FMO DATABASE

FMODB ID: YVJ22

Calculation Name: 4HJG-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HJG

Chain ID: E

ChEMBL ID:

UniProt ID: P0A015

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-327318.628561
FMO2-HF: Nuclear repulsion	303796.620968
FMO2-HF: Total energy	-23522.007592
FMO2-MP2: Total energy	-23591.345467

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(E:20:GLU)

Summations of interaction energy for fragment #1(E:20:GLU)

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.
23.256	31.526	7.622	-6.361	-9.529	0.006

Interaction energy analysis for fragmet #1(E:20:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.993 / q_NPA : -1.006

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	E	22	THR	0	-0.036	-0.024	2.690	8.525	10.958	1.112	-1.316	-2.229	-0.004
4	E	23	ILE	0	0.013	0.032	4.750	-4.359	-4.288	-0.001	-0.013	-0.057	0.000
5	E	24	LYS	1	0.862	0.919	8.175	-27.140	-27.140	0.000	0.000	0.000	0.000
6	E	25	VAL	0	0.024	0.000	10.926	-1.309	-1.309	0.000	0.000	0.000	0.000
7	E	26	ASN	0	-0.001	-0.002	14.086	0.468	0.468	0.000	0.000	0.000	0.000
8	E	27	LEU	0	-0.026	-0.006	16.458	-0.232	-0.232	0.000	0.000	0.000	0.000
9	E	28	ILE	0	0.023	0.001	19.772	-0.446	-0.446	0.000	0.000	0.000	0.000
10	E	29	PHE	0	0.002	-0.005	21.542	-0.190	-0.190	0.000	0.000	0.000	0.000
11	E	30	ALA	0	-0.003	-0.003	26.124	-0.243	-0.243	0.000	0.000	0.000	0.000
12	E	31	ASP	-1	-0.864	-0.921	29.205	10.593	10.593	0.000	0.000	0.000	0.000
13	E	32	GLY	0	-0.003	0.003	28.812	-0.226	-0.226	0.000	0.000	0.000	0.000
14	E	33	LYS	1	0.840	0.913	25.983	-10.504	-10.504	0.000	0.000	0.000	0.000
15	E	34	ILE	0	0.011	0.006	21.129	0.179	0.179	0.000	0.000	0.000	0.000
16	E	35	GLN	0	-0.046	-0.020	18.880	0.435	0.435	0.000	0.000	0.000	0.000
17	E	36	THR	0	0.010	0.005	15.127	-0.366	-0.366	0.000	0.000	0.000	0.000
18	E	37	ALA	0	-0.036	-0.012	12.744	0.032	0.032	0.000	0.000	0.000	0.000
19	E	38	GLU	-1	-0.821	-0.904	7.239	37.700	37.700	0.000	0.000	0.000	0.000
20	E	39	PHE	0	-0.018	0.002	7.849	-0.551	-0.551	0.000	0.000	0.000	0.000
21	E	40	LYS	1	0.837	0.903	2.533	-70.774	-66.916	1.977	-2.499	-3.335	0.037
22	E	41	GLY	0	0.058	0.041	2.002	-5.625	-5.234	2.179	-0.795	-1.775	-0.001
23	E	42	THR	0	-0.017	-0.044	2.507	-0.301	1.166	2.356	-1.734	-2.089	-0.026
24	E	43	PHE	0	0.017	0.010	4.446	0.308	0.358	-0.001	-0.004	-0.044	0.000
25	E	44	GLU	-1	-0.865	-0.934	6.981	24.916	24.916	0.000	0.000	0.000	0.000
26	E	45	GLU	-1	-0.851	-0.899	6.163	36.869	36.869	0.000	0.000	0.000	0.000
27	E	46	ALA	0	-0.008	0.002	5.558	-1.747	-1.747	0.000	0.000	0.000	0.000
28	E	47	THR	0	0.024	-0.010	7.561	-2.677	-2.677	0.000	0.000	0.000	0.000
29	E	48	ALA	0	-0.035	-0.017	11.103	-1.752	-1.752	0.000	0.000	0.000	0.000
30	E	49	GLU	-1	-0.799	-0.876	10.099	20.849	20.849	0.000	0.000	0.000	0.000
31	E	50	ALA	0	0.022	0.032	11.465	-1.326	-1.326	0.000	0.000	0.000	0.000
32	E	51	TYR	0	0.010	-0.007	13.001	-1.578	-1.578	0.000	0.000	0.000	0.000
33	E	52	ARG	1	0.762	0.854	14.331	-21.198	-21.198	0.000	0.000	0.000	0.000
34	E	53	TYR	0	-0.010	-0.012	14.904	-1.163	-1.163	0.000	0.000	0.000	0.000
35	E	54	ALA	0	0.028	0.021	16.816	-1.015	-1.015	0.000	0.000	0.000	0.000
36	E	55	ALA	0	0.019	0.000	19.109	-0.991	-0.991	0.000	0.000	0.000	0.000
37	E	56	LEU	0	-0.076	-0.039	19.302	-0.904	-0.904	0.000	0.000	0.000	0.000
38	E	57	LEU	0	0.019	0.008	19.441	-0.799	-0.799	0.000	0.000	0.000	0.000
39	E	58	ALA	0	0.056	0.027	22.616	-0.673	-0.673	0.000	0.000	0.000	0.000
40	E	59	LYS	1	0.832	0.931	23.858	-13.730	-13.730	0.000	0.000	0.000	0.000
41	E	60	VAL	0	-0.039	-0.012	26.665	-0.443	-0.443	0.000	0.000	0.000	0.000
42	E	61	ASN	0	-0.049	-0.033	24.826	-0.558	-0.558	0.000	0.000	0.000	0.000
43	E	62	GLY	0	0.022	0.024	27.768	-0.239	-0.239	0.000	0.000	0.000	0.000
44	E	63	GLU	-1	-0.953	-0.986	26.814	10.944	10.944	0.000	0.000	0.000	0.000
45	E	64	TYR	0	-0.010	-0.016	20.156	0.161	0.161	0.000	0.000	0.000	0.000
46	E	65	THR	0	-0.013	0.006	24.101	-0.174	-0.174	0.000	0.000	0.000	0.000
47	E	66	ALA	0	0.012	-0.025	18.600	0.402	0.402	0.000	0.000	0.000	0.000
48	E	67	ASP	-1	-0.871	-0.912	19.962	13.185	13.185	0.000	0.000	0.000	0.000
49	E	68	LEU	0	-0.021	-0.014	15.595	0.869	0.869	0.000	0.000	0.000	0.000
50	E	69	GLU	-1	-0.869	-0.937	16.355	14.420	14.420	0.000	0.000	0.000	0.000
51	E	70	ASP	-1	-0.896	-0.956	12.766	21.532	21.532	0.000	0.000	0.000	0.000
52	E	71	GLY	0	-0.015	-0.006	13.563	1.170	1.170	0.000	0.000	0.000	0.000
53	E	72	GLY	0	-0.004	-0.002	13.611	0.085	0.085	0.000	0.000	0.000	0.000
54	E	73	ASN	0	-0.048	-0.028	9.014	3.315	3.315	0.000	0.000	0.000	0.000
55	E	74	HIS	0	-0.032	-0.011	10.549	2.794	2.794	0.000	0.000	0.000	0.000
56	E	75	MET	0	0.001	0.011	12.498	-1.114	-1.114	0.000	0.000	0.000	0.000
57	E	76	ASN	0	-0.042	-0.031	15.755	0.389	0.389	0.000	0.000	0.000	0.000
58	E	77	ILE	0	0.026	0.012	16.262	-0.505	-0.505	0.000	0.000	0.000	0.000
59	E	78	LYS	1	0.893	0.959	20.303	-11.235	-11.235	0.000	0.000	0.000	0.000
60	E	79	PHE	0	0.010	0.004	20.564	-0.149	-0.149	0.000	0.000	0.000	0.000
61	E	80	ALA	0	-0.036	-0.014	25.976	-0.304	-0.304	0.000	0.000	0.000	0.000
62	E	81	GLY	0	-0.017	-0.010	29.657	-0.344	-0.344	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:20:GLU)