FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R5G98

Calculation Name: 3PC7-A-Xray372

Preferred Name: DNA ligase 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3PC7

Chain ID: A

ChEMBL ID: CHEMBL4295773

UniProt ID: P49916

Base Structure: X-ray

Registration Date: 2023-06-19

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 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 81
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -537187.758023
FMO2-HF: Nuclear repulsion 505012.631362
FMO2-HF: Total energy -32175.126661
FMO2-MP2: Total energy -32269.975605


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:842:SER)


Summations of interaction energy for fragment #1(A:842:SER)
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.
2.6734.353-0.007-0.724-0.950.003
Interaction energy analysis for fragmet #1(A:842:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.000
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].
3A844THR00.0320.0053.785-1.475-0.057-0.013-0.657-0.7480.003
4A845LYS10.8930.9373.1573.5693.8310.006-0.067-0.2020.000
5A846VAL00.0030.0118.3060.2270.2270.0000.0000.0000.000
6A847LEU0-0.039-0.01011.495-0.083-0.0830.0000.0000.0000.000
7A848LEU0-0.025-0.02412.690-0.003-0.0030.0000.0000.0000.000
8A849ASP-1-0.837-0.91415.829-0.352-0.3520.0000.0000.0000.000
9A850ILE0-0.126-0.04918.1610.0160.0160.0000.0000.0000.000
10A851PHE0-0.064-0.05821.1890.0260.0260.0000.0000.0000.000
11A852THR00.0690.02722.9810.0140.0140.0000.0000.0000.000
12A853GLY0-0.045-0.01825.1040.0090.0090.0000.0000.0000.000
13A854VAL0-0.090-0.03727.7040.0130.0130.0000.0000.0000.000
14A855ARG10.8440.91129.5990.1010.1010.0000.0000.0000.000
15A856LEU0-0.008-0.00930.3610.0080.0080.0000.0000.0000.000
16A857TYR0-0.027-0.02532.755-0.003-0.0030.0000.0000.0000.000
17A858LEU0-0.032-0.02029.7780.0010.0010.0000.0000.0000.000
18A859PRO00.0460.02333.8110.0010.0010.0000.0000.0000.000
19A860PRO00.0560.03035.091-0.002-0.0020.0000.0000.0000.000
20A861SER0-0.0080.00336.0470.0000.0000.0000.0000.0000.000
21A862THR0-0.074-0.04633.2110.0020.0020.0000.0000.0000.000
22A863PRO00.0490.01834.251-0.001-0.0010.0000.0000.0000.000
23A864ASP-1-0.778-0.87928.145-0.097-0.0970.0000.0000.0000.000
24A865PHE00.0450.03729.261-0.010-0.0100.0000.0000.0000.000
25A866SER0-0.012-0.00327.701-0.012-0.0120.0000.0000.0000.000
26A867ARG10.8530.87924.2690.0770.0770.0000.0000.0000.000
27A868LEU00.0320.02524.526-0.016-0.0160.0000.0000.0000.000
28A869ARG11.0011.00325.8570.1110.1110.0000.0000.0000.000
29A870ARG10.9140.96217.4480.1620.1620.0000.0000.0000.000
30A871TYR0-0.016-0.02918.182-0.014-0.0140.0000.0000.0000.000
31A872PHE0-0.0070.01221.624-0.023-0.0230.0000.0000.0000.000
32A873VAL00.0150.00522.466-0.009-0.0090.0000.0000.0000.000
33A874ALA0-0.058-0.02117.928-0.015-0.0150.0000.0000.0000.000
34A875PHE0-0.060-0.04415.613-0.036-0.0360.0000.0000.0000.000
35A876ASP-1-0.759-0.86420.148-0.235-0.2350.0000.0000.0000.000
36A877GLY0-0.0040.01222.5170.0150.0150.0000.0000.0000.000
37A878ASP-1-0.862-0.91725.819-0.132-0.1320.0000.0000.0000.000
38A879LEU0-0.054-0.03928.2190.0100.0100.0000.0000.0000.000
39A880VAL00.0190.01930.5830.0010.0010.0000.0000.0000.000
40A881GLN0-0.006-0.02133.2620.0060.0060.0000.0000.0000.000
41A882GLU-1-0.823-0.90036.492-0.061-0.0610.0000.0000.0000.000
42A883PHE0-0.032-0.02738.1410.0010.0010.0000.0000.0000.000
43A884ASP-1-0.818-0.89237.297-0.084-0.0840.0000.0000.0000.000
44A885MET00.0000.01338.674-0.002-0.0020.0000.0000.0000.000
45A886THR0-0.036-0.02539.750-0.001-0.0010.0000.0000.0000.000
46A887SER0-0.065-0.04038.189-0.001-0.0010.0000.0000.0000.000
47A888ALA0-0.051-0.00936.090-0.005-0.0050.0000.0000.0000.000
48A889THR00.0510.00733.1620.0030.0030.0000.0000.0000.000
49A890HIS0-0.0110.01431.3540.0040.0040.0000.0000.0000.000
50A891VAL00.018-0.00235.1310.0010.0010.0000.0000.0000.000
51A892LEU00.0030.02333.0080.0000.0000.0000.0000.0000.000
52A893GLY00.0030.00037.0720.0030.0030.0000.0000.0000.000
53A894SER0-0.024-0.04840.593-0.002-0.0020.0000.0000.0000.000
54A895ARG10.9160.95440.8340.0580.0580.0000.0000.0000.000
55A896ASP-1-0.874-0.90043.597-0.048-0.0480.0000.0000.0000.000
56A897LYS10.9010.94743.8000.0580.0580.0000.0000.0000.000
57A898ASN0-0.024-0.01740.1010.0010.0010.0000.0000.0000.000
58A899PRO00.0600.03142.529-0.003-0.0030.0000.0000.0000.000
59A900ALA0-0.0050.00541.6580.0000.0000.0000.0000.0000.000
60A901ALA00.0040.03338.228-0.003-0.0030.0000.0000.0000.000
61A902GLN0-0.019-0.02234.4240.0050.0050.0000.0000.0000.000
62A903GLN0-0.039-0.03536.314-0.002-0.0020.0000.0000.0000.000
63A904VAL0-0.014-0.00432.098-0.002-0.0020.0000.0000.0000.000
64A905SER0-0.012-0.04532.8850.0040.0040.0000.0000.0000.000
65A906PRO00.0690.02230.653-0.008-0.0080.0000.0000.0000.000
66A907GLU-1-0.846-0.90929.297-0.090-0.0900.0000.0000.0000.000
67A908TRP0-0.0010.00328.768-0.009-0.0090.0000.0000.0000.000
68A909ILE00.0490.03525.647-0.012-0.0120.0000.0000.0000.000
69A910TRP00.009-0.00822.433-0.022-0.0220.0000.0000.0000.000
70A911ALA0-0.051-0.03023.777-0.013-0.0130.0000.0000.0000.000
71A912CYS00.0220.02923.782-0.008-0.0080.0000.0000.0000.000
72A913ILE0-0.0210.00019.353-0.023-0.0230.0000.0000.0000.000
73A914ARG10.8960.95319.1840.0990.0990.0000.0000.0000.000
74A915LYS10.9180.96019.2940.1290.1290.0000.0000.0000.000
75A916ARG10.9150.96511.2230.6210.6210.0000.0000.0000.000
76A917ARG10.9630.98618.5400.2150.2150.0000.0000.0000.000
77A918LEU00.0650.03321.5760.0130.0130.0000.0000.0000.000
78A919VAL0-0.052-0.03525.0330.0030.0030.0000.0000.0000.000
79A920ALA00.0310.01527.3490.0020.0020.0000.0000.0000.000
80A921PRO00.0050.00231.118-0.002-0.0020.0000.0000.0000.000
81A922SER00.0020.00631.7940.0030.0030.0000.0000.0000.000