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: 43Y8N

Calculation Name: 3K5B-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5B

Chain ID: E

ChEMBL ID:

UniProt ID: P74901

Base Structure: X-ray

Registration Date: 2023-03-14

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1333912.500663
FMO2-HF: Nuclear repulsion 1262936.058176
FMO2-HF: Total energy -70976.442488
FMO2-MP2: Total energy -71185.83039


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:3:LYS)


Summations of interaction energy for fragment #1(E:3: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.
-187.971-189.30430.584-15.761-13.49-0.161
Interaction energy analysis for fragmet #1(E:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.895 / q_NPA : 0.925
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].
3E5GLU-1-0.837-0.8871.641-166.723-170.71729.628-14.634-11.001-0.161
4E6ALA00.0190.0132.2998.98710.9020.951-0.929-1.9360.000
5E7ILE00.0130.0023.4656.7047.4500.005-0.198-0.5530.000
6E8LEU00.0190.0115.7553.4383.4380.0000.0000.0000.000
7E9SER0-0.016-0.0276.6603.7433.7430.0000.0000.0000.000
8E10GLN0-0.054-0.0307.7892.6832.6830.0000.0000.0000.000
9E11GLU-1-0.934-0.9539.429-20.976-20.9760.0000.0000.0000.000
10E12VAL0-0.010-0.00811.7151.9491.9490.0000.0000.0000.000
11E13GLU-1-0.910-0.92912.097-17.386-17.3860.0000.0000.0000.000
12E14ALA0-0.005-0.02213.9060.2930.2930.0000.0000.0000.000
13E15GLU-1-0.921-0.95015.663-14.705-14.7050.0000.0000.0000.000
14E16ILE0-0.031-0.02117.0811.1931.1930.0000.0000.0000.000
15E17GLN0-0.018-0.01717.0490.5990.5990.0000.0000.0000.000
16E18ALA00.0270.02119.8470.9350.9350.0000.0000.0000.000
17E19LEU0-0.008-0.01121.6340.8520.8520.0000.0000.0000.000
18E20LEU0-0.010-0.00521.7770.7120.7120.0000.0000.0000.000
19E21GLN0-0.035-0.02221.7580.1670.1670.0000.0000.0000.000
20E22GLU-1-0.829-0.89225.853-10.215-10.2150.0000.0000.0000.000
21E23ALA0-0.010-0.00927.5210.4940.4940.0000.0000.0000.000
22E24GLU-1-0.901-0.95928.641-9.572-9.5720.0000.0000.0000.000
23E25ALA0-0.037-0.02129.9020.4070.4070.0000.0000.0000.000
24E26LYS10.7650.85830.47910.73310.7330.0000.0000.0000.000
25E27ALA00.0100.02533.1700.3370.3370.0000.0000.0000.000
26E28GLU-1-0.875-0.93834.481-7.907-7.9070.0000.0000.0000.000
27E29ALA00.0420.03036.1040.2920.2920.0000.0000.0000.000
28E30VAL0-0.017-0.01737.8210.2770.2770.0000.0000.0000.000
29E31LYS10.8160.90639.0937.7607.7600.0000.0000.0000.000
30E32ARG10.8010.88839.2197.8987.8980.0000.0000.0000.000
31E33GLU-1-0.954-0.96142.252-6.903-6.9030.0000.0000.0000.000
32E34ALA00.0690.02643.8090.2300.2300.0000.0000.0000.000
33E35GLU-1-0.828-0.90343.951-6.976-6.9760.0000.0000.0000.000
34E36GLU-1-0.913-0.95644.223-6.869-6.8690.0000.0000.0000.000
35E37LYS10.9380.97847.9536.4046.4040.0000.0000.0000.000
36E38ALA0-0.007-0.01449.4180.1850.1850.0000.0000.0000.000
37E39LYS10.9640.97950.8266.0916.0910.0000.0000.0000.000
38E40ALA0-0.006-0.00652.4770.1550.1550.0000.0000.0000.000
39E41LEU0-0.058-0.02253.9570.1480.1480.0000.0000.0000.000
40E42LEU00.0080.00155.5150.1260.1260.0000.0000.0000.000
41E43GLN0-0.030-0.02655.8260.1280.1280.0000.0000.0000.000
42E44ALA0-0.0110.00358.5310.1060.1060.0000.0000.0000.000
43E45ARG10.9380.97059.4545.4515.4510.0000.0000.0000.000
44E46GLU-1-0.793-0.89458.969-5.282-5.2820.0000.0000.0000.000
45E47ARG10.8830.92559.3785.3255.3250.0000.0000.0000.000
46E48ALA0-0.0150.01164.7280.0870.0870.0000.0000.0000.000
47E49LEU00.0190.00764.7530.0850.0850.0000.0000.0000.000
48E50GLU-1-0.773-0.85367.615-4.455-4.4550.0000.0000.0000.000
49E51ALA0-0.0110.00169.2610.0890.0890.0000.0000.0000.000
50E52GLN0-0.016-0.02068.6650.0250.0250.0000.0000.0000.000
51E53TYR0-0.0020.01071.9830.0780.0780.0000.0000.0000.000
52E54ARG10.8440.86971.7274.4744.4740.0000.0000.0000.000
53E55ALA0-0.040-0.01175.2330.0690.0690.0000.0000.0000.000
54E56ALA0-0.015-0.01276.5040.0680.0680.0000.0000.0000.000
55E57LEU0-0.0070.00276.8410.0590.0590.0000.0000.0000.000
56E58ARG11.0231.02578.8854.0844.0840.0000.0000.0000.000
57E59ARG10.9100.97581.2533.9053.9050.0000.0000.0000.000
58E60ALA00.0190.00282.4660.0560.0560.0000.0000.0000.000
59E61GLU-1-0.884-0.95581.426-3.899-3.8990.0000.0000.0000.000
60E62SER0-0.034-0.02985.3660.0580.0580.0000.0000.0000.000
61E63ALA0-0.037-0.01787.0400.0500.0500.0000.0000.0000.000
62E64GLY00.0230.01488.1920.0450.0450.0000.0000.0000.000
63E65GLU-1-0.895-0.95289.819-3.500-3.5000.0000.0000.0000.000
64E66LEU0-0.032-0.01791.5930.0550.0550.0000.0000.0000.000
65E67LEU0-0.0020.01991.7650.0490.0490.0000.0000.0000.000
66E68VAL00.0320.01593.7110.0520.0520.0000.0000.0000.000
67E69ALA0-0.023-0.01595.8520.0500.0500.0000.0000.0000.000
68E70THR0-0.029-0.02796.7600.0490.0490.0000.0000.0000.000
69E71ALA00.0430.03198.6410.0420.0420.0000.0000.0000.000
70E72ARG10.9200.95299.1073.2683.2680.0000.0000.0000.000
71E73THR0-0.066-0.043101.3760.0420.0420.0000.0000.0000.000
72E74GLN0-0.070-0.039103.2760.0050.0050.0000.0000.0000.000
73E75ALA00.0700.042104.9390.0340.0340.0000.0000.0000.000
74E76ARG10.9090.956104.8743.1013.1010.0000.0000.0000.000
75E77GLY00.0120.005107.7920.0320.0320.0000.0000.0000.000
76E78GLU-1-0.817-0.906107.573-2.993-2.9930.0000.0000.0000.000
77E79VAL0-0.023-0.007110.9800.0350.0350.0000.0000.0000.000
78E80LEU0-0.028-0.021111.0650.0340.0340.0000.0000.0000.000
79E81GLU-1-0.945-0.964113.651-2.848-2.8480.0000.0000.0000.000
80E82GLU-1-0.719-0.818115.411-2.705-2.7050.0000.0000.0000.000
81E83VAL0-0.034-0.021117.0960.0340.0340.0000.0000.0000.000
82E84ARG10.8170.883117.6472.7642.7640.0000.0000.0000.000
83E85ARG10.7330.845119.5562.7172.7170.0000.0000.0000.000
84E86ARG10.8740.908120.1222.7282.7280.0000.0000.0000.000
85E87VAL0-0.013-0.006122.6810.0270.0270.0000.0000.0000.000
86E88ARG10.9430.969121.3632.6902.6900.0000.0000.0000.000
87E89GLU-1-0.846-0.913124.913-2.598-2.5980.0000.0000.0000.000
88E90ALA0-0.009-0.010127.2840.0230.0230.0000.0000.0000.000
89E91LEU0-0.044-0.020127.6710.0230.0230.0000.0000.0000.000
90E92GLU-1-0.864-0.940129.057-2.509-2.5090.0000.0000.0000.000
91E93ALA0-0.0100.011131.2420.0180.0180.0000.0000.0000.000
92E94LEU0-0.040-0.030133.3870.0130.0130.0000.0000.0000.000
93E95PRO00.0320.003135.2230.0150.0150.0000.0000.0000.000
94E96GLN0-0.0130.009136.5080.0120.0120.0000.0000.0000.000
95E97LYS10.8350.927135.4122.4062.4060.0000.0000.0000.000
96E98PRO00.0240.015140.5930.0120.0120.0000.0000.0000.000
97E99GLU-1-0.812-0.910138.136-2.373-2.3730.0000.0000.0000.000
98E100TRP0-0.012-0.008136.229-0.013-0.0130.0000.0000.0000.000
99E101PRO00.011-0.013140.487-0.001-0.0010.0000.0000.0000.000
100E102GLU-1-0.962-0.966142.335-2.252-2.2520.0000.0000.0000.000
101E103VAL0-0.022-0.007136.525-0.006-0.0060.0000.0000.0000.000
102E104VAL00.0250.011139.553-0.006-0.0060.0000.0000.0000.000
103E105ARG10.8630.930140.9082.2242.2240.0000.0000.0000.000
104E106LYS10.7850.880138.5482.3552.3550.0000.0000.0000.000
105E107LEU0-0.038-0.027135.076-0.010-0.0100.0000.0000.0000.000
106E108ALA00.0350.011138.686-0.008-0.0080.0000.0000.0000.000
107E109LEU00.0020.005141.6470.0030.0030.0000.0000.0000.000
108E110GLU-1-0.732-0.852136.051-2.407-2.4070.0000.0000.0000.000
109E111ALA0-0.053-0.026138.763-0.012-0.0120.0000.0000.0000.000
110E112LEU0-0.072-0.045139.7220.0040.0040.0000.0000.0000.000
111E113GLU-1-0.862-0.905140.402-2.319-2.3190.0000.0000.0000.000
112E114ALA0-0.032-0.007136.912-0.009-0.0090.0000.0000.0000.000
113E115LEU0-0.017-0.026134.4960.0110.0110.0000.0000.0000.000
114E116PRO0-0.048-0.013138.0570.0060.0060.0000.0000.0000.000
115E117GLY00.0310.035140.8360.0120.0120.0000.0000.0000.000
116E118ALA00.0240.005144.068-0.011-0.0110.0000.0000.0000.000
117E119LYS10.8770.943145.9002.2112.2110.0000.0000.0000.000
118E120ALA0-0.027-0.012145.7070.0190.0190.0000.0000.0000.000
119E121LEU0-0.0270.006141.567-0.021-0.0210.0000.0000.0000.000
120E122VAL0-0.015-0.008140.3300.0140.0140.0000.0000.0000.000
121E123ALA00.0580.025140.475-0.020-0.0200.0000.0000.0000.000
122E124ASN0-0.013-0.016138.709-0.009-0.0090.0000.0000.0000.000
123E125PRO00.0120.007141.4760.0120.0120.0000.0000.0000.000
124E126GLU-1-0.908-0.971142.688-2.244-2.2440.0000.0000.0000.000
125E127ASP-1-0.834-0.928140.786-2.330-2.3300.0000.0000.0000.000
126E128LEU0-0.0320.001144.1500.0130.0130.0000.0000.0000.000
127E129PRO0-0.033-0.028147.2660.0160.0160.0000.0000.0000.000
128E130HIS0-0.038-0.016144.4410.0180.0180.0000.0000.0000.000
129E131LEU00.0060.006143.664-0.008-0.0080.0000.0000.0000.000
130E132GLU-1-0.751-0.854147.517-2.153-2.1530.0000.0000.0000.000
131E133ALA0-0.044-0.018150.1010.0130.0130.0000.0000.0000.000
132E134MET00.028-0.005148.2480.0130.0130.0000.0000.0000.000
133E135ALA0-0.0300.005150.2450.0030.0030.0000.0000.0000.000
134E136ARG10.8370.893151.5352.1302.1300.0000.0000.0000.000
135E137GLU-1-0.878-0.911152.435-2.095-2.0950.0000.0000.0000.000
136E138ARG10.8080.873152.6952.0852.0850.0000.0000.0000.000
137E139GLY00.0480.062149.630-0.005-0.0050.0000.0000.0000.000
138E140VAL0-0.073-0.052150.233-0.001-0.0010.0000.0000.0000.000
139E141GLU-1-0.796-0.912144.600-2.281-2.2810.0000.0000.0000.000
140E142LEU0-0.039-0.031143.8480.0160.0160.0000.0000.0000.000
141E143GLN0-0.023-0.017146.330-0.016-0.0160.0000.0000.0000.000
142E144ALA00.0320.013145.420-0.007-0.0070.0000.0000.0000.000
143E145GLU-1-0.829-0.915138.871-2.367-2.3670.0000.0000.0000.000
144E146PRO0-0.050-0.026138.634-0.010-0.0100.0000.0000.0000.000
145E147ALA0-0.014-0.005135.421-0.020-0.0200.0000.0000.0000.000
146E148LEU0-0.0190.001135.075-0.021-0.0210.0000.0000.0000.000
147E149ARG10.8480.923130.6852.4682.4680.0000.0000.0000.000
148E150LEU0-0.005-0.006132.2410.0090.0090.0000.0000.0000.000
149E151GLY0-0.010-0.017134.332-0.016-0.0160.0000.0000.0000.000
150E152VAL00.0110.028136.1050.0120.0120.0000.0000.0000.000
151E153ARG10.8400.917135.4552.3952.3950.0000.0000.0000.000
152E154ALA00.0340.010138.5270.0200.0200.0000.0000.0000.000
153E155VAL0-0.037-0.020139.855-0.018-0.0180.0000.0000.0000.000
154E156GLY00.0510.020141.8590.0160.0160.0000.0000.0000.000
155E157ALA0-0.028-0.021143.2950.0170.0170.0000.0000.0000.000
156E158GLU-1-0.858-0.933144.187-2.245-2.2450.0000.0000.0000.000
157E159GLY0-0.056-0.021142.099-0.012-0.0120.0000.0000.0000.000
158E160LYS10.9530.979139.3742.3262.3260.0000.0000.0000.000
159E161THR0-0.018-0.013138.1310.0110.0110.0000.0000.0000.000
160E162GLN0-0.046-0.029134.967-0.002-0.0020.0000.0000.0000.000
161E163VAL00.0460.036134.905-0.021-0.0210.0000.0000.0000.000
162E164GLU-1-0.862-0.933133.014-2.445-2.4450.0000.0000.0000.000
163E165ASN0-0.082-0.025133.514-0.043-0.0430.0000.0000.0000.000
164E166SER00.0790.027131.8720.0120.0120.0000.0000.0000.000
165E167LEU00.0400.021131.037-0.022-0.0220.0000.0000.0000.000
166E168LEU00.0400.017126.638-0.024-0.0240.0000.0000.0000.000
167E169ALA00.0380.025126.547-0.024-0.0240.0000.0000.0000.000
168E170ARG10.8040.890126.9642.4532.4530.0000.0000.0000.000
169E171MET0-0.0090.022123.936-0.027-0.0270.0000.0000.0000.000
170E172ASP-1-0.751-0.868122.126-2.711-2.7110.0000.0000.0000.000
171E173ARG10.8330.904121.4972.5472.5470.0000.0000.0000.000
172E174ALA00.0060.008122.7340.0050.0050.0000.0000.0000.000
173E175TRP0-0.025-0.026115.744-0.007-0.0070.0000.0000.0000.000
174E176ASP-1-0.901-0.943115.906-2.833-2.8330.0000.0000.0000.000
175E177ALA00.0320.022117.046-0.018-0.0180.0000.0000.0000.000
176E178MET0-0.028-0.010118.5330.0070.0070.0000.0000.0000.000
177E179SER00.0160.009114.031-0.013-0.0130.0000.0000.0000.000
178E180SER0-0.012-0.015112.958-0.005-0.0050.0000.0000.0000.000
179E181LYS10.8930.940113.9032.7602.7600.0000.0000.0000.000
180E182VAL00.0430.025115.9200.0020.0020.0000.0000.0000.000
181E183ALA00.0270.008111.302-0.008-0.0080.0000.0000.0000.000
182E184GLN0-0.011-0.016112.6180.0010.0010.0000.0000.0000.000
183E185ALA0-0.028-0.012113.631-0.001-0.0010.0000.0000.0000.000
184E186LEU0-0.0280.006113.4270.0090.0090.0000.0000.0000.000
185E187TRP0-0.041-0.022108.931-0.014-0.0140.0000.0000.0000.000
186E188GLY0-0.0390.001109.730-0.018-0.0180.0000.0000.0000.000