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: 7635K

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1700478.023318
FMO2-HF: Nuclear repulsion 1632219.469936
FMO2-HF: Total energy -68258.553382
FMO2-MP2: Total energy -68456.040218


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.
-12.961-25.19226.996-8.652-6.1140.034
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 : 0.062 / q_NPA : 0.051
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].
3B24ARG10.9630.9883.8581.6153.031-0.018-0.866-0.5320.000
4B25ARG10.9490.9837.4560.0490.0490.0000.0000.0000.000
5B26PRO00.0610.0147.8550.5520.5520.0000.0000.0000.000
6B27GLY00.0080.0128.561-0.219-0.2190.0000.0000.0000.000
7B28GLU-1-0.816-0.8844.243-0.943-0.814-0.001-0.025-0.1030.000
8B29THR0-0.014-0.0421.769-10.294-23.97725.943-8.040-4.2210.034
9B30ARG11.0341.0193.216-3.311-3.6340.0180.649-0.3440.001
10B31THR0-0.015-0.0126.415-0.592-0.5920.0000.0000.0000.000
11B32ARG10.8240.8982.4520.7530.8361.055-0.334-0.803-0.001
12B33GLU-1-0.853-0.9404.1141.2101.357-0.001-0.036-0.1110.000
13B34ALA00.0110.0256.167-0.317-0.3170.0000.0000.0000.000
14B35ILE00.0150.0018.321-0.161-0.1610.0000.0000.0000.000
15B36LEU0-0.019-0.0065.525-0.104-0.1040.0000.0000.0000.000
16B37THR0-0.037-0.0239.367-0.096-0.0960.0000.0000.0000.000
17B38ALA00.0250.01311.792-0.047-0.0470.0000.0000.0000.000
18B39ALA0-0.005-0.00412.255-0.032-0.0320.0000.0000.0000.000
19B40ARG10.8730.9238.9360.1800.1800.0000.0000.0000.000
20B41VAL00.0070.01215.134-0.010-0.0100.0000.0000.0000.000
21B42CYS0-0.027-0.01417.368-0.010-0.0100.0000.0000.0000.000
22B43PHE0-0.024-0.02714.971-0.009-0.0090.0000.0000.0000.000
23B44ALA0-0.015-0.00319.185-0.008-0.0080.0000.0000.0000.000
24B45GLU-1-0.871-0.90120.9920.0300.0300.0000.0000.0000.000
25B46ARG10.7700.85722.825-0.016-0.0160.0000.0000.0000.000
26B47GLY00.0840.05622.701-0.004-0.0040.0000.0000.0000.000
27B48PHE00.0150.00018.2700.0060.0060.0000.0000.0000.000
28B49ASP-1-0.802-0.90421.935-0.085-0.0850.0000.0000.0000.000
29B50ALA0-0.0100.02524.7910.0060.0060.0000.0000.0000.000
30B51THR0-0.002-0.00619.3560.0210.0210.0000.0000.0000.000
31B52SER00.000-0.00220.842-0.010-0.0100.0000.0000.0000.000
32B53LEU00.0480.00715.0300.0110.0110.0000.0000.0000.000
33B54ARG10.8630.92917.043-0.020-0.0200.0000.0000.0000.000
34B55ARG10.9240.96419.0270.0090.0090.0000.0000.0000.000
35B56ILE00.0170.01613.6560.0170.0170.0000.0000.0000.000
36B57ALA0-0.005-0.00814.5350.0340.0340.0000.0000.0000.000
37B58GLU-1-0.823-0.89915.6100.1050.1050.0000.0000.0000.000
38B59THR0-0.056-0.04016.4560.0180.0180.0000.0000.0000.000
39B60ALA0-0.033-0.00911.8770.0230.0230.0000.0000.0000.000
40B61GLY0-0.0350.00313.2610.0730.0730.0000.0000.0000.000
41B62VAL0-0.058-0.02711.7630.0230.0230.0000.0000.0000.000
42B63ASP-1-0.729-0.85215.1210.0580.0580.0000.0000.0000.000
43B64GLN00.007-0.01515.4510.0010.0010.0000.0000.0000.000
44B65SER0-0.062-0.04516.061-0.028-0.0280.0000.0000.0000.000
45B66LEU00.0360.01312.165-0.031-0.0310.0000.0000.0000.000
46B67VAL00.0090.00411.490-0.043-0.0430.0000.0000.0000.000
47B68HIS0-0.056-0.04712.039-0.054-0.0540.0000.0000.0000.000
48B69HIS0-0.022-0.0059.954-0.079-0.0790.0000.0000.0000.000
49B70PHE0-0.048-0.0247.276-0.033-0.0330.0000.0000.0000.000
50B71TYR00.0070.0045.787-0.302-0.3020.0000.0000.0000.000
51B72GLY00.0470.04810.864-0.013-0.0130.0000.0000.0000.000
52B73THR0-0.021-0.02414.5120.0490.0490.0000.0000.0000.000
53B74LYS10.8230.89514.8930.0690.0690.0000.0000.0000.000
54B75GLU-1-0.800-0.90816.116-0.223-0.2230.0000.0000.0000.000
55B76ASN0-0.030-0.02110.455-0.046-0.0460.0000.0000.0000.000
56B77LEU0-0.002-0.00510.232-0.048-0.0480.0000.0000.0000.000
57B78PHE0-0.002-0.00112.2390.0070.0070.0000.0000.0000.000
58B79LEU0-0.001-0.00213.599-0.005-0.0050.0000.0000.0000.000
59B80GLN0-0.029-0.0176.917-0.172-0.1720.0000.0000.0000.000
60B81ALA0-0.013-0.0089.915-0.004-0.0040.0000.0000.0000.000
61B82LEU00.0350.01311.7490.0210.0210.0000.0000.0000.000
62B83GLU-1-0.840-0.89710.343-0.265-0.2650.0000.0000.0000.000
63B84LEU0-0.002-0.00912.203-0.051-0.0510.0000.0000.0000.000
64B85PRO00.0010.00113.218-0.005-0.0050.0000.0000.0000.000
65B86GLY00.0480.02211.092-0.005-0.0050.0000.0000.0000.000
66B87LYS10.7880.88612.1420.3120.3120.0000.0000.0000.000
67B88ILE0-0.0010.00114.3710.0280.0280.0000.0000.0000.000
68B89GLU-1-0.768-0.86014.126-0.428-0.4280.0000.0000.0000.000
69B90GLU-1-0.922-0.94312.583-0.589-0.5890.0000.0000.0000.000
70B91ALA0-0.007-0.00415.4770.0460.0460.0000.0000.0000.000
71B92ILE0-0.044-0.02518.3920.0350.0350.0000.0000.0000.000
72B93THR00.0390.00518.1160.0300.0300.0000.0000.0000.000
73B94ALA0-0.020-0.00718.8750.0240.0240.0000.0000.0000.000
74B95ALA0-0.053-0.02620.7930.0260.0260.0000.0000.0000.000
75B96ALA00.0190.00523.4600.0220.0220.0000.0000.0000.000
76B97GLN0-0.0200.00621.305-0.002-0.0020.0000.0000.0000.000
77B98GLY0-0.0010.00325.4910.0090.0090.0000.0000.0000.000
78B99GLY00.0220.00928.960-0.001-0.0010.0000.0000.0000.000
79B100LEU00.0970.03631.757-0.005-0.0050.0000.0000.0000.000
80B101ASP-1-0.898-0.93933.467-0.090-0.0900.0000.0000.0000.000
81B102GLY0-0.009-0.01033.625-0.002-0.0020.0000.0000.0000.000
82B103ILE0-0.0220.00428.213-0.003-0.0030.0000.0000.0000.000
83B104GLY00.0440.01629.183-0.009-0.0090.0000.0000.0000.000
84B105GLU-1-0.783-0.87230.060-0.092-0.0920.0000.0000.0000.000
85B106ARG10.7670.89127.0030.1360.1360.0000.0000.0000.000
86B107VAL00.0430.02325.156-0.010-0.0100.0000.0000.0000.000
87B108VAL00.0060.00625.181-0.009-0.0090.0000.0000.0000.000
88B109ARG10.7710.84926.5580.0950.0950.0000.0000.0000.000
89B110ALA00.0150.02521.6820.0000.0000.0000.0000.0000.000
90B111HIS0-0.007-0.01021.935-0.022-0.0220.0000.0000.0000.000
91B112LEU0-0.001-0.00822.701-0.003-0.0030.0000.0000.0000.000
92B113SER0-0.025-0.01021.953-0.002-0.0020.0000.0000.0000.000
93B114VAL0-0.013-0.00517.450-0.002-0.0020.0000.0000.0000.000
94B115TRP00.0250.00019.3010.0020.0020.0000.0000.0000.000
95B116ASP-1-0.761-0.80621.839-0.097-0.0970.0000.0000.0000.000
96B117ASP-1-0.770-0.85016.538-0.195-0.1950.0000.0000.0000.000
97B118VAL0-0.033-0.03116.5160.0120.0120.0000.0000.0000.000
98B119SER0-0.021-0.05019.1270.0200.0200.0000.0000.0000.000
99B120SER0-0.041-0.01820.8790.0180.0180.0000.0000.0000.000
100B121ARG10.7660.86812.8610.2140.2140.0000.0000.0000.000
101B122PRO00.0360.01119.898-0.007-0.0070.0000.0000.0000.000
102B123ALA00.0100.02418.111-0.002-0.0020.0000.0000.0000.000
103B124LEU00.0290.00914.2290.0010.0010.0000.0000.0000.000
104B125MET00.0630.04718.192-0.013-0.0130.0000.0000.0000.000
105B126THR0-0.035-0.01521.6930.0050.0050.0000.0000.0000.000
106B127MET0-0.0480.00415.0030.0050.0050.0000.0000.0000.000
107B128VAL00.001-0.00619.571-0.007-0.0070.0000.0000.0000.000
108B129ARG10.8570.90921.7390.0580.0580.0000.0000.0000.000
109B130SER0-0.035-0.00923.1470.0100.0100.0000.0000.0000.000
110B131ALA0-0.079-0.02221.9810.0010.0010.0000.0000.0000.000
111B141LEU00.0390.01218.2870.0060.0060.0000.0000.0000.000
112B142ARG10.9250.94720.8610.1060.1060.0000.0000.0000.000
113B143GLU-1-0.851-0.92823.625-0.156-0.1560.0000.0000.0000.000
114B144THR0-0.015-0.00817.041-0.002-0.0020.0000.0000.0000.000
115B145ALA00.0030.00619.842-0.021-0.0210.0000.0000.0000.000
116B146THR00.0260.00620.912-0.010-0.0100.0000.0000.0000.000
117B147GLY00.0280.01621.9250.0030.0030.0000.0000.0000.000
118B148ILE0-0.079-0.03216.203-0.009-0.0090.0000.0000.0000.000
119B149LEU0-0.024-0.00519.579-0.002-0.0020.0000.0000.0000.000
120B150ALA00.005-0.00922.5120.0070.0070.0000.0000.0000.000
121B151ARG10.7610.86016.6300.3900.3900.0000.0000.0000.000
122B152ALA00.0140.00419.5080.0060.0060.0000.0000.0000.000
123B153LEU0-0.009-0.00621.1640.0120.0120.0000.0000.0000.000
124B154GLY00.0100.00024.0560.0190.0190.0000.0000.0000.000
125B155GLY0-0.031-0.01425.665-0.006-0.0060.0000.0000.0000.000
126B156VAL0-0.037-0.01226.8720.0110.0110.0000.0000.0000.000
127B157ILE0-0.0070.00929.6140.0110.0110.0000.0000.0000.000
128B158THR0-0.022-0.01932.056-0.002-0.0020.0000.0000.0000.000
129B159GLY00.0330.02134.7210.0040.0040.0000.0000.0000.000
130B160GLU-1-0.909-0.96137.628-0.079-0.0790.0000.0000.0000.000
131B161ASP-1-0.837-0.92437.679-0.092-0.0920.0000.0000.0000.000
132B162ALA0-0.0200.00633.403-0.004-0.0040.0000.0000.0000.000
133B163MET00.0030.00729.413-0.005-0.0050.0000.0000.0000.000
134B164LEU00.0250.02331.598-0.007-0.0070.0000.0000.0000.000
135B165ARG10.8680.90933.2850.0960.0960.0000.0000.0000.000
136B166THR0-0.001-0.01027.662-0.004-0.0040.0000.0000.0000.000
137B167SER0-0.060-0.04529.013-0.006-0.0060.0000.0000.0000.000
138B168MET0-0.0020.01630.0860.0000.0000.0000.0000.0000.000
139B169VAL00.0390.02428.1430.0010.0010.0000.0000.0000.000
140B170ALA0-0.003-0.00325.985-0.003-0.0030.0000.0000.0000.000
141B171THR0-0.013-0.02327.166-0.002-0.0020.0000.0000.0000.000
142B172GLN0-0.022-0.01429.762-0.001-0.0010.0000.0000.0000.000
143B173LEU00.0360.03425.2370.0060.0060.0000.0000.0000.000
144B174VAL00.0100.00424.2010.0000.0000.0000.0000.0000.000
145B175GLY00.0040.00026.5620.0050.0050.0000.0000.0000.000
146B176LEU0-0.009-0.00228.2750.0060.0060.0000.0000.0000.000
147B177ALA00.0060.00824.6070.0060.0060.0000.0000.0000.000
148B178MET00.0050.00724.6920.0080.0080.0000.0000.0000.000
149B179MET00.000-0.00128.4110.0090.0090.0000.0000.0000.000
150B180ARG10.8050.89828.4690.0940.0940.0000.0000.0000.000
151B181TYR0-0.013-0.04025.6330.0020.0020.0000.0000.0000.000
152B182VAL0-0.067-0.04025.7720.0020.0020.0000.0000.0000.000
153B183ALA0-0.023-0.02528.4800.0060.0060.0000.0000.0000.000
154B184HIS0-0.043-0.01228.7350.0080.0080.0000.0000.0000.000
155B185LEU00.0150.01233.0940.0050.0050.0000.0000.0000.000
156B186GLU-1-0.778-0.84435.849-0.054-0.0540.0000.0000.0000.000
157B187PRO0-0.065-0.03937.9080.0000.0000.0000.0000.0000.000
158B188LEU0-0.004-0.01832.505-0.002-0.0020.0000.0000.0000.000
159B189ALA0-0.0170.00932.200-0.006-0.0060.0000.0000.0000.000
160B190SER0-0.017-0.05432.463-0.002-0.0020.0000.0000.0000.000
161B191ALA0-0.0460.00234.9940.0020.0020.0000.0000.0000.000
162B192ASP-1-0.814-0.89233.055-0.061-0.0610.0000.0000.0000.000
163B193THR0-0.024-0.04127.1490.0010.0010.0000.0000.0000.000
164B194ASP-1-0.780-0.85630.499-0.078-0.0780.0000.0000.0000.000
165B195THR0-0.004-0.03032.568-0.001-0.0010.0000.0000.0000.000
166B196VAL00.0160.01931.5170.0000.0000.0000.0000.0000.000
167B197ALA00.0080.00130.221-0.002-0.0020.0000.0000.0000.000
168B198ARG10.8460.91932.0890.0650.0650.0000.0000.0000.000
169B199HIS0-0.048-0.02535.5510.0050.0050.0000.0000.0000.000
170B200TYR0-0.012-0.03831.0710.0030.0030.0000.0000.0000.000
171B201GLY00.0340.01432.254-0.004-0.0040.0000.0000.0000.000
172B202ARG10.7890.86933.1460.0830.0830.0000.0000.0000.000
173B203ALA00.0070.00635.3320.0000.0000.0000.0000.0000.000
174B204VAL00.0230.03229.984-0.001-0.0010.0000.0000.0000.000
175B205GLN0-0.015-0.02533.342-0.005-0.0050.0000.0000.0000.000
176B206ALA0-0.0070.00635.0560.0010.0010.0000.0000.0000.000
177B207ILE00.0280.01334.1440.0020.0020.0000.0000.0000.000
178B208VAL0-0.047-0.01332.132-0.003-0.0030.0000.0000.0000.000
179B209THR0-0.072-0.04034.8890.0010.0010.0000.0000.0000.000
180B210ASP-1-0.904-0.92638.145-0.087-0.0870.0000.0000.0000.000