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

tag_button

FMODB ID: 76M3K

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2215590.126611
FMO2-HF: Nuclear repulsion 2137376.342106
FMO2-HF: Total energy -78213.784505
FMO2-MP2: Total energy -78438.553102


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.
-21.549-10.32816.131-10.101-17.252-0.047
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 : 0.019 / q_NPA : 0.014
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].
3A4TYR0-0.013-0.0082.388-2.978-1.0204.768-1.821-4.9050.003
4A5ASP-1-0.797-0.9354.3890.5040.582-0.001-0.010-0.0680.000
5A6TYR00.0700.0297.784-0.085-0.0850.0000.0000.0000.000
6A7PHE00.0910.02311.3840.0210.0210.0000.0000.0000.000
7A8ARG10.8960.95513.860-0.049-0.0490.0000.0000.0000.000
8A9SER0-0.029-0.00113.246-0.011-0.0110.0000.0000.0000.000
9A10THR00.0920.03915.1110.0310.0310.0000.0000.0000.000
10A11ALA0-0.026-0.01014.1790.0360.0360.0000.0000.0000.000
11A12CYS0-0.0170.0049.4880.0050.0050.0000.0000.0000.000
12A13TYR00.0250.04612.1180.0930.0930.0000.0000.0000.000
13A14ARG10.9460.97914.569-0.163-0.1630.0000.0000.0000.000
14A15VAL0-0.005-0.0068.8610.0220.0220.0000.0000.0000.000
15A16ARG10.8070.8919.729-0.327-0.3270.0000.0000.0000.000
16A17ILE00.0150.01411.4270.0840.0840.0000.0000.0000.000
17A18ALA0-0.025-0.01312.5410.0100.0100.0000.0000.0000.000
18A19LEU0-0.017-0.0136.8510.0110.0110.0000.0000.0000.000
19A20ASN0-0.0160.00610.8130.1960.1960.0000.0000.0000.000
20A21LEU00.0180.00913.444-0.045-0.0450.0000.0000.0000.000
21A22LYS10.8080.91913.259-0.759-0.7590.0000.0000.0000.000
22A23LYS10.8770.92713.603-0.465-0.4650.0000.0000.0000.000
23A24ILE00.0050.0197.572-0.046-0.0460.0000.0000.0000.000
24A25ALA0-0.022-0.0108.5600.1700.1700.0000.0000.0000.000
25A26TYR0-0.041-0.0244.0630.2250.6580.005-0.137-0.3010.001
26A27GLU-1-0.913-0.9562.657-6.169-3.2670.648-1.344-2.206-0.005
27A28LYS10.7960.8972.264-2.028-1.5644.443-2.573-2.334-0.022
28A29ILE00.0360.0202.268-1.475-0.7271.824-0.479-2.0940.000
29A30GLU-1-0.806-0.8854.9510.3400.343-0.001-0.0020.0010.000
30A31VAL0-0.026-0.0077.408-0.087-0.0870.0000.0000.0000.000
31A32HIS0-0.005-0.01410.2000.0680.0680.0000.0000.0000.000
32A33LEU0-0.025-0.00612.9840.0090.0090.0000.0000.0000.000
33A53LEU0-0.026-0.0259.8490.0200.0200.0000.0000.0000.000
34A54VAL0-0.0090.0508.204-0.054-0.0540.0000.0000.0000.000
35A55PRO0-0.009-0.0588.6350.0090.0090.0000.0000.0000.000
36A56SER0-0.072-0.0476.451-0.099-0.0990.0000.0000.0000.000
37A57LEU00.0220.0083.854-0.4390.0140.000-0.167-0.2850.000
38A58ASP-1-0.872-0.9391.946-5.726-4.0063.198-1.859-3.0590.000
39A59ILE0-0.005-0.0152.446-6.331-3.8691.247-1.709-2.001-0.024
40A60ASN0-0.011-0.0114.8560.5160.5160.0000.0000.0000.000
41A61GLY0-0.0120.0055.1180.5610.5610.0000.0000.0000.000
42A62GLN0-0.062-0.0306.7700.3130.3130.0000.0000.0000.000
43A63ILE00.0420.0326.818-0.242-0.2420.0000.0000.0000.000
44A64LEU0-0.0090.0097.6000.2370.2370.0000.0000.0000.000
45A65SER00.014-0.0118.9360.0420.0420.0000.0000.0000.000
46A66GLN00.0120.00411.2690.0690.0690.0000.0000.0000.000
47A67SER00.0270.01912.6530.0270.0270.0000.0000.0000.000
48A68MET00.0210.00613.6770.0680.0680.0000.0000.0000.000
49A69ALA00.0370.02113.9360.0230.0230.0000.0000.0000.000
50A70ILE0-0.022-0.0148.6660.0180.0180.0000.0000.0000.000
51A71ILE00.013-0.00410.8630.1320.1320.0000.0000.0000.000
52A72ASP-1-0.861-0.93313.0300.2810.2810.0000.0000.0000.000
53A73TYR00.0170.0127.693-0.098-0.0980.0000.0000.0000.000
54A74LEU0-0.003-0.0037.4920.0500.0500.0000.0000.0000.000
55A75GLU-1-0.855-0.94311.1890.4140.4140.0000.0000.0000.000
56A76GLU-1-0.985-0.97114.3200.1280.1280.0000.0000.0000.000
57A77ILE0-0.047-0.0338.738-0.014-0.0140.0000.0000.0000.000
58A78HIS0-0.058-0.0259.644-0.050-0.0500.0000.0000.0000.000
59A79PRO00.0130.01414.0430.0210.0210.0000.0000.0000.000
60A80GLU-1-0.941-0.97316.9130.3780.3780.0000.0000.0000.000
61A81MET0-0.052-0.02016.5080.0300.0300.0000.0000.0000.000
62A82PRO00.0030.02018.5200.0250.0250.0000.0000.0000.000
63A83LEU00.018-0.00415.592-0.008-0.0080.0000.0000.0000.000
64A84LEU0-0.056-0.03620.015-0.041-0.0410.0000.0000.0000.000
65A85PRO00.0570.03222.9450.0020.0020.0000.0000.0000.000
66A86LYS10.9540.95825.673-0.169-0.1690.0000.0000.0000.000
67A87ASP-1-0.841-0.92927.5010.1000.1000.0000.0000.0000.000
68A88PRO0-0.0010.00128.6450.0060.0060.0000.0000.0000.000
69A89PHE00.0440.03129.3460.0010.0010.0000.0000.0000.000
70A90MET00.0540.03430.081-0.001-0.0010.0000.0000.0000.000
71A91LYS10.9290.97723.289-0.168-0.1680.0000.0000.0000.000
72A92ALA00.004-0.01125.8760.0090.0090.0000.0000.0000.000
73A93THR0-0.013-0.00927.711-0.004-0.0040.0000.0000.0000.000
74A94LEU00.0450.01625.4180.0000.0000.0000.0000.0000.000
75A95LYS10.8770.94419.991-0.186-0.1860.0000.0000.0000.000
76A96SER0-0.039-0.02124.626-0.003-0.0030.0000.0000.0000.000
77A97MET00.0130.01827.305-0.007-0.0070.0000.0000.0000.000
78A98ALA00.0210.00321.7980.0020.0020.0000.0000.0000.000
79A99LEU0-0.043-0.02922.547-0.002-0.0020.0000.0000.0000.000
80A100ILE00.0510.03924.825-0.009-0.0090.0000.0000.0000.000
81A101VAL00.0020.01322.418-0.007-0.0070.0000.0000.0000.000
82A102ALA0-0.080-0.05820.557-0.008-0.0080.0000.0000.0000.000
83A103CYS0-0.095-0.05622.297-0.014-0.0140.0000.0000.0000.000
84A104ASP-1-0.863-0.92424.9260.0600.0600.0000.0000.0000.000
85A105MET0-0.0620.01425.8930.0010.0010.0000.0000.0000.000
86A106HIS0-0.034-0.02218.601-0.008-0.0080.0000.0000.0000.000
87A107PRO0-0.052-0.02522.694-0.011-0.0110.0000.0000.0000.000
88A108LEU00.0190.01023.713-0.012-0.0120.0000.0000.0000.000
89A109ASN00.0450.02925.367-0.014-0.0140.0000.0000.0000.000
90A110ASN00.0000.01018.904-0.011-0.0110.0000.0000.0000.000
91A111LEU00.0690.03420.805-0.006-0.0060.0000.0000.0000.000
92A112ARG10.9440.95521.1400.0110.0110.0000.0000.0000.000
93A113VAL0-0.012-0.00323.625-0.007-0.0070.0000.0000.0000.000
94A114LEU00.0150.01526.046-0.003-0.0030.0000.0000.0000.000
95A115ASN0-0.014-0.02224.6970.0020.0020.0000.0000.0000.000
96A116ARG10.8780.95127.9990.0160.0160.0000.0000.0000.000
97A117LEU00.0200.00829.781-0.002-0.0020.0000.0000.0000.000
98A118LYS10.9210.96528.734-0.012-0.0120.0000.0000.0000.000
99A119GLU-1-0.921-0.95030.880-0.024-0.0240.0000.0000.0000.000
100A120GLN0-0.0100.00933.074-0.001-0.0010.0000.0000.0000.000
101A121PHE0-0.037-0.02834.8010.0000.0000.0000.0000.0000.000
102A122ASN0-0.052-0.01136.0530.0000.0000.0000.0000.0000.000
103A123ALA0-0.005-0.01234.0650.0020.0020.0000.0000.0000.000
104A124ASN00.0100.01735.1950.0020.0020.0000.0000.0000.000
105A125GLU-1-0.907-0.98034.5080.0320.0320.0000.0000.0000.000
106A126GLU-1-0.886-0.95835.0950.0270.0270.0000.0000.0000.000
107A127GLN00.0210.02536.7610.0010.0010.0000.0000.0000.000
108A128VAL0-0.031-0.01830.1740.0020.0020.0000.0000.0000.000
109A129LEU0-0.018-0.02132.0990.0050.0050.0000.0000.0000.000
110A130GLU-1-0.909-0.93233.8180.0360.0360.0000.0000.0000.000
111A131TRP0-0.044-0.02929.3810.0010.0010.0000.0000.0000.000
112A132TYR0-0.018-0.02424.7650.0070.0070.0000.0000.0000.000
113A133HIS0-0.031-0.05430.8810.0060.0060.0000.0000.0000.000
114A134HIS0-0.0370.01133.3390.0040.0040.0000.0000.0000.000
115A135TRP00.011-0.01229.9620.0020.0020.0000.0000.0000.000
116A136LEU0-0.048-0.01728.0760.0070.0070.0000.0000.0000.000
117A137LYS10.9731.00131.158-0.050-0.0500.0000.0000.0000.000
118A138THR0-0.026-0.00533.4090.0010.0010.0000.0000.0000.000
119A139GLY00.007-0.02230.3480.0010.0010.0000.0000.0000.000
120A140PHE00.008-0.02127.7560.0090.0090.0000.0000.0000.000
121A141ASP-1-0.809-0.88732.3120.0700.0700.0000.0000.0000.000
122A142ALA0-0.035-0.01432.8170.0020.0020.0000.0000.0000.000
123A143PHE0-0.028-0.02926.6490.0040.0040.0000.0000.0000.000
124A144GLU-1-0.712-0.88831.9830.1110.1110.0000.0000.0000.000
125A145GLU-1-0.955-0.98034.5140.0710.0710.0000.0000.0000.000
126A146LYS10.9110.96031.790-0.088-0.0880.0000.0000.0000.000
127A147LEU0-0.043-0.00330.5550.0050.0050.0000.0000.0000.000
128A148GLY00.0110.01233.8960.0030.0030.0000.0000.0000.000
129A149ALA0-0.054-0.01236.560-0.004-0.0040.0000.0000.0000.000
130A150LEU0-0.104-0.04731.4470.0020.0020.0000.0000.0000.000
131A151GLU-1-0.915-0.94935.3340.0940.0940.0000.0000.0000.000
132A152ARG10.7780.88031.982-0.122-0.1220.0000.0000.0000.000
133A153ASP-1-0.886-0.94332.9560.1240.1240.0000.0000.0000.000
134A154LYS10.8640.92328.952-0.183-0.1830.0000.0000.0000.000
135A155PRO00.0260.02130.566-0.001-0.0010.0000.0000.0000.000
136A156VAL00.0260.02126.6880.0140.0140.0000.0000.0000.000
137A157CYS0-0.036-0.03926.715-0.018-0.0180.0000.0000.0000.000
138A158PHE00.010-0.01628.470-0.015-0.0150.0000.0000.0000.000
139A159GLY0-0.0060.02628.8400.0130.0130.0000.0000.0000.000
140A160SER00.021-0.01329.692-0.005-0.0050.0000.0000.0000.000
141A161GLU-1-0.914-0.97223.9160.2950.2950.0000.0000.0000.000
142A162VAL0-0.0290.01021.538-0.011-0.0110.0000.0000.0000.000
143A163GLY00.0240.01021.6180.0180.0180.0000.0000.0000.000
144A164LEU0-0.026-0.02718.1750.0060.0060.0000.0000.0000.000
145A165ALA00.008-0.00220.736-0.001-0.0010.0000.0000.0000.000
146A166ASP-1-0.671-0.83122.8070.2200.2200.0000.0000.0000.000
147A167VAL0-0.027-0.01316.5360.0020.0020.0000.0000.0000.000
148A168CYS0-0.083-0.04519.2460.0060.0060.0000.0000.0000.000
149A169LEU00.0140.02220.876-0.017-0.0170.0000.0000.0000.000
150A170ILE00.0450.02620.782-0.014-0.0140.0000.0000.0000.000
151A171PRO0-0.028-0.02518.554-0.021-0.0210.0000.0000.0000.000
152A172GLN0-0.014-0.00420.916-0.014-0.0140.0000.0000.0000.000
153A173VAL00.0470.02023.750-0.018-0.0180.0000.0000.0000.000
154A174TYR0-0.088-0.05321.220-0.016-0.0160.0000.0000.0000.000
155A175ASN0-0.062-0.05221.378-0.011-0.0110.0000.0000.0000.000
156A176ALA00.0410.02524.699-0.014-0.0140.0000.0000.0000.000
157A177HIS00.0770.05127.944-0.016-0.0160.0000.0000.0000.000
158A178ARG10.9501.00221.575-0.103-0.1030.0000.0000.0000.000
159A179PHE0-0.089-0.04025.010-0.011-0.0110.0000.0000.0000.000
160A180HIS10.8770.93829.778-0.069-0.0690.0000.0000.0000.000
161A181PHE0-0.008-0.00431.630-0.006-0.0060.0000.0000.0000.000
162A182ASP-1-0.901-0.96133.3260.0780.0780.0000.0000.0000.000
163A183MET00.0060.00830.672-0.003-0.0030.0000.0000.0000.000
164A184ALA00.0230.02934.8270.0030.0030.0000.0000.0000.000
165A185SER0-0.039-0.02637.779-0.002-0.0020.0000.0000.0000.000
166A186TYR0-0.084-0.04634.146-0.002-0.0020.0000.0000.0000.000
167A187PRO00.0450.02334.6110.0070.0070.0000.0000.0000.000
168A188ILE00.0470.02933.0660.0060.0060.0000.0000.0000.000
169A189ILE0-0.007-0.01729.6920.0120.0120.0000.0000.0000.000
170A190ASN0-0.087-0.06930.3720.0160.0160.0000.0000.0000.000
171A191GLU-1-0.924-0.95531.5760.1210.1210.0000.0000.0000.000
172A192ILE0-0.044-0.01927.0040.0100.0100.0000.0000.0000.000
173A193ASN0-0.020-0.02325.8520.0300.0300.0000.0000.0000.000
174A194GLU-1-0.923-0.96126.7130.1440.1440.0000.0000.0000.000
175A195TYR00.001-0.00126.5090.0060.0060.0000.0000.0000.000
176A196CYS0-0.008-0.00723.2460.0170.0170.0000.0000.0000.000
177A197LEU0-0.054-0.01622.6730.0290.0290.0000.0000.0000.000
178A198THR0-0.094-0.04024.3380.0030.0030.0000.0000.0000.000
179A199LEU0-0.040-0.01921.6550.0080.0080.0000.0000.0000.000
180A200PRO00.0310.01619.2530.0110.0110.0000.0000.0000.000
181A201ALA00.0080.01616.4790.0300.0300.0000.0000.0000.000
182A202PHE00.0550.01016.3920.0550.0550.0000.0000.0000.000
183A203HIS0-0.020-0.00818.246-0.013-0.0130.0000.0000.0000.000
184A204ASP-1-0.887-0.96515.5060.4070.4070.0000.0000.0000.000
185A205ALA0-0.050-0.01113.9180.0450.0450.0000.0000.0000.000
186A206ALA00.0200.01314.893-0.015-0.0150.0000.0000.0000.000
187A207PRO00.004-0.00816.2530.0190.0190.0000.0000.0000.000
188A208GLU-1-0.826-0.91517.2950.1800.1800.0000.0000.0000.000
189A209ALA0-0.0070.01416.288-0.017-0.0170.0000.0000.0000.000
190A210ILE0-0.092-0.03212.4350.0090.0090.0000.0000.0000.000
191A211SER0-0.064-0.02214.977-0.039-0.0390.0000.0000.0000.000