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: 7MLVK

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 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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -827038.996344
FMO2-HF: Nuclear repulsion 783369.675276
FMO2-HF: Total energy -43669.321068
FMO2-MP2: Total energy -43792.996923


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.
-0.8340.262-0.006-0.533-0.5580.003
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 : 0.118 / q_NPA : 0.024
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].
4A142ASN00.1050.0503.831-0.6960.400-0.006-0.533-0.5580.003
5A142ASN0-0.0250.0956.8600.4140.4140.0000.0000.0000.000
6A143MET00.146-0.1026.3310.7290.7290.0000.0000.0000.000
7A143MET0-0.1140.1068.5460.0820.0820.0000.0000.0000.000
8A144ARG00.097-0.0978.9980.2850.2850.0000.0000.0000.000
9A144ARG10.8941.08310.9810.2590.2590.0000.0000.0000.000
10A145THR00.008-0.0908.5770.0830.0830.0000.0000.0000.000
11A145THR0-0.0110.0787.674-0.014-0.0140.0000.0000.0000.000
12A146ARG00.076-0.0738.4150.2140.2140.0000.0000.0000.000
13A146ARG10.9001.0745.250-1.453-1.4530.0000.0000.0000.000
14A147VAL00.067-0.0739.2150.1220.1220.0000.0000.0000.000
15A147VAL0-0.0840.07312.088-0.022-0.0220.0000.0000.0000.000
16A148CYS00.162-0.10312.8170.0100.0100.0000.0000.0000.000
17A148CYS0-0.1350.09813.056-0.041-0.0410.0000.0000.0000.000
18A149THR0-0.009-0.08211.756-0.131-0.1310.0000.0000.0000.000
19A149THR0-0.0410.05510.8340.1400.1400.0000.0000.0000.000
20A150VAL00.101-0.06813.0850.0200.0200.0000.0000.0000.000
21A150VAL0-0.1020.08612.775-0.011-0.0110.0000.0000.0000.000
22A151ILE00.031-0.10214.989-0.020-0.0200.0000.0000.0000.000
23A151ILE0-0.0640.08116.779-0.014-0.0140.0000.0000.0000.000
24A152ASN00.031-0.08516.722-0.049-0.0490.0000.0000.0000.000
25A152ASN0-0.0850.06615.806-0.056-0.0560.0000.0000.0000.000
26A153ASN00.157-0.08217.574-0.033-0.0330.0000.0000.0000.000
27A153ASN0-0.0900.09615.6180.0080.0080.0000.0000.0000.000
28A154ASN00.081-0.09618.826-0.024-0.0240.0000.0000.0000.000
29A154ASN0-0.1420.07221.877-0.022-0.0220.0000.0000.0000.000
30A155ILE00.095-0.05722.002-0.003-0.0030.0000.0000.0000.000
31A155ILE0-0.0810.10620.820-0.001-0.0010.0000.0000.0000.000
32A156ALA00.105-0.10622.901-0.017-0.0170.0000.0000.0000.000
33A156ALA0-0.0380.11927.486-0.002-0.0020.0000.0000.0000.000
34A157HIS00.036-0.09324.104-0.028-0.0280.0000.0000.0000.000
35A157HIS0-0.0480.09122.9680.0000.0000.0000.0000.0000.000
36A158GLU00.125-0.07824.787-0.003-0.0030.0000.0000.0000.000
37A158GLU-1-1.058-0.87227.3120.1490.1490.0000.0000.0000.000
38A159TRP00.064-0.13221.7670.0010.0010.0000.0000.0000.000
39A159TRP0-0.1130.09919.323-0.011-0.0110.0000.0000.0000.000
40A160THR00.044-0.07922.386-0.028-0.0280.0000.0000.0000.000
41A160THR0-0.0310.05323.7360.0080.0080.0000.0000.0000.000
42A161LEU00.196-0.05919.9080.0360.0360.0000.0000.0000.000
43A161LEU0-0.1560.08118.545-0.006-0.0060.0000.0000.0000.000
44A162ALA00.133-0.08819.2570.0290.0290.0000.0000.0000.000
45A162ALA0-0.0770.09922.944-0.005-0.0050.0000.0000.0000.000
46A163ARG00.072-0.08920.4000.0190.0190.0000.0000.0000.000
47A163ARG10.8021.04221.759-0.210-0.2100.0000.0000.0000.000
48A164ILE00.114-0.06217.2240.0470.0470.0000.0000.0000.000
49A164ILE0-0.0680.08815.187-0.010-0.0100.0000.0000.0000.000
50A165ALA00.124-0.08315.6970.0930.0930.0000.0000.0000.000
51A165ALA0-0.0970.08817.285-0.016-0.0160.0000.0000.0000.000
52A166SER0-0.021-0.08916.1270.0470.0470.0000.0000.0000.000
53A166SER0-0.0220.07119.464-0.027-0.0270.0000.0000.0000.000
54A167GLU00.064-0.11116.2600.0000.0000.0000.0000.0000.000
55A167GLU-1-0.955-0.85715.4490.6440.6440.0000.0000.0000.000
56A168LEU0-0.012-0.10612.4230.1370.1370.0000.0000.0000.000
57A168LEU0-0.0980.08810.5710.0030.0030.0000.0000.0000.000
58A169LEU00.043-0.10512.3340.0470.0470.0000.0000.0000.000
59A169LEU0-0.0690.11913.576-0.005-0.0050.0000.0000.0000.000
60A170MET00.116-0.10514.367-0.017-0.0170.0000.0000.0000.000
61A170MET0-0.1420.07811.8190.0100.0100.0000.0000.0000.000
62A171SER00.054-0.05915.283-0.002-0.0020.0000.0000.0000.000
63A171SER0-0.0250.07118.682-0.011-0.0110.0000.0000.0000.000
64A172PRO00.084-0.08017.530-0.010-0.0100.0000.0000.0000.000
65A173SER00.0080.00618.990-0.013-0.0130.0000.0000.0000.000
66A173SER0-0.0160.07120.8170.0030.0030.0000.0000.0000.000
67A174LEU00.135-0.06216.060-0.049-0.0490.0000.0000.0000.000
68A174LEU0-0.0780.10113.282-0.004-0.0040.0000.0000.0000.000
69A175LEU00.083-0.10114.380-0.068-0.0680.0000.0000.0000.000
70A175LEU0-0.0450.11613.1770.0060.0060.0000.0000.0000.000
71A176LYS00.102-0.09915.434-0.034-0.0340.0000.0000.0000.000
72A176LYS10.8541.06019.7060.0200.0200.0000.0000.0000.000
73A177LYS00.092-0.07317.494-0.025-0.0250.0000.0000.0000.000
74A177LYS10.8491.06216.7940.1780.1780.0000.0000.0000.000
75A178LYS00.061-0.10012.614-0.047-0.0470.0000.0000.0000.000
76A178LYS10.8651.06010.5760.4920.4920.0000.0000.0000.000
77A179LEU00.077-0.07413.576-0.110-0.1100.0000.0000.0000.000
78A179LEU0-0.1100.07013.0390.0160.0160.0000.0000.0000.000
79A180ARG00.165-0.03515.046-0.035-0.0350.0000.0000.0000.000
80A180ARG10.7721.02118.7200.2230.2230.0000.0000.0000.000
81A181GLU00.037-0.13015.3620.0280.0280.0000.0000.0000.000
82A181GLU-1-0.973-0.86114.173-0.468-0.4680.0000.0000.0000.000
83A182GLU00.024-0.08313.731-0.070-0.0700.0000.0000.0000.000
84A182GLU-1-0.911-0.85410.207-0.766-0.7660.0000.0000.0000.000
85A183GLU00.023-0.13415.0010.0230.0230.0000.0000.0000.000
86A183GLU-1-0.958-0.82018.475-0.261-0.2610.0000.0000.0000.000
87A184THR00.050-0.04017.5430.0180.0180.0000.0000.0000.000
88A184THR0-0.0010.03915.5260.0250.0250.0000.0000.0000.000
89A185SER00.024-0.09418.547-0.008-0.0080.0000.0000.0000.000
90A185SER0-0.0260.08220.9250.0140.0140.0000.0000.0000.000
91A186TYR00.133-0.06617.955-0.001-0.0010.0000.0000.0000.000
92A186TYR0-0.0690.09018.5470.0020.0020.0000.0000.0000.000
93A187SER00.040-0.08318.9360.0290.0290.0000.0000.0000.000
94A187SER0-0.0230.08523.668-0.003-0.0030.0000.0000.0000.000
95A188GLN00.035-0.11921.2770.0190.0190.0000.0000.0000.000
96A188GLN0-0.0530.11520.586-0.018-0.0180.0000.0000.0000.000
97A189LEU00.144-0.06417.329-0.010-0.0100.0000.0000.0000.000
98A189LEU0-0.1040.09514.6240.0080.0080.0000.0000.0000.000
99A190LEU00.117-0.07818.6660.0290.0290.0000.0000.0000.000
100A190LEU0-0.1120.08121.101-0.001-0.0010.0000.0000.0000.000
101A191THR00.002-0.08020.9780.0230.0230.0000.0000.0000.000
102A191THR0-0.0430.06023.779-0.002-0.0020.0000.0000.0000.000
103A192GLU00.130-0.10220.4330.0110.0110.0000.0000.0000.000
104A192GLU-1-0.987-0.82819.092-0.034-0.0340.0000.0000.0000.000
105A193CYS00.117-0.12019.713-0.007-0.0070.0000.0000.0000.000
106A193CYS0-0.1570.07817.9460.0260.0260.0000.0000.0000.000
107A194ARG00.081-0.07920.3690.0190.0190.0000.0000.0000.000
108A194ARG10.7901.03823.438-0.177-0.1770.0000.0000.0000.000
109A195MET00.051-0.12424.0410.0100.0100.0000.0000.0000.000
110A195MET0-0.0860.13324.357-0.006-0.0060.0000.0000.0000.000
111A196GLN00.100-0.08121.416-0.018-0.0180.0000.0000.0000.000
112A196GLN0-0.0770.10918.0960.0370.0370.0000.0000.0000.000
113A197ARG00.096-0.12522.9440.0010.0010.0000.0000.0000.000
114A197ARG10.8111.08020.207-0.314-0.3140.0000.0000.0000.000
115A198ALA00.151-0.09924.3370.0050.0050.0000.0000.0000.000
116A198ALA0-0.0880.10827.892-0.003-0.0030.0000.0000.0000.000
117A199LEU00.011-0.14326.513-0.006-0.0060.0000.0000.0000.000
118A199LEU0-0.0890.12325.6500.0000.0000.0000.0000.0000.000
119A200GLN00.076-0.09625.997-0.014-0.0140.0000.0000.0000.000
120A200GLN0-0.0690.08921.9120.0170.0170.0000.0000.0000.000
121A201LEU00.018-0.10527.1960.0000.0000.0000.0000.0000.000
122A201LEU0-0.0950.07527.7010.0010.0010.0000.0000.0000.000
123A202ILE00.070-0.07730.130-0.001-0.0010.0000.0000.0000.000
124A202ILE0-0.0870.10230.827-0.002-0.0020.0000.0000.0000.000
125A203VAL00.098-0.08931.679-0.008-0.0080.0000.0000.0000.000
126A203VAL0-0.0430.09731.3130.0000.0000.0000.0000.0000.000
127A204ILE00.063-0.07233.156-0.007-0.0070.0000.0000.0000.000
128A204ILE0-0.1050.08731.5410.0020.0020.0000.0000.0000.000
129A205HIS00.140-0.08634.417-0.003-0.0030.0000.0000.0000.000
130A205HIS0-0.0420.10338.7660.0000.0000.0000.0000.0000.000
131A206GLY0-0.014-0.10038.2040.0050.0050.0000.0000.0000.000
132A207PHE00.078-0.03835.591-0.001-0.0010.0000.0000.0000.000
133A207PHE0-0.0710.11832.7640.0030.0030.0000.0000.0000.000
134A208SER00.060-0.04037.100-0.004-0.0040.0000.0000.0000.000
135A208SER0-0.0420.04939.4870.0010.0010.0000.0000.0000.000
136A209ILE00.137-0.09736.1030.0090.0090.0000.0000.0000.000
137A209ILE0-0.0420.13036.0990.0000.0000.0000.0000.0000.000
138A210LYS00.102-0.08135.6560.0040.0040.0000.0000.0000.000
139A210LYS10.8691.05439.246-0.080-0.0800.0000.0000.0000.000
140A211ARG00.065-0.09835.9620.0030.0030.0000.0000.0000.000
141A211ARG10.8271.08833.974-0.122-0.1220.0000.0000.0000.000
142A212VAL00.123-0.10932.2210.0150.0150.0000.0000.0000.000
143A212VAL0-0.0480.14230.7350.0000.0000.0000.0000.0000.000
144A213ALA00.115-0.06431.1950.0140.0140.0000.0000.0000.000
145A213ALA0-0.0810.08933.624-0.002-0.0020.0000.0000.0000.000
146A214VAL00.058-0.08831.2810.0070.0070.0000.0000.0000.000
147A214VAL0-0.0710.08333.425-0.001-0.0010.0000.0000.0000.000
148A215SER0-0.003-0.08830.3990.0100.0100.0000.0000.0000.000
149A215SER0-0.0550.04329.8150.0020.0020.0000.0000.0000.000
150A216CYS00.029-0.13826.9930.0270.0270.0000.0000.0000.000
151A216CYS0-0.1360.09427.251-0.001-0.0010.0000.0000.0000.000
152A217GLY00.028-0.07726.9180.0050.0050.0000.0000.0000.000
153A218TYR00.0360.00928.807-0.004-0.0040.0000.0000.0000.000
154A218TYR0-0.1030.08327.3690.0000.0000.0000.0000.0000.000
155A219HIS00.115-0.10831.5030.0020.0020.0000.0000.0000.000
156A219HIS0-0.0500.13531.524-0.007-0.0070.0000.0000.0000.000
157A220SER00.063-0.07634.493-0.004-0.0040.0000.0000.0000.000
158A220SER0-0.0800.06735.583-0.002-0.0020.0000.0000.0000.000
159A221VAL00.103-0.11935.2260.0010.0010.0000.0000.0000.000
160A221VAL0-0.0350.12637.0170.0000.0000.0000.0000.0000.000
161A222SER00.032-0.06836.754-0.001-0.0010.0000.0000.0000.000
162A222SER00.0000.07439.1850.0000.0000.0000.0000.0000.000
163A223TYR00.141-0.05034.797-0.007-0.0070.0000.0000.0000.000
164A223TYR0-0.0820.09629.8430.0040.0040.0000.0000.0000.000
165A224PHE00.066-0.07632.104-0.006-0.0060.0000.0000.0000.000
166A224PHE0-0.0390.07529.9170.0010.0010.0000.0000.0000.000
167A225ILE00.033-0.08132.7080.0000.0000.0000.0000.0000.000
168A225ILE0-0.0730.05236.7920.0000.0000.0000.0000.0000.000
169A226TYR00.070-0.08034.614-0.004-0.0040.0000.0000.0000.000
170A226TYR0-0.1130.07132.211-0.002-0.0020.0000.0000.0000.000
171A227VAL00.146-0.09430.292-0.011-0.0110.0000.0000.0000.000
172A227VAL0-0.1180.09828.2810.0000.0000.0000.0000.0000.000
173A228PHE00.177-0.07029.896-0.007-0.0070.0000.0000.0000.000
174A228PHE0-0.1430.07529.9980.0030.0030.0000.0000.0000.000
175A229ARG00.072-0.07331.105-0.004-0.0040.0000.0000.0000.000
176A229ARG10.8641.04935.162-0.011-0.0110.0000.0000.0000.000
177A230ASN00.057-0.09831.342-0.006-0.0060.0000.0000.0000.000
178A230ASN0-0.1390.05430.500-0.002-0.0020.0000.0000.0000.000
179A231TYR00.119-0.05527.771-0.014-0.0140.0000.0000.0000.000
180A231TYR0-0.0920.08122.0860.0020.0020.0000.0000.0000.000
181A232TYR0-0.024-0.12028.251-0.010-0.0100.0000.0000.0000.000
182A232TYR0-0.1240.04525.471-0.001-0.0010.0000.0000.0000.000
183A233GLY00.044-0.08030.431-0.004-0.0040.0000.0000.0000.000
184A234MET00.035-0.01433.764-0.003-0.0030.0000.0000.0000.000
185A234MET0-0.0690.11533.5190.0030.0030.0000.0000.0000.000
186A235THR0-0.001-0.12434.5040.0040.0040.0000.0000.0000.000
187A235THR0-0.0610.04638.1770.0020.0020.0000.0000.0000.000
188A236PRO0-0.035-0.10633.6800.0000.0000.0000.0000.0000.000
189A237THR00.0680.03335.2840.0040.0040.0000.0000.0000.000
190A237THR0-0.0050.07940.1200.0010.0010.0000.0000.0000.000
191A238GLU00.117-0.04638.4990.0020.0020.0000.0000.0000.000
192A238GLU-1-0.897-0.83837.6910.0110.0110.0000.0000.0000.000
193A239TYR00.117-0.08134.007-0.003-0.0030.0000.0000.0000.000
194A239TYR0-0.0730.07529.5030.0040.0040.0000.0000.0000.000
195A240GLN00.097-0.09135.3640.0000.0000.0000.0000.0000.000
196A240GLN0-0.1470.07136.001-0.005-0.0050.0000.0000.0000.000
197A241GLU00.051-0.11836.6560.0050.0050.0000.0000.0000.000
198A241GLU-1-1.036-0.85740.4420.0320.0320.0000.0000.0000.000
199A242ARG0-0.007-0.10937.047-0.003-0.0030.0000.0000.0000.000
200A242ARG10.8511.03236.048-0.019-0.0190.0000.0000.0000.000
201A243SER0-0.104-0.14234.873-0.003-0.0030.0000.0000.0000.000
202A243SER00.0860.07234.0220.0040.0040.0000.0000.0000.000