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: VQ651

Calculation Name: 1N7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1N7K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y948

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2664679.002248
FMO2-HF: Nuclear repulsion 2580404.54479
FMO2-HF: Total energy -84274.457458
FMO2-MP2: Total energy -84525.017628


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-4.4631.1285.857-3.598-7.851-0.017
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.007
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].
3A4ALA00.039-0.0033.778-0.7331.003-0.005-0.855-0.8750.005
4A5ARG10.9770.9736.0960.4710.4710.0000.0000.0000.000
5A6ASP-1-0.776-0.8402.447-1.1440.6421.015-1.248-1.552-0.009
6A7ILE0-0.0130.0032.638-0.4720.1860.314-0.198-0.7750.000
7A8LEU0-0.014-0.0065.0520.0710.116-0.001-0.005-0.0390.000
8A9GLN0-0.067-0.0407.5850.0350.0350.0000.0000.0000.000
9A10GLN00.0360.0222.994-0.3710.0740.040-0.123-0.3630.000
10A11GLY00.0120.0007.9150.0070.0070.0000.0000.0000.000
11A12LEU0-0.063-0.04010.3480.0240.0240.0000.0000.0000.000
12A13ASP-1-0.874-0.92510.2280.1550.1550.0000.0000.0000.000
13A14ARG10.7560.8727.013-0.016-0.0160.0000.0000.0000.000
14A15LEU0-0.064-0.03313.744-0.004-0.0040.0000.0000.0000.000
15A16GLY00.0470.04216.132-0.010-0.0100.0000.0000.0000.000
16A17SER0-0.048-0.04318.679-0.004-0.0040.0000.0000.0000.000
17A18PRO0-0.009-0.02220.949-0.010-0.0100.0000.0000.0000.000
18A19GLU-1-0.817-0.91422.951-0.061-0.0610.0000.0000.0000.000
19A20ASP-1-0.822-0.86518.833-0.034-0.0340.0000.0000.0000.000
20A21LEU0-0.049-0.02917.857-0.010-0.0100.0000.0000.0000.000
21A22ALA00.0130.00119.921-0.009-0.0090.0000.0000.0000.000
22A23SER00.0460.00821.6890.0010.0010.0000.0000.0000.000
23A24ARG10.8470.92114.9600.0720.0720.0000.0000.0000.000
24A25ILE0-0.044-0.01419.138-0.019-0.0190.0000.0000.0000.000
25A26ASP-1-0.728-0.84721.115-0.091-0.0910.0000.0000.0000.000
26A27SER00.0380.01023.012-0.017-0.0170.0000.0000.0000.000
27A28THR0-0.051-0.04024.2870.0060.0060.0000.0000.0000.000
28A29LEU00.0270.02126.684-0.005-0.0050.0000.0000.0000.000
29A30LEU0-0.019-0.00526.2900.0050.0050.0000.0000.0000.000
30A31SER00.0000.00230.119-0.005-0.0050.0000.0000.0000.000
31A32PRO00.018-0.00332.5110.0050.0050.0000.0000.0000.000
32A33ARG10.9400.95735.3770.0910.0910.0000.0000.0000.000
33A34ALA0-0.0170.02034.2350.0020.0020.0000.0000.0000.000
34A35THR00.000-0.01036.3630.0050.0050.0000.0000.0000.000
35A36GLU-1-0.813-0.93738.357-0.051-0.0510.0000.0000.0000.000
36A37GLU-1-0.773-0.85839.553-0.051-0.0510.0000.0000.0000.000
37A38ASP-1-0.837-0.89035.619-0.074-0.0740.0000.0000.0000.000
38A39VAL00.011-0.00434.760-0.003-0.0030.0000.0000.0000.000
39A40ARG10.8120.88735.5590.0480.0480.0000.0000.0000.000
40A41ASN0-0.021-0.01036.2990.0030.0030.0000.0000.0000.000
41A42LEU0-0.0090.01229.101-0.001-0.0010.0000.0000.0000.000
42A43VAL00.000-0.01732.126-0.001-0.0010.0000.0000.0000.000
43A44ARG10.8610.91833.8160.0520.0520.0000.0000.0000.000
44A45GLU-1-0.871-0.93231.841-0.079-0.0790.0000.0000.0000.000
45A46ALA0-0.068-0.03829.564-0.002-0.0020.0000.0000.0000.000
46A47SER00.0100.00330.2070.0020.0020.0000.0000.0000.000
47A48ASP-1-0.978-0.98132.569-0.050-0.0500.0000.0000.0000.000
48A49TYR0-0.109-0.08327.9720.0010.0010.0000.0000.0000.000
49A50GLY00.0060.02727.960-0.001-0.0010.0000.0000.0000.000
50A51PHE0-0.075-0.04724.730-0.004-0.0040.0000.0000.0000.000
51A52ARG10.8140.92221.0240.0740.0740.0000.0000.0000.000
52A53CYS0-0.102-0.06024.4300.0070.0070.0000.0000.0000.000
53A54ALA00.0310.02926.689-0.009-0.0090.0000.0000.0000.000
54A55VAL0-0.036-0.02924.2860.0030.0030.0000.0000.0000.000
55A56LEU00.002-0.00527.754-0.005-0.0050.0000.0000.0000.000
56A57THR00.0290.00430.5740.0010.0010.0000.0000.0000.000
57A58PRO00.0750.04332.4060.0030.0030.0000.0000.0000.000
58A59VAL00.0040.00034.8960.0030.0030.0000.0000.0000.000
59A60TYR0-0.033-0.04135.1860.0040.0040.0000.0000.0000.000
60A61THR00.0050.00333.0560.0010.0010.0000.0000.0000.000
61A62VAL00.0330.01335.2280.0030.0030.0000.0000.0000.000
62A63LYS10.8750.95238.7390.0480.0480.0000.0000.0000.000
63A64ILE00.0040.00635.2780.0020.0020.0000.0000.0000.000
64A65SER00.0100.00537.3530.0010.0010.0000.0000.0000.000
65A66GLY00.0500.03738.3750.0020.0020.0000.0000.0000.000
66A67LEU0-0.045-0.02838.4590.0020.0020.0000.0000.0000.000
67A68ALA00.011-0.01434.8270.0010.0010.0000.0000.0000.000
68A69GLU-1-0.919-0.94336.458-0.023-0.0230.0000.0000.0000.000
69A70LYS10.9000.95238.3800.0310.0310.0000.0000.0000.000
70A71LEU0-0.066-0.04636.7350.0020.0020.0000.0000.0000.000
71A72GLY00.0260.04035.514-0.001-0.0010.0000.0000.0000.000
72A73VAL0-0.052-0.02030.883-0.002-0.0020.0000.0000.0000.000
73A74LYS10.8920.93725.1540.0450.0450.0000.0000.0000.000
74A75LEU00.0220.01030.052-0.006-0.0060.0000.0000.0000.000
75A76CYS0-0.053-0.01924.8570.0030.0030.0000.0000.0000.000
76A77SER00.0810.04128.526-0.004-0.0040.0000.0000.0000.000
77A78VAL0-0.075-0.03226.129-0.001-0.0010.0000.0000.0000.000
78A79ILE00.0150.00328.0920.0060.0060.0000.0000.0000.000
79A80GLY00.006-0.01128.802-0.005-0.0050.0000.0000.0000.000
80A81PHE0-0.0250.01724.706-0.008-0.0080.0000.0000.0000.000
81A82PRO0-0.016-0.02727.1810.0060.0060.0000.0000.0000.000
82A83LEU00.005-0.02627.047-0.007-0.0070.0000.0000.0000.000
83A84GLY00.0820.05028.647-0.001-0.0010.0000.0000.0000.000
84A85GLN0-0.058-0.02829.6660.0020.0020.0000.0000.0000.000
85A86ALA00.0210.03432.5430.0040.0040.0000.0000.0000.000
86A87PRO00.0470.00633.989-0.001-0.0010.0000.0000.0000.000
87A88LEU00.0500.01632.382-0.001-0.0010.0000.0000.0000.000
88A89GLU-1-0.923-0.95734.937-0.030-0.0300.0000.0000.0000.000
89A90VAL00.0190.00236.6950.0000.0000.0000.0000.0000.000
90A91LYS10.7260.84429.3140.0680.0680.0000.0000.0000.000
91A92LEU0-0.011-0.00634.2890.0000.0000.0000.0000.0000.000
92A93VAL00.0070.01835.9120.0010.0010.0000.0000.0000.000
93A94GLU-1-0.830-0.91433.315-0.063-0.0630.0000.0000.0000.000
94A95ALA00.004-0.01732.708-0.001-0.0010.0000.0000.0000.000
95A96GLN00.0070.01934.3450.0010.0010.0000.0000.0000.000
96A97THR0-0.036-0.01237.5210.0000.0000.0000.0000.0000.000
97A98VAL0-0.035-0.02232.9880.0000.0000.0000.0000.0000.000
98A99LEU0-0.055-0.02532.0010.0000.0000.0000.0000.0000.000
99A100GLU-1-0.885-0.93635.716-0.024-0.0240.0000.0000.0000.000
100A101ALA0-0.063-0.02937.6840.0010.0010.0000.0000.0000.000
101A102GLY00.0340.02536.5770.0000.0000.0000.0000.0000.000
102A103ALA0-0.079-0.02631.698-0.001-0.0010.0000.0000.0000.000
103A104THR00.0550.01829.9340.0020.0020.0000.0000.0000.000
104A105GLU-1-0.797-0.87024.353-0.059-0.0590.0000.0000.0000.000
105A106LEU00.0440.02126.546-0.002-0.0020.0000.0000.0000.000
106A107ASP-1-0.793-0.88422.676-0.124-0.1240.0000.0000.0000.000
107A108VAL00.025-0.00724.652-0.002-0.0020.0000.0000.0000.000
108A109VAL0-0.0080.01024.144-0.011-0.0110.0000.0000.0000.000
109A110PRO00.0030.01224.0080.0090.0090.0000.0000.0000.000
110A111HIS00.0320.00626.809-0.012-0.0120.0000.0000.0000.000
111A112LEU0-0.024-0.02921.9230.0060.0060.0000.0000.0000.000
112A113SER00.0060.00225.4170.0050.0050.0000.0000.0000.000
113A114LEU0-0.0130.01027.0200.0050.0050.0000.0000.0000.000
114A115GLY00.0000.01025.8860.0080.0080.0000.0000.0000.000
115A116PRO00.027-0.01022.4750.0020.0020.0000.0000.0000.000
116A117GLU-1-0.782-0.85524.578-0.007-0.0070.0000.0000.0000.000
117A118ALA00.0060.00627.7590.0030.0030.0000.0000.0000.000
118A119VAL00.0380.01823.4210.0010.0010.0000.0000.0000.000
119A120TYR0-0.0040.01125.7020.0020.0020.0000.0000.0000.000
120A121ARG10.8380.90926.9000.0160.0160.0000.0000.0000.000
121A122GLU-1-0.784-0.87728.968-0.059-0.0590.0000.0000.0000.000
122A123VAL00.006-0.00824.3320.0000.0000.0000.0000.0000.000
123A124SER00.007-0.01427.6780.0050.0050.0000.0000.0000.000
124A125GLY0-0.063-0.01729.4240.0040.0040.0000.0000.0000.000
125A126ILE00.018-0.00327.1760.0020.0020.0000.0000.0000.000
126A127VAL00.0020.01626.1320.0010.0010.0000.0000.0000.000
127A128LYS10.9310.97029.2190.0090.0090.0000.0000.0000.000
128A129LEU00.0040.01032.5920.0020.0020.0000.0000.0000.000
129A130ALA00.0510.02029.6830.0010.0010.0000.0000.0000.000
130A131LYS10.9080.95425.8560.0090.0090.0000.0000.0000.000
131A132SER0-0.100-0.03431.9460.0020.0020.0000.0000.0000.000
132A133TYR00.005-0.02933.8770.0020.0020.0000.0000.0000.000
133A134GLY0-0.057-0.02031.6820.0000.0000.0000.0000.0000.000
134A135ALA0-0.026-0.00829.768-0.001-0.0010.0000.0000.0000.000
135A136VAL0-0.066-0.03423.0800.0020.0020.0000.0000.0000.000
136A137VAL0-0.003-0.00824.079-0.007-0.0070.0000.0000.0000.000
137A138LYS10.7660.86520.2680.0890.0890.0000.0000.0000.000
138A139VAL00.013-0.00320.484-0.002-0.0020.0000.0000.0000.000
139A140ILE0-0.046-0.01819.409-0.020-0.0200.0000.0000.0000.000
140A141LEU00.0390.00816.4930.0110.0110.0000.0000.0000.000
141A142GLU-1-0.764-0.83519.152-0.203-0.2030.0000.0000.0000.000
142A143ALA00.0480.01813.6510.0010.0010.0000.0000.0000.000
143A144PRO0-0.049-0.03315.138-0.004-0.0040.0000.0000.0000.000
144A145LEU0-0.0240.00416.1510.0020.0020.0000.0000.0000.000
145A146TRP0-0.035-0.01817.0820.0320.0320.0000.0000.0000.000
146A147ASP-1-0.763-0.85615.063-0.187-0.1870.0000.0000.0000.000
147A148ASP-1-0.779-0.88710.572-0.408-0.4080.0000.0000.0000.000
148A149LYS10.9230.97613.3270.0660.0660.0000.0000.0000.000
149A150THR0-0.035-0.05016.1930.0280.0280.0000.0000.0000.000
150A151LEU00.0230.01712.0840.0130.0130.0000.0000.0000.000
151A152SER00.0410.02114.0110.0240.0240.0000.0000.0000.000
152A153LEU0-0.055-0.02615.4120.0220.0220.0000.0000.0000.000
153A154LEU00.0110.01118.6220.0110.0110.0000.0000.0000.000
154A155VAL00.0200.01914.0040.0070.0070.0000.0000.0000.000
155A156ASP-1-0.802-0.88417.3570.0520.0520.0000.0000.0000.000
156A157SER0-0.048-0.04019.2740.0120.0120.0000.0000.0000.000
157A158SER0-0.006-0.02119.4800.0010.0010.0000.0000.0000.000
158A159ARG10.9130.95618.522-0.039-0.0390.0000.0000.0000.000
159A160ARG10.7720.86220.988-0.028-0.0280.0000.0000.0000.000
160A161ALA0-0.020-0.00224.3020.0030.0030.0000.0000.0000.000
161A162GLY0-0.026-0.00924.414-0.001-0.0010.0000.0000.0000.000
162A163ALA0-0.027-0.01421.798-0.001-0.0010.0000.0000.0000.000
163A164ASP-1-0.827-0.91321.201-0.012-0.0120.0000.0000.0000.000
164A165ILE0-0.039-0.01716.8900.0020.0020.0000.0000.0000.000
165A166VAL00.0220.03715.3140.0020.0020.0000.0000.0000.000
166A167LYS10.8290.89015.8350.1340.1340.0000.0000.0000.000
167A168THR0-0.0150.01213.7200.0090.0090.0000.0000.0000.000
168A169SER0-0.041-0.03415.570-0.002-0.0020.0000.0000.0000.000
169A170THR00.014-0.02018.8310.0130.0130.0000.0000.0000.000
170A171GLY0-0.055-0.02621.3600.0100.0100.0000.0000.0000.000
171A172VAL0-0.062-0.03422.3030.0030.0030.0000.0000.0000.000
172A173TYR00.0110.00024.3720.0010.0010.0000.0000.0000.000
173A174THR00.0260.02118.968-0.018-0.0180.0000.0000.0000.000
174A175LYS10.8390.90018.7980.2380.2380.0000.0000.0000.000
175A176GLY00.0600.02715.094-0.025-0.0250.0000.0000.0000.000
176A177GLY00.0000.00014.033-0.013-0.0130.0000.0000.0000.000
177A178ASP-1-0.786-0.86411.286-0.773-0.7730.0000.0000.0000.000
178A179PRO00.0570.0066.974-0.006-0.0060.0000.0000.0000.000
179A180VAL00.0200.0246.932-0.234-0.2340.0000.0000.0000.000
180A181THR0-0.038-0.0567.9200.0060.0060.0000.0000.0000.000
181A182VAL0-0.052-0.0298.1700.0760.0760.0000.0000.0000.000
182A183PHE00.0520.0282.514-2.449-1.5284.494-1.169-4.247-0.013
183A184ARG10.7700.8705.9230.6980.6980.0000.0000.0000.000
184A185LEU0-0.0100.0048.1680.1600.1600.0000.0000.0000.000
185A186ALA00.006-0.0046.7540.1170.1170.0000.0000.0000.000
186A187SER0-0.068-0.0445.3130.2130.2130.0000.0000.0000.000
187A188LEU0-0.003-0.0027.2140.1880.1880.0000.0000.0000.000
188A189ALA00.008-0.00910.7990.0570.0570.0000.0000.0000.000
189A190LYS10.8430.9048.7570.1060.1060.0000.0000.0000.000
190A191PRO0-0.0310.0029.7710.0300.0300.0000.0000.0000.000
191A192LEU0-0.015-0.00912.6090.0070.0070.0000.0000.0000.000
192A193GLY0-0.031-0.02114.787-0.015-0.0150.0000.0000.0000.000
193A194MET0-0.072-0.00415.299-0.015-0.0150.0000.0000.0000.000
194A195GLY00.0150.01214.208-0.001-0.0010.0000.0000.0000.000
195A196VAL00.000-0.00910.558-0.016-0.0160.0000.0000.0000.000
196A197LYS10.7850.88213.6480.1340.1340.0000.0000.0000.000
197A198ALA00.0410.02212.661-0.023-0.0230.0000.0000.0000.000
198A199SER0-0.002-0.02314.6560.0490.0490.0000.0000.0000.000
199A200GLY00.0350.00917.355-0.019-0.0190.0000.0000.0000.000
200A201GLY0-0.021-0.01918.030-0.030-0.0300.0000.0000.0000.000
201A202ILE0-0.0080.02615.037-0.009-0.0090.0000.0000.0000.000
202A203ARG10.9080.95118.7730.2190.2190.0000.0000.0000.000
203A204SER0-0.011-0.01218.6770.0310.0310.0000.0000.0000.000
204A205GLY00.0700.03518.382-0.014-0.0140.0000.0000.0000.000
205A206ILE00.021-0.00315.434-0.009-0.0090.0000.0000.0000.000
206A207ASP-1-0.780-0.87814.070-0.358-0.3580.0000.0000.0000.000
207A208ALA00.000-0.00313.638-0.042-0.0420.0000.0000.0000.000
208A209VAL00.0340.01612.181-0.013-0.0130.0000.0000.0000.000
209A210LEU0-0.026-0.0119.520-0.025-0.0250.0000.0000.0000.000
210A211ALA0-0.0010.0078.798-0.111-0.1110.0000.0000.0000.000
211A212VAL00.0370.0139.644-0.022-0.0220.0000.0000.0000.000
212A213GLY00.0250.0217.9970.0630.0630.0000.0000.0000.000
213A214ALA0-0.089-0.0425.0320.0450.0450.0000.0000.0000.000
214A215GLY00.0210.0005.674-0.097-0.0970.0000.0000.0000.000
215A216ALA0-0.037-0.0047.6910.0820.0820.0000.0000.0000.000
216A217ASP-1-0.815-0.89511.216-0.037-0.0370.0000.0000.0000.000
217A218ILE0-0.039-0.02414.0480.0180.0180.0000.0000.0000.000
218A219ILE00.0300.01015.404-0.039-0.0390.0000.0000.0000.000
219A220GLY00.0030.01117.3670.0250.0250.0000.0000.0000.000
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