Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 762JK

Calculation Name: 2NYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYI

Chain ID: A

ChEMBL ID:

UniProt ID: J3QW32

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptH
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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1518061.297318
FMO2-HF: Nuclear repulsion 1451998.092154
FMO2-HF: Total energy -66063.205165
FMO2-MP2: Total energy -66257.064548


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:2:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-9.7879999999999-4.03299999999997.878-6.703-6.9310.063
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.924 / q_NPA : -0.967
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].
3A4GLN0-0.058-0.0021.988-15.325-10.7717.879-6.208-6.2260.060
4A5SER00.0730.0404.872-4.483-4.432-0.001-0.006-0.0450.000
5A6PHE0-0.004-0.0178.0940.8480.8480.0000.0000.0000.000
6A7VAL00.0060.00811.517-0.672-0.6720.0000.0000.0000.000
7A8VAL0-0.003-0.00615.146-0.028-0.0280.0000.0000.0000.000
8A9SER0-0.0170.00017.794-0.443-0.4430.0000.0000.0000.000
9A10VAL00.002-0.00521.5430.0700.0700.0000.0000.0000.000
10A11ALA00.0300.01624.289-0.164-0.1640.0000.0000.0000.000
11A12GLY00.011-0.00127.9950.0720.0720.0000.0000.0000.000
12A13SER00.0300.02431.142-0.071-0.0710.0000.0000.0000.000
13A14ASP-1-0.865-0.95433.1819.2879.2870.0000.0000.0000.000
14A15ARG10.7940.89829.647-9.977-9.9770.0000.0000.0000.000
15A16VAL00.0500.01933.2000.2480.2480.0000.0000.0000.000
16A17GLY0-0.006-0.01430.861-0.006-0.0060.0000.0000.0000.000
17A18ILE00.0180.04426.9850.2700.2700.0000.0000.0000.000
18A19VAL00.0800.03224.5580.3980.3980.0000.0000.0000.000
19A20HIS0-0.024-0.00724.9210.6310.6310.0000.0000.0000.000
20A21ASP-1-0.797-0.89824.93910.70710.7070.0000.0000.0000.000
21A22PHE00.018-0.00218.7330.4610.4610.0000.0000.0000.000
22A23SER0-0.009-0.02220.7380.8300.8300.0000.0000.0000.000
23A24TRP0-0.054-0.02320.2690.6420.6420.0000.0000.0000.000
24A25ALA00.0130.00220.3230.3510.3510.0000.0000.0000.000
25A26LEU00.009-0.00215.7390.6730.6730.0000.0000.0000.000
26A27LYS10.9590.98515.588-12.273-12.2730.0000.0000.0000.000
27A28ASN0-0.065-0.02516.5780.2510.2510.0000.0000.0000.000
28A29ILE0-0.053-0.01513.6230.0750.0750.0000.0000.0000.000
29A30SER0-0.064-0.03011.4181.1681.1680.0000.0000.0000.000
30A31ALA0-0.0110.00211.0121.7651.7650.0000.0000.0000.000
31A32ASN0-0.033-0.02311.919-2.037-2.0370.0000.0000.0000.000
32A33VAL00.0180.00413.2880.9120.9120.0000.0000.0000.000
33A34GLU-1-0.988-0.98511.73022.64622.6460.0000.0000.0000.000
34A35SER00.002-0.01314.652-0.935-0.9350.0000.0000.0000.000
35A36SER0-0.028-0.02017.8170.1960.1960.0000.0000.0000.000
36A37ARG10.9600.99520.600-12.902-12.9020.0000.0000.0000.000
37A38MET0-0.015-0.01023.8850.2410.2410.0000.0000.0000.000
38A39ALA00.0380.02426.577-0.217-0.2170.0000.0000.0000.000
39A40CYS0-0.038-0.01629.9930.2250.2250.0000.0000.0000.000
40A41LEU00.0480.01932.950-0.169-0.1690.0000.0000.0000.000
41A42GLY0-0.0030.00736.2730.0480.0480.0000.0000.0000.000
42A43GLY0-0.0130.00337.911-0.117-0.1170.0000.0000.0000.000
43A44ASP-1-0.898-0.92733.4638.8998.8990.0000.0000.0000.000
44A45PHE0-0.021-0.04326.1240.1070.1070.0000.0000.0000.000
45A46ALA00.0430.01227.6030.1320.1320.0000.0000.0000.000
46A47MET0-0.052-0.01922.128-0.097-0.0970.0000.0000.0000.000
47A48ILE00.0060.00919.3320.3650.3650.0000.0000.0000.000
48A49VAL0-0.017-0.01916.605-0.163-0.1630.0000.0000.0000.000
49A50LEU0-0.0070.01413.4290.6320.6320.0000.0000.0000.000
50A51VAL00.0270.00812.147-0.378-0.3780.0000.0000.0000.000
51A52SER0-0.011-0.0078.5332.3302.3300.0000.0000.0000.000
52A53LEU00.0470.0087.768-1.945-1.9450.0000.0000.0000.000
53A54ASN00.0010.0114.1603.7053.9160.000-0.053-0.1580.000
54A55ALA00.011-0.0064.884-1.870-1.686-0.001-0.012-0.1700.000
55A56LYS10.9570.9743.719-62.996-62.2410.001-0.424-0.3320.003
56A57ASP-1-0.893-0.9536.85822.44722.4470.0000.0000.0000.000
57A58GLY00.0770.03010.4410.0520.0520.0000.0000.0000.000
58A59LYS10.9300.96912.828-19.345-19.3450.0000.0000.0000.000
59A60LEU00.0030.00811.730-1.022-1.0220.0000.0000.0000.000
60A61ILE00.0410.01811.645-0.794-0.7940.0000.0000.0000.000
61A62GLN0-0.042-0.04615.422-0.204-0.2040.0000.0000.0000.000
62A63SER00.003-0.00117.955-0.983-0.9830.0000.0000.0000.000
63A64ALA0-0.035-0.01317.520-0.722-0.7220.0000.0000.0000.000
64A65LEU0-0.011-0.01218.651-0.650-0.6500.0000.0000.0000.000
65A66GLU-1-0.856-0.91021.32412.23312.2330.0000.0000.0000.000
66A67SER0-0.096-0.03822.951-0.687-0.6870.0000.0000.0000.000
67A68ALA0-0.008-0.00323.314-0.425-0.4250.0000.0000.0000.000
68A69LEU0-0.067-0.02424.141-0.391-0.3910.0000.0000.0000.000
69A70PRO00.0510.02826.9950.0290.0290.0000.0000.0000.000
70A71GLY0-0.036-0.02829.141-0.245-0.2450.0000.0000.0000.000
71A72PHE0-0.033-0.00327.118-0.133-0.1330.0000.0000.0000.000
72A73GLN0-0.018-0.00126.4850.3720.3720.0000.0000.0000.000
73A74ILE00.0100.00020.9440.2170.2170.0000.0000.0000.000
74A75SER0-0.029-0.00520.7430.1340.1340.0000.0000.0000.000
75A76THR00.0490.01914.3310.4390.4390.0000.0000.0000.000
76A77ARG10.8920.94814.916-18.296-18.2960.0000.0000.0000.000
77A78ARG10.8850.9205.295-39.356-39.3560.0000.0000.0000.000
78A79ALA0-0.015-0.00210.075-1.767-1.7670.0000.0000.0000.000
79A80SER0-0.023-0.02810.9871.5491.5490.0000.0000.0000.000
80A81SER00.0260.02310.9520.2380.2380.0000.0000.0000.000
81A82VAL00.0220.00312.021-0.061-0.0610.0000.0000.0000.000
82A83ALA00.035-0.00114.011-0.396-0.3960.0000.0000.0000.000
83A84GLU-1-0.804-0.86312.06924.09624.0960.0000.0000.0000.000
84A85ARG10.7480.84213.449-21.595-21.5950.0000.0000.0000.000
85A86HIS0-0.0180.00218.327-0.041-0.0410.0000.0000.0000.000
86A87VAL00.0270.02819.880-0.529-0.5290.0000.0000.0000.000
87A88SER00.0120.01023.4160.2700.2700.0000.0000.0000.000
88A89PRO00.0350.01324.8360.0890.0890.0000.0000.0000.000
89A90ASP-1-0.877-0.93625.97010.40810.4080.0000.0000.0000.000
90A91THR0-0.094-0.04326.373-0.454-0.4540.0000.0000.0000.000
91A92ARG10.8430.92428.082-10.429-10.4290.0000.0000.0000.000
92A93GLU-1-0.837-0.91325.94411.95511.9550.0000.0000.0000.000
93A94TYR00.0010.00430.332-0.176-0.1760.0000.0000.0000.000
94A95GLU-1-0.868-0.93532.3419.8119.8110.0000.0000.0000.000
95A96LEU0-0.044-0.02535.186-0.201-0.2010.0000.0000.0000.000
96A97TYR00.000-0.00736.6440.1360.1360.0000.0000.0000.000
97A98VAL00.0060.00740.448-0.106-0.1060.0000.0000.0000.000
98A99GLU-1-0.909-0.96343.1786.8066.8060.0000.0000.0000.000
99A100GLY00.0600.03446.212-0.100-0.1000.0000.0000.0000.000
100A101PRO0-0.043-0.02049.2070.0400.0400.0000.0000.0000.000
101A102ASP-1-0.858-0.95047.1396.8056.8050.0000.0000.0000.000
102A103SER0-0.061-0.03948.449-0.159-0.1590.0000.0000.0000.000
103A104GLU-1-0.961-0.98747.7946.5056.5050.0000.0000.0000.000
104A105GLY00.006-0.00246.5790.1370.1370.0000.0000.0000.000
105A106ILE00.0150.04244.2500.1120.1120.0000.0000.0000.000
106A107VAL00.0440.01839.4730.1360.1360.0000.0000.0000.000
107A108GLU-1-0.948-0.96540.8267.5577.5570.0000.0000.0000.000
108A109ALA00.0780.04641.8420.1310.1310.0000.0000.0000.000
109A110VAL00.002-0.00439.1820.0930.0930.0000.0000.0000.000
110A111THR0-0.044-0.05536.8170.2030.2030.0000.0000.0000.000
111A112ALA00.0070.02237.6500.2210.2210.0000.0000.0000.000
112A113VAL0-0.061-0.02939.3950.0980.0980.0000.0000.0000.000
113A114LEU00.0110.00234.9790.1360.1360.0000.0000.0000.000
114A115ALA00.0230.01234.4040.2330.2330.0000.0000.0000.000
115A116LYS10.8840.93835.203-7.332-7.3320.0000.0000.0000.000
116A117LYS10.8560.94236.622-7.869-7.8690.0000.0000.0000.000
117A118GLY0-0.020-0.00132.6900.1420.1420.0000.0000.0000.000
118A119ALA0-0.028-0.00130.9770.3630.3630.0000.0000.0000.000
119A120ASN0-0.060-0.03025.991-0.074-0.0740.0000.0000.0000.000
120A121ILE00.0280.01129.402-0.076-0.0760.0000.0000.0000.000
121A122VAL0-0.102-0.04725.0330.4300.4300.0000.0000.0000.000
122A123GLU-1-0.946-0.98926.98111.16111.1610.0000.0000.0000.000
123A124LEU0-0.024-0.01729.607-0.212-0.2120.0000.0000.0000.000
124A125GLU-1-0.956-0.95332.9768.9498.9490.0000.0000.0000.000
125A126THR00.006-0.00835.623-0.110-0.1100.0000.0000.0000.000
126A127GLU-1-0.913-0.94839.2177.4607.4600.0000.0000.0000.000
127A128THR00.006-0.00842.106-0.064-0.0640.0000.0000.0000.000
128A129LEU0-0.056-0.02145.129-0.026-0.0260.0000.0000.0000.000
129A130PRO0-0.024-0.01048.422-0.096-0.0960.0000.0000.0000.000
130A131ALA00.0140.01651.9300.0060.0060.0000.0000.0000.000
131A132PRO0-0.043-0.02954.748-0.033-0.0330.0000.0000.0000.000
132A133PHE0-0.039-0.01057.270-0.101-0.1010.0000.0000.0000.000
133A134ALA00.001-0.01858.0690.0790.0790.0000.0000.0000.000
134A135GLY0-0.010-0.01458.278-0.044-0.0440.0000.0000.0000.000
135A136PHE00.0110.00952.478-0.019-0.0190.0000.0000.0000.000
136A137THR00.0110.01349.272-0.044-0.0440.0000.0000.0000.000
137A138LEU0-0.0270.01048.045-0.024-0.0240.0000.0000.0000.000
138A139PHE00.0480.01941.6800.1140.1140.0000.0000.0000.000
139A140ARG10.9160.95642.666-7.068-7.0680.0000.0000.0000.000
140A141MET0-0.027-0.01936.9530.0960.0960.0000.0000.0000.000
141A142GLY00.0410.03937.320-0.117-0.1170.0000.0000.0000.000
142A143SER0-0.057-0.05133.1890.2000.2000.0000.0000.0000.000
143A144ARG10.9280.98327.843-10.908-10.9080.0000.0000.0000.000
144A145VAL00.000-0.00530.6260.2630.2630.0000.0000.0000.000
145A146ALA00.0170.00027.9050.0430.0430.0000.0000.0000.000
146A147PHE00.0300.00129.8580.0190.0190.0000.0000.0000.000
147A148PRO00.000-0.00330.2590.0480.0480.0000.0000.0000.000
148A149PHE00.1060.04631.924-0.314-0.3140.0000.0000.0000.000
149A150PRO0-0.078-0.03633.961-0.307-0.3070.0000.0000.0000.000
150A151LEU0-0.0160.00234.636-0.248-0.2480.0000.0000.0000.000
151A152TYR0-0.013-0.00637.696-0.213-0.2130.0000.0000.0000.000
152A153GLN00.0350.00938.823-0.208-0.2080.0000.0000.0000.000
153A154GLU-1-0.904-0.96240.2247.8017.8010.0000.0000.0000.000
154A155VAL0-0.029-0.01337.249-0.121-0.1210.0000.0000.0000.000
155A156VAL00.0710.03540.656-0.100-0.1000.0000.0000.0000.000
156A157THR0-0.020-0.00243.221-0.204-0.2040.0000.0000.0000.000
157A158ALA0-0.098-0.04042.698-0.158-0.1580.0000.0000.0000.000
158A159LEU00.022-0.00540.028-0.069-0.0690.0000.0000.0000.000
159A160SER00.0160.00244.429-0.130-0.1300.0000.0000.0000.000
160A161ARG10.9170.95247.809-6.535-6.5350.0000.0000.0000.000
161A162VAL0-0.0030.00944.332-0.102-0.1020.0000.0000.0000.000
162A163GLU-1-0.825-0.91047.2286.6066.6060.0000.0000.0000.000
163A164GLU-1-0.992-0.99449.2985.8285.8280.0000.0000.0000.000
164A165GLU-1-1.071-1.03550.5646.2586.2580.0000.0000.0000.000
165A166PHE0-0.053-0.04248.480-0.056-0.0560.0000.0000.0000.000
166A167GLY0-0.0320.00751.082-0.031-0.0310.0000.0000.0000.000
167A168VAL0-0.119-0.05546.5420.0020.0020.0000.0000.0000.000
168A169ASP-1-0.865-0.92648.1066.2876.2870.0000.0000.0000.000
169A170ILE0-0.100-0.08142.3170.2020.2020.0000.0000.0000.000
170A171ASP-1-0.891-0.91542.3137.0807.0800.0000.0000.0000.000
171A172LEU0-0.060-0.05536.6850.2370.2370.0000.0000.0000.000
172A173GLU-1-0.928-0.95438.1497.5797.5790.0000.0000.0000.000
173A174GLU-1-0.958-0.98933.9689.5039.5030.0000.0000.0000.000
174A175VAL0-0.027-0.01029.818-0.084-0.0840.0000.0000.0000.000
175A176VAL0-0.062-0.03130.4340.2150.2150.0000.0000.0000.000