FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: GN3Z1

Calculation Name: 3V42-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V42

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NFG4

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptH
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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299646.71888
FMO2-HF: Nuclear repulsion 2219904.070431
FMO2-HF: Total energy -79742.648449
FMO2-MP2: Total energy -79973.99869


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:343:LEU)


Summations of interaction energy for fragment #1(A:343:LEU)
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.
-0.3453.0270.081-1.316-2.1370
Interaction energy analysis for fragmet #1(A:343:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.002
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].
3A345VAL00.0340.0142.793-1.4931.1490.060-1.129-1.573-0.001
4A346PHE0-0.004-0.0225.131-0.195-0.153-0.001-0.006-0.0350.000
5A347LYS10.9080.9453.0691.0661.5470.024-0.137-0.3680.001
6A348SER00.0520.0228.8940.0690.0690.0000.0000.0000.000
7A349LEU00.0900.04212.631-0.014-0.0140.0000.0000.0000.000
8A350ARG10.8430.93114.7730.1550.1550.0000.0000.0000.000
9A351HIS00.0130.0237.2000.0330.0330.0000.0000.0000.000
10A352MET00.0170.01812.1700.0080.0080.0000.0000.0000.000
11A353ARG10.9440.97213.8100.1390.1390.0000.0000.0000.000
12A354GLN0-0.070-0.03712.596-0.016-0.0160.0000.0000.0000.000
13A355VAL0-0.026-0.01610.3780.0080.0080.0000.0000.0000.000
14A356LEU0-0.0090.01113.6160.0250.0250.0000.0000.0000.000
15A357GLY00.0530.04016.6610.0190.0190.0000.0000.0000.000
16A358ALA0-0.035-0.02719.1600.0040.0040.0000.0000.0000.000
17A359PRO00.0270.00222.1780.0010.0010.0000.0000.0000.000
18A360SER00.0530.02920.5490.0070.0070.0000.0000.0000.000
19A361PHE00.0120.00217.8890.0020.0020.0000.0000.0000.000
20A362ARG10.8450.91421.0600.0590.0590.0000.0000.0000.000
21A363MET00.0480.04224.5020.0040.0040.0000.0000.0000.000
22A364LEU0-0.012-0.01317.7110.0030.0030.0000.0000.0000.000
23A365ALA0-0.002-0.02521.7950.0030.0030.0000.0000.0000.000
24A366TRP0-0.0270.00022.9090.0030.0030.0000.0000.0000.000
25A367HIS00.0690.03224.6630.0040.0040.0000.0000.0000.000
26A368VAL0-0.036-0.01120.5880.0030.0030.0000.0000.0000.000
27A369LEU0-0.054-0.02723.7340.0040.0040.0000.0000.0000.000
28A370MET0-0.035-0.01926.3820.0030.0030.0000.0000.0000.000
29A371GLY0-0.020-0.01627.0530.0030.0030.0000.0000.0000.000
30A372ASN0-0.037-0.01927.4070.0070.0070.0000.0000.0000.000
31A373GLN0-0.056-0.00324.585-0.002-0.0020.0000.0000.0000.000
32A374VAL0-0.017-0.01119.467-0.002-0.0020.0000.0000.0000.000
33A375ILE0-0.020-0.01220.7480.0050.0050.0000.0000.0000.000
34A376TRP00.0320.01713.131-0.013-0.0130.0000.0000.0000.000
35A377LYS10.8740.96217.441-0.049-0.0490.0000.0000.0000.000
36A378SER00.0770.03112.1030.0120.0120.0000.0000.0000.000
37A379ARG10.9751.00413.082-0.337-0.3370.0000.0000.0000.000
38A380ASP-1-0.864-0.9207.8421.1501.1500.0000.0000.0000.000
39A381VAL00.0300.02510.456-0.075-0.0750.0000.0000.0000.000
40A382ASP-1-0.826-0.9266.0950.7720.7720.0000.0000.0000.000
41A383LEU0-0.081-0.0177.171-0.281-0.2810.0000.0000.0000.000
42A384VAL00.0310.0268.007-0.160-0.1600.0000.0000.0000.000
43A385GLN00.0250.0229.739-0.029-0.0290.0000.0000.0000.000
44A386SER0-0.047-0.0507.151-0.120-0.1200.0000.0000.0000.000
45A387ALA00.0330.0139.278-0.034-0.0340.0000.0000.0000.000
46A388PHE00.001-0.01812.166-0.004-0.0040.0000.0000.0000.000
47A389GLU-1-0.940-0.96611.320-0.100-0.1000.0000.0000.0000.000
48A390VAL00.0180.01111.3720.0030.0030.0000.0000.0000.000
49A391LEU0-0.008-0.00614.0160.0170.0170.0000.0000.0000.000
50A392ARG10.9480.99016.3380.0750.0750.0000.0000.0000.000
51A393THR0-0.077-0.03816.5630.0120.0120.0000.0000.0000.000
52A394MET00.001-0.00919.3020.0040.0040.0000.0000.0000.000
53A395LEU0-0.0120.01222.0380.0070.0070.0000.0000.0000.000
54A396PRO00.0030.01123.662-0.004-0.0040.0000.0000.0000.000
55A397VAL00.025-0.00922.7190.0020.0020.0000.0000.0000.000
56A398GLY00.0070.00324.6360.0030.0030.0000.0000.0000.000
57A399CYS0-0.0330.00226.3470.0030.0030.0000.0000.0000.000
58A400VAL0-0.035-0.00220.3740.0000.0000.0000.0000.0000.000
59A401ARG10.9030.95423.6710.0090.0090.0000.0000.0000.000
60A402ILE00.0110.00317.637-0.001-0.0010.0000.0000.0000.000
61A403ILE00.0120.00920.9130.0050.0050.0000.0000.0000.000
62A404PRO00.0200.00315.6920.0020.0020.0000.0000.0000.000
63A405TYR0-0.042-0.07514.8770.0190.0190.0000.0000.0000.000
64A406SER00.0360.03717.4550.0080.0080.0000.0000.0000.000
65A407SER0-0.011-0.01820.7220.0070.0070.0000.0000.0000.000
66A408GLN0-0.028-0.01622.913-0.001-0.0010.0000.0000.0000.000
67A409TYR0-0.004-0.03124.8560.0010.0010.0000.0000.0000.000
68A410GLU-1-0.790-0.87525.2880.0370.0370.0000.0000.0000.000
69A411GLU-1-0.796-0.91326.9780.0120.0120.0000.0000.0000.000
70A412ALA00.0440.01728.0910.0000.0000.0000.0000.0000.000
71A413TYR0-0.010-0.01828.931-0.002-0.0020.0000.0000.0000.000
72A414ARG10.7990.88227.603-0.031-0.0310.0000.0000.0000.000
73A415CYS0-0.053-0.00123.4130.0020.0020.0000.0000.0000.000
74A416ASN00.0430.01124.3210.0030.0030.0000.0000.0000.000
75A417PHE0-0.0280.01118.634-0.006-0.0060.0000.0000.0000.000
76A418LEU00.0600.01320.5510.0060.0060.0000.0000.0000.000
77A419GLY00.0210.01716.997-0.005-0.0050.0000.0000.0000.000
78A420LEU0-0.047-0.02717.6660.0040.0040.0000.0000.0000.000
79A421SER00.0420.02017.5230.0200.0200.0000.0000.0000.000
80A422PRO00.015-0.00617.245-0.018-0.0180.0000.0000.0000.000
81A423HIS00.002-0.02619.719-0.023-0.0230.0000.0000.0000.000
82A424VAL0-0.0110.03122.004-0.007-0.0070.0000.0000.0000.000
83A425GLN0-0.007-0.01724.334-0.007-0.0070.0000.0000.0000.000
84A426ILE0-0.014-0.00123.558-0.001-0.0010.0000.0000.0000.000
85A427PRO00.0380.03427.886-0.001-0.0010.0000.0000.0000.000
86A428PRO00.0460.00331.159-0.002-0.0020.0000.0000.0000.000
87A429HIS0-0.017-0.01833.076-0.002-0.0020.0000.0000.0000.000
88A430VAL0-0.0010.00527.377-0.003-0.0030.0000.0000.0000.000
89A431LEU0-0.035-0.01027.659-0.003-0.0030.0000.0000.0000.000
90A432SER0-0.029-0.01030.029-0.003-0.0030.0000.0000.0000.000
91A433SER00.0080.02330.784-0.003-0.0030.0000.0000.0000.000
92A434GLU-1-0.889-0.94530.938-0.013-0.0130.0000.0000.0000.000
93A435PHE0-0.101-0.06530.741-0.004-0.0040.0000.0000.0000.000
94A436ALA0-0.028-0.01526.6150.0010.0010.0000.0000.0000.000
95A437VAL0-0.0140.02422.247-0.002-0.0020.0000.0000.0000.000
96A438ILE00.0280.01421.9580.0040.0040.0000.0000.0000.000
97A439VAL0-0.024-0.01716.614-0.008-0.0080.0000.0000.0000.000
98A440GLU-1-0.912-0.96318.3340.0590.0590.0000.0000.0000.000
99A441VAL0-0.044-0.02212.622-0.017-0.0170.0000.0000.0000.000
100A442HIS00.0060.00915.8810.0460.0460.0000.0000.0000.000
101A443ALA0-0.057-0.03713.435-0.009-0.0090.0000.0000.0000.000
102A444ALA00.0360.02113.215-0.015-0.0150.0000.0000.0000.000
103A445ALA0-0.018-0.00514.8530.0140.0140.0000.0000.0000.000
104A459SER00.0100.0124.3710.0010.127-0.001-0.012-0.1130.000
105A460LEU0-0.046-0.0534.311-0.500-0.419-0.001-0.032-0.0480.000
106A461SER00.0410.0227.1440.0980.0980.0000.0000.0000.000
107A462LYS10.9340.9926.919-0.510-0.5100.0000.0000.0000.000
108A463TYR0-0.104-0.0627.7620.0690.0690.0000.0000.0000.000
109A464GLU-1-0.908-0.93911.743-0.072-0.0720.0000.0000.0000.000
110A465PHE0-0.021-0.03211.0220.0200.0200.0000.0000.0000.000
111A466VAL00.0080.00716.635-0.007-0.0070.0000.0000.0000.000
112A467VAL00.0080.00219.5960.0060.0060.0000.0000.0000.000
113A468THR0-0.035-0.01322.0230.0010.0010.0000.0000.0000.000
114A469SER0-0.001-0.03325.3860.0000.0000.0000.0000.0000.000
115A470GLY00.0400.04728.0470.0000.0000.0000.0000.0000.000
116A471SER0-0.053-0.04931.748-0.003-0.0030.0000.0000.0000.000
117A472PRO00.0210.03632.1690.0010.0010.0000.0000.0000.000
118A473VAL00.0200.02235.2180.0020.0020.0000.0000.0000.000
119A474ALA0-0.033-0.02637.2080.0000.0000.0000.0000.0000.000
120A475ALA00.009-0.01732.729-0.001-0.0010.0000.0000.0000.000
121A476ASP-1-0.862-0.92829.172-0.038-0.0380.0000.0000.0000.000
122A477ARG10.8870.94232.3380.0270.0270.0000.0000.0000.000
123A478VAL00.0410.00932.542-0.003-0.0030.0000.0000.0000.000
124A479GLY0-0.0310.03233.080-0.002-0.0020.0000.0000.0000.000
125A480PRO00.0690.02029.7680.0000.0000.0000.0000.0000.000
126A481THR00.034-0.02131.208-0.003-0.0030.0000.0000.0000.000
127A482ILE0-0.012-0.00327.370-0.003-0.0030.0000.0000.0000.000
128A483LEU00.0620.04125.337-0.006-0.0060.0000.0000.0000.000
129A484ASN00.0350.03226.800-0.007-0.0070.0000.0000.0000.000
130A485LYS10.9090.95627.9170.0450.0450.0000.0000.0000.000
131A486ILE00.0510.02022.421-0.004-0.0040.0000.0000.0000.000
132A487GLU-1-0.889-0.93923.193-0.083-0.0830.0000.0000.0000.000
133A488ALA0-0.010-0.01323.667-0.006-0.0060.0000.0000.0000.000
134A489ALA00.0130.00323.334-0.002-0.0020.0000.0000.0000.000
135A490LEU0-0.034-0.02218.383-0.009-0.0090.0000.0000.0000.000
136A491THR0-0.048-0.01519.870-0.010-0.0100.0000.0000.0000.000
137A492ASN0-0.045-0.01222.034-0.002-0.0020.0000.0000.0000.000
138A493GLN00.046-0.01716.947-0.018-0.0180.0000.0000.0000.000
139A494ASN0-0.016-0.00519.967-0.009-0.0090.0000.0000.0000.000
140A495LEU0-0.0350.03120.8820.0040.0040.0000.0000.0000.000
141A496SER00.0490.01619.152-0.014-0.0140.0000.0000.0000.000
142A497VAL00.062-0.00314.1320.0000.0000.0000.0000.0000.000
143A498ASP-1-0.792-0.89117.533-0.112-0.1120.0000.0000.0000.000
144A499VAL0-0.095-0.02720.2490.0080.0080.0000.0000.0000.000
145A500VAL0-0.062-0.03518.8280.0050.0050.0000.0000.0000.000
146A501ASP-1-0.879-0.93417.682-0.149-0.1490.0000.0000.0000.000
147A502GLN0-0.021-0.01920.5250.0060.0060.0000.0000.0000.000
148A503ALA00.011-0.00324.0200.0070.0070.0000.0000.0000.000
149A504LEU0-0.010-0.00220.5380.0070.0070.0000.0000.0000.000
150A505VAL0-0.021-0.01223.0600.0060.0060.0000.0000.0000.000
151A506ALA00.0410.01925.3100.0060.0060.0000.0000.0000.000
152A507LEU0-0.014-0.00126.5460.0050.0050.0000.0000.0000.000
153A508LYS10.8530.92722.4760.0770.0770.0000.0000.0000.000
154A509GLU-1-0.931-0.96527.948-0.040-0.0400.0000.0000.0000.000
155A510GLU-1-0.923-0.95230.558-0.040-0.0400.0000.0000.0000.000
156A511TRP00.024-0.02130.8050.0050.0050.0000.0000.0000.000
157A512MET00.007-0.00530.1710.0040.0040.0000.0000.0000.000
158A513ASN0-0.050-0.02032.7730.0050.0050.0000.0000.0000.000
159A514LYS10.8800.96135.5790.0380.0380.0000.0000.0000.000
160A515VAL00.0100.02033.5770.0020.0020.0000.0000.0000.000
161A516LYS10.9550.98133.7020.0320.0320.0000.0000.0000.000
162A517VAL0-0.040-0.01438.5750.0020.0020.0000.0000.0000.000
163A518LEU00.0130.00539.3620.0020.0020.0000.0000.0000.000
164A519PHE00.0430.01639.8790.0010.0010.0000.0000.0000.000
165A520LYS10.8920.93941.7920.0180.0180.0000.0000.0000.000
166A521PHE0-0.002-0.00544.3310.0010.0010.0000.0000.0000.000
167A522THR0-0.048-0.02344.0960.0010.0010.0000.0000.0000.000
168A523LYS10.9430.98945.1580.0150.0150.0000.0000.0000.000
169A524VAL00.011-0.00247.9420.0000.0000.0000.0000.0000.000
170A525ASP-1-0.823-0.88051.414-0.008-0.0080.0000.0000.0000.000
171A526SER0-0.041-0.03052.673-0.001-0.0010.0000.0000.0000.000
172A527ARG10.8580.92252.3190.0120.0120.0000.0000.0000.000
173A528PRO0-0.046-0.00453.6970.0000.0000.0000.0000.0000.000
174A529LYS10.9130.92448.5610.0110.0110.0000.0000.0000.000
175A530GLU-1-0.835-0.92349.752-0.013-0.0130.0000.0000.0000.000
176A531ASP-1-0.787-0.90450.682-0.014-0.0140.0000.0000.0000.000
177A532THR0-0.071-0.02745.614-0.001-0.0010.0000.0000.0000.000
178A533GLN00.0270.00643.610-0.001-0.0010.0000.0000.0000.000
179A534LYS10.9000.94846.4170.0130.0130.0000.0000.0000.000
180A535LEU00.0100.01244.563-0.001-0.0010.0000.0000.0000.000
181A536LEU0-0.005-0.01540.880-0.001-0.0010.0000.0000.0000.000
182A537SER0-0.029-0.00942.490-0.002-0.0020.0000.0000.0000.000
183A538ILE00.0190.01444.108-0.001-0.0010.0000.0000.0000.000
184A539LEU0-0.063-0.02240.345-0.001-0.0010.0000.0000.0000.000
185A540GLY00.0010.00439.400-0.002-0.0020.0000.0000.0000.000
186A541ALA0-0.040-0.04237.974-0.002-0.0020.0000.0000.0000.000
187A542SER0-0.021-0.00339.2020.0000.0000.0000.0000.0000.000
188A543GLU-1-0.868-0.92938.641-0.031-0.0310.0000.0000.0000.000
189A544GLU-1-0.936-0.97038.028-0.023-0.0230.0000.0000.0000.000
190A545ASP-1-0.739-0.89033.801-0.031-0.0310.0000.0000.0000.000
191A546ASN0-0.004-0.00934.629-0.003-0.0030.0000.0000.0000.000
192A547VAL0-0.0050.00235.8600.0000.0000.0000.0000.0000.000
193A548LYS10.9430.96834.7550.0200.0200.0000.0000.0000.000
194A549LEU00.0630.03529.4970.0010.0010.0000.0000.0000.000
195A550LEU0-0.050-0.02732.8450.0000.0000.0000.0000.0000.000
196A551LYS10.9530.98535.1760.0150.0150.0000.0000.0000.000
197A552PHE00.0010.02227.3890.0020.0020.0000.0000.0000.000
198A553TRP00.0350.00026.9920.0000.0000.0000.0000.0000.000
199A554MET0-0.042-0.01331.7380.0000.0000.0000.0000.0000.000
200A555THR0-0.077-0.04431.5090.0010.0010.0000.0000.0000.000
201A556GLY0-0.0120.00530.4210.0010.0010.0000.0000.0000.000
202A557LEU0-0.066-0.04331.150-0.002-0.0020.0000.0000.0000.000
203A558SER00.0040.01534.3280.0020.0020.0000.0000.0000.000