FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 82Y4Y

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 OptHSide
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 -2299753.320305
FMO2-HF: Nuclear repulsion 2220008.215884
FMO2-HF: Total energy -79745.104422
FMO2-MP2: Total energy -79976.65806


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.
-0.2733.270.067-1.388-2.2190.001
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 : 0.023 / q_NPA : 0.001
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].
3A345VAL00.0350.0142.987-1.6691.0220.042-1.136-1.5970.000
4A346PHE00.023-0.0105.100-0.214-0.168-0.001-0.006-0.0380.000
5A347LYS10.8530.9203.1691.6052.2160.028-0.205-0.4330.001
6A348SER00.0620.0308.8510.0710.0710.0000.0000.0000.000
7A349LEU00.0750.03612.540-0.012-0.0120.0000.0000.0000.000
8A350ARG10.8410.92414.7220.1720.1720.0000.0000.0000.000
9A351HIS00.0010.0097.5250.0140.0140.0000.0000.0000.000
10A352MET00.0040.01812.0650.0140.0140.0000.0000.0000.000
11A353ARG10.8360.90013.7040.1400.1400.0000.0000.0000.000
12A354GLN0-0.051-0.02812.686-0.017-0.0170.0000.0000.0000.000
13A355VAL0-0.036-0.01910.3800.0090.0090.0000.0000.0000.000
14A356LEU0-0.0100.01013.6870.0280.0280.0000.0000.0000.000
15A357GLY00.0520.03616.7360.0200.0200.0000.0000.0000.000
16A358ALA0-0.035-0.02219.2300.0030.0030.0000.0000.0000.000
17A359PRO00.0410.00522.1240.0010.0010.0000.0000.0000.000
18A360SER00.0400.02220.4570.0070.0070.0000.0000.0000.000
19A361PHE00.013-0.00117.5130.0020.0020.0000.0000.0000.000
20A362ARG10.8360.91220.9610.0610.0610.0000.0000.0000.000
21A363MET00.0300.03124.3980.0040.0040.0000.0000.0000.000
22A364LEU0-0.002-0.01017.7000.0030.0030.0000.0000.0000.000
23A365ALA0-0.005-0.01921.7610.0030.0030.0000.0000.0000.000
24A366TRP0-0.026-0.00522.8860.0030.0030.0000.0000.0000.000
25A367HIS00.0680.02824.6610.0040.0040.0000.0000.0000.000
26A368VAL0-0.034-0.01320.4380.0030.0030.0000.0000.0000.000
27A369LEU0-0.049-0.02523.7110.0040.0040.0000.0000.0000.000
28A370MET0-0.042-0.02126.3650.0030.0030.0000.0000.0000.000
29A371GLY0-0.016-0.01527.0270.0040.0040.0000.0000.0000.000
30A372ASN0-0.035-0.00727.3360.0060.0060.0000.0000.0000.000
31A373GLN0-0.057-0.01624.330-0.002-0.0020.0000.0000.0000.000
32A374VAL0-0.011-0.00919.422-0.001-0.0010.0000.0000.0000.000
33A375ILE0-0.021-0.01220.7210.0050.0050.0000.0000.0000.000
34A376TRP00.0330.01813.317-0.013-0.0130.0000.0000.0000.000
35A377LYS10.8280.91317.394-0.055-0.0550.0000.0000.0000.000
36A378SER00.0700.02412.0710.0140.0140.0000.0000.0000.000
37A379ARG10.9850.99613.231-0.384-0.3840.0000.0000.0000.000
38A380ASP-1-0.862-0.8907.9731.1851.1850.0000.0000.0000.000
39A381VAL00.0490.03110.471-0.079-0.0790.0000.0000.0000.000
40A382ASP-1-0.837-0.9316.0400.6690.6690.0000.0000.0000.000
41A383LEU0-0.082-0.0167.128-0.299-0.2990.0000.0000.0000.000
42A384VAL00.0350.0277.961-0.165-0.1650.0000.0000.0000.000
43A385GLN00.0090.0149.671-0.027-0.0270.0000.0000.0000.000
44A386SER0-0.035-0.0527.125-0.127-0.1270.0000.0000.0000.000
45A387ALA00.0270.0109.259-0.036-0.0360.0000.0000.0000.000
46A388PHE00.012-0.01112.139-0.005-0.0050.0000.0000.0000.000
47A389GLU-1-0.870-0.92011.327-0.101-0.1010.0000.0000.0000.000
48A390VAL00.0250.01611.3210.0030.0030.0000.0000.0000.000
49A391LEU0-0.0020.00414.0090.0190.0190.0000.0000.0000.000
50A392ARG10.8830.93816.1850.0900.0900.0000.0000.0000.000
51A393THR0-0.050-0.03116.4690.0140.0140.0000.0000.0000.000
52A394MET00.0000.00519.3030.0040.0040.0000.0000.0000.000
53A395LEU0-0.0120.01722.0330.0080.0080.0000.0000.0000.000
54A396PRO00.0150.01323.661-0.005-0.0050.0000.0000.0000.000
55A397VAL00.012-0.00722.6190.0020.0020.0000.0000.0000.000
56A398GLY00.0170.00624.6370.0030.0030.0000.0000.0000.000
57A399CYS0-0.0300.00726.2450.0030.0030.0000.0000.0000.000
58A400VAL0-0.040-0.00620.4530.0000.0000.0000.0000.0000.000
59A401ARG10.8860.94723.6590.0090.0090.0000.0000.0000.000
60A402ILE00.008-0.00517.5690.0000.0000.0000.0000.0000.000
61A403ILE00.0130.01220.8860.0050.0050.0000.0000.0000.000
62A404PRO00.0260.01115.4660.0030.0030.0000.0000.0000.000
63A405TYR0-0.029-0.05014.6650.0200.0200.0000.0000.0000.000
64A406SER00.0240.02517.4190.0080.0080.0000.0000.0000.000
65A407SER00.016-0.00820.6790.0100.0100.0000.0000.0000.000
66A408GLN0-0.073-0.04622.8710.0000.0000.0000.0000.0000.000
67A409TYR00.005-0.02224.8150.0000.0000.0000.0000.0000.000
68A410GLU-1-0.766-0.83925.3300.0400.0400.0000.0000.0000.000
69A411GLU-1-0.777-0.88626.9400.0140.0140.0000.0000.0000.000
70A412ALA00.0510.02628.0620.0000.0000.0000.0000.0000.000
71A413TYR00.007-0.00828.902-0.002-0.0020.0000.0000.0000.000
72A414ARG10.7860.86327.634-0.034-0.0340.0000.0000.0000.000
73A415CYS0-0.070-0.00923.3750.0020.0020.0000.0000.0000.000
74A416ASN00.0480.00824.3690.0030.0030.0000.0000.0000.000
75A417PHE0-0.0330.00818.165-0.006-0.0060.0000.0000.0000.000
76A418LEU00.0510.01720.5090.0060.0060.0000.0000.0000.000
77A419GLY00.0260.01416.959-0.004-0.0040.0000.0000.0000.000
78A420LEU0-0.048-0.02317.6060.0030.0030.0000.0000.0000.000
79A421SER00.0270.01417.4740.0230.0230.0000.0000.0000.000
80A422PRO00.006-0.01617.168-0.018-0.0180.0000.0000.0000.000
81A423HIS0-0.003-0.01419.665-0.022-0.0220.0000.0000.0000.000
82A424VAL0-0.0230.02022.023-0.008-0.0080.0000.0000.0000.000
83A425GLN0-0.012-0.01324.283-0.007-0.0070.0000.0000.0000.000
84A426ILE0-0.014-0.00523.391-0.001-0.0010.0000.0000.0000.000
85A427PRO00.0300.02427.836-0.001-0.0010.0000.0000.0000.000
86A428PRO00.0590.01431.111-0.002-0.0020.0000.0000.0000.000
87A429HIS0-0.019-0.02432.749-0.002-0.0020.0000.0000.0000.000
88A430VAL0-0.0010.00027.396-0.003-0.0030.0000.0000.0000.000
89A431LEU0-0.040-0.00927.698-0.003-0.0030.0000.0000.0000.000
90A432SER0-0.023-0.01729.981-0.003-0.0030.0000.0000.0000.000
91A433SER0-0.0140.01030.603-0.004-0.0040.0000.0000.0000.000
92A434GLU-1-0.920-0.95530.896-0.012-0.0120.0000.0000.0000.000
93A435PHE0-0.057-0.04430.750-0.004-0.0040.0000.0000.0000.000
94A436ALA0-0.036-0.01626.6570.0010.0010.0000.0000.0000.000
95A437VAL0-0.0020.03422.329-0.002-0.0020.0000.0000.0000.000
96A438ILE00.0320.01922.1220.0040.0040.0000.0000.0000.000
97A439VAL0-0.022-0.01416.671-0.008-0.0080.0000.0000.0000.000
98A440GLU-1-0.811-0.88518.2850.0770.0770.0000.0000.0000.000
99A441VAL0-0.044-0.02712.476-0.018-0.0180.0000.0000.0000.000
100A442HIS0-0.017-0.00915.9390.0470.0470.0000.0000.0000.000
101A443ALA0-0.066-0.03813.522-0.005-0.0050.0000.0000.0000.000
102A444ALA00.0250.01913.250-0.018-0.0180.0000.0000.0000.000
103A445ALA0-0.031-0.01014.9380.0190.0190.0000.0000.0000.000
104A459SER00.0250.0174.390-0.0410.089-0.001-0.013-0.1150.000
105A460LEU0-0.035-0.0424.392-0.428-0.363-0.001-0.028-0.0360.000
106A461SER00.0140.0117.2280.0960.0960.0000.0000.0000.000
107A462LYS10.9280.9797.189-0.744-0.7440.0000.0000.0000.000
108A463TYR0-0.105-0.0828.2340.0930.0930.0000.0000.0000.000
109A464GLU-1-0.860-0.92311.833-0.045-0.0450.0000.0000.0000.000
110A465PHE0-0.013-0.03010.8890.0200.0200.0000.0000.0000.000
111A466VAL00.0150.01116.721-0.008-0.0080.0000.0000.0000.000
112A467VAL0-0.0050.00019.5220.0060.0060.0000.0000.0000.000
113A468THR0-0.035-0.01921.9780.0010.0010.0000.0000.0000.000
114A469SER00.001-0.04225.3420.0000.0000.0000.0000.0000.000
115A470GLY00.0390.04528.0030.0000.0000.0000.0000.0000.000
116A471SER0-0.041-0.04431.704-0.003-0.0030.0000.0000.0000.000
117A472PRO00.0240.03232.2370.0020.0020.0000.0000.0000.000
118A473VAL00.0240.02435.1800.0010.0010.0000.0000.0000.000
119A474ALA0-0.037-0.01937.3680.0000.0000.0000.0000.0000.000
120A475ALA00.013-0.01033.201-0.001-0.0010.0000.0000.0000.000
121A476ASP-1-0.873-0.93229.278-0.036-0.0360.0000.0000.0000.000
122A477ARG10.8240.90532.4830.0260.0260.0000.0000.0000.000
123A478VAL00.0280.00332.518-0.004-0.0040.0000.0000.0000.000
124A479GLY0-0.0030.04933.026-0.003-0.0030.0000.0000.0000.000
125A480PRO00.0520.00829.8000.0000.0000.0000.0000.0000.000
126A481THR00.044-0.01731.194-0.004-0.0040.0000.0000.0000.000
127A482ILE0-0.017-0.00227.338-0.003-0.0030.0000.0000.0000.000
128A483LEU00.0660.04725.345-0.007-0.0070.0000.0000.0000.000
129A484ASN00.0140.01426.685-0.008-0.0080.0000.0000.0000.000
130A485LYS10.8430.92927.8050.0520.0520.0000.0000.0000.000
131A486ILE00.0410.01222.266-0.005-0.0050.0000.0000.0000.000
132A487GLU-1-0.794-0.87623.076-0.090-0.0900.0000.0000.0000.000
133A488ALA0-0.0130.00423.560-0.007-0.0070.0000.0000.0000.000
134A489ALA00.0090.00423.270-0.002-0.0020.0000.0000.0000.000
135A490LEU0-0.011-0.01517.894-0.010-0.0100.0000.0000.0000.000
136A491THR0-0.047-0.03519.769-0.010-0.0100.0000.0000.0000.000
137A492ASN0-0.0280.00421.943-0.005-0.0050.0000.0000.0000.000
138A493GLN00.0490.00116.380-0.014-0.0140.0000.0000.0000.000
139A494ASN0-0.023-0.01219.886-0.010-0.0100.0000.0000.0000.000
140A495LEU0-0.0580.01120.9450.0050.0050.0000.0000.0000.000
141A496SER00.0570.02219.071-0.017-0.0170.0000.0000.0000.000
142A497VAL00.0530.00314.0770.0020.0020.0000.0000.0000.000
143A498ASP-1-0.842-0.91517.430-0.139-0.1390.0000.0000.0000.000
144A499VAL0-0.042-0.01720.1470.0090.0090.0000.0000.0000.000
145A500VAL0-0.060-0.02718.5410.0070.0070.0000.0000.0000.000
146A501ASP-1-0.881-0.94217.220-0.176-0.1760.0000.0000.0000.000
147A502GLN0-0.020-0.01320.4090.0070.0070.0000.0000.0000.000
148A503ALA00.001-0.00523.9130.0090.0090.0000.0000.0000.000
149A504LEU0-0.002-0.00220.3190.0080.0080.0000.0000.0000.000
150A505VAL0-0.006-0.00422.9090.0080.0080.0000.0000.0000.000
151A506ALA00.0380.02125.3220.0070.0070.0000.0000.0000.000
152A507LEU0-0.020-0.00626.3240.0060.0060.0000.0000.0000.000
153A508LYS10.8310.89522.4830.0900.0900.0000.0000.0000.000
154A509GLU-1-0.912-0.95727.952-0.047-0.0470.0000.0000.0000.000
155A510GLU-1-0.858-0.91530.567-0.046-0.0460.0000.0000.0000.000
156A511TRP00.013-0.02630.7580.0050.0050.0000.0000.0000.000
157A512MET00.0330.01830.0630.0040.0040.0000.0000.0000.000
158A513ASN0-0.0040.00332.7750.0060.0060.0000.0000.0000.000
159A514LYS10.8520.93935.2520.0430.0430.0000.0000.0000.000
160A515VAL00.0080.02033.6010.0030.0030.0000.0000.0000.000
161A516LYS10.9090.95333.8910.0390.0390.0000.0000.0000.000
162A517VAL0-0.047-0.02238.5770.0020.0020.0000.0000.0000.000
163A518LEU00.0240.01039.2890.0020.0020.0000.0000.0000.000
164A519PHE00.0390.02039.8160.0020.0020.0000.0000.0000.000
165A520LYS10.9000.94541.7890.0220.0220.0000.0000.0000.000
166A521PHE0-0.003-0.01044.3310.0010.0010.0000.0000.0000.000
167A522THR0-0.047-0.02544.0090.0010.0010.0000.0000.0000.000
168A523LYS10.9360.98344.8710.0170.0170.0000.0000.0000.000
169A524VAL00.001-0.01747.9380.0000.0000.0000.0000.0000.000
170A525ASP-1-0.792-0.85951.409-0.009-0.0090.0000.0000.0000.000
171A526SER0-0.049-0.03553.038-0.001-0.0010.0000.0000.0000.000
172A527ARG10.8640.91852.2970.0130.0130.0000.0000.0000.000
173A528PRO0-0.0400.00653.752-0.001-0.0010.0000.0000.0000.000
174A529LYS10.9200.92348.7140.0120.0120.0000.0000.0000.000
175A530GLU-1-0.802-0.88949.739-0.014-0.0140.0000.0000.0000.000
176A531ASP-1-0.769-0.88250.672-0.016-0.0160.0000.0000.0000.000
177A532THR0-0.067-0.03045.606-0.001-0.0010.0000.0000.0000.000
178A533GLN00.017-0.00243.628-0.001-0.0010.0000.0000.0000.000
179A534LYS10.8360.90446.4080.0140.0140.0000.0000.0000.000
180A535LEU0-0.0050.00444.579-0.001-0.0010.0000.0000.0000.000
181A536LEU00.002-0.01540.484-0.001-0.0010.0000.0000.0000.000
182A537SER00.0180.00542.484-0.002-0.0020.0000.0000.0000.000
183A538ILE0-0.044-0.00744.102-0.001-0.0010.0000.0000.0000.000
184A539LEU0-0.053-0.01540.343-0.001-0.0010.0000.0000.0000.000
185A540GLY0-0.0020.00439.398-0.002-0.0020.0000.0000.0000.000
186A541ALA0-0.031-0.03438.013-0.002-0.0020.0000.0000.0000.000
187A542SER00.0160.01339.1940.0000.0000.0000.0000.0000.000
188A543GLU-1-0.855-0.91738.502-0.034-0.0340.0000.0000.0000.000
189A544GLU-1-0.828-0.90538.157-0.024-0.0240.0000.0000.0000.000
190A545ASP-1-0.708-0.87533.765-0.032-0.0320.0000.0000.0000.000
191A546ASN0-0.003-0.00434.578-0.003-0.0030.0000.0000.0000.000
192A547VAL0-0.0060.00335.8460.0000.0000.0000.0000.0000.000
193A548LYS10.8130.89434.7490.0260.0260.0000.0000.0000.000
194A549LEU00.0540.02829.4270.0010.0010.0000.0000.0000.000
195A550LEU0-0.040-0.02032.8320.0000.0000.0000.0000.0000.000
196A551LYS10.9590.98235.1650.0160.0160.0000.0000.0000.000
197A552PHE00.0100.02927.2090.0020.0020.0000.0000.0000.000
198A553TRP00.031-0.00226.8790.0000.0000.0000.0000.0000.000
199A554MET0-0.052-0.02231.7290.0000.0000.0000.0000.0000.000
200A555THR0-0.071-0.04631.4380.0010.0010.0000.0000.0000.000
201A556GLY0-0.019-0.00130.4180.0010.0010.0000.0000.0000.000
202A557LEU0-0.063-0.03731.145-0.003-0.0030.0000.0000.0000.000
203A558SER00.0040.01434.3260.0020.0020.0000.0000.0000.000