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: 4JN4N

Calculation Name: 4OZR-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OZR

Chain ID: E

ChEMBL ID:

UniProt ID: E0VVT4

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2274804.536405
FMO2-HF: Nuclear repulsion 2194069.869189
FMO2-HF: Total energy -80734.667216
FMO2-MP2: Total energy -80968.385393


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:282:LYS)


Summations of interaction energy for fragment #1(E:282:LYS)
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.
-20.799-18.4160.033-1.08-1.334-0.003
Interaction energy analysis for fragmet #1(E:282:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.994 / q_NPA : 0.977
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].
3E284ILE00.0220.0303.9110.0251.1710.000-0.482-0.6630.001
4E285SER00.0250.0135.9441.9721.9720.0000.0000.0000.000
5E286PRO0-0.0180.0088.6920.7980.7980.0000.0000.0000.000
6E287GLU-1-0.862-0.95212.119-15.771-15.7710.0000.0000.0000.000
7E288GLN0-0.017-0.02011.175-0.098-0.0980.0000.0000.0000.000
8E289GLU-1-0.810-0.88613.022-17.329-17.3290.0000.0000.0000.000
9E290GLU-1-0.801-0.88614.745-11.786-11.7860.0000.0000.0000.000
10E291LEU0-0.041-0.02216.5730.6410.6410.0000.0000.0000.000
11E292ILE0-0.007-0.00712.3870.3980.3980.0000.0000.0000.000
12E293HIS0-0.023-0.02216.7790.9580.9580.0000.0000.0000.000
13E294ARG10.8340.92119.54412.09012.0900.0000.0000.0000.000
14E295LEU0-0.052-0.01319.5030.5430.5430.0000.0000.0000.000
15E296VAL00.000-0.01218.7200.3890.3890.0000.0000.0000.000
16E297TYR0-0.091-0.06021.6200.3310.3310.0000.0000.0000.000
17E298PHE00.051-0.00424.7290.3760.3760.0000.0000.0000.000
18E299GLN0-0.062-0.04421.7900.2070.2070.0000.0000.0000.000
19E300ASN0-0.029-0.02424.7460.0890.0890.0000.0000.0000.000
20E301GLU-1-0.846-0.89427.410-8.726-8.7260.0000.0000.0000.000
21E302TYR0-0.0060.00429.6290.2430.2430.0000.0000.0000.000
22E303GLU-1-0.769-0.85728.065-9.653-9.6530.0000.0000.0000.000
23E304GLN0-0.068-0.02630.675-0.077-0.0770.0000.0000.0000.000
24E305PRO0-0.042-0.03134.454-0.090-0.0900.0000.0000.0000.000
25E306SER0-0.041-0.02337.669-0.073-0.0730.0000.0000.0000.000
26E307ASP-1-0.875-0.92538.693-6.813-6.8130.0000.0000.0000.000
27E308GLU-1-0.930-0.98140.128-7.164-7.1640.0000.0000.0000.000
28E309ASP-1-1.008-0.98243.422-5.924-5.9240.0000.0000.0000.000
29E328PHE00.002-0.01050.8360.0150.0150.0000.0000.0000.000
30E329ARG10.8800.94449.2925.7465.7460.0000.0000.0000.000
31E330HIS00.0430.01548.881-0.093-0.0930.0000.0000.0000.000
32E331ILE00.0870.05246.829-0.068-0.0680.0000.0000.0000.000
33E332THR0-0.043-0.02343.287-0.165-0.1650.0000.0000.0000.000
34E333GLU-1-0.886-0.94343.379-6.280-6.2800.0000.0000.0000.000
35E334ILE00.0710.03239.779-0.130-0.1300.0000.0000.0000.000
36E335THR0-0.021-0.01138.596-0.228-0.2280.0000.0000.0000.000
37E336ILE00.001-0.00138.521-0.205-0.2050.0000.0000.0000.000
38E337LEU00.0400.04038.360-0.148-0.1480.0000.0000.0000.000
39E338THR0-0.050-0.04134.653-0.230-0.2300.0000.0000.0000.000
40E339VAL0-0.002-0.00934.433-0.243-0.2430.0000.0000.0000.000
41E340GLN00.0010.00035.021-0.120-0.1200.0000.0000.0000.000
42E341LEU00.0240.02232.985-0.135-0.1350.0000.0000.0000.000
43E342ILE0-0.030-0.00529.934-0.309-0.3090.0000.0000.0000.000
44E343VAL0-0.027-0.02630.741-0.244-0.2440.0000.0000.0000.000
45E344GLU-1-0.794-0.84932.463-8.416-8.4160.0000.0000.0000.000
46E345PHE00.0010.00023.230-0.171-0.1710.0000.0000.0000.000
47E346ALA00.0190.01227.613-0.264-0.2640.0000.0000.0000.000
48E347LYS10.8120.89828.2628.1978.1970.0000.0000.0000.000
49E348ARG10.7500.86627.0108.9928.9920.0000.0000.0000.000
50E349LEU00.0090.01123.048-0.360-0.3600.0000.0000.0000.000
51E350PRO0-0.028-0.00722.4330.3040.3040.0000.0000.0000.000
52E351GLY00.0300.02523.531-0.446-0.4460.0000.0000.0000.000
53E352PHE00.0700.02325.6990.3090.3090.0000.0000.0000.000
54E353ASP-1-0.824-0.90028.228-9.809-9.8090.0000.0000.0000.000
55E354LYS10.8110.89727.49710.55410.5540.0000.0000.0000.000
56E355LEU0-0.0120.01028.2750.0730.0730.0000.0000.0000.000
57E356LEU00.0210.03331.7380.1990.1990.0000.0000.0000.000
58E357ARG10.8740.92335.0627.7637.7630.0000.0000.0000.000
59E358GLU-1-0.840-0.94137.168-7.556-7.5560.0000.0000.0000.000
60E359ASP-1-0.697-0.85632.740-8.705-8.7050.0000.0000.0000.000
61E360GLN0-0.0080.01032.2210.1510.1510.0000.0000.0000.000
62E361ILE0-0.024-0.01533.694-0.040-0.0400.0000.0000.0000.000
63E362ALA0-0.046-0.02534.8790.0390.0390.0000.0000.0000.000
64E363LEU00.0480.02328.3920.0230.0230.0000.0000.0000.000
65E364LEU00.0160.01431.165-0.048-0.0480.0000.0000.0000.000
66E365LYS10.9270.96032.9807.6527.6520.0000.0000.0000.000
67E366ALA0-0.027-0.01032.3630.0710.0710.0000.0000.0000.000
68E367CYS0-0.0400.00528.514-0.120-0.1200.0000.0000.0000.000
69E368SER00.002-0.00230.357-0.078-0.0780.0000.0000.0000.000
70E369SER00.018-0.00132.2600.0220.0220.0000.0000.0000.000
71E370GLU-1-0.785-0.86127.872-9.935-9.9350.0000.0000.0000.000
72E371VAL00.0410.00826.940-0.215-0.2150.0000.0000.0000.000
73E372MET0-0.032-0.00928.640-0.013-0.0130.0000.0000.0000.000
74E373MET0-0.0080.00829.0610.0650.0650.0000.0000.0000.000
75E374LEU0-0.007-0.00223.255-0.106-0.1060.0000.0000.0000.000
76E375ARG10.8330.91226.5728.6728.6720.0000.0000.0000.000
77E376MET00.0000.01028.7920.0880.0880.0000.0000.0000.000
78E377ALA00.0370.00626.0410.0380.0380.0000.0000.0000.000
79E378ARG10.7590.87423.36810.44810.4480.0000.0000.0000.000
80E379ARG10.7970.86826.2939.4149.4140.0000.0000.0000.000
81E380TYR0-0.0270.00028.5800.1830.1830.0000.0000.0000.000
82E381ASP-1-0.811-0.89228.384-9.900-9.9000.0000.0000.0000.000
83E382VAL0-0.091-0.04029.6860.2640.2640.0000.0000.0000.000
84E383GLY00.0510.01232.036-0.026-0.0260.0000.0000.0000.000
85E384SER0-0.074-0.04134.8470.0080.0080.0000.0000.0000.000
86E385ASP-1-0.849-0.89736.003-7.139-7.1390.0000.0000.0000.000
87E386SER0-0.083-0.04836.901-0.130-0.1300.0000.0000.0000.000
88E387ILE0-0.017-0.01136.233-0.082-0.0820.0000.0000.0000.000
89E388LEU0-0.0020.00738.2920.2160.2160.0000.0000.0000.000
90E407ALA0-0.019-0.02942.2410.0220.0220.0000.0000.0000.000
91E408THR00.0400.02437.260-0.019-0.0190.0000.0000.0000.000
92E409VAL00.0540.02737.059-0.213-0.2130.0000.0000.0000.000
93E410ASP-1-0.905-0.95435.956-7.986-7.9860.0000.0000.0000.000
94E411ASP-1-0.776-0.87533.149-8.690-8.6900.0000.0000.0000.000
95E412LEU00.0020.01131.012-0.318-0.3180.0000.0000.0000.000
96E413LEU00.1140.04431.122-0.282-0.2820.0000.0000.0000.000
97E414ARG10.7790.90129.3818.8038.8030.0000.0000.0000.000
98E415PHE00.0340.01825.362-0.340-0.3400.0000.0000.0000.000
99E416CYS0-0.017-0.00726.384-0.370-0.3700.0000.0000.0000.000
100E417ARG10.8900.92226.6958.4698.4690.0000.0000.0000.000
101E418GLN0-0.0070.00222.5440.0120.0120.0000.0000.0000.000
102E419MET0-0.0010.00021.014-0.661-0.6610.0000.0000.0000.000
103E420TYR00.005-0.01621.891-0.621-0.6210.0000.0000.0000.000
104E421GLY0-0.020-0.00823.079-0.193-0.1930.0000.0000.0000.000
105E422MET0-0.122-0.06218.188-0.664-0.6640.0000.0000.0000.000
106E423LYS10.8120.91317.82010.75910.7590.0000.0000.0000.000
107E424VAL0-0.0180.00717.681-0.507-0.5070.0000.0000.0000.000
108E425ASP-1-0.746-0.85415.042-15.194-15.1940.0000.0000.0000.000
109E426ASN00.044-0.00218.4690.3650.3650.0000.0000.0000.000
110E427ALA00.0570.03815.3970.3610.3610.0000.0000.0000.000
111E428GLU-1-0.807-0.90013.693-16.441-16.4410.0000.0000.0000.000
112E429TYR00.0290.00316.3280.2200.2200.0000.0000.0000.000
113E430ALA00.0280.05019.5430.2930.2930.0000.0000.0000.000
114E431LEU00.0240.00113.9900.2430.2430.0000.0000.0000.000
115E432LEU0-0.006-0.01217.5140.1330.1330.0000.0000.0000.000
116E433THR0-0.025-0.02519.5370.5380.5380.0000.0000.0000.000
117E434ALA00.0040.00420.1660.3930.3930.0000.0000.0000.000
118E435ILE0-0.051-0.02516.2910.2020.2020.0000.0000.0000.000
119E436VAL0-0.004-0.00420.9520.2650.2650.0000.0000.0000.000
120E437ILE0-0.015-0.01624.3130.3850.3850.0000.0000.0000.000
121E438PHE0-0.028-0.02522.3570.4010.4010.0000.0000.0000.000
122E439SER00.0040.02323.686-0.126-0.1260.0000.0000.0000.000
123E440GLU-1-0.819-0.92025.142-9.708-9.7080.0000.0000.0000.000
124E441ARG10.7210.82227.46810.02110.0210.0000.0000.0000.000
125E442PRO00.0320.01831.1540.0280.0280.0000.0000.0000.000
126E443SER0-0.106-0.07034.4920.1780.1780.0000.0000.0000.000
127E444LEU00.0160.03530.5810.1630.1630.0000.0000.0000.000
128E445ILE0-0.049-0.03934.6600.0490.0490.0000.0000.0000.000
129E446GLU-1-0.856-0.92531.616-9.156-9.1560.0000.0000.0000.000
130E447GLY00.0570.03529.779-0.295-0.2950.0000.0000.0000.000
131E448TRP00.0300.01027.770-0.494-0.4940.0000.0000.0000.000
132E449LYS10.7730.88126.4949.0669.0660.0000.0000.0000.000
133E450VAL00.000-0.00325.682-0.385-0.3850.0000.0000.0000.000
134E451GLU-1-0.857-0.91522.683-12.736-12.7360.0000.0000.0000.000
135E452LYS10.7950.86121.50712.82812.8280.0000.0000.0000.000
136E453ILE0-0.042-0.00621.207-0.499-0.4990.0000.0000.0000.000
137E454GLN00.009-0.00319.948-0.321-0.3210.0000.0000.0000.000
138E455GLU-1-0.844-0.91217.445-15.143-15.1430.0000.0000.0000.000
139E456ILE00.0080.00915.782-1.050-1.0500.0000.0000.0000.000
140E457TYR0-0.005-0.02415.232-0.776-0.7760.0000.0000.0000.000
141E458LEU0-0.017-0.00614.938-0.557-0.5570.0000.0000.0000.000
142E459GLU-1-0.901-0.9559.807-25.132-25.1320.0000.0000.0000.000
143E460ALA0-0.010-0.00710.382-1.487-1.4870.0000.0000.0000.000
144E461LEU0-0.012-0.00411.008-0.763-0.7630.0000.0000.0000.000
145E462LYS10.8420.9175.65930.18530.1850.0000.0000.0000.000
146E463VAL00.008-0.0055.816-1.892-1.8920.0000.0000.0000.000
147E464TYR0-0.032-0.0296.209-1.794-1.7940.0000.0000.0000.000
148E465VAL0-0.034-0.0288.121-0.558-0.5580.0000.0000.0000.000
149E466ASP-1-0.926-0.9653.337-37.152-36.5990.023-0.328-0.248-0.002
150E467ASN0-0.041-0.0283.623-4.258-3.5740.010-0.270-0.423-0.002
151E468ARG10.8490.9265.61122.35122.3510.0000.0000.0000.000
152E469ARG10.8190.9198.49918.59618.5960.0000.0000.0000.000
153E470LYS10.9640.9838.64315.45215.4520.0000.0000.0000.000
154E471PRO0-0.020-0.0015.1721.7311.7310.0000.0000.0000.000
155E472ARG10.9940.9926.65024.12624.1260.0000.0000.0000.000
156E473SER0-0.040-0.0198.4132.5422.5420.0000.0000.0000.000
157E474GLY00.0820.0326.591-2.588-2.5880.0000.0000.0000.000
158E475THR0-0.018-0.0159.2780.1970.1970.0000.0000.0000.000
159E476ILE00.006-0.00311.5750.8120.8120.0000.0000.0000.000
160E477PHE00.0870.05910.3450.5750.5750.0000.0000.0000.000
161E478ALA00.0510.02412.4730.8220.8220.0000.0000.0000.000
162E479LYS10.9150.96015.37815.26115.2610.0000.0000.0000.000
163E480LEU00.0580.03014.2660.8080.8080.0000.0000.0000.000
164E481LEU00.0150.01315.0530.5780.5780.0000.0000.0000.000
165E482SER0-0.097-0.06118.2340.7430.7430.0000.0000.0000.000
166E483VAL00.0270.00920.2590.5640.5640.0000.0000.0000.000
167E484LEU00.0330.01119.7570.5210.5210.0000.0000.0000.000
168E485THR0-0.016-0.00623.5460.3260.3260.0000.0000.0000.000
169E486GLU-1-0.912-0.95825.620-9.777-9.7770.0000.0000.0000.000
170E487LEU0-0.025-0.00524.4870.4100.4100.0000.0000.0000.000
171E488ARG10.8720.94626.21610.68210.6820.0000.0000.0000.000
172E489THR00.0100.00929.9260.3450.3450.0000.0000.0000.000
173E490LEU00.007-0.00429.2870.3060.3060.0000.0000.0000.000
174E491GLY00.0130.00531.8210.2420.2420.0000.0000.0000.000
175E492ASN0-0.075-0.02033.2960.1780.1780.0000.0000.0000.000
176E493LEU00.0860.05135.9060.2270.2270.0000.0000.0000.000
177E494ASN0-0.031-0.02235.8800.3240.3240.0000.0000.0000.000
178E495SER0-0.044-0.04037.4640.2280.2280.0000.0000.0000.000
179E496GLU-1-0.824-0.92239.199-7.194-7.1940.0000.0000.0000.000
180E497MET0-0.0190.01040.0770.3230.3230.0000.0000.0000.000
181E498CYS00.0120.00741.1600.2460.2460.0000.0000.0000.000
182E499PHE0-0.019-0.01843.1030.1950.1950.0000.0000.0000.000
183E500SER0-0.007-0.02345.1200.2040.2040.0000.0000.0000.000
184E501LEU0-0.065-0.02845.9910.1840.1840.0000.0000.0000.000
185E502LYS10.9430.96045.9406.5466.5460.0000.0000.0000.000
186E503LEU0-0.019-0.00748.7810.1340.1340.0000.0000.0000.000
187E504LYS10.9360.98149.1616.1256.1250.0000.0000.0000.000
188E505ASN0-0.071-0.03651.1780.0170.0170.0000.0000.0000.000
189E506LYS10.8710.91353.5195.1305.1300.0000.0000.0000.000
190E507LYS10.9710.99055.3205.2985.2980.0000.0000.0000.000
191E508LEU0-0.029-0.02357.388-0.006-0.0060.0000.0000.0000.000
192E509PRO00.0160.02461.0860.0190.0190.0000.0000.0000.000
193E510PRO00.017-0.00763.8890.0000.0000.0000.0000.0000.000
194E511PHE0-0.0040.00662.9670.0430.0430.0000.0000.0000.000
195E512LEU00.0140.01466.553-0.027-0.0270.0000.0000.0000.000
196E513ALA0-0.020-0.02161.825-0.068-0.0680.0000.0000.0000.000
197E514GLU-1-0.787-0.86059.469-5.056-5.0560.0000.0000.0000.000