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: MN6JZ

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1695166.281382
FMO2-HF: Nuclear repulsion 1626908.302621
FMO2-HF: Total energy -68257.978761
FMO2-MP2: Total energy -68455.418535


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.
-1.013-3.60619.129-9.197-7.34-0.022
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 : 0.040 / q_NPA : 0.002
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].
3B24ARG10.9560.9673.7400.9873.614-0.039-1.503-1.0850.006
4B25ARG10.9781.0116.4581.0021.0020.0000.0000.0000.000
5B26PRO00.0870.0316.573-0.039-0.0390.0000.0000.0000.000
6B27GLY0-0.019-0.0177.8840.0350.0350.0000.0000.0000.000
7B28GLU-1-0.827-0.8852.990-1.747-1.4570.081-0.125-0.2460.000
8B29THR00.0260.0001.799-4.974-4.76911.968-8.170-4.003-0.020
9B30ARG11.0361.0312.7164.3781.0730.0333.688-0.416-0.003
10B31THR0-0.023-0.0135.768-0.198-0.1980.0000.0000.0000.000
11B32ARG10.8350.9282.1320.583-1.8587.086-3.038-1.607-0.005
12B33GLU-1-0.854-0.9434.3573.1923.2230.000-0.0490.0170.000
13B34ALA0-0.014-0.0026.437-0.984-0.9840.0000.0000.0000.000
14B35ILE0-0.002-0.0078.023-0.390-0.3900.0000.0000.0000.000
15B36LEU0-0.020-0.0065.419-0.386-0.3860.0000.0000.0000.000
16B37THR0-0.037-0.0249.249-0.415-0.4150.0000.0000.0000.000
17B38ALA00.0520.02111.921-0.227-0.2270.0000.0000.0000.000
18B39ALA00.0050.00312.179-0.165-0.1650.0000.0000.0000.000
19B40ARG10.8990.9479.355-1.520-1.5200.0000.0000.0000.000
20B41VAL0-0.0180.00515.258-0.095-0.0950.0000.0000.0000.000
21B42CYS0-0.027-0.01117.244-0.082-0.0820.0000.0000.0000.000
22B43PHE0-0.001-0.02314.517-0.067-0.0670.0000.0000.0000.000
23B44ALA0-0.034-0.01418.973-0.055-0.0550.0000.0000.0000.000
24B45GLU-1-0.851-0.91020.8520.3090.3090.0000.0000.0000.000
25B46ARG10.7680.87722.587-0.315-0.3150.0000.0000.0000.000
26B47GLY00.0790.05622.591-0.028-0.0280.0000.0000.0000.000
27B48PHE00.0160.00817.9420.0210.0210.0000.0000.0000.000
28B49ASP-1-0.874-0.95021.5050.1850.1850.0000.0000.0000.000
29B50ALA0-0.0070.01924.326-0.005-0.0050.0000.0000.0000.000
30B51THR0-0.013-0.00218.6540.0150.0150.0000.0000.0000.000
31B52SER0-0.009-0.00920.805-0.002-0.0020.0000.0000.0000.000
32B53LEU00.0530.00014.7410.0340.0340.0000.0000.0000.000
33B54ARG10.8610.91316.958-0.198-0.1980.0000.0000.0000.000
34B55ARG10.9340.97819.281-0.290-0.2900.0000.0000.0000.000
35B56ILE00.0320.01713.5250.0240.0240.0000.0000.0000.000
36B57ALA0-0.048-0.01614.8030.0830.0830.0000.0000.0000.000
37B58GLU-1-0.820-0.90215.8650.3450.3450.0000.0000.0000.000
38B59THR0-0.048-0.02816.743-0.009-0.0090.0000.0000.0000.000
39B60ALA0-0.032-0.01712.0890.0410.0410.0000.0000.0000.000
40B61GLY0-0.0170.01813.3900.0670.0670.0000.0000.0000.000
41B62VAL0-0.066-0.03311.177-0.019-0.0190.0000.0000.0000.000
42B63ASP-1-0.772-0.87814.6290.2440.2440.0000.0000.0000.000
43B64GLN00.029-0.01515.1870.0230.0230.0000.0000.0000.000
44B65SER0-0.061-0.03215.595-0.002-0.0020.0000.0000.0000.000
45B66LEU00.0360.01911.267-0.014-0.0140.0000.0000.0000.000
46B67VAL00.005-0.00311.1110.0180.0180.0000.0000.0000.000
47B68HIS0-0.044-0.03911.606-0.001-0.0010.0000.0000.0000.000
48B69HIS0-0.041-0.0099.284-0.180-0.1800.0000.0000.0000.000
49B70PHE0-0.060-0.0326.764-0.040-0.0400.0000.0000.0000.000
50B71TYR00.014-0.0015.5050.0520.0520.0000.0000.0000.000
51B72GLY00.0710.06910.167-0.066-0.0660.0000.0000.0000.000
52B73THR0-0.003-0.01213.6720.0320.0320.0000.0000.0000.000
53B74LYS10.9040.94314.128-0.204-0.2040.0000.0000.0000.000
54B75GLU-1-0.825-0.92915.4880.2340.2340.0000.0000.0000.000
55B76ASN0-0.051-0.02810.2980.0080.0080.0000.0000.0000.000
56B77LEU0-0.015-0.01810.0500.0440.0440.0000.0000.0000.000
57B78PHE0-0.016-0.00411.8280.1320.1320.0000.0000.0000.000
58B79LEU00.0100.00513.7180.0480.0480.0000.0000.0000.000
59B80GLN0-0.013-0.0086.9820.1040.1040.0000.0000.0000.000
60B81ALA0-0.018-0.00610.1950.1740.1740.0000.0000.0000.000
61B82LEU00.0260.01111.5590.0180.0180.0000.0000.0000.000
62B83GLU-1-0.847-0.90610.7470.7420.7420.0000.0000.0000.000
63B84LEU00.020-0.01112.685-0.093-0.0930.0000.0000.0000.000
64B85PRO0-0.0100.01314.255-0.054-0.0540.0000.0000.0000.000
65B86GLY00.0470.01911.475-0.060-0.0600.0000.0000.0000.000
66B87LYS10.7710.86612.450-0.478-0.4780.0000.0000.0000.000
67B88ILE0-0.005-0.00114.461-0.036-0.0360.0000.0000.0000.000
68B89GLU-1-0.779-0.85314.688-0.219-0.2190.0000.0000.0000.000
69B90GLU-1-0.917-0.94312.523-0.419-0.4190.0000.0000.0000.000
70B91ALA0-0.029-0.00915.510-0.004-0.0040.0000.0000.0000.000
71B92ILE0-0.041-0.03518.572-0.001-0.0010.0000.0000.0000.000
72B93THR00.031-0.00118.023-0.003-0.0030.0000.0000.0000.000
73B94ALA0-0.0050.00618.863-0.003-0.0030.0000.0000.0000.000
74B95ALA0-0.043-0.01720.7590.0080.0080.0000.0000.0000.000
75B96ALA0-0.010-0.00923.3910.0100.0100.0000.0000.0000.000
76B97GLN0-0.0060.01621.558-0.013-0.0130.0000.0000.0000.000
77B98GLY0-0.005-0.00525.6850.0130.0130.0000.0000.0000.000
78B99GLY00.0160.00528.998-0.001-0.0010.0000.0000.0000.000
79B100LEU00.0940.03131.8880.0030.0030.0000.0000.0000.000
80B101ASP-1-0.896-0.93333.662-0.046-0.0460.0000.0000.0000.000
81B102GLY0-0.019-0.01633.759-0.001-0.0010.0000.0000.0000.000
82B103ILE0-0.031-0.00528.4430.0030.0030.0000.0000.0000.000
83B104GLY00.0650.02529.6530.0010.0010.0000.0000.0000.000
84B105GLU-1-0.786-0.88430.275-0.002-0.0020.0000.0000.0000.000
85B106ARG10.8030.91027.0240.0780.0780.0000.0000.0000.000
86B107VAL00.0440.03025.5690.0040.0040.0000.0000.0000.000
87B108VAL00.0080.00525.6170.0090.0090.0000.0000.0000.000
88B109ARG10.7570.83926.7320.0060.0060.0000.0000.0000.000
89B110ALA00.0240.02121.9550.0130.0130.0000.0000.0000.000
90B111HIS0-0.007-0.00221.8790.0100.0100.0000.0000.0000.000
91B112LEU00.001-0.01822.9090.0200.0200.0000.0000.0000.000
92B113SER0-0.0320.00321.8280.0140.0140.0000.0000.0000.000
93B114VAL00.0110.00917.6760.0270.0270.0000.0000.0000.000
94B115TRP00.0100.00219.4860.0520.0520.0000.0000.0000.000
95B116ASP-1-0.772-0.83321.9950.1200.1200.0000.0000.0000.000
96B117ASP-1-0.754-0.85416.4090.3400.3400.0000.0000.0000.000
97B118VAL0-0.033-0.04016.6770.0400.0400.0000.0000.0000.000
98B119SER0-0.027-0.03519.1920.0250.0250.0000.0000.0000.000
99B120SER0-0.036-0.00920.838-0.008-0.0080.0000.0000.0000.000
100B121ARG10.7640.86813.347-0.468-0.4680.0000.0000.0000.000
101B122PRO00.0410.02620.5240.0080.0080.0000.0000.0000.000
102B123ALA00.0340.02918.423-0.014-0.0140.0000.0000.0000.000
103B124LEU00.0090.00614.689-0.010-0.0100.0000.0000.0000.000
104B125MET00.0840.04518.679-0.023-0.0230.0000.0000.0000.000
105B126THR0-0.080-0.03422.128-0.042-0.0420.0000.0000.0000.000
106B127MET0-0.0270.00315.211-0.001-0.0010.0000.0000.0000.000
107B128VAL0-0.005-0.00420.436-0.024-0.0240.0000.0000.0000.000
108B129ARG10.8510.91122.398-0.240-0.2400.0000.0000.0000.000
109B130SER0-0.044-0.01723.580-0.017-0.0170.0000.0000.0000.000
110B131ALA0-0.051-0.00922.064-0.024-0.0240.0000.0000.0000.000
111B141LEU00.0490.01118.8770.0000.0000.0000.0000.0000.000
112B142ARG10.9160.93021.248-0.102-0.1020.0000.0000.0000.000
113B143GLU-1-0.870-0.92423.8320.0160.0160.0000.0000.0000.000
114B144THR0-0.029-0.01617.324-0.015-0.0150.0000.0000.0000.000
115B145ALA00.0030.00020.539-0.024-0.0240.0000.0000.0000.000
116B146THR00.0600.03021.485-0.018-0.0180.0000.0000.0000.000
117B147GLY00.0300.02622.388-0.014-0.0140.0000.0000.0000.000
118B148ILE0-0.086-0.04516.652-0.018-0.0180.0000.0000.0000.000
119B149LEU0-0.018-0.00920.217-0.019-0.0190.0000.0000.0000.000
120B150ALA00.0140.00322.929-0.009-0.0090.0000.0000.0000.000
121B151ARG10.7600.84617.0790.1740.1740.0000.0000.0000.000
122B152ALA00.0060.00220.098-0.013-0.0130.0000.0000.0000.000
123B153LEU0-0.023-0.00921.617-0.003-0.0030.0000.0000.0000.000
124B154GLY00.0400.02224.4650.0090.0090.0000.0000.0000.000
125B155GLY0-0.050-0.03026.127-0.010-0.0100.0000.0000.0000.000
126B156VAL0-0.0170.00327.0280.0050.0050.0000.0000.0000.000
127B157ILE0-0.042-0.00129.7640.0070.0070.0000.0000.0000.000
128B158THR0-0.001-0.00732.461-0.004-0.0040.0000.0000.0000.000
129B159GLY00.0190.01135.0080.0060.0060.0000.0000.0000.000
130B160GLU-1-0.923-0.96737.852-0.040-0.0400.0000.0000.0000.000
131B161ASP-1-0.843-0.92238.092-0.036-0.0360.0000.0000.0000.000
132B162ALA00.0060.01233.6220.0020.0020.0000.0000.0000.000
133B163MET00.0070.00229.8160.0000.0000.0000.0000.0000.000
134B164LEU00.0310.01832.3590.0030.0030.0000.0000.0000.000
135B165ARG10.8780.92534.0560.0500.0500.0000.0000.0000.000
136B166THR00.002-0.01028.1670.0020.0020.0000.0000.0000.000
137B167SER0-0.053-0.03529.5190.0050.0050.0000.0000.0000.000
138B168MET0-0.0130.01430.6910.0090.0090.0000.0000.0000.000
139B169VAL00.0400.02128.4680.0080.0080.0000.0000.0000.000
140B170ALA0-0.005-0.00426.7070.0080.0080.0000.0000.0000.000
141B171THR0-0.007-0.02228.0200.0130.0130.0000.0000.0000.000
142B172GLN0-0.0050.00330.5640.0060.0060.0000.0000.0000.000
143B173LEU00.0350.04325.5070.0090.0090.0000.0000.0000.000
144B174VAL00.007-0.00125.1060.0150.0150.0000.0000.0000.000
145B175GLY0-0.004-0.00127.3930.0120.0120.0000.0000.0000.000
146B176LEU0-0.002-0.00228.8210.0060.0060.0000.0000.0000.000
147B177ALA00.0010.00025.2460.0070.0070.0000.0000.0000.000
148B178MET00.0090.01425.2640.0150.0150.0000.0000.0000.000
149B179MET00.0000.00129.0970.0080.0080.0000.0000.0000.000
150B180ARG10.8090.91228.688-0.075-0.0750.0000.0000.0000.000
151B181TYR0-0.015-0.04926.1690.0000.0000.0000.0000.0000.000
152B182VAL0-0.054-0.03026.4040.0160.0160.0000.0000.0000.000
153B183ALA0-0.035-0.02829.0700.0020.0020.0000.0000.0000.000
154B184HIS0-0.031-0.00729.342-0.008-0.0080.0000.0000.0000.000
155B185LEU00.0140.01233.516-0.004-0.0040.0000.0000.0000.000
156B186GLU-1-0.796-0.83536.0570.0720.0720.0000.0000.0000.000
157B187PRO0-0.045-0.04638.598-0.004-0.0040.0000.0000.0000.000
158B188LEU0-0.019-0.03432.8920.0000.0000.0000.0000.0000.000
159B189ALA0-0.012-0.00832.6990.0010.0010.0000.0000.0000.000
160B190SER0-0.034-0.04432.7430.0070.0070.0000.0000.0000.000
161B191ALA0-0.0430.00735.186-0.003-0.0030.0000.0000.0000.000
162B192ASP-1-0.860-0.92733.3160.0590.0590.0000.0000.0000.000
163B193THR0-0.004-0.03527.529-0.006-0.0060.0000.0000.0000.000
164B194ASP-1-0.788-0.86030.8890.0100.0100.0000.0000.0000.000
165B195THR00.0160.00032.950-0.008-0.0080.0000.0000.0000.000
166B196VAL00.0310.03631.687-0.005-0.0050.0000.0000.0000.000
167B197ALA00.0290.00930.257-0.005-0.0050.0000.0000.0000.000
168B198ARG10.8400.92832.138-0.021-0.0210.0000.0000.0000.000
169B199HIS0-0.039-0.04035.451-0.006-0.0060.0000.0000.0000.000
170B200TYR0-0.033-0.04231.475-0.003-0.0030.0000.0000.0000.000
171B201GLY00.0280.01032.760-0.004-0.0040.0000.0000.0000.000
172B202ARG10.8110.88833.7200.0040.0040.0000.0000.0000.000
173B203ALA00.0230.01835.476-0.003-0.0030.0000.0000.0000.000
174B204VAL00.0110.01930.372-0.003-0.0030.0000.0000.0000.000
175B205GLN0-0.037-0.04733.777-0.005-0.0050.0000.0000.0000.000
176B206ALA00.0070.01735.512-0.004-0.0040.0000.0000.0000.000
177B207ILE00.0090.02034.560-0.001-0.0010.0000.0000.0000.000
178B208VAL0-0.031-0.02532.145-0.005-0.0050.0000.0000.0000.000
179B209THR0-0.058-0.04235.072-0.003-0.0030.0000.0000.0000.000
180B210ASP-1-0.935-0.94038.533-0.035-0.0350.0000.0000.0000.000