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: 6YGLZ

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2221409.952823
FMO2-HF: Nuclear repulsion 2143194.740121
FMO2-HF: Total energy -78215.212701
FMO2-MP2: Total energy -78439.852168


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.
-20.874-7.8429.285-8.341-13.982-0.063
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 : -0.012 / 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].
3A4TYR00.0020.0053.201-2.9850.1820.513-1.158-2.523-0.001
4A5ASP-1-0.741-0.8904.6840.5810.639-0.001-0.006-0.0510.000
5A6TYR00.0610.0208.128-0.083-0.0830.0000.0000.0000.000
6A7PHE00.0640.01811.7200.0250.0250.0000.0000.0000.000
7A8ARG10.9100.95414.2130.0010.0010.0000.0000.0000.000
8A9SER0-0.029-0.00813.872-0.001-0.0010.0000.0000.0000.000
9A10THR00.0420.00715.6530.0330.0330.0000.0000.0000.000
10A11ALA0-0.014-0.00815.0530.0320.0320.0000.0000.0000.000
11A12CYS0-0.045-0.00910.1600.0130.0130.0000.0000.0000.000
12A13TYR0-0.0230.00212.4380.0950.0950.0000.0000.0000.000
13A14ARG10.9330.97514.637-0.169-0.1690.0000.0000.0000.000
14A15VAL00.0100.0069.0300.0210.0210.0000.0000.0000.000
15A16ARG10.7500.8659.749-0.221-0.2210.0000.0000.0000.000
16A17ILE00.0090.01811.3410.0610.0610.0000.0000.0000.000
17A18ALA0-0.006-0.00412.7310.0030.0030.0000.0000.0000.000
18A19LEU0-0.006-0.0067.0130.0040.0040.0000.0000.0000.000
19A20ASN00.0060.00810.9590.1110.1110.0000.0000.0000.000
20A21LEU0-0.020-0.01413.258-0.062-0.0620.0000.0000.0000.000
21A22LYS10.7650.88013.415-0.709-0.7090.0000.0000.0000.000
22A23LYS10.9070.95413.749-0.431-0.4310.0000.0000.0000.000
23A24ILE00.0010.0237.930-0.033-0.0330.0000.0000.0000.000
24A25ALA0-0.014-0.0128.8730.2230.2230.0000.0000.0000.000
25A26TYR0-0.058-0.0324.3570.3450.575-0.001-0.032-0.1970.000
26A27GLU-1-0.902-0.9452.439-8.537-5.0681.718-2.063-3.125-0.020
27A28LYS10.8580.9202.557-1.0520.4491.486-1.511-1.477-0.016
28A29ILE00.0040.0072.625-1.020-0.5321.458-0.332-1.6140.001
29A30GLU-1-0.806-0.8965.1880.1920.181-0.001-0.0010.0130.000
30A31VAL0-0.018-0.0117.661-0.078-0.0780.0000.0000.0000.000
31A32HIS0-0.014-0.01210.3870.0680.0680.0000.0000.0000.000
32A33LEU0-0.022-0.00413.4930.0120.0120.0000.0000.0000.000
33A53LEU0-0.022-0.02010.4770.0200.0200.0000.0000.0000.000
34A54VAL00.0050.0428.742-0.067-0.0670.0000.0000.0000.000
35A55PRO0-0.027-0.0349.0790.0150.0150.0000.0000.0000.000
36A56SER0-0.060-0.0537.081-0.070-0.0700.0000.0000.0000.000
37A57LEU00.0080.0042.979-0.945-0.1100.157-0.354-0.6390.001
38A58ASP-1-0.877-0.9262.089-3.481-1.9741.676-0.882-2.3020.000
39A59ILE00.0140.0072.237-6.217-4.4292.280-2.002-2.067-0.028
40A60ASN0-0.034-0.0294.8540.3810.3810.0000.0000.0000.000
41A61GLY00.0250.0135.2910.3700.3700.0000.0000.0000.000
42A62GLN0-0.094-0.0427.0210.2670.2670.0000.0000.0000.000
43A63ILE00.0040.0086.946-0.122-0.1220.0000.0000.0000.000
44A64LEU00.0340.0387.1690.2020.2020.0000.0000.0000.000
45A65SER0-0.013-0.0438.608-0.072-0.0720.0000.0000.0000.000
46A66GLN00.0260.00811.2270.0690.0690.0000.0000.0000.000
47A67SER00.0210.01212.5560.0390.0390.0000.0000.0000.000
48A68MET00.0120.00313.3690.0800.0800.0000.0000.0000.000
49A69ALA00.0370.02313.7450.0270.0270.0000.0000.0000.000
50A70ILE0-0.0050.0038.1580.0200.0200.0000.0000.0000.000
51A71ILE00.0130.00310.6790.1450.1450.0000.0000.0000.000
52A72ASP-1-0.794-0.87712.8870.3090.3090.0000.0000.0000.000
53A73TYR00.0130.0037.385-0.016-0.0160.0000.0000.0000.000
54A74LEU00.003-0.0097.3800.0440.0440.0000.0000.0000.000
55A75GLU-1-0.846-0.90411.3250.4360.4360.0000.0000.0000.000
56A76GLU-1-0.994-0.99014.3910.1900.1900.0000.0000.0000.000
57A77ILE0-0.057-0.0358.530-0.019-0.0190.0000.0000.0000.000
58A78HIS00.0040.0069.180-0.068-0.0680.0000.0000.0000.000
59A79PRO0-0.0180.00214.2370.0120.0120.0000.0000.0000.000
60A80GLU-1-0.914-0.96717.0580.3680.3680.0000.0000.0000.000
61A81MET0-0.054-0.03216.8050.0210.0210.0000.0000.0000.000
62A82PRO0-0.0190.01418.5830.0270.0270.0000.0000.0000.000
63A83LEU00.0270.00716.036-0.024-0.0240.0000.0000.0000.000
64A84LEU0-0.021-0.01920.172-0.041-0.0410.0000.0000.0000.000
65A85PRO00.0520.03322.9210.0000.0000.0000.0000.0000.000
66A86LYS11.0170.99725.861-0.177-0.1770.0000.0000.0000.000
67A87ASP-1-0.778-0.87927.3620.1170.1170.0000.0000.0000.000
68A88PRO0-0.009-0.01128.3530.0110.0110.0000.0000.0000.000
69A89PHE00.0380.02829.0140.0040.0040.0000.0000.0000.000
70A90MET00.0330.01729.858-0.001-0.0010.0000.0000.0000.000
71A91LYS10.7960.90823.363-0.170-0.1700.0000.0000.0000.000
72A92ALA00.0190.00425.7350.0090.0090.0000.0000.0000.000
73A93THR0-0.002-0.00127.639-0.003-0.0030.0000.0000.0000.000
74A94LEU00.0340.02225.137-0.001-0.0010.0000.0000.0000.000
75A95LYS10.8040.88019.278-0.237-0.2370.0000.0000.0000.000
76A96SER0-0.048-0.04224.473-0.005-0.0050.0000.0000.0000.000
77A97MET00.0040.01527.098-0.006-0.0060.0000.0000.0000.000
78A98ALA00.0270.00521.4990.0000.0000.0000.0000.0000.000
79A99LEU0-0.028-0.02122.269-0.001-0.0010.0000.0000.0000.000
80A100ILE00.0260.02624.423-0.008-0.0080.0000.0000.0000.000
81A101VAL0-0.001-0.00422.679-0.008-0.0080.0000.0000.0000.000
82A102ALA0-0.062-0.04920.697-0.006-0.0060.0000.0000.0000.000
83A103CYS0-0.108-0.06122.445-0.007-0.0070.0000.0000.0000.000
84A104ASP-1-0.842-0.92125.1440.0730.0730.0000.0000.0000.000
85A105MET0-0.0600.01326.390-0.001-0.0010.0000.0000.0000.000
86A106HIS0-0.024-0.01319.009-0.004-0.0040.0000.0000.0000.000
87A107PRO0-0.050-0.02623.064-0.011-0.0110.0000.0000.0000.000
88A108LEU00.0030.01224.209-0.012-0.0120.0000.0000.0000.000
89A109ASN00.0270.02125.952-0.013-0.0130.0000.0000.0000.000
90A110ASN0-0.0070.00819.192-0.010-0.0100.0000.0000.0000.000
91A111LEU00.0580.01821.418-0.008-0.0080.0000.0000.0000.000
92A112ARG10.9300.96421.117-0.004-0.0040.0000.0000.0000.000
93A113VAL00.0150.01824.065-0.007-0.0070.0000.0000.0000.000
94A114LEU00.0350.02326.422-0.003-0.0030.0000.0000.0000.000
95A115ASN0-0.001-0.00524.8720.0010.0010.0000.0000.0000.000
96A116ARG10.8320.90728.2250.0110.0110.0000.0000.0000.000
97A117LEU00.0190.00830.004-0.002-0.0020.0000.0000.0000.000
98A118LYS10.8940.93628.675-0.004-0.0040.0000.0000.0000.000
99A119GLU-1-0.888-0.92130.928-0.020-0.0200.0000.0000.0000.000
100A120GLN0-0.006-0.00133.402-0.001-0.0010.0000.0000.0000.000
101A121PHE0-0.022-0.02235.1740.0000.0000.0000.0000.0000.000
102A122ASN0-0.070-0.01936.5580.0000.0000.0000.0000.0000.000
103A123ALA00.0020.01834.6460.0010.0010.0000.0000.0000.000
104A124ASN0-0.020-0.02935.4070.0010.0010.0000.0000.0000.000
105A125GLU-1-0.937-0.97634.0800.0280.0280.0000.0000.0000.000
106A126GLU-1-0.832-0.90735.3800.0230.0230.0000.0000.0000.000
107A127GLN00.0550.03137.5210.0010.0010.0000.0000.0000.000
108A128VAL0-0.037-0.02130.8890.0020.0020.0000.0000.0000.000
109A129LEU0-0.026-0.02032.1460.0050.0050.0000.0000.0000.000
110A130GLU-1-0.932-0.95234.0700.0350.0350.0000.0000.0000.000
111A131TRP0-0.034-0.02929.6860.0020.0020.0000.0000.0000.000
112A132TYR0-0.027-0.02424.8770.0080.0080.0000.0000.0000.000
113A133HIS0-0.007-0.02331.3290.0070.0070.0000.0000.0000.000
114A134HIS00.0030.02133.8460.0030.0030.0000.0000.0000.000
115A135TRP0-0.006-0.00430.2290.0030.0030.0000.0000.0000.000
116A136LEU0-0.022-0.00528.0980.0070.0070.0000.0000.0000.000
117A137LYS10.8470.90731.516-0.057-0.0570.0000.0000.0000.000
118A138THR0-0.032-0.02733.5830.0010.0010.0000.0000.0000.000
119A139GLY00.002-0.01130.7990.0010.0010.0000.0000.0000.000
120A140PHE00.014-0.01628.2030.0080.0080.0000.0000.0000.000
121A141ASP-1-0.761-0.83432.6240.0680.0680.0000.0000.0000.000
122A142ALA0-0.016-0.00632.8480.0010.0010.0000.0000.0000.000
123A143PHE0-0.015-0.01826.2920.0050.0050.0000.0000.0000.000
124A144GLU-1-0.730-0.89231.8820.1080.1080.0000.0000.0000.000
125A145GLU-1-0.988-0.97834.5650.0770.0770.0000.0000.0000.000
126A146LYS10.8950.93630.957-0.106-0.1060.0000.0000.0000.000
127A147LEU0-0.063-0.01530.5880.0050.0050.0000.0000.0000.000
128A148GLY00.0410.02133.5820.0020.0020.0000.0000.0000.000
129A149ALA0-0.063-0.01736.571-0.003-0.0030.0000.0000.0000.000
130A150LEU0-0.077-0.03531.6140.0030.0030.0000.0000.0000.000
131A151GLU-1-0.865-0.93435.3460.0960.0960.0000.0000.0000.000
132A152ARG10.7480.86432.029-0.118-0.1180.0000.0000.0000.000
133A153ASP-1-0.870-0.89332.7740.1300.1300.0000.0000.0000.000
134A154LYS10.8560.92629.299-0.167-0.1670.0000.0000.0000.000
135A155PRO00.0560.02830.5030.0000.0000.0000.0000.0000.000
136A156VAL00.0030.01026.6340.0140.0140.0000.0000.0000.000
137A157CYS0-0.036-0.04426.825-0.016-0.0160.0000.0000.0000.000
138A158PHE0-0.019-0.02228.581-0.014-0.0140.0000.0000.0000.000
139A159GLY00.0010.01629.0730.0120.0120.0000.0000.0000.000
140A160SER0-0.018-0.05429.834-0.002-0.0020.0000.0000.0000.000
141A161GLU-1-0.923-0.97024.4860.2750.2750.0000.0000.0000.000
142A162VAL0-0.0230.00221.291-0.011-0.0110.0000.0000.0000.000
143A163GLY00.0330.01521.9850.0170.0170.0000.0000.0000.000
144A164LEU0-0.031-0.03317.7400.0030.0030.0000.0000.0000.000
145A165ALA00.0070.00720.701-0.002-0.0020.0000.0000.0000.000
146A166ASP-1-0.666-0.83122.8900.2120.2120.0000.0000.0000.000
147A167VAL0-0.022-0.01116.627-0.002-0.0020.0000.0000.0000.000
148A168CYS0-0.083-0.03719.1320.0080.0080.0000.0000.0000.000
149A169LEU00.0220.01521.041-0.015-0.0150.0000.0000.0000.000
150A170ILE00.0450.03921.156-0.015-0.0150.0000.0000.0000.000
151A171PRO0-0.021-0.01918.597-0.022-0.0220.0000.0000.0000.000
152A172GLN00.0160.00321.106-0.011-0.0110.0000.0000.0000.000
153A173VAL00.0440.02024.274-0.019-0.0190.0000.0000.0000.000
154A174TYR0-0.079-0.05621.363-0.015-0.0150.0000.0000.0000.000
155A175ASN0-0.033-0.02821.999-0.008-0.0080.0000.0000.0000.000
156A176ALA00.0230.01525.174-0.013-0.0130.0000.0000.0000.000
157A177HIS00.0700.03628.181-0.016-0.0160.0000.0000.0000.000
158A178ARG10.8870.96520.715-0.096-0.0960.0000.0000.0000.000
159A179PHE0-0.067-0.03325.351-0.011-0.0110.0000.0000.0000.000
160A180HIS10.8970.94730.019-0.057-0.0570.0000.0000.0000.000
161A181PHE00.0210.00232.021-0.005-0.0050.0000.0000.0000.000
162A182ASP-1-0.872-0.93633.7280.0710.0710.0000.0000.0000.000
163A183MET0-0.0010.00430.8810.0000.0000.0000.0000.0000.000
164A184ALA00.0170.01134.6490.0030.0030.0000.0000.0000.000
165A185SER0-0.077-0.03937.980-0.002-0.0020.0000.0000.0000.000
166A186TYR0-0.052-0.04434.222-0.002-0.0020.0000.0000.0000.000
167A187PRO00.0350.02034.6030.0070.0070.0000.0000.0000.000
168A188ILE00.0650.03633.0760.0050.0050.0000.0000.0000.000
169A189ILE0-0.005-0.01829.4920.0120.0120.0000.0000.0000.000
170A190ASN0-0.095-0.05629.9930.0120.0120.0000.0000.0000.000
171A191GLU-1-0.908-0.95031.0210.1150.1150.0000.0000.0000.000
172A192ILE0-0.035-0.01826.7400.0090.0090.0000.0000.0000.000
173A193ASN0-0.011-0.01526.2760.0250.0250.0000.0000.0000.000
174A194GLU-1-0.939-0.97126.5450.1260.1260.0000.0000.0000.000
175A195TYR00.010-0.00126.4650.0030.0030.0000.0000.0000.000
176A196CYS0-0.022-0.00423.0660.0150.0150.0000.0000.0000.000
177A197LEU0-0.027-0.01222.3140.0240.0240.0000.0000.0000.000
178A198THR0-0.091-0.04524.210-0.001-0.0010.0000.0000.0000.000
179A199LEU0-0.021-0.00121.8680.0050.0050.0000.0000.0000.000
180A200PRO00.0260.00219.3190.0180.0180.0000.0000.0000.000
181A201ALA0-0.0060.00116.3840.0210.0210.0000.0000.0000.000
182A202PHE00.0630.01016.2320.0580.0580.0000.0000.0000.000
183A203HIS0-0.041-0.02218.479-0.026-0.0260.0000.0000.0000.000
184A204ASP-1-0.847-0.92915.7570.3170.3170.0000.0000.0000.000
185A205ALA0-0.037-0.00513.8690.0360.0360.0000.0000.0000.000
186A206ALA00.0490.02514.847-0.008-0.0080.0000.0000.0000.000
187A207PRO0-0.040-0.02816.5040.0030.0030.0000.0000.0000.000
188A208GLU-1-0.788-0.88717.3950.1370.1370.0000.0000.0000.000
189A209ALA00.0050.03717.034-0.020-0.0200.0000.0000.0000.000
190A210ILE0-0.069-0.02312.4900.0120.0120.0000.0000.0000.000
191A211SER0-0.123-0.06914.878-0.055-0.0550.0000.0000.0000.000