FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R9RR8

Calculation Name: 2NLZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NLZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KEI5

Base Structure: X-ray

Registration Date: 2023-09-20

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 540
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11452170.791903
FMO2-HF: Nuclear repulsion 11245284.211849
FMO2-HF: Total energy -206886.580053
FMO2-MP2: Total energy -207492.416771


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:3:VAL)


Summations of interaction energy for fragment #1(A:3:VAL)
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.
-1.080.424-0.015-0.754-0.7350.002
Interaction energy analysis for fragmet #1(A:3:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.032
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].
3A5PHE0-0.013-0.0123.885-1.1610.343-0.015-0.754-0.7350.002
4A6ASP-1-0.922-0.9536.6470.2960.2960.0000.0000.0000.000
5A7PRO0-0.0190.0077.2990.2760.2760.0000.0000.0000.000
6A8GLN0-0.027-0.0218.697-0.019-0.0190.0000.0000.0000.000
7A9SER0-0.034-0.02312.149-0.023-0.0230.0000.0000.0000.000
8A10TYR00.0300.00913.823-0.023-0.0230.0000.0000.0000.000
9A11PRO0-0.026-0.01015.5350.0010.0010.0000.0000.0000.000
10A12TYR0-0.011-0.00117.410-0.010-0.0100.0000.0000.0000.000
11A13PRO00.0190.02121.5910.0120.0120.0000.0000.0000.000
12A14SER00.005-0.00822.886-0.009-0.0090.0000.0000.0000.000
13A15ARG10.8940.92825.007-0.011-0.0110.0000.0000.0000.000
14A16ARG10.9150.99924.400-0.089-0.0890.0000.0000.0000.000
15A17ASN0-0.002-0.01029.170-0.007-0.0070.0000.0000.0000.000
16A18VAL00.0190.01832.7590.0040.0040.0000.0000.0000.000
17A19VAL0-0.0170.01332.648-0.003-0.0030.0000.0000.0000.000
18A20TYR00.003-0.01935.5910.0000.0000.0000.0000.0000.000
19A21ALA0-0.014-0.00438.7730.0010.0010.0000.0000.0000.000
20A22LYS10.8100.90641.223-0.024-0.0240.0000.0000.0000.000
21A23ASN00.003-0.01744.1820.0000.0000.0000.0000.0000.000
22A24GLY00.0200.00942.2760.0010.0010.0000.0000.0000.000
23A25MET0-0.099-0.02137.4320.0000.0000.0000.0000.0000.000
24A26VAL00.0280.02034.5270.0010.0010.0000.0000.0000.000
25A27ALA0-0.0050.00233.2960.0000.0000.0000.0000.0000.000
26A28THR00.005-0.00430.3940.0030.0030.0000.0000.0000.000
27A29SER0-0.040-0.02527.195-0.004-0.0040.0000.0000.0000.000
28A30GLN00.0310.00823.7230.0220.0220.0000.0000.0000.000
29A31PRO00.0270.01724.026-0.009-0.0090.0000.0000.0000.000
30A32LEU00.0230.01824.441-0.010-0.0100.0000.0000.0000.000
31A33ALA00.0330.02728.031-0.006-0.0060.0000.0000.0000.000
32A34ALA00.0230.00830.398-0.008-0.0080.0000.0000.0000.000
33A35GLN0-0.048-0.03130.303-0.009-0.0090.0000.0000.0000.000
34A36ALA00.0280.01632.215-0.005-0.0050.0000.0000.0000.000
35A37GLY00.0460.02134.374-0.005-0.0050.0000.0000.0000.000
36A38LEU0-0.021-0.02133.838-0.005-0.0050.0000.0000.0000.000
37A39ASP-1-0.882-0.92034.8570.0670.0670.0000.0000.0000.000
38A40ILE0-0.0210.00137.468-0.004-0.0040.0000.0000.0000.000
39A41LEU00.0120.01239.969-0.003-0.0030.0000.0000.0000.000
40A42LYS10.7740.88034.816-0.063-0.0630.0000.0000.0000.000
41A43ALA0-0.045-0.01041.630-0.003-0.0030.0000.0000.0000.000
42A44GLY00.0080.01443.626-0.001-0.0010.0000.0000.0000.000
43A45GLY0-0.027-0.01244.380-0.001-0.0010.0000.0000.0000.000
44A46ASN0-0.030-0.03345.0550.0000.0000.0000.0000.0000.000
45A47ALA00.019-0.00942.9000.0030.0030.0000.0000.0000.000
46A48ILE0-0.0030.00842.5780.0040.0040.0000.0000.0000.000
47A49ASP-1-0.752-0.85443.1920.0520.0520.0000.0000.0000.000
48A50ALA00.0390.01739.3200.0040.0040.0000.0000.0000.000
49A51ALA0-0.0010.01238.3880.0060.0060.0000.0000.0000.000
50A52ILE00.0340.02038.5620.0050.0050.0000.0000.0000.000
51A53ALA00.0220.02837.6690.0050.0050.0000.0000.0000.000
52A54THR0-0.051-0.03733.3890.0070.0070.0000.0000.0000.000
53A55ALA0-0.001-0.00733.9800.0080.0080.0000.0000.0000.000
54A56THR0-0.014-0.02535.1360.0070.0070.0000.0000.0000.000
55A57ALA00.0280.00731.8380.0070.0070.0000.0000.0000.000
56A58LEU0-0.004-0.01529.5400.0130.0130.0000.0000.0000.000
57A59THR0-0.047-0.01130.5710.0100.0100.0000.0000.0000.000
58A60VAL0-0.037-0.01028.8370.0060.0060.0000.0000.0000.000
59A61LEU0-0.029-0.00926.2650.0160.0160.0000.0000.0000.000
60A62GLU-1-0.774-0.84425.5140.1690.1690.0000.0000.0000.000
61A63PRO00.0090.00425.878-0.008-0.0080.0000.0000.0000.000
62A64THR0-0.029-0.00923.4190.0000.0000.0000.0000.0000.000
63A65SER0-0.076-0.05426.863-0.002-0.0020.0000.0000.0000.000
64A66ASN00.0010.01629.756-0.019-0.0190.0000.0000.0000.000
65A67GLY00.0490.03031.7770.0100.0100.0000.0000.0000.000
66A68ILE00.0130.00734.088-0.006-0.0060.0000.0000.0000.000
67A69GLY00.0370.01236.974-0.006-0.0060.0000.0000.0000.000
68A70SER0-0.026-0.02436.1300.0000.0000.0000.0000.0000.000
69A71ASP-1-0.779-0.87138.4530.0690.0690.0000.0000.0000.000
70A72ALA00.005-0.00739.9190.0040.0040.0000.0000.0000.000
71A73PHE00.0120.01541.787-0.004-0.0040.0000.0000.0000.000
72A74ALA0-0.019-0.01542.4650.0030.0030.0000.0000.0000.000
73A75LEU0-0.0160.01644.586-0.003-0.0030.0000.0000.0000.000
74A76VAL00.022-0.00545.4590.0020.0020.0000.0000.0000.000
75A77TRP00.0220.02447.715-0.001-0.0010.0000.0000.0000.000
76A78THR00.001-0.03449.3400.0000.0000.0000.0000.0000.000
77A79LYS10.8930.93951.863-0.036-0.0360.0000.0000.0000.000
78A80GLY00.0070.01554.604-0.001-0.0010.0000.0000.0000.000
79A81LYS10.8460.91354.814-0.034-0.0340.0000.0000.0000.000
80A82LEU00.0190.02048.6660.0010.0010.0000.0000.0000.000
81A83HIS0-0.007-0.00751.168-0.001-0.0010.0000.0000.0000.000
82A84GLY00.0500.02549.2810.0020.0020.0000.0000.0000.000
83A85LEU0-0.066-0.02146.564-0.001-0.0010.0000.0000.0000.000
84A86ASN00.014-0.01547.0690.0050.0050.0000.0000.0000.000
85A87GLY00.0300.00745.776-0.001-0.0010.0000.0000.0000.000
86A88SER0-0.031-0.01545.1690.0040.0040.0000.0000.0000.000
87A89GLY00.0160.00745.116-0.003-0.0030.0000.0000.0000.000
88A90ARG10.7760.87246.605-0.048-0.0480.0000.0000.0000.000
89A91ALA00.0270.00648.5790.0030.0030.0000.0000.0000.000
90A92PRO00.0070.00748.057-0.002-0.0020.0000.0000.0000.000
91A93MET0-0.017-0.01850.994-0.001-0.0010.0000.0000.0000.000
92A94SER0-0.029-0.01052.418-0.001-0.0010.0000.0000.0000.000
93A95LEU0-0.040-0.01547.3410.0000.0000.0000.0000.0000.000
94A96THR0-0.045-0.06651.883-0.001-0.0010.0000.0000.0000.000
95A97MET00.0300.02852.6350.0010.0010.0000.0000.0000.000
96A98GLU-1-0.810-0.89053.3740.0430.0430.0000.0000.0000.000
97A99ALA0-0.014-0.00553.5320.0000.0000.0000.0000.0000.000
98A100VAL0-0.024-0.00747.6570.0020.0020.0000.0000.0000.000
99A101LYS10.8710.91550.206-0.043-0.0430.0000.0000.0000.000
100A102ALA0-0.056-0.03052.4550.0000.0000.0000.0000.0000.000
101A103LYS10.8820.94647.871-0.060-0.0600.0000.0000.0000.000
102A104GLY0-0.0090.00848.5100.0020.0020.0000.0000.0000.000
103A105TYR0-0.042-0.02243.2090.0010.0010.0000.0000.0000.000
104A106GLU-1-0.791-0.90047.8300.0440.0440.0000.0000.0000.000
105A107GLN0-0.0310.00345.363-0.002-0.0020.0000.0000.0000.000
106A108GLU-1-0.817-0.91040.8730.0750.0750.0000.0000.0000.000
107A109LEU00.0130.01944.0260.0010.0010.0000.0000.0000.000
108A110PRO00.0390.02040.5590.0020.0020.0000.0000.0000.000
109A111PRO0-0.0020.01036.048-0.001-0.0010.0000.0000.0000.000
110A112TYR0-0.0030.00832.2300.0050.0050.0000.0000.0000.000
111A113GLY00.0720.04737.525-0.005-0.0050.0000.0000.0000.000
112A114VAL0-0.011-0.02239.4200.0000.0000.0000.0000.0000.000
113A115ILE00.0020.00842.520-0.004-0.0040.0000.0000.0000.000
114A116PRO0-0.047-0.00940.086-0.003-0.0030.0000.0000.0000.000
115A117VAL0-0.033-0.02040.7640.0020.0020.0000.0000.0000.000
116A118THR00.000-0.00943.183-0.003-0.0030.0000.0000.0000.000
117A119VAL0-0.018-0.01444.0420.0030.0030.0000.0000.0000.000
118A120PRO0-0.0150.00941.242-0.001-0.0010.0000.0000.0000.000
119A121GLY00.0810.05543.184-0.002-0.0020.0000.0000.0000.000
120A122ALA0-0.010-0.00540.182-0.003-0.0030.0000.0000.0000.000
121A123PRO00.0320.01041.172-0.002-0.0020.0000.0000.0000.000
122A124GLY00.0440.01943.229-0.003-0.0030.0000.0000.0000.000
123A125ALA0-0.025-0.00743.906-0.003-0.0030.0000.0000.0000.000
124A126TRP0-0.023-0.02338.045-0.002-0.0020.0000.0000.0000.000
125A127ALA00.0380.02744.130-0.002-0.0020.0000.0000.0000.000
126A128GLU-1-0.840-0.91947.2660.0420.0420.0000.0000.0000.000
127A129LEU0-0.010-0.00444.066-0.002-0.0020.0000.0000.0000.000
128A130ALA00.007-0.00346.208-0.002-0.0020.0000.0000.0000.000
129A131LYS10.8250.90147.953-0.045-0.0450.0000.0000.0000.000
130A132MET0-0.067-0.01151.246-0.002-0.0020.0000.0000.0000.000
131A133TYR0-0.032-0.03149.783-0.002-0.0020.0000.0000.0000.000
132A134GLY00.0010.01648.0370.0000.0000.0000.0000.0000.000
133A135ASN0-0.045-0.03247.994-0.003-0.0030.0000.0000.0000.000
134A136LEU0-0.043-0.02044.064-0.001-0.0010.0000.0000.0000.000
135A137PRO00.0000.00947.5820.0010.0010.0000.0000.0000.000
136A138LEU00.0490.01543.2760.0020.0020.0000.0000.0000.000
137A139ALA00.009-0.00743.3210.0030.0030.0000.0000.0000.000
138A140ALA0-0.035-0.00742.6420.0020.0020.0000.0000.0000.000
139A141SER00.006-0.00541.5390.0030.0030.0000.0000.0000.000
140A142LEU00.0420.01138.6840.0030.0030.0000.0000.0000.000
141A143ALA00.0270.02237.7320.0060.0060.0000.0000.0000.000
142A144PRO0-0.021-0.02434.2840.0050.0050.0000.0000.0000.000
143A145ALA00.0000.01233.2510.0080.0080.0000.0000.0000.000
144A146ILE00.0160.01633.1900.0080.0080.0000.0000.0000.000
145A147ARG10.9460.99131.479-0.084-0.0840.0000.0000.0000.000
146A148TYR0-0.017-0.03528.5720.0060.0060.0000.0000.0000.000
147A149ALA0-0.0230.00828.7980.0150.0150.0000.0000.0000.000
148A150GLU-1-0.766-0.84830.5460.1020.1020.0000.0000.0000.000
149A151GLU-1-0.941-0.96628.5710.1160.1160.0000.0000.0000.000
150A152GLY0-0.003-0.01225.7550.0120.0120.0000.0000.0000.000
151A153TYR0-0.058-0.05022.594-0.006-0.0060.0000.0000.0000.000
152A154PRO0-0.020-0.00218.1010.0170.0170.0000.0000.0000.000
153A155VAL00.0070.00718.202-0.025-0.0250.0000.0000.0000.000
154A156THR00.013-0.01316.8340.0670.0670.0000.0000.0000.000
155A157PRO00.0520.00513.5390.0240.0240.0000.0000.0000.000
156A158THR0-0.025-0.02715.4240.0080.0080.0000.0000.0000.000
157A159LEU00.0010.01018.802-0.004-0.0040.0000.0000.0000.000
158A160ALA00.0320.00715.930-0.009-0.0090.0000.0000.0000.000
159A161LYS10.8440.92416.805-0.249-0.2490.0000.0000.0000.000
160A162TYR00.013-0.00217.934-0.009-0.0090.0000.0000.0000.000
161A163TRP00.003-0.01420.367-0.011-0.0110.0000.0000.0000.000
162A164LYS10.7500.84415.909-0.447-0.4470.0000.0000.0000.000
163A165ALA00.0050.00819.660-0.015-0.0150.0000.0000.0000.000
164A166ALA0-0.0120.00321.855-0.020-0.0200.0000.0000.0000.000
165A167TYR0-0.024-0.03821.256-0.017-0.0170.0000.0000.0000.000
166A168ASP-1-0.810-0.89619.1200.3570.3570.0000.0000.0000.000
167A169ARG10.8400.91222.538-0.162-0.1620.0000.0000.0000.000
168A170VAL00.0460.02425.738-0.013-0.0130.0000.0000.0000.000
169A171LYS10.8420.94024.366-0.192-0.1920.0000.0000.0000.000
170A172THR0-0.025-0.02226.841-0.005-0.0050.0000.0000.0000.000
171A173GLU-1-0.854-0.91028.9540.1240.1240.0000.0000.0000.000
172A174TRP0-0.052-0.01030.269-0.006-0.0060.0000.0000.0000.000
173A175THR0-0.049-0.03731.5570.0080.0080.0000.0000.0000.000
174A176ASP-1-0.846-0.92733.8240.0850.0850.0000.0000.0000.000
175A177ASP-1-0.865-0.92835.7440.1010.1010.0000.0000.0000.000
176A178VAL0-0.058-0.03537.3250.0030.0030.0000.0000.0000.000
177A179TYR0-0.014-0.01232.8700.0020.0020.0000.0000.0000.000
178A180GLN0-0.068-0.03030.1780.0110.0110.0000.0000.0000.000
179A181PRO00.0550.02331.8300.0100.0100.0000.0000.0000.000
180A182TRP0-0.0150.01225.3080.0100.0100.0000.0000.0000.000
181A183PHE00.001-0.01426.4310.0180.0180.0000.0000.0000.000
182A184ASP-1-0.854-0.91227.4000.1580.1580.0000.0000.0000.000
183A185THR0-0.060-0.03328.8410.0040.0040.0000.0000.0000.000
184A186PHE0-0.014-0.02326.2040.0070.0070.0000.0000.0000.000
185A187ALA00.0130.01723.4320.0270.0270.0000.0000.0000.000
186A188PRO00.0370.02824.3160.0080.0080.0000.0000.0000.000
187A189LYS10.8180.90419.245-0.351-0.3510.0000.0000.0000.000
188A190GLY00.0310.01520.5650.0320.0320.0000.0000.0000.000
189A191ARG10.7660.88816.720-0.448-0.4480.0000.0000.0000.000
190A192ALA00.0560.03619.375-0.008-0.0080.0000.0000.0000.000
191A193PRO0-0.032-0.00618.3080.0520.0520.0000.0000.0000.000
192A194ARG10.9320.96411.500-0.833-0.8330.0000.0000.0000.000
193A195VAL00.0550.01811.582-0.066-0.0660.0000.0000.0000.000
194A196GLY0-0.0050.00612.8800.1060.1060.0000.0000.0000.000
195A197GLU-1-0.832-0.88915.0850.4570.4570.0000.0000.0000.000
196A198VAL0-0.013-0.00716.809-0.032-0.0320.0000.0000.0000.000
197A199TRP0-0.071-0.03620.4940.0110.0110.0000.0000.0000.000
198A200ARG10.8770.91423.332-0.165-0.1650.0000.0000.0000.000
199A201SER0-0.062-0.03327.0840.0030.0030.0000.0000.0000.000
200A202GLN00.080-0.00130.403-0.006-0.0060.0000.0000.0000.000
201A203GLY00.0340.04633.519-0.007-0.0070.0000.0000.0000.000
202A204HIS00.0190.00931.550-0.006-0.0060.0000.0000.0000.000
203A205ALA00.0170.00834.190-0.006-0.0060.0000.0000.0000.000
204A206ASP-1-0.793-0.89535.8470.0830.0830.0000.0000.0000.000
205A207THR0-0.046-0.01737.480-0.007-0.0070.0000.0000.0000.000
206A208LEU0-0.024-0.01935.198-0.005-0.0050.0000.0000.0000.000
207A209ARG10.7920.86237.498-0.090-0.0900.0000.0000.0000.000
208A210SER00.0580.04141.555-0.005-0.0050.0000.0000.0000.000
209A211ILE0-0.0170.00840.890-0.004-0.0040.0000.0000.0000.000
210A212ALA00.0060.00642.700-0.004-0.0040.0000.0000.0000.000
211A213GLU-1-0.966-0.98944.5030.0600.0600.0000.0000.0000.000
212A214SER0-0.061-0.04847.304-0.003-0.0030.0000.0000.0000.000
213A215ASN0-0.049-0.02947.790-0.001-0.0010.0000.0000.0000.000
214A216GLY00.0310.00645.995-0.001-0.0010.0000.0000.0000.000
215A217GLU-1-0.758-0.86147.0490.0500.0500.0000.0000.0000.000
216A218SER00.002-0.01046.633-0.001-0.0010.0000.0000.0000.000
217A219PHE00.007-0.01341.1010.0010.0010.0000.0000.0000.000
218A220TYR0-0.080-0.05445.1640.0010.0010.0000.0000.0000.000
219A221ARG10.7370.83349.507-0.051-0.0510.0000.0000.0000.000
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