FMO DATABASE

FMODB ID: 945Z2

Calculation Name: 5HOD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HOD

Chain ID: A

ChEMBL ID:

UniProt ID: Q969G2

Base Structure: X-ray

Registration Date: 2023-09-20

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-350096.739635
FMO2-HF: Nuclear repulsion	325417.332267
FMO2-HF: Total energy	-24679.407369
FMO2-MP2: Total energy	-24752.666101

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:84:GLY)

Summations of interaction energy for fragment #1(A:84: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.
-4.804	-2.904	-0.026	-1.012	-0.861	-0.002

Interaction energy analysis for fragmet #1(A:84:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : -0.004

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	86	LYS	1	0.989	0.999	3.797	0.860	2.760	-0.026	-1.012	-0.861	-0.002
4	A	87	ARG	1	0.955	0.971	4.816	-3.098	-3.098	0.000	0.000	0.000	0.000
5	A	88	PRO	0	0.048	0.048	7.511	0.104	0.104	0.000	0.000	0.000	0.000
6	A	89	ARG	1	0.961	0.968	11.084	-0.220	-0.220	0.000	0.000	0.000	0.000
7	A	90	THR	0	0.057	0.038	14.254	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	91	THR	0	-0.064	-0.030	16.629	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	92	ILE	0	0.035	0.013	19.922	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	93	THR	0	0.061	0.032	22.158	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	94	ALA	0	0.064	0.006	25.834	0.010	0.010	0.000	0.000	0.000	0.000
12	A	95	LYS	1	1.069	1.038	28.439	-0.059	-0.059	0.000	0.000	0.000	0.000
13	A	96	GLN	0	0.031	0.014	22.165	0.013	0.013	0.000	0.000	0.000	0.000
14	A	97	LEU	0	-0.062	-0.026	24.867	0.014	0.014	0.000	0.000	0.000	0.000
15	A	98	GLU	-1	-0.924	-0.966	26.193	0.109	0.109	0.000	0.000	0.000	0.000
16	A	99	THR	0	0.020	0.016	27.169	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	100	LEU	0	-0.015	-0.008	22.033	0.007	0.007	0.000	0.000	0.000	0.000
18	A	101	LYS	1	0.931	0.944	26.252	-0.124	-0.124	0.000	0.000	0.000	0.000
19	A	102	ASN	0	-0.057	-0.032	28.798	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	103	ALA	0	0.022	0.013	27.211	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	104	TYR	0	-0.106	-0.047	25.909	0.018	0.018	0.000	0.000	0.000	0.000
22	A	105	LYS	1	0.983	0.992	28.474	-0.103	-0.103	0.000	0.000	0.000	0.000
23	A	106	ASN	0	0.058	0.049	31.005	0.004	0.004	0.000	0.000	0.000	0.000
24	A	107	SER	0	-0.016	-0.018	28.743	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	108	PRO	0	0.102	0.054	27.347	0.013	0.013	0.000	0.000	0.000	0.000
26	A	109	LYS	1	0.880	0.924	23.620	-0.234	-0.234	0.000	0.000	0.000	0.000
27	A	110	PRO	0	0.049	0.060	23.131	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	111	ALA	0	0.060	0.020	23.512	0.030	0.030	0.000	0.000	0.000	0.000
29	A	112	ARG	1	0.934	0.957	17.531	-0.252	-0.252	0.000	0.000	0.000	0.000
30	A	113	HIS	0	0.152	0.063	22.542	0.010	0.010	0.000	0.000	0.000	0.000
31	A	114	VAL	0	0.035	0.024	25.246	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	115	ARG	1	0.894	0.939	18.472	-0.341	-0.341	0.000	0.000	0.000	0.000
33	A	116	GLU	-1	-0.911	-0.963	21.368	0.155	0.155	0.000	0.000	0.000	0.000
34	A	117	GLN	0	0.031	0.018	22.511	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	118	LEU	0	0.025	0.016	23.487	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	119	SER	0	-0.055	-0.024	19.243	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	120	SER	0	-0.020	-0.002	21.524	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	121	GLU	-1	-0.918	-0.954	24.221	0.091	0.091	0.000	0.000	0.000	0.000
39	A	122	THR	0	-0.118	-0.088	22.376	0.000	0.000	0.000	0.000	0.000	0.000
40	A	123	GLY	0	0.051	0.029	21.834	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	124	LEU	0	-0.079	-0.032	17.995	0.004	0.004	0.000	0.000	0.000	0.000
42	A	125	ASP	-1	-0.774	-0.885	11.972	0.454	0.454	0.000	0.000	0.000	0.000
43	A	126	MET	0	0.028	0.021	15.022	0.032	0.032	0.000	0.000	0.000	0.000
44	A	127	ARG	1	0.933	0.964	9.160	-0.881	-0.881	0.000	0.000	0.000	0.000
45	A	128	VAL	0	0.018	0.020	13.338	0.037	0.037	0.000	0.000	0.000	0.000
46	A	129	VAL	0	0.063	0.041	15.081	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	130	GLN	0	-0.032	-0.020	15.304	0.010	0.010	0.000	0.000	0.000	0.000
48	A	131	VAL	0	-0.004	-0.008	12.595	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	132	TRP	0	0.017	0.025	15.993	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	133	PHE	0	0.035	0.002	19.127	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	134	GLN	0	-0.106	-0.051	15.368	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	135	ASN	0	0.032	0.010	17.581	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	136	ARG	1	0.915	0.976	20.618	-0.211	-0.211	0.000	0.000	0.000	0.000
54	A	137	ARG	1	0.927	0.958	20.837	-0.327	-0.327	0.000	0.000	0.000	0.000
55	A	138	ALA	0	-0.024	-0.009	22.143	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	139	LYS	1	0.887	0.926	24.175	-0.202	-0.202	0.000	0.000	0.000	0.000
57	A	140	GLU	-1	-0.885	-0.952	26.066	0.150	0.150	0.000	0.000	0.000	0.000
58	A	141	LYS	1	0.953	0.976	27.171	-0.212	-0.212	0.000	0.000	0.000	0.000
59	A	142	ARG	1	0.859	0.952	22.939	-0.254	-0.254	0.000	0.000	0.000	0.000
60	A	143	LEU	0	-0.050	-0.045	28.760	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	144	LYS	1	1.042	1.060	32.213	-0.137	-0.137	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:84:GLY)