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: 7222K

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2236307.987663
FMO2-HF: Nuclear repulsion 2160641.794544
FMO2-HF: Total energy -75666.19312
FMO2-MP2: Total energy -75889.661385


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.
-21.868-20.63217.414-10.363-8.285-0.08
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 : 0.010 / q_NPA : -0.004
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].
3A586VAL00.0300.0092.637-4.162-1.7170.285-1.232-1.4980.005
4A587ASP-1-0.754-0.8731.838-21.310-23.30917.127-8.732-6.395-0.086
5A588SER0-0.040-0.0033.9531.7452.5350.002-0.399-0.3920.001
6A589ILE0-0.018-0.0145.8290.4270.4270.0000.0000.0000.000
7A590GLN00.0320.0067.2400.4380.4380.0000.0000.0000.000
8A591SER00.0270.0377.0580.1260.1260.0000.0000.0000.000
9A592VAL0-0.0100.0089.5330.2130.2130.0000.0000.0000.000
10A593LEU00.0010.00611.5850.0830.0830.0000.0000.0000.000
11A594THR00.013-0.01611.6800.0820.0820.0000.0000.0000.000
12A595THR00.0120.00612.7150.0790.0790.0000.0000.0000.000
13A596ILE00.0060.00715.2750.0740.0740.0000.0000.0000.000
14A597SER00.0120.00717.2570.0580.0580.0000.0000.0000.000
15A598SER0-0.020-0.02317.1000.0430.0430.0000.0000.0000.000
16A599ILE00.0460.01018.4640.0440.0440.0000.0000.0000.000
17A600LEU0-0.042-0.02021.2270.0400.0400.0000.0000.0000.000
18A601SER0-0.027-0.02922.3750.0380.0380.0000.0000.0000.000
19A602LEU00.0040.00823.5430.0230.0230.0000.0000.0000.000
20A603LYS10.8800.92824.5320.2030.2030.0000.0000.0000.000
21A604ARG10.9180.97925.3710.2150.2150.0000.0000.0000.000
22A605GLU-1-0.841-0.90729.058-0.160-0.1600.0000.0000.0000.000
23A606LYS10.8620.93531.0030.1220.1220.0000.0000.0000.000
24A607PRO00.0080.01428.7800.0080.0080.0000.0000.0000.000
25A608ASP-1-0.804-0.88032.092-0.122-0.1220.0000.0000.0000.000
26A609ASN0-0.064-0.05933.4320.0050.0050.0000.0000.0000.000
27A610LEU0-0.0020.00526.137-0.010-0.0100.0000.0000.0000.000
28A611ALA00.0070.01028.9680.0130.0130.0000.0000.0000.000
29A612ILE0-0.004-0.00323.921-0.020-0.0200.0000.0000.0000.000
30A613ILE0-0.023-0.01124.9270.0170.0170.0000.0000.0000.000
31A614LEU00.0130.00721.896-0.040-0.0400.0000.0000.0000.000
32A615GLN00.010-0.00821.586-0.009-0.0090.0000.0000.0000.000
33A616ILE00.0210.00220.521-0.060-0.0600.0000.0000.0000.000
34A617ASP-1-0.792-0.87119.018-0.406-0.4060.0000.0000.0000.000
35A618PHE00.0870.02019.405-0.037-0.0370.0000.0000.0000.000
36A619THR0-0.068-0.03720.4760.0150.0150.0000.0000.0000.000
37A620LYS10.8270.90915.2550.6050.6050.0000.0000.0000.000
38A621LEU0-0.060-0.01715.135-0.085-0.0850.0000.0000.0000.000
39A622LYS10.8140.88411.2550.3530.3530.0000.0000.0000.000
40A623GLU-1-0.768-0.84814.026-0.250-0.2500.0000.0000.0000.000
41A624GLU-1-0.769-0.87217.444-0.271-0.2710.0000.0000.0000.000
42A625ASP-1-0.858-0.93619.276-0.161-0.1610.0000.0000.0000.000
43A626SER0-0.018-0.02216.649-0.019-0.0190.0000.0000.0000.000
44A627LEU0-0.029-0.02118.724-0.013-0.0130.0000.0000.0000.000
45A628ILE00.0100.00822.1800.0120.0120.0000.0000.0000.000
46A629VAL00.0100.01918.7940.0110.0110.0000.0000.0000.000
47A630VAL0-0.0190.00320.500-0.003-0.0030.0000.0000.0000.000
48A631TYR0-0.038-0.02822.6970.0070.0070.0000.0000.0000.000
49A632ASN00.0300.00124.2140.0110.0110.0000.0000.0000.000
50A633SER0-0.014-0.02722.1110.0090.0090.0000.0000.0000.000
51A634LEU0-0.031-0.01024.5090.0030.0030.0000.0000.0000.000
52A635LYS10.8470.90927.0050.1400.1400.0000.0000.0000.000
53A636ALA00.0270.03326.5550.0100.0100.0000.0000.0000.000
54A637LEU00.022-0.00224.8080.0090.0090.0000.0000.0000.000
55A638THR0-0.095-0.06228.7250.0090.0090.0000.0000.0000.000
56A639ILE0-0.0110.00530.9780.0090.0090.0000.0000.0000.000
57A640LYS10.8520.95230.4330.1530.1530.0000.0000.0000.000
58A641PHE0-0.018-0.00628.6210.0030.0030.0000.0000.0000.000
59A642ALA00.0650.02733.532-0.006-0.0060.0000.0000.0000.000
60A643ARG10.8300.88635.7120.1310.1310.0000.0000.0000.000
61A644LEU00.0220.03528.529-0.006-0.0060.0000.0000.0000.000
62A645GLN0-0.045-0.02731.8370.0050.0050.0000.0000.0000.000
63A646PHE00.0090.00028.683-0.019-0.0190.0000.0000.0000.000
64A647CYS0-0.049-0.02528.3880.0140.0140.0000.0000.0000.000
65A648PHE00.0400.03625.231-0.025-0.0250.0000.0000.0000.000
66A649VAL0-0.006-0.00525.6490.0190.0190.0000.0000.0000.000
67A650ASP-1-0.700-0.85025.348-0.318-0.3180.0000.0000.0000.000
68A651ARG10.8870.93021.9240.3380.3380.0000.0000.0000.000
69A652ASN0-0.075-0.04323.993-0.021-0.0210.0000.0000.0000.000
70A653ASN00.0300.01626.587-0.002-0.0020.0000.0000.0000.000
71A654TYR0-0.0030.00927.8110.0150.0150.0000.0000.0000.000
72A655VAL00.0190.00429.681-0.014-0.0140.0000.0000.0000.000
73A656LEU0-0.0350.00727.4030.0160.0160.0000.0000.0000.000
74A657ASP-1-0.796-0.89931.291-0.148-0.1480.0000.0000.0000.000
75A658TYR00.0110.00131.573-0.018-0.0180.0000.0000.0000.000
76A659GLY00.0300.02833.3810.0140.0140.0000.0000.0000.000
77A660SER00.0400.00133.672-0.012-0.0120.0000.0000.0000.000
78A661VAL00.0340.00929.7410.0040.0040.0000.0000.0000.000
79A662LEU0-0.0150.01232.7420.0060.0060.0000.0000.0000.000
80A663HIS00.0230.00935.4090.0010.0010.0000.0000.0000.000
81A664LYS10.7920.89035.5760.1580.1580.0000.0000.0000.000
82A665ILE00.0130.01829.582-0.008-0.0080.0000.0000.0000.000
83A666ASP-1-0.803-0.84533.542-0.112-0.1120.0000.0000.0000.000
84A667SER0-0.0010.00133.4690.0070.0070.0000.0000.0000.000
85A668LEU00.0190.00525.979-0.011-0.0110.0000.0000.0000.000
86A669ASP-1-0.855-0.93829.362-0.130-0.1300.0000.0000.0000.000
87A670SER0-0.046-0.05031.824-0.006-0.0060.0000.0000.0000.000
88A671ILE0-0.018-0.00325.711-0.010-0.0100.0000.0000.0000.000
89A672SER0-0.020-0.01627.414-0.016-0.0160.0000.0000.0000.000
90A673ASN00.0450.00828.450-0.006-0.0060.0000.0000.0000.000
91A674LEU0-0.038-0.02028.7680.0010.0010.0000.0000.0000.000
92A675LYS10.7940.89024.6350.2060.2060.0000.0000.0000.000
93A676SER0-0.044-0.01928.294-0.001-0.0010.0000.0000.0000.000
94A677LYS10.8060.92631.5730.1810.1810.0000.0000.0000.000
95A678SER00.0330.01632.691-0.012-0.0120.0000.0000.0000.000
96A679SER0-0.014-0.04233.6410.0050.0050.0000.0000.0000.000
97A680SER0-0.005-0.01035.6430.0030.0030.0000.0000.0000.000
98A681THR00.0040.01535.1730.0030.0030.0000.0000.0000.000
99A682GLN0-0.032-0.01330.350-0.019-0.0190.0000.0000.0000.000
100A683PHE00.0110.00727.3770.0130.0130.0000.0000.0000.000
101A684SER00.0440.02530.302-0.002-0.0020.0000.0000.0000.000
102A685PRO00.0240.01728.5520.0130.0130.0000.0000.0000.000
103A686ILE00.0610.01831.2190.0120.0120.0000.0000.0000.000
104A687TRP0-0.0110.00332.0210.0060.0060.0000.0000.0000.000
105A688LEU00.0140.01729.7760.0090.0090.0000.0000.0000.000
106A689LYS10.9140.94733.8250.1640.1640.0000.0000.0000.000
107A690ASN0-0.012-0.02035.8380.0080.0080.0000.0000.0000.000
108A691THR0-0.053-0.02136.6920.0110.0110.0000.0000.0000.000
109A692LEU0-0.060-0.03334.0220.0050.0050.0000.0000.0000.000
110A693TYR0-0.060-0.05334.8770.0010.0010.0000.0000.0000.000
111A694PRO00.0210.01939.3350.0000.0000.0000.0000.0000.000
112A695GLU-1-0.900-0.94142.500-0.103-0.1030.0000.0000.0000.000
113A696ASN0-0.066-0.02840.566-0.004-0.0040.0000.0000.0000.000
114A697ILE0-0.022-0.01135.7310.0010.0010.0000.0000.0000.000
115A698HIS0-0.014-0.01139.0750.0020.0020.0000.0000.0000.000
116A699GLU-1-0.776-0.83636.507-0.134-0.1340.0000.0000.0000.000
117A700HIS10.8320.89633.8900.1250.1250.0000.0000.0000.000
118A701LEU00.0150.01131.719-0.002-0.0020.0000.0000.0000.000
119A702GLY0-0.014-0.00728.712-0.003-0.0030.0000.0000.0000.000
120A703ILE0-0.039-0.02126.0300.0050.0050.0000.0000.0000.000
121A704VAL00.0300.00221.536-0.019-0.0190.0000.0000.0000.000
122A705ALA00.0010.01622.2120.0180.0180.0000.0000.0000.000
123A706VAL00.0330.01917.266-0.053-0.0530.0000.0000.0000.000
124A707SER00.002-0.00917.7740.0460.0460.0000.0000.0000.000
125A708ASN00.0510.03115.341-0.056-0.0560.0000.0000.0000.000
126A709SER0-0.062-0.02016.320-0.021-0.0210.0000.0000.0000.000
127A710ASN00.0440.00117.233-0.076-0.0760.0000.0000.0000.000
128A711MET00.0290.04015.4420.0660.0660.0000.0000.0000.000
129A712GLU-1-0.851-0.93618.578-0.362-0.3620.0000.0000.0000.000
130A713ALA00.0350.01522.2200.0040.0040.0000.0000.0000.000
131A714LYS10.8830.94124.0070.2740.2740.0000.0000.0000.000
132A715LYS10.8390.92023.9370.3430.3430.0000.0000.0000.000
133A716SER00.0370.02819.0670.0170.0170.0000.0000.0000.000
134A717ILE00.022-0.00622.1810.0110.0110.0000.0000.0000.000
135A718LEU0-0.0080.00817.0030.0290.0290.0000.0000.0000.000
136A719PHE00.0380.02119.7230.0070.0070.0000.0000.0000.000
137A720GLN0-0.031-0.00823.3300.0550.0550.0000.0000.0000.000
138A721ASP-1-0.781-0.86826.004-0.269-0.2690.0000.0000.0000.000
139A722TYR00.012-0.02024.6090.0300.0300.0000.0000.0000.000
140A723ARG10.8800.90829.2750.2530.2530.0000.0000.0000.000
141A724CYS0-0.0180.01931.7310.0110.0110.0000.0000.0000.000
142A725PHE00.004-0.01131.2450.0120.0120.0000.0000.0000.000
143A726THR0-0.101-0.05133.131-0.004-0.0040.0000.0000.0000.000
144A727SER00.0290.01834.2480.0070.0070.0000.0000.0000.000
145A728PHE00.0480.01636.707-0.002-0.0020.0000.0000.0000.000
146A729GLY00.0180.01438.5230.0010.0010.0000.0000.0000.000
147A730ARG10.7550.86332.2330.1560.1560.0000.0000.0000.000
148A731ARG10.9790.97530.2840.1950.1950.0000.0000.0000.000
149A732ARG10.7550.84724.7740.3200.3200.0000.0000.0000.000
150A733PRO00.0130.02028.3590.0160.0160.0000.0000.0000.000
151A734ASN00.004-0.00627.633-0.025-0.0250.0000.0000.0000.000
152A735GLU-1-0.820-0.91124.291-0.327-0.3270.0000.0000.0000.000
153A736LEU00.0180.01318.758-0.005-0.0050.0000.0000.0000.000
154A737LYS10.8270.92819.4060.4330.4330.0000.0000.0000.000
155A738ILE00.0260.00214.628-0.045-0.0450.0000.0000.0000.000
156A739LYS10.8300.90712.5311.2851.2850.0000.0000.0000.000
157A740VAL0-0.0030.00212.170-0.175-0.1750.0000.0000.0000.000
158A741GLY0-0.002-0.0079.6060.1420.1420.0000.0000.0000.000
159A742TYR0-0.036-0.0375.3130.0040.0040.0000.0000.0000.000
160A743LEU0-0.035-0.0068.1450.3480.3480.0000.0000.0000.000
161A744ASN0-0.046-0.0236.647-0.274-0.2740.0000.0000.0000.000
162A745VAL0-0.025-0.0159.8900.2340.2340.0000.0000.0000.000
163A746ASP-1-0.785-0.86513.232-0.810-0.8100.0000.0000.0000.000
164A747TYR0-0.025-0.03514.5880.0810.0810.0000.0000.0000.000
165A748SER00.001-0.02015.7030.0430.0430.0000.0000.0000.000
166A749ASP-1-0.840-0.89218.144-0.413-0.4130.0000.0000.0000.000
167A750LYS10.7420.84320.4510.5130.5130.0000.0000.0000.000
168A751ILE0-0.051-0.02717.7120.0090.0090.0000.0000.0000.000
169A752ASP-1-0.772-0.85319.404-0.417-0.4170.0000.0000.0000.000
170A753GLU-1-0.973-0.99417.785-0.378-0.3780.0000.0000.0000.000
171A754LEU0-0.051-0.01114.3830.0200.0200.0000.0000.0000.000
172A755VAL0-0.0040.00913.290-0.063-0.0630.0000.0000.0000.000
173A756GLU-1-0.821-0.9259.407-2.072-2.0720.0000.0000.0000.000
174A757ALA00.004-0.0089.137-0.067-0.0670.0000.0000.0000.000
175A758SER00.0190.0157.0720.0630.0630.0000.0000.0000.000
176A759SER00.010-0.0038.8410.1910.1910.0000.0000.0000.000
177A760TRP00.018-0.00312.395-0.003-0.0030.0000.0000.0000.000
178A761THR00.0560.02414.6280.0110.0110.0000.0000.0000.000
179A762PHE00.0380.03312.3970.0170.0170.0000.0000.0000.000
180A763VAL00.0070.01713.9240.0410.0410.0000.0000.0000.000
181A764LEU0-0.008-0.00816.1500.0490.0490.0000.0000.0000.000
182A765GLU-1-0.789-0.87617.700-0.134-0.1340.0000.0000.0000.000
183A766THR0-0.026-0.02516.0390.0450.0450.0000.0000.0000.000
184A767LEU0-0.027-0.00118.6710.0320.0320.0000.0000.0000.000
185A768CYS0-0.030-0.01821.4510.0320.0320.0000.0000.0000.000
186A769TYR0-0.010-0.02418.9300.0260.0260.0000.0000.0000.000
187A770SER0-0.053-0.02920.7280.0180.0180.0000.0000.0000.000
188A771PHE0-0.060-0.04223.3300.0120.0120.0000.0000.0000.000
189A772GLY0-0.0110.00526.1960.0120.0120.0000.0000.0000.000
190A773LEU0-0.065-0.01526.4460.0120.0120.0000.0000.0000.000
191A774SER00.0130.00924.0450.0070.0070.0000.0000.0000.000