FMO DATABASE

FMODB ID: VRJK1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-314102.647642
FMO2-HF: Nuclear repulsion	291000.87241
FMO2-HF: Total energy	-23101.775233
FMO2-MP2: Total energy	-23169.103275

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.
0.399	1.353	-0.015	-0.491	-0.449	0

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 : 0.017 / q_NPA : -0.001

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].
3	I	86	SER	0	-0.020	-0.014	3.789	-0.064	0.890	-0.015	-0.491	-0.449
4	I	87	LYS	1	0.970	0.983	6.490	0.260	0.260	0.000	0.000	0.000
5	I	88	PRO	0	-0.004	-0.008	8.958	-0.082	-0.082	0.000	0.000	0.000
6	I	89	LYS	1	1.002	0.993	12.533	0.285	0.285	0.000	0.000	0.000
7	I	90	VAL	0	0.058	0.059	15.450	0.007	0.007	0.000	0.000	0.000
8	I	91	ALA	0	-0.015	0.007	15.248	0.014	0.014	0.000	0.000	0.000
9	I	92	THR	0	-0.002	-0.008	16.424	0.033	0.033	0.000	0.000	0.000
10	I	93	PRO	0	0.069	0.011	15.979	-0.003	-0.003	0.000	0.000	0.000
11	I	94	LYS	1	1.019	1.017	18.611	-0.047	-0.047	0.000	0.000	0.000
12	I	95	VAL	0	0.024	0.017	20.659	-0.002	-0.002	0.000	0.000	0.000
13	I	96	VAL	0	-0.029	-0.034	17.661	-0.003	-0.003	0.000	0.000	0.000
14	I	97	GLU	-1	-0.923	-0.952	21.056	0.108	0.108	0.000	0.000	0.000
15	I	98	LYS	1	0.927	0.977	23.714	-0.043	-0.043	0.000	0.000	0.000
16	I	99	ILE	0	-0.021	0.000	22.137	-0.004	-0.004	0.000	0.000	0.000
17	I	100	ALA	0	-0.002	-0.003	24.518	-0.002	-0.002	0.000	0.000	0.000
18	I	101	GLU	-1	-0.928	-0.970	26.376	0.054	0.054	0.000	0.000	0.000
19	I	102	TYR	0	-0.091	-0.118	28.994	-0.005	-0.005	0.000	0.000	0.000
20	I	103	LYS	1	0.915	0.962	27.745	-0.054	-0.054	0.000	0.000	0.000
21	I	104	ARG	1	0.946	0.974	30.525	-0.079	-0.079	0.000	0.000	0.000
22	I	105	GLN	0	0.030	0.045	32.439	-0.001	-0.001	0.000	0.000	0.000
23	I	106	ASN	0	0.034	0.014	34.481	0.000	0.000	0.000	0.000	0.000
24	I	107	PRO	0	0.037	0.010	32.778	-0.002	-0.002	0.000	0.000	0.000
25	I	108	THR	0	-0.044	-0.020	33.523	0.001	0.001	0.000	0.000	0.000
26	I	109	MET	0	-0.051	0.009	32.281	-0.002	-0.002	0.000	0.000	0.000
27	I	110	PHE	0	0.001	-0.005	32.468	0.003	0.003	0.000	0.000	0.000
28	I	111	ALA	0	-0.016	-0.029	27.562	0.000	0.000	0.000	0.000	0.000
29	I	112	TRP	0	-0.016	-0.028	29.268	-0.002	-0.002	0.000	0.000	0.000
30	I	113	GLU	-1	-0.761	-0.857	31.236	0.015	0.015	0.000	0.000	0.000
31	I	114	ILE	0	-0.027	-0.015	26.788	0.001	0.001	0.000	0.000	0.000
32	I	115	ARG	1	0.905	0.939	26.544	0.034	0.034	0.000	0.000	0.000
33	I	116	ASP	-1	-0.856	-0.919	28.969	-0.008	-0.008	0.000	0.000	0.000
34	I	117	ARG	1	0.851	0.917	32.216	-0.031	-0.031	0.000	0.000	0.000
35	I	118	LEU	0	-0.055	-0.014	24.585	0.001	0.001	0.000	0.000	0.000
36	I	119	LEU	0	0.005	-0.001	28.658	-0.003	-0.003	0.000	0.000	0.000
37	I	120	ALA	0	0.014	0.015	30.591	-0.002	-0.002	0.000	0.000	0.000
38	I	121	GLU	-1	-0.902	-0.923	31.631	0.028	0.028	0.000	0.000	0.000
39	I	122	ARG	1	0.939	0.956	31.091	0.008	0.008	0.000	0.000	0.000
40	I	123	VAL	0	-0.022	0.008	25.779	0.002	0.002	0.000	0.000	0.000
41	I	124	CYS	0	-0.087	-0.041	24.463	0.002	0.002	0.000	0.000	0.000
42	I	125	ASP	-1	-0.793	-0.886	25.762	-0.031	-0.031	0.000	0.000	0.000
43	I	126	ASN	0	-0.022	-0.022	26.500	0.004	0.004	0.000	0.000	0.000
44	I	127	ASP	-1	-0.889	-0.943	25.229	-0.073	-0.073	0.000	0.000	0.000
45	I	128	THR	0	-0.113	-0.060	21.264	-0.016	-0.016	0.000	0.000	0.000
46	I	129	VAL	0	-0.015	-0.005	22.380	0.009	0.009	0.000	0.000	0.000
47	I	130	PRO	0	-0.027	-0.017	21.282	-0.012	-0.012	0.000	0.000	0.000
48	I	131	SER	0	0.041	0.006	22.011	0.007	0.007	0.000	0.000	0.000
49	I	132	VAL	0	0.123	0.039	23.583	0.009	0.009	0.000	0.000	0.000
50	I	133	SER	0	-0.019	-0.017	22.113	0.007	0.007	0.000	0.000	0.000
51	I	134	SER	0	-0.043	-0.025	19.499	0.007	0.007	0.000	0.000	0.000
52	I	135	ILE	0	0.057	0.046	20.600	0.019	0.019	0.000	0.000	0.000
53	I	136	ASN	0	0.055	0.014	23.198	0.019	0.019	0.000	0.000	0.000
54	I	137	ARG	1	0.903	0.961	15.788	0.020	0.020	0.000	0.000	0.000
55	I	138	ILE	0	-0.016	-0.019	17.822	0.021	0.021	0.000	0.000	0.000
56	I	139	ILE	0	-0.016	-0.008	20.041	0.018	0.018	0.000	0.000	0.000
57	I	140	ARG	1	0.892	0.957	20.015	-0.055	-0.055	0.000	0.000	0.000
58	I	141	THR	0	-0.030	0.008	15.679	0.029	0.029	0.000	0.000	0.000

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