Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: MVVVZ

Calculation Name: 4F2H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F2H

Chain ID: A

ChEMBL ID:

UniProt ID: P32917

Base Structure: X-ray

Registration Date: 2023-06-21

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2235367.357704
FMO2-HF: Nuclear repulsion 2159702.07255
FMO2-HF: Total energy -75665.285155
FMO2-MP2: Total energy -75888.863039


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:584:SER)


Summations of interaction energy for fragment #1(A:584:SER)
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.
-23.674-23.33122.337-12.445-10.235-0.071
Interaction energy analysis for fragmet #1(A:584:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / 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].
3A586VAL00.0280.0052.588-5.727-2.8391.248-1.809-2.3260.011
4A587ASP-1-0.773-0.8841.888-20.071-23.83221.071-10.174-7.137-0.083
5A588SER0-0.044-0.0173.5121.1102.1770.019-0.445-0.6410.001
6A589ILE0-0.021-0.0075.4220.2380.2380.0000.0000.0000.000
7A590GLN00.0500.0136.7940.3390.3390.0000.0000.0000.000
8A591SER00.0520.0676.5680.1330.1330.0000.0000.0000.000
9A592VAL0-0.0140.0119.0790.2090.2090.0000.0000.0000.000
10A593LEU0-0.0010.00011.4280.0670.0670.0000.0000.0000.000
11A594THR0-0.002-0.03211.1010.0620.0620.0000.0000.0000.000
12A595THR0-0.003-0.00712.1570.0710.0710.0000.0000.0000.000
13A596ILE0-0.026-0.02114.5820.0720.0720.0000.0000.0000.000
14A597SER0-0.0290.00616.4850.0550.0550.0000.0000.0000.000
15A598SER00.038-0.01116.5060.0390.0390.0000.0000.0000.000
16A599ILE00.017-0.00417.7920.0410.0410.0000.0000.0000.000
17A600LEU0-0.022-0.00820.5000.0390.0390.0000.0000.0000.000
18A601SER0-0.024-0.02321.7510.0390.0390.0000.0000.0000.000
19A602LEU00.0100.01723.1520.0230.0230.0000.0000.0000.000
20A603LYS10.8720.91823.9080.2000.2000.0000.0000.0000.000
21A604ARG10.9310.98525.2200.1920.1920.0000.0000.0000.000
22A605GLU-1-0.853-0.90828.257-0.155-0.1550.0000.0000.0000.000
23A606LYS10.8620.93730.2570.1170.1170.0000.0000.0000.000
24A607PRO0-0.0080.00528.4800.0060.0060.0000.0000.0000.000
25A608ASP-1-0.808-0.88931.753-0.116-0.1160.0000.0000.0000.000
26A609ASN0-0.054-0.05132.9130.0040.0040.0000.0000.0000.000
27A610LEU00.0010.00525.810-0.010-0.0100.0000.0000.0000.000
28A611ALA00.0180.01628.7150.0120.0120.0000.0000.0000.000
29A612ILE0-0.020-0.02023.557-0.020-0.0200.0000.0000.0000.000
30A613ILE0-0.009-0.00524.8800.0170.0170.0000.0000.0000.000
31A614LEU0-0.007-0.00821.504-0.039-0.0390.0000.0000.0000.000
32A615GLN00.003-0.01721.592-0.009-0.0090.0000.0000.0000.000
33A616ILE00.0210.00020.187-0.060-0.0600.0000.0000.0000.000
34A617ASP-1-0.831-0.90818.827-0.392-0.3920.0000.0000.0000.000
35A618PHE00.1160.01519.307-0.034-0.0340.0000.0000.0000.000
36A619THR0-0.092-0.03020.5860.0190.0190.0000.0000.0000.000
37A620LYS10.8680.93315.4420.6320.6320.0000.0000.0000.000
38A621LEU0-0.081-0.02115.066-0.077-0.0770.0000.0000.0000.000
39A622LYS10.8320.89511.4490.2910.2910.0000.0000.0000.000
40A623GLU-1-0.789-0.84914.065-0.232-0.2320.0000.0000.0000.000
41A624GLU-1-0.734-0.87417.688-0.283-0.2830.0000.0000.0000.000
42A625ASP-1-0.893-0.93119.579-0.162-0.1620.0000.0000.0000.000
43A626SER00.030-0.01316.521-0.018-0.0180.0000.0000.0000.000
44A627LEU0-0.102-0.06218.743-0.025-0.0250.0000.0000.0000.000
45A628ILE00.0090.00322.0780.0120.0120.0000.0000.0000.000
46A629VAL00.0430.02818.9990.0130.0130.0000.0000.0000.000
47A630VAL00.0120.02520.4700.0010.0010.0000.0000.0000.000
48A631TYR0-0.044-0.01022.6490.0070.0070.0000.0000.0000.000
49A632ASN00.0370.00424.4910.0130.0130.0000.0000.0000.000
50A633SER0-0.020-0.03522.0640.0050.0050.0000.0000.0000.000
51A634LEU0-0.036-0.01724.4540.0060.0060.0000.0000.0000.000
52A635LYS10.8640.92026.9630.1410.1410.0000.0000.0000.000
53A636ALA00.0330.04526.6460.0100.0100.0000.0000.0000.000
54A637LEU00.0370.00324.4720.0100.0100.0000.0000.0000.000
55A638THR0-0.120-0.07428.5970.0080.0080.0000.0000.0000.000
56A639ILE0-0.022-0.00430.9380.0100.0100.0000.0000.0000.000
57A640LYS10.8650.96129.9330.1470.1470.0000.0000.0000.000
58A641PHE0-0.029-0.03128.2990.0040.0040.0000.0000.0000.000
59A642ALA00.0900.04633.128-0.006-0.0060.0000.0000.0000.000
60A643ARG10.8130.88535.7890.1260.1260.0000.0000.0000.000
61A644LEU00.0390.04828.313-0.007-0.0070.0000.0000.0000.000
62A645GLN0-0.047-0.02831.5470.0050.0050.0000.0000.0000.000
63A646PHE0-0.0070.00228.418-0.018-0.0180.0000.0000.0000.000
64A647CYS0-0.045-0.02828.0620.0130.0130.0000.0000.0000.000
65A648PHE00.0420.04424.916-0.024-0.0240.0000.0000.0000.000
66A649VAL00.0160.02525.5930.0200.0200.0000.0000.0000.000
67A650ASP-1-0.682-0.84825.393-0.302-0.3020.0000.0000.0000.000
68A651ARG10.8840.93021.8550.3230.3230.0000.0000.0000.000
69A652ASN0-0.103-0.05323.929-0.024-0.0240.0000.0000.0000.000
70A653ASN00.0180.00326.513-0.002-0.0020.0000.0000.0000.000
71A654TYR0-0.003-0.00427.6850.0170.0170.0000.0000.0000.000
72A655VAL00.0050.00229.604-0.012-0.0120.0000.0000.0000.000
73A656LEU0-0.052-0.02027.5650.0140.0140.0000.0000.0000.000
74A657ASP-1-0.783-0.89531.300-0.151-0.1510.0000.0000.0000.000
75A658TYR0-0.013-0.01431.545-0.016-0.0160.0000.0000.0000.000
76A659GLY00.0350.04033.1630.0140.0140.0000.0000.0000.000
77A660SER00.032-0.00333.643-0.011-0.0110.0000.0000.0000.000
78A661VAL00.0440.01629.4880.0050.0050.0000.0000.0000.000
79A662LEU0-0.0100.00632.5540.0060.0060.0000.0000.0000.000
80A663HIS00.0120.00135.2880.0020.0020.0000.0000.0000.000
81A664LYS10.7900.88434.9980.1550.1550.0000.0000.0000.000
82A665ILE0-0.0190.00429.721-0.006-0.0060.0000.0000.0000.000
83A666ASP-1-0.806-0.88333.583-0.113-0.1130.0000.0000.0000.000
84A667SER0-0.020-0.00233.7290.0060.0060.0000.0000.0000.000
85A668LEU00.0200.01326.127-0.010-0.0100.0000.0000.0000.000
86A669ASP-1-0.827-0.92729.463-0.129-0.1290.0000.0000.0000.000
87A670SER0-0.030-0.01031.425-0.008-0.0080.0000.0000.0000.000
88A671ILE0-0.014-0.00625.424-0.007-0.0070.0000.0000.0000.000
89A672SER0-0.040-0.02127.415-0.017-0.0170.0000.0000.0000.000
90A673ASN00.047-0.00428.466-0.005-0.0050.0000.0000.0000.000
91A674LEU0-0.075-0.02728.9620.0000.0000.0000.0000.0000.000
92A675LYS10.8330.91024.3920.2080.2080.0000.0000.0000.000
93A676SER0-0.059-0.02828.428-0.005-0.0050.0000.0000.0000.000
94A677LYS10.9070.97631.5240.1720.1720.0000.0000.0000.000
95A678SER00.0200.01332.392-0.011-0.0110.0000.0000.0000.000
96A679SER0-0.042-0.05933.3690.0070.0070.0000.0000.0000.000
97A680SER00.0150.00735.017-0.002-0.0020.0000.0000.0000.000
98A681THR00.0030.00834.9380.0060.0060.0000.0000.0000.000
99A682GLN0-0.030-0.00730.239-0.019-0.0190.0000.0000.0000.000
100A683PHE0-0.0020.00227.1430.0120.0120.0000.0000.0000.000
101A684SER00.0400.01730.172-0.002-0.0020.0000.0000.0000.000
102A685PRO00.0300.01528.5470.0130.0130.0000.0000.0000.000
103A686ILE00.0620.00731.1570.0100.0100.0000.0000.0000.000
104A687TRP00.0140.04031.9180.0060.0060.0000.0000.0000.000
105A688LEU00.0480.03329.6020.0090.0090.0000.0000.0000.000
106A689LYS10.8640.92733.6570.1600.1600.0000.0000.0000.000
107A690ASN0-0.003-0.01035.4710.0080.0080.0000.0000.0000.000
108A691THR0-0.068-0.02836.1950.0100.0100.0000.0000.0000.000
109A692LEU0-0.078-0.05233.4890.0040.0040.0000.0000.0000.000
110A693TYR0-0.101-0.07034.2760.0010.0010.0000.0000.0000.000
111A694PRO00.0240.01339.079-0.001-0.0010.0000.0000.0000.000
112A695GLU-1-0.908-0.94742.347-0.097-0.0970.0000.0000.0000.000
113A696ASN0-0.071-0.02640.357-0.004-0.0040.0000.0000.0000.000
114A697ILE00.003-0.00835.663-0.002-0.0020.0000.0000.0000.000
115A698HIS00.0030.00638.9270.0020.0020.0000.0000.0000.000
116A699GLU-1-0.793-0.85236.137-0.137-0.1370.0000.0000.0000.000
117A700HIS10.8450.90833.5640.1230.1230.0000.0000.0000.000
118A701LEU00.0150.01631.1690.0000.0000.0000.0000.0000.000
119A702GLY0-0.012-0.00628.099-0.004-0.0040.0000.0000.0000.000
120A703ILE0-0.028-0.01825.7000.0050.0050.0000.0000.0000.000
121A704VAL00.0340.01621.180-0.020-0.0200.0000.0000.0000.000
122A705ALA0-0.0090.00721.7770.0160.0160.0000.0000.0000.000
123A706VAL00.0220.01716.908-0.053-0.0530.0000.0000.0000.000
124A707SER00.004-0.00617.5550.0460.0460.0000.0000.0000.000
125A708ASN00.0610.04014.992-0.052-0.0520.0000.0000.0000.000
126A709SER0-0.049-0.01015.998-0.014-0.0140.0000.0000.0000.000
127A710ASN00.028-0.01817.238-0.072-0.0720.0000.0000.0000.000
128A711MET00.0160.02315.4110.0570.0570.0000.0000.0000.000
129A712GLU-1-0.886-0.93118.623-0.349-0.3490.0000.0000.0000.000
130A713ALA00.0490.01422.2150.0120.0120.0000.0000.0000.000
131A714LYS10.9050.94823.7690.2590.2590.0000.0000.0000.000
132A715LYS10.8730.94223.9890.3320.3320.0000.0000.0000.000
133A716SER00.0410.04619.6550.0010.0010.0000.0000.0000.000
134A717ILE00.0570.01422.1100.0230.0230.0000.0000.0000.000
135A718LEU0-0.0100.01216.8730.0280.0280.0000.0000.0000.000
136A719PHE00.008-0.00619.0430.0130.0130.0000.0000.0000.000
137A720GLN0-0.035-0.00922.7760.0540.0540.0000.0000.0000.000
138A721ASP-1-0.785-0.86425.595-0.256-0.2560.0000.0000.0000.000
139A722TYR0-0.004-0.03924.2620.0280.0280.0000.0000.0000.000
140A723ARG10.9170.91928.8820.2430.2430.0000.0000.0000.000
141A724CYS0-0.0670.01231.1240.0110.0110.0000.0000.0000.000
142A725PHE00.044-0.00630.9090.0100.0100.0000.0000.0000.000
143A726THR0-0.119-0.05632.502-0.002-0.0020.0000.0000.0000.000
144A727SER00.0110.01133.6170.0060.0060.0000.0000.0000.000
145A728PHE00.0420.00536.297-0.001-0.0010.0000.0000.0000.000
146A729GLY00.009-0.00337.9710.0010.0010.0000.0000.0000.000
147A730ARG10.7870.90231.4560.1540.1540.0000.0000.0000.000
148A731ARG10.9830.97830.1300.1760.1760.0000.0000.0000.000
149A732ARG10.7740.86224.1570.3080.3080.0000.0000.0000.000
150A733PRO00.0080.01827.6810.0150.0150.0000.0000.0000.000
151A734ASN00.0010.00726.798-0.024-0.0240.0000.0000.0000.000
152A735GLU-1-0.820-0.91923.652-0.315-0.3150.0000.0000.0000.000
153A736LEU00.0140.00718.364-0.010-0.0100.0000.0000.0000.000
154A737LYS10.8470.93219.0800.4270.4270.0000.0000.0000.000
155A738ILE00.010-0.00413.980-0.053-0.0530.0000.0000.0000.000
156A739LYS10.8440.91412.2231.3151.3150.0000.0000.0000.000
157A740VAL0-0.031-0.01611.921-0.185-0.1850.0000.0000.0000.000
158A741GLY0-0.006-0.0119.2490.1590.1590.0000.0000.0000.000
159A742TYR0-0.025-0.0304.616-0.251-0.102-0.001-0.017-0.1310.000
160A743LEU0-0.038-0.0137.7710.4270.4270.0000.0000.0000.000
161A744ASN0-0.025-0.0117.049-0.433-0.4330.0000.0000.0000.000
162A745VAL0-0.053-0.0339.5400.2370.2370.0000.0000.0000.000
163A746ASP-1-0.792-0.85912.567-0.786-0.7860.0000.0000.0000.000
164A747TYR0-0.032-0.04114.1780.0920.0920.0000.0000.0000.000
165A748SER0-0.002-0.02915.3510.0390.0390.0000.0000.0000.000
166A749ASP-1-0.874-0.89317.656-0.385-0.3850.0000.0000.0000.000
167A750LYS10.7920.86420.3180.4730.4730.0000.0000.0000.000
168A751ILE0-0.068-0.03117.4870.0180.0180.0000.0000.0000.000
169A752ASP-1-0.767-0.87619.477-0.402-0.4020.0000.0000.0000.000
170A753GLU-1-0.959-0.96216.902-0.347-0.3470.0000.0000.0000.000
171A754LEU0-0.038-0.01713.9100.0350.0350.0000.0000.0000.000
172A755VAL0-0.012-0.00512.627-0.054-0.0540.0000.0000.0000.000
173A756GLU-1-0.813-0.9108.901-2.186-2.1860.0000.0000.0000.000
174A757ALA00.0130.0129.037-0.126-0.1260.0000.0000.0000.000
175A758SER00.0300.0147.0170.0070.0070.0000.0000.0000.000
176A759SER00.0170.0019.0200.2100.2100.0000.0000.0000.000
177A760TRP00.0110.00312.400-0.023-0.0230.0000.0000.0000.000
178A761THR00.0320.00814.4890.0210.0210.0000.0000.0000.000
179A762PHE00.0500.02112.0970.0200.0200.0000.0000.0000.000
180A763VAL00.0070.02013.7350.0550.0550.0000.0000.0000.000
181A764LEU00.0040.00715.9520.0540.0540.0000.0000.0000.000
182A765GLU-1-0.792-0.87617.703-0.159-0.1590.0000.0000.0000.000
183A766THR0-0.017-0.02615.8690.0470.0470.0000.0000.0000.000
184A767LEU0-0.041-0.00918.4470.0350.0350.0000.0000.0000.000
185A768CYS0-0.040-0.02720.8970.0310.0310.0000.0000.0000.000
186A769TYR00.007-0.00718.7240.0310.0310.0000.0000.0000.000
187A770SER0-0.061-0.02620.7290.0200.0200.0000.0000.0000.000
188A771PHE0-0.051-0.03823.2600.0150.0150.0000.0000.0000.000
189A772GLY0-0.016-0.00326.0950.0120.0120.0000.0000.0000.000
190A773LEU0-0.043-0.00626.4460.0110.0110.0000.0000.0000.000
191A774SER00.0040.00824.3450.0060.0060.0000.0000.0000.000