FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 2NL7R

Calculation Name: 3NIV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NIV

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZT82

Base Structure: X-ray

Registration Date: 2023-09-21

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2214955.190674
FMO2-HF: Nuclear repulsion 2136740.47931
FMO2-HF: Total energy -78214.711363
FMO2-MP2: Total energy -78439.408488


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:2:ILE)


Summations of interaction energy for fragment #1(A:2:ILE)
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.
-22.948-10.33313.474-9.945-16.145-0.059
Interaction energy analysis for fragmet #1(A:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / 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].
3A4TYR0-0.0010.0002.919-3.4380.0171.313-1.469-3.2980.001
4A5ASP-1-0.771-0.9064.7350.4970.551-0.001-0.005-0.0490.000
5A6TYR00.0660.0268.192-0.074-0.0740.0000.0000.0000.000
6A7PHE00.0900.02611.7640.0280.0280.0000.0000.0000.000
7A8ARG10.8900.94614.020-0.033-0.0330.0000.0000.0000.000
8A9SER0-0.037-0.00813.575-0.006-0.0060.0000.0000.0000.000
9A10THR00.0810.03815.5110.0280.0280.0000.0000.0000.000
10A11ALA0-0.021-0.00614.4450.0340.0340.0000.0000.0000.000
11A12CYS0-0.029-0.0049.9250.0130.0130.0000.0000.0000.000
12A13TYR00.0140.03212.2670.0820.0820.0000.0000.0000.000
13A14ARG10.9440.97614.530-0.174-0.1740.0000.0000.0000.000
14A15VAL0-0.004-0.0058.8670.0280.0280.0000.0000.0000.000
15A16ARG10.7850.8789.731-0.266-0.2660.0000.0000.0000.000
16A17ILE00.0220.01511.3830.0750.0750.0000.0000.0000.000
17A18ALA0-0.020-0.00912.5930.0090.0090.0000.0000.0000.000
18A19LEU0-0.014-0.0127.0010.0270.0270.0000.0000.0000.000
19A20ASN0-0.037-0.00810.8130.1440.1440.0000.0000.0000.000
20A21LEU00.0250.01513.385-0.043-0.0430.0000.0000.0000.000
21A22LYS10.8030.91313.420-0.758-0.7580.0000.0000.0000.000
22A23LYS10.8920.93713.584-0.409-0.4090.0000.0000.0000.000
23A24ILE0-0.0130.0117.572-0.034-0.0340.0000.0000.0000.000
24A25ALA0-0.019-0.0098.5340.1490.1490.0000.0000.0000.000
25A26TYR0-0.021-0.0184.1270.1620.6010.004-0.129-0.3130.001
26A27GLU-1-0.906-0.9552.471-8.833-5.2221.670-2.144-3.137-0.015
27A28LYS10.8460.9292.259-2.107-1.6904.514-2.635-2.297-0.024
28A29ILE00.0420.0232.428-0.911-0.9902.921-0.547-2.2960.000
29A30GLU-1-0.839-0.9074.9480.3070.306-0.001-0.0020.0040.000
30A31VAL0-0.026-0.0127.556-0.065-0.0650.0000.0000.0000.000
31A32HIS0-0.005-0.01510.2610.0590.0590.0000.0000.0000.000
32A33LEU0-0.017-0.00113.2670.0130.0130.0000.0000.0000.000
33A53LEU0-0.029-0.0239.7760.0120.0120.0000.0000.0000.000
34A54VAL0-0.0010.0628.408-0.036-0.0360.0000.0000.0000.000
35A55PRO00.001-0.0458.8360.0020.0020.0000.0000.0000.000
36A56SER0-0.067-0.0646.594-0.063-0.0630.0000.0000.0000.000
37A57LEU00.0070.0063.979-0.507-0.0620.002-0.157-0.2890.000
38A58ASP-1-0.874-0.9352.144-4.023-2.2031.824-1.119-2.5260.001
39A59ILE00.001-0.0132.444-6.171-3.7171.228-1.738-1.944-0.023
40A60ASN0-0.017-0.0144.8850.3880.3880.0000.0000.0000.000
41A61GLY0-0.0010.0055.0710.4440.4440.0000.0000.0000.000
42A62GLN0-0.064-0.0306.8670.2560.2560.0000.0000.0000.000
43A63ILE00.0180.0226.613-0.180-0.1800.0000.0000.0000.000
44A64LEU00.0030.0147.6600.1650.1650.0000.0000.0000.000
45A65SER00.008-0.0158.6970.0290.0290.0000.0000.0000.000
46A66GLN00.0340.01211.0680.0560.0560.0000.0000.0000.000
47A67SER00.0300.02012.7200.0280.0280.0000.0000.0000.000
48A68MET00.010-0.00213.7390.0680.0680.0000.0000.0000.000
49A69ALA00.0240.01614.0800.0180.0180.0000.0000.0000.000
50A70ILE0-0.023-0.0158.5400.0250.0250.0000.0000.0000.000
51A71ILE00.012-0.00210.8770.1280.1280.0000.0000.0000.000
52A72ASP-1-0.794-0.87413.0460.3020.3020.0000.0000.0000.000
53A73TYR00.0450.0217.363-0.091-0.0910.0000.0000.0000.000
54A74LEU0-0.0020.0017.3760.0400.0400.0000.0000.0000.000
55A75GLU-1-0.859-0.94811.2010.4020.4020.0000.0000.0000.000
56A76GLU-1-0.995-0.97914.3020.1530.1530.0000.0000.0000.000
57A77ILE0-0.051-0.0288.650-0.018-0.0180.0000.0000.0000.000
58A78HIS0-0.042-0.0219.262-0.075-0.0750.0000.0000.0000.000
59A79PRO00.0140.01614.0510.0170.0170.0000.0000.0000.000
60A80GLU-1-0.940-0.97717.1790.3510.3510.0000.0000.0000.000
61A81MET0-0.057-0.02316.4710.0280.0280.0000.0000.0000.000
62A82PRO0-0.0020.00918.4110.0270.0270.0000.0000.0000.000
63A83LEU00.0230.00915.802-0.010-0.0100.0000.0000.0000.000
64A84LEU0-0.044-0.02720.029-0.040-0.0400.0000.0000.0000.000
65A85PRO00.0690.04122.9580.0000.0000.0000.0000.0000.000
66A86LYS10.9900.98125.686-0.167-0.1670.0000.0000.0000.000
67A87ASP-1-0.788-0.89927.5130.1090.1090.0000.0000.0000.000
68A88PRO0-0.004-0.00228.6480.0060.0060.0000.0000.0000.000
69A89PHE00.0400.02929.3600.0020.0020.0000.0000.0000.000
70A90MET00.0440.02530.028-0.001-0.0010.0000.0000.0000.000
71A91LYS10.8090.91223.447-0.168-0.1680.0000.0000.0000.000
72A92ALA00.0180.00025.8910.0100.0100.0000.0000.0000.000
73A93THR0-0.008-0.01027.726-0.003-0.0030.0000.0000.0000.000
74A94LEU00.0360.01825.405-0.001-0.0010.0000.0000.0000.000
75A95LYS10.8040.88319.411-0.223-0.2230.0000.0000.0000.000
76A96SER0-0.031-0.02524.642-0.003-0.0030.0000.0000.0000.000
77A97MET00.0020.00427.309-0.008-0.0080.0000.0000.0000.000
78A98ALA00.0140.00421.8020.0010.0010.0000.0000.0000.000
79A99LEU0-0.031-0.02522.5560.0000.0000.0000.0000.0000.000
80A100ILE00.0470.04124.841-0.008-0.0080.0000.0000.0000.000
81A101VAL0-0.0070.00122.826-0.007-0.0070.0000.0000.0000.000
82A102ALA0-0.079-0.05520.685-0.007-0.0070.0000.0000.0000.000
83A103CYS0-0.099-0.05822.383-0.005-0.0050.0000.0000.0000.000
84A104ASP-1-0.852-0.92224.9920.0750.0750.0000.0000.0000.000
85A105MET0-0.0540.02126.139-0.001-0.0010.0000.0000.0000.000
86A106HIS0-0.039-0.02618.982-0.004-0.0040.0000.0000.0000.000
87A107PRO0-0.044-0.02122.561-0.010-0.0100.0000.0000.0000.000
88A108LEU00.0140.01223.831-0.010-0.0100.0000.0000.0000.000
89A109ASN00.0250.01325.596-0.013-0.0130.0000.0000.0000.000
90A110ASN0-0.0050.00518.981-0.009-0.0090.0000.0000.0000.000
91A111LEU00.0710.03520.994-0.007-0.0070.0000.0000.0000.000
92A112ARG10.9340.95920.719-0.018-0.0180.0000.0000.0000.000
93A113VAL0-0.0010.00123.761-0.007-0.0070.0000.0000.0000.000
94A114LEU00.0260.02226.299-0.004-0.0040.0000.0000.0000.000
95A115ASN0-0.002-0.01224.759-0.001-0.0010.0000.0000.0000.000
96A116ARG10.8370.92228.1330.0000.0000.0000.0000.0000.000
97A117LEU00.0260.01229.891-0.002-0.0020.0000.0000.0000.000
98A118LYS10.8810.94128.594-0.016-0.0160.0000.0000.0000.000
99A119GLU-1-0.868-0.91030.778-0.009-0.0090.0000.0000.0000.000
100A120GLN0-0.0050.00333.199-0.001-0.0010.0000.0000.0000.000
101A121PHE0-0.033-0.02934.925-0.001-0.0010.0000.0000.0000.000
102A122ASN0-0.067-0.02036.1890.0000.0000.0000.0000.0000.000
103A123ALA0-0.010-0.00134.2800.0010.0010.0000.0000.0000.000
104A124ASN0-0.024-0.02735.4450.0010.0010.0000.0000.0000.000
105A125GLU-1-0.925-0.97934.2710.0330.0330.0000.0000.0000.000
106A126GLU-1-0.839-0.92035.4220.0280.0280.0000.0000.0000.000
107A127GLN00.0470.03137.2820.0020.0020.0000.0000.0000.000
108A128VAL0-0.037-0.02030.5460.0030.0030.0000.0000.0000.000
109A129LEU0-0.020-0.01932.2720.0050.0050.0000.0000.0000.000
110A130GLU-1-0.910-0.93734.1410.0380.0380.0000.0000.0000.000
111A131TRP0-0.022-0.01729.5030.0010.0010.0000.0000.0000.000
112A132TYR0-0.031-0.02824.9860.0070.0070.0000.0000.0000.000
113A133HIS0-0.005-0.02631.1670.0060.0060.0000.0000.0000.000
114A134HIS0-0.0220.01333.6470.0030.0030.0000.0000.0000.000
115A135TRP0-0.001-0.01230.2230.0020.0020.0000.0000.0000.000
116A136LEU0-0.014-0.00228.0780.0070.0070.0000.0000.0000.000
117A137LYS10.8720.92731.442-0.056-0.0560.0000.0000.0000.000
118A138THR0-0.037-0.01833.5240.0010.0010.0000.0000.0000.000
119A139GLY00.012-0.02230.5800.0010.0010.0000.0000.0000.000
120A140PHE00.008-0.01828.2430.0090.0090.0000.0000.0000.000
121A141ASP-1-0.761-0.83032.5740.0700.0700.0000.0000.0000.000
122A142ALA0-0.028-0.00932.9980.0010.0010.0000.0000.0000.000
123A143PHE0-0.019-0.02626.4480.0040.0040.0000.0000.0000.000
124A144GLU-1-0.742-0.89231.9830.1080.1080.0000.0000.0000.000
125A145GLU-1-0.960-0.98134.5140.0740.0740.0000.0000.0000.000
126A146LYS10.9040.95831.181-0.102-0.1020.0000.0000.0000.000
127A147LEU0-0.053-0.00430.7790.0040.0040.0000.0000.0000.000
128A148GLY00.0330.01933.8960.0020.0020.0000.0000.0000.000
129A149ALA0-0.057-0.01636.578-0.004-0.0040.0000.0000.0000.000
130A150LEU0-0.101-0.04531.4970.0020.0020.0000.0000.0000.000
131A151GLU-1-0.885-0.93435.3370.0930.0930.0000.0000.0000.000
132A152ARG10.7640.86932.170-0.117-0.1170.0000.0000.0000.000
133A153ASP-1-0.840-0.88432.8110.1240.1240.0000.0000.0000.000
134A154LYS10.8600.91729.076-0.170-0.1700.0000.0000.0000.000
135A155PRO00.0260.02230.7260.0000.0000.0000.0000.0000.000
136A156VAL00.0200.01526.6330.0130.0130.0000.0000.0000.000
137A157CYS0-0.047-0.04626.754-0.016-0.0160.0000.0000.0000.000
138A158PHE00.002-0.01728.471-0.014-0.0140.0000.0000.0000.000
139A159GLY0-0.0070.02428.8400.0120.0120.0000.0000.0000.000
140A160SER0-0.029-0.06329.697-0.004-0.0040.0000.0000.0000.000
141A161GLU-1-0.919-0.96824.2140.2780.2780.0000.0000.0000.000
142A162VAL0-0.0200.00821.331-0.011-0.0110.0000.0000.0000.000
143A163GLY00.0290.00921.6210.0180.0180.0000.0000.0000.000
144A164LEU0-0.024-0.02518.0260.0050.0050.0000.0000.0000.000
145A165ALA00.0120.00320.7510.0000.0000.0000.0000.0000.000
146A166ASP-1-0.663-0.82822.8000.2120.2120.0000.0000.0000.000
147A167VAL0-0.029-0.01416.6160.0010.0010.0000.0000.0000.000
148A168CYS0-0.100-0.05219.2210.0070.0070.0000.0000.0000.000
149A169LEU00.0180.01920.876-0.017-0.0170.0000.0000.0000.000
150A170ILE00.0400.02620.849-0.014-0.0140.0000.0000.0000.000
151A171PRO0-0.025-0.01718.473-0.021-0.0210.0000.0000.0000.000
152A172GLN0-0.007-0.00721.025-0.012-0.0120.0000.0000.0000.000
153A173VAL00.0480.02424.096-0.018-0.0180.0000.0000.0000.000
154A174TYR0-0.080-0.05821.537-0.015-0.0150.0000.0000.0000.000
155A175ASN0-0.066-0.05621.694-0.011-0.0110.0000.0000.0000.000
156A176ALA00.0450.02825.104-0.013-0.0130.0000.0000.0000.000
157A177HIS00.0780.05128.083-0.016-0.0160.0000.0000.0000.000
158A178ARG10.9410.99521.506-0.101-0.1010.0000.0000.0000.000
159A179PHE0-0.085-0.03525.526-0.010-0.0100.0000.0000.0000.000
160A180HIS10.8730.92630.191-0.064-0.0640.0000.0000.0000.000
161A181PHE00.004-0.00631.950-0.005-0.0050.0000.0000.0000.000
162A182ASP-1-0.880-0.94333.7380.0740.0740.0000.0000.0000.000
163A183MET00.0040.00730.786-0.002-0.0020.0000.0000.0000.000
164A184ALA00.0110.01534.9330.0030.0030.0000.0000.0000.000
165A185SER0-0.050-0.02837.994-0.002-0.0020.0000.0000.0000.000
166A186TYR0-0.072-0.05734.136-0.001-0.0010.0000.0000.0000.000
167A187PRO00.0430.02334.5690.0070.0070.0000.0000.0000.000
168A188ILE00.0630.03233.3120.0060.0060.0000.0000.0000.000
169A189ILE0-0.005-0.01329.5130.0110.0110.0000.0000.0000.000
170A190ASN0-0.080-0.05830.3270.0140.0140.0000.0000.0000.000
171A191GLU-1-0.935-0.96031.5320.1120.1120.0000.0000.0000.000
172A192ILE0-0.036-0.01627.0030.0090.0090.0000.0000.0000.000
173A193ASN0-0.024-0.02126.1440.0250.0250.0000.0000.0000.000
174A194GLU-1-0.921-0.96026.6680.1280.1280.0000.0000.0000.000
175A195TYR00.000-0.00526.5900.0040.0040.0000.0000.0000.000
176A196CYS0-0.018-0.00323.2550.0140.0140.0000.0000.0000.000
177A197LEU0-0.055-0.02022.5650.0250.0250.0000.0000.0000.000
178A198THR0-0.082-0.04424.2960.0000.0000.0000.0000.0000.000
179A199LEU0-0.036-0.01521.7410.0060.0060.0000.0000.0000.000
180A200PRO00.0470.01719.2150.0110.0110.0000.0000.0000.000
181A201ALA0-0.0070.01016.4250.0260.0260.0000.0000.0000.000
182A202PHE00.0600.01116.3430.0540.0540.0000.0000.0000.000
183A203HIS0-0.042-0.02918.204-0.015-0.0150.0000.0000.0000.000
184A204ASP-1-0.866-0.94515.5860.3350.3350.0000.0000.0000.000
185A205ALA0-0.054-0.01213.8800.0350.0350.0000.0000.0000.000
186A206ALA00.0290.01814.856-0.011-0.0110.0000.0000.0000.000
187A207PRO0-0.001-0.01016.2890.0110.0110.0000.0000.0000.000
188A208GLU-1-0.826-0.90317.2700.1520.1520.0000.0000.0000.000
189A209ALA00.0040.02916.332-0.021-0.0210.0000.0000.0000.000
190A210ILE0-0.092-0.03112.4680.0040.0040.0000.0000.0000.000
191A211SER0-0.089-0.04715.026-0.045-0.0450.0000.0000.0000.000