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: 7263K

Calculation Name: 5N9J-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: E

ChEMBL ID:

UniProt ID: P87310

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1577680.71004
FMO2-HF: Nuclear repulsion 1495548.021917
FMO2-HF: Total energy -82132.688123
FMO2-MP2: Total energy -82370.546267


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(E:10:PHE)


Summations of interaction energy for fragment #1(E:10:PHE)
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.
0.1962.195-0.011-0.947-1.0410.004
Interaction energy analysis for fragmet #1(E:10:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.006
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].
3E12ALA0-0.014-0.0063.8251.1803.179-0.011-0.947-1.0410.004
4E13PHE00.0100.0006.560-0.638-0.6380.0000.0000.0000.000
5E14PRO00.0010.01410.3310.1340.1340.0000.0000.0000.000
6E15PRO00.0090.00613.161-0.002-0.0020.0000.0000.0000.000
7E16PRO00.0170.00814.965-0.072-0.0720.0000.0000.0000.000
8E17PRO00.0190.00318.4650.0050.0050.0000.0000.0000.000
9E18PRO00.0500.00821.5070.0040.0040.0000.0000.0000.000
10E19TYR00.0500.01322.8290.0000.0000.0000.0000.0000.000
11E20TYR00.0040.00219.267-0.004-0.0040.0000.0000.0000.000
12E21LYS10.9460.97620.114-0.362-0.3620.0000.0000.0000.000
13E22LEU0-0.028-0.00124.022-0.011-0.0110.0000.0000.0000.000
14E23PHE00.0120.00727.300-0.020-0.0200.0000.0000.0000.000
15E24THR00.0190.02028.4060.0040.0040.0000.0000.0000.000
16E25ARG11.0010.97831.038-0.121-0.1210.0000.0000.0000.000
17E26GLU-1-0.887-0.93333.8440.0950.0950.0000.0000.0000.000
18E27ASN00.0630.01732.5480.0020.0020.0000.0000.0000.000
19E28ILE0-0.060-0.03132.285-0.004-0.0040.0000.0000.0000.000
20E29GLU-1-0.862-0.94436.2610.0780.0780.0000.0000.0000.000
21E30LYS10.8840.95338.738-0.094-0.0940.0000.0000.0000.000
22E31VAL0-0.036-0.01637.568-0.004-0.0040.0000.0000.0000.000
23E32ILE0-0.0040.01840.281-0.004-0.0040.0000.0000.0000.000
24E33SER0-0.021-0.01842.348-0.005-0.0050.0000.0000.0000.000
25E34ASN0-0.049-0.04242.901-0.002-0.0020.0000.0000.0000.000
26E35MET0-0.030-0.01544.161-0.002-0.0020.0000.0000.0000.000
27E36GLU-1-0.934-0.97045.8210.0490.0490.0000.0000.0000.000
28E37LYS10.8680.94548.029-0.058-0.0580.0000.0000.0000.000
29E38GLU-1-0.844-0.89246.7850.0600.0600.0000.0000.0000.000
30E55GLU-1-0.885-0.95342.7770.0720.0720.0000.0000.0000.000
31E56ILE00.0340.01337.5170.0040.0040.0000.0000.0000.000
32E57GLU-1-0.816-0.90638.5630.0850.0850.0000.0000.0000.000
33E58SER00.007-0.01239.8170.0010.0010.0000.0000.0000.000
34E59LEU0-0.006-0.00336.5240.0010.0010.0000.0000.0000.000
35E60ALA0-0.0180.00235.3750.0070.0070.0000.0000.0000.000
36E61LYS10.8180.88835.743-0.065-0.0650.0000.0000.0000.000
37E62LEU0-0.045-0.03137.0320.0000.0000.0000.0000.0000.000
38E63PHE0-0.010-0.00228.3540.0040.0040.0000.0000.0000.000
39E64LYS10.7970.91531.654-0.129-0.1290.0000.0000.0000.000
40E65LYS10.9410.98634.712-0.073-0.0730.0000.0000.0000.000
41E66PRO00.0290.00733.8070.0050.0050.0000.0000.0000.000
42E67SER0-0.061-0.03634.733-0.003-0.0030.0000.0000.0000.000
43E68CYS00.0240.02835.0810.0020.0020.0000.0000.0000.000
44E69LEU00.0040.00634.454-0.002-0.0020.0000.0000.0000.000
45E70THR0-0.010-0.00736.940-0.001-0.0010.0000.0000.0000.000
46E71SER00.000-0.01538.031-0.004-0.0040.0000.0000.0000.000
47E72GLY00.0430.02637.3450.0030.0030.0000.0000.0000.000
48E73THR0-0.032-0.02032.1680.0010.0010.0000.0000.0000.000
49E74TYR00.0060.00726.9480.0050.0050.0000.0000.0000.000
50E75GLN0-0.0060.00925.453-0.004-0.0040.0000.0000.0000.000
51E76MET00.0050.01022.3530.0130.0130.0000.0000.0000.000
52E186PRO0-0.011-0.03532.2580.0020.0020.0000.0000.0000.000
53E187LEU0-0.038-0.01133.4360.0020.0020.0000.0000.0000.000
54E188ASP-1-0.933-0.94635.9330.0180.0180.0000.0000.0000.000
55E189SER0-0.025-0.02235.723-0.001-0.0010.0000.0000.0000.000
56E190GLN0-0.041-0.01335.0340.0020.0020.0000.0000.0000.000
57E191ASP-1-0.807-0.92237.091-0.001-0.0010.0000.0000.0000.000
58E192THR00.009-0.02340.053-0.001-0.0010.0000.0000.0000.000
59E193GLY0-0.016-0.00641.699-0.001-0.0010.0000.0000.0000.000
60E194ALA0-0.034-0.01339.9740.0000.0000.0000.0000.0000.000
61E195VAL0-0.074-0.01537.0960.0000.0000.0000.0000.0000.000
62E196SER0-0.035-0.03539.632-0.002-0.0020.0000.0000.0000.000
63E197ALA00.0080.01242.6380.0010.0010.0000.0000.0000.000
64E198SER00.0100.00245.899-0.002-0.0020.0000.0000.0000.000
65E199SER0-0.062-0.05347.2860.0010.0010.0000.0000.0000.000
66E200VAL00.0030.00149.6970.0000.0000.0000.0000.0000.000
67E201ASN0-0.031-0.01350.0740.0010.0010.0000.0000.0000.000
68E202GLU-1-0.821-0.89950.350-0.008-0.0080.0000.0000.0000.000
69E203GLY00.0700.04052.3570.0010.0010.0000.0000.0000.000
70E204PHE0-0.057-0.03953.857-0.001-0.0010.0000.0000.0000.000
71E205ARG10.8970.93855.3890.0030.0030.0000.0000.0000.000
72E206ALA00.0400.01656.608-0.001-0.0010.0000.0000.0000.000
73E207ASP-1-0.851-0.92157.005-0.002-0.0020.0000.0000.0000.000
74E208GLN00.0200.00758.0920.0000.0000.0000.0000.0000.000
75E209LYS10.8820.95056.4290.0040.0040.0000.0000.0000.000
76E210SER0-0.0130.01557.1840.0000.0000.0000.0000.0000.000
77E211LYS10.9120.94857.8320.0090.0090.0000.0000.0000.000
78E212ASP-1-0.808-0.88860.059-0.006-0.0060.0000.0000.0000.000
79E213GLY0-0.066-0.05761.557-0.001-0.0010.0000.0000.0000.000
80E214GLU-1-0.889-0.92760.780-0.009-0.0090.0000.0000.0000.000
81E215THR0-0.011-0.02962.785-0.001-0.0010.0000.0000.0000.000
82E216SER00.0160.01859.2930.0000.0000.0000.0000.0000.000
83E217ASP-1-0.752-0.84458.429-0.017-0.0170.0000.0000.0000.000
84E218LEU0-0.052-0.01461.7680.0000.0000.0000.0000.0000.000
85E219ILE0-0.0160.02158.2930.0000.0000.0000.0000.0000.000
86E220LYS11.0261.00161.4060.0090.0090.0000.0000.0000.000
87E221ILE0-0.045-0.01455.7870.0000.0000.0000.0000.0000.000
88E222PRO00.009-0.02454.5570.0010.0010.0000.0000.0000.000
89E223ARG10.9480.97055.6310.0060.0060.0000.0000.0000.000
90E224ARG10.7770.85548.5630.0060.0060.0000.0000.0000.000
91E225ALA00.0240.01050.635-0.001-0.0010.0000.0000.0000.000
92E226TYR0-0.039-0.01851.686-0.002-0.0020.0000.0000.0000.000
93E227GLU-1-0.826-0.92251.071-0.012-0.0120.0000.0000.0000.000
94E228LEU00.0240.01546.457-0.001-0.0010.0000.0000.0000.000
95E229ARG10.8890.93849.1510.0160.0160.0000.0000.0000.000
96E230PHE0-0.057-0.01250.804-0.001-0.0010.0000.0000.0000.000
97E231LEU00.0790.03146.853-0.001-0.0010.0000.0000.0000.000
98E232SER0-0.055-0.00846.197-0.001-0.0010.0000.0000.0000.000
99E233ARG10.8350.85547.6800.0170.0170.0000.0000.0000.000
100E234SER00.0260.02150.006-0.001-0.0010.0000.0000.0000.000
101E235LEU00.0150.01642.397-0.001-0.0010.0000.0000.0000.000
102E236MET0-0.008-0.01246.783-0.001-0.0010.0000.0000.0000.000
103E237LEU0-0.006-0.00647.845-0.001-0.0010.0000.0000.0000.000
104E238ASN00.0160.00547.2330.0000.0000.0000.0000.0000.000
105E239PHE00.0210.01041.208-0.001-0.0010.0000.0000.0000.000
106E240LEU0-0.0090.00346.190-0.001-0.0010.0000.0000.0000.000
107E241GLU-1-0.845-0.92749.146-0.021-0.0210.0000.0000.0000.000
108E242LEU0-0.030-0.00441.8680.0000.0000.0000.0000.0000.000
109E243LEU00.0240.00044.106-0.001-0.0010.0000.0000.0000.000
110E244GLY0-0.016-0.00746.8730.0000.0000.0000.0000.0000.000
111E245ILE0-0.048-0.02546.8240.0000.0000.0000.0000.0000.000
112E246MET0-0.0090.00342.686-0.001-0.0010.0000.0000.0000.000
113E247ALA0-0.036-0.01146.4350.0000.0000.0000.0000.0000.000
114E248LYS10.8670.94148.9660.0240.0240.0000.0000.0000.000
115E249ALA00.0040.00049.5840.0010.0010.0000.0000.0000.000
116E250PRO00.0990.04844.3540.0000.0000.0000.0000.0000.000
117E251GLU-1-0.916-0.96544.593-0.027-0.0270.0000.0000.0000.000
118E252GLN0-0.010-0.01645.6810.0020.0020.0000.0000.0000.000
119E253PHE0-0.039-0.00939.0200.0010.0010.0000.0000.0000.000
120E254PRO00.003-0.00141.9450.0000.0000.0000.0000.0000.000
121E255SER00.0260.01643.1830.0010.0010.0000.0000.0000.000
122E256LYS10.8950.93445.7830.0210.0210.0000.0000.0000.000
123E257VAL0-0.001-0.00540.0350.0000.0000.0000.0000.0000.000
124E258GLU-1-0.820-0.88940.628-0.020-0.0200.0000.0000.0000.000
125E259ASN0-0.035-0.01443.1710.0010.0010.0000.0000.0000.000
126E260ILE0-0.036-0.02140.7890.0000.0000.0000.0000.0000.000
127E261ARG10.8820.93438.1120.0190.0190.0000.0000.0000.000
128E262VAL00.0450.01640.8190.0010.0010.0000.0000.0000.000
129E263LEU0-0.0060.01343.3700.0010.0010.0000.0000.0000.000
130E264LEU0-0.014-0.00738.1230.0000.0000.0000.0000.0000.000
131E265LEU00.005-0.00637.2300.0000.0000.0000.0000.0000.000
132E266ASN0-0.0060.01840.6120.0030.0030.0000.0000.0000.000
133E267LEU00.006-0.00442.0150.0010.0010.0000.0000.0000.000
134E268HIS0-0.024-0.00635.8800.0020.0020.0000.0000.0000.000
135E269HIS00.0420.05740.4480.0010.0010.0000.0000.0000.000
136E270LEU00.0310.00842.0140.0010.0010.0000.0000.0000.000
137E271ILE0-0.018-0.01840.0630.0010.0010.0000.0000.0000.000
138E272ASN0-0.023-0.02337.997-0.001-0.0010.0000.0000.0000.000
139E273ASP-1-0.808-0.88441.147-0.002-0.0020.0000.0000.0000.000
140E274TYR0-0.070-0.03944.1580.0010.0010.0000.0000.0000.000
141E275ARG10.9000.95736.4890.0200.0200.0000.0000.0000.000
142E276PRO00.0410.02942.1270.0000.0000.0000.0000.0000.000
143E277HIS0-0.001-0.01743.1450.0020.0020.0000.0000.0000.000
144E278GLN00.0350.02139.550-0.001-0.0010.0000.0000.0000.000
145E279SER00.004-0.00239.1810.0000.0000.0000.0000.0000.000
146E280ARG10.9290.97541.3720.0010.0010.0000.0000.0000.000
147E281GLU-1-0.883-0.93744.398-0.010-0.0100.0000.0000.0000.000
148E282SER00.0170.00440.744-0.001-0.0010.0000.0000.0000.000
149E283LEU0-0.026-0.00741.3070.0000.0000.0000.0000.0000.000
150E284ILE0-0.015-0.00942.9770.0010.0010.0000.0000.0000.000
151E285MET00.0300.02444.1670.0000.0000.0000.0000.0000.000
152E286LEU0-0.030-0.01439.5380.0000.0000.0000.0000.0000.000
153E287LEU00.002-0.01043.3670.0010.0010.0000.0000.0000.000
154E288GLU-1-0.940-0.96445.990-0.005-0.0050.0000.0000.0000.000
155E289LYS10.9530.97840.6670.0050.0050.0000.0000.0000.000
156E290GLN0-0.077-0.03544.3630.0000.0000.0000.0000.0000.000
157E291LEU00.0530.02446.0730.0010.0010.0000.0000.0000.000
158E292LYS11.0021.01148.7190.0090.0090.0000.0000.0000.000
159E293HIS0-0.055-0.01645.0140.0000.0000.0000.0000.0000.000
160E294GLU-1-0.875-0.94148.2310.0060.0060.0000.0000.0000.000
161E295GLU-1-0.928-0.96550.325-0.002-0.0020.0000.0000.0000.000
162E296SER0-0.077-0.06550.5830.0000.0000.0000.0000.0000.000
163E297GLN0-0.043-0.01448.9720.0000.0000.0000.0000.0000.000
164E298VAL00.0310.01551.5790.0000.0000.0000.0000.0000.000
165E299GLU-1-0.847-0.90754.7420.0000.0000.0000.0000.0000.000
166E300LEU0-0.004-0.00251.1650.0000.0000.0000.0000.0000.000
167E301LEU00.0200.02352.8940.0000.0000.0000.0000.0000.000
168E302ARG10.8640.90955.466-0.001-0.0010.0000.0000.0000.000
169E303THR0-0.085-0.04757.3960.0000.0000.0000.0000.0000.000
170E304HIS00.0170.00955.3670.0000.0000.0000.0000.0000.000
171E305ASN00.0250.00057.8500.0000.0000.0000.0000.0000.000
172E306ARG10.8220.88960.0500.0020.0020.0000.0000.0000.000
173E307GLN00.0360.01459.2460.0000.0000.0000.0000.0000.000
174E308MET0-0.0020.01359.0670.0000.0000.0000.0000.0000.000
175E309THR0-0.026-0.02161.6440.0000.0000.0000.0000.0000.000
176E310GLU-1-0.808-0.86464.943-0.001-0.0010.0000.0000.0000.000
177E311THR0-0.052-0.04262.6230.0000.0000.0000.0000.0000.000
178E312LEU0-0.034-0.01863.9880.0000.0000.0000.0000.0000.000
179E313GLU-1-0.799-0.90265.7450.0030.0030.0000.0000.0000.000
180E314LYS10.8770.95167.3640.0020.0020.0000.0000.0000.000
181E315TYR0-0.034-0.03065.8360.0000.0000.0000.0000.0000.000
182E316LYS10.7930.90968.800-0.003-0.0030.0000.0000.0000.000
183E317SER0-0.007-0.01369.8170.0000.0000.0000.0000.0000.000
184E318LEU0-0.058-0.01367.7330.0000.0000.0000.0000.0000.000
185E319ASP-1-0.889-0.94569.9220.0040.0040.0000.0000.0000.000
186E320PHE0-0.026-0.02269.5860.0000.0000.0000.0000.0000.000
187E321ASN0-0.025-0.02070.5860.0000.0000.0000.0000.0000.000
188E322MET00.1080.06267.0530.0000.0000.0000.0000.0000.000
189E323GLU-1-0.862-0.91871.4830.0050.0050.0000.0000.0000.000
190E324LYS10.8490.91472.723-0.005-0.0050.0000.0000.0000.000
191E325GLU-1-0.841-0.93173.6990.0020.0020.0000.0000.0000.000
192E326GLY0-0.0060.00773.1800.0000.0000.0000.0000.0000.000
193E327ASP-1-0.913-0.98173.9820.0030.0030.0000.0000.0000.000
194E328VAL00.0270.02377.1030.0000.0000.0000.0000.0000.000
195E329ILE00.0210.01174.7200.0000.0000.0000.0000.0000.000
196E330GLN0-0.051-0.01274.573-0.001-0.0010.0000.0000.0000.000
197E331GLN0-0.059-0.04378.2370.0000.0000.0000.0000.0000.000
198E332LEU0-0.0010.01080.0630.0000.0000.0000.0000.0000.000
199E333LYS10.8530.92077.3060.0000.0000.0000.0000.0000.000
200E334SER0-0.082-0.03780.4520.0000.0000.0000.0000.0000.000
201E335SER0-0.0390.00083.0760.0000.0000.0000.0000.0000.000