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: 98QV2

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2293051.14478
FMO2-HF: Nuclear repulsion 2212816.572596
FMO2-HF: Total energy -80234.572184
FMO2-MP2: Total energy -80466.217791


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.
-0.4691.247-0.029-0.813-0.8730
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 : -0.037 / q_NPA : -0.027
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].
3A2ASN00.0300.0143.822-0.2671.388-0.028-0.810-0.8170.000
4A3ALA0-0.001-0.0077.0310.0940.0940.0000.0000.0000.000
5A4ILE0-0.026-0.00810.7620.0210.0210.0000.0000.0000.000
6A5ILE0-0.018-0.00314.3500.0220.0220.0000.0000.0000.000
7A6ILE0-0.026-0.02216.881-0.004-0.0040.0000.0000.0000.000
8A7ASP-1-0.776-0.90220.4770.0150.0150.0000.0000.0000.000
9A8ASP-1-0.869-0.93623.058-0.022-0.0220.0000.0000.0000.000
10A9HIS00.0090.01625.6090.0060.0060.0000.0000.0000.000
11A10PRO00.0250.00124.8000.0040.0040.0000.0000.0000.000
12A11LEU0-0.011-0.00724.4870.0050.0050.0000.0000.0000.000
13A12ALA0-0.0010.00323.2530.0110.0110.0000.0000.0000.000
14A13ILE00.0290.02619.7670.0110.0110.0000.0000.0000.000
15A14ALA0-0.028-0.00419.3770.0100.0100.0000.0000.0000.000
16A15ALA0-0.003-0.01719.2430.0170.0170.0000.0000.0000.000
17A16ILE00.0380.01315.7940.0310.0310.0000.0000.0000.000
18A17ARG10.8450.89015.0080.0120.0120.0000.0000.0000.000
19A18ASN0-0.026-0.00814.2820.0560.0560.0000.0000.0000.000
20A19LEU0-0.034-0.02114.5240.0440.0440.0000.0000.0000.000
21A20LEU00.0290.00810.8620.0790.0790.0000.0000.0000.000
22A21ILE00.0290.02110.1910.1160.1160.0000.0000.0000.000
23A22LYS10.8650.92910.534-0.185-0.1850.0000.0000.0000.000
24A23ASN0-0.130-0.08010.2320.0450.0450.0000.0000.0000.000
25A24ASP-1-0.916-0.9525.6371.9921.9920.0000.0000.0000.000
26A25ILE0-0.051-0.0085.1980.2280.289-0.001-0.003-0.0560.000
27A26GLU-1-0.941-0.9676.135-0.714-0.7140.0000.0000.0000.000
28A27ILE0-0.036-0.0367.815-0.093-0.0930.0000.0000.0000.000
29A28LEU00.0020.0168.4350.0440.0440.0000.0000.0000.000
30A29ALA0-0.047-0.03412.0400.0410.0410.0000.0000.0000.000
31A30GLU-1-0.774-0.84515.706-0.014-0.0140.0000.0000.0000.000
32A31LEU0-0.045-0.02518.380-0.006-0.0060.0000.0000.0000.000
33A32THR00.0530.01221.4840.0090.0090.0000.0000.0000.000
34A33GLU-1-0.858-0.89624.771-0.075-0.0750.0000.0000.0000.000
35A34GLY00.0610.03024.754-0.009-0.0090.0000.0000.0000.000
36A35GLY0-0.054-0.03326.009-0.006-0.0060.0000.0000.0000.000
37A36SER0-0.073-0.06223.815-0.009-0.0090.0000.0000.0000.000
38A37ALA00.0100.00821.578-0.016-0.0160.0000.0000.0000.000
39A38VAL00.017-0.00620.553-0.019-0.0190.0000.0000.0000.000
40A39GLN00.0160.01120.690-0.009-0.0090.0000.0000.0000.000
41A40ARG10.9800.99317.8850.1360.1360.0000.0000.0000.000
42A41VAL00.0600.03915.805-0.032-0.0320.0000.0000.0000.000
43A42GLU-1-0.762-0.83215.678-0.220-0.2200.0000.0000.0000.000
44A43THR0-0.099-0.06017.076-0.013-0.0130.0000.0000.0000.000
45A44LEU0-0.039-0.03213.055-0.005-0.0050.0000.0000.0000.000
46A45LYS10.8230.92511.6800.2890.2890.0000.0000.0000.000
47A46PRO00.0500.0469.600-0.109-0.1090.0000.0000.0000.000
48A47ASP-1-0.795-0.8916.076-2.129-2.1290.0000.0000.0000.000
49A48ILE0-0.030-0.0218.7210.2120.2120.0000.0000.0000.000
50A49VAL0-0.012-0.00311.663-0.007-0.0070.0000.0000.0000.000
51A50ILE00.000-0.00113.8050.0360.0360.0000.0000.0000.000
52A51ILE0-0.010-0.00217.224-0.003-0.0030.0000.0000.0000.000
53A52ASP-1-0.760-0.87620.8890.0090.0090.0000.0000.0000.000
54A53VAL0-0.045-0.04023.982-0.010-0.0100.0000.0000.0000.000
55A54ASP-1-0.884-0.92826.870-0.014-0.0140.0000.0000.0000.000
56A55ILE0-0.0190.01624.5060.0010.0010.0000.0000.0000.000
57A56PRO00.0240.00927.637-0.002-0.0020.0000.0000.0000.000
58A57GLY0-0.008-0.00429.219-0.007-0.0070.0000.0000.0000.000
59A58VAL0-0.062-0.02727.8970.0020.0020.0000.0000.0000.000
60A59ASN00.0910.03128.048-0.003-0.0030.0000.0000.0000.000
61A60GLY00.1170.06125.417-0.008-0.0080.0000.0000.0000.000
62A61ILE00.0320.00525.053-0.009-0.0090.0000.0000.0000.000
63A62GLN0-0.078-0.02627.1140.0010.0010.0000.0000.0000.000
64A63VAL00.0340.01822.365-0.008-0.0080.0000.0000.0000.000
65A64LEU0-0.0180.01821.691-0.012-0.0120.0000.0000.0000.000
66A65GLU-1-0.768-0.86823.701-0.070-0.0700.0000.0000.0000.000
67A66THR0-0.102-0.06125.628-0.003-0.0030.0000.0000.0000.000
68A67LEU00.0440.01619.270-0.005-0.0050.0000.0000.0000.000
69A68ARG10.7670.89817.2040.1520.1520.0000.0000.0000.000
70A69LYS10.9670.99023.1730.0840.0840.0000.0000.0000.000
71A70ARG10.6710.78423.6080.1470.1470.0000.0000.0000.000
72A71GLN0-0.043-0.02521.806-0.015-0.0150.0000.0000.0000.000
73A72TYR00.0120.00613.2150.0160.0160.0000.0000.0000.000
74A73SER0-0.009-0.02015.5810.0160.0160.0000.0000.0000.000
75A74GLY00.0400.03113.071-0.018-0.0180.0000.0000.0000.000
76A75ILE00.0020.00110.1430.0890.0890.0000.0000.0000.000
77A76ILE0-0.020-0.00814.001-0.012-0.0120.0000.0000.0000.000
78A77ILE0-0.024-0.01514.8290.0260.0260.0000.0000.0000.000
79A78ILE00.0030.00618.405-0.003-0.0030.0000.0000.0000.000
80A79VAL0-0.004-0.00920.2030.0180.0180.0000.0000.0000.000
81A80SER00.024-0.01723.112-0.010-0.0100.0000.0000.0000.000
82A81ALA00.0310.02426.5310.0100.0100.0000.0000.0000.000
83A82LYS10.8800.94628.5040.0010.0010.0000.0000.0000.000
84A83ASN00.0230.02029.638-0.001-0.0010.0000.0000.0000.000
85A84ASP-1-0.762-0.86530.0120.0060.0060.0000.0000.0000.000
86A85HIS00.009-0.00530.6400.0010.0010.0000.0000.0000.000
87A86PHE00.007-0.01330.8400.0000.0000.0000.0000.0000.000
88A87TYR00.0090.01129.916-0.005-0.0050.0000.0000.0000.000
89A88GLY00.0660.03227.107-0.006-0.0060.0000.0000.0000.000
90A89LYS10.8410.91427.2210.0110.0110.0000.0000.0000.000
91A90HIS0-0.0080.00628.919-0.007-0.0070.0000.0000.0000.000
92A91CYS0-0.031-0.01024.711-0.007-0.0070.0000.0000.0000.000
93A92ALA00.0010.00124.469-0.009-0.0090.0000.0000.0000.000
94A93ASP-1-0.855-0.91325.552-0.029-0.0290.0000.0000.0000.000
95A94ALA0-0.044-0.02026.757-0.005-0.0050.0000.0000.0000.000
96A95GLY00.0360.02023.435-0.011-0.0110.0000.0000.0000.000
97A96ALA0-0.023-0.00720.594-0.017-0.0170.0000.0000.0000.000
98A97ASN00.0390.01216.113-0.014-0.0140.0000.0000.0000.000
99A98GLY00.0500.01018.7410.0240.0240.0000.0000.0000.000
100A99PHE0-0.060-0.02320.280-0.014-0.0140.0000.0000.0000.000
101A100VAL00.019-0.00119.9690.0110.0110.0000.0000.0000.000
102A101SER0-0.017-0.01723.185-0.006-0.0060.0000.0000.0000.000
103A102LYS10.8090.86122.600-0.005-0.0050.0000.0000.0000.000
104A103LYS10.8560.95224.921-0.029-0.0290.0000.0000.0000.000
105A104GLU-1-0.900-0.96026.1910.0650.0650.0000.0000.0000.000
106A105GLY0-0.0050.01324.1920.0110.0110.0000.0000.0000.000
107A106MET00.001-0.02118.686-0.006-0.0060.0000.0000.0000.000
108A107ASN00.0130.00218.7800.0030.0030.0000.0000.0000.000
109A108ASN00.0600.03818.9740.0230.0230.0000.0000.0000.000
110A109ILE0-0.0070.00115.767-0.011-0.0110.0000.0000.0000.000
111A110ILE00.0460.02111.376-0.025-0.0250.0000.0000.0000.000
112A111ALA00.0010.01814.1040.0410.0410.0000.0000.0000.000
113A112ALA00.008-0.00116.130-0.005-0.0050.0000.0000.0000.000
114A113ILE00.0190.01210.555-0.034-0.0340.0000.0000.0000.000
115A114GLU-1-0.839-0.91410.3880.8840.8840.0000.0000.0000.000
116A115ALA0-0.0170.00112.541-0.024-0.0240.0000.0000.0000.000
117A116ALA00.0180.00813.042-0.027-0.0270.0000.0000.0000.000
118A117LYS10.8060.8986.990-1.243-1.2430.0000.0000.0000.000
119A118ASN0-0.097-0.04710.649-0.031-0.0310.0000.0000.0000.000
120A119GLY0-0.0060.00513.225-0.023-0.0230.0000.0000.0000.000
121A120TYR0-0.058-0.02815.421-0.013-0.0130.0000.0000.0000.000
122A121CYS0-0.032-0.01216.798-0.003-0.0030.0000.0000.0000.000
123A122TYR0-0.032-0.02818.9360.0160.0160.0000.0000.0000.000
124A123PHE00.0200.00820.849-0.007-0.0070.0000.0000.0000.000
125A124PRO0-0.0070.00424.2830.0070.0070.0000.0000.0000.000
126A125PHE00.0490.03027.396-0.006-0.0060.0000.0000.0000.000
127A126SER0-0.010-0.01929.8040.0020.0020.0000.0000.0000.000
128A127LEU00.0540.02933.392-0.003-0.0030.0000.0000.0000.000
129A128ASN00.0210.00235.867-0.001-0.0010.0000.0000.0000.000
130A129ARG10.8290.90432.220-0.008-0.0080.0000.0000.0000.000
131A130PHE0-0.042-0.03133.112-0.002-0.0020.0000.0000.0000.000
132A131VAL00.0280.02538.8880.0000.0000.0000.0000.0000.000
133A132GLY00.0100.01041.2240.0010.0010.0000.0000.0000.000
134A133SER0-0.003-0.01844.153-0.001-0.0010.0000.0000.0000.000
135A134LEU0-0.023-0.00842.154-0.001-0.0010.0000.0000.0000.000
136A135THR00.0450.03841.236-0.001-0.0010.0000.0000.0000.000
137A136SER00.0620.03041.619-0.001-0.0010.0000.0000.0000.000
138A137ASP-1-0.755-0.86143.0190.0040.0040.0000.0000.0000.000
139A138GLN0-0.048-0.02936.5140.0010.0010.0000.0000.0000.000
140A139GLN00.0290.01338.2640.0000.0000.0000.0000.0000.000
141A140LYS10.8400.92839.877-0.003-0.0030.0000.0000.0000.000
142A141LEU0-0.0130.00537.397-0.002-0.0020.0000.0000.0000.000
143A142ASP-1-0.813-0.90035.181-0.004-0.0040.0000.0000.0000.000
144A143SER0-0.055-0.03136.570-0.003-0.0030.0000.0000.0000.000
145A144LEU0-0.050-0.00737.605-0.002-0.0020.0000.0000.0000.000
146A145SER00.023-0.00937.043-0.003-0.0030.0000.0000.0000.000
147A146LYS10.8770.88531.1560.0540.0540.0000.0000.0000.000
148A147GLN00.0240.00835.0340.0010.0010.0000.0000.0000.000
149A148GLU-1-0.776-0.85937.766-0.018-0.0180.0000.0000.0000.000
150A149ILE00.0550.03633.8510.0030.0030.0000.0000.0000.000
151A150SER0-0.017-0.00535.0170.0020.0020.0000.0000.0000.000
152A151VAL00.0210.01036.4770.0020.0020.0000.0000.0000.000
153A152MET0-0.026-0.00638.0950.0020.0020.0000.0000.0000.000
154A153ARG10.7460.84931.6070.0090.0090.0000.0000.0000.000
155A154TYR00.0400.02135.0240.0020.0020.0000.0000.0000.000
156A155ILE0-0.019-0.01139.7520.0010.0010.0000.0000.0000.000
157A156LEU0-0.052-0.03339.5720.0010.0010.0000.0000.0000.000
158A157ASP-1-0.859-0.91337.5100.0040.0040.0000.0000.0000.000
159A158GLY0-0.043-0.01240.3290.0010.0010.0000.0000.0000.000
160A159LYS10.8200.92239.3060.0020.0020.0000.0000.0000.000
161A160ASP-1-0.852-0.91943.685-0.006-0.0060.0000.0000.0000.000
162A161ASN0-0.037-0.05845.6690.0000.0000.0000.0000.0000.000
163A162ASN00.0440.03346.436-0.003-0.0030.0000.0000.0000.000
164A163ASP-1-0.794-0.89042.775-0.008-0.0080.0000.0000.0000.000
165A164ILE0-0.035-0.02241.113-0.002-0.0020.0000.0000.0000.000
166A165ALA0-0.069-0.02641.586-0.002-0.0020.0000.0000.0000.000
167A166GLU-1-0.904-0.94541.552-0.018-0.0180.0000.0000.0000.000
168A167LYS10.9220.96234.5430.0150.0150.0000.0000.0000.000
169A168MET0-0.116-0.06137.479-0.001-0.0010.0000.0000.0000.000
170A169PHE0-0.020-0.00235.286-0.003-0.0030.0000.0000.0000.000
171A170ILE0-0.060-0.02440.424-0.001-0.0010.0000.0000.0000.000
172A171SER00.0550.02043.5120.0020.0020.0000.0000.0000.000
173A172ASN00.069-0.01746.8850.0010.0010.0000.0000.0000.000
174A173LYS10.9800.99248.8980.0150.0150.0000.0000.0000.000
175A174THR00.0100.02544.3980.0010.0010.0000.0000.0000.000
176A175VAL00.0550.04243.7870.0000.0000.0000.0000.0000.000
177A176SER0-0.001-0.01545.8370.0010.0010.0000.0000.0000.000
178A177THR0-0.048-0.01947.1130.0010.0010.0000.0000.0000.000
179A178TYR0-0.004-0.00341.1760.0000.0000.0000.0000.0000.000
180A179LYS10.9310.95444.9930.0080.0080.0000.0000.0000.000
181A180SER00.0060.00746.5930.0010.0010.0000.0000.0000.000
182A181ARG10.9610.97842.6460.0220.0220.0000.0000.0000.000
183A182LEU0-0.028-0.00441.7390.0010.0010.0000.0000.0000.000
184A183MET0-0.031-0.00944.7300.0010.0010.0000.0000.0000.000
185A184GLU-1-0.930-0.94947.708-0.010-0.0100.0000.0000.0000.000
186A185LYS10.8060.88740.8940.0180.0180.0000.0000.0000.000
187A186LEU0-0.047-0.02641.8190.0010.0010.0000.0000.0000.000
188A187GLU-1-0.873-0.91945.8610.0000.0000.0000.0000.0000.000
189A188CYS0-0.124-0.06848.0170.0020.0020.0000.0000.0000.000
190A189LYS10.8960.94250.3590.0010.0010.0000.0000.0000.000
191A190SER0-0.007-0.03252.8080.0000.0000.0000.0000.0000.000
192A191LEU00.0820.01449.3050.0000.0000.0000.0000.0000.000
193A192MET00.0480.02850.0390.0010.0010.0000.0000.0000.000
194A193ASP-1-0.811-0.84650.8890.0020.0020.0000.0000.0000.000
195A194LEU00.0270.00144.3330.0010.0010.0000.0000.0000.000
196A195TYR00.0230.01046.3020.0010.0010.0000.0000.0000.000
197A196THR0-0.004-0.01646.7760.0020.0020.0000.0000.0000.000
198A197PHE00.0060.00341.8610.0020.0020.0000.0000.0000.000
199A198ALA00.002-0.01142.4330.0010.0010.0000.0000.0000.000
200A199GLN0-0.0110.00042.3220.0020.0020.0000.0000.0000.000
201A200ARG10.8260.90943.630-0.005-0.0050.0000.0000.0000.000
202A201ASN0-0.062-0.06140.3050.0030.0030.0000.0000.0000.000
203A202LYS10.8390.93838.490-0.020-0.0200.0000.0000.0000.000
204A203ILE00.0120.01636.8250.0020.0020.0000.0000.0000.000