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: N1YJQ

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2305013.129238
FMO2-HF: Nuclear repulsion 2225267.248309
FMO2-HF: Total energy -79745.880929
FMO2-MP2: Total energy -79978.370182


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.
-4.0120.280.316-1.921-2.6860.009
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 : 0.055 / q_NPA : 0.020
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].
3A345VAL00.0490.0183.112-1.7591.4080.260-1.511-1.9160.007
4A346PHE00.032-0.0025.504-0.371-0.322-0.001-0.008-0.0400.000
5A347LYS10.8150.8942.982-2.429-1.5920.058-0.347-0.5480.002
6A348SER00.0600.0288.807-0.099-0.0990.0000.0000.0000.000
7A349LEU00.0720.03312.620-0.023-0.0230.0000.0000.0000.000
8A350ARG10.8110.90714.911-0.174-0.1740.0000.0000.0000.000
9A351HIS00.0150.0097.3760.1360.1360.0000.0000.0000.000
10A352MET0-0.0090.01211.985-0.072-0.0720.0000.0000.0000.000
11A353ARG10.8180.89313.655-0.146-0.1460.0000.0000.0000.000
12A354GLN0-0.046-0.02612.810-0.010-0.0100.0000.0000.0000.000
13A355VAL0-0.043-0.01610.012-0.035-0.0350.0000.0000.0000.000
14A356LEU0-0.0070.00313.369-0.022-0.0220.0000.0000.0000.000
15A357GLY00.0470.04516.675-0.016-0.0160.0000.0000.0000.000
16A358ALA0-0.004-0.01419.0650.0150.0150.0000.0000.0000.000
17A359PRO00.0200.00121.6530.0110.0110.0000.0000.0000.000
18A360SER00.0300.00620.2450.0040.0040.0000.0000.0000.000
19A361PHE00.0260.00517.3090.0140.0140.0000.0000.0000.000
20A362ARG10.8300.91020.774-0.065-0.0650.0000.0000.0000.000
21A363MET00.0340.03224.3440.0070.0070.0000.0000.0000.000
22A364LEU00.0060.00018.0930.0070.0070.0000.0000.0000.000
23A365ALA00.003-0.01121.6330.0110.0110.0000.0000.0000.000
24A366TRP0-0.007-0.00223.0250.0050.0050.0000.0000.0000.000
25A367HIS00.0330.01925.3030.0060.0060.0000.0000.0000.000
26A368VAL0-0.025-0.01720.9690.0020.0020.0000.0000.0000.000
27A369LEU0-0.039-0.02124.365-0.002-0.0020.0000.0000.0000.000
28A370MET0-0.059-0.02626.893-0.006-0.0060.0000.0000.0000.000
29A371GLY0-0.002-0.01827.567-0.006-0.0060.0000.0000.0000.000
30A372ASN0-0.042-0.02127.816-0.003-0.0030.0000.0000.0000.000
31A373GLN0-0.060-0.01425.0600.0040.0040.0000.0000.0000.000
32A374VAL0-0.008-0.00520.065-0.007-0.0070.0000.0000.0000.000
33A375ILE0-0.025-0.01521.1900.0200.0200.0000.0000.0000.000
34A376TRP00.0230.00013.7690.0090.0090.0000.0000.0000.000
35A377LYS10.8400.93017.234-0.021-0.0210.0000.0000.0000.000
36A378SER00.0750.03312.206-0.039-0.0390.0000.0000.0000.000
37A379ARG10.9510.97513.5100.1090.1090.0000.0000.0000.000
38A380ASP-1-0.850-0.8767.9910.0500.0500.0000.0000.0000.000
39A381VAL00.0800.03710.6290.0610.0610.0000.0000.0000.000
40A382ASP-1-0.867-0.9316.3750.7280.7280.0000.0000.0000.000
41A383LEU0-0.048-0.0157.6460.3240.3240.0000.0000.0000.000
42A384VAL00.0180.0248.3200.0250.0250.0000.0000.0000.000
43A385GLN0-0.016-0.01610.415-0.069-0.0690.0000.0000.0000.000
44A386SER0-0.042-0.0397.8800.0150.0150.0000.0000.0000.000
45A387ALA00.0270.0069.995-0.072-0.0720.0000.0000.0000.000
46A388PHE00.0160.00212.860-0.061-0.0610.0000.0000.0000.000
47A389GLU-1-0.829-0.89812.1870.4690.4690.0000.0000.0000.000
48A390VAL0-0.0020.00611.560-0.056-0.0560.0000.0000.0000.000
49A391LEU00.0020.00414.413-0.075-0.0750.0000.0000.0000.000
50A392ARG10.8720.92017.015-0.437-0.4370.0000.0000.0000.000
51A393THR0-0.044-0.02616.700-0.051-0.0510.0000.0000.0000.000
52A394MET0-0.0080.00619.676-0.036-0.0360.0000.0000.0000.000
53A395LEU00.0000.02022.447-0.024-0.0240.0000.0000.0000.000
54A396PRO00.0070.00024.3690.0160.0160.0000.0000.0000.000
55A397VAL00.0120.00123.4690.0020.0020.0000.0000.0000.000
56A398GLY00.0160.01225.4110.0040.0040.0000.0000.0000.000
57A399CYS0-0.054-0.00827.067-0.009-0.0090.0000.0000.0000.000
58A400VAL0-0.013-0.00421.2210.0030.0030.0000.0000.0000.000
59A401ARG10.8700.94424.473-0.126-0.1260.0000.0000.0000.000
60A402ILE00.0250.00518.115-0.005-0.0050.0000.0000.0000.000
61A403ILE00.0190.01121.331-0.007-0.0070.0000.0000.0000.000
62A404PRO00.0070.00415.724-0.011-0.0110.0000.0000.0000.000
63A405TYR0-0.012-0.04614.6360.0140.0140.0000.0000.0000.000
64A406SER00.0230.02117.503-0.018-0.0180.0000.0000.0000.000
65A407SER00.0160.00020.577-0.001-0.0010.0000.0000.0000.000
66A408GLN0-0.073-0.04322.893-0.019-0.0190.0000.0000.0000.000
67A409TYR00.025-0.02024.7070.0090.0090.0000.0000.0000.000
68A410GLU-1-0.765-0.84225.4060.0930.0930.0000.0000.0000.000
69A411GLU-1-0.771-0.88827.3830.0770.0770.0000.0000.0000.000
70A412ALA00.0540.03628.9700.0080.0080.0000.0000.0000.000
71A413TYR00.005-0.00429.9540.0080.0080.0000.0000.0000.000
72A414ARG10.7720.86128.313-0.093-0.0930.0000.0000.0000.000
73A415CYS0-0.065-0.01724.1620.0090.0090.0000.0000.0000.000
74A416ASN00.0230.00425.140-0.003-0.0030.0000.0000.0000.000
75A417PHE0-0.0100.01018.8960.0060.0060.0000.0000.0000.000
76A418LEU00.0350.01120.9050.0010.0010.0000.0000.0000.000
77A419GLY00.0350.02017.138-0.003-0.0030.0000.0000.0000.000
78A420LEU0-0.066-0.03017.963-0.017-0.0170.0000.0000.0000.000
79A421SER00.0570.02117.891-0.004-0.0040.0000.0000.0000.000
80A422PRO0-0.042-0.03217.103-0.005-0.0050.0000.0000.0000.000
81A423HIS00.0130.00019.6490.0000.0000.0000.0000.0000.000
82A424VAL0-0.042-0.00222.358-0.003-0.0030.0000.0000.0000.000
83A425GLN0-0.015-0.00424.4280.0000.0000.0000.0000.0000.000
84A426ILE00.0210.00523.6370.0070.0070.0000.0000.0000.000
85A427PRO00.0100.00828.076-0.006-0.0060.0000.0000.0000.000
86A428PRO00.0530.01631.5650.0030.0030.0000.0000.0000.000
87A429HIS0-0.0070.00033.496-0.004-0.0040.0000.0000.0000.000
88A430VAL0-0.012-0.00727.9500.0020.0020.0000.0000.0000.000
89A431LEU0-0.032-0.02328.0130.0030.0030.0000.0000.0000.000
90A432SER0-0.034-0.02230.367-0.003-0.0030.0000.0000.0000.000
91A433SER00.0000.01531.156-0.002-0.0020.0000.0000.0000.000
92A434GLU-1-0.908-0.94831.0720.0550.0550.0000.0000.0000.000
93A435PHE0-0.045-0.03431.5360.0050.0050.0000.0000.0000.000
94A436ALA0-0.037-0.02027.4150.0080.0080.0000.0000.0000.000
95A437VAL00.0060.02723.023-0.007-0.0070.0000.0000.0000.000
96A438ILE00.0100.00122.6620.0140.0140.0000.0000.0000.000
97A439VAL0-0.009-0.00116.960-0.014-0.0140.0000.0000.0000.000
98A440GLU-1-0.823-0.88818.8030.0390.0390.0000.0000.0000.000
99A441VAL0-0.042-0.02712.544-0.005-0.0050.0000.0000.0000.000
100A442HIS0-0.015-0.01815.601-0.013-0.0130.0000.0000.0000.000
101A443ALA0-0.063-0.03913.263-0.022-0.0220.0000.0000.0000.000
102A444ALA00.0050.01412.6580.0210.0210.0000.0000.0000.000
103A445ALA0-0.046-0.01614.420-0.026-0.0260.0000.0000.0000.000
104A459SER00.0400.0314.159-0.0320.1370.000-0.028-0.1400.000
105A460LEU0-0.003-0.0254.426-0.568-0.498-0.001-0.027-0.0420.000
106A461SER0-0.009-0.0087.1430.0620.0620.0000.0000.0000.000
107A462LYS10.9270.9866.4160.6090.6090.0000.0000.0000.000
108A463TYR0-0.116-0.1078.279-0.013-0.0130.0000.0000.0000.000
109A464GLU-1-0.842-0.90411.506-0.129-0.1290.0000.0000.0000.000
110A465PHE0-0.008-0.02510.5720.0310.0310.0000.0000.0000.000
111A466VAL00.0080.01516.509-0.006-0.0060.0000.0000.0000.000
112A467VAL0-0.007-0.01119.8280.0160.0160.0000.0000.0000.000
113A468THR0-0.036-0.00922.214-0.011-0.0110.0000.0000.0000.000
114A469SER00.025-0.02125.7870.0100.0100.0000.0000.0000.000
115A470GLY00.0280.02428.590-0.007-0.0070.0000.0000.0000.000
116A471SER0-0.019-0.01932.3920.0010.0010.0000.0000.0000.000
117A472PRO00.0580.03532.483-0.003-0.0030.0000.0000.0000.000
118A473VAL0-0.041-0.02035.557-0.001-0.0010.0000.0000.0000.000
119A474ALA0-0.064-0.02637.592-0.003-0.0030.0000.0000.0000.000
120A475ALA00.0220.00133.417-0.001-0.0010.0000.0000.0000.000
121A476ASP-1-0.869-0.92529.5650.0680.0680.0000.0000.0000.000
122A477ARG10.7920.87532.777-0.053-0.0530.0000.0000.0000.000
123A478VAL00.0530.02732.4740.0030.0030.0000.0000.0000.000
124A479GLY0-0.0180.02232.9710.0010.0010.0000.0000.0000.000
125A480PRO00.0610.01329.6400.0010.0010.0000.0000.0000.000
126A481THR00.014-0.02430.8960.0030.0030.0000.0000.0000.000
127A482ILE0-0.0090.00427.4600.0000.0000.0000.0000.0000.000
128A483LEU00.0500.03325.0580.0090.0090.0000.0000.0000.000
129A484ASN00.009-0.00226.5760.0050.0050.0000.0000.0000.000
130A485LYS10.8190.90427.968-0.091-0.0910.0000.0000.0000.000
131A486ILE00.0390.02022.2760.0020.0020.0000.0000.0000.000
132A487GLU-1-0.771-0.87023.1940.0940.0940.0000.0000.0000.000
133A488ALA00.0010.01923.718-0.006-0.0060.0000.0000.0000.000
134A489ALA00.0050.00423.274-0.005-0.0050.0000.0000.0000.000
135A490LEU0-0.014-0.01418.1070.0050.0050.0000.0000.0000.000
136A491THR0-0.023-0.02319.560-0.006-0.0060.0000.0000.0000.000
137A492ASN0-0.0020.00421.824-0.013-0.0130.0000.0000.0000.000
138A493GLN00.020-0.00915.9100.0110.0110.0000.0000.0000.000
139A494ASN0-0.0040.00719.490-0.003-0.0030.0000.0000.0000.000
140A495LEU0-0.069-0.00921.3670.0000.0000.0000.0000.0000.000
141A496SER00.028-0.00418.8750.0080.0080.0000.0000.0000.000
142A497VAL00.0320.01014.172-0.003-0.0030.0000.0000.0000.000
143A498ASP-1-0.805-0.88817.4700.2010.2010.0000.0000.0000.000
144A499VAL0-0.033-0.01420.367-0.007-0.0070.0000.0000.0000.000
145A500VAL0-0.040-0.01718.757-0.009-0.0090.0000.0000.0000.000
146A501ASP-1-0.872-0.93716.9570.3400.3400.0000.0000.0000.000
147A502GLN0-0.012-0.01120.361-0.004-0.0040.0000.0000.0000.000
148A503ALA0-0.007-0.00123.848-0.012-0.0120.0000.0000.0000.000
149A504LEU0-0.004-0.00720.078-0.011-0.0110.0000.0000.0000.000
150A505VAL0-0.011-0.00522.881-0.005-0.0050.0000.0000.0000.000
151A506ALA00.0350.01825.300-0.010-0.0100.0000.0000.0000.000
152A507LEU0-0.028-0.01526.011-0.011-0.0110.0000.0000.0000.000
153A508LYS10.8540.90423.063-0.236-0.2360.0000.0000.0000.000
154A509GLU-1-0.922-0.96128.1280.1110.1110.0000.0000.0000.000
155A510GLU-1-0.810-0.88430.8840.0830.0830.0000.0000.0000.000
156A511TRP0-0.010-0.01931.107-0.008-0.0080.0000.0000.0000.000
157A512MET00.0460.02430.590-0.005-0.0050.0000.0000.0000.000
158A513ASN0-0.0050.00733.259-0.006-0.0060.0000.0000.0000.000
159A514LYS10.8250.91335.120-0.087-0.0870.0000.0000.0000.000
160A515VAL00.0110.02034.286-0.005-0.0050.0000.0000.0000.000
161A516LYS10.8990.94234.157-0.109-0.1090.0000.0000.0000.000
162A517VAL0-0.030-0.01139.012-0.005-0.0050.0000.0000.0000.000
163A518LEU00.0320.01939.848-0.004-0.0040.0000.0000.0000.000
164A519PHE00.0350.02140.376-0.004-0.0040.0000.0000.0000.000
165A520LYS10.9030.94442.362-0.062-0.0620.0000.0000.0000.000
166A521PHE0-0.020-0.01144.874-0.003-0.0030.0000.0000.0000.000
167A522THR0-0.027-0.03744.421-0.002-0.0020.0000.0000.0000.000
168A523LYS10.8870.96745.031-0.063-0.0630.0000.0000.0000.000
169A524VAL0-0.019-0.01648.434-0.001-0.0010.0000.0000.0000.000
170A525ASP-1-0.755-0.85052.0950.0360.0360.0000.0000.0000.000
171A526SER0-0.055-0.03753.6090.0010.0010.0000.0000.0000.000
172A527ARG10.8560.90952.940-0.040-0.0400.0000.0000.0000.000
173A528PRO00.0170.01354.3160.0020.0020.0000.0000.0000.000
174A529LYS10.8760.92149.564-0.042-0.0420.0000.0000.0000.000
175A530GLU-1-0.796-0.87349.9470.0370.0370.0000.0000.0000.000
176A531ASP-1-0.776-0.87850.3560.0400.0400.0000.0000.0000.000
177A532THR0-0.052-0.03245.8600.0020.0020.0000.0000.0000.000
178A533GLN00.019-0.00143.8870.0020.0020.0000.0000.0000.000
179A534LYS10.8160.89846.465-0.036-0.0360.0000.0000.0000.000
180A535LEU00.0050.00744.5250.0010.0010.0000.0000.0000.000
181A536LEU00.014-0.01040.4830.0020.0020.0000.0000.0000.000
182A537SER00.0160.00342.1280.0020.0020.0000.0000.0000.000
183A538ILE0-0.052-0.01643.8740.0000.0000.0000.0000.0000.000
184A539LEU0-0.040-0.01540.1130.0020.0020.0000.0000.0000.000
185A540GLY0-0.0100.01139.1990.0050.0050.0000.0000.0000.000
186A541ALA0-0.039-0.03837.8050.0040.0040.0000.0000.0000.000
187A542SER00.0280.02339.0130.0020.0020.0000.0000.0000.000
188A543GLU-1-0.807-0.88938.4040.0590.0590.0000.0000.0000.000
189A544GLU-1-0.790-0.87538.5750.0600.0600.0000.0000.0000.000
190A545ASP-1-0.713-0.86533.9160.0710.0710.0000.0000.0000.000
191A546ASN0-0.028-0.01934.6630.0120.0120.0000.0000.0000.000
192A547VAL00.0060.00636.1480.0040.0040.0000.0000.0000.000
193A548LYS10.7760.88134.958-0.065-0.0650.0000.0000.0000.000
194A549LEU00.0660.03129.5950.0020.0020.0000.0000.0000.000
195A550LEU0-0.051-0.02633.4180.0050.0050.0000.0000.0000.000
196A551LYS10.9470.97635.734-0.066-0.0660.0000.0000.0000.000
197A552PHE0-0.0060.03927.8810.0000.0000.0000.0000.0000.000
198A553TRP00.029-0.00427.2890.0040.0040.0000.0000.0000.000
199A554MET0-0.050-0.01932.4240.0010.0010.0000.0000.0000.000
200A555THR0-0.040-0.03531.9220.0010.0010.0000.0000.0000.000
201A556GLY0-0.0160.00231.0020.0040.0040.0000.0000.0000.000
202A557LEU0-0.070-0.04531.7190.0020.0020.0000.0000.0000.000
203A558SER00.0010.01435.071-0.004-0.0040.0000.0000.0000.000