FMO DATABASE

FMODB ID: QVJ9Y

Calculation Name: 4EMH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMH

Chain ID: A

ChEMBL ID:

UniProt ID: O14352

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	OptH
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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-357261.896924
FMO2-HF: Nuclear repulsion	331852.026245
FMO2-HF: Total energy	-25409.870679
FMO2-MP2: Total energy	-25482.06165

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
1.102	-1.366	12.71	-6.416	-3.827	0.009

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : -0.020

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	14	PRO	0	-0.014	0.013	3.095	-0.761	0.633	0.061	-0.685	-0.770	0.003
4	A	15	ILE	0	-0.009	0.007	3.604	-1.025	-0.548	0.021	-0.227	-0.272	-0.001
5	A	16	LEU	0	0.007	0.009	5.643	0.452	0.452	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.006	-0.015	9.060	-0.033	-0.033	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.832	-0.911	11.556	-0.260	-0.260	0.000	0.000	0.000	0.000
8	A	19	LEU	0	0.000	-0.001	14.873	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	20	LYS	1	0.883	0.921	17.835	0.292	0.292	0.000	0.000	0.000	0.000
10	A	21	ASN	0	-0.035	-0.012	20.995	0.006	0.006	0.000	0.000	0.000	0.000
11	A	22	GLY	0	0.034	0.017	20.752	0.019	0.019	0.000	0.000	0.000	0.000
12	A	23	GLU	-1	-0.829	-0.891	19.146	-0.271	-0.271	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.028	-0.016	14.108	-0.043	-0.043	0.000	0.000	0.000	0.000
14	A	25	PHE	0	0.002	-0.010	13.540	0.047	0.047	0.000	0.000	0.000	0.000
15	A	26	ASN	0	-0.020	-0.008	9.599	-0.241	-0.241	0.000	0.000	0.000	0.000
16	A	27	GLY	0	0.103	0.051	9.230	0.186	0.186	0.000	0.000	0.000	0.000
17	A	28	HIS	0	-0.078	-0.028	7.425	-0.411	-0.411	0.000	0.000	0.000	0.000
18	A	29	LEU	0	-0.007	-0.017	5.907	0.316	0.316	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.943	-0.986	8.105	-0.157	-0.157	0.000	0.000	0.000	0.000
20	A	31	ASN	0	-0.001	-0.019	11.145	0.154	0.154	0.000	0.000	0.000	0.000
21	A	32	CYS	0	0.003	0.003	9.889	-0.153	-0.153	0.000	0.000	0.000	0.000
22	A	33	ASP	-1	-0.744	-0.825	11.875	-0.268	-0.268	0.000	0.000	0.000	0.000
23	A	34	ASN	0	0.020	-0.015	14.000	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	35	TYR	0	-0.069	-0.025	15.960	0.026	0.026	0.000	0.000	0.000	0.000
25	A	36	MET	0	-0.017	-0.016	9.787	0.008	0.008	0.000	0.000	0.000	0.000
26	A	37	ASN	0	-0.106	-0.062	14.239	-0.031	-0.031	0.000	0.000	0.000	0.000
27	A	38	LEU	0	0.004	-0.002	10.410	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	39	THR	0	-0.004	0.000	12.790	0.094	0.094	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.013	-0.002	9.212	-0.155	-0.155	0.000	0.000	0.000	0.000
30	A	41	ARG	1	0.969	0.977	11.552	0.426	0.426	0.000	0.000	0.000	0.000
31	A	42	GLU	-1	-0.945	-0.975	12.202	-0.330	-0.330	0.000	0.000	0.000	0.000
32	A	43	VAL	0	-0.038	-0.021	13.113	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	44	ILE	0	-0.040	-0.024	13.680	0.083	0.083	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.858	0.922	14.926	0.202	0.202	0.000	0.000	0.000	0.000
35	A	46	THR	0	-0.050	-0.025	16.666	0.050	0.050	0.000	0.000	0.000	0.000
36	A	47	MET	0	0.028	0.011	18.918	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	48	PRO	0	0.000	-0.018	21.979	0.001	0.001	0.000	0.000	0.000	0.000
38	A	49	ASP	-1	-0.914	-0.959	23.348	-0.146	-0.146	0.000	0.000	0.000	0.000
39	A	50	GLY	0	-0.012	0.008	22.833	0.012	0.012	0.000	0.000	0.000	0.000
40	A	51	ASP	-1	-0.894	-0.924	23.106	-0.139	-0.139	0.000	0.000	0.000	0.000
41	A	52	LYS	1	0.890	0.924	17.320	0.200	0.200	0.000	0.000	0.000	0.000
42	A	53	PHE	0	-0.017	0.007	20.231	0.021	0.021	0.000	0.000	0.000	0.000
43	A	54	PHE	0	0.004	-0.019	17.718	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	55	ARG	1	0.952	0.975	17.461	0.162	0.162	0.000	0.000	0.000	0.000
45	A	56	LEU	0	0.011	0.018	17.586	0.026	0.026	0.000	0.000	0.000	0.000
46	A	57	PRO	0	0.030	0.026	16.989	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.916	-0.983	16.248	-0.322	-0.322	0.000	0.000	0.000	0.000
48	A	59	CYS	0	-0.058	-0.005	15.536	0.047	0.047	0.000	0.000	0.000	0.000
49	A	60	TYR	0	0.058	0.039	15.472	-0.054	-0.054	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.001	-0.007	13.728	0.040	0.040	0.000	0.000	0.000	0.000
51	A	62	ARG	1	0.919	0.957	16.459	0.235	0.235	0.000	0.000	0.000	0.000
52	A	63	GLY	0	0.125	0.066	16.380	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	64	ASN	0	-0.015	-0.022	17.364	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	65	ASN	0	-0.043	-0.022	19.414	0.043	0.043	0.000	0.000	0.000	0.000
55	A	66	ILE	0	-0.001	0.017	13.270	0.002	0.002	0.000	0.000	0.000	0.000
56	A	67	LYS	1	0.895	0.961	16.577	0.306	0.306	0.000	0.000	0.000	0.000
57	A	68	TYR	0	-0.069	-0.059	12.171	0.007	0.007	0.000	0.000	0.000	0.000
58	A	69	LEU	0	0.044	0.035	6.671	0.005	0.005	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.889	0.947	8.163	0.526	0.526	0.000	0.000	0.000	0.000
60	A	71	ILE	0	0.037	0.046	1.883	2.186	-2.153	12.628	-5.504	-2.785	0.007

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)