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: 8984Y

Calculation Name: 2NYV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYV

Chain ID: A

ChEMBL ID:

UniProt ID: O67359

Base Structure: X-ray

Registration Date: 2023-09-20

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2599728.376483
FMO2-HF: Nuclear repulsion 2516382.596345
FMO2-HF: Total energy -83345.780139
FMO2-MP2: Total energy -83594.994347


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.496-16.14117.646-7.902-15.098-0.031
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.007
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].
3A3LEU0-0.025-0.0122.729-0.8972.3950.252-1.250-2.2940.003
4A4ARG10.8070.8655.3030.4720.490-0.001-0.003-0.0140.000
5A5VAL0-0.0060.0018.5920.0580.0580.0000.0000.0000.000
6A6ILE0-0.0160.0008.8320.2480.2480.0000.0000.0000.000
7A7LEU0-0.023-0.01311.012-0.118-0.1180.0000.0000.0000.000
8A8PHE00.000-0.01013.0290.1090.1090.0000.0000.0000.000
9A9ASP-1-0.727-0.87015.4960.1680.1680.0000.0000.0000.000
10A10LEU0-0.059-0.05018.063-0.034-0.0340.0000.0000.0000.000
11A11ASP-1-0.772-0.85021.3580.0650.0650.0000.0000.0000.000
12A12GLY00.0120.00522.0350.0170.0170.0000.0000.0000.000
13A13THR0-0.010-0.00216.3720.0210.0210.0000.0000.0000.000
14A14LEU00.0160.01517.889-0.030-0.0300.0000.0000.0000.000
15A15ILE0-0.047-0.03920.602-0.028-0.0280.0000.0000.0000.000
16A16ASP-1-0.784-0.85924.2430.0420.0420.0000.0000.0000.000
17A17SER0-0.022-0.05426.505-0.007-0.0070.0000.0000.0000.000
18A18ALA00.005-0.00728.646-0.001-0.0010.0000.0000.0000.000
19A19LYS10.8680.92730.223-0.019-0.0190.0000.0000.0000.000
20A20ASP-1-0.642-0.77032.4360.0140.0140.0000.0000.0000.000
21A21ILE0-0.0030.00628.7080.0010.0010.0000.0000.0000.000
22A22ALA0-0.022-0.01333.2240.0010.0010.0000.0000.0000.000
23A23LEU00.0100.00835.703-0.001-0.0010.0000.0000.0000.000
24A24ALA00.0120.01335.868-0.001-0.0010.0000.0000.0000.000
25A25LEU00.0150.01535.6860.0010.0010.0000.0000.0000.000
26A26GLU-1-0.906-0.96238.1500.0230.0230.0000.0000.0000.000
27A27LYS10.8340.91940.902-0.020-0.0200.0000.0000.0000.000
28A28THR0-0.065-0.06439.6290.0000.0000.0000.0000.0000.000
29A29LEU0-0.031-0.01040.3480.0000.0000.0000.0000.0000.000
30A30LYS10.9951.02543.652-0.021-0.0210.0000.0000.0000.000
31A31GLU-1-0.887-0.90245.2040.0300.0300.0000.0000.0000.000
32A32LEU0-0.060-0.04142.8290.0000.0000.0000.0000.0000.000
33A33GLY0-0.0260.01346.9440.0010.0010.0000.0000.0000.000
34A34LEU0-0.027-0.02144.0130.0010.0010.0000.0000.0000.000
35A35GLU-1-0.849-0.94844.4800.0300.0300.0000.0000.0000.000
36A36GLU-1-0.930-0.97044.6280.0360.0360.0000.0000.0000.000
37A37TYR0-0.045-0.03241.2540.0020.0020.0000.0000.0000.000
38A38TYR0-0.048-0.01838.2780.0040.0040.0000.0000.0000.000
39A39PRO0-0.042-0.01135.675-0.001-0.0010.0000.0000.0000.000
40A40ASP-1-0.897-0.95037.5960.0390.0390.0000.0000.0000.000
41A41ASN0-0.038-0.03630.595-0.003-0.0030.0000.0000.0000.000
42A42VAL00.0520.01432.3110.0060.0060.0000.0000.0000.000
43A43THR0-0.023-0.03527.9410.0070.0070.0000.0000.0000.000
44A44LYN00.0130.02527.6130.0080.0080.0000.0000.0000.000
45A45TYR0-0.063-0.02528.2270.0100.0100.0000.0000.0000.000
46A46ILE0-0.0290.00125.4590.0010.0010.0000.0000.0000.000
47A47GLY00.0720.03923.5320.0050.0050.0000.0000.0000.000
48A48GLY0-0.0050.00323.4520.0150.0150.0000.0000.0000.000
49A49GLY00.0240.01225.5030.0000.0000.0000.0000.0000.000
50A50VAL0-0.008-0.01027.939-0.003-0.0030.0000.0000.0000.000
51A51ARG10.7580.84131.395-0.099-0.0990.0000.0000.0000.000
52A52ALA00.0590.04128.750-0.003-0.0030.0000.0000.0000.000
53A53LEU0-0.026-0.01030.624-0.004-0.0040.0000.0000.0000.000
54A54LEU00.0290.00031.910-0.005-0.0050.0000.0000.0000.000
55A55GLU-1-0.819-0.88932.9120.0980.0980.0000.0000.0000.000
56A56LYS10.9100.96028.444-0.121-0.1210.0000.0000.0000.000
57A57VAL0-0.006-0.00434.425-0.004-0.0040.0000.0000.0000.000
58A58LEU00.0130.00136.790-0.003-0.0030.0000.0000.0000.000
59A59LYS10.8340.92637.676-0.067-0.0670.0000.0000.0000.000
60A60ASP-1-0.850-0.91239.3690.0530.0530.0000.0000.0000.000
61A61LYS10.8230.90442.524-0.048-0.0480.0000.0000.0000.000
62A62PHE0-0.031-0.00836.903-0.002-0.0020.0000.0000.0000.000
63A63ARG10.8360.90140.915-0.049-0.0490.0000.0000.0000.000
64A64GLU-1-0.736-0.84037.3050.0810.0810.0000.0000.0000.000
65A65GLU-1-0.791-0.88139.3160.0510.0510.0000.0000.0000.000
66A66TYR00.005-0.01640.035-0.003-0.0030.0000.0000.0000.000
67A67VAL00.0080.00234.540-0.001-0.0010.0000.0000.0000.000
68A68GLU-1-0.933-0.96937.2490.0450.0450.0000.0000.0000.000
69A69VAL0-0.030-0.00339.059-0.003-0.0030.0000.0000.0000.000
70A70PHE00.0210.01333.528-0.002-0.0020.0000.0000.0000.000
71A71ARG10.7990.85230.701-0.083-0.0830.0000.0000.0000.000
72A72LYS10.8860.93536.406-0.034-0.0340.0000.0000.0000.000
73A73HIS10.8120.86639.643-0.032-0.0320.0000.0000.0000.000
74A74TYR00.013-0.00330.3790.0020.0020.0000.0000.0000.000
75A75LEU00.0070.00634.477-0.003-0.0030.0000.0000.0000.000
76A76GLU-1-0.868-0.88937.0540.0170.0170.0000.0000.0000.000
77A77ASN0-0.087-0.05938.013-0.003-0.0030.0000.0000.0000.000
78A78PRO00.0170.02633.1650.0020.0020.0000.0000.0000.000
79A79VAL0-0.002-0.01031.5420.0020.0020.0000.0000.0000.000
80A80VAL0-0.068-0.02634.121-0.004-0.0040.0000.0000.0000.000
81A81TYR0-0.049-0.05934.235-0.007-0.0070.0000.0000.0000.000
82A82THR0-0.052-0.04928.461-0.001-0.0010.0000.0000.0000.000
83A83LYS10.8670.93328.7810.0050.0050.0000.0000.0000.000
84A84PRO00.0330.02223.9680.0100.0100.0000.0000.0000.000
85A85TYR00.0630.04621.749-0.004-0.0040.0000.0000.0000.000
86A86PRO00.024-0.00723.116-0.016-0.0160.0000.0000.0000.000
87A87GLU-1-0.776-0.86719.149-0.125-0.1250.0000.0000.0000.000
88A88ILE00.0050.03618.351-0.026-0.0260.0000.0000.0000.000
89A89PRO00.001-0.00319.532-0.017-0.0170.0000.0000.0000.000
90A90TYR0-0.0090.00216.988-0.013-0.0130.0000.0000.0000.000
91A91THR00.020-0.01714.399-0.049-0.0490.0000.0000.0000.000
92A92LEU0-0.017-0.00215.672-0.044-0.0440.0000.0000.0000.000
93A93GLU-1-0.862-0.91417.269-0.283-0.2830.0000.0000.0000.000
94A94ALA0-0.014-0.00215.157-0.038-0.0380.0000.0000.0000.000
95A95LEU0-0.015-0.00710.761-0.085-0.0850.0000.0000.0000.000
96A96LYS10.8800.93713.7230.1270.1270.0000.0000.0000.000
97A97SER0-0.052-0.02516.349-0.044-0.0440.0000.0000.0000.000
98A98LYN0-0.023-0.0048.679-0.253-0.2530.0000.0000.0000.000
99A99GLY0-0.034-0.03112.980-0.134-0.1340.0000.0000.0000.000
100A100PHE0-0.040-0.0177.1070.0680.0680.0000.0000.0000.000
101A101LYS10.8130.90012.4670.2600.2600.0000.0000.0000.000
102A102LEU0-0.036-0.02513.0250.0360.0360.0000.0000.0000.000
103A103ALA0-0.018-0.00515.333-0.011-0.0110.0000.0000.0000.000
104A104VAL0-0.0260.00216.6200.0350.0350.0000.0000.0000.000
105A105VAL00.0200.00217.183-0.011-0.0110.0000.0000.0000.000
106A106SER00.0180.02218.9530.0130.0130.0000.0000.0000.000
107A107ASN0-0.011-0.01921.588-0.007-0.0070.0000.0000.0000.000
108A108LYS10.7600.89024.716-0.086-0.0860.0000.0000.0000.000
109A109LEU00.0250.01126.6940.0040.0040.0000.0000.0000.000
110A110GLU-1-0.754-0.83926.5050.0520.0520.0000.0000.0000.000
111A111GLU-1-0.941-0.97228.3130.0240.0240.0000.0000.0000.000
112A112LEU00.0130.00130.494-0.007-0.0070.0000.0000.0000.000
113A113SER0-0.027-0.02925.353-0.002-0.0020.0000.0000.0000.000
114A114LYS10.8680.91726.563-0.042-0.0420.0000.0000.0000.000
115A115LYS10.8510.95328.609-0.007-0.0070.0000.0000.0000.000
116A116ILE00.0600.00627.717-0.008-0.0080.0000.0000.0000.000
117A117LEU00.0060.00923.467-0.008-0.0080.0000.0000.0000.000
118A118ASP-1-0.831-0.90627.361-0.025-0.0250.0000.0000.0000.000
119A119ILE0-0.076-0.03130.269-0.008-0.0080.0000.0000.0000.000
120A120LEU0-0.076-0.04227.300-0.005-0.0050.0000.0000.0000.000
121A121ASN0-0.054-0.02828.298-0.006-0.0060.0000.0000.0000.000
122A122LEU00.0160.00022.815-0.012-0.0120.0000.0000.0000.000
123A123SER0-0.004-0.01223.518-0.003-0.0030.0000.0000.0000.000
124A124GLY00.0060.00623.8970.0000.0000.0000.0000.0000.000
125A125TYR0-0.070-0.04319.658-0.004-0.0040.0000.0000.0000.000
126A126PHE0-0.044-0.03417.716-0.021-0.0210.0000.0000.0000.000
127A127ASP-1-0.824-0.90817.788-0.159-0.1590.0000.0000.0000.000
128A128LEU0-0.012-0.01319.7140.0120.0120.0000.0000.0000.000
129A129ILE0-0.038-0.01520.3090.0130.0130.0000.0000.0000.000
130A130VAL0-0.007-0.00621.002-0.009-0.0090.0000.0000.0000.000
131A131GLY00.0270.01022.7070.0100.0100.0000.0000.0000.000
132A132GLY00.0220.00725.1340.0080.0080.0000.0000.0000.000
133A133ASP-1-0.867-0.94826.3570.0860.0860.0000.0000.0000.000
134A134THR0-0.029-0.02325.006-0.001-0.0010.0000.0000.0000.000
135A135PHE00.0190.00821.643-0.006-0.0060.0000.0000.0000.000
136A136GLY00.0040.00426.9090.0020.0020.0000.0000.0000.000
137A137GLU-1-0.784-0.86427.7030.1060.1060.0000.0000.0000.000
138A138LYS10.9220.96028.894-0.090-0.0900.0000.0000.0000.000
139A139LYS10.7610.88225.694-0.135-0.1350.0000.0000.0000.000
140A140PRO00.0460.03724.5730.0030.0030.0000.0000.0000.000
141A141SER00.0330.02919.2580.0190.0190.0000.0000.0000.000
142A142PRO00.0280.01116.765-0.019-0.0190.0000.0000.0000.000
143A143THR00.007-0.03718.5550.0030.0030.0000.0000.0000.000
144A144PRO00.0330.02020.152-0.004-0.0040.0000.0000.0000.000
145A145VAL00.0460.04113.891-0.021-0.0210.0000.0000.0000.000
146A146LEU00.0050.00415.6630.0010.0010.0000.0000.0000.000
147A147LYN00.0810.05617.569-0.032-0.0320.0000.0000.0000.000
148A148THR0-0.022-0.02816.552-0.046-0.0460.0000.0000.0000.000
149A149LEU0-0.018-0.01112.125-0.031-0.0310.0000.0000.0000.000
150A150GLU-1-0.923-0.97115.8020.1540.1540.0000.0000.0000.000
151A151ILE0-0.058-0.02918.614-0.037-0.0370.0000.0000.0000.000
152A152LEU0-0.044-0.01315.516-0.033-0.0330.0000.0000.0000.000
153A153GLY00.0060.02016.918-0.055-0.0550.0000.0000.0000.000
154A154GLU-1-0.795-0.85511.799-0.303-0.3030.0000.0000.0000.000
155A155GLU-1-0.860-0.92810.5190.2040.2040.0000.0000.0000.000
156A156PRO00.0300.0049.9830.0230.0230.0000.0000.0000.000
157A157GLU-1-0.865-0.9047.1021.0251.0250.0000.0000.0000.000
158A158LYS10.7740.8745.3490.7420.7420.0000.0000.0000.000
159A159ALA00.0220.0076.619-0.420-0.4200.0000.0000.0000.000
160A160LEU0-0.018-0.0105.2370.7170.908-0.001-0.013-0.1760.000
161A161ILE00.0100.0167.510-0.519-0.5190.0000.0000.0000.000
162A162VAL0-0.023-0.01610.0590.1120.1120.0000.0000.0000.000
163A163GLY00.0430.00812.142-0.080-0.0800.0000.0000.0000.000
164A164ASP-1-0.774-0.88514.4370.1950.1950.0000.0000.0000.000
165A165THR0-0.006-0.02017.146-0.014-0.0140.0000.0000.0000.000
166A166ASP-1-0.737-0.86316.0750.3030.3030.0000.0000.0000.000
167A167ALA0-0.016-0.01016.3610.0430.0430.0000.0000.0000.000
168A168ASP-1-0.799-0.87415.2150.3370.3370.0000.0000.0000.000
169A169ILE0-0.011-0.00710.6620.0910.0910.0000.0000.0000.000
170A170GLU-1-0.883-0.93012.6410.4230.4230.0000.0000.0000.000
171A171ALA0-0.036-0.02115.1820.0180.0180.0000.0000.0000.000
172A172GLY00.0720.02611.3850.0000.0000.0000.0000.0000.000
173A173LYS10.8220.8989.799-0.534-0.5340.0000.0000.0000.000
174A174ARG10.7590.87512.048-0.370-0.3700.0000.0000.0000.000
175A175ALA0-0.024-0.01813.146-0.043-0.0430.0000.0000.0000.000
176A176GLY0-0.0090.01111.066-0.044-0.0440.0000.0000.0000.000
177A177THR0-0.054-0.0238.2810.0060.0060.0000.0000.0000.000
178A178LYS10.8810.9462.713-6.521-9.1998.577-1.695-4.2040.009
179A179THR0-0.085-0.0485.595-1.107-1.089-0.001-0.0170.0000.000
180A180ALA00.028-0.0126.4860.0000.0000.0000.0000.0000.000
181A181LEU0-0.0010.0138.851-0.075-0.0750.0000.0000.0000.000
182A182ALA0-0.0050.00412.187-0.049-0.0490.0000.0000.0000.000
183A183LEU0-0.014-0.03114.787-0.016-0.0160.0000.0000.0000.000
184A184TRP0-0.074-0.03214.827-0.013-0.0130.0000.0000.0000.000
185A185GLY00.0090.02119.371-0.013-0.0130.0000.0000.0000.000
186A186TYR0-0.099-0.08521.076-0.015-0.0150.0000.0000.0000.000
187A187VAL0-0.048-0.00819.851-0.010-0.0100.0000.0000.0000.000
188A188LYS10.9340.96721.169-0.068-0.0680.0000.0000.0000.000
189A189LEU0-0.043-0.02721.057-0.007-0.0070.0000.0000.0000.000
190A190ASN0-0.017-0.01516.297-0.015-0.0150.0000.0000.0000.000
191A191SER0-0.088-0.06217.963-0.011-0.0110.0000.0000.0000.000
192A192GLN00.0070.01013.3200.0560.0560.0000.0000.0000.000
193A193ILE0-0.006-0.0099.612-0.020-0.0200.0000.0000.0000.000
194A194PRO00.0090.0278.1780.0700.0700.0000.0000.0000.000
195A195ASP-1-0.846-0.9112.6950.8441.8300.158-0.397-0.748-0.003
196A196PHE00.001-0.0092.517-2.802-1.8682.302-0.671-2.566-0.002
197A197THR00.007-0.0036.7990.1190.1190.0000.0000.0000.000
198A198LEU0-0.044-0.0189.741-0.080-0.0800.0000.0000.0000.000
199A199SER0-0.075-0.03812.7420.0210.0210.0000.0000.0000.000
200A200ARG10.8540.90315.9750.1140.1140.0000.0000.0000.000
201A201PRO00.0180.01515.570-0.013-0.0130.0000.0000.0000.000
202A202SER0-0.003-0.03114.512-0.034-0.0340.0000.0000.0000.000
203A203ASP-1-0.816-0.90212.743-0.210-0.2100.0000.0000.0000.000
204A204LEU0-0.010-0.0129.222-0.074-0.0740.0000.0000.0000.000
205A205VAL00.0090.0059.673-0.198-0.1980.0000.0000.0000.000
206A206LYS10.9800.99411.1450.1830.1830.0000.0000.0000.000
207A207LEU0-0.0050.0076.472-0.088-0.0880.0000.0000.0000.000
208A208MET00.0180.0276.598-0.528-0.5280.0000.0000.0000.000
209A209ASP-1-0.896-0.9428.100-0.947-0.9470.0000.0000.0000.000
210A210ASN0-0.149-0.0828.5160.1280.1280.0000.0000.0000.000
211A211HIS10.8350.9255.7172.0262.0260.0000.0000.0000.000
212A212ILE0-0.0160.0063.682-1.398-0.4760.007-0.376-0.552-0.002
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