Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 669GZ

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:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1989555.796583
FMO2-HF: Nuclear repulsion 1916967.70973
FMO2-HF: Total energy -72588.086853
FMO2-MP2: Total energy -72799.113183


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.
-5.395-1.7162.562-2.131-4.11-0.013
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 : 0.005 / q_NPA : -0.010
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].
3A0HIS0-0.0080.0002.693-5.468-2.0622.564-2.120-3.850-0.013
4A1GLY00.0570.0314.839-0.1280.025-0.001-0.008-0.1440.000
5A2SER00.004-0.0144.683-0.0550.065-0.001-0.003-0.1160.000
6A3SER0-0.023-0.0036.409-0.069-0.0690.0000.0000.0000.000
7A4LEU0-0.0040.0148.053-0.123-0.1230.0000.0000.0000.000
8A5ILE0-0.037-0.0279.971-0.206-0.2060.0000.0000.0000.000
9A6SER0-0.036-0.03611.5960.0790.0790.0000.0000.0000.000
10A7LYS10.8180.8609.556-1.031-1.0310.0000.0000.0000.000
11A8THR0-0.030-0.01913.033-0.132-0.1320.0000.0000.0000.000
12A9ILE0-0.071-0.00915.160-0.034-0.0340.0000.0000.0000.000
13A10LYS10.8810.93316.2060.1860.1860.0000.0000.0000.000
14A11TYR0-0.002-0.01613.1730.0540.0540.0000.0000.0000.000
15A12ASP-1-0.784-0.88315.044-0.744-0.7440.0000.0000.0000.000
16A13PRO00.0180.01011.8650.0790.0790.0000.0000.0000.000
17A14ALA0-0.0310.00015.0910.0330.0330.0000.0000.0000.000
18A15LYS10.7050.82717.2400.5070.5070.0000.0000.0000.000
19A16ASP-1-0.796-0.87918.627-0.296-0.2960.0000.0000.0000.000
20A17LYS10.8230.90017.9520.0780.0780.0000.0000.0000.000
21A18LEU00.0420.02414.1730.0000.0000.0000.0000.0000.000
22A19ILE0-0.047-0.02318.2530.0130.0130.0000.0000.0000.000
23A20THR00.0380.00917.530-0.004-0.0040.0000.0000.0000.000
24A21LEU0-0.042-0.00520.1840.0090.0090.0000.0000.0000.000
25A22ALA00.0640.03323.7240.0040.0040.0000.0000.0000.000
26A23CYS00.0040.01225.795-0.010-0.0100.0000.0000.0000.000
27A24GLY00.0210.01528.923-0.012-0.0120.0000.0000.0000.000
28A25CYS0-0.015-0.00728.5090.0110.0110.0000.0000.0000.000
29A26PHE00.0700.03023.322-0.022-0.0220.0000.0000.0000.000
30A27TRP0-0.005-0.01125.727-0.019-0.0190.0000.0000.0000.000
31A28GLY0-0.0050.00429.098-0.017-0.0170.0000.0000.0000.000
32A29THR0-0.006-0.03026.561-0.009-0.0090.0000.0000.0000.000
33A30GLU-1-0.815-0.92324.5030.0160.0160.0000.0000.0000.000
34A31HIS0-0.0080.00227.938-0.022-0.0220.0000.0000.0000.000
35A32MET0-0.018-0.00331.662-0.015-0.0150.0000.0000.0000.000
36A33TYR00.016-0.02127.959-0.006-0.0060.0000.0000.0000.000
37A34ARG10.9010.93826.4930.0410.0410.0000.0000.0000.000
38A35LYS10.8980.96630.540-0.002-0.0020.0000.0000.0000.000
39A36TYR0-0.053-0.04033.310-0.005-0.0050.0000.0000.0000.000
40A37LEU0-0.003-0.00530.161-0.004-0.0040.0000.0000.0000.000
41A38ASN0-0.008-0.00629.069-0.010-0.0100.0000.0000.0000.000
42A39ASP-1-0.874-0.92329.241-0.104-0.1040.0000.0000.0000.000
43A40ARG10.7220.83130.2000.0730.0730.0000.0000.0000.000
44A41ILE0-0.052-0.01025.003-0.002-0.0020.0000.0000.0000.000
45A42VAL0-0.053-0.01821.235-0.008-0.0080.0000.0000.0000.000
46A43ASP-1-0.778-0.88420.733-0.160-0.1600.0000.0000.0000.000
47A44CYS0-0.089-0.04221.6990.0070.0070.0000.0000.0000.000
48A45LYS10.8790.94518.6830.0640.0640.0000.0000.0000.000
49A46VAL00.0190.02120.6790.0250.0250.0000.0000.0000.000
50A47GLY00.0110.00118.9330.0060.0060.0000.0000.0000.000
51A48TYR0-0.037-0.02218.533-0.039-0.0390.0000.0000.0000.000
52A49ALA00.0210.00617.3190.0660.0660.0000.0000.0000.000
53A50ASN00.016-0.00417.136-0.006-0.0060.0000.0000.0000.000
54A51GLY00.1130.02017.5500.0250.0250.0000.0000.0000.000
55A52GLU-1-0.962-0.97216.5410.6000.6000.0000.0000.0000.000
56A53GLU-1-0.876-0.90219.6340.3670.3670.0000.0000.0000.000
57A63SER00.0650.04029.414-0.012-0.0120.0000.0000.0000.000
58A64TYR00.018-0.00929.4460.0200.0200.0000.0000.0000.000
59A65LYS10.9040.95130.416-0.205-0.2050.0000.0000.0000.000
60A66ARG10.8310.90021.837-0.532-0.5320.0000.0000.0000.000
61A67VAL00.0010.02523.963-0.036-0.0360.0000.0000.0000.000
62A68CYS0-0.0640.00424.1050.0390.0390.0000.0000.0000.000
63A69GLY00.0640.04124.3290.0150.0150.0000.0000.0000.000
64A70GLY00.0380.01821.4800.0400.0400.0000.0000.0000.000
65A71ASP-1-0.796-0.88619.7630.6490.6490.0000.0000.0000.000
66A72THR0-0.062-0.04622.608-0.011-0.0110.0000.0000.0000.000
67A73ASP-1-0.788-0.87521.0750.5330.5330.0000.0000.0000.000
68A74PHE00.0140.02516.598-0.022-0.0220.0000.0000.0000.000
69A75ALA0-0.026-0.01321.733-0.045-0.0450.0000.0000.0000.000
70A76GLU-1-0.790-0.85122.1080.2250.2250.0000.0000.0000.000
71A77VAL0-0.051-0.02619.447-0.019-0.0190.0000.0000.0000.000
72A78LEU0-0.033-0.01022.402-0.005-0.0050.0000.0000.0000.000
73A79GLN00.0110.00914.703-0.041-0.0410.0000.0000.0000.000
74A80VAL0-0.004-0.01519.973-0.028-0.0280.0000.0000.0000.000
75A81SER00.014-0.00118.865-0.007-0.0070.0000.0000.0000.000
76A82TYR00.0520.00220.305-0.003-0.0030.0000.0000.0000.000
77A83ASN00.0700.02421.999-0.004-0.0040.0000.0000.0000.000
78A84PRO0-0.004-0.00722.5610.0240.0240.0000.0000.0000.000
79A85LYS10.9090.96325.5940.2370.2370.0000.0000.0000.000
80A86VAL0-0.0230.00527.8770.0050.0050.0000.0000.0000.000
81A87ILE0-0.0080.00227.0450.0180.0180.0000.0000.0000.000
82A88THR0-0.001-0.01927.155-0.006-0.0060.0000.0000.0000.000
83A89LEU00.0310.01323.3500.0070.0070.0000.0000.0000.000
84A90ARG10.9120.92826.5580.0250.0250.0000.0000.0000.000
85A91GLU-1-0.764-0.83230.133-0.056-0.0560.0000.0000.0000.000
86A92LEU00.0200.01524.8200.0100.0100.0000.0000.0000.000
87A93THR00.017-0.00627.8180.0200.0200.0000.0000.0000.000
88A94ASP-1-0.796-0.87929.5660.0160.0160.0000.0000.0000.000
89A95PHE0-0.051-0.01930.8270.0030.0030.0000.0000.0000.000
90A96PHE00.0560.03027.4020.0030.0030.0000.0000.0000.000
91A97PHE0-0.034-0.02431.0490.0100.0100.0000.0000.0000.000
92A98ARG10.8020.86234.098-0.013-0.0130.0000.0000.0000.000
93A99ILE0-0.045-0.01030.263-0.001-0.0010.0000.0000.0000.000
94A100HIS00.0100.02931.4460.0190.0190.0000.0000.0000.000
95A101ASP-1-0.736-0.80935.4240.0880.0880.0000.0000.0000.000
96A102PRO0-0.0070.01433.4950.0110.0110.0000.0000.0000.000
97A103THR0-0.062-0.06134.2920.0080.0080.0000.0000.0000.000
98A104THR00.011-0.00836.8290.0030.0030.0000.0000.0000.000
99A105SER0-0.063-0.04338.4040.0020.0020.0000.0000.0000.000
100A106ASN0-0.038-0.00334.8700.0040.0040.0000.0000.0000.000
101A107SER0-0.012-0.04335.2760.0060.0060.0000.0000.0000.000
102A108GLN0-0.070-0.02137.1070.0170.0170.0000.0000.0000.000
103A109GLY00.1030.02838.252-0.008-0.0080.0000.0000.0000.000
104A110PRO0-0.119-0.03637.3230.0110.0110.0000.0000.0000.000
105A111ASP-1-0.848-0.90438.6790.1280.1280.0000.0000.0000.000
106A112LYS10.8000.88432.936-0.155-0.1550.0000.0000.0000.000
107A113GLY00.0110.01231.5590.0050.0050.0000.0000.0000.000
108A114THR00.018-0.01128.014-0.015-0.0150.0000.0000.0000.000
109A115GLN00.0340.02725.7340.0080.0080.0000.0000.0000.000
110A116TYR0-0.070-0.05026.870-0.005-0.0050.0000.0000.0000.000
111A117ARG10.7740.88423.530-0.352-0.3520.0000.0000.0000.000
112A118SER00.0280.01228.2430.0030.0030.0000.0000.0000.000
113A119GLY0-0.012-0.02725.5690.0130.0130.0000.0000.0000.000
114A120LEU0-0.036-0.00924.067-0.014-0.0140.0000.0000.0000.000
115A121PHE00.0170.00218.7900.0080.0080.0000.0000.0000.000
116A122ALA00.0240.00619.293-0.026-0.0260.0000.0000.0000.000
117A123HIS00.0470.03314.0750.0710.0710.0000.0000.0000.000
118A124SER00.000-0.02215.418-0.041-0.0410.0000.0000.0000.000
119A125ASP-1-0.818-0.91517.6890.1280.1280.0000.0000.0000.000
120A126ALA0-0.041-0.02220.4010.0010.0010.0000.0000.0000.000
121A127ASP-1-0.814-0.87519.451-0.041-0.0410.0000.0000.0000.000
122A128LEU00.0100.01321.3790.0020.0020.0000.0000.0000.000
123A129LYS10.9740.99023.239-0.025-0.0250.0000.0000.0000.000
124A130GLU-1-0.846-0.92625.731-0.016-0.0160.0000.0000.0000.000
125A131LEU00.0280.00823.1300.0000.0000.0000.0000.0000.000
126A132ALA00.0000.00327.1510.0030.0030.0000.0000.0000.000
127A133LYS10.7410.86628.953-0.015-0.0150.0000.0000.0000.000
128A134ILE0-0.031-0.01328.605-0.002-0.0020.0000.0000.0000.000
129A135LYS10.8730.93030.941-0.134-0.1340.0000.0000.0000.000
130A136GLU-1-0.837-0.91732.6600.0820.0820.0000.0000.0000.000
131A137GLU-1-0.805-0.87534.0530.0060.0060.0000.0000.0000.000
132A138TRP0-0.015-0.02335.044-0.002-0.0020.0000.0000.0000.000
133A139GLN0-0.028-0.01536.1780.0040.0040.0000.0000.0000.000
134A140PRO00.0170.01338.3620.0010.0010.0000.0000.0000.000
135A141LYS10.8160.91739.415-0.031-0.0310.0000.0000.0000.000
136A142TRP00.0130.00936.9500.0010.0010.0000.0000.0000.000
137A143GLY00.0170.01340.5560.0060.0060.0000.0000.0000.000
138A144ASN0-0.064-0.04439.8730.0010.0010.0000.0000.0000.000
139A145LYS10.9250.96439.004-0.076-0.0760.0000.0000.0000.000
140A146ILE00.0050.01532.9410.0070.0070.0000.0000.0000.000
141A147ALA00.003-0.00833.6150.0060.0060.0000.0000.0000.000
142A148THR0-0.046-0.03228.1870.0100.0100.0000.0000.0000.000
143A149VAL00.0100.02225.202-0.007-0.0070.0000.0000.0000.000
144A150ILE0-0.019-0.01924.812-0.008-0.0080.0000.0000.0000.000
145A151GLH0-0.049-0.05020.9420.0120.0120.0000.0000.0000.000
146A152PRO00.0480.02717.171-0.036-0.0360.0000.0000.0000.000
147A153ILE0-0.037-0.01213.8520.0420.0420.0000.0000.0000.000
148A154LYS10.7930.91514.255-0.595-0.5950.0000.0000.0000.000
149A155ASN0-0.029-0.02611.7830.1460.1460.0000.0000.0000.000
150A156PHE00.0010.00212.411-0.200-0.2000.0000.0000.0000.000
151A157TYR0-0.0050.00512.2320.2190.2190.0000.0000.0000.000
152A158ASP-1-0.690-0.82114.6770.1730.1730.0000.0000.0000.000
153A159ALA00.0060.00917.1960.0530.0530.0000.0000.0000.000
154A160GLU-1-0.891-0.95919.8200.1820.1820.0000.0000.0000.000
155A161GLU-1-0.809-0.87612.8010.8460.8460.0000.0000.0000.000
156A162TYR0-0.007-0.02617.5430.0720.0720.0000.0000.0000.000
157A163HIS10.8700.92118.687-0.275-0.2750.0000.0000.0000.000
158A164GLN0-0.024-0.01718.511-0.004-0.0040.0000.0000.0000.000
159A165LEU0-0.0310.00414.8250.0110.0110.0000.0000.0000.000
160A166TYR0-0.030-0.02217.9290.0490.0490.0000.0000.0000.000
161A167LEU0-0.051-0.03921.500-0.043-0.0430.0000.0000.0000.000
162A168ASP-1-0.765-0.84621.9670.3870.3870.0000.0000.0000.000
163A169LYS10.7730.87123.878-0.425-0.4250.0000.0000.0000.000
164A170ASN0-0.060-0.03627.039-0.041-0.0410.0000.0000.0000.000
165A171PRO00.1090.06427.6880.0000.0000.0000.0000.0000.000
166A172GLN00.045-0.00528.701-0.010-0.0100.0000.0000.0000.000
167A173GLY00.0300.03129.031-0.012-0.0120.0000.0000.0000.000
168A174TYR00.003-0.01129.924-0.011-0.0110.0000.0000.0000.000
169A175ALA0-0.013-0.01630.8940.0190.0190.0000.0000.0000.000
170A177PRO0-0.007-0.00829.618-0.013-0.0130.0000.0000.0000.000
171A178THR0-0.003-0.01225.851-0.005-0.0050.0000.0000.0000.000
172A179HIS00.0220.01129.0780.0010.0010.0000.0000.0000.000
173A180TYR0-0.018-0.02426.9720.0090.0090.0000.0000.0000.000
174A181LEU00.0280.02628.9360.0030.0030.0000.0000.0000.000
175A182ARG10.7850.89329.375-0.164-0.1640.0000.0000.0000.000
176A183GLU-1-0.888-0.94828.8710.0830.0830.0000.0000.0000.000
177A184MET0-0.066-0.00531.7000.0080.0080.0000.0000.0000.000