FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 226LR

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 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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1984659.700561
FMO2-HF: Nuclear repulsion 1912071.898491
FMO2-HF: Total energy -72587.80207
FMO2-MP2: Total energy -72798.844803


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.
-6.309-2.8371.661-1.779-3.353-0.012
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 : -0.006 / q_NPA : -0.015
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].
3A0HIS00.0250.0062.784-6.202-3.0011.663-1.768-3.095-0.012
4A1GLY00.0580.0335.169-0.159-0.029-0.001-0.005-0.1250.000
5A2SER0-0.005-0.0154.549-0.186-0.045-0.001-0.006-0.1330.000
6A3SER0-0.018-0.0056.288-0.132-0.1320.0000.0000.0000.000
7A4LEU0-0.0050.0118.126-0.149-0.1490.0000.0000.0000.000
8A5ILE0-0.037-0.01410.166-0.153-0.1530.0000.0000.0000.000
9A6SER0-0.050-0.05211.5560.0410.0410.0000.0000.0000.000
10A7LYS10.8340.8769.773-0.616-0.6160.0000.0000.0000.000
11A8THR0-0.035-0.01913.207-0.140-0.1400.0000.0000.0000.000
12A9ILE0-0.064-0.00415.209-0.024-0.0240.0000.0000.0000.000
13A10LYS10.9460.97916.5480.2590.2590.0000.0000.0000.000
14A11TYR00.0310.00113.0220.0610.0610.0000.0000.0000.000
15A12ASP-1-0.808-0.87315.010-0.783-0.7830.0000.0000.0000.000
16A13PRO00.0250.00611.8270.0870.0870.0000.0000.0000.000
17A14ALA0-0.036-0.00115.0790.0550.0550.0000.0000.0000.000
18A15LYS10.7470.85317.4660.5550.5550.0000.0000.0000.000
19A16ASP-1-0.841-0.92718.525-0.331-0.3310.0000.0000.0000.000
20A17LYS10.8200.88818.0670.1090.1090.0000.0000.0000.000
21A18LEU00.0260.01314.1630.0030.0030.0000.0000.0000.000
22A19ILE0-0.045-0.01918.2770.0210.0210.0000.0000.0000.000
23A20THR00.0260.00217.606-0.013-0.0130.0000.0000.0000.000
24A21LEU0-0.046-0.01020.3120.0190.0190.0000.0000.0000.000
25A22ALA00.0630.03423.8860.0030.0030.0000.0000.0000.000
26A23CYS00.0010.00825.745-0.009-0.0090.0000.0000.0000.000
27A24GLY00.0440.03528.896-0.012-0.0120.0000.0000.0000.000
28A25CYS0-0.042-0.02428.5470.0060.0060.0000.0000.0000.000
29A26PHE00.0970.03423.396-0.017-0.0170.0000.0000.0000.000
30A27TRP0-0.0160.00125.885-0.016-0.0160.0000.0000.0000.000
31A28GLY0-0.0070.00229.270-0.015-0.0150.0000.0000.0000.000
32A29THR00.001-0.02326.612-0.009-0.0090.0000.0000.0000.000
33A30GLU-1-0.841-0.94824.942-0.046-0.0460.0000.0000.0000.000
34A31HIS0-0.014-0.00428.061-0.021-0.0210.0000.0000.0000.000
35A32MET0-0.035-0.01131.626-0.012-0.0120.0000.0000.0000.000
36A33TYR00.028-0.00828.005-0.004-0.0040.0000.0000.0000.000
37A34ARG10.9490.97726.5630.0920.0920.0000.0000.0000.000
38A35LYS10.9120.97030.7570.0260.0260.0000.0000.0000.000
39A36TYR0-0.054-0.04633.634-0.004-0.0040.0000.0000.0000.000
40A37LEU0-0.004-0.00730.439-0.003-0.0030.0000.0000.0000.000
41A38ASN0-0.0250.00129.573-0.012-0.0120.0000.0000.0000.000
42A39ASP-1-0.886-0.93429.663-0.134-0.1340.0000.0000.0000.000
43A40ARG10.7140.82130.2980.0920.0920.0000.0000.0000.000
44A41ILE0-0.053-0.01325.245-0.002-0.0020.0000.0000.0000.000
45A42VAL0-0.060-0.02221.139-0.006-0.0060.0000.0000.0000.000
46A43ASP-1-0.803-0.89920.889-0.223-0.2230.0000.0000.0000.000
47A44CYS0-0.098-0.04021.7360.0120.0120.0000.0000.0000.000
48A45LYS10.8970.95118.7960.1470.1470.0000.0000.0000.000
49A46VAL00.0070.01520.7350.0250.0250.0000.0000.0000.000
50A47GLY00.0300.01019.105-0.002-0.0020.0000.0000.0000.000
51A48TYR0-0.041-0.01718.733-0.030-0.0300.0000.0000.0000.000
52A49ALA00.0210.00317.4700.0530.0530.0000.0000.0000.000
53A50ASN0-0.002-0.01217.1230.0020.0020.0000.0000.0000.000
54A51GLY00.1100.03117.4150.0270.0270.0000.0000.0000.000
55A52GLU-1-0.973-0.96615.9640.5900.5900.0000.0000.0000.000
56A53GLU-1-0.865-0.90119.4240.3180.3180.0000.0000.0000.000
57A63SER00.0590.03429.829-0.011-0.0110.0000.0000.0000.000
58A64TYR00.014-0.01829.7490.0160.0160.0000.0000.0000.000
59A65LYS10.9040.96030.420-0.172-0.1720.0000.0000.0000.000
60A66ARG10.8390.91921.789-0.466-0.4660.0000.0000.0000.000
61A67VAL00.0040.02224.228-0.036-0.0360.0000.0000.0000.000
62A68CYS0-0.088-0.00424.2710.0340.0340.0000.0000.0000.000
63A69GLY00.0760.03624.3770.0120.0120.0000.0000.0000.000
64A70GLY00.0290.01121.6970.0370.0370.0000.0000.0000.000
65A71ASP-1-0.793-0.90019.4060.5900.5900.0000.0000.0000.000
66A72THR0-0.036-0.03022.480-0.011-0.0110.0000.0000.0000.000
67A73ASP-1-0.796-0.86921.1490.4730.4730.0000.0000.0000.000
68A74PHE00.0020.01516.613-0.020-0.0200.0000.0000.0000.000
69A75ALA0-0.020-0.01721.876-0.038-0.0380.0000.0000.0000.000
70A76GLU-1-0.796-0.87622.2430.1630.1630.0000.0000.0000.000
71A77VAL0-0.046-0.02819.559-0.013-0.0130.0000.0000.0000.000
72A78LEU0-0.030-0.01222.576-0.008-0.0080.0000.0000.0000.000
73A79GLN0-0.0060.00014.718-0.055-0.0550.0000.0000.0000.000
74A80VAL00.001-0.01219.977-0.030-0.0300.0000.0000.0000.000
75A81SER00.0150.00118.781-0.004-0.0040.0000.0000.0000.000
76A82TYR00.041-0.00620.4240.0040.0040.0000.0000.0000.000
77A83ASN00.0840.03122.145-0.002-0.0020.0000.0000.0000.000
78A84PRO00.0070.00222.7400.0250.0250.0000.0000.0000.000
79A85LYS10.9140.96225.7850.2450.2450.0000.0000.0000.000
80A86VAL0-0.037-0.00227.8690.0080.0080.0000.0000.0000.000
81A87ILE0-0.0030.00427.2940.0180.0180.0000.0000.0000.000
82A88THR00.000-0.01327.471-0.006-0.0060.0000.0000.0000.000
83A89LEU00.0570.02223.5270.0060.0060.0000.0000.0000.000
84A90ARG10.9040.92126.7880.0350.0350.0000.0000.0000.000
85A91GLU-1-0.770-0.83830.280-0.075-0.0750.0000.0000.0000.000
86A92LEU00.0140.01525.0690.0080.0080.0000.0000.0000.000
87A93THR00.007-0.01427.9290.0170.0170.0000.0000.0000.000
88A94ASP-1-0.794-0.88629.5990.0000.0000.0000.0000.0000.000
89A95PHE0-0.060-0.02130.9560.0050.0050.0000.0000.0000.000
90A96PHE00.0830.03827.4730.0040.0040.0000.0000.0000.000
91A97PHE0-0.027-0.01831.1150.0100.0100.0000.0000.0000.000
92A98ARG10.7880.86633.9910.0100.0100.0000.0000.0000.000
93A99ILE0-0.038-0.00930.625-0.002-0.0020.0000.0000.0000.000
94A100HIS00.0060.03931.4130.0170.0170.0000.0000.0000.000
95A101ASP-1-0.744-0.83635.3680.0660.0660.0000.0000.0000.000
96A102PRO0-0.0060.01433.4600.0100.0100.0000.0000.0000.000
97A103THR0-0.041-0.04334.4940.0090.0090.0000.0000.0000.000
98A104THR0-0.004-0.01336.8330.0070.0070.0000.0000.0000.000
99A105SER0-0.060-0.03338.2930.0020.0020.0000.0000.0000.000
100A106ASN0-0.0090.01435.3860.0030.0030.0000.0000.0000.000
101A107SER00.027-0.01935.8170.0030.0030.0000.0000.0000.000
102A108GLN0-0.108-0.03237.8500.0130.0130.0000.0000.0000.000
103A109GLY00.0730.02038.122-0.007-0.0070.0000.0000.0000.000
104A110PRO0-0.094-0.03237.4570.0100.0100.0000.0000.0000.000
105A111ASP-1-0.847-0.90138.6600.1020.1020.0000.0000.0000.000
106A112LYS10.8140.88933.654-0.121-0.1210.0000.0000.0000.000
107A113GLY00.0310.02331.7640.0060.0060.0000.0000.0000.000
108A114THR00.021-0.01528.314-0.013-0.0130.0000.0000.0000.000
109A115GLN00.0510.03126.0020.0050.0050.0000.0000.0000.000
110A116TYR0-0.111-0.05627.060-0.007-0.0070.0000.0000.0000.000
111A117ARG10.7970.91523.651-0.295-0.2950.0000.0000.0000.000
112A118SER00.0220.00028.3040.0010.0010.0000.0000.0000.000
113A119GLY0-0.013-0.03525.7400.0140.0140.0000.0000.0000.000
114A120LEU0-0.044-0.01024.069-0.016-0.0160.0000.0000.0000.000
115A121PHE00.0220.00318.8260.0150.0150.0000.0000.0000.000
116A122ALA00.0050.00219.574-0.032-0.0320.0000.0000.0000.000
117A123HIS00.0600.03913.9330.0630.0630.0000.0000.0000.000
118A124SER0-0.006-0.03015.350-0.032-0.0320.0000.0000.0000.000
119A125ASP-1-0.824-0.91017.7140.1320.1320.0000.0000.0000.000
120A126ALA0-0.042-0.03120.1250.0050.0050.0000.0000.0000.000
121A127ASP-1-0.789-0.85619.889-0.071-0.0710.0000.0000.0000.000
122A128LEU00.0200.01921.2080.0030.0030.0000.0000.0000.000
123A129LYS10.9620.98623.187-0.026-0.0260.0000.0000.0000.000
124A130GLU-1-0.924-0.97425.808-0.043-0.0430.0000.0000.0000.000
125A131LEU00.018-0.00423.1300.0000.0000.0000.0000.0000.000
126A132ALA00.0030.00427.2230.0020.0020.0000.0000.0000.000
127A133LYS10.8190.91229.167-0.004-0.0040.0000.0000.0000.000
128A134ILE0-0.033-0.00628.664-0.003-0.0030.0000.0000.0000.000
129A135LYS10.8910.93830.850-0.111-0.1110.0000.0000.0000.000
130A136GLU-1-0.870-0.94732.5720.0650.0650.0000.0000.0000.000
131A137GLU-1-0.782-0.86134.566-0.003-0.0030.0000.0000.0000.000
132A138TRP0-0.012-0.02234.740-0.002-0.0020.0000.0000.0000.000
133A139GLN0-0.0050.00136.3610.0010.0010.0000.0000.0000.000
134A140PRO00.0220.02538.5680.0010.0010.0000.0000.0000.000
135A141LYS10.8180.91639.786-0.015-0.0150.0000.0000.0000.000
136A142TRP0-0.015-0.00136.8700.0000.0000.0000.0000.0000.000
137A143GLY00.0170.00840.6480.0060.0060.0000.0000.0000.000
138A144ASN0-0.077-0.05940.0520.0020.0020.0000.0000.0000.000
139A145LYS10.9550.98439.377-0.064-0.0640.0000.0000.0000.000
140A146ILE0-0.0150.00933.2700.0060.0060.0000.0000.0000.000
141A147ALA0-0.012-0.02433.7750.0050.0050.0000.0000.0000.000
142A148THR0-0.046-0.02428.2720.0090.0090.0000.0000.0000.000
143A149VAL00.0010.01625.408-0.005-0.0050.0000.0000.0000.000
144A150ILE0-0.018-0.01124.574-0.006-0.0060.0000.0000.0000.000
145A151GLH0-0.066-0.07221.1770.0120.0120.0000.0000.0000.000
146A152PRO00.0420.02817.467-0.037-0.0370.0000.0000.0000.000
147A153ILE0-0.033-0.01013.9530.0450.0450.0000.0000.0000.000
148A154LYS10.7910.90514.117-0.574-0.5740.0000.0000.0000.000
149A155ASN0-0.039-0.03411.9280.1490.1490.0000.0000.0000.000
150A156PHE00.0160.00612.662-0.165-0.1650.0000.0000.0000.000
151A157TYR0-0.0070.00612.4230.1630.1630.0000.0000.0000.000
152A158ASP-1-0.697-0.82214.9280.0150.0150.0000.0000.0000.000
153A159ALA00.0130.01217.3350.0530.0530.0000.0000.0000.000
154A160GLU-1-0.925-0.98119.8140.0800.0800.0000.0000.0000.000
155A161GLU-1-0.789-0.88112.6240.5590.5590.0000.0000.0000.000
156A162TYR0-0.011-0.02617.4950.0790.0790.0000.0000.0000.000
157A163HIS10.8500.91718.652-0.178-0.1780.0000.0000.0000.000
158A164GLN0-0.005-0.00718.8440.0140.0140.0000.0000.0000.000
159A165LEU0-0.0090.02114.9460.0100.0100.0000.0000.0000.000
160A166TYR0-0.046-0.03417.8090.0500.0500.0000.0000.0000.000
161A167LEU0-0.071-0.04321.540-0.032-0.0320.0000.0000.0000.000
162A168ASP-1-0.760-0.84521.7770.3000.3000.0000.0000.0000.000
163A169LYS10.7890.87923.780-0.330-0.3300.0000.0000.0000.000
164A170ASN0-0.068-0.03626.929-0.037-0.0370.0000.0000.0000.000
165A171PRO00.1030.05928.1310.0000.0000.0000.0000.0000.000
166A172GLN00.0520.00929.109-0.012-0.0120.0000.0000.0000.000
167A173GLY00.0280.02929.252-0.009-0.0090.0000.0000.0000.000
168A174TYR0-0.010-0.01630.103-0.009-0.0090.0000.0000.0000.000
169A175ALA0-0.011-0.01431.1870.0160.0160.0000.0000.0000.000
170A177PRO0-0.011-0.01029.440-0.012-0.0120.0000.0000.0000.000
171A178THR0-0.003-0.00526.143-0.005-0.0050.0000.0000.0000.000
172A179HIS00.0210.01729.353-0.002-0.0020.0000.0000.0000.000
173A180TYR00.003-0.02327.3670.0080.0080.0000.0000.0000.000
174A181LEU00.0180.01429.3540.0050.0050.0000.0000.0000.000
175A182ARG10.7910.90129.767-0.117-0.1170.0000.0000.0000.000
176A183GLU-1-0.902-0.94629.2810.0240.0240.0000.0000.0000.000
177A184MET0-0.059-0.02131.9710.0120.0120.0000.0000.0000.000