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: KGR63

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2271379.968361
FMO2-HF: Nuclear repulsion 2190646.056897
FMO2-HF: Total energy -80733.911463
FMO2-MP2: Total energy -80967.735849


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.
-24.307-22.0110.011-1.083-1.224-0.001
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 : 0.978 / q_NPA : 0.969
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].
3E284ILE00.0500.0243.564-1.2750.2510.000-0.769-0.7570.001
4E285SER00.0380.0236.2701.4851.4850.0000.0000.0000.000
5E286PRO0-0.0220.0028.7670.8080.8080.0000.0000.0000.000
6E287GLU-1-0.845-0.93412.342-15.832-15.8320.0000.0000.0000.000
7E288GLN0-0.028-0.03211.137-0.231-0.2310.0000.0000.0000.000
8E289GLU-1-0.848-0.93212.845-17.224-17.2240.0000.0000.0000.000
9E290GLU-1-0.829-0.90814.673-11.945-11.9450.0000.0000.0000.000
10E291LEU0-0.049-0.01716.7210.6620.6620.0000.0000.0000.000
11E292ILE0-0.002-0.02012.8290.5470.5470.0000.0000.0000.000
12E293HIS0-0.0070.00316.6380.8290.8290.0000.0000.0000.000
13E294ARG10.8830.94619.62211.92711.9270.0000.0000.0000.000
14E295LEU0-0.060-0.02119.4130.5120.5120.0000.0000.0000.000
15E296VAL00.005-0.00818.7840.4220.4220.0000.0000.0000.000
16E297TYR0-0.091-0.04921.6890.3470.3470.0000.0000.0000.000
17E298PHE00.058-0.00224.7590.3900.3900.0000.0000.0000.000
18E299GLN0-0.057-0.03721.6490.2930.2930.0000.0000.0000.000
19E300ASN0-0.051-0.04524.9930.0720.0720.0000.0000.0000.000
20E301GLU-1-0.861-0.89127.337-8.737-8.7370.0000.0000.0000.000
21E302TYR0-0.025-0.01229.5860.2430.2430.0000.0000.0000.000
22E303GLU-1-0.766-0.85728.222-9.669-9.6690.0000.0000.0000.000
23E304GLN0-0.033-0.02330.795-0.071-0.0710.0000.0000.0000.000
24E305PRO0-0.049-0.02834.465-0.064-0.0640.0000.0000.0000.000
25E306SER0-0.053-0.01737.870-0.030-0.0300.0000.0000.0000.000
26E307ASP-1-0.871-0.92638.919-6.792-6.7920.0000.0000.0000.000
27E308GLU-1-0.949-0.98540.785-7.076-7.0760.0000.0000.0000.000
28E309ASP-1-1.015-0.98943.962-5.900-5.9000.0000.0000.0000.000
29E328PHE0-0.002-0.01251.2130.0140.0140.0000.0000.0000.000
30E329ARG10.9120.96749.3475.7995.7990.0000.0000.0000.000
31E330HIS00.043-0.00249.290-0.094-0.0940.0000.0000.0000.000
32E331ILE00.0580.05347.506-0.020-0.0200.0000.0000.0000.000
33E332THR0-0.042-0.02543.824-0.164-0.1640.0000.0000.0000.000
34E333GLU-1-0.866-0.92744.032-6.300-6.3000.0000.0000.0000.000
35E334ILE00.0910.03639.983-0.129-0.1290.0000.0000.0000.000
36E335THR0-0.033-0.02139.179-0.244-0.2440.0000.0000.0000.000
37E336ILE00.008-0.00839.033-0.191-0.1910.0000.0000.0000.000
38E337LEU00.0560.04638.311-0.149-0.1490.0000.0000.0000.000
39E338THR0-0.035-0.02634.859-0.242-0.2420.0000.0000.0000.000
40E339VAL00.000-0.00334.643-0.250-0.2500.0000.0000.0000.000
41E340GLN00.0010.00535.134-0.139-0.1390.0000.0000.0000.000
42E341LEU00.0080.01133.117-0.146-0.1460.0000.0000.0000.000
43E342ILE0-0.026-0.00830.182-0.302-0.3020.0000.0000.0000.000
44E343VAL0-0.027-0.02530.839-0.263-0.2630.0000.0000.0000.000
45E344GLU-1-0.777-0.85432.538-8.407-8.4070.0000.0000.0000.000
46E345PHE0-0.017-0.01623.143-0.201-0.2010.0000.0000.0000.000
47E346ALA00.007-0.00727.660-0.297-0.2970.0000.0000.0000.000
48E347LYS10.8570.94428.7428.1888.1880.0000.0000.0000.000
49E348ARG10.7110.85227.5228.8378.8370.0000.0000.0000.000
50E349LEU00.0170.02423.427-0.380-0.3800.0000.0000.0000.000
51E350PRO0-0.0070.00222.5400.2830.2830.0000.0000.0000.000
52E351GLY00.0290.02324.064-0.362-0.3620.0000.0000.0000.000
53E352PHE00.0650.02126.0880.2750.2750.0000.0000.0000.000
54E353ASP-1-0.840-0.90828.732-9.703-9.7030.0000.0000.0000.000
55E354LYS10.8170.90027.91310.45810.4580.0000.0000.0000.000
56E355LEU0-0.0210.00428.7130.1050.1050.0000.0000.0000.000
57E356LEU00.0210.03032.2000.2010.2010.0000.0000.0000.000
58E357ARG10.8790.92135.6887.7717.7710.0000.0000.0000.000
59E358GLU-1-0.845-0.94637.637-7.555-7.5550.0000.0000.0000.000
60E359ASP-1-0.737-0.88632.870-8.787-8.7870.0000.0000.0000.000
61E360GLN0-0.0050.01132.6360.1290.1290.0000.0000.0000.000
62E361ILE0-0.026-0.01233.902-0.028-0.0280.0000.0000.0000.000
63E362ALA0-0.027-0.01335.0200.0260.0260.0000.0000.0000.000
64E363LEU00.0450.02328.6720.0160.0160.0000.0000.0000.000
65E364LEU00.0260.01031.433-0.074-0.0740.0000.0000.0000.000
66E365LYS10.9090.94833.2827.6457.6450.0000.0000.0000.000
67E366ALA0-0.037-0.01432.6420.1130.1130.0000.0000.0000.000
68E367CYS0-0.061-0.00528.974-0.099-0.0990.0000.0000.0000.000
69E368SER00.0250.01630.718-0.089-0.0890.0000.0000.0000.000
70E369SER00.0210.00932.7050.0440.0440.0000.0000.0000.000
71E370GLU-1-0.761-0.85028.321-10.033-10.0330.0000.0000.0000.000
72E371VAL00.0550.01127.248-0.206-0.2060.0000.0000.0000.000
73E372MET0-0.019-0.00928.997-0.035-0.0350.0000.0000.0000.000
74E373MET0-0.023-0.00429.4950.0750.0750.0000.0000.0000.000
75E374LEU0-0.006-0.00223.633-0.087-0.0870.0000.0000.0000.000
76E375ARG10.8380.91226.9918.6928.6920.0000.0000.0000.000
77E376MET0-0.0270.00029.0710.1640.1640.0000.0000.0000.000
78E377ALA00.008-0.01026.5590.0650.0650.0000.0000.0000.000
79E378ARG10.7860.89023.70210.50010.5000.0000.0000.0000.000
80E379ARG10.8230.89326.5949.2979.2970.0000.0000.0000.000
81E380TYR0-0.054-0.02028.6240.1520.1520.0000.0000.0000.000
82E381ASP-1-0.801-0.90628.938-9.752-9.7520.0000.0000.0000.000
83E382VAL0-0.121-0.01029.9560.2960.2960.0000.0000.0000.000
84E383GLY00.1080.03132.489-0.059-0.0590.0000.0000.0000.000
85E384SER0-0.077-0.06535.095-0.008-0.0080.0000.0000.0000.000
86E385ASP-1-0.872-0.91836.099-7.176-7.1760.0000.0000.0000.000
87E386SER0-0.095-0.04437.096-0.129-0.1290.0000.0000.0000.000
88E387ILE0-0.022-0.01236.727-0.061-0.0610.0000.0000.0000.000
89E388LEU00.0090.01138.7450.1940.1940.0000.0000.0000.000
90E407ALA0-0.021-0.02542.6680.0210.0210.0000.0000.0000.000
91E408THR00.0290.01837.854-0.029-0.0290.0000.0000.0000.000
92E409VAL00.0690.03137.660-0.195-0.1950.0000.0000.0000.000
93E410ASP-1-0.906-0.95436.389-8.015-8.0150.0000.0000.0000.000
94E411ASP-1-0.777-0.87833.709-8.659-8.6590.0000.0000.0000.000
95E412LEU0-0.0060.00331.656-0.319-0.3190.0000.0000.0000.000
96E413LEU00.0990.03131.690-0.283-0.2830.0000.0000.0000.000
97E414ARG10.7800.88430.1588.7568.7560.0000.0000.0000.000
98E415PHE00.0380.02325.957-0.330-0.3300.0000.0000.0000.000
99E416CYS0-0.014-0.00727.043-0.384-0.3840.0000.0000.0000.000
100E417ARG10.9130.95427.2998.4768.4760.0000.0000.0000.000
101E418GLN0-0.0150.00222.7860.0210.0210.0000.0000.0000.000
102E419MET0-0.003-0.00521.541-0.641-0.6410.0000.0000.0000.000
103E420TYR00.000-0.01622.454-0.647-0.6470.0000.0000.0000.000
104E421GLY0-0.020-0.00723.411-0.224-0.2240.0000.0000.0000.000
105E422MET0-0.119-0.05518.558-0.679-0.6790.0000.0000.0000.000
106E423LYS10.8210.92018.13610.80710.8070.0000.0000.0000.000
107E424VAL0-0.0290.00417.894-0.590-0.5900.0000.0000.0000.000
108E425ASP-1-0.767-0.85414.997-15.301-15.3010.0000.0000.0000.000
109E426ASN00.0810.00618.5100.3150.3150.0000.0000.0000.000
110E427ALA00.0550.04215.3950.3920.3920.0000.0000.0000.000
111E428GLU-1-0.802-0.90013.801-16.652-16.6520.0000.0000.0000.000
112E429TYR00.0240.00316.6230.2590.2590.0000.0000.0000.000
113E430ALA00.0160.03719.5750.3160.3160.0000.0000.0000.000
114E431LEU00.017-0.00414.2950.2720.2720.0000.0000.0000.000
115E432LEU0-0.017-0.00418.1220.1100.1100.0000.0000.0000.000
116E433THR0-0.032-0.02419.9870.5140.5140.0000.0000.0000.000
117E434ALA0-0.001-0.00620.4430.3690.3690.0000.0000.0000.000
118E435ILE0-0.027-0.01416.7330.2070.2070.0000.0000.0000.000
119E436VAL0-0.0080.00421.3990.2640.2640.0000.0000.0000.000
120E437ILE00.008-0.00924.6150.3980.3980.0000.0000.0000.000
121E438PHE0-0.064-0.03322.8530.4110.4110.0000.0000.0000.000
122E439SER0-0.004-0.00424.521-0.288-0.2880.0000.0000.0000.000
123E440GLU-1-0.878-0.94825.907-9.895-9.8950.0000.0000.0000.000
124E441ARG10.7060.82027.82010.12010.1200.0000.0000.0000.000
125E442PRO00.0380.01331.5430.0130.0130.0000.0000.0000.000
126E443SER0-0.082-0.05334.7200.2060.2060.0000.0000.0000.000
127E444LEU00.0180.03030.9490.1530.1530.0000.0000.0000.000
128E445ILE0-0.044-0.02234.9820.0330.0330.0000.0000.0000.000
129E446GLU-1-0.860-0.92332.079-9.217-9.2170.0000.0000.0000.000
130E447GLY00.0650.03430.306-0.198-0.1980.0000.0000.0000.000
131E448TRP00.0240.00428.056-0.510-0.5100.0000.0000.0000.000
132E449LYS10.7980.90326.6129.0629.0620.0000.0000.0000.000
133E450VAL00.0180.00625.772-0.428-0.4280.0000.0000.0000.000
134E451GLU-1-0.849-0.90723.187-12.761-12.7610.0000.0000.0000.000
135E452LYS10.7930.86422.14812.80712.8070.0000.0000.0000.000
136E453ILE0-0.033-0.01521.155-0.605-0.6050.0000.0000.0000.000
137E454GLN00.0040.00520.313-0.264-0.2640.0000.0000.0000.000
138E455GLU-1-0.852-0.92617.836-15.233-15.2330.0000.0000.0000.000
139E456ILE00.0110.01016.114-1.088-1.0880.0000.0000.0000.000
140E457TYR0-0.028-0.02715.508-0.785-0.7850.0000.0000.0000.000
141E458LEU0-0.017-0.01215.175-0.597-0.5970.0000.0000.0000.000
142E459GLU-1-0.913-0.95210.480-25.024-25.0240.0000.0000.0000.000
143E460ALA0-0.009-0.00610.736-1.524-1.5240.0000.0000.0000.000
144E461LEU0-0.004-0.00910.913-0.948-0.9480.0000.0000.0000.000
145E462LYS10.8520.9226.77929.55529.5550.0000.0000.0000.000
146E463VAL00.000-0.0066.098-1.761-1.7610.0000.0000.0000.000
147E464TYR0-0.066-0.0396.227-1.778-1.7780.0000.0000.0000.000
148E465VAL0-0.011-0.0238.104-0.464-0.4640.0000.0000.0000.000
149E466ASP-1-0.973-0.9844.048-34.385-34.300-0.001-0.037-0.0470.000
150E467ASN0-0.070-0.0333.441-5.386-4.7010.012-0.277-0.420-0.002
151E468ARG10.9050.9655.64421.00821.0080.0000.0000.0000.000
152E469ARG10.8240.9149.12918.16718.1670.0000.0000.0000.000
153E470LYS10.9900.9928.84215.36015.3600.0000.0000.0000.000
154E471PRO0-0.019-0.0095.8421.5991.5990.0000.0000.0000.000
155E472ARG10.9681.0137.15124.55624.5560.0000.0000.0000.000
156E473SER0-0.053-0.0228.7742.4392.4390.0000.0000.0000.000
157E474GLY00.1160.0377.007-2.593-2.5930.0000.0000.0000.000
158E475THR0-0.024-0.02510.090-0.151-0.1510.0000.0000.0000.000
159E476ILE00.011-0.02111.8610.9920.9920.0000.0000.0000.000
160E477PHE00.0950.06611.0530.5090.5090.0000.0000.0000.000
161E478ALA00.0510.02113.1780.7910.7910.0000.0000.0000.000
162E479LYS10.9180.95616.13615.47715.4770.0000.0000.0000.000
163E480LEU00.0510.02414.3900.7840.7840.0000.0000.0000.000
164E481LEU00.0180.00915.7220.6060.6060.0000.0000.0000.000
165E482SER0-0.090-0.03218.8480.6720.6720.0000.0000.0000.000
166E483VAL00.0370.01020.9720.6040.6040.0000.0000.0000.000
167E484LEU00.0430.02420.7100.5170.5170.0000.0000.0000.000
168E485THR0-0.008-0.01424.2210.3650.3650.0000.0000.0000.000
169E486GLU-1-0.924-0.96025.901-9.874-9.8740.0000.0000.0000.000
170E487LEU0-0.048-0.01625.1300.4630.4630.0000.0000.0000.000
171E488ARG10.9280.98226.91210.67210.6720.0000.0000.0000.000
172E489THR00.0310.02430.5500.3450.3450.0000.0000.0000.000
173E490LEU00.0100.00129.7390.3080.3080.0000.0000.0000.000
174E491GLY00.0130.00932.3190.2610.2610.0000.0000.0000.000
175E492ASN0-0.049-0.01233.7970.1990.1990.0000.0000.0000.000
176E493LEU00.0590.03736.3100.2420.2420.0000.0000.0000.000
177E494ASN0-0.023-0.02136.4830.3650.3650.0000.0000.0000.000
178E495SER0-0.048-0.03637.7730.2230.2230.0000.0000.0000.000
179E496GLU-1-0.819-0.92239.486-7.185-7.1850.0000.0000.0000.000
180E497MET0-0.040-0.00940.7920.3200.3200.0000.0000.0000.000
181E498CYS0-0.006-0.00741.3610.2430.2430.0000.0000.0000.000
182E499PHE00.001-0.00443.3490.1980.1980.0000.0000.0000.000
183E500SER0-0.001-0.01645.3850.2000.2000.0000.0000.0000.000
184E501LEU0-0.074-0.02546.3300.1920.1920.0000.0000.0000.000
185E502LYS10.9300.95246.3346.5706.5700.0000.0000.0000.000
186E503LEU0-0.030-0.00749.0420.1290.1290.0000.0000.0000.000
187E504LYS10.9310.97449.9436.0956.0950.0000.0000.0000.000
188E505ASN0-0.057-0.02851.3480.0210.0210.0000.0000.0000.000
189E506LYS10.8940.93554.0455.1535.1530.0000.0000.0000.000
190E507LYS10.9700.99156.0885.3315.3310.0000.0000.0000.000
191E508LEU0-0.026-0.03457.9130.0080.0080.0000.0000.0000.000
192E509PRO00.0080.03561.7190.0100.0100.0000.0000.0000.000
193E510PRO0-0.012-0.02264.559-0.001-0.0010.0000.0000.0000.000
194E511PHE00.0320.01163.6040.0250.0250.0000.0000.0000.000
195E512LEU00.0040.00466.722-0.036-0.0360.0000.0000.0000.000
196E513ALA0-0.007-0.00862.339-0.071-0.0710.0000.0000.0000.000
197E514GLU-1-0.827-0.89060.325-5.054-5.0540.0000.0000.0000.000