FMO DATABASE

FMODB ID: 1486Z

Calculation Name: 1K78-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K78

Chain ID: I

ChEMBL ID:

UniProt ID: P27577

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	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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-313892.974988
FMO2-HF: Nuclear repulsion	290790.8114
FMO2-HF: Total energy	-23102.163588
FMO2-MP2: Total energy	-23169.44127

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(I:84:GLY)

Summations of interaction energy for fragment #1(I: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.
0.775	2.451	-0.016	-0.972	-0.689	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.029

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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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	I	86	SER	0	-0.023	-0.020	3.789	-0.026	1.650	-0.016	-0.972	-0.689	0.004
4	I	87	LYS	1	0.977	0.990	6.489	-0.174	-0.174	0.000	0.000	0.000	0.000
5	I	88	PRO	0	-0.002	-0.007	8.958	-0.085	-0.085	0.000	0.000	0.000	0.000
6	I	89	LYS	1	0.989	0.989	12.532	0.477	0.477	0.000	0.000	0.000	0.000
7	I	90	VAL	0	0.056	0.039	15.449	0.023	0.023	0.000	0.000	0.000	0.000
8	I	91	ALA	0	-0.015	0.008	15.195	0.026	0.026	0.000	0.000	0.000	0.000
9	I	92	THR	0	0.005	-0.006	16.422	0.029	0.029	0.000	0.000	0.000	0.000
10	I	93	PRO	0	0.080	0.016	15.946	-0.007	-0.007	0.000	0.000	0.000	0.000
11	I	94	LYS	1	1.012	1.015	18.610	-0.030	-0.030	0.000	0.000	0.000	0.000
12	I	95	VAL	0	0.020	0.013	20.602	-0.002	-0.002	0.000	0.000	0.000	0.000
13	I	96	VAL	0	-0.039	-0.037	17.670	-0.009	-0.009	0.000	0.000	0.000	0.000
14	I	97	GLU	-1	-0.932	-0.948	21.053	0.039	0.039	0.000	0.000	0.000	0.000
15	I	98	LYS	1	0.884	0.953	23.712	0.018	0.018	0.000	0.000	0.000	0.000
16	I	99	ILE	0	-0.012	0.000	22.332	-0.004	-0.004	0.000	0.000	0.000	0.000
17	I	100	ALA	0	0.001	0.001	24.474	-0.001	-0.001	0.000	0.000	0.000	0.000
18	I	101	GLU	-1	-0.901	-0.962	26.373	-0.006	-0.006	0.000	0.000	0.000	0.000
19	I	102	TYR	0	-0.084	-0.095	28.992	-0.002	-0.002	0.000	0.000	0.000	0.000
20	I	103	LYS	1	0.839	0.920	28.079	0.074	0.074	0.000	0.000	0.000	0.000
21	I	104	ARG	1	0.927	0.972	30.521	-0.008	-0.008	0.000	0.000	0.000	0.000
22	I	105	GLN	0	0.027	0.029	32.436	-0.001	-0.001	0.000	0.000	0.000	0.000
23	I	106	ASN	0	0.036	0.014	34.457	0.003	0.003	0.000	0.000	0.000	0.000
24	I	107	PRO	0	0.054	0.021	32.779	-0.006	-0.006	0.000	0.000	0.000	0.000
25	I	108	THR	0	-0.024	-0.007	33.518	-0.005	-0.005	0.000	0.000	0.000	0.000
26	I	109	MET	0	-0.033	0.016	32.403	-0.002	-0.002	0.000	0.000	0.000	0.000
27	I	110	PHE	0	0.010	0.002	32.472	-0.008	-0.008	0.000	0.000	0.000	0.000
28	I	111	ALA	0	-0.014	-0.026	27.585	0.000	0.000	0.000	0.000	0.000	0.000
29	I	112	TRP	0	0.004	-0.019	29.264	-0.004	-0.004	0.000	0.000	0.000	0.000
30	I	113	GLU	-1	-0.765	-0.865	31.232	-0.066	-0.066	0.000	0.000	0.000	0.000
31	I	114	ILE	0	-0.042	-0.023	26.855	0.004	0.004	0.000	0.000	0.000	0.000
32	I	115	ARG	1	0.888	0.928	25.892	0.145	0.145	0.000	0.000	0.000	0.000
33	I	116	ASP	-1	-0.849	-0.920	28.966	-0.083	-0.083	0.000	0.000	0.000	0.000
34	I	117	ARG	1	0.845	0.907	32.238	0.044	0.044	0.000	0.000	0.000	0.000
35	I	118	LEU	0	-0.053	-0.012	24.459	0.004	0.004	0.000	0.000	0.000	0.000
36	I	119	LEU	0	0.007	-0.003	28.657	-0.001	-0.001	0.000	0.000	0.000	0.000
37	I	120	ALA	0	0.018	0.015	30.590	0.004	0.004	0.000	0.000	0.000	0.000
38	I	121	GLU	-1	-0.870	-0.905	31.712	-0.027	-0.027	0.000	0.000	0.000	0.000
39	I	122	ARG	1	0.941	0.957	31.068	0.040	0.040	0.000	0.000	0.000	0.000
40	I	123	VAL	0	-0.013	0.008	25.835	0.006	0.006	0.000	0.000	0.000	0.000
41	I	124	CYS	0	-0.069	-0.031	24.436	-0.009	-0.009	0.000	0.000	0.000	0.000
42	I	125	ASP	-1	-0.783	-0.863	25.580	-0.070	-0.070	0.000	0.000	0.000	0.000
43	I	126	ASN	0	-0.071	-0.041	26.499	-0.010	-0.010	0.000	0.000	0.000	0.000
44	I	127	ASP	-1	-0.841	-0.926	25.326	-0.136	-0.136	0.000	0.000	0.000	0.000
45	I	128	THR	0	-0.131	-0.090	21.198	-0.023	-0.023	0.000	0.000	0.000	0.000
46	I	129	VAL	0	-0.015	-0.001	22.378	-0.006	-0.006	0.000	0.000	0.000	0.000
47	I	130	PRO	0	-0.013	-0.006	21.181	-0.024	-0.024	0.000	0.000	0.000	0.000
48	I	131	SER	0	0.042	0.034	21.918	0.013	0.013	0.000	0.000	0.000	0.000
49	I	132	VAL	0	0.126	0.041	23.579	-0.003	-0.003	0.000	0.000	0.000	0.000
50	I	133	SER	0	0.001	-0.007	22.125	0.011	0.011	0.000	0.000	0.000	0.000
51	I	134	SER	0	-0.041	-0.031	19.384	-0.028	-0.028	0.000	0.000	0.000	0.000
52	I	135	ILE	0	0.050	0.046	20.596	0.002	0.002	0.000	0.000	0.000	0.000
53	I	136	ASN	0	0.018	-0.005	23.194	0.022	0.022	0.000	0.000	0.000	0.000
54	I	137	ARG	1	0.898	0.961	15.826	0.403	0.403	0.000	0.000	0.000	0.000
55	I	138	ILE	0	-0.013	-0.011	17.790	-0.004	-0.004	0.000	0.000	0.000	0.000
56	I	139	ILE	0	-0.003	0.003	20.036	0.017	0.017	0.000	0.000	0.000	0.000
57	I	140	ARG	1	0.913	0.964	20.502	0.239	0.239	0.000	0.000	0.000	0.000
58	I	141	THR	0	-0.056	-0.013	15.607	0.002	0.002	0.000	0.000	0.000	0.000

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