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: 98NK2

Calculation Name: 2NP3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NP3

Chain ID: B

ChEMBL ID:

UniProt ID: Q9RCV4

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1693821.961335
FMO2-HF: Nuclear repulsion 1625564.910169
FMO2-HF: Total energy -68257.051167
FMO2-MP2: Total energy -68454.54651


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(B:22:GLY)


Summations of interaction energy for fragment #1(B:22:GLY)
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.
4.025-4.28725.051-9.942-6.797-0.013
Interaction energy analysis for fragmet #1(B:22:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.045
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].
3B24ARG10.9610.9673.7401.2202.836-0.036-0.821-0.7590.001
4B25ARG10.9761.0146.4560.3990.3990.0000.0000.0000.000
5B26PRO00.0800.0286.5660.3410.3410.0000.0000.0000.000
6B27GLY0-0.019-0.0267.880-0.137-0.1370.0000.0000.0000.000
7B28GLU-1-0.839-0.9002.987-1.395-1.1260.083-0.128-0.2240.000
8B29THR00.0320.0031.7940.419-0.13511.062-7.286-3.222-0.006
9B30ARG11.0411.0292.7130.681-2.6230.0193.673-0.388-0.003
10B31THR0-0.017-0.0035.771-0.463-0.4630.0000.0000.0000.000
11B32ARG10.8460.9692.0073.908-2.60713.915-5.289-2.111-0.004
12B33GLU-1-0.882-0.9543.2470.4610.6370.008-0.091-0.093-0.001
13B34ALA0-0.005-0.0055.703-0.272-0.2720.0000.0000.0000.000
14B35ILE0-0.002-0.0067.951-0.159-0.1590.0000.0000.0000.000
15B36LEU0-0.022-0.0135.653-0.115-0.1150.0000.0000.0000.000
16B37THR0-0.028-0.0099.256-0.088-0.0880.0000.0000.0000.000
17B38ALA00.0600.01711.293-0.039-0.0390.0000.0000.0000.000
18B39ALA0-0.0120.00112.192-0.026-0.0260.0000.0000.0000.000
19B40ARG10.9240.9608.5140.1790.1790.0000.0000.0000.000
20B41VAL0-0.0290.00215.033-0.006-0.0060.0000.0000.0000.000
21B42CYS0-0.007-0.00217.213-0.008-0.0080.0000.0000.0000.000
22B43PHE0-0.023-0.03114.565-0.008-0.0080.0000.0000.0000.000
23B44ALA0-0.041-0.01518.891-0.006-0.0060.0000.0000.0000.000
24B45GLU-1-0.950-0.96820.6910.0360.0360.0000.0000.0000.000
25B46ARG10.8760.94422.593-0.008-0.0080.0000.0000.0000.000
26B47GLY00.0830.05322.604-0.003-0.0030.0000.0000.0000.000
27B48PHE00.0170.00618.1460.0070.0070.0000.0000.0000.000
28B49ASP-1-0.879-0.96321.512-0.063-0.0630.0000.0000.0000.000
29B50ALA0-0.0180.01724.3360.0050.0050.0000.0000.0000.000
30B51THR0-0.017-0.00818.6490.0170.0170.0000.0000.0000.000
31B52SER0-0.006-0.01220.821-0.009-0.0090.0000.0000.0000.000
32B53LEU00.0610.00814.7830.0060.0060.0000.0000.0000.000
33B54ARG10.9120.96216.978-0.015-0.0150.0000.0000.0000.000
34B55ARG10.9470.98919.301-0.003-0.0030.0000.0000.0000.000
35B56ILE00.0340.02413.6260.0130.0130.0000.0000.0000.000
36B57ALA0-0.050-0.01214.8200.0310.0310.0000.0000.0000.000
37B58GLU-1-0.857-0.94315.8740.0880.0880.0000.0000.0000.000
38B59THR0-0.044-0.03616.5460.0080.0080.0000.0000.0000.000
39B60ALA0-0.039-0.02012.0840.0180.0180.0000.0000.0000.000
40B61GLY0-0.0130.01913.3970.0560.0560.0000.0000.0000.000
41B62VAL0-0.082-0.03511.2320.0210.0210.0000.0000.0000.000
42B63ASP-1-0.828-0.93114.6360.0750.0750.0000.0000.0000.000
43B64GLN00.041-0.01915.1960.0070.0070.0000.0000.0000.000
44B65SER0-0.0020.02315.619-0.026-0.0260.0000.0000.0000.000
45B66LEU00.0450.01810.903-0.021-0.0210.0000.0000.0000.000
46B67VAL0-0.012-0.00911.132-0.021-0.0210.0000.0000.0000.000
47B68HIS0-0.037-0.03411.628-0.035-0.0350.0000.0000.0000.000
48B69HIS0-0.038-0.0049.654-0.089-0.0890.0000.0000.0000.000
49B70PHE0-0.059-0.0346.743-0.007-0.0070.0000.0000.0000.000
50B71TYR0-0.003-0.0025.600-0.173-0.1730.0000.0000.0000.000
51B72GLY00.0700.06910.183-0.039-0.0390.0000.0000.0000.000
52B73THR00.005-0.00613.6890.0420.0420.0000.0000.0000.000
53B74LYS10.8860.93714.1410.0460.0460.0000.0000.0000.000
54B75GLU-1-0.849-0.93715.498-0.184-0.1840.0000.0000.0000.000
55B76ASN0-0.053-0.03410.139-0.036-0.0360.0000.0000.0000.000
56B77LEU0-0.021-0.0209.979-0.042-0.0420.0000.0000.0000.000
57B78PHE00.0010.00011.833-0.011-0.0110.0000.0000.0000.000
58B79LEU00.0200.00813.704-0.010-0.0100.0000.0000.0000.000
59B80GLN0-0.019-0.0157.368-0.159-0.1590.0000.0000.0000.000
60B81ALA0-0.015-0.00610.189-0.031-0.0310.0000.0000.0000.000
61B82LEU00.0110.00811.5580.0180.0180.0000.0000.0000.000
62B83GLU-1-0.927-0.95210.419-0.215-0.2150.0000.0000.0000.000
63B84LEU00.025-0.01312.658-0.044-0.0440.0000.0000.0000.000
64B85PRO0-0.0260.01214.0990.0000.0000.0000.0000.0000.000
65B86GLY00.0470.01611.486-0.008-0.0080.0000.0000.0000.000
66B87LYS10.8530.90812.4600.2520.2520.0000.0000.0000.000
67B88ILE0-0.0060.00414.4690.0270.0270.0000.0000.0000.000
68B89GLU-1-0.817-0.89814.648-0.362-0.3620.0000.0000.0000.000
69B90GLU-1-0.928-0.95012.698-0.418-0.4180.0000.0000.0000.000
70B91ALA0-0.023-0.01115.5140.0380.0380.0000.0000.0000.000
71B92ILE0-0.041-0.03318.5770.0260.0260.0000.0000.0000.000
72B93THR00.0360.01118.0060.0240.0240.0000.0000.0000.000
73B94ALA0-0.0090.01018.8970.0180.0180.0000.0000.0000.000
74B95ALA0-0.040-0.02020.7600.0210.0210.0000.0000.0000.000
75B96ALA0-0.015-0.01523.3940.0170.0170.0000.0000.0000.000
76B97GLN0-0.0130.01021.504-0.007-0.0070.0000.0000.0000.000
77B98GLY0-0.009-0.00925.6850.0070.0070.0000.0000.0000.000
78B99GLY00.0030.00228.997-0.001-0.0010.0000.0000.0000.000
79B100LEU00.0930.04531.889-0.003-0.0030.0000.0000.0000.000
80B101ASP-1-0.893-0.93333.663-0.063-0.0630.0000.0000.0000.000
81B102GLY0-0.020-0.02133.7600.0000.0000.0000.0000.0000.000
82B103ILE0-0.0300.00028.377-0.002-0.0020.0000.0000.0000.000
83B104GLY00.0730.02329.657-0.006-0.0060.0000.0000.0000.000
84B105GLU-1-0.813-0.91030.280-0.065-0.0650.0000.0000.0000.000
85B106ARG10.8090.90227.0680.0960.0960.0000.0000.0000.000
86B107VAL00.0480.03025.573-0.007-0.0070.0000.0000.0000.000
87B108VAL00.0030.00525.623-0.007-0.0070.0000.0000.0000.000
88B109ARG10.7950.86626.6750.0650.0650.0000.0000.0000.000
89B110ALA00.0150.01721.8980.0000.0000.0000.0000.0000.000
90B111HIS00.005-0.00121.886-0.020-0.0200.0000.0000.0000.000
91B112LEU0-0.001-0.00922.918-0.004-0.0040.0000.0000.0000.000
92B113SER0-0.0330.00121.8270.0010.0010.0000.0000.0000.000
93B114VAL00.0220.01917.7300.0020.0020.0000.0000.0000.000
94B115TRP00.005-0.00319.496-0.001-0.0010.0000.0000.0000.000
95B116ASP-1-0.768-0.84222.005-0.067-0.0670.0000.0000.0000.000
96B117ASP-1-0.835-0.89716.399-0.136-0.1360.0000.0000.0000.000
97B118VAL0-0.024-0.03816.5630.0110.0110.0000.0000.0000.000
98B119SER0-0.033-0.02818.9870.0140.0140.0000.0000.0000.000
99B120SER0-0.0200.00120.2420.0150.0150.0000.0000.0000.000
100B121ARG10.8020.89313.2970.1390.1390.0000.0000.0000.000
101B122PRO00.0470.03619.896-0.010-0.0100.0000.0000.0000.000
102B123ALA00.0390.04317.526-0.005-0.0050.0000.0000.0000.000
103B124LEU00.0310.01214.085-0.001-0.0010.0000.0000.0000.000
104B125MET00.0590.03418.134-0.010-0.0100.0000.0000.0000.000
105B126THR0-0.076-0.05821.5010.0070.0070.0000.0000.0000.000
106B127MET0-0.040-0.00815.2800.0050.0050.0000.0000.0000.000
107B128VAL0-0.009-0.00820.256-0.005-0.0050.0000.0000.0000.000
108B129ARG10.8680.93122.3720.0460.0460.0000.0000.0000.000
109B130SER0-0.032-0.00823.6810.0050.0050.0000.0000.0000.000
110B131ALA0-0.049-0.00822.0160.0010.0010.0000.0000.0000.000
111B141LEU00.0570.01319.1520.0040.0040.0000.0000.0000.000
112B142ARG10.9110.92321.2440.0880.0880.0000.0000.0000.000
113B143GLU-1-0.863-0.91823.868-0.128-0.1280.0000.0000.0000.000
114B144THR0-0.050-0.02217.342-0.005-0.0050.0000.0000.0000.000
115B145ALA00.0040.00120.527-0.014-0.0140.0000.0000.0000.000
116B146THR00.0430.02221.475-0.008-0.0080.0000.0000.0000.000
117B147GLY00.0480.03622.3810.0030.0030.0000.0000.0000.000
118B148ILE0-0.092-0.05016.595-0.008-0.0080.0000.0000.0000.000
119B149LEU0-0.016-0.01320.224-0.001-0.0010.0000.0000.0000.000
120B150ALA00.0240.01222.9370.0070.0070.0000.0000.0000.000
121B151ARG10.7980.88016.5490.3450.3450.0000.0000.0000.000
122B152ALA00.0150.01020.1340.0040.0040.0000.0000.0000.000
123B153LEU0-0.029-0.01221.6210.0110.0110.0000.0000.0000.000
124B154GLY00.0410.02124.4670.0150.0150.0000.0000.0000.000
125B155GLY0-0.051-0.03126.130-0.003-0.0030.0000.0000.0000.000
126B156VAL0-0.0120.00927.0570.0090.0090.0000.0000.0000.000
127B157ILE0-0.040-0.00329.7660.0090.0090.0000.0000.0000.000
128B158THR0-0.020-0.00932.463-0.002-0.0020.0000.0000.0000.000
129B159GLY00.0210.00435.0110.0030.0030.0000.0000.0000.000
130B160GLU-1-0.915-0.96337.855-0.065-0.0650.0000.0000.0000.000
131B161ASP-1-0.854-0.92538.136-0.073-0.0730.0000.0000.0000.000
132B162ALA00.0080.01333.613-0.003-0.0030.0000.0000.0000.000
133B163MET00.001-0.00729.767-0.003-0.0030.0000.0000.0000.000
134B164LEU00.0410.02432.369-0.005-0.0050.0000.0000.0000.000
135B165ARG10.8800.92534.0630.0770.0770.0000.0000.0000.000
136B166THR00.0170.00428.260-0.003-0.0030.0000.0000.0000.000
137B167SER0-0.048-0.03229.525-0.005-0.0050.0000.0000.0000.000
138B168MET0-0.0150.01230.6990.0000.0000.0000.0000.0000.000
139B169VAL00.0550.03128.3430.0010.0010.0000.0000.0000.000
140B170ALA0-0.010-0.00726.719-0.002-0.0020.0000.0000.0000.000
141B171THR0-0.013-0.02428.029-0.001-0.0010.0000.0000.0000.000
142B172GLN0-0.0100.00130.574-0.001-0.0010.0000.0000.0000.000
143B173LEU00.0380.04125.4160.0050.0050.0000.0000.0000.000
144B174VAL00.007-0.00325.1360.0010.0010.0000.0000.0000.000
145B175GLY0-0.014-0.00827.4040.0040.0040.0000.0000.0000.000
146B176LEU00.0010.00028.8400.0050.0050.0000.0000.0000.000
147B177ALA0-0.005-0.00325.2680.0050.0050.0000.0000.0000.000
148B178MET00.0110.01725.1630.0050.0050.0000.0000.0000.000
149B179MET00.0040.00329.1100.0070.0070.0000.0000.0000.000
150B180ARG10.8140.91428.8290.0670.0670.0000.0000.0000.000
151B181TYR0-0.016-0.04926.0320.0010.0010.0000.0000.0000.000
152B182VAL0-0.054-0.03126.2060.0010.0010.0000.0000.0000.000
153B183ALA0-0.041-0.02728.8830.0050.0050.0000.0000.0000.000
154B184HIS0-0.021-0.00829.1670.0040.0040.0000.0000.0000.000
155B185LEU00.0200.01333.3430.0040.0040.0000.0000.0000.000
156B186GLU-1-0.815-0.86436.042-0.038-0.0380.0000.0000.0000.000
157B187PRO0-0.036-0.04138.5390.0000.0000.0000.0000.0000.000
158B188LEU0-0.024-0.03533.070-0.001-0.0010.0000.0000.0000.000
159B189ALA0-0.020-0.00832.677-0.003-0.0030.0000.0000.0000.000
160B190SER0-0.022-0.01932.6760.0000.0000.0000.0000.0000.000
161B191ALA0-0.0470.00235.1000.0020.0020.0000.0000.0000.000
162B192ASP-1-0.849-0.91733.302-0.038-0.0380.0000.0000.0000.000
163B193THR0-0.015-0.03927.659-0.001-0.0010.0000.0000.0000.000
164B194ASP-1-0.810-0.89130.897-0.051-0.0510.0000.0000.0000.000
165B195THR00.0110.00132.956-0.001-0.0010.0000.0000.0000.000
166B196VAL00.0240.02331.872-0.001-0.0010.0000.0000.0000.000
167B197ALA00.0290.00530.261-0.002-0.0020.0000.0000.0000.000
168B198ARG10.8480.93132.1450.0430.0430.0000.0000.0000.000
169B199HIS0-0.030-0.03135.4570.0010.0010.0000.0000.0000.000
170B200TYR0-0.034-0.03931.3580.0020.0020.0000.0000.0000.000
171B201GLY00.0280.01032.766-0.003-0.0030.0000.0000.0000.000
172B202ARG10.8430.92433.7260.0580.0580.0000.0000.0000.000
173B203ALA00.0240.01535.4310.0010.0010.0000.0000.0000.000
174B204VAL00.0090.02230.457-0.001-0.0010.0000.0000.0000.000
175B205GLN0-0.007-0.01633.783-0.004-0.0040.0000.0000.0000.000
176B206ALA0-0.0020.00635.5170.0000.0000.0000.0000.0000.000
177B207ILE00.0430.04634.5350.0010.0010.0000.0000.0000.000
178B208VAL0-0.031-0.02932.271-0.001-0.0010.0000.0000.0000.000
179B209THR0-0.113-0.07935.0760.0010.0010.0000.0000.0000.000
180B210ASP-1-0.950-0.94038.537-0.064-0.0640.0000.0000.0000.000