FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: K22V3

Calculation Name: 4MCK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MCK

Chain ID: A

ChEMBL ID:

UniProt ID: P29022

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2284661.912037
FMO2-HF: Nuclear repulsion 2205858.115456
FMO2-HF: Total energy -78803.796581
FMO2-MP2: Total energy -79030.682395


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(A:-4:PHE)


Summations of interaction energy for fragment #1(A:-4: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.
-19.408-12.92318.833-10.072-15.245-0.047
Interaction energy analysis for fragmet #1(A:-4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.005
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].
3A-2ALA00.027-0.0023.856-1.2860.8070.029-0.889-1.2330.007
4A-1GLU-1-0.869-0.9165.6510.1570.1570.0000.0000.0000.000
5A0PHE0-0.003-0.0102.517-2.840-1.2031.986-0.870-2.7520.003
6A1VAL0-0.0180.0023.263-0.6210.0560.046-0.144-0.5790.000
7A2VAL0-0.0220.0025.9680.0890.0890.0000.0000.0000.000
8A3SER00.0540.0409.150-0.037-0.0370.0000.0000.0000.000
9A4ASP-1-0.805-0.93411.490-0.101-0.1010.0000.0000.0000.000
10A5ALA0-0.052-0.01815.061-0.002-0.0020.0000.0000.0000.000
11A6PHE0-0.0190.00011.2950.0160.0160.0000.0000.0000.000
12A7PHE00.0340.01013.221-0.006-0.0060.0000.0000.0000.000
13A8ASN0-0.019-0.03315.109-0.014-0.0140.0000.0000.0000.000
14A9GLY0-0.0120.01017.7710.0030.0030.0000.0000.0000.000
15A10ILE0-0.0090.01114.2000.0020.0020.0000.0000.0000.000
16A11LYS10.9460.98418.6100.0800.0800.0000.0000.0000.000
17A12ASN0-0.062-0.04020.769-0.008-0.0080.0000.0000.0000.000
18A13GLN0-0.056-0.01821.7740.0080.0080.0000.0000.0000.000
19A14ALA00.0150.00824.316-0.008-0.0080.0000.0000.0000.000
20A15GLY00.0270.03426.137-0.008-0.0080.0000.0000.0000.000
21A16SER00.002-0.03928.0950.0040.0040.0000.0000.0000.000
22A17GLY0-0.012-0.00130.284-0.003-0.0030.0000.0000.0000.000
23A18CYS0-0.0670.01221.3780.0010.0010.0000.0000.0000.000
24A19GLU-1-0.772-0.89227.467-0.086-0.0860.0000.0000.0000.000
25A20GLY0-0.001-0.00224.464-0.006-0.0060.0000.0000.0000.000
26A21LYS10.9110.95823.7370.0340.0340.0000.0000.0000.000
27A22ASN0-0.053-0.04024.3990.0010.0010.0000.0000.0000.000
28A23PHE00.0080.03021.987-0.004-0.0040.0000.0000.0000.000
29A24TYR0-0.021-0.04718.697-0.024-0.0240.0000.0000.0000.000
30A25THR00.0160.00018.4880.0100.0100.0000.0000.0000.000
31A26ARG10.8640.91110.1260.1180.1180.0000.0000.0000.000
32A27SER00.0130.00714.170-0.048-0.0480.0000.0000.0000.000
33A28ALA00.0290.00915.921-0.022-0.0220.0000.0000.0000.000
34A29PHE00.009-0.0057.845-0.018-0.0180.0000.0000.0000.000
35A30LEU00.0160.0039.708-0.107-0.1070.0000.0000.0000.000
36A31SER0-0.011-0.00212.056-0.019-0.0190.0000.0000.0000.000
37A32ALA0-0.059-0.03413.360-0.009-0.0090.0000.0000.0000.000
38A33VAL00.0200.0017.418-0.057-0.0570.0000.0000.0000.000
39A34ASN0-0.023-0.00210.031-0.104-0.1040.0000.0000.0000.000
40A35ALA0-0.060-0.01911.7620.0150.0150.0000.0000.0000.000
41A36TYR0-0.066-0.04110.8730.0550.0550.0000.0000.0000.000
42A37PRO00.0580.0298.283-0.276-0.2760.0000.0000.0000.000
43A38GLY00.0210.0057.090-0.295-0.2950.0000.0000.0000.000
44A39PHE00.015-0.0186.298-0.138-0.1380.0000.0000.0000.000
45A40ALA0-0.064-0.0182.082-0.904-1.2733.121-1.389-1.3630.002
46A41HIS0-0.017-0.0171.881-10.111-10.52711.882-5.437-6.029-0.062
47A42GLY00.0130.0134.5420.6020.686-0.001-0.032-0.0520.000
48A43GLY00.0120.0056.1290.1440.1440.0000.0000.0000.000
49A44THR0-0.062-0.0416.7090.1960.1960.0000.0000.0000.000
50A45GLU-1-0.867-0.9372.4212.9214.2550.563-0.523-1.3730.002
51A46VAL0-0.025-0.0164.3141.8882.1010.000-0.015-0.1970.000
52A47GLU-1-0.831-0.9006.7720.4650.4650.0000.0000.0000.000
53A48GLY00.0490.0332.323-1.835-1.3281.033-0.867-0.6730.002
54A49LYS10.9590.9623.268-5.067-4.8240.0400.281-0.5640.000
55A50ARG10.9000.9494.848-1.816-1.818-0.001-0.0050.0080.000
56A51GLU-1-0.739-0.8415.554-1.499-1.4990.0000.0000.0000.000
57A52ILE00.0060.0072.660-0.2910.1930.135-0.182-0.438-0.001
58A53ALA0-0.005-0.0036.4180.0050.0050.0000.0000.0000.000
59A54ALA0-0.015-0.0249.495-0.048-0.0480.0000.0000.0000.000
60A55PHE00.0110.0089.292-0.004-0.0040.0000.0000.0000.000
61A56PHE00.0290.0038.8310.0470.0470.0000.0000.0000.000
62A57ALA0-0.0310.01612.4750.0320.0320.0000.0000.0000.000
63A58HIS00.015-0.00314.1900.0150.0150.0000.0000.0000.000
64A59VAL00.0380.02514.1790.0130.0130.0000.0000.0000.000
65A60THR0-0.045-0.00215.9700.0200.0200.0000.0000.0000.000
66A61HIS00.0170.00018.2670.0140.0140.0000.0000.0000.000
67A62GLN0-0.012-0.00719.2150.0030.0030.0000.0000.0000.000
68A63THR0-0.0090.00619.6680.0050.0050.0000.0000.0000.000
69A64GLY00.0200.01422.1770.0060.0060.0000.0000.0000.000
70A65HIS0-0.027-0.03620.1840.0030.0030.0000.0000.0000.000
71A66PHE0-0.013-0.01115.304-0.004-0.0040.0000.0000.0000.000
72A68TYR00.014-0.00724.3560.0030.0030.0000.0000.0000.000
73A69ILE0-0.0270.02423.640-0.014-0.0140.0000.0000.0000.000
74A70SER0-0.038-0.03724.894-0.013-0.0130.0000.0000.0000.000
75A71GLU-1-0.796-0.87127.558-0.076-0.0760.0000.0000.0000.000
76A72ILE0-0.007-0.00928.8890.0020.0020.0000.0000.0000.000
77A73ASN0-0.0110.00231.9000.0070.0070.0000.0000.0000.000
78A74LYS10.9450.96931.5070.0710.0710.0000.0000.0000.000
79A75SER0-0.030-0.02534.527-0.002-0.0020.0000.0000.0000.000
80A76ASN00.0500.02834.2850.0020.0020.0000.0000.0000.000
81A77ALA00.0640.01534.197-0.005-0.0050.0000.0000.0000.000
82A78TYR0-0.042-0.01629.332-0.006-0.0060.0000.0000.0000.000
83A79CYS0-0.023-0.03431.938-0.012-0.0120.0000.0000.0000.000
84A80ASP-1-0.839-0.92432.510-0.078-0.0780.0000.0000.0000.000
85A81ALA00.015-0.02534.340-0.005-0.0050.0000.0000.0000.000
86A82SER00.0070.02235.7230.0030.0030.0000.0000.0000.000
87A83ASN0-0.0140.00531.219-0.008-0.0080.0000.0000.0000.000
88A84ARG10.9350.97030.7290.1080.1080.0000.0000.0000.000
89A86TRP00.0100.00026.853-0.006-0.0060.0000.0000.0000.000
90A87PRO00.0090.01731.9250.0020.0020.0000.0000.0000.000
91A89ALA00.0360.02834.9700.0050.0050.0000.0000.0000.000
92A90ALA00.0390.00836.7950.0010.0010.0000.0000.0000.000
93A91GLY0-0.011-0.00139.277-0.001-0.0010.0000.0000.0000.000
94A92GLN0-0.038-0.00733.748-0.003-0.0030.0000.0000.0000.000
95A93LYS10.8890.95433.6160.0710.0710.0000.0000.0000.000
96A94TYR0-0.067-0.04328.952-0.004-0.0040.0000.0000.0000.000
97A95TYR00.0730.03128.879-0.004-0.0040.0000.0000.0000.000
98A96GLY00.0330.02725.652-0.009-0.0090.0000.0000.0000.000
99A97ARG10.8000.88524.4730.1260.1260.0000.0000.0000.000
100A98GLY00.0570.03121.003-0.017-0.0170.0000.0000.0000.000
101A99PRO0-0.026-0.01216.4500.0150.0150.0000.0000.0000.000
102A100LEU0-0.002-0.00514.4380.0080.0080.0000.0000.0000.000
103A101GLN0-0.088-0.04118.7140.0200.0200.0000.0000.0000.000
104A102ILE00.0230.03620.7100.0100.0100.0000.0000.0000.000
105A103SER00.019-0.01222.5470.0180.0180.0000.0000.0000.000
106A104TRP00.0240.00425.842-0.005-0.0050.0000.0000.0000.000
107A105ASN00.0060.00227.537-0.012-0.0120.0000.0000.0000.000
108A106TYR0-0.039-0.02226.183-0.009-0.0090.0000.0000.0000.000
109A107ASN0-0.013-0.01023.214-0.019-0.0190.0000.0000.0000.000
110A108TYR0-0.004-0.01323.936-0.017-0.0170.0000.0000.0000.000
111A109GLY0-0.017-0.00825.671-0.006-0.0060.0000.0000.0000.000
112A110PRO0-0.039-0.01523.130-0.004-0.0040.0000.0000.0000.000
113A111ALA00.0580.03421.063-0.016-0.0160.0000.0000.0000.000
114A112GLY0-0.002-0.00321.910-0.014-0.0140.0000.0000.0000.000
115A113ARG10.8870.94324.5640.1580.1580.0000.0000.0000.000
116A114ASP-1-0.818-0.91217.930-0.374-0.3740.0000.0000.0000.000
117A115ILE0-0.047-0.02018.802-0.005-0.0050.0000.0000.0000.000
118A116GLY00.0000.01321.0810.0030.0030.0000.0000.0000.000
119A117PHE0-0.062-0.03822.7610.0160.0160.0000.0000.0000.000
120A118ASN00.0340.02226.763-0.006-0.0060.0000.0000.0000.000
121A119GLY00.0570.02927.0800.0040.0040.0000.0000.0000.000
122A120LEU0-0.035-0.01627.8340.0040.0040.0000.0000.0000.000
123A121ALA00.0060.00331.2260.0070.0070.0000.0000.0000.000
124A122ASP-1-0.874-0.93330.185-0.105-0.1050.0000.0000.0000.000
125A123PRO00.0180.01428.092-0.010-0.0100.0000.0000.0000.000
126A124ASN00.026-0.00927.603-0.008-0.0080.0000.0000.0000.000
127A125ARG10.9730.99426.8420.1420.1420.0000.0000.0000.000
128A126VAL0-0.024-0.00622.116-0.006-0.0060.0000.0000.0000.000
129A127ALA0-0.009-0.02123.724-0.006-0.0060.0000.0000.0000.000
130A128GLN0-0.041-0.01626.2980.0030.0030.0000.0000.0000.000
131A129ASP-1-0.826-0.90722.789-0.178-0.1780.0000.0000.0000.000
132A130ALA00.0410.01920.061-0.015-0.0150.0000.0000.0000.000
133A131VAL00.0030.00417.767-0.032-0.0320.0000.0000.0000.000
134A132ILE0-0.0170.00218.172-0.037-0.0370.0000.0000.0000.000
135A133ALA00.0130.00919.637-0.020-0.0200.0000.0000.0000.000
136A134PHE0-0.010-0.01614.093-0.015-0.0150.0000.0000.0000.000
137A135LYS10.9861.00614.9940.2590.2590.0000.0000.0000.000
138A136THR0-0.041-0.01816.354-0.017-0.0170.0000.0000.0000.000
139A137ALA0-0.0180.00315.1990.0020.0020.0000.0000.0000.000
140A138LEU00.0270.0069.707-0.008-0.0080.0000.0000.0000.000
141A139TRP00.0130.02713.245-0.027-0.0270.0000.0000.0000.000
142A140PHE0-0.001-0.00816.0380.0020.0020.0000.0000.0000.000
143A141TRP0-0.002-0.0379.7140.0920.0920.0000.0000.0000.000
144A142MET0-0.0150.0079.311-0.020-0.0200.0000.0000.0000.000
145A143ASN0-0.061-0.02813.1630.0520.0520.0000.0000.0000.000
146A144ASN0-0.100-0.04816.3270.0680.0680.0000.0000.0000.000
147A145VAL0-0.012-0.00313.6790.0420.0420.0000.0000.0000.000
148A146HIS0-0.026-0.0337.6990.1480.1480.0000.0000.0000.000
149A147ARG10.9360.95911.8520.2490.2490.0000.0000.0000.000
150A148LEU0-0.021-0.02014.3240.0520.0520.0000.0000.0000.000
151A149MET00.0140.0288.9140.0530.0530.0000.0000.0000.000
152A150PRO0-0.0110.00111.4390.0960.0960.0000.0000.0000.000
153A151GLN0-0.035-0.01312.9800.0520.0520.0000.0000.0000.000
154A152GLY00.0190.02414.5240.0220.0220.0000.0000.0000.000
155A153PHE00.0360.01513.657-0.040-0.0400.0000.0000.0000.000
156A154GLY00.0640.03815.556-0.040-0.0400.0000.0000.0000.000
157A155ALA0-0.051-0.02817.180-0.019-0.0190.0000.0000.0000.000
158A156THR0-0.031-0.02713.418-0.029-0.0290.0000.0000.0000.000
159A157ILE00.002-0.00816.866-0.019-0.0190.0000.0000.0000.000
160A158ARG10.8490.89519.7480.0140.0140.0000.0000.0000.000
161A159ALA0-0.021-0.00118.082-0.003-0.0030.0000.0000.0000.000
162A160ILE0-0.0230.00716.196-0.016-0.0160.0000.0000.0000.000
163A161ASN0-0.008-0.00920.540-0.003-0.0030.0000.0000.0000.000
164A162GLY00.0530.03024.1900.0000.0000.0000.0000.0000.000
165A164LEU0-0.055-0.02326.7780.0090.0090.0000.0000.0000.000
166A165GLU-1-0.773-0.85924.069-0.042-0.0420.0000.0000.0000.000
167A198CYS0-0.051-0.00122.2460.0020.0020.0000.0000.0000.000
168A167ASN0-0.021-0.03126.910-0.008-0.0080.0000.0000.0000.000
169A168GLY00.0690.03729.6590.0000.0000.0000.0000.0000.000
170A169ASN0-0.0140.00930.2620.0020.0020.0000.0000.0000.000
171A170ASN0-0.010-0.02028.4840.0010.0010.0000.0000.0000.000
172A171PRO00.0130.01027.8130.0000.0000.0000.0000.0000.000
173A172ALA00.0240.01327.1910.0050.0050.0000.0000.0000.000
174A173GLN00.0610.03025.2410.0070.0070.0000.0000.0000.000
175A174MET00.0010.04423.2020.0050.0050.0000.0000.0000.000
176A175ASN00.005-0.03722.3310.0140.0140.0000.0000.0000.000
177A176ALA0-0.0140.01722.8040.0120.0120.0000.0000.0000.000
178A177ARG10.7780.85118.7300.0780.0780.0000.0000.0000.000
179A178VAL0-0.007-0.00617.9890.0140.0140.0000.0000.0000.000
180A179GLY0-0.017-0.00418.4080.0300.0300.0000.0000.0000.000
181A180TYR00.0280.01016.8620.0220.0220.0000.0000.0000.000
182A181TYR0-0.031-0.01710.9650.0410.0410.0000.0000.0000.000
183A182LYS10.9520.96814.070-0.092-0.0920.0000.0000.0000.000
184A183GLN0-0.0200.00015.9620.0390.0390.0000.0000.0000.000
185A184TYR0-0.027-0.04511.6090.0410.0410.0000.0000.0000.000
186A185CYS0-0.0140.00811.2080.1100.1100.0000.0000.0000.000
187A186GLN0-0.013-0.00112.2870.1050.1050.0000.0000.0000.000
188A187GLN0-0.027-0.01413.3450.0100.0100.0000.0000.0000.000
189A188LEU0-0.055-0.0187.067-0.016-0.0160.0000.0000.0000.000
190A189ARG10.9010.9589.160-0.203-0.2030.0000.0000.0000.000
191A190VAL0-0.0200.0008.6520.1710.1710.0000.0000.0000.000
192A191ASP-1-0.849-0.92111.2640.4110.4110.0000.0000.0000.000
193A192PRO00.001-0.01112.4350.0830.0830.0000.0000.0000.000
194A193GLY00.0060.01514.060-0.020-0.0200.0000.0000.0000.000
195A194PRO00.0290.00715.370-0.033-0.0330.0000.0000.0000.000
196A195ASN0-0.035-0.02617.388-0.009-0.0090.0000.0000.0000.000
197A196LEU00.0020.01016.490-0.016-0.0160.0000.0000.0000.000
198A197THR00.0960.03219.233-0.016-0.0160.0000.0000.0000.000