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: K3VM3

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1331219.990401
FMO2-HF: Nuclear repulsion 1260244.722839
FMO2-HF: Total energy -70975.267562
FMO2-MP2: Total energy -71184.7885


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.
-186.486-186.99126.257-13.963-11.789-0.147
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 : 0.884 / q_NPA : 0.924
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-1-0.855-0.9011.649-162.840-165.48425.750-13.311-9.795-0.145
4E6ALA00.0260.0002.6409.24010.8500.506-0.540-1.576-0.002
5E7ILE00.0160.0113.9136.7737.3020.001-0.112-0.4180.000
6E8LEU00.0290.0136.2913.7273.7270.0000.0000.0000.000
7E9SER0-0.027-0.0306.6563.9823.9820.0000.0000.0000.000
8E10GLN0-0.069-0.0327.8512.3732.3730.0000.0000.0000.000
9E11GLU-1-0.937-0.9599.575-21.677-21.6770.0000.0000.0000.000
10E12VAL0-0.024-0.00411.5991.8951.8950.0000.0000.0000.000
11E13GLU-1-0.898-0.93113.018-17.118-17.1180.0000.0000.0000.000
12E14ALA00.025-0.00814.331-0.156-0.1560.0000.0000.0000.000
13E15GLU-1-0.902-0.93716.270-14.846-14.8460.0000.0000.0000.000
14E16ILE0-0.100-0.05616.3151.1631.1630.0000.0000.0000.000
15E17GLN0-0.005-0.01317.7590.0520.0520.0000.0000.0000.000
16E18ALA00.0340.02820.4250.9070.9070.0000.0000.0000.000
17E19LEU00.001-0.00721.8070.8390.8390.0000.0000.0000.000
18E20LEU0-0.012-0.01022.1840.6900.6900.0000.0000.0000.000
19E21GLN0-0.040-0.01222.3190.0390.0390.0000.0000.0000.000
20E22GLU-1-0.840-0.90326.154-10.306-10.3060.0000.0000.0000.000
21E23ALA0-0.056-0.04527.9590.5120.5120.0000.0000.0000.000
22E24GLU-1-0.929-0.96229.300-9.828-9.8280.0000.0000.0000.000
23E25ALA0-0.0150.00230.5820.2690.2690.0000.0000.0000.000
24E26LYS10.7740.86530.91310.68810.6880.0000.0000.0000.000
25E27ALA00.0150.01933.8460.3350.3350.0000.0000.0000.000
26E28GLU-1-0.891-0.94535.203-8.181-8.1810.0000.0000.0000.000
27E29ALA00.0640.03636.7230.2910.2910.0000.0000.0000.000
28E30VAL0-0.015-0.02038.3300.2550.2550.0000.0000.0000.000
29E31LYS10.8370.90739.7017.7787.7780.0000.0000.0000.000
30E32ARG10.8370.92739.8507.8847.8840.0000.0000.0000.000
31E33GLU-1-0.930-0.95042.730-7.039-7.0390.0000.0000.0000.000
32E34ALA00.0470.01944.1690.2130.2130.0000.0000.0000.000
33E35GLU-1-0.854-0.92044.375-7.015-7.0150.0000.0000.0000.000
34E36GLU-1-0.955-0.99944.934-6.940-6.9400.0000.0000.0000.000
35E37LYS10.9461.00248.4336.3806.3800.0000.0000.0000.000
36E38ALA00.016-0.00650.0240.1870.1870.0000.0000.0000.000
37E39LYS11.0101.00551.4076.1716.1710.0000.0000.0000.000
38E40ALA00.0240.00453.0060.1590.1590.0000.0000.0000.000
39E41LEU0-0.104-0.04854.2580.1260.1260.0000.0000.0000.000
40E42LEU00.004-0.00556.0200.1040.1040.0000.0000.0000.000
41E43GLN0-0.0220.00156.5930.1300.1300.0000.0000.0000.000
42E44ALA0-0.006-0.00359.0210.1090.1090.0000.0000.0000.000
43E45ARG10.9520.97760.0405.4435.4430.0000.0000.0000.000
44E46GLU-1-0.833-0.91659.448-5.306-5.3060.0000.0000.0000.000
45E47ARG10.8920.92859.7525.3645.3640.0000.0000.0000.000
46E48ALA0-0.0210.00265.1010.0910.0910.0000.0000.0000.000
47E49LEU00.0240.00665.6670.0870.0870.0000.0000.0000.000
48E50GLU-1-0.774-0.85368.293-4.493-4.4930.0000.0000.0000.000
49E51ALA00.0280.02669.9850.0920.0920.0000.0000.0000.000
50E52GLN0-0.031-0.03669.0760.0240.0240.0000.0000.0000.000
51E53TYR00.0100.01372.6880.0610.0610.0000.0000.0000.000
52E54ARG10.8010.86572.0064.4954.4950.0000.0000.0000.000
53E55ALA0-0.044-0.02075.7520.0700.0700.0000.0000.0000.000
54E56ALA0-0.003-0.00777.0390.0670.0670.0000.0000.0000.000
55E57LEU00.0350.01277.4690.0560.0560.0000.0000.0000.000
56E58ARG11.0151.02979.2244.0884.0880.0000.0000.0000.000
57E59ARG10.8940.95481.7203.9173.9170.0000.0000.0000.000
58E60ALA00.004-0.01282.8860.0570.0570.0000.0000.0000.000
59E61GLU-1-0.878-0.92982.179-3.908-3.9080.0000.0000.0000.000
60E62SER00.005-0.00186.1400.0530.0530.0000.0000.0000.000
61E63ALA0-0.039-0.00687.5420.0510.0510.0000.0000.0000.000
62E64GLY00.0480.01988.5900.0480.0480.0000.0000.0000.000
63E65GLU-1-0.908-0.95890.127-3.544-3.5440.0000.0000.0000.000
64E66LEU0-0.082-0.05591.9490.0560.0560.0000.0000.0000.000
65E67LEU0-0.046-0.02591.7150.0470.0470.0000.0000.0000.000
66E68VAL00.0330.03594.2740.0440.0440.0000.0000.0000.000
67E69ALA0-0.006-0.00696.4930.0500.0500.0000.0000.0000.000
68E70THR00.000-0.00397.3550.0490.0490.0000.0000.0000.000
69E71ALA00.0700.04799.1820.0410.0410.0000.0000.0000.000
70E72ARG10.9260.96099.7983.2623.2620.0000.0000.0000.000
71E73THR0-0.068-0.040101.9960.0420.0420.0000.0000.0000.000
72E74GLN0-0.052-0.028103.7690.0010.0010.0000.0000.0000.000
73E75ALA00.0520.037105.2000.0330.0330.0000.0000.0000.000
74E76ARG10.9100.939105.0723.1173.1170.0000.0000.0000.000
75E77GLY0-0.002-0.008108.0520.0320.0320.0000.0000.0000.000
76E78GLU-1-0.822-0.911108.268-2.993-2.9930.0000.0000.0000.000
77E79VAL0-0.0230.001111.3270.0330.0330.0000.0000.0000.000
78E80LEU0-0.027-0.019111.5990.0340.0340.0000.0000.0000.000
79E81GLU-1-0.959-0.986113.550-2.867-2.8670.0000.0000.0000.000
80E82GLU-1-0.742-0.841115.755-2.721-2.7210.0000.0000.0000.000
81E83VAL0-0.046-0.034117.3890.0330.0330.0000.0000.0000.000
82E84ARG10.8250.895118.4052.7662.7660.0000.0000.0000.000
83E85ARG10.7660.875119.8202.7202.7200.0000.0000.0000.000
84E86ARG10.8710.918120.3582.7362.7360.0000.0000.0000.000
85E87VAL0-0.004-0.003123.1700.0280.0280.0000.0000.0000.000
86E88ARG10.9690.974121.5182.7002.7000.0000.0000.0000.000
87E89GLU-1-0.842-0.910125.681-2.598-2.5980.0000.0000.0000.000
88E90ALA0-0.038-0.015127.9040.0240.0240.0000.0000.0000.000
89E91LEU0-0.015-0.023128.6520.0230.0230.0000.0000.0000.000
90E92GLU-1-0.852-0.919129.753-2.512-2.5120.0000.0000.0000.000
91E93ALA00.0000.011131.8510.0180.0180.0000.0000.0000.000
92E94LEU0-0.068-0.031133.8250.0130.0130.0000.0000.0000.000
93E95PRO00.0480.006135.7180.0160.0160.0000.0000.0000.000
94E96GLN0-0.044-0.009137.0350.0100.0100.0000.0000.0000.000
95E97LYS10.9040.951134.8872.4252.4250.0000.0000.0000.000
96E98PRO00.0200.019140.5790.0090.0090.0000.0000.0000.000
97E99GLU-1-0.886-0.950138.919-2.369-2.3690.0000.0000.0000.000
98E100TRP00.0180.020136.880-0.020-0.0200.0000.0000.0000.000
99E101PRO0-0.007-0.014140.898-0.003-0.0030.0000.0000.0000.000
100E102GLU-1-0.959-0.988142.712-2.265-2.2650.0000.0000.0000.000
101E103VAL0-0.031-0.006136.901-0.008-0.0080.0000.0000.0000.000
102E104VAL00.0150.008139.898-0.006-0.0060.0000.0000.0000.000
103E105ARG10.9010.951141.1842.2242.2240.0000.0000.0000.000
104E106LYS10.8730.939139.0502.3592.3590.0000.0000.0000.000
105E107LEU0-0.021-0.008135.438-0.012-0.0120.0000.0000.0000.000
106E108ALA00.0350.005139.056-0.008-0.0080.0000.0000.0000.000
107E109LEU0-0.013-0.006141.8220.0080.0080.0000.0000.0000.000
108E110GLU-1-0.756-0.857136.308-2.411-2.4110.0000.0000.0000.000
109E111ALA0-0.046-0.024139.227-0.008-0.0080.0000.0000.0000.000
110E112LEU0-0.049-0.029140.1990.0010.0010.0000.0000.0000.000
111E113GLU-1-0.938-0.961140.802-2.325-2.3250.0000.0000.0000.000
112E114ALA0-0.050-0.014137.377-0.007-0.0070.0000.0000.0000.000
113E115LEU0-0.033-0.028134.9320.0090.0090.0000.0000.0000.000
114E116PRO0-0.037-0.016138.4950.0100.0100.0000.0000.0000.000
115E117GLY00.0440.043141.4700.0100.0100.0000.0000.0000.000
116E118ALA00.017-0.001144.914-0.008-0.0080.0000.0000.0000.000
117E119LYS10.9200.948146.9502.2152.2150.0000.0000.0000.000
118E120ALA0-0.039-0.004146.2330.0200.0200.0000.0000.0000.000
119E121LEU0-0.0170.014141.824-0.021-0.0210.0000.0000.0000.000
120E122VAL0-0.018-0.004141.0000.0140.0140.0000.0000.0000.000
121E123ALA00.0390.004140.898-0.018-0.0180.0000.0000.0000.000
122E124ASN0-0.007-0.002138.959-0.007-0.0070.0000.0000.0000.000
123E125PRO00.0440.016141.9510.0100.0100.0000.0000.0000.000
124E126GLU-1-0.928-0.979143.046-2.247-2.2470.0000.0000.0000.000
125E127ASP-1-0.842-0.944141.130-2.340-2.3400.0000.0000.0000.000
126E128LEU0-0.050-0.010144.4050.0130.0130.0000.0000.0000.000
127E129PRO0-0.034-0.010147.4140.0150.0150.0000.0000.0000.000
128E130HIS0-0.069-0.025145.2420.0200.0200.0000.0000.0000.000
129E131LEU0-0.023-0.013144.137-0.010-0.0100.0000.0000.0000.000
130E132GLU-1-0.722-0.852148.121-2.159-2.1590.0000.0000.0000.000
131E133ALA0-0.041-0.024150.3580.0160.0160.0000.0000.0000.000
132E134MET00.0440.004149.0240.0150.0150.0000.0000.0000.000
133E135ALA0-0.0440.008150.9510.0020.0020.0000.0000.0000.000
134E136ARG10.8470.890152.1832.1322.1320.0000.0000.0000.000
135E137GLU-1-0.906-0.932153.129-2.092-2.0920.0000.0000.0000.000
136E138ARG10.8110.892153.3372.0902.0900.0000.0000.0000.000
137E139GLY00.0450.039150.356-0.010-0.0100.0000.0000.0000.000
138E140VAL0-0.079-0.041150.510-0.002-0.0020.0000.0000.0000.000
139E141GLU-1-0.784-0.902145.037-2.282-2.2820.0000.0000.0000.000
140E142LEU0-0.037-0.030144.3470.0150.0150.0000.0000.0000.000
141E143GLN0-0.031-0.030146.777-0.019-0.0190.0000.0000.0000.000
142E144ALA00.0650.031145.763-0.009-0.0090.0000.0000.0000.000
143E145GLU-1-0.877-0.933138.990-2.373-2.3730.0000.0000.0000.000
144E146PRO0-0.032-0.023138.758-0.008-0.0080.0000.0000.0000.000
145E147ALA0-0.0180.000135.813-0.021-0.0210.0000.0000.0000.000
146E148LEU0-0.039-0.014135.540-0.019-0.0190.0000.0000.0000.000
147E149ARG10.8340.912130.6332.4782.4780.0000.0000.0000.000
148E150LEU00.0080.008132.9230.0110.0110.0000.0000.0000.000
149E151GLY0-0.001-0.016134.788-0.018-0.0180.0000.0000.0000.000
150E152VAL00.0090.023136.4650.0120.0120.0000.0000.0000.000
151E153ARG10.8450.918136.0682.4012.4010.0000.0000.0000.000
152E154ALA00.0600.023138.8570.0190.0190.0000.0000.0000.000
153E155VAL0-0.067-0.037140.272-0.019-0.0190.0000.0000.0000.000
154E156GLY00.0550.023141.9110.0150.0150.0000.0000.0000.000
155E157ALA0-0.020-0.017143.3310.0170.0170.0000.0000.0000.000
156E158GLU-1-0.891-0.942145.037-2.243-2.2430.0000.0000.0000.000
157E159GLY0-0.0220.002142.427-0.014-0.0140.0000.0000.0000.000
158E160LYS10.9410.933139.2532.3452.3450.0000.0000.0000.000
159E161THR0-0.0140.021138.3550.0090.0090.0000.0000.0000.000
160E162GLN0-0.046-0.035135.527-0.005-0.0050.0000.0000.0000.000
161E163VAL00.0460.035135.569-0.019-0.0190.0000.0000.0000.000
162E164GLU-1-0.869-0.927133.374-2.449-2.4490.0000.0000.0000.000
163E165ASN0-0.070-0.022133.727-0.044-0.0440.0000.0000.0000.000
164E166SER00.0770.019132.1150.0110.0110.0000.0000.0000.000
165E167LEU00.0650.033131.520-0.020-0.0200.0000.0000.0000.000
166E168LEU00.0280.015127.441-0.024-0.0240.0000.0000.0000.000
167E169ALA00.0410.018126.973-0.023-0.0230.0000.0000.0000.000
168E170ARG10.8230.899126.9032.4552.4550.0000.0000.0000.000
169E171MET0-0.0360.013124.419-0.023-0.0230.0000.0000.0000.000
170E172ASP-1-0.786-0.890122.588-2.712-2.7120.0000.0000.0000.000
171E173ARG10.8420.931121.9962.5522.5520.0000.0000.0000.000
172E174ALA00.033-0.006122.4580.0170.0170.0000.0000.0000.000
173E175TRP0-0.038-0.022116.214-0.007-0.0070.0000.0000.0000.000
174E176ASP-1-0.930-0.957116.197-2.848-2.8480.0000.0000.0000.000
175E177ALA0-0.0090.016117.709-0.011-0.0110.0000.0000.0000.000
176E178MET0-0.031-0.026118.845-0.003-0.0030.0000.0000.0000.000
177E179SER00.0340.022114.324-0.008-0.0080.0000.0000.0000.000
178E180SER00.0180.009113.392-0.006-0.0060.0000.0000.0000.000
179E181LYS10.9330.960114.4282.7662.7660.0000.0000.0000.000
180E182VAL00.0650.035116.3220.0030.0030.0000.0000.0000.000
181E183ALA00.0500.020111.854-0.006-0.0060.0000.0000.0000.000
182E184GLN0-0.076-0.045113.289-0.003-0.0030.0000.0000.0000.000
183E185ALA0-0.033-0.018114.311-0.002-0.0020.0000.0000.0000.000
184E186LEU0-0.0420.002113.8660.0050.0050.0000.0000.0000.000
185E187TRP0-0.047-0.023109.506-0.011-0.0110.0000.0000.0000.000
186E188GLY0-0.0060.009110.360-0.004-0.0040.0000.0000.0000.000