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: MNZ1Z

Calculation Name: 5F64-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F64

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACZ7

Base Structure: X-ray

Registration Date: 2023-09-23

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2303859.551912
FMO2-HF: Nuclear repulsion 2223624.540773
FMO2-HF: Total energy -80235.011138
FMO2-MP2: Total energy -80466.776103


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-2.1620.111-0.019-1.185-1.0690.004
Interaction energy analysis for fragmet #1(A:0:ALA)
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 : 0.010
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].
3A2ASN0-0.043-0.0293.878-0.3601.709-0.017-1.176-0.8760.004
4A3ALA00.007-0.0076.8300.0470.0470.0000.0000.0000.000
5A4ILE0-0.022-0.00710.6390.1360.1360.0000.0000.0000.000
6A5ILE0-0.020-0.00114.075-0.019-0.0190.0000.0000.0000.000
7A6ILE0-0.013-0.01317.1540.0380.0380.0000.0000.0000.000
8A7ASP-1-0.790-0.90520.618-0.241-0.2410.0000.0000.0000.000
9A8ASP-1-0.856-0.94123.043-0.162-0.1620.0000.0000.0000.000
10A9HIS00.0100.02025.9710.0110.0110.0000.0000.0000.000
11A10PRO00.0290.00124.888-0.013-0.0130.0000.0000.0000.000
12A11LEU0-0.008-0.00724.093-0.004-0.0040.0000.0000.0000.000
13A12ALA0-0.0020.01022.972-0.007-0.0070.0000.0000.0000.000
14A13ILE00.0300.02519.793-0.024-0.0240.0000.0000.0000.000
15A14ALA0-0.0040.00019.042-0.022-0.0220.0000.0000.0000.000
16A15ALA0-0.014-0.00619.169-0.003-0.0030.0000.0000.0000.000
17A16ILE00.0250.00015.626-0.018-0.0180.0000.0000.0000.000
18A17ARG10.8270.87514.8620.1420.1420.0000.0000.0000.000
19A18ASN0-0.027-0.01014.202-0.020-0.0200.0000.0000.0000.000
20A19LEU0-0.035-0.02114.2130.0180.0180.0000.0000.0000.000
21A20LEU00.0310.01610.560-0.009-0.0090.0000.0000.0000.000
22A21ILE00.0570.0369.780-0.066-0.0660.0000.0000.0000.000
23A22LYS10.8280.91310.4260.2600.2600.0000.0000.0000.000
24A23ASN0-0.110-0.07510.0190.0990.0990.0000.0000.0000.000
25A24ASP-1-0.925-0.9484.9830.4220.556-0.001-0.004-0.1290.000
26A25ILE0-0.057-0.0094.780-0.602-0.532-0.001-0.005-0.0640.000
27A26GLU-1-0.863-0.9325.865-0.122-0.1220.0000.0000.0000.000
28A27ILE0-0.034-0.0327.681-0.177-0.1770.0000.0000.0000.000
29A28LEU00.0100.0208.2870.1360.1360.0000.0000.0000.000
30A29ALA0-0.053-0.03711.5640.0940.0940.0000.0000.0000.000
31A30GLU-1-0.765-0.83915.228-0.293-0.2930.0000.0000.0000.000
32A31LEU0-0.049-0.02518.0590.0250.0250.0000.0000.0000.000
33A32THR00.0340.01421.290-0.009-0.0090.0000.0000.0000.000
34A33GLU-1-0.825-0.89224.394-0.179-0.1790.0000.0000.0000.000
35A34GLY00.0480.01924.328-0.020-0.0200.0000.0000.0000.000
36A35GLY0-0.048-0.03025.871-0.003-0.0030.0000.0000.0000.000
37A36SER0-0.057-0.05723.177-0.003-0.0030.0000.0000.0000.000
38A37ALA00.0020.00721.083-0.014-0.0140.0000.0000.0000.000
39A38VAL00.0170.00320.211-0.027-0.0270.0000.0000.0000.000
40A39GLN00.0440.01820.537-0.017-0.0170.0000.0000.0000.000
41A40ARG10.9450.98018.1130.2190.2190.0000.0000.0000.000
42A41VAL00.0560.03815.664-0.020-0.0200.0000.0000.0000.000
43A42GLU-1-0.765-0.85315.609-0.295-0.2950.0000.0000.0000.000
44A43THR0-0.104-0.05917.2420.0190.0190.0000.0000.0000.000
45A44LEU0-0.041-0.03312.9380.0270.0270.0000.0000.0000.000
46A45LYS10.8210.91911.6850.2820.2820.0000.0000.0000.000
47A46PRO00.0550.0479.364-0.059-0.0590.0000.0000.0000.000
48A47ASP-1-0.790-0.8786.195-3.022-3.0220.0000.0000.0000.000
49A48ILE0-0.047-0.0289.1190.2160.2160.0000.0000.0000.000
50A49VAL0-0.012-0.00511.9920.0800.0800.0000.0000.0000.000
51A50ILE0-0.0020.00213.8810.0160.0160.0000.0000.0000.000
52A51ILE0-0.006-0.00517.4170.0360.0360.0000.0000.0000.000
53A52ASP-1-0.782-0.89221.111-0.212-0.2120.0000.0000.0000.000
54A53VAL0-0.036-0.03124.1980.0030.0030.0000.0000.0000.000
55A54ASP-1-0.852-0.91927.336-0.141-0.1410.0000.0000.0000.000
56A55ILE0-0.0310.01424.6920.0120.0120.0000.0000.0000.000
57A56PRO00.0200.01928.0720.0040.0040.0000.0000.0000.000
58A57GLY0-0.008-0.00329.033-0.009-0.0090.0000.0000.0000.000
59A58VAL0-0.058-0.03327.7430.0060.0060.0000.0000.0000.000
60A59ASN00.0940.04327.905-0.024-0.0240.0000.0000.0000.000
61A60GLY00.1180.06025.379-0.006-0.0060.0000.0000.0000.000
62A61ILE00.013-0.00125.288-0.017-0.0170.0000.0000.0000.000
63A62GLN0-0.066-0.02527.4860.0070.0070.0000.0000.0000.000
64A63VAL00.0170.02222.3120.0000.0000.0000.0000.0000.000
65A64LEU00.0110.01721.981-0.010-0.0100.0000.0000.0000.000
66A65GLU-1-0.753-0.84123.802-0.185-0.1850.0000.0000.0000.000
67A66THR0-0.098-0.07425.7370.0130.0130.0000.0000.0000.000
68A67LEU00.0250.01319.2480.0080.0080.0000.0000.0000.000
69A68ARG10.7700.87917.8290.4650.4650.0000.0000.0000.000
70A69LYS10.8480.91923.3650.1870.1870.0000.0000.0000.000
71A70ARG10.7630.84823.5560.2330.2330.0000.0000.0000.000
72A71GLN0-0.043-0.02321.988-0.009-0.0090.0000.0000.0000.000
73A72TYR0-0.023-0.01512.9300.0160.0160.0000.0000.0000.000
74A73SER0-0.006-0.00915.679-0.011-0.0110.0000.0000.0000.000
75A74GLY00.0370.03413.472-0.040-0.0400.0000.0000.0000.000
76A75ILE00.0080.00010.8590.1440.1440.0000.0000.0000.000
77A76ILE0-0.006-0.00314.5330.0100.0100.0000.0000.0000.000
78A77ILE0-0.034-0.00915.0970.0350.0350.0000.0000.0000.000
79A78ILE00.0010.00018.6820.0110.0110.0000.0000.0000.000
80A79VAL0-0.007-0.00420.274-0.002-0.0020.0000.0000.0000.000
81A80SER00.022-0.02123.2000.0200.0200.0000.0000.0000.000
82A81ALA00.0210.01426.603-0.003-0.0030.0000.0000.0000.000
83A82LYS10.8660.93628.6440.1430.1430.0000.0000.0000.000
84A83ASN00.0070.01329.553-0.004-0.0040.0000.0000.0000.000
85A84ASP-1-0.794-0.86929.925-0.177-0.1770.0000.0000.0000.000
86A85HIS00.014-0.00830.864-0.010-0.0100.0000.0000.0000.000
87A86PHE00.0150.00031.434-0.006-0.0060.0000.0000.0000.000
88A87TYR00.0120.01330.625-0.001-0.0010.0000.0000.0000.000
89A88GLY00.0760.03427.541-0.011-0.0110.0000.0000.0000.000
90A89LYS10.8030.90127.6020.1550.1550.0000.0000.0000.000
91A90HIS0-0.003-0.00129.438-0.012-0.0120.0000.0000.0000.000
92A91CYS0-0.051-0.02325.276-0.005-0.0050.0000.0000.0000.000
93A92ALA00.0180.01425.251-0.021-0.0210.0000.0000.0000.000
94A93ASP-1-0.844-0.90926.319-0.191-0.1910.0000.0000.0000.000
95A94ALA0-0.056-0.02527.1530.0030.0030.0000.0000.0000.000
96A95GLY00.0360.02024.243-0.010-0.0100.0000.0000.0000.000
97A96ALA0-0.019-0.00721.246-0.038-0.0380.0000.0000.0000.000
98A97ASN00.0440.01516.6410.0180.0180.0000.0000.0000.000
99A98GLY00.0410.00419.212-0.006-0.0060.0000.0000.0000.000
100A99PHE0-0.052-0.01920.8980.0050.0050.0000.0000.0000.000
101A100VAL00.013-0.00220.1350.0120.0120.0000.0000.0000.000
102A101SER0-0.039-0.03623.3470.0050.0050.0000.0000.0000.000
103A102LYS10.8080.86022.5470.2290.2290.0000.0000.0000.000
104A103LYS10.8440.93424.6540.1380.1380.0000.0000.0000.000
105A104GLU-1-0.852-0.92426.356-0.142-0.1420.0000.0000.0000.000
106A105GLY00.0070.01424.0360.0010.0010.0000.0000.0000.000
107A106MET00.008-0.01918.645-0.024-0.0240.0000.0000.0000.000
108A107ASN00.0130.00318.435-0.041-0.0410.0000.0000.0000.000
109A108ASN00.0410.03218.375-0.032-0.0320.0000.0000.0000.000
110A109ILE00.0250.02015.883-0.020-0.0200.0000.0000.0000.000
111A110ILE00.0350.02610.959-0.059-0.0590.0000.0000.0000.000
112A111ALA00.0020.01314.038-0.069-0.0690.0000.0000.0000.000
113A112ALA0-0.004-0.00716.207-0.020-0.0200.0000.0000.0000.000
114A113ILE00.0130.00310.519-0.028-0.0280.0000.0000.0000.000
115A114GLU-1-0.829-0.89710.150-1.173-1.1730.0000.0000.0000.000
116A115ALA0-0.009-0.00212.664-0.001-0.0010.0000.0000.0000.000
117A116ALA0-0.008-0.00313.5310.0140.0140.0000.0000.0000.000
118A117LYS10.8250.8906.9051.5551.5550.0000.0000.0000.000
119A118ASN0-0.095-0.04411.1060.0640.0640.0000.0000.0000.000
120A119GLY0-0.0040.01113.7330.0890.0890.0000.0000.0000.000
121A120TYR0-0.063-0.02416.0420.0900.0900.0000.0000.0000.000
122A121CYS0-0.040-0.02617.649-0.037-0.0370.0000.0000.0000.000
123A122TYR0-0.017-0.01919.2410.0250.0250.0000.0000.0000.000
124A123PHE00.0230.01321.213-0.007-0.0070.0000.0000.0000.000
125A124PRO0-0.0030.00624.7250.0110.0110.0000.0000.0000.000
126A125PHE00.0480.02927.9630.0070.0070.0000.0000.0000.000
127A126SER0-0.033-0.02530.1500.0070.0070.0000.0000.0000.000
128A127LEU00.0480.03533.6820.0030.0030.0000.0000.0000.000
129A128ASN00.026-0.00135.8540.0070.0070.0000.0000.0000.000
130A129ARG10.8250.90932.7620.1560.1560.0000.0000.0000.000
131A130PHE0-0.037-0.02033.3330.0010.0010.0000.0000.0000.000
132A131VAL00.0150.01039.0480.0050.0050.0000.0000.0000.000
133A132GLY00.0270.01941.331-0.002-0.0020.0000.0000.0000.000
134A133SER0-0.020-0.02744.206-0.001-0.0010.0000.0000.0000.000
135A134LEU0-0.0070.00142.1260.0020.0020.0000.0000.0000.000
136A135THR00.0240.03241.231-0.003-0.0030.0000.0000.0000.000
137A136SER00.0580.02841.777-0.005-0.0050.0000.0000.0000.000
138A137ASP-1-0.733-0.83743.263-0.087-0.0870.0000.0000.0000.000
139A138GLN0-0.027-0.02536.361-0.006-0.0060.0000.0000.0000.000
140A139GLN00.0420.01738.620-0.003-0.0030.0000.0000.0000.000
141A140LYS10.8180.90940.5040.0810.0810.0000.0000.0000.000
142A141LEU0-0.0090.00937.671-0.001-0.0010.0000.0000.0000.000
143A142ASP-1-0.799-0.89335.813-0.149-0.1490.0000.0000.0000.000
144A143SER0-0.048-0.02437.422-0.001-0.0010.0000.0000.0000.000
145A144LEU0-0.0260.00138.3060.0040.0040.0000.0000.0000.000
146A145SER00.007-0.03037.612-0.008-0.0080.0000.0000.0000.000
147A146LYS10.9070.91031.6800.1710.1710.0000.0000.0000.000
148A147GLN00.0320.03535.361-0.007-0.0070.0000.0000.0000.000
149A148GLU-1-0.744-0.83638.135-0.103-0.1030.0000.0000.0000.000
150A149ILE00.0120.01134.0930.0040.0040.0000.0000.0000.000
151A150SER0-0.027-0.02335.159-0.002-0.0020.0000.0000.0000.000
152A151VAL00.0240.00336.7490.0040.0040.0000.0000.0000.000
153A152MET0-0.0160.00138.3080.0050.0050.0000.0000.0000.000
154A153ARG10.7860.86431.7140.1620.1620.0000.0000.0000.000
155A154TYR00.0140.00433.9840.0000.0000.0000.0000.0000.000
156A155ILE00.012-0.00139.6230.0050.0050.0000.0000.0000.000
157A156LEU0-0.053-0.03339.9800.0040.0040.0000.0000.0000.000
158A157ASP-1-0.856-0.88737.249-0.111-0.1110.0000.0000.0000.000
159A158GLY0-0.030-0.02040.1570.0020.0020.0000.0000.0000.000
160A159LYS10.7890.89739.5290.0970.0970.0000.0000.0000.000
161A160ASP-1-0.781-0.89943.693-0.066-0.0660.0000.0000.0000.000
162A161ASN0-0.100-0.06345.412-0.005-0.0050.0000.0000.0000.000
163A162ASN00.0370.01246.291-0.002-0.0020.0000.0000.0000.000
164A163ASP-1-0.803-0.89042.638-0.078-0.0780.0000.0000.0000.000
165A164ILE0-0.037-0.02741.123-0.005-0.0050.0000.0000.0000.000
166A165ALA0-0.063-0.03441.510-0.004-0.0040.0000.0000.0000.000
167A166GLU-1-0.921-0.95340.990-0.081-0.0810.0000.0000.0000.000
168A167LYS10.8940.93934.0780.1200.1200.0000.0000.0000.000
169A168MET0-0.093-0.03537.065-0.007-0.0070.0000.0000.0000.000
170A169PHE0-0.0060.00734.938-0.001-0.0010.0000.0000.0000.000
171A170ILE0-0.044-0.01340.3260.0030.0030.0000.0000.0000.000
172A171SER00.0470.00643.4060.0040.0040.0000.0000.0000.000
173A172ASN00.1140.02246.810-0.003-0.0030.0000.0000.0000.000
174A173LYS10.9640.98748.7600.0640.0640.0000.0000.0000.000
175A174THR00.0040.03144.3840.0010.0010.0000.0000.0000.000
176A175VAL00.0430.03743.774-0.003-0.0030.0000.0000.0000.000
177A176SER00.017-0.00845.785-0.002-0.0020.0000.0000.0000.000
178A177THR0-0.058-0.02347.7130.0020.0020.0000.0000.0000.000
179A178TYR00.007-0.00241.397-0.002-0.0020.0000.0000.0000.000
180A179LYS10.9320.96144.9890.0730.0730.0000.0000.0000.000
181A180SER0-0.022-0.01646.4580.0020.0020.0000.0000.0000.000
182A181ARG10.9370.96243.0450.0920.0920.0000.0000.0000.000
183A182LEU0-0.027-0.00541.903-0.001-0.0010.0000.0000.0000.000
184A183MET0-0.047-0.01644.913-0.002-0.0020.0000.0000.0000.000
185A184GLU-1-0.927-0.96048.114-0.073-0.0730.0000.0000.0000.000
186A185LYS10.8120.88841.7560.1050.1050.0000.0000.0000.000
187A186LEU0-0.039-0.01642.153-0.002-0.0020.0000.0000.0000.000
188A187GLU-1-0.857-0.90746.229-0.072-0.0720.0000.0000.0000.000
189A188CYS0-0.100-0.02948.1790.0030.0030.0000.0000.0000.000
190A189LYS10.8740.91850.5670.0640.0640.0000.0000.0000.000
191A190SER00.004-0.02653.6810.0010.0010.0000.0000.0000.000
192A191LEU00.0570.00149.043-0.003-0.0030.0000.0000.0000.000
193A192MET00.0550.03449.939-0.003-0.0030.0000.0000.0000.000
194A193ASP-1-0.813-0.84751.083-0.064-0.0640.0000.0000.0000.000
195A194LEU00.0380.00744.518-0.002-0.0020.0000.0000.0000.000
196A195TYR00.0200.01245.974-0.003-0.0030.0000.0000.0000.000
197A196THR0-0.012-0.02946.669-0.002-0.0020.0000.0000.0000.000
198A197PHE0-0.007-0.01441.888-0.001-0.0010.0000.0000.0000.000
199A198ALA00.0020.00242.498-0.004-0.0040.0000.0000.0000.000
200A199GLN0-0.012-0.00442.270-0.006-0.0060.0000.0000.0000.000
201A200ARG10.8270.90743.7170.0770.0770.0000.0000.0000.000
202A201ASN0-0.048-0.05240.678-0.001-0.0010.0000.0000.0000.000
203A202LYS10.8360.93238.4860.0850.0850.0000.0000.0000.000
204A203ILE00.0060.01237.007-0.008-0.0080.0000.0000.0000.000