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: 7GLMK

Calculation Name: 3PIM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PIM

Chain ID: A

ChEMBL ID:

UniProt ID: P40029

Base Structure: X-ray

Registration Date: 2023-06-20

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1983708.920794
FMO2-HF: Nuclear repulsion 1911121.808225
FMO2-HF: Total energy -72587.112569
FMO2-MP2: Total energy -72798.065261


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:-2:HIS)


Summations of interaction energy for fragment #1(A:-2:HIS)
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.
-6.505-2.890.483-1.499-2.598-0.008
Interaction energy analysis for fragmet #1(A:-2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.013
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].
3A0HIS00.0220.0083.077-5.692-2.3440.485-1.493-2.341-0.008
4A1GLY00.0590.0305.178-0.182-0.051-0.001-0.004-0.1250.000
5A2SER0-0.007-0.0134.433-0.702-0.566-0.001-0.002-0.1320.000
6A3SER0-0.041-0.0196.352-0.175-0.1750.0000.0000.0000.000
7A4LEU00.0180.0228.204-0.126-0.1260.0000.0000.0000.000
8A5ILE0-0.036-0.0129.974-0.114-0.1140.0000.0000.0000.000
9A6SER0-0.042-0.05211.6060.0010.0010.0000.0000.0000.000
10A7LYS10.9260.9539.972-0.092-0.0920.0000.0000.0000.000
11A8THR0-0.035-0.01913.222-0.126-0.1260.0000.0000.0000.000
12A9ILE0-0.078-0.01215.2070.0010.0010.0000.0000.0000.000
13A10LYS10.9420.97116.0800.2900.2900.0000.0000.0000.000
14A11TYR00.017-0.01012.6650.1030.1030.0000.0000.0000.000
15A12ASP-1-0.877-0.93514.809-0.733-0.7330.0000.0000.0000.000
16A13PRO00.0200.00612.1050.0830.0830.0000.0000.0000.000
17A14ALA0-0.033-0.00515.1420.0610.0610.0000.0000.0000.000
18A15LYS10.8320.91517.6950.4610.4610.0000.0000.0000.000
19A16ASP-1-0.857-0.93018.224-0.333-0.3330.0000.0000.0000.000
20A17LYS10.8170.89718.0860.1090.1090.0000.0000.0000.000
21A18LEU00.0160.00814.141-0.002-0.0020.0000.0000.0000.000
22A19ILE0-0.036-0.01018.3460.0280.0280.0000.0000.0000.000
23A20THR00.019-0.01217.636-0.025-0.0250.0000.0000.0000.000
24A21LEU0-0.040-0.01220.3980.0230.0230.0000.0000.0000.000
25A22ALA00.0560.03023.974-0.002-0.0020.0000.0000.0000.000
26A23CYS0-0.023-0.00825.836-0.005-0.0050.0000.0000.0000.000
27A24GLY00.0520.03428.975-0.008-0.0080.0000.0000.0000.000
28A25CYS0-0.043-0.01928.6280.0020.0020.0000.0000.0000.000
29A26PHE00.0990.03323.535-0.014-0.0140.0000.0000.0000.000
30A27TRP0-0.032-0.00225.878-0.013-0.0130.0000.0000.0000.000
31A28GLY00.0020.00429.327-0.012-0.0120.0000.0000.0000.000
32A29THR00.011-0.00826.807-0.005-0.0050.0000.0000.0000.000
33A30GLU-1-0.869-0.95925.263-0.103-0.1030.0000.0000.0000.000
34A31HIS0-0.015-0.00428.118-0.017-0.0170.0000.0000.0000.000
35A32MET0-0.047-0.01831.584-0.008-0.0080.0000.0000.0000.000
36A33TYR00.039-0.00228.057-0.001-0.0010.0000.0000.0000.000
37A34ARG10.9710.99226.7630.1340.1340.0000.0000.0000.000
38A35LYS10.8980.96530.8030.0480.0480.0000.0000.0000.000
39A36TYR0-0.048-0.04533.705-0.001-0.0010.0000.0000.0000.000
40A37LEU0-0.010-0.00930.3320.0000.0000.0000.0000.0000.000
41A38ASN00.0120.01629.083-0.012-0.0120.0000.0000.0000.000
42A39ASP-1-0.910-0.94329.485-0.148-0.1480.0000.0000.0000.000
43A40ARG10.7400.85830.1980.0970.0970.0000.0000.0000.000
44A41ILE0-0.048-0.01425.2460.0010.0010.0000.0000.0000.000
45A42VAL0-0.077-0.02720.846-0.004-0.0040.0000.0000.0000.000
46A43ASP-1-0.824-0.92420.765-0.298-0.2980.0000.0000.0000.000
47A44CYS0-0.081-0.03521.7520.0200.0200.0000.0000.0000.000
48A45LYS10.9711.00618.7280.2370.2370.0000.0000.0000.000
49A46VAL0-0.0040.01020.7930.0260.0260.0000.0000.0000.000
50A47GLY00.0390.01319.168-0.014-0.0140.0000.0000.0000.000
51A48TYR0-0.035-0.00418.801-0.018-0.0180.0000.0000.0000.000
52A49ALA00.0250.00617.5490.0370.0370.0000.0000.0000.000
53A50ASN00.0150.00517.1720.0000.0000.0000.0000.0000.000
54A51GLY00.0990.02817.5220.0210.0210.0000.0000.0000.000
55A52GLU-1-0.990-0.97915.6580.5290.5290.0000.0000.0000.000
56A53GLU-1-0.874-0.90919.5270.2510.2510.0000.0000.0000.000
57A63SER00.0500.02629.935-0.010-0.0100.0000.0000.0000.000
58A64TYR00.008-0.01329.7490.0150.0150.0000.0000.0000.000
59A65LYS10.9170.95930.420-0.126-0.1260.0000.0000.0000.000
60A66ARG10.9210.96922.031-0.344-0.3440.0000.0000.0000.000
61A67VAL00.0160.02924.309-0.031-0.0310.0000.0000.0000.000
62A68CYS0-0.106-0.00724.3450.0230.0230.0000.0000.0000.000
63A69GLY00.0690.03224.4390.0060.0060.0000.0000.0000.000
64A70GLY00.0290.00721.7510.0310.0310.0000.0000.0000.000
65A71ASP-1-0.900-0.95719.7340.4840.4840.0000.0000.0000.000
66A72THR0-0.053-0.04022.480-0.015-0.0150.0000.0000.0000.000
67A73ASP-1-0.826-0.90721.6240.3700.3700.0000.0000.0000.000
68A74PHE0-0.0150.00616.798-0.013-0.0130.0000.0000.0000.000
69A75ALA0-0.020-0.01821.970-0.030-0.0300.0000.0000.0000.000
70A76GLU-1-0.833-0.91322.3290.0860.0860.0000.0000.0000.000
71A77VAL0-0.047-0.02919.618-0.006-0.0060.0000.0000.0000.000
72A78LEU0-0.019-0.01122.646-0.013-0.0130.0000.0000.0000.000
73A79GLN0-0.0010.00414.730-0.055-0.0550.0000.0000.0000.000
74A80VAL0-0.002-0.01120.045-0.029-0.0290.0000.0000.0000.000
75A81SER00.0150.00318.7540.0040.0040.0000.0000.0000.000
76A82TYR00.036-0.00520.4730.0100.0100.0000.0000.0000.000
77A83ASN00.1370.07322.148-0.005-0.0050.0000.0000.0000.000
78A84PRO00.0210.00322.7340.0230.0230.0000.0000.0000.000
79A85LYS10.8930.94525.8030.2060.2060.0000.0000.0000.000
80A86VAL0-0.059-0.01327.8920.0070.0070.0000.0000.0000.000
81A87ILE0-0.0060.00127.3430.0150.0150.0000.0000.0000.000
82A88THR00.0160.01027.492-0.005-0.0050.0000.0000.0000.000
83A89LEU00.0630.02723.6390.0030.0030.0000.0000.0000.000
84A90ARG10.8950.92326.8640.0300.0300.0000.0000.0000.000
85A91GLU-1-0.805-0.89030.361-0.077-0.0770.0000.0000.0000.000
86A92LEU00.0090.00925.1430.0060.0060.0000.0000.0000.000
87A93THR00.003-0.00727.7900.0130.0130.0000.0000.0000.000
88A94ASP-1-0.886-0.94929.684-0.011-0.0110.0000.0000.0000.000
89A95PHE0-0.095-0.04630.8660.0050.0050.0000.0000.0000.000
90A96PHE00.0790.03527.8610.0030.0030.0000.0000.0000.000
91A97PHE0-0.022-0.01931.1880.0090.0090.0000.0000.0000.000
92A98ARG10.9120.95034.0820.0230.0230.0000.0000.0000.000
93A99ILE0-0.035-0.00530.686-0.002-0.0020.0000.0000.0000.000
94A100HIS00.0170.04531.6380.0130.0130.0000.0000.0000.000
95A101ASP-1-0.753-0.83935.4560.0440.0440.0000.0000.0000.000
96A102PRO0-0.0010.01133.5350.0080.0080.0000.0000.0000.000
97A103THR0-0.036-0.04234.5980.0090.0090.0000.0000.0000.000
98A104THR0-0.015-0.02136.9350.0050.0050.0000.0000.0000.000
99A105SER0-0.060-0.03438.3980.0020.0020.0000.0000.0000.000
100A106ASN00.0110.02835.3820.0010.0010.0000.0000.0000.000
101A107SER00.012-0.02135.9160.0020.0020.0000.0000.0000.000
102A108GLN0-0.100-0.02437.9500.0110.0110.0000.0000.0000.000
103A109GLY00.0840.02338.301-0.005-0.0050.0000.0000.0000.000
104A110PRO0-0.106-0.03837.6400.0080.0080.0000.0000.0000.000
105A111ASP-1-0.846-0.90638.7620.0700.0700.0000.0000.0000.000
106A112LYS10.8150.89533.721-0.085-0.0850.0000.0000.0000.000
107A113GLY00.0260.01931.8390.0060.0060.0000.0000.0000.000
108A114THR00.009-0.02228.451-0.008-0.0080.0000.0000.0000.000
109A115GLN00.0790.04826.1620.0070.0070.0000.0000.0000.000
110A116TYR0-0.070-0.02227.149-0.006-0.0060.0000.0000.0000.000
111A117ARG10.8260.92023.770-0.223-0.2230.0000.0000.0000.000
112A118SER00.0150.00228.4010.0000.0000.0000.0000.0000.000
113A119GLY0-0.018-0.03625.8420.0140.0140.0000.0000.0000.000
114A120LEU0-0.039-0.00624.154-0.017-0.0170.0000.0000.0000.000
115A121PHE00.0230.00718.8730.0160.0160.0000.0000.0000.000
116A122ALA00.0160.00219.671-0.033-0.0330.0000.0000.0000.000
117A123HIS00.0600.05013.9870.0620.0620.0000.0000.0000.000
118A124SER00.0040.01015.444-0.021-0.0210.0000.0000.0000.000
119A125ASP-1-0.806-0.90317.7480.1630.1630.0000.0000.0000.000
120A126ALA0-0.061-0.03920.1310.0020.0020.0000.0000.0000.000
121A127ASP-1-0.817-0.91420.505-0.064-0.0640.0000.0000.0000.000
122A128LEU00.0200.01621.4850.0000.0000.0000.0000.0000.000
123A129LYS10.9610.98523.290-0.044-0.0440.0000.0000.0000.000
124A130GLU-1-0.947-0.97825.815-0.041-0.0410.0000.0000.0000.000
125A131LEU00.018-0.00623.161-0.001-0.0010.0000.0000.0000.000
126A132ALA0-0.0020.00227.3220.0010.0010.0000.0000.0000.000
127A133LYS10.8990.94929.273-0.004-0.0040.0000.0000.0000.000
128A134ILE0-0.021-0.00428.860-0.003-0.0030.0000.0000.0000.000
129A135LYS10.9100.94330.900-0.095-0.0950.0000.0000.0000.000
130A136GLU-1-0.933-0.97832.6750.0520.0520.0000.0000.0000.000
131A137GLU-1-0.825-0.89935.1300.0000.0000.0000.0000.0000.000
132A138TRP0-0.050-0.04434.359-0.003-0.0030.0000.0000.0000.000
133A139GLN00.0500.02935.742-0.003-0.0030.0000.0000.0000.000
134A140PRO00.0180.02738.6720.0000.0000.0000.0000.0000.000
135A141LYS10.8600.93440.250-0.005-0.0050.0000.0000.0000.000
136A142TRP0-0.0260.00137.0590.0000.0000.0000.0000.0000.000
137A143GLY00.0140.00340.7490.0050.0050.0000.0000.0000.000
138A144ASN0-0.074-0.05740.1790.0030.0030.0000.0000.0000.000
139A145LYS10.9450.97839.494-0.050-0.0500.0000.0000.0000.000
140A146ILE0-0.033-0.00633.3720.0040.0040.0000.0000.0000.000
141A147ALA0-0.016-0.02633.8830.0050.0050.0000.0000.0000.000
142A148THR0-0.037-0.02328.4500.0080.0080.0000.0000.0000.000
143A149VAL0-0.0020.01625.223-0.002-0.0020.0000.0000.0000.000
144A150ILE0-0.020-0.01424.555-0.008-0.0080.0000.0000.0000.000
145A151GLH0-0.084-0.07521.5240.0140.0140.0000.0000.0000.000
146A152PRO00.0460.03417.620-0.036-0.0360.0000.0000.0000.000
147A153ILE0-0.021-0.00714.0920.0360.0360.0000.0000.0000.000
148A154LYS10.8490.94814.226-0.517-0.5170.0000.0000.0000.000
149A155ASN0-0.045-0.03712.1380.1020.1020.0000.0000.0000.000
150A156PHE00.0180.00312.757-0.130-0.1300.0000.0000.0000.000
151A157TYR0-0.0200.00612.6930.0780.0780.0000.0000.0000.000
152A158ASP-1-0.684-0.81815.337-0.170-0.1700.0000.0000.0000.000
153A159ALA0-0.0050.00017.3810.0480.0480.0000.0000.0000.000
154A160GLU-1-0.932-0.99019.906-0.063-0.0630.0000.0000.0000.000
155A161GLU-1-0.865-0.93912.5770.2600.2600.0000.0000.0000.000
156A162TYR0-0.025-0.03817.5250.0680.0680.0000.0000.0000.000
157A163HIS10.8400.90618.702-0.064-0.0640.0000.0000.0000.000
158A164GLN00.009-0.00418.6780.0130.0130.0000.0000.0000.000
159A165LEU0-0.0050.02414.8800.0140.0140.0000.0000.0000.000
160A166TYR0-0.023-0.01816.9120.0350.0350.0000.0000.0000.000
161A167LEU0-0.083-0.05121.523-0.016-0.0160.0000.0000.0000.000
162A168ASP-1-0.882-0.91421.7140.1540.1540.0000.0000.0000.000
163A169LYS10.9150.95323.726-0.184-0.1840.0000.0000.0000.000
164A170ASN0-0.068-0.03626.878-0.024-0.0240.0000.0000.0000.000
165A171PRO00.1020.05828.091-0.001-0.0010.0000.0000.0000.000
166A172GLN00.0620.01129.069-0.013-0.0130.0000.0000.0000.000
167A173GLY00.0200.02229.284-0.006-0.0060.0000.0000.0000.000
168A174TYR0-0.009-0.01730.147-0.005-0.0050.0000.0000.0000.000
169A175ALA0-0.014-0.01331.2420.0130.0130.0000.0000.0000.000
170A177PRO0-0.012-0.00629.361-0.011-0.0110.0000.0000.0000.000
171A178THR00.000-0.00226.208-0.004-0.0040.0000.0000.0000.000
172A179HIS00.0220.01329.412-0.004-0.0040.0000.0000.0000.000
173A180TYR00.011-0.02327.3740.0030.0030.0000.0000.0000.000
174A181LEU00.0180.01529.3910.0090.0090.0000.0000.0000.000
175A182ARG10.8020.91229.787-0.050-0.0500.0000.0000.0000.000
176A183GLU-1-0.906-0.94829.117-0.044-0.0440.0000.0000.0000.000
177A184MET0-0.067-0.02131.9810.0120.0120.0000.0000.0000.000