Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 1NR4Z

Calculation Name: 1Z9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z9S

Chain ID: A

ChEMBL ID:

UniProt ID: P26926

Base Structure: X-ray

Registration Date: 2023-09-24

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2218281.30563
FMO2-HF: Nuclear repulsion 2138844.354645
FMO2-HF: Total energy -79436.950985
FMO2-MP2: Total energy -79672.062927


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:9:SER)


Summations of interaction energy for fragment #1(A:9:SER)
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.
-0.0783.097-0.008-1.615-1.5520.006
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.019
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].
3A11GLU-1-0.834-0.9093.5900.0193.194-0.008-1.615-1.5520.006
4A12TYR0-0.048-0.0365.972-0.297-0.2970.0000.0000.0000.000
5A13GLY00.0250.0209.3340.1540.1540.0000.0000.0000.000
6A14VAL0-0.020-0.00712.433-0.044-0.0440.0000.0000.0000.000
7A15THR0-0.0010.00716.1540.0430.0430.0000.0000.0000.000
8A16ILE0-0.009-0.00818.923-0.019-0.0190.0000.0000.0000.000
9A17GLY0-0.021-0.01822.5220.0130.0130.0000.0000.0000.000
10A18GLU-1-0.883-0.93425.193-0.008-0.0080.0000.0000.0000.000
11A19SER00.006-0.00724.960-0.006-0.0060.0000.0000.0000.000
12A20ARG10.8130.90225.926-0.018-0.0180.0000.0000.0000.000
13A21ILE00.0470.03128.885-0.002-0.0020.0000.0000.0000.000
14A22ILE0-0.0040.00831.8560.0000.0000.0000.0000.0000.000
15A23TYR0-0.007-0.03035.483-0.003-0.0030.0000.0000.0000.000
16A24PRO0-0.0010.00337.3330.0010.0010.0000.0000.0000.000
17A25LEU0-0.020-0.00841.095-0.002-0.0020.0000.0000.0000.000
18A26ASP-1-0.804-0.89642.884-0.017-0.0170.0000.0000.0000.000
19A27ALA0-0.0150.01440.900-0.001-0.0010.0000.0000.0000.000
20A28ALA00.0270.01441.864-0.002-0.0020.0000.0000.0000.000
21A29GLY00.000-0.01738.150-0.004-0.0040.0000.0000.0000.000
22A30VAL0-0.044-0.00533.5660.0030.0030.0000.0000.0000.000
23A31MET0-0.020-0.00932.358-0.005-0.0050.0000.0000.0000.000
24A32VAL00.0690.04426.8770.0050.0050.0000.0000.0000.000
25A33SER0-0.0040.00025.926-0.008-0.0080.0000.0000.0000.000
26A34VAL00.0150.01321.2340.0050.0050.0000.0000.0000.000
27A35LYS10.9010.94919.2400.0650.0650.0000.0000.0000.000
28A36ASN0-0.015-0.01415.544-0.001-0.0010.0000.0000.0000.000
29A37THR0-0.044-0.03413.336-0.003-0.0030.0000.0000.0000.000
30A38GLN00.0430.0459.3100.1270.1270.0000.0000.0000.000
31A39ASP-1-0.841-0.92811.097-0.251-0.2510.0000.0000.0000.000
32A40TYR0-0.018-0.0289.3940.0380.0380.0000.0000.0000.000
33A41PRO0-0.0180.00314.2000.0500.0500.0000.0000.0000.000
34A42VAL00.0130.00114.973-0.061-0.0610.0000.0000.0000.000
35A43LEU0-0.009-0.00317.9240.0450.0450.0000.0000.0000.000
36A44ILE00.0000.00419.415-0.011-0.0110.0000.0000.0000.000
37A45GLN0-0.020-0.02221.6360.0150.0150.0000.0000.0000.000
38A46SER00.0180.01023.1890.0050.0050.0000.0000.0000.000
39A47ARG10.9040.95625.4580.1230.1230.0000.0000.0000.000
40A48ILE00.0460.02527.6290.0040.0040.0000.0000.0000.000
41A49TYR0-0.038-0.02026.063-0.007-0.0070.0000.0000.0000.000
42A50ASP-1-0.724-0.87531.059-0.025-0.0250.0000.0000.0000.000
43A51GLU-1-0.839-0.89532.075-0.007-0.0070.0000.0000.0000.000
44A52ASN0-0.045-0.03132.5900.0070.0070.0000.0000.0000.000
45A53LYS10.8100.91925.6400.0240.0240.0000.0000.0000.000
46A54GLU-1-0.885-0.94029.946-0.040-0.0400.0000.0000.0000.000
47A55LYS10.6820.81130.1000.0690.0690.0000.0000.0000.000
48A56GLU-1-0.737-0.84733.040-0.063-0.0630.0000.0000.0000.000
49A57SER0-0.052-0.02936.6820.0030.0030.0000.0000.0000.000
50A58GLU-1-0.862-0.91038.802-0.032-0.0320.0000.0000.0000.000
51A59ASP-1-0.914-0.95238.954-0.053-0.0530.0000.0000.0000.000
52A60PRO0-0.0220.00336.2020.0020.0020.0000.0000.0000.000
53A61PHE00.007-0.00134.7910.0020.0020.0000.0000.0000.000
54A62VAL00.0210.01334.643-0.005-0.0050.0000.0000.0000.000
55A63VAL0-0.006-0.00828.6870.0030.0030.0000.0000.0000.000
56A64THR0-0.0640.00031.967-0.006-0.0060.0000.0000.0000.000
57A65PRO00.037-0.00628.7770.0050.0050.0000.0000.0000.000
58A66PRO00.0520.02128.572-0.004-0.0040.0000.0000.0000.000
59A67LEU0-0.013-0.03123.957-0.009-0.0090.0000.0000.0000.000
60A68PHE00.0020.01224.7800.0060.0060.0000.0000.0000.000
61A69ARG10.8540.89821.4570.2610.2610.0000.0000.0000.000
62A70LEU0-0.030-0.00520.4890.0210.0210.0000.0000.0000.000
63A71ASP-1-0.741-0.85119.611-0.297-0.2970.0000.0000.0000.000
64A72ALA00.0550.03216.2080.0190.0190.0000.0000.0000.000
65A73LYS10.8040.89512.4980.2010.2010.0000.0000.0000.000
66A74GLN0-0.028-0.00318.4010.0510.0510.0000.0000.0000.000
67A75GLN0-0.013-0.02120.9390.0030.0030.0000.0000.0000.000
68A76ASN00.0210.01623.5410.0070.0070.0000.0000.0000.000
69A77SER0-0.027-0.01626.2200.0080.0080.0000.0000.0000.000
70A78LEU0-0.0020.01225.678-0.006-0.0060.0000.0000.0000.000
71A79ARG10.9490.96929.6010.0530.0530.0000.0000.0000.000
72A80ILE0-0.023-0.01329.726-0.005-0.0050.0000.0000.0000.000
73A81ALA00.013-0.01133.8080.0050.0050.0000.0000.0000.000
74A82GLN00.0360.03537.430-0.001-0.0010.0000.0000.0000.000
75A83ALA0-0.027-0.01939.6720.0010.0010.0000.0000.0000.000
76A84GLY00.0070.01841.4130.0000.0000.0000.0000.0000.000
77A85GLY00.0450.01043.4290.0000.0000.0000.0000.0000.000
78A86VAL0-0.029-0.02244.5500.0010.0010.0000.0000.0000.000
79A87PHE00.0190.00439.7960.0000.0000.0000.0000.0000.000
80A88PRO0-0.0280.00143.4140.0010.0010.0000.0000.0000.000
81A89ARG10.8540.87245.3430.0140.0140.0000.0000.0000.000
82A90ASP-1-0.840-0.90247.647-0.002-0.0020.0000.0000.0000.000
83A91LYS10.9310.94743.2510.0060.0060.0000.0000.0000.000
84A92GLU-1-0.719-0.83338.3800.0010.0010.0000.0000.0000.000
85A93SER0-0.022-0.00939.1410.0000.0000.0000.0000.0000.000
86A94LEU0-0.061-0.01531.5620.0000.0000.0000.0000.0000.000
87A95LYS10.8890.94633.1030.0280.0280.0000.0000.0000.000
88A96TRP0-0.038-0.02925.9750.0070.0070.0000.0000.0000.000
89A97LEU00.0580.04026.240-0.006-0.0060.0000.0000.0000.000
90A98CYS0-0.102-0.03519.524-0.002-0.0020.0000.0000.0000.000
91A99VAL00.0410.00420.943-0.009-0.0090.0000.0000.0000.000
92A100LYS10.9740.98417.8220.2310.2310.0000.0000.0000.000
93A101GLY00.0100.01216.5010.0050.0050.0000.0000.0000.000
94A102ILE0-0.074-0.05015.596-0.041-0.0410.0000.0000.0000.000
95A103PRO00.0300.01912.4370.0160.0160.0000.0000.0000.000
96A104PRO0-0.0130.00713.538-0.005-0.0050.0000.0000.0000.000
97A125ASP-1-0.927-0.97916.9920.0240.0240.0000.0000.0000.000
98A126VAL0-0.036-0.01116.458-0.027-0.0270.0000.0000.0000.000
99A127GLY00.0290.02714.0840.0190.0190.0000.0000.0000.000
100A128VAL0-0.021-0.01711.100-0.031-0.0310.0000.0000.0000.000
101A129PHE00.0280.0048.655-0.108-0.1080.0000.0000.0000.000
102A130VAL00.0300.0228.3510.0610.0610.0000.0000.0000.000
103A131GLN00.0400.0298.553-0.438-0.4380.0000.0000.0000.000
104A132PHE00.0000.0017.2730.1680.1680.0000.0000.0000.000
105A133ALA00.017-0.01311.310-0.057-0.0570.0000.0000.0000.000
106A134ILE00.0050.02210.9870.0470.0470.0000.0000.0000.000
107A135ASN00.027-0.01014.595-0.008-0.0080.0000.0000.0000.000
108A136ASN0-0.0200.00118.0320.0280.0280.0000.0000.0000.000
109A138ILE00.0250.01823.0990.0130.0130.0000.0000.0000.000
110A139LYS10.8460.92725.746-0.018-0.0180.0000.0000.0000.000
111A140LEU00.0240.02529.3940.0010.0010.0000.0000.0000.000
112A141LEU0-0.018-0.02032.0680.0000.0000.0000.0000.0000.000
113A142VAL00.0140.01835.1840.0000.0000.0000.0000.0000.000
114A143ARG10.7640.82237.4670.0000.0000.0000.0000.0000.000
115A144PRO00.0200.02540.990-0.001-0.0010.0000.0000.0000.000
116A145ASN0-0.0020.00144.7230.0020.0020.0000.0000.0000.000
117A146GLU-1-0.835-0.92246.512-0.008-0.0080.0000.0000.0000.000
118A147LEU0-0.052-0.01043.0910.0020.0020.0000.0000.0000.000
119A148LYS10.9150.95646.727-0.001-0.0010.0000.0000.0000.000
120A149GLY00.0140.00745.3230.0010.0010.0000.0000.0000.000
121A150THR0-0.007-0.00739.790-0.001-0.0010.0000.0000.0000.000
122A151PRO00.0560.01837.1090.0020.0020.0000.0000.0000.000
123A152ILE00.034-0.00137.5850.0010.0010.0000.0000.0000.000
124A153GLN0-0.0350.00140.0290.0010.0010.0000.0000.0000.000
125A154PHE00.0190.00442.4950.0000.0000.0000.0000.0000.000
126A155ALA00.0160.02239.0910.0000.0000.0000.0000.0000.000
127A156GLU-1-0.910-0.94940.8270.0300.0300.0000.0000.0000.000
128A157ASN0-0.062-0.06143.335-0.001-0.0010.0000.0000.0000.000
129A158LEU0-0.0060.03038.529-0.001-0.0010.0000.0000.0000.000
130A159SER0-0.058-0.03043.1270.0020.0020.0000.0000.0000.000
131A160TRP00.0750.00836.7660.0010.0010.0000.0000.0000.000
132A161LYS10.9120.94243.403-0.020-0.0200.0000.0000.0000.000
133A162VAL0-0.016-0.00842.2860.0010.0010.0000.0000.0000.000
134A163ASP-1-0.816-0.89943.5120.0190.0190.0000.0000.0000.000
135A164GLY00.0450.02943.1940.0010.0010.0000.0000.0000.000
136A165GLY0-0.038-0.01041.8780.0010.0010.0000.0000.0000.000
137A166LYS10.8340.89736.238-0.027-0.0270.0000.0000.0000.000
138A167LEU0-0.0140.00536.792-0.001-0.0010.0000.0000.0000.000
139A168ILE0-0.008-0.00738.6770.0000.0000.0000.0000.0000.000
140A169ALA0-0.0070.01038.6390.0010.0010.0000.0000.0000.000
141A170GLU-1-0.860-0.91440.6970.0150.0150.0000.0000.0000.000
142A171ASN0-0.024-0.02539.9080.0020.0020.0000.0000.0000.000
143A172PRO00.0330.02042.878-0.002-0.0020.0000.0000.0000.000
144A173SER0-0.016-0.01542.430-0.002-0.0020.0000.0000.0000.000
145A174PRO00.018-0.00644.0130.0000.0000.0000.0000.0000.000
146A175PHE00.023-0.00539.608-0.002-0.0020.0000.0000.0000.000
147A176TYR0-0.018-0.03135.4220.0020.0020.0000.0000.0000.000
148A177MET0-0.0110.02236.7480.0030.0030.0000.0000.0000.000
149A178ASN00.002-0.02131.2220.0010.0010.0000.0000.0000.000
150A179ILE00.0010.00532.0960.0030.0030.0000.0000.0000.000
151A180GLY00.010-0.00928.825-0.001-0.0010.0000.0000.0000.000
152A181GLU-1-0.883-0.94128.3920.0840.0840.0000.0000.0000.000
153A182LEU00.0210.01730.695-0.006-0.0060.0000.0000.0000.000
154A183THR0-0.022-0.00532.2250.0070.0070.0000.0000.0000.000
155A184PHE00.0320.01134.637-0.005-0.0050.0000.0000.0000.000
156A185GLY00.009-0.01637.0540.0020.0020.0000.0000.0000.000
157A186GLY0-0.014-0.00436.5010.0020.0020.0000.0000.0000.000
158A187LYS10.9060.96633.252-0.070-0.0700.0000.0000.0000.000
159A188SER00.0560.02629.133-0.003-0.0030.0000.0000.0000.000
160A189ILE0-0.033-0.01430.7820.0010.0010.0000.0000.0000.000
161A190PRO0-0.0070.00626.6400.0020.0020.0000.0000.0000.000
162A191SER00.0170.00027.928-0.006-0.0060.0000.0000.0000.000
163A192HIS10.8890.94128.719-0.021-0.0210.0000.0000.0000.000
164A193TYR0-0.080-0.04930.7820.0030.0030.0000.0000.0000.000
165A194ILE00.0070.01733.2480.0000.0000.0000.0000.0000.000
166A195PRO00.0200.01336.695-0.001-0.0010.0000.0000.0000.000
167A196PRO0-0.0180.00438.6890.0020.0020.0000.0000.0000.000
168A197LYS10.7760.88041.776-0.003-0.0030.0000.0000.0000.000
169A198SER00.0150.02141.661-0.001-0.0010.0000.0000.0000.000
170A199THR0-0.004-0.00441.3600.0020.0020.0000.0000.0000.000
171A200TRP00.0370.00333.030-0.004-0.0040.0000.0000.0000.000
172A201ALA0-0.0010.00837.5990.0020.0020.0000.0000.0000.000
173A202PHE0-0.025-0.01832.0780.0000.0000.0000.0000.0000.000
174A203ASP-1-0.818-0.90632.8650.0340.0340.0000.0000.0000.000
175A204LEU0-0.003-0.00834.1070.0040.0040.0000.0000.0000.000
176A205PRO00.007-0.00734.4370.0050.0050.0000.0000.0000.000
177A206LYS10.9140.98928.582-0.082-0.0820.0000.0000.0000.000
178A207GLY0-0.006-0.01733.8490.0040.0040.0000.0000.0000.000
179A208LEU00.009-0.02236.4000.0020.0020.0000.0000.0000.000
180A209ALA00.002-0.00239.661-0.002-0.0020.0000.0000.0000.000
181A210GLY00.0490.03342.654-0.003-0.0030.0000.0000.0000.000
182A211ALA0-0.0610.01441.2170.0000.0000.0000.0000.0000.000
183A212ARG10.9270.94143.173-0.035-0.0350.0000.0000.0000.000
184A213ASN00.0100.03340.345-0.004-0.0040.0000.0000.0000.000
185A214VAL0-0.005-0.00338.4690.0030.0030.0000.0000.0000.000
186A215SER0-0.026-0.02937.025-0.002-0.0020.0000.0000.0000.000
187A216TRP0-0.015-0.01535.1940.0040.0040.0000.0000.0000.000
188A217ARG10.9340.97431.966-0.068-0.0680.0000.0000.0000.000
189A218ILE0-0.013-0.00333.1480.0010.0010.0000.0000.0000.000
190A219ILE0-0.0250.00128.2930.0030.0030.0000.0000.0000.000
191A220ASN00.0360.02231.865-0.006-0.0060.0000.0000.0000.000
192A221ASP-1-0.712-0.85532.4550.0090.0090.0000.0000.0000.000
193A222GLN00.0170.00631.972-0.001-0.0010.0000.0000.0000.000
194A223GLY0-0.048-0.02828.5220.0010.0010.0000.0000.0000.000
195A224GLY0-0.009-0.00328.1810.0080.0080.0000.0000.0000.000
196A225LEU0-0.027-0.02427.794-0.005-0.0050.0000.0000.0000.000
197A226ASP-1-0.835-0.91231.0930.0360.0360.0000.0000.0000.000
198A227ARG10.9040.94134.715-0.029-0.0290.0000.0000.0000.000
199A228LEU0-0.050-0.01935.377-0.001-0.0010.0000.0000.0000.000
200A229TYR00.0340.03237.887-0.003-0.0030.0000.0000.0000.000
201A230SER00.001-0.01339.6710.0040.0040.0000.0000.0000.000
202A231LYS10.8630.94342.172-0.029-0.0290.0000.0000.0000.000
203A232ASN0-0.010-0.02043.6400.0040.0040.0000.0000.0000.000
204A233VAL0-0.0120.00643.142-0.002-0.0020.0000.0000.0000.000
205A234THR00.007-0.00445.8060.0000.0000.0000.0000.0000.000