name: 3VUB-A-Xray22

Preferred Name:

Target Type:

Ligand Name: chloride ion

ligand 3-letter code: CL

PDB ID: 3VUB

Chain ID: A

ChEMBL ID:

UniProt ID: P62554

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:

Apendix: None


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 170
LigandResidueName
LigandFragmentNumber 0
LigandCharge CL-=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -955093.105165
FMO2-HF: Nuclear repulsion 907739.778232
FMO2-HF: Total energy -47353.326933
FMO2-MP2: Total energy -47485.800006


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(A:1:MET)


Summations of interaction energy for fragment #1(A: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.
-33.221-59.89282.473-35.598-20.2-0.047
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : 0.056
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].
3A3PHE0-0.017-0.0223.7760.0021.389-0.009-0.577-0.8010.002
4A4LYS10.8410.9622.305-4.307-3.0671.404-0.777-1.8670.000
5A5VAL0-0.017-0.0184.806-0.533-0.504-0.001-0.010-0.0170.000
6A6TYR00.020-0.0072.002-9.932-12.37210.651-3.803-4.4070.018
7A7THR00.0060.0158.644-0.505-0.5050.0000.0000.0000.000
8A8TYR0-0.041-0.01510.8930.1270.1270.0000.0000.0000.000
9A9LYS10.9220.96111.108-0.855-0.8550.0000.0000.0000.000
10A10ARG10.8960.95914.534-0.190-0.1900.0000.0000.0000.000
11A11GLU-1-0.848-0.91416.7570.2790.2790.0000.0000.0000.000
12A12SER0-0.030-0.01416.352-0.064-0.0640.0000.0000.0000.000
13A13ARG10.9390.98518.433-0.027-0.0270.0000.0000.0000.000
14A14TYR0-0.067-0.03615.7670.0060.0060.0000.0000.0000.000
15A15ARG10.9840.97716.128-0.324-0.3240.0000.0000.0000.000
16A16LEU00.0380.01812.3570.1190.1190.0000.0000.0000.000
17A17PHE0-0.020-0.0055.924-0.202-0.2020.0000.0000.0000.000
18A18VAL00.0280.0227.5300.4470.4470.0000.0000.0000.000
19A19ASP-1-0.733-0.8321.904-12.947-15.3788.772-3.244-3.096-0.040
20A20VAL00.0300.0034.975-0.298-0.309-0.001-0.0090.0210.000
21A21GLN0-0.0110.0145.6530.5690.5690.0000.0000.0000.000
22A22SER00.0200.0015.277-0.977-0.9770.0000.0000.0000.000
23A23ASP-1-0.716-0.8692.658-10.742-8.6530.982-1.510-1.561-0.015
24A24ILE0-0.0220.0195.2130.2100.266-0.0010.000-0.0540.000
25A25ILE0-0.037-0.0028.0490.4040.4040.0000.0000.0000.000
26A26ASP-1-0.880-0.9488.244-1.768-1.7680.0000.0000.0000.000
27A27THR0-0.007-0.0099.2370.1970.1970.0000.0000.0000.000
28A28PRO00.0290.01610.024-0.102-0.1020.0000.0000.0000.000
29A29GLY00.0190.0119.5800.1310.1310.0000.0000.0000.000
30A30ARG10.8680.9379.2830.8120.8120.0000.0000.0000.000
31A31ARG10.8930.9552.8944.8966.3000.184-0.617-0.972-0.001
32A32MET00.0070.0156.7120.5840.5840.0000.0000.0000.000
33A33VAL0-0.007-0.0035.995-0.419-0.4190.0000.0000.0000.000
34A34ILE00.0220.0078.4860.0700.0700.0000.0000.0000.000
35A35PRO0-0.0120.00511.0860.1340.1340.0000.0000.0000.000
36A36LEU00.0290.02912.017-0.065-0.0650.0000.0000.0000.000
37A37ALA00.0050.00615.0410.0480.0480.0000.0000.0000.000
38A38SER0-0.0070.01918.754-0.010-0.0100.0000.0000.0000.000
39A39ALA00.0540.02021.233-0.033-0.0330.0000.0000.0000.000
40A40ARG10.8900.94223.232-0.218-0.2180.0000.0000.0000.000
41A41LEU0-0.017-0.00826.334-0.013-0.0130.0000.0000.0000.000
42A42LEU0-0.031-0.01122.936-0.016-0.0160.0000.0000.0000.000
43A43SER00.0010.00527.0340.0010.0010.0000.0000.0000.000
44A44ASP-1-0.861-0.94227.5460.0070.0070.0000.0000.0000.000
45A45LYS10.9020.94629.287-0.002-0.0020.0000.0000.0000.000
46A46VAL0-0.0190.00924.439-0.012-0.0120.0000.0000.0000.000
47A47SER00.0280.01125.2270.0000.0000.0000.0000.0000.000
48A48ARG11.0060.97522.9860.0560.0560.0000.0000.0000.000
49A49GLU-1-0.896-0.92121.767-0.130-0.1300.0000.0000.0000.000
50A50LEU00.0560.04220.232-0.034-0.0340.0000.0000.0000.000
51A51TYR0-0.056-0.00719.187-0.025-0.0250.0000.0000.0000.000
52A52PRO00.0380.02817.1840.0490.0490.0000.0000.0000.000
53A53VAL0-0.017-0.00918.5740.0220.0220.0000.0000.0000.000
54A54VAL00.0000.00214.497-0.019-0.0190.0000.0000.0000.000
55A55HIS00.013-0.00516.9480.0330.0330.0000.0000.0000.000
56A56ILE00.0340.00912.4760.0420.0420.0000.0000.0000.000
57A57GLY00.0280.02116.233-0.035-0.0350.0000.0000.0000.000
58A58ASP-1-0.932-0.95418.3040.3380.3380.0000.0000.0000.000
59A59GLU-1-0.913-0.94520.0310.2520.2520.0000.0000.0000.000
60A60SER00.0170.00119.6980.0060.0060.0000.0000.0000.000
61A61TRP0-0.049-0.03616.955-0.003-0.0030.0000.0000.0000.000
62A62ARG10.8320.91718.758-0.017-0.0170.0000.0000.0000.000
63A63MET00.0300.02513.5380.0240.0240.0000.0000.0000.000
64A64MET0-0.022-0.01115.818-0.031-0.0310.0000.0000.0000.000
65A65THR00.029-0.03715.466-0.031-0.0310.0000.0000.0000.000
66A66THR00.0600.02216.344-0.041-0.0410.0000.0000.0000.000
67A67ASP-1-0.898-0.94416.836-0.086-0.0860.0000.0000.0000.000
68A68MET0-0.053-0.00911.994-0.020-0.0200.0000.0000.0000.000
69A69ALA0-0.012-0.00212.2860.0350.0350.0000.0000.0000.000
70A70SER00.0160.01010.341-0.043-0.0430.0000.0000.0000.000
71A71VAL0-0.023-0.0088.2280.1780.1780.0000.0000.0000.000
72A72PRO0-0.046-0.0229.345-0.195-0.1950.0000.0000.0000.000
73A73VAL00.1150.0226.4490.1760.1760.0000.0000.0000.000
74A74SER0-0.051-0.0208.6390.3090.3090.0000.0000.0000.000
75A75VAL00.007-0.01411.0240.0840.0840.0000.0000.0000.000
76A76ILE00.0030.0325.223-0.102-0.1020.0000.0000.0000.000
77A77GLY00.0070.0018.804-0.011-0.0110.0000.0000.0000.000
78A78GLU-1-0.895-0.9498.4431.8131.8130.0000.0000.0000.000
79A79GLU-1-0.810-0.9024.4797.7088.0500.005-0.049-0.2970.000
80A80VAL0-0.022-0.0248.319-0.463-0.4630.0000.0000.0000.000
81A81ALA00.0150.0008.818-0.355-0.3550.0000.0000.0000.000
82A82ASP-1-0.774-0.8917.2200.9880.9880.0000.0000.0000.000
83A83LEU00.013-0.0078.074-0.172-0.1720.0000.0000.0000.000
84A84SER00.0050.0147.447-0.196-0.1960.0000.0000.0000.000
85A85HIS0-0.0190.0009.328-0.118-0.1180.0000.0000.0000.000
86A86ARG10.7370.83912.3700.0500.0500.0000.0000.0000.000
87A87GLU-1-0.849-0.91510.985-0.758-0.7580.0000.0000.0000.000
88A88ASN00.0520.01712.618-0.074-0.0740.0000.0000.0000.000
89A89ASP-1-0.762-0.87916.284-0.180-0.1800.0000.0000.0000.000
90A90ILE0-0.0070.00111.1700.0120.0120.0000.0000.0000.000
91A91LYS10.9340.97714.3530.5860.5860.0000.0000.0000.000
92A92ASN0-0.024-0.02415.353-0.024-0.0240.0000.0000.0000.000
93A93ALA00.0080.01216.7480.0230.0230.0000.0000.0000.000
94A94ILE0-0.018-0.01112.1170.0140.0140.0000.0000.0000.000
95A95ASN0-0.051-0.03116.641-0.021-0.0210.0000.0000.0000.000
96A96LEU0-0.031-0.00119.3560.0290.0290.0000.0000.0000.000
97A97MET0-0.065-0.01116.4060.0460.0460.0000.0000.0000.000
98A98PHE0-0.080-0.03916.1360.0130.0130.0000.0000.0000.000
99A99TRP0-0.029-0.03419.6690.0300.0300.0000.0000.0000.000
100A100GLY0-0.0120.02824.0880.0210.0210.0000.0000.0000.000
101A101ILE-1-0.918-0.95925.523-0.256-0.2560.0000.0000.0000.000
102A200CL--1-0.866-0.90616.7950.1540.1540.0000.0000.0000.000
103A201HOH00.0170.00615.397-0.043-0.0430.0000.0000.0000.000
104A203HOH00.0140.00617.159-0.018-0.0180.0000.0000.0000.000
105A204HOH0-0.020-0.0711.756-1.217-33.42258.270-21.856-4.2090.005
106A205HOH0-0.016-0.0224.5800.0130.046-0.001-0.002-0.0310.000
107A206HOH00.0310.01714.981-0.027-0.0270.0000.0000.0000.000
108A207HOH0-0.024-0.0206.933-0.085-0.0850.0000.0000.0000.000
109A208HOH0-0.036-0.0283.046-0.0020.7240.051-0.419-0.357-0.003
110A209HOH0-0.027-0.02619.1320.0130.0130.0000.0000.0000.000
111A210HOH00.0240.01218.1180.0000.0000.0000.0000.0000.000
112A211HOH00.004-0.00317.341-0.006-0.0060.0000.0000.0000.000
113A212HOH0-0.055-0.0432.429-3.511-1.6421.053-1.420-1.502-0.012
114A215HOH0-0.009-0.01215.3520.0030.0030.0000.0000.0000.000
115A217HOH0-0.018-0.01113.640-0.047-0.0470.0000.0000.0000.000
116A218HOH0-0.020-0.01312.357-0.082-0.0820.0000.0000.0000.000
117A219HOH0-0.037-0.02617.2540.0060.0060.0000.0000.0000.000
118A220HOH00.0130.0056.3690.1110.1110.0000.0000.0000.000
119A221HOH0-0.034-0.0282.166-2.300-1.0591.114-1.305-1.050-0.001
120A222HOH00.016-0.00314.8710.0140.0140.0000.0000.0000.000
121A223HOH00.0220.00715.0190.0300.0300.0000.0000.0000.000
122A224HOH00.0150.02312.5220.0480.0480.0000.0000.0000.000
123A225HOH00.0130.01412.086-0.008-0.0080.0000.0000.0000.000
124A227HOH0-0.020-0.0179.2360.1180.1180.0000.0000.0000.000
125A229HOH00.0310.05221.009-0.019-0.0190.0000.0000.0000.000
126A230HOH0-0.037-0.0247.290-0.270-0.2700.0000.0000.0000.000
127A232HOH0-0.044-0.03420.9040.0110.0110.0000.0000.0000.000
128A234HOH0-0.016-0.01916.860-0.020-0.0200.0000.0000.0000.000
129A235HOH0-0.031-0.01713.9050.0300.0300.0000.0000.0000.000
130A237HOH0-0.035-0.0278.865-0.043-0.0430.0000.0000.0000.000
131A238HOH00.0150.0218.7760.0120.0120.0000.0000.0000.000
132A239HOH0-0.020-0.0225.228-0.575-0.5750.0000.0000.0000.000
133A240HOH0-0.038-0.0255.948-0.309-0.3090.0000.0000.0000.000
134A241HOH0-0.016-0.00420.812-0.006-0.0060.0000.0000.0000.000
135A243HOH0-0.061-0.04215.739-0.001-0.0010.0000.0000.0000.000
136A246HOH00.0340.0235.6420.3060.3060.0000.0000.0000.000
137A248HOH0-0.057-0.03421.171-0.014-0.0140.0000.0000.0000.000
138A250HOH0-0.046-0.0218.076-0.020-0.0200.0000.0000.0000.000
139A251HOH0-0.024-0.01211.6020.0600.0600.0000.0000.0000.000
140A254HOH0-0.003-0.00620.7320.0060.0060.0000.0000.0000.000
141A255HOH0-0.017-0.03024.187-0.002-0.0020.0000.0000.0000.000
142A258HOH00.0350.02124.993-0.006-0.0060.0000.0000.0000.000
143A260HOH0-0.023-0.0139.8660.0550.0550.0000.0000.0000.000
144A262HOH0-0.032-0.0185.6380.2980.2980.0000.0000.0000.000
145A265HOH00.003-0.00523.444-0.014-0.0140.0000.0000.0000.000
146A267HOH00.0140.00416.0440.0080.0080.0000.0000.0000.000
147A271HOH0-0.044-0.02320.7140.0130.0130.0000.0000.0000.000
148A273HOH0-0.037-0.02911.6390.0760.0760.0000.0000.0000.000
149A275HOH00.0230.02114.9200.0170.0170.0000.0000.0000.000
150A279HOH0-0.040-0.02323.787-0.011-0.0110.0000.0000.0000.000
151A282HOH0-0.013-0.00924.020-0.008-0.0080.0000.0000.0000.000
152A287HOH0-0.031-0.01519.080-0.015-0.0150.0000.0000.0000.000
153A292HOH0-0.0010.00321.0560.0120.0120.0000.0000.0000.000
154A294HOH0-0.027-0.01714.463-0.001-0.0010.0000.0000.0000.000
155A295HOH0-0.011-0.01022.6470.0100.0100.0000.0000.0000.000
156A297HOH0-0.010-0.01620.163-0.020-0.0200.0000.0000.0000.000
157A298HOH0-0.027-0.01913.7150.0070.0070.0000.0000.0000.000
158A299HOH00.0060.00413.1030.0150.0150.0000.0000.0000.000
159A305HOH0-0.015-0.00634.138-0.002-0.0020.0000.0000.0000.000
160A306HOH0-0.008-0.0127.6010.2110.2110.0000.0000.0000.000
161A307HOH0-0.037-0.01822.7010.0090.0090.0000.0000.0000.000
162A308HOH0-0.054-0.03120.095-0.002-0.0020.0000.0000.0000.000
163A309HOH0-0.047-0.0279.246-0.117-0.1170.0000.0000.0000.000
164A314HOH00.0360.02227.4370.0020.0020.0000.0000.0000.000
165A323HOH00.0130.00417.1040.0020.0020.0000.0000.0000.000
166A329HOH00.001-0.00321.586-0.004-0.0040.0000.0000.0000.000
167A333HOH0-0.0090.00728.3080.0070.0070.0000.0000.0000.000
168A340HOH0-0.0050.00320.6630.0120.0120.0000.0000.0000.000
169A342HOH00.0150.0127.208-0.053-0.0530.0000.0000.0000.000
170A344HOH0-0.046-0.07222.778-0.011-0.0110.0000.0000.0000.000