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: 9GN62

Calculation Name: 3V42-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2321134.462228
FMO2-HF: Nuclear repulsion 2241050.161509
FMO2-HF: Total energy -80084.30072
FMO2-MP2: Total energy -80316.762487


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:342:ACE )


Summations of interaction energy for fragment #1(A:342: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.
2.7284.3940.047-0.791-0.923-0.001
Interaction energy analysis for fragmet #1(A:342:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.013
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].
3A344PRO 00.0060.0033.473-0.1831.2870.042-0.746-0.766-0.001
4A345VAL 00.0340.0153.6790.1590.3550.005-0.045-0.1570.000
5A346PHE 0-0.004-0.0216.425-0.155-0.1550.0000.0000.0000.000
6A347LYS 10.9150.9496.8251.2181.2180.0000.0000.0000.000
7A348SER 00.0510.02110.5380.0380.0380.0000.0000.0000.000
8A349LEU 00.0890.04114.136-0.001-0.0010.0000.0000.0000.000
9A350ARG 10.8400.93017.1600.1220.1220.0000.0000.0000.000
10A351HIS 00.0120.02410.2030.0120.0120.0000.0000.0000.000
11A352MET 00.0210.01914.0610.0050.0050.0000.0000.0000.000
12A353ARG 10.9430.97215.6450.0850.0850.0000.0000.0000.000
13A354GLN 0-0.075-0.03917.131-0.016-0.0160.0000.0000.0000.000
14A355VAL 0-0.025-0.01513.6320.0020.0020.0000.0000.0000.000
15A356LEU 0-0.0090.01016.7270.0130.0130.0000.0000.0000.000
16A357GLY 00.0540.04119.1460.0080.0080.0000.0000.0000.000
17A358ALA 0-0.036-0.02822.2200.0070.0070.0000.0000.0000.000
18A359PRO 00.0330.00524.8720.0040.0040.0000.0000.0000.000
19A360SER 00.0490.02822.5520.0070.0070.0000.0000.0000.000
20A361PHE 00.0170.00419.0200.0050.0050.0000.0000.0000.000
21A362ARG 10.8480.91722.3920.0290.0290.0000.0000.0000.000
22A363MET 00.0540.03925.7550.0060.0060.0000.0000.0000.000
23A364LEU 0-0.005-0.00918.5920.0060.0060.0000.0000.0000.000
24A365ALA 00.005-0.02222.7910.0070.0070.0000.0000.0000.000
25A366TRP 0-0.040-0.00423.7830.0050.0050.0000.0000.0000.000
26A367HIS 00.0690.03625.3110.0070.0070.0000.0000.0000.000
27A368VAL 0-0.039-0.01321.1440.0060.0060.0000.0000.0000.000
28A369LEU 0-0.063-0.03024.1810.0040.0040.0000.0000.0000.000
29A370MET 0-0.031-0.01726.8540.0020.0020.0000.0000.0000.000
30A371GLY 0-0.018-0.01627.1730.0020.0020.0000.0000.0000.000
31A372ASN 0-0.042-0.02127.8140.0060.0060.0000.0000.0000.000
32A373GLN 0-0.050-0.00124.620-0.002-0.0020.0000.0000.0000.000
33A374VAL 0-0.023-0.01219.792-0.005-0.0050.0000.0000.0000.000
34A375ILE 0-0.019-0.01120.8560.0140.0140.0000.0000.0000.000
35A376TRP 00.0320.01614.052-0.011-0.0110.0000.0000.0000.000
36A377LYS 10.8770.96317.517-0.046-0.0460.0000.0000.0000.000
37A378SER 00.0760.03012.558-0.013-0.0130.0000.0000.0000.000
38A379ARG 10.9781.00412.987-0.129-0.1290.0000.0000.0000.000
39A380ASP -1-0.868-0.9217.9810.5420.5420.0000.0000.0000.000
40A381VAL 00.0270.0249.291-0.034-0.0340.0000.0000.0000.000
41A382ASP -1-0.828-0.9285.2151.7771.7770.0000.0000.0000.000
42A383LEU 0-0.074-0.0147.276-0.151-0.1510.0000.0000.0000.000
43A384VAL 00.0270.0268.320-0.093-0.0930.0000.0000.0000.000
44A385GLN 00.0260.0238.983-0.063-0.0630.0000.0000.0000.000
45A386SER 0-0.046-0.0497.245-0.113-0.1130.0000.0000.0000.000
46A387ALA 00.0320.0139.342-0.069-0.0690.0000.0000.0000.000
47A388PHE 00.000-0.01812.620-0.027-0.0270.0000.0000.0000.000
48A389GLU -1-0.938-0.96510.8360.1490.1490.0000.0000.0000.000
49A390VAL 00.0170.01011.911-0.029-0.0290.0000.0000.0000.000
50A391LEU 0-0.003-0.00514.449-0.009-0.0090.0000.0000.0000.000
51A392ARG 10.9480.98915.942-0.120-0.1200.0000.0000.0000.000
52A393THR 0-0.075-0.03716.746-0.006-0.0060.0000.0000.0000.000
53A394MET 0-0.001-0.00819.511-0.010-0.0100.0000.0000.0000.000
54A395LEU 0-0.0150.00922.274-0.001-0.0010.0000.0000.0000.000
55A396PRO 00.0040.01223.6340.0020.0020.0000.0000.0000.000
56A397VAL 00.026-0.00822.1620.0040.0040.0000.0000.0000.000
57A398GLY 00.0070.00424.2290.0060.0060.0000.0000.0000.000
58A399CYS 0-0.0400.00026.082-0.001-0.0010.0000.0000.0000.000
59A400VAL 0-0.030-0.00119.9140.0010.0010.0000.0000.0000.000
60A401ARG 10.9060.95423.261-0.055-0.0550.0000.0000.0000.000
61A402ILE 00.0080.00217.005-0.005-0.0050.0000.0000.0000.000
62A403ILE 00.0140.00920.1270.0090.0090.0000.0000.0000.000
63A404PRO 00.0210.00414.730-0.007-0.0070.0000.0000.0000.000
64A405TYR 0-0.043-0.07514.5210.0200.0200.0000.0000.0000.000
65A406SER 00.0330.03416.6690.0050.0050.0000.0000.0000.000
66A407SER 0-0.010-0.01820.0940.0010.0010.0000.0000.0000.000
67A408GLN 0-0.027-0.01622.168-0.013-0.0130.0000.0000.0000.000
68A409TYR 0-0.004-0.03124.3010.0060.0060.0000.0000.0000.000
69A410GLU -1-0.787-0.87424.5850.0900.0900.0000.0000.0000.000
70A411GLU -1-0.796-0.91326.6530.0460.0460.0000.0000.0000.000
71A412ALA 00.0430.01727.8490.0040.0040.0000.0000.0000.000
72A413TYR 0-0.008-0.01628.5750.0020.0020.0000.0000.0000.000
73A414ARG 10.7970.88226.894-0.084-0.0840.0000.0000.0000.000
74A415CYS 0-0.054-0.00222.9330.0080.0080.0000.0000.0000.000
75A416ASN 00.0440.01124.1270.0010.0010.0000.0000.0000.000
76A417PHE 0-0.0310.01118.400-0.005-0.0050.0000.0000.0000.000
77A418LEU 00.0620.01320.2310.0110.0110.0000.0000.0000.000
78A419GLY 00.0230.01716.603-0.007-0.0070.0000.0000.0000.000
79A420LEU 0-0.049-0.02717.514-0.002-0.0020.0000.0000.0000.000
80A421SER 00.0440.02017.3590.0120.0120.0000.0000.0000.000
81A422PRO 00.014-0.00617.022-0.017-0.0170.0000.0000.0000.000
82A423HIS 00.003-0.02419.607-0.018-0.0180.0000.0000.0000.000
83A424VAL 0-0.0130.03021.669-0.006-0.0060.0000.0000.0000.000
84A425GLN 0-0.003-0.01624.138-0.009-0.0090.0000.0000.0000.000
85A426ILE 0-0.017-0.00223.7560.0030.0030.0000.0000.0000.000
86A427PRO 00.0410.03427.955-0.004-0.0040.0000.0000.0000.000
87A428PRO 00.0440.00331.350-0.001-0.0010.0000.0000.0000.000
88A429HIS 0-0.016-0.01732.988-0.004-0.0040.0000.0000.0000.000
89A430VAL 00.0000.00527.532-0.002-0.0020.0000.0000.0000.000
90A431LEU 0-0.037-0.00928.087-0.002-0.0020.0000.0000.0000.000
91A432SER 0-0.029-0.01030.498-0.004-0.0040.0000.0000.0000.000
92A433SER 00.0110.02431.174-0.004-0.0040.0000.0000.0000.000
93A434GLU -1-0.881-0.94631.5240.0090.0090.0000.0000.0000.000
94A435PHE 0-0.087-0.06331.194-0.002-0.0020.0000.0000.0000.000
95A436ALA 0-0.025-0.01226.9300.0050.0050.0000.0000.0000.000
96A437VAL 0-0.0140.02422.861-0.005-0.0050.0000.0000.0000.000
97A438ILE 00.0310.01422.5710.0100.0100.0000.0000.0000.000
98A439VAL 0-0.026-0.01717.556-0.011-0.0110.0000.0000.0000.000
99A440GLU -1-0.910-0.96218.9640.0580.0580.0000.0000.0000.000
100A441VAL 0-0.043-0.02113.596-0.016-0.0160.0000.0000.0000.000
101A442HIS 00.0020.00716.9160.0210.0210.0000.0000.0000.000
102A443ALA 0-0.057-0.03715.517-0.016-0.0160.0000.0000.0000.000
103A444ALA 00.0430.02116.2090.0030.0030.0000.0000.0000.000
104A445ALA 0-0.016-0.01018.2290.0040.0040.0000.0000.0000.000
105A446NME 0-0.0090.00319.439-0.015-0.0150.0000.0000.0000.000
106A458ACE 00.0390.00912.8780.0160.0160.0000.0000.0000.000
107A459SER 0-0.063-0.0449.922-0.027-0.0270.0000.0000.0000.000
108A460LEU 0-0.011-0.0088.796-0.099-0.0990.0000.0000.0000.000
109A461SER 00.0490.02711.6910.0420.0420.0000.0000.0000.000
110A462LYS 10.9330.9929.0260.1390.1390.0000.0000.0000.000
111A463TYR 0-0.104-0.0628.9460.0210.0210.0000.0000.0000.000
112A464GLU -1-0.905-0.93814.748-0.073-0.0730.0000.0000.0000.000
113A465PHE 0-0.020-0.03112.8840.0180.0180.0000.0000.0000.000
114A466VAL 00.0080.00718.758-0.005-0.0050.0000.0000.0000.000
115A467VAL 00.0020.00020.7030.0100.0100.0000.0000.0000.000
116A468THR 0-0.032-0.01323.128-0.003-0.0030.0000.0000.0000.000
117A469SER 00.002-0.03226.2030.0040.0040.0000.0000.0000.000
118A470GLY 00.0380.04628.875-0.003-0.0030.0000.0000.0000.000
119A471SER 0-0.048-0.04632.530-0.002-0.0020.0000.0000.0000.000
120A472PRO 00.0200.03433.1600.0010.0010.0000.0000.0000.000
121A473VAL 00.025-0.00536.1610.0010.0010.0000.0000.0000.000
122A474ALA 0-0.007-0.04235.655-0.001-0.0010.0000.0000.0000.000
123A475ALA 00.0040.00032.398-0.002-0.0020.0000.0000.0000.000
124A476ASP -1-0.917-0.94530.969-0.010-0.0100.0000.0000.0000.000
125A477ARG 10.9070.98232.9860.0040.0040.0000.0000.0000.000
126A478VAL 00.0170.00433.637-0.002-0.0020.0000.0000.0000.000
127A479GLY 0-0.0320.03034.091-0.002-0.0020.0000.0000.0000.000
128A480PRO 00.0630.01730.6370.0000.0000.0000.0000.0000.000
129A481THR 00.041-0.01932.138-0.003-0.0030.0000.0000.0000.000
130A482ILE 0-0.019-0.00528.097-0.004-0.0040.0000.0000.0000.000
131A483LEU 00.0620.04226.303-0.004-0.0040.0000.0000.0000.000
132A484ASN 00.0380.03328.211-0.006-0.0060.0000.0000.0000.000
133A485LYS 10.9150.95829.8970.0160.0160.0000.0000.0000.000
134A486ILE 00.0440.01723.621-0.005-0.0050.0000.0000.0000.000
135A487GLU -1-0.889-0.93925.289-0.048-0.0480.0000.0000.0000.000
136A488ALA 0-0.006-0.01226.335-0.008-0.0080.0000.0000.0000.000
137A489ALA 00.0130.00225.637-0.005-0.0050.0000.0000.0000.000
138A490LEU 0-0.040-0.02520.519-0.010-0.0100.0000.0000.0000.000
139A491THR 0-0.045-0.01423.312-0.012-0.0120.0000.0000.0000.000
140A492ASN 0-0.046-0.01325.856-0.007-0.0070.0000.0000.0000.000
141A493GLN 00.046-0.01721.575-0.010-0.0100.0000.0000.0000.000
142A494ASN 0-0.016-0.00424.639-0.014-0.0140.0000.0000.0000.000
143A495LEU 0-0.0370.03024.4980.0040.0040.0000.0000.0000.000
144A496SER 00.0500.01522.923-0.013-0.0130.0000.0000.0000.000
145A497VAL 00.063-0.00217.0560.0030.0030.0000.0000.0000.000
146A498ASP -1-0.792-0.89220.354-0.080-0.0800.0000.0000.0000.000
147A499VAL 0-0.095-0.02722.3440.0110.0110.0000.0000.0000.000
148A500VAL 0-0.063-0.03520.9550.0080.0080.0000.0000.0000.000
149A501ASP -1-0.878-0.93318.784-0.079-0.0790.0000.0000.0000.000
150A502GLN 0-0.020-0.01821.6580.0090.0090.0000.0000.0000.000
151A503ALA 00.011-0.00325.0560.0070.0070.0000.0000.0000.000
152A504LEU 0-0.008-0.00121.0980.0060.0060.0000.0000.0000.000
153A505VAL 0-0.025-0.01323.3880.0080.0080.0000.0000.0000.000
154A506ALA 00.0430.01925.6430.0050.0050.0000.0000.0000.000
155A507LEU 0-0.014-0.00127.6040.0030.0030.0000.0000.0000.000
156A508LYS 10.8540.92822.594-0.008-0.0080.0000.0000.0000.000
157A509GLU -1-0.931-0.96528.289-0.001-0.0010.0000.0000.0000.000
158A510GLU -1-0.924-0.95230.747-0.011-0.0110.0000.0000.0000.000
159A511TRP 00.024-0.02131.2140.0030.0030.0000.0000.0000.000
160A512MET 00.010-0.00530.2240.0030.0030.0000.0000.0000.000
161A513ASN 0-0.050-0.02032.8730.0020.0020.0000.0000.0000.000
162A514LYS 10.8780.96136.0340.0070.0070.0000.0000.0000.000
163A515VAL 00.0170.02233.6600.0010.0010.0000.0000.0000.000
164A516LYS 10.9530.98233.544-0.012-0.0120.0000.0000.0000.000
165A517VAL 0-0.041-0.01538.5100.0000.0000.0000.0000.0000.000
166A518LEU 00.0130.00439.5230.0000.0000.0000.0000.0000.000
167A519PHE 00.0420.01839.7410.0010.0010.0000.0000.0000.000
168A520LYS 10.9030.94541.694-0.007-0.0070.0000.0000.0000.000
169A521PHE 00.0160.00644.1940.0000.0000.0000.0000.0000.000
170A522THR 0-0.030-0.02444.0610.0000.0000.0000.0000.0000.000
171A523LYS 10.9551.00144.785-0.012-0.0120.0000.0000.0000.000
172A524VAL 0-0.019-0.02947.745-0.001-0.0010.0000.0000.0000.000
173A525ASP -1-0.869-0.90750.3410.0100.0100.0000.0000.0000.000
174A526SER 00.0360.02052.0220.0000.0000.0000.0000.0000.000
175A527ARG 10.8830.95449.795-0.006-0.0060.0000.0000.0000.000
176A528PRO 0-0.025-0.00554.3320.0000.0000.0000.0000.0000.000
177A529LYS 10.9050.92250.624-0.008-0.0080.0000.0000.0000.000
178A530GLU -1-0.872-0.93250.0520.0020.0020.0000.0000.0000.000
179A531ASP -1-0.851-0.94551.1050.0020.0020.0000.0000.0000.000
180A532THR 0-0.074-0.03245.8730.0000.0000.0000.0000.0000.000
181A533GLN 00.0280.00844.203-0.001-0.0010.0000.0000.0000.000
182A534LYS 10.8980.94746.959-0.002-0.0020.0000.0000.0000.000
183A535LEU 00.0060.00844.887-0.001-0.0010.0000.0000.0000.000
184A536LEU 0-0.006-0.01541.294-0.001-0.0010.0000.0000.0000.000
185A537SER 0-0.028-0.00943.074-0.001-0.0010.0000.0000.0000.000
186A538ILE 00.0210.01644.814-0.001-0.0010.0000.0000.0000.000
187A539LEU 0-0.066-0.02440.830-0.001-0.0010.0000.0000.0000.000
188A540GLY 00.0020.00540.011-0.001-0.0010.0000.0000.0000.000
189A541ALA 0-0.041-0.04238.508-0.001-0.0010.0000.0000.0000.000
190A542SER 0-0.030-0.00739.8280.0010.0010.0000.0000.0000.000
191A543GLU -1-0.860-0.92539.460-0.009-0.0090.0000.0000.0000.000
192A544GLU -1-0.934-0.96938.8010.0010.0010.0000.0000.0000.000
193A545ASP -1-0.744-0.89134.5640.0000.0000.0000.0000.0000.000
194A546ASN 0-0.006-0.01035.3280.0010.0010.0000.0000.0000.000
195A547VAL 00.0010.00536.4330.0020.0020.0000.0000.0000.000
196A548LYS 10.9440.96935.194-0.008-0.0080.0000.0000.0000.000
197A549LEU 00.0590.03329.9830.0020.0020.0000.0000.0000.000
198A550LEU 0-0.051-0.02833.0940.0020.0020.0000.0000.0000.000
199A551LYS 10.9540.98635.364-0.015-0.0150.0000.0000.0000.000
200A552PHE 00.0010.02227.4820.0020.0020.0000.0000.0000.000
201A553TRP 00.033-0.00227.3660.0030.0030.0000.0000.0000.000
202A554MET 0-0.040-0.01231.7630.0010.0010.0000.0000.0000.000
203A555THR 0-0.079-0.04531.2750.0030.0030.0000.0000.0000.000
204A556GLY 0-0.0100.00630.1390.0040.0040.0000.0000.0000.000
205A557LEU 0-0.070-0.04530.815-0.002-0.0020.0000.0000.0000.000
206A558SER 0-0.004-0.00533.9250.0010.0010.0000.0000.0000.000
207A559NME 00.0130.02036.636-0.002-0.0020.0000.0000.0000.000