FMO DATABASE

FMODB ID: 53VGZ

Calculation Name: 4GI3-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GI3

Chain ID: C

ChEMBL ID:

UniProt ID: P85064

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	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	53
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-300979.527884
FMO2-HF: Nuclear repulsion	276526.045245
FMO2-HF: Total energy	-24453.482638
FMO2-MP2: Total energy	-24517.283363

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(C:21:CYS)

Summations of interaction energy for fragment #1(C:21:CYS)

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.
-37.175	-28.684	9.512	-4.277	-13.727	-0.03

Interaction energy analysis for fragmet #1(C:21:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.100 / q_NPA : -0.054

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	C	23	SER	0	0.054	0.013	3.839	-0.787	0.627	-0.006	-0.558	-0.850	0.002
4	C	24	ILE	0	-0.087	-0.042	5.210	0.960	1.094	-0.002	-0.008	-0.124	0.000
5	C	25	CYS	0	-0.051	-0.009	8.131	-1.099	-1.099	0.000	0.000	0.000	0.000
6	C	26	PRO	0	0.007	0.001	10.385	0.269	0.269	0.000	0.000	0.000	0.000
7	C	27	LEU	0	0.019	0.014	14.199	-0.188	-0.188	0.000	0.000	0.000	0.000
8	C	28	ILE	0	-0.020	-0.004	15.602	0.166	0.166	0.000	0.000	0.000	0.000
9	C	29	TYR	0	0.019	0.009	16.375	-0.199	-0.199	0.000	0.000	0.000	0.000
10	C	30	ALA	0	-0.002	-0.009	16.236	0.173	0.173	0.000	0.000	0.000	0.000
11	C	31	PRO	0	-0.016	0.008	15.332	-0.161	-0.161	0.000	0.000	0.000	0.000
12	C	32	VAL	0	0.015	0.006	11.676	0.231	0.231	0.000	0.000	0.000	0.000
13	C	33	CYS	0	-0.069	0.003	13.247	-0.293	-0.293	0.000	0.000	0.000	0.000
14	C	34	VAL	0	-0.012	-0.014	8.468	-0.050	-0.050	0.000	0.000	0.000	0.000
15	C	35	GLU	-1	-0.834	-0.904	11.550	-0.610	-0.610	0.000	0.000	0.000	0.000
16	C	36	ASP	-1	-0.804	-0.917	9.057	-1.447	-1.447	0.000	0.000	0.000	0.000
17	C	37	SER	0	-0.013	-0.010	9.524	0.381	0.381	0.000	0.000	0.000	0.000
18	C	38	ASN	0	-0.124	-0.069	11.348	0.354	0.354	0.000	0.000	0.000	0.000
19	C	39	GLN	0	-0.094	-0.056	13.774	0.123	0.123	0.000	0.000	0.000	0.000
20	C	40	ASP	-1	-0.847	-0.877	13.486	-0.857	-0.857	0.000	0.000	0.000	0.000
21	C	41	PHE	0	-0.027	-0.023	13.509	-0.167	-0.167	0.000	0.000	0.000	0.000
22	C	42	TYR	0	-0.083	-0.068	10.941	-0.049	-0.049	0.000	0.000	0.000	0.000
23	C	43	LEU	0	0.023	0.005	12.459	-0.183	-0.183	0.000	0.000	0.000	0.000
24	C	44	PHE	0	0.034	0.018	7.376	-0.079	-0.079	0.000	0.000	0.000	0.000
25	C	45	VAL	0	0.021	-0.013	12.119	0.257	0.257	0.000	0.000	0.000	0.000
26	C	46	ASN	0	-0.034	-0.031	11.713	-0.070	-0.070	0.000	0.000	0.000	0.000
27	C	47	GLU	-1	-0.763	-0.875	9.933	-2.944	-2.944	0.000	0.000	0.000	0.000
28	C	49	GLU	-1	-0.773	-0.895	6.590	-6.224	-6.224	0.000	0.000	0.000	0.000
29	C	50	VAL	0	-0.030	0.012	5.588	-1.389	-1.389	0.000	0.000	0.000	0.000
30	C	51	ARG	1	0.853	0.902	3.891	-1.610	-0.979	0.018	-0.277	-0.373	-0.002
31	C	52	LYS	1	0.772	0.900	2.052	-8.493	-6.869	4.789	-2.581	-3.833	-0.032
32	C	53	CYS	0	-0.011	0.008	2.548	-4.161	-0.952	2.471	-2.414	-3.267	-0.021
35	C	57	ALA	0	-0.023	-0.011	3.552	-0.764	1.355	0.038	-0.606	-1.552	0.002
36	C	58	GLY	0	-0.012	0.011	2.520	-4.658	-2.719	2.051	-1.822	-2.167	0.020
37	C	59	PHE	0	-0.030	-0.013	2.939	-2.319	-4.642	0.137	3.244	-1.057	0.004
38	C	60	VAL	0	0.020	0.008	3.421	-3.299	-3.689	0.010	0.714	-0.333	-0.003
39	C	61	TYR	0	-0.020	-0.014	3.631	-0.555	-0.421	0.006	0.031	-0.171	0.000
40	C	62	THR	0	0.011	0.004	7.763	0.345	0.345	0.000	0.000	0.000	0.000
41	C	63	PHE	0	-0.012	-0.009	9.195	-0.252	-0.252	0.000	0.000	0.000	0.000
42	C	64	VAL	0	0.002	0.009	12.296	0.283	0.283	0.000	0.000	0.000	0.000
43	C	65	PRO	0	0.019	-0.001	15.739	-0.088	-0.088	0.000	0.000	0.000	0.000
44	C	66	ARG	1	0.914	0.954	18.131	1.104	1.104	0.000	0.000	0.000	0.000
45	C	67	GLU	-1	-0.896	-0.968	19.145	-0.849	-0.849	0.000	0.000	0.000	0.000
46	C	68	MET	0	-0.037	-0.005	17.638	0.095	0.095	0.000	0.000	0.000	0.000
47	C	70	LYS	1	0.973	0.985	18.307	1.042	1.042	0.000	0.000	0.000	0.000
48	C	71	ALA	0	0.011	-0.002	19.365	-0.088	-0.088	0.000	0.000	0.000	0.000
49	C	72	THR	0	-0.039	-0.019	20.125	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	73	THR	0	-0.005	0.000	15.635	-0.005	-0.005	0.000	0.000	0.000	0.000
51	C	74	SER	0	-0.051	-0.027	13.352	0.241	0.241	0.000	0.000	0.000	0.000
52	C	75	LEU	0	-0.014	-0.012	11.697	-0.226	-0.226	0.000	0.000	0.000	0.000
53	C	77	PRO	0	-0.014	0.014	7.659	0.965	0.965	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:21:CYS)