FMO DATABASE

FMODB ID: 1NLGZ

Calculation Name: 3C8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8P

Chain ID: A

ChEMBL ID:

UniProt ID: P83554

Base Structure: X-ray

Registration Date: 2023-09-23

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	43
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-201413.644022
FMO2-HF: Nuclear repulsion	182793.454079
FMO2-HF: Total energy	-18620.189942
FMO2-MP2: Total energy	-18669.298471

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)

Summations of interaction energy for fragment #1(A:1:LYS)

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.
13.537	17.703	37.25	-20.007	-21.41	-0.21

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.898

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	3	CYS	0	-0.028	0.005	1.839	-50.832	-49.987	14.473	-7.114	-8.205	-0.075
4	A	4	CYS	0	-0.100	-0.037	4.910	5.266	5.360	-0.002	-0.007	-0.085	0.000
5	A	5	PRO	0	0.050	0.037	8.417	-1.548	-1.548	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.031	0.009	11.527	0.579	0.579	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.044	0.005	11.669	-1.892	-1.892	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.043	0.027	13.094	-0.273	-0.273	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.062	0.044	12.623	0.431	0.431	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.822	0.859	4.451	40.174	40.271	-0.001	-0.005	-0.091	0.000
11	A	11	ASN	0	0.029	0.005	10.620	-0.861	-0.861	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.037	0.038	13.938	0.551	0.551	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.026	-0.022	6.585	-0.380	-0.380	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.004	-0.024	9.511	-0.988	-0.988	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.023	0.003	11.758	0.928	0.928	0.000	0.000	0.000	0.000
16	A	16	CYS	0	0.016	0.025	10.233	1.209	1.209	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.869	0.912	8.508	20.285	20.285	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.015	0.003	12.213	0.416	0.416	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.008	0.017	15.287	0.521	0.521	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.012	0.015	15.025	0.608	0.608	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.019	-0.003	14.527	0.163	0.163	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.010	-0.010	12.030	-1.355	-1.355	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.995	0.972	4.851	22.855	22.855	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.786	-0.878	8.808	-17.391	-17.391	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.073	0.039	10.673	-0.080	-0.080	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.044	-0.001	8.891	-0.552	-0.552	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.836	0.910	10.773	15.376	15.376	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.015	0.009	14.499	0.252	0.252	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.019	-0.026	11.739	-0.327	-0.327	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.033	0.025	13.474	-0.483	-0.483	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.884	0.945	7.712	25.838	25.838	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.021	-0.015	3.498	-4.671	-3.962	0.055	-0.309	-0.457	0.002
33	A	35	ILE	0	0.027	0.007	2.751	3.224	4.491	0.059	-0.422	-0.903	0.000
34	A	36	SER	0	0.026	0.021	1.968	-15.225	-15.838	7.487	-3.615	-3.259	-0.042
35	A	37	ALA	0	0.014	0.006	3.072	5.293	5.885	0.023	-0.181	-0.434	0.001
36	A	38	SER	0	0.073	0.038	2.767	-16.686	-13.261	1.655	-2.137	-2.942	-0.020
37	A	39	THR	0	0.033	0.032	1.764	-39.069	-41.584	13.500	-6.120	-4.865	-0.075
38	A	41	PRO	0	0.053	0.047	3.860	4.980	5.245	0.001	-0.097	-0.169	-0.001
39	A	42	SER	0	0.047	0.007	7.718	-1.199	-1.199	0.000	0.000	0.000	0.000
40	A	43	ASN	0	0.039	0.020	10.240	-0.743	-0.743	0.000	0.000	0.000	0.000
41	A	44	TYR	0	-0.028	-0.023	7.976	2.128	2.128	0.000	0.000	0.000	0.000
42	A	45	PRO	0	0.060	0.034	6.805	-6.129	-6.129	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.957	1.000	5.717	23.144	23.144	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)