FMO DATABASE

FMODB ID: MVK4Z

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	OptHSide
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	-350457.255545
FMO2-HF: Nuclear repulsion	325777.137856
FMO2-HF: Total energy	-24680.117689
FMO2-MP2: Total energy	-24753.338872

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.
-4.987	-2.978	-0.027	-1.055	-0.926	-0.001

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 : 0.013 / q_NPA : -0.005

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	0.986	0.997	3.797	0.702	2.630	-0.026	-1.039	-0.862	-0.001
4	A	87	ARG	1	0.966	0.976	4.493	-3.374	-3.293	-0.001	-0.016	-0.064	0.000
5	A	88	PRO	0	0.035	0.045	7.511	0.080	0.080	0.000	0.000	0.000	0.000
6	A	89	ARG	1	0.959	0.965	11.082	-0.186	-0.186	0.000	0.000	0.000	0.000
7	A	90	THR	0	0.041	0.024	14.253	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	91	THR	0	-0.045	-0.018	16.630	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	92	ILE	0	0.038	0.013	19.511	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	93	THR	0	0.062	0.034	22.161	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	94	ALA	0	0.063	0.010	25.836	0.010	0.010	0.000	0.000	0.000	0.000
12	A	95	LYS	1	1.053	1.036	28.458	-0.065	-0.065	0.000	0.000	0.000	0.000
13	A	96	GLN	0	0.057	0.027	21.774	0.014	0.014	0.000	0.000	0.000	0.000
14	A	97	LEU	0	-0.036	-0.013	24.816	0.012	0.012	0.000	0.000	0.000	0.000
15	A	98	GLU	-1	-0.815	-0.903	26.197	0.109	0.109	0.000	0.000	0.000	0.000
16	A	99	THR	0	0.004	0.013	27.113	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	100	LEU	0	-0.004	-0.003	21.999	0.006	0.006	0.000	0.000	0.000	0.000
18	A	101	LYS	1	0.848	0.894	26.257	-0.109	-0.109	0.000	0.000	0.000	0.000
19	A	102	ASN	0	-0.038	-0.024	28.802	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	103	ALA	0	0.021	0.011	27.216	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	104	TYR	0	-0.077	-0.040	25.715	0.015	0.015	0.000	0.000	0.000	0.000
22	A	105	LYS	1	0.925	0.960	28.480	-0.100	-0.100	0.000	0.000	0.000	0.000
23	A	106	ASN	0	0.043	0.038	31.011	0.002	0.002	0.000	0.000	0.000	0.000
24	A	107	SER	0	-0.023	-0.021	28.610	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	108	PRO	0	0.098	0.060	27.342	0.012	0.012	0.000	0.000	0.000	0.000
26	A	109	LYS	1	0.904	0.939	23.883	-0.217	-0.217	0.000	0.000	0.000	0.000
27	A	110	PRO	0	0.052	0.061	23.156	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	111	ALA	0	0.070	0.031	23.519	0.030	0.030	0.000	0.000	0.000	0.000
29	A	112	ARG	1	0.879	0.921	17.866	-0.259	-0.259	0.000	0.000	0.000	0.000
30	A	113	HIS	0	0.153	0.065	22.550	0.013	0.013	0.000	0.000	0.000	0.000
31	A	114	VAL	0	0.031	0.024	25.255	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	115	ARG	1	0.855	0.917	18.465	-0.337	-0.337	0.000	0.000	0.000	0.000
33	A	116	GLU	-1	-0.834	-0.916	21.519	0.190	0.190	0.000	0.000	0.000	0.000
34	A	117	GLN	0	0.016	0.004	22.520	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	118	LEU	0	0.028	0.018	23.494	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	119	SER	0	-0.056	-0.031	19.207	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	120	SER	0	0.003	0.007	21.531	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	121	GLU	-1	-0.955	-0.972	24.228	0.096	0.096	0.000	0.000	0.000	0.000
39	A	122	THR	0	-0.106	-0.077	22.371	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	123	GLY	0	0.036	0.019	21.840	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	124	LEU	0	-0.075	-0.023	18.033	0.007	0.007	0.000	0.000	0.000	0.000
42	A	125	ASP	-1	-0.741	-0.865	12.227	0.495	0.495	0.000	0.000	0.000	0.000
43	A	126	MET	0	0.029	0.025	15.171	0.029	0.029	0.000	0.000	0.000	0.000
44	A	127	ARG	1	0.884	0.933	9.229	-0.791	-0.791	0.000	0.000	0.000	0.000
45	A	128	VAL	0	0.005	0.011	13.345	0.024	0.024	0.000	0.000	0.000	0.000
46	A	129	VAL	0	0.061	0.040	15.086	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	130	GLN	0	-0.041	-0.032	15.497	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	131	VAL	0	-0.007	-0.009	12.582	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	132	TRP	0	0.015	0.021	15.997	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	133	PHE	0	0.034	0.003	19.131	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	134	GLN	0	-0.061	-0.034	15.148	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	135	ASN	0	0.023	0.007	16.995	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	136	ARG	1	0.764	0.873	20.621	-0.190	-0.190	0.000	0.000	0.000	0.000
54	A	137	ARG	1	0.922	0.958	20.760	-0.305	-0.305	0.000	0.000	0.000	0.000
55	A	138	ALA	0	-0.028	-0.012	22.150	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	139	LYS	1	0.908	0.950	24.177	-0.180	-0.180	0.000	0.000	0.000	0.000
57	A	140	GLU	-1	-0.751	-0.864	26.068	0.150	0.150	0.000	0.000	0.000	0.000
58	A	141	LYS	1	0.949	0.978	27.209	-0.189	-0.189	0.000	0.000	0.000	0.000
59	A	142	ARG	1	0.880	0.956	22.780	-0.228	-0.228	0.000	0.000	0.000	0.000
60	A	143	LEU	0	-0.063	-0.048	28.761	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	144	LYS	1	1.043	1.057	32.214	-0.127	-0.127	0.000	0.000	0.000	0.000

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