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: LN1V9

Calculation Name: 2NR7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NR7

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXB3

Base Structure: X-ray

Registration Date: 2023-09-24

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2180172.636469
FMO2-HF: Nuclear repulsion 2104289.511962
FMO2-HF: Total energy -75883.124507
FMO2-MP2: Total energy -76110.872663


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:ASN)


Summations of interaction energy for fragment #1(A:-1:ASN)
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.
-3.742-1.1550.223-0.985-1.8260.003
Interaction energy analysis for fragmet #1(A:-1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.022
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].
3A1MET00.0060.0302.972-1.8520.1850.221-0.796-1.4630.004
4A2ALA0-0.026-0.0035.8551.0341.0340.0000.0000.0000.000
5A3ASN00.018-0.0079.558-0.025-0.0250.0000.0000.0000.000
6A4VAL00.0710.03211.8470.2150.2150.0000.0000.0000.000
7A5LYS10.9290.94914.9720.8770.8770.0000.0000.0000.000
8A6LEU0-0.020-0.00712.9390.1140.1140.0000.0000.0000.000
9A7LEU0-0.0050.01716.9780.0800.0800.0000.0000.0000.000
10A8LEU00.004-0.00418.8630.0740.0740.0000.0000.0000.000
11A9PRO00.0380.01720.6060.0540.0540.0000.0000.0000.000
12A10TYR0-0.020-0.02222.1100.0420.0420.0000.0000.0000.000
13A11ILE0-0.002-0.00222.5380.0400.0400.0000.0000.0000.000
14A12LEU00.0200.00725.2020.0360.0360.0000.0000.0000.000
15A13LYS10.9170.97426.5380.3090.3090.0000.0000.0000.000
16A14TRP0-0.071-0.04126.8000.0460.0460.0000.0000.0000.000
17A15GLU-1-0.724-0.83828.566-0.284-0.2840.0000.0000.0000.000
18A16GLY00.0280.01931.1130.0170.0170.0000.0000.0000.000
19A17GLY0-0.024-0.00732.5810.0190.0190.0000.0000.0000.000
20A18PHE0-0.021-0.01532.9980.0160.0160.0000.0000.0000.000
21A19VAL0-0.016-0.00532.420-0.014-0.0140.0000.0000.0000.000
22A20HIS00.0380.02531.4420.0190.0190.0000.0000.0000.000
23A21ASP-1-0.856-0.91534.471-0.153-0.1530.0000.0000.0000.000
24A22PRO00.010-0.00934.748-0.009-0.0090.0000.0000.0000.000
25A23ALA00.028-0.01035.5630.0070.0070.0000.0000.0000.000
26A24ASP-1-0.951-0.96837.448-0.124-0.1240.0000.0000.0000.000
27A25ALA0-0.019-0.00239.7180.0080.0080.0000.0000.0000.000
28A26GLY0-0.028-0.01841.0720.0030.0030.0000.0000.0000.000
29A27GLY0-0.066-0.02337.718-0.003-0.0030.0000.0000.0000.000
30A28ALA0-0.0020.01637.976-0.008-0.0080.0000.0000.0000.000
31A29THR00.002-0.00535.945-0.005-0.0050.0000.0000.0000.000
32A30ASN0-0.053-0.02137.4750.0130.0130.0000.0000.0000.000
33A31LYS10.8550.92236.8770.1860.1860.0000.0000.0000.000
34A32GLY00.0200.00937.3000.0120.0120.0000.0000.0000.000
35A33VAL0-0.050-0.03235.278-0.002-0.0020.0000.0000.0000.000
36A34THR0-0.008-0.01134.490-0.010-0.0100.0000.0000.0000.000
37A35ILE0-0.108-0.03731.9420.0140.0140.0000.0000.0000.000
38A36ALA00.0500.03131.722-0.018-0.0180.0000.0000.0000.000
39A37THR0-0.070-0.06529.0550.0080.0080.0000.0000.0000.000
40A38TRP00.0090.01227.6450.0120.0120.0000.0000.0000.000
41A39LYS10.8730.90529.7790.2900.2900.0000.0000.0000.000
42A40ARG10.8430.92031.6570.2520.2520.0000.0000.0000.000
43A41VAL0-0.036-0.00830.8350.0170.0170.0000.0000.0000.000
44A42GLY0-0.0030.00031.946-0.007-0.0070.0000.0000.0000.000
45A43TYR0-0.095-0.04828.132-0.008-0.0080.0000.0000.0000.000
46A44ASP-1-0.867-0.92630.890-0.198-0.1980.0000.0000.0000.000
47A45LYS10.8460.88630.2070.1900.1900.0000.0000.0000.000
48A46ASP-1-0.856-0.90630.477-0.225-0.2250.0000.0000.0000.000
49A47GLY00.0180.00627.485-0.019-0.0190.0000.0000.0000.000
50A48ASP-1-0.850-0.90926.191-0.312-0.3120.0000.0000.0000.000
51A49GLY0-0.005-0.00527.030-0.022-0.0220.0000.0000.0000.000
52A50ASP-1-0.861-0.91228.210-0.214-0.2140.0000.0000.0000.000
53A51ILE0-0.0180.02026.5800.0100.0100.0000.0000.0000.000
54A52ASP-1-0.867-0.93229.753-0.234-0.2340.0000.0000.0000.000
55A53VAL0-0.031-0.01930.891-0.004-0.0040.0000.0000.0000.000
56A54GLU-1-0.915-0.94733.610-0.173-0.1730.0000.0000.0000.000
57A55ASP-1-0.773-0.88835.523-0.213-0.2130.0000.0000.0000.000
58A56LEU0-0.0010.00428.629-0.003-0.0030.0000.0000.0000.000
59A57LYS10.7400.84731.7860.2050.2050.0000.0000.0000.000
60A58LEU0-0.023-0.00133.9330.0050.0050.0000.0000.0000.000
61A59LEU0-0.0330.00329.7660.0020.0020.0000.0000.0000.000
62A60THR00.013-0.01228.847-0.010-0.0100.0000.0000.0000.000
63A61ASP-1-0.835-0.93325.396-0.362-0.3620.0000.0000.0000.000
64A62ASP-1-0.856-0.94322.696-0.524-0.5240.0000.0000.0000.000
65A63ASP-1-0.830-0.87624.219-0.360-0.3600.0000.0000.0000.000
66A64VAL00.0200.01524.903-0.015-0.0150.0000.0000.0000.000
67A65LEU0-0.021-0.01618.341-0.035-0.0350.0000.0000.0000.000
68A66ASN0-0.077-0.05720.547-0.097-0.0970.0000.0000.0000.000
69A67ARG10.8330.90522.1570.3310.3310.0000.0000.0000.000
70A68VAL0-0.0010.01324.3370.0190.0190.0000.0000.0000.000
71A69LEU0-0.004-0.00420.115-0.019-0.0190.0000.0000.0000.000
72A70LYS10.7580.84713.5141.1781.1780.0000.0000.0000.000
73A71PRO00.0170.02318.682-0.042-0.0420.0000.0000.0000.000
74A72PHE0-0.005-0.00120.5310.0040.0040.0000.0000.0000.000
75A73TYR0-0.047-0.01921.0280.0270.0270.0000.0000.0000.000
76A74TRP0-0.023-0.03711.9030.1420.1420.0000.0000.0000.000
77A75ASP-1-0.780-0.89615.100-1.133-1.1330.0000.0000.0000.000
78A76ARG10.8410.94416.7060.3920.3920.0000.0000.0000.000
79A77TRP0-0.021-0.03215.8100.0450.0450.0000.0000.0000.000
80A78LYS10.8610.91812.6380.5750.5750.0000.0000.0000.000
81A79ALA00.0650.02811.689-0.195-0.1950.0000.0000.0000.000
82A80ASP-1-0.819-0.8799.427-1.865-1.8650.0000.0000.0000.000
83A81LEU0-0.045-0.0306.904-0.742-0.7420.0000.0000.0000.000
84A82ILE0-0.0270.0047.8870.1480.1480.0000.0000.0000.000
85A83GLU-1-0.842-0.9313.882-2.404-1.8540.002-0.189-0.363-0.001
86A84SER0-0.0010.0196.5580.0400.0400.0000.0000.0000.000
87A85GLN00.040-0.0019.414-0.059-0.0590.0000.0000.0000.000
88A86LYS10.8620.92711.5380.5730.5730.0000.0000.0000.000
89A87VAL00.0360.01812.6610.0910.0910.0000.0000.0000.000
90A88ALA00.0430.02312.3980.0960.0960.0000.0000.0000.000
91A89ASN00.0150.00214.3660.0270.0270.0000.0000.0000.000
92A90ILE0-0.0150.00217.2080.0710.0710.0000.0000.0000.000
93A91LEU00.0440.02615.5930.0740.0740.0000.0000.0000.000
94A92VAL00.0050.00916.5690.0620.0620.0000.0000.0000.000
95A93ASP-1-0.784-0.87419.584-0.350-0.3500.0000.0000.0000.000
96A94TRP0-0.0020.00522.1600.0410.0410.0000.0000.0000.000
97A95VAL0-0.0080.00021.7630.0400.0400.0000.0000.0000.000
98A96TRP0-0.040-0.02223.7400.0230.0230.0000.0000.0000.000
99A97GLY00.0450.02025.3860.0290.0290.0000.0000.0000.000
100A98SER0-0.038-0.05927.4550.0240.0240.0000.0000.0000.000
101A99GLY00.0150.01927.0410.0200.0200.0000.0000.0000.000
102A100LYS10.8910.93226.1270.1920.1920.0000.0000.0000.000
103A101TYR00.006-0.00126.4370.0010.0010.0000.0000.0000.000
104A102GLY00.0070.00524.2840.0050.0050.0000.0000.0000.000
105A103ILE0-0.027-0.01021.052-0.043-0.0430.0000.0000.0000.000
106A104VAL00.015-0.00123.0630.0090.0090.0000.0000.0000.000
107A105ILE0-0.034-0.00625.7040.0230.0230.0000.0000.0000.000
108A106PRO00.0410.01220.2350.0200.0200.0000.0000.0000.000
109A107GLN00.010-0.00321.1790.0080.0080.0000.0000.0000.000
110A108ARG10.9520.98922.5460.1950.1950.0000.0000.0000.000
111A109ILE0-0.088-0.04721.2090.0240.0240.0000.0000.0000.000
112A110LEU0-0.0050.00417.0020.0170.0170.0000.0000.0000.000
113A111GLY0-0.0040.02320.6240.0310.0310.0000.0000.0000.000
114A112VAL0-0.093-0.05119.3360.0310.0310.0000.0000.0000.000
115A113GLN0-0.016-0.02022.793-0.007-0.0070.0000.0000.0000.000
116A114ALA00.0140.00623.988-0.023-0.0230.0000.0000.0000.000
117A115ASP-1-0.850-0.91923.536-0.220-0.2200.0000.0000.0000.000
118A116GLY0-0.022-0.02024.5390.0010.0010.0000.0000.0000.000
119A117ILE0-0.052-0.01920.792-0.035-0.0350.0000.0000.0000.000
120A118VAL00.0320.02715.7210.0290.0290.0000.0000.0000.000
121A119GLY00.0360.02217.156-0.051-0.0510.0000.0000.0000.000
122A120ASN00.0340.00012.794-0.070-0.0700.0000.0000.0000.000
123A121LYS10.9700.98814.3220.0180.0180.0000.0000.0000.000
124A122THR00.0380.01516.5530.0410.0410.0000.0000.0000.000
125A123LEU00.0430.02111.0830.0140.0140.0000.0000.0000.000
126A124GLN0-0.032-0.01310.9390.0330.0330.0000.0000.0000.000
127A125ALA0-0.0100.01312.9320.0570.0570.0000.0000.0000.000
128A126VAL0-0.037-0.02711.9260.0250.0250.0000.0000.0000.000
129A127ASN0-0.027-0.0457.242-0.057-0.0570.0000.0000.0000.000
130A128SER0-0.063-0.02910.0050.1410.1410.0000.0000.0000.000
131A129ALA0-0.038-0.00512.3270.0670.0670.0000.0000.0000.000
132A130ASP-1-0.772-0.88312.438-0.315-0.3150.0000.0000.0000.000
133A131PRO0-0.022-0.0239.778-0.060-0.0600.0000.0000.0000.000
134A132ASP-1-0.849-0.92012.885-0.426-0.4260.0000.0000.0000.000
135A133GLU-1-0.917-0.95215.679-0.095-0.0950.0000.0000.0000.000
136A134LEU0-0.0010.00814.3860.0070.0070.0000.0000.0000.000
137A135PHE0-0.039-0.03416.084-0.006-0.0060.0000.0000.0000.000
138A136GLU-1-0.763-0.86617.903-0.267-0.2670.0000.0000.0000.000
139A137SER0-0.0150.00120.7100.0320.0320.0000.0000.0000.000
140A138ILE0-0.045-0.03217.8200.0120.0120.0000.0000.0000.000
141A139PHE00.010-0.01021.9380.0190.0190.0000.0000.0000.000
142A140ASP-1-0.868-0.93023.690-0.173-0.1730.0000.0000.0000.000
143A141ALA00.0270.01525.0430.0130.0130.0000.0000.0000.000
144A142ARG10.7750.87222.6820.3910.3910.0000.0000.0000.000
145A143ARG10.8700.93626.8770.2130.2130.0000.0000.0000.000
146A144GLU-1-0.907-0.95229.667-0.154-0.1540.0000.0000.0000.000
147A145PHE0-0.025-0.01229.4710.0100.0100.0000.0000.0000.000
148A146LEU0-0.010-0.00529.8110.0100.0100.0000.0000.0000.000
149A147GLU-1-0.843-0.92932.865-0.136-0.1360.0000.0000.0000.000
150A148ASP-1-0.819-0.85634.441-0.129-0.1290.0000.0000.0000.000
151A149ILE00.002-0.00733.5660.0120.0120.0000.0000.0000.000
152A150THR0-0.045-0.03736.6910.0060.0060.0000.0000.0000.000
153A151ALA00.0150.00938.9580.0080.0080.0000.0000.0000.000
154A152ARG10.8190.86437.4200.1350.1350.0000.0000.0000.000
155A153SER0-0.057-0.00840.9110.0050.0050.0000.0000.0000.000
156A154ILE00.008-0.01242.6030.0050.0050.0000.0000.0000.000
157A155LYS10.8450.91144.5550.0890.0890.0000.0000.0000.000
158A156LYS10.9730.98941.6690.1290.1290.0000.0000.0000.000
159A157TYR0-0.015-0.02146.9340.0030.0030.0000.0000.0000.000
160A158GLU-1-0.756-0.88148.901-0.081-0.0810.0000.0000.0000.000
161A159ASP-1-0.825-0.89748.996-0.079-0.0790.0000.0000.0000.000
162A160SER0-0.053-0.01951.2240.0020.0020.0000.0000.0000.000
163A161ILE0-0.108-0.04752.9260.0030.0030.0000.0000.0000.000
164A162GLY00.0220.02854.7440.0030.0030.0000.0000.0000.000
165A163ARG10.7920.86355.0460.0750.0750.0000.0000.0000.000
166A164LYS10.8340.90449.5910.0790.0790.0000.0000.0000.000
167A165ALA0-0.0080.00250.3580.0020.0020.0000.0000.0000.000
168A166THR0-0.012-0.02952.162-0.001-0.0010.0000.0000.0000.000
169A167GLU-1-0.808-0.90546.874-0.101-0.1010.0000.0000.0000.000
170A168ARG10.9860.98248.9090.0800.0800.0000.0000.0000.000
171A169GLU-1-0.756-0.82050.103-0.083-0.0830.0000.0000.0000.000
172A170LEU00.0390.02146.164-0.004-0.0040.0000.0000.0000.000
173A171LEU0-0.0010.01444.114-0.006-0.0060.0000.0000.0000.000
174A172ARG10.8700.93545.7800.0930.0930.0000.0000.0000.000
175A173HIS00.0040.01047.291-0.006-0.0060.0000.0000.0000.000
176A174THR0-0.016-0.00543.987-0.001-0.0010.0000.0000.0000.000
177A175ASN00.038-0.00238.510-0.003-0.0030.0000.0000.0000.000
178A176LYS10.8820.94239.5910.1010.1010.0000.0000.0000.000
179A177ARG10.8310.92041.1980.1320.1320.0000.0000.0000.000
180A178PHE00.003-0.00936.8260.0010.0010.0000.0000.0000.000
181A179LEU00.0130.03734.925-0.010-0.0100.0000.0000.0000.000
182A180ARG10.9830.98935.0900.1280.1280.0000.0000.0000.000
183A181GLY00.0080.00634.516-0.006-0.0060.0000.0000.0000.000
184A182TRP00.0660.01131.893-0.012-0.0120.0000.0000.0000.000
185A183LEU00.0250.02330.326-0.019-0.0190.0000.0000.0000.000
186A184ASN0-0.029-0.02129.903-0.006-0.0060.0000.0000.0000.000
187A185ARG10.8260.89826.0080.3380.3380.0000.0000.0000.000
188A186LEU0-0.0040.01224.703-0.025-0.0250.0000.0000.0000.000
189A187GLU-1-0.834-0.93425.003-0.252-0.2520.0000.0000.0000.000
190A188ASP-1-0.868-0.94325.066-0.298-0.2980.0000.0000.0000.000
191A189ILE0-0.0050.00620.331-0.021-0.0210.0000.0000.0000.000
192A190ARG10.7300.84820.2050.2240.2240.0000.0000.0000.000
193A191LYS10.7930.89519.9750.2470.2470.0000.0000.0000.000
194A192LEU0-0.0350.01216.9890.0030.0030.0000.0000.0000.000