FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 9MJV2

Calculation Name: 3MKL-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MKL

Chain ID: A

ChEMBL ID:

UniProt ID: P37639

Base Structure: X-ray

Registration Date: 2025-07-10

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 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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -827898.067263
FMO2-HF: Nuclear repulsion 784227.932767
FMO2-HF: Total energy -43670.134497
FMO2-MP2: Total energy -43793.802298


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:140:GLN)


Summations of interaction energy for fragment #1(A:140:GLN)
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.
-0.940.169-0.006-0.534-0.5690.002
Interaction energy analysis for fragmet #1(A:140:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.127 / q_NPA : 0.032
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].
4A142ASN00.1160.0573.831-0.8740.235-0.006-0.534-0.5690.002
5A142ASN0-0.0350.0966.8360.3690.3690.0000.0000.0000.000
6A143MET00.149-0.0966.3410.7150.7150.0000.0000.0000.000
7A143MET0-0.1150.1038.6510.0820.0820.0000.0000.0000.000
8A144ARG00.087-0.0929.0010.2770.2770.0000.0000.0000.000
9A144ARG10.8761.07511.2700.1560.1560.0000.0000.0000.000
10A145THR00.010-0.1008.5750.0590.0590.0000.0000.0000.000
11A145THR0-0.0090.0727.6620.0020.0020.0000.0000.0000.000
12A146ARG00.078-0.0698.4420.2240.2240.0000.0000.0000.000
13A146ARG10.9031.0625.420-1.311-1.3110.0000.0000.0000.000
14A147VAL00.082-0.0699.1780.1030.1030.0000.0000.0000.000
15A147VAL0-0.1050.08512.014-0.023-0.0230.0000.0000.0000.000
16A148CYS00.157-0.11012.786-0.001-0.0010.0000.0000.0000.000
17A148CYS0-0.1400.09012.992-0.042-0.0420.0000.0000.0000.000
18A149THR00.003-0.07711.682-0.139-0.1390.0000.0000.0000.000
19A149THR0-0.0500.05510.7580.1400.1400.0000.0000.0000.000
20A150VAL00.096-0.05513.0330.0120.0120.0000.0000.0000.000
21A150VAL0-0.1130.08212.774-0.007-0.0070.0000.0000.0000.000
22A151ILE00.058-0.09114.941-0.024-0.0240.0000.0000.0000.000
23A151ILE0-0.0790.07816.980-0.014-0.0140.0000.0000.0000.000
24A152ASN00.037-0.09316.665-0.055-0.0550.0000.0000.0000.000
25A152ASN0-0.0860.06816.126-0.051-0.0510.0000.0000.0000.000
26A153ASN00.146-0.08217.520-0.032-0.0320.0000.0000.0000.000
27A153ASN0-0.0630.09615.1960.0140.0140.0000.0000.0000.000
28A154ASN00.088-0.07618.786-0.026-0.0260.0000.0000.0000.000
29A154ASN0-0.1390.06821.739-0.021-0.0210.0000.0000.0000.000
30A155ILE00.147-0.06121.954-0.005-0.0050.0000.0000.0000.000
31A155ILE0-0.1140.10721.0770.0020.0020.0000.0000.0000.000
32A156ALA00.133-0.11922.853-0.016-0.0160.0000.0000.0000.000
33A156ALA0-0.0620.12927.313-0.001-0.0010.0000.0000.0000.000
34A157HIS00.039-0.10224.056-0.028-0.0280.0000.0000.0000.000
35A157HIS0-0.0470.10122.267-0.012-0.0120.0000.0000.0000.000
36A158GLU00.168-0.06224.7480.0010.0010.0000.0000.0000.000
37A158GLU-1-1.014-0.84327.5850.1520.1520.0000.0000.0000.000
38A159TRP00.017-0.14321.751-0.002-0.0020.0000.0000.0000.000
39A159TRP0-0.1160.10019.046-0.013-0.0130.0000.0000.0000.000
40A160THR00.037-0.06822.396-0.027-0.0270.0000.0000.0000.000
41A160THR0-0.0400.04323.9620.0060.0060.0000.0000.0000.000
42A161LEU00.202-0.06019.8970.0370.0370.0000.0000.0000.000
43A161LEU0-0.1390.07918.607-0.006-0.0060.0000.0000.0000.000
44A162ALA00.138-0.08019.2410.0290.0290.0000.0000.0000.000
45A162ALA0-0.0780.09522.944-0.005-0.0050.0000.0000.0000.000
46A163ARG00.068-0.08120.3790.0160.0160.0000.0000.0000.000
47A163ARG10.7951.01221.664-0.210-0.2100.0000.0000.0000.000
48A164ILE00.121-0.05117.2390.0450.0450.0000.0000.0000.000
49A164ILE0-0.0810.08615.147-0.008-0.0080.0000.0000.0000.000
50A165ALA00.122-0.07415.6770.0920.0920.0000.0000.0000.000
51A165ALA0-0.0990.07817.278-0.016-0.0160.0000.0000.0000.000
52A166SER0-0.021-0.09416.1080.0410.0410.0000.0000.0000.000
53A166SER0-0.0230.06519.569-0.026-0.0260.0000.0000.0000.000
54A167GLU00.062-0.10616.245-0.005-0.0050.0000.0000.0000.000
55A167GLU-1-0.932-0.85015.5370.6120.6120.0000.0000.0000.000
56A168LEU0-0.018-0.09212.3980.1340.1340.0000.0000.0000.000
57A168LEU0-0.1000.07110.3300.0100.0100.0000.0000.0000.000
58A169LEU00.059-0.10712.3150.0420.0420.0000.0000.0000.000
59A169LEU0-0.0620.12513.615-0.007-0.0070.0000.0000.0000.000
60A170MET00.109-0.11314.298-0.026-0.0260.0000.0000.0000.000
61A170MET0-0.1420.07711.6720.0200.0200.0000.0000.0000.000
62A171SER00.069-0.05415.2750.0010.0010.0000.0000.0000.000
63A171SER0-0.0340.07618.710-0.010-0.0100.0000.0000.0000.000
64A172PRO00.087-0.08417.533-0.009-0.0090.0000.0000.0000.000
65A173SER0-0.0040.00918.996-0.010-0.0100.0000.0000.0000.000
66A173SER0-0.0150.06820.8030.0040.0040.0000.0000.0000.000
67A174LEU00.155-0.07416.107-0.046-0.0460.0000.0000.0000.000
68A174LEU0-0.0850.11613.312-0.002-0.0020.0000.0000.0000.000
69A175LEU00.080-0.09914.377-0.066-0.0660.0000.0000.0000.000
70A175LEU0-0.0550.11613.2230.0040.0040.0000.0000.0000.000
71A176LYS00.104-0.08315.441-0.029-0.0290.0000.0000.0000.000
72A176LYS10.8401.04919.7140.0170.0170.0000.0000.0000.000
73A177LYS00.098-0.07017.518-0.020-0.0200.0000.0000.0000.000
74A177LYS10.8461.06016.9060.2130.2130.0000.0000.0000.000
75A178LYS00.049-0.11112.638-0.050-0.0500.0000.0000.0000.000
76A178LYS10.7490.99211.5870.5140.5140.0000.0000.0000.000
77A179LEU00.084-0.08513.601-0.105-0.1050.0000.0000.0000.000
78A179LEU0-0.1000.07713.0650.0160.0160.0000.0000.0000.000
79A180ARG00.148-0.05015.059-0.030-0.0300.0000.0000.0000.000
80A180ARG10.7070.95018.8240.2070.2070.0000.0000.0000.000
81A181GLU00.023-0.12015.3630.0250.0250.0000.0000.0000.000
82A181GLU-1-0.856-0.80914.022-0.492-0.4920.0000.0000.0000.000
83A182GLU0-0.005-0.08113.764-0.073-0.0730.0000.0000.0000.000
84A182GLU-1-0.867-0.84310.094-0.606-0.6060.0000.0000.0000.000
85A183GLU00.055-0.09615.0270.0270.0270.0000.0000.0000.000
86A183GLU-1-0.889-0.74718.733-0.229-0.2290.0000.0000.0000.000
87A184THR00.042-0.07317.5460.0180.0180.0000.0000.0000.000
88A184THR0-0.0210.05215.5260.0240.0240.0000.0000.0000.000
89A185SER00.047-0.08518.555-0.012-0.0120.0000.0000.0000.000
90A185SER0-0.0610.05620.9530.0120.0120.0000.0000.0000.000
91A186TYR00.143-0.07217.9430.0040.0040.0000.0000.0000.000
92A186TYR0-0.0820.09118.441-0.006-0.0060.0000.0000.0000.000
93A187SER00.045-0.05918.9240.0320.0320.0000.0000.0000.000
94A187SER0-0.0320.06223.569-0.006-0.0060.0000.0000.0000.000
95A188GLN00.077-0.09921.3250.0190.0190.0000.0000.0000.000
96A188GLN0-0.0230.13620.499-0.009-0.0090.0000.0000.0000.000
97A189LEU00.112-0.06917.301-0.011-0.0110.0000.0000.0000.000
98A189LEU0-0.0820.09414.6110.0100.0100.0000.0000.0000.000
99A190LEU00.127-0.05818.6480.0320.0320.0000.0000.0000.000
100A190LEU0-0.1090.08621.069-0.001-0.0010.0000.0000.0000.000
101A191THR00.023-0.10520.9510.0230.0230.0000.0000.0000.000
102A191THR0-0.0600.06023.652-0.004-0.0040.0000.0000.0000.000
103A192GLU00.073-0.08820.3290.0060.0060.0000.0000.0000.000
104A192GLU-1-0.943-0.85318.5570.0050.0050.0000.0000.0000.000
105A193CYS00.138-0.08719.656-0.007-0.0070.0000.0000.0000.000
106A193CYS0-0.1600.07117.9230.0280.0280.0000.0000.0000.000
107A194ARG00.072-0.08120.3690.0200.0200.0000.0000.0000.000
108A194ARG10.7591.02923.328-0.197-0.1970.0000.0000.0000.000
109A195MET00.052-0.13024.0410.0070.0070.0000.0000.0000.000
110A195MET0-0.0910.13124.322-0.006-0.0060.0000.0000.0000.000
111A196GLN00.102-0.08721.457-0.021-0.0210.0000.0000.0000.000
112A196GLN0-0.0680.11518.1180.0450.0450.0000.0000.0000.000
113A197ARG00.083-0.10822.9900.0010.0010.0000.0000.0000.000
114A197ARG10.7291.01920.171-0.353-0.3530.0000.0000.0000.000
115A198ALA00.133-0.08424.3840.0030.0030.0000.0000.0000.000
116A198ALA0-0.0910.09027.855-0.003-0.0030.0000.0000.0000.000
117A199LEU00.039-0.12026.556-0.008-0.0080.0000.0000.0000.000
118A199LEU0-0.1060.11525.9970.0000.0000.0000.0000.0000.000
119A200GLN00.091-0.10126.022-0.015-0.0150.0000.0000.0000.000
120A200GLN0-0.0640.09021.7690.0140.0140.0000.0000.0000.000
121A201LEU00.030-0.10027.243-0.001-0.0010.0000.0000.0000.000
122A201LEU0-0.0960.07427.9340.0010.0010.0000.0000.0000.000
123A202ILE00.090-0.08430.178-0.002-0.0020.0000.0000.0000.000
124A202ILE0-0.1040.11730.900-0.002-0.0020.0000.0000.0000.000
125A203VAL00.095-0.09931.727-0.010-0.0100.0000.0000.0000.000
126A203VAL0-0.0660.10531.1670.0000.0000.0000.0000.0000.000
127A204ILE00.100-0.07133.191-0.007-0.0070.0000.0000.0000.000
128A204ILE0-0.1130.09531.6250.0020.0020.0000.0000.0000.000
129A205HIS00.130-0.10834.463-0.003-0.0030.0000.0000.0000.000
130A205HIS0-0.0510.10838.8000.0000.0000.0000.0000.0000.000
131A206GLY0-0.022-0.10438.2500.0050.0050.0000.0000.0000.000
132A207PHE00.084-0.02335.643-0.002-0.0020.0000.0000.0000.000
133A207PHE0-0.0670.12032.9000.0030.0030.0000.0000.0000.000
134A208SER00.066-0.03837.147-0.003-0.0030.0000.0000.0000.000
135A208SER0-0.0410.04739.5600.0010.0010.0000.0000.0000.000
136A209ILE00.135-0.09636.1470.0100.0100.0000.0000.0000.000
137A209ILE0-0.0530.13435.9750.0000.0000.0000.0000.0000.000
138A210LYS00.112-0.06535.6560.0050.0050.0000.0000.0000.000
139A210LYS10.8751.05538.868-0.089-0.0890.0000.0000.0000.000
140A211ARG00.060-0.10436.0080.0030.0030.0000.0000.0000.000
141A211ARG10.8321.08034.417-0.131-0.1310.0000.0000.0000.000
142A212VAL00.122-0.11032.2680.0140.0140.0000.0000.0000.000
143A212VAL0-0.0470.14130.7310.0000.0000.0000.0000.0000.000
144A213ALA00.123-0.05931.1950.0150.0150.0000.0000.0000.000
145A213ALA0-0.0870.07833.658-0.003-0.0030.0000.0000.0000.000
146A214VAL00.103-0.09031.2390.0080.0080.0000.0000.0000.000
147A214VAL0-0.1110.09233.457-0.001-0.0010.0000.0000.0000.000
148A215SER0-0.005-0.10130.3490.0090.0090.0000.0000.0000.000
149A215SER0-0.0450.03929.7640.0020.0020.0000.0000.0000.000
150A216CYS00.047-0.10826.9470.0270.0270.0000.0000.0000.000
151A216CYS0-0.1560.08427.2460.0000.0000.0000.0000.0000.000
152A217GLY00.017-0.08926.8770.0060.0060.0000.0000.0000.000
153A218TYR00.0360.01228.766-0.004-0.0040.0000.0000.0000.000
154A218TYR0-0.1040.08027.1260.0010.0010.0000.0000.0000.000
155A219HIS00.112-0.10231.4660.0020.0020.0000.0000.0000.000
156A219HIS0-0.0880.11031.245-0.007-0.0070.0000.0000.0000.000
157A220SER00.077-0.08134.458-0.004-0.0040.0000.0000.0000.000
158A220SER0-0.0710.06435.582-0.002-0.0020.0000.0000.0000.000
159A221VAL00.094-0.11335.1930.0020.0020.0000.0000.0000.000
160A221VAL0-0.0430.11837.0790.0000.0000.0000.0000.0000.000
161A222SER00.049-0.04236.7540.0000.0000.0000.0000.0000.000
162A222SER0-0.0100.06739.1880.0010.0010.0000.0000.0000.000
163A223TYR00.148-0.05834.792-0.007-0.0070.0000.0000.0000.000
164A223TYR0-0.0860.09029.9450.0030.0030.0000.0000.0000.000
165A224PHE00.060-0.07432.098-0.005-0.0050.0000.0000.0000.000
166A224PHE0-0.0410.07829.7560.0010.0010.0000.0000.0000.000
167A225ILE00.071-0.08232.7080.0010.0010.0000.0000.0000.000
168A225ILE0-0.1040.06736.6260.0000.0000.0000.0000.0000.000
169A226TYR00.073-0.07734.614-0.003-0.0030.0000.0000.0000.000
170A226TYR0-0.1210.06632.705-0.002-0.0020.0000.0000.0000.000
171A227VAL00.150-0.09430.293-0.011-0.0110.0000.0000.0000.000
172A227VAL0-0.1170.08528.2940.0010.0010.0000.0000.0000.000
173A228PHE00.166-0.05329.896-0.005-0.0050.0000.0000.0000.000
174A228PHE0-0.1340.06929.7800.0030.0030.0000.0000.0000.000
175A229ARG00.094-0.07531.105-0.003-0.0030.0000.0000.0000.000
176A229ARG10.8691.05835.169-0.023-0.0230.0000.0000.0000.000
177A230ASN00.027-0.09331.405-0.006-0.0060.0000.0000.0000.000
178A230ASN0-0.1470.04230.706-0.002-0.0020.0000.0000.0000.000
179A231TYR00.141-0.05427.779-0.014-0.0140.0000.0000.0000.000
180A231TYR0-0.0950.07821.7070.0060.0060.0000.0000.0000.000
181A232TYR0-0.023-0.12328.251-0.009-0.0090.0000.0000.0000.000
182A232TYR0-0.1210.04725.6580.0000.0000.0000.0000.0000.000
183A233GLY00.044-0.08130.431-0.004-0.0040.0000.0000.0000.000
184A234MET00.036-0.01933.764-0.004-0.0040.0000.0000.0000.000
185A234MET0-0.0690.11833.4230.0030.0030.0000.0000.0000.000
186A235THR0-0.006-0.13234.4910.0050.0050.0000.0000.0000.000
187A235THR0-0.0860.01238.0860.0020.0020.0000.0000.0000.000
188A236PRO0-0.034-0.11533.6820.0000.0000.0000.0000.0000.000
189A237THR00.1080.03335.3290.0040.0040.0000.0000.0000.000
190A237THR0-0.0370.07640.0780.0000.0000.0000.0000.0000.000
191A238GLU00.107-0.05538.5430.0020.0020.0000.0000.0000.000
192A238GLU-1-0.866-0.78437.7660.0250.0250.0000.0000.0000.000
193A239TYR00.120-0.06534.058-0.003-0.0030.0000.0000.0000.000
194A239TYR0-0.0740.07029.4810.0040.0040.0000.0000.0000.000
195A240GLN00.112-0.07735.4080.0010.0010.0000.0000.0000.000
196A240GLN0-0.1560.03836.287-0.005-0.0050.0000.0000.0000.000
197A241GLU00.030-0.17136.7010.0040.0040.0000.0000.0000.000
198A241GLU-1-0.907-0.80440.2560.0380.0380.0000.0000.0000.000
199A242ARG0-0.025-0.06637.129-0.003-0.0030.0000.0000.0000.000
200A242ARG10.7380.99136.119-0.034-0.0340.0000.0000.0000.000
201A243SER0-0.098-0.14834.913-0.004-0.0040.0000.0000.0000.000
202A243SER00.0800.06734.0710.0040.0040.0000.0000.0000.000