FMO DATABASE

FMODB ID: 6Y2ZZ

Calculation Name: 3KGK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KGK

Chain ID: A

ChEMBL ID:

UniProt ID: P46003

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:

Apendix: None

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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-640374.776662
FMO2-HF: Nuclear repulsion	604007.996393
FMO2-HF: Total energy	-36366.780269
FMO2-MP2: Total energy	-36472.199164

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-9.495	-2.415	5.789	-3.931	-8.94	-0.019

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.024

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

Sort

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	3	THR	0	-0.014	0.001	2.613	-4.681	-1.769	0.736	-1.704	-1.945	-0.013
4	A	4	LEU	0	-0.022	-0.019	5.267	0.790	0.874	-0.001	-0.005	-0.077	0.000
5	A	5	MET	0	0.009	0.012	7.747	-0.114	-0.114	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.036	-0.025	11.430	0.146	0.146	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.036	0.013	13.994	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.734	-0.851	17.655	-0.069	-0.069	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.057	0.018	19.777	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.029	-0.009	23.258	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	24	GLN	0	0.022	0.006	23.482	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	25	ALA	0	0.037	0.013	21.140	0.003	0.003	0.000	0.000	0.000	0.000
13	A	26	LEU	0	0.035	0.012	19.707	0.011	0.011	0.000	0.000	0.000	0.000
14	A	27	VAL	0	-0.023	-0.002	19.446	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	28	ASP	-1	-0.852	-0.938	18.823	0.072	0.072	0.000	0.000	0.000	0.000
16	A	29	PHE	0	0.028	0.008	12.433	0.004	0.004	0.000	0.000	0.000	0.000
17	A	30	SER	0	-0.027	-0.014	14.754	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	31	THR	0	0.007	0.003	15.143	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	32	ASP	-1	-0.833	-0.907	12.452	0.197	0.197	0.000	0.000	0.000	0.000
20	A	33	VAL	0	-0.022	-0.010	10.648	0.023	0.023	0.000	0.000	0.000	0.000
21	A	34	GLN	0	-0.005	-0.007	10.236	-0.130	-0.130	0.000	0.000	0.000	0.000
22	A	35	TRP	0	0.024	0.016	8.824	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	36	LEU	0	0.023	0.018	5.969	-0.102	-0.102	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.909	0.955	6.119	0.329	0.329	0.000	0.000	0.000	0.000
25	A	38	GLN	0	-0.049	-0.021	8.238	-0.214	-0.214	0.000	0.000	0.000	0.000
26	A	39	SER	0	-0.051	-0.030	4.842	0.094	0.094	0.000	0.000	0.000	0.000
27	A	40	GLY	0	-0.024	-0.001	4.363	-0.769	-0.620	-0.001	-0.026	-0.121	0.000
28	A	41	VAL	0	-0.040	-0.014	2.330	-2.620	-1.508	1.869	-0.599	-2.383	0.000
29	A	42	GLN	0	-0.002	0.004	3.524	0.815	0.985	0.007	0.097	-0.275	0.000
30	A	43	ILE	0	-0.019	-0.020	6.081	0.159	0.159	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.940	-0.964	8.577	-0.818	-0.818	0.000	0.000	0.000	0.000
32	A	45	ARG	1	0.803	0.873	11.983	0.243	0.243	0.000	0.000	0.000	0.000
33	A	46	PHE	0	0.032	0.029	13.990	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	47	ASN	0	0.045	0.006	18.302	0.049	0.049	0.000	0.000	0.000	0.000
35	A	48	LEU	0	0.050	0.011	21.640	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	49	ALA	0	-0.020	0.004	25.078	0.004	0.004	0.000	0.000	0.000	0.000
37	A	50	GLN	0	-0.041	-0.015	23.163	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	51	GLN	0	0.019	0.012	20.161	0.003	0.003	0.000	0.000	0.000	0.000
39	A	52	PRO	0	0.059	0.032	22.617	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	53	MET	0	0.009	-0.012	24.994	0.012	0.012	0.000	0.000	0.000	0.000
41	A	54	SER	0	0.058	0.027	19.385	0.007	0.007	0.000	0.000	0.000	0.000
42	A	55	PHE	0	-0.055	-0.033	20.857	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	56	VAL	0	-0.038	-0.012	22.683	0.021	0.021	0.000	0.000	0.000	0.000
44	A	57	GLN	0	0.000	0.002	22.137	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	58	ASN	0	0.024	0.031	16.289	0.035	0.035	0.000	0.000	0.000	0.000
46	A	59	GLU	-1	-0.862	-0.953	20.242	-0.062	-0.062	0.000	0.000	0.000	0.000
47	A	60	LYS	1	0.851	0.930	16.057	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	61	VAL	0	-0.026	-0.009	18.356	0.025	0.025	0.000	0.000	0.000	0.000
49	A	62	LYS	1	0.971	1.000	20.856	0.069	0.069	0.000	0.000	0.000	0.000
50	A	63	ALA	0	0.013	0.006	23.756	0.011	0.011	0.000	0.000	0.000	0.000
51	A	64	PHE	0	-0.015	-0.009	21.809	0.014	0.014	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.027	-0.016	23.758	0.007	0.007	0.000	0.000	0.000	0.000
53	A	66	GLU	-1	-0.992	-0.987	25.973	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	67	ALA	0	-0.044	-0.018	26.786	0.006	0.006	0.000	0.000	0.000	0.000
55	A	68	SER	0	-0.059	-0.034	25.761	0.012	0.012	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.073	0.059	27.749	0.002	0.002	0.000	0.000	0.000	0.000
57	A	70	ALA	0	-0.018	-0.036	26.038	0.003	0.003	0.000	0.000	0.000	0.000
58	A	71	GLU	-1	-0.946	-0.981	25.906	0.005	0.005	0.000	0.000	0.000	0.000
59	A	72	GLY	0	-0.015	0.003	25.287	0.010	0.010	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.090	-0.025	20.746	0.013	0.013	0.000	0.000	0.000	0.000
61	A	74	PRO	0	-0.018	-0.012	17.615	0.004	0.004	0.000	0.000	0.000	0.000
62	A	75	LEU	0	-0.015	0.004	16.890	0.037	0.037	0.000	0.000	0.000	0.000
63	A	76	LEU	0	-0.043	-0.027	12.064	-0.040	-0.040	0.000	0.000	0.000	0.000
64	A	77	LEU	0	0.003	-0.002	12.305	0.071	0.071	0.000	0.000	0.000	0.000
65	A	78	LEU	0	-0.016	-0.012	5.993	-0.093	-0.093	0.000	0.000	0.000	0.000
66	A	79	ASP	-1	-0.808	-0.918	6.648	-0.890	-0.890	0.000	0.000	0.000	0.000
67	A	80	GLY	0	0.004	0.009	9.119	0.134	0.134	0.000	0.000	0.000	0.000
68	A	81	GLU	-1	-0.912	-0.956	11.896	0.225	0.225	0.000	0.000	0.000	0.000
69	A	82	THR	0	0.001	-0.006	12.893	0.006	0.006	0.000	0.000	0.000	0.000
70	A	83	VAL	0	-0.029	-0.003	11.093	0.070	0.070	0.000	0.000	0.000	0.000
71	A	84	MET	0	-0.097	-0.040	14.296	0.045	0.045	0.000	0.000	0.000	0.000
72	A	85	ALA	0	0.002	-0.005	16.527	-0.044	-0.044	0.000	0.000	0.000	0.000
73	A	86	GLY	0	0.067	0.058	19.488	0.018	0.018	0.000	0.000	0.000	0.000
74	A	87	ARG	1	0.746	0.848	17.914	-0.322	-0.322	0.000	0.000	0.000	0.000
75	A	88	TYR	0	-0.008	-0.034	15.881	0.013	0.013	0.000	0.000	0.000	0.000
76	A	89	PRO	0	-0.042	-0.009	12.508	0.004	0.004	0.000	0.000	0.000	0.000
77	A	90	LYS	1	0.985	0.977	15.242	-0.287	-0.287	0.000	0.000	0.000	0.000
78	A	91	ARG	1	0.957	0.964	12.053	-0.046	-0.046	0.000	0.000	0.000	0.000
79	A	92	ALA	0	0.011	0.000	11.617	0.150	0.150	0.000	0.000	0.000	0.000
80	A	93	GLU	-1	-0.824	-0.892	12.335	0.577	0.577	0.000	0.000	0.000	0.000
81	A	94	LEU	0	0.047	0.020	8.862	0.183	0.183	0.000	0.000	0.000	0.000
82	A	95	ALA	0	0.029	0.013	7.580	0.620	0.620	0.000	0.000	0.000	0.000
83	A	96	ARG	1	0.939	0.977	7.826	-0.484	-0.484	0.000	0.000	0.000	0.000
84	A	97	TRP	0	-0.045	-0.036	7.795	0.214	0.214	0.000	0.000	0.000	0.000
85	A	98	PHE	0	-0.012	-0.020	2.811	-2.011	-1.102	2.626	-0.926	-2.609	0.005
86	A	99	GLY	0	-0.002	0.020	3.548	0.146	1.688	0.554	-0.746	-1.350	-0.011
87	A	100	ILE	0	-0.033	-0.014	4.210	-0.822	-0.620	-0.001	-0.022	-0.180	0.000
88	A	101	PRO	0	-0.022	-0.014	5.744	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	102	LEU	0	0.003	-0.003	8.866	-0.094	-0.094	0.000	0.000	0.000	0.000
90	A	103	ASP	-1	-0.897	-0.943	11.916	0.148	0.148	0.000	0.000	0.000	0.000
91	A	104	LYS	1	0.880	0.932	12.951	-0.326	-0.326	0.000	0.000	0.000	0.000
92	A	105	VAL	0	0.021	0.023	16.876	-0.018	-0.018	0.000	0.000	0.000	0.000

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