FMO DATABASE

FMODB ID: YY452

Calculation Name: 3KIK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIK

Chain ID: B

ChEMBL ID:

UniProt ID: Q03067

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

Total energy (hartree)

FMO2-HF: Electronic energy	-598656.040359
FMO2-HF: Nuclear repulsion	561548.82638
FMO2-HF: Total energy	-37107.213979
FMO2-MP2: Total energy	-37215.794735

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(B:4:ASP)

Summations of interaction energy for fragment #1(B:4:ASP)

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.
16.116	22.162	0.325	-2.893	-3.478	0.016

Interaction energy analysis for fragmet #1(B:4:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.868 / q_NPA : -0.949

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	B	6	ALA	0	-0.043	-0.012	3.188	-15.395	-11.880	0.064	-1.848	-1.731	0.011
4	B	7	GLN	0	0.010	-0.004	2.742	-6.109	-4.448	0.259	-0.707	-1.213	0.004
5	B	8	LEU	0	0.046	0.013	3.720	-8.052	-7.182	0.002	-0.338	-0.534	0.001
6	B	9	LYS	1	0.944	0.978	5.498	-39.103	-39.103	0.000	0.000	0.000	0.000
7	B	10	SER	0	0.040	0.019	8.065	-2.446	-2.446	0.000	0.000	0.000	0.000
8	B	11	GLN	0	-0.007	-0.001	6.335	-0.270	-0.270	0.000	0.000	0.000	0.000
9	B	12	ILE	0	0.024	0.022	9.326	-2.333	-2.333	0.000	0.000	0.000	0.000
10	B	13	GLN	0	-0.030	-0.026	11.429	-1.288	-1.288	0.000	0.000	0.000	0.000
11	B	14	GLN	0	-0.015	-0.004	11.066	0.011	0.011	0.000	0.000	0.000	0.000
12	B	15	TYR	0	0.096	0.050	13.307	-1.219	-1.219	0.000	0.000	0.000	0.000
13	B	16	LEU	0	-0.033	-0.005	15.158	-1.321	-1.321	0.000	0.000	0.000	0.000
14	B	17	VAL	0	-0.062	-0.037	17.104	-1.216	-1.216	0.000	0.000	0.000	0.000
15	B	18	GLU	-1	-0.973	-0.989	16.046	18.093	18.093	0.000	0.000	0.000	0.000
16	B	19	SER	0	-0.011	-0.004	19.050	-0.743	-0.743	0.000	0.000	0.000	0.000
17	B	20	GLY	0	-0.005	0.007	20.831	-0.613	-0.613	0.000	0.000	0.000	0.000
18	B	21	ASN	0	-0.027	-0.038	20.277	-0.454	-0.454	0.000	0.000	0.000	0.000
19	B	22	TYR	0	-0.011	0.000	18.685	-0.519	-0.519	0.000	0.000	0.000	0.000
20	B	23	GLU	-1	-0.934	-0.978	21.426	11.068	11.068	0.000	0.000	0.000	0.000
21	B	24	LEU	0	-0.014	0.006	25.002	-0.469	-0.469	0.000	0.000	0.000	0.000
22	B	25	ILE	0	0.046	0.025	20.595	-0.366	-0.366	0.000	0.000	0.000	0.000
23	B	26	SER	0	-0.042	-0.004	23.829	-0.488	-0.488	0.000	0.000	0.000	0.000
24	B	27	ASN	0	0.004	-0.013	25.227	-0.515	-0.515	0.000	0.000	0.000	0.000
25	B	28	GLU	-1	-0.771	-0.847	27.680	10.800	10.800	0.000	0.000	0.000	0.000
26	B	29	LEU	0	0.024	0.011	24.215	-0.377	-0.377	0.000	0.000	0.000	0.000
27	B	30	LYS	1	0.881	0.924	27.863	-11.253	-11.253	0.000	0.000	0.000	0.000
28	B	31	ALA	0	0.003	0.008	30.316	-0.388	-0.388	0.000	0.000	0.000	0.000
29	B	32	ARG	1	0.809	0.892	29.887	-10.736	-10.736	0.000	0.000	0.000	0.000
30	B	33	LEU	0	0.026	0.008	27.942	-0.320	-0.320	0.000	0.000	0.000	0.000
31	B	34	LEU	0	-0.014	-0.010	32.343	-0.289	-0.289	0.000	0.000	0.000	0.000
32	B	35	GLN	0	-0.020	-0.011	35.156	-0.048	-0.048	0.000	0.000	0.000	0.000
33	B	36	GLU	-1	-0.814	-0.879	32.164	9.781	9.781	0.000	0.000	0.000	0.000
34	B	37	GLY	0	0.035	0.009	36.489	-0.114	-0.114	0.000	0.000	0.000	0.000
35	B	38	TRP	0	-0.048	-0.021	28.858	-0.214	-0.214	0.000	0.000	0.000	0.000
36	B	39	VAL	0	0.033	0.008	33.173	-0.031	-0.031	0.000	0.000	0.000	0.000
37	B	40	ASP	-1	-0.823	-0.908	35.067	8.022	8.022	0.000	0.000	0.000	0.000
38	B	41	LYS	1	0.855	0.934	35.384	-9.224	-9.224	0.000	0.000	0.000	0.000
39	B	42	VAL	0	0.074	0.033	31.972	-0.085	-0.085	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.780	0.902	35.222	-8.234	-8.234	0.000	0.000	0.000	0.000
41	B	44	ASP	-1	-0.849	-0.923	38.174	7.474	7.474	0.000	0.000	0.000	0.000
42	B	45	LEU	0	0.003	0.020	32.924	-0.139	-0.139	0.000	0.000	0.000	0.000
43	B	46	THR	0	-0.009	-0.029	35.466	0.017	0.017	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.814	0.893	37.109	-7.683	-7.683	0.000	0.000	0.000	0.000
45	B	48	SER	0	0.026	0.026	39.367	-0.221	-0.221	0.000	0.000	0.000	0.000
46	B	49	GLU	-1	-0.787	-0.874	34.872	8.933	8.933	0.000	0.000	0.000	0.000
47	B	50	MET	0	-0.064	-0.032	37.915	-0.018	-0.018	0.000	0.000	0.000	0.000
48	B	51	ASN	0	-0.073	-0.038	39.820	-0.294	-0.294	0.000	0.000	0.000	0.000
49	B	52	ILE	0	-0.039	-0.005	38.289	-0.131	-0.131	0.000	0.000	0.000	0.000
50	B	53	ASN	0	-0.078	-0.036	35.968	0.062	0.062	0.000	0.000	0.000	0.000
51	B	54	GLU	-1	-0.905	-0.950	39.737	7.308	7.308	0.000	0.000	0.000	0.000
52	B	55	SER	0	-0.021	-0.012	36.523	-0.056	-0.056	0.000	0.000	0.000	0.000
53	B	56	THR	0	0.031	0.003	37.831	0.163	0.163	0.000	0.000	0.000	0.000
54	B	57	ASN	0	-0.067	-0.021	35.292	-0.011	-0.011	0.000	0.000	0.000	0.000
55	B	58	PHE	0	0.060	0.018	29.570	0.109	0.109	0.000	0.000	0.000	0.000
56	B	59	THR	0	0.021	0.003	28.337	0.090	0.090	0.000	0.000	0.000	0.000
57	B	60	GLN	0	0.028	0.018	30.038	0.200	0.200	0.000	0.000	0.000	0.000
58	B	61	ILE	0	0.053	0.049	32.130	0.133	0.133	0.000	0.000	0.000	0.000
59	B	62	LEU	0	-0.009	0.002	26.943	0.032	0.032	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.067	-0.044	27.753	0.243	0.243	0.000	0.000	0.000	0.000
61	B	64	THR	0	-0.021	-0.031	28.703	0.187	0.187	0.000	0.000	0.000	0.000
62	B	65	VAL	0	0.009	0.006	31.160	-0.041	-0.041	0.000	0.000	0.000	0.000
63	B	66	GLU	-1	-0.911	-0.961	23.772	12.845	12.845	0.000	0.000	0.000	0.000
64	B	67	PRO	0	0.000	-0.008	26.173	0.206	0.206	0.000	0.000	0.000	0.000
65	B	68	LYS	1	0.818	0.885	27.252	-9.387	-9.387	0.000	0.000	0.000	0.000
66	B	69	ALA	0	0.016	0.005	29.069	-0.099	-0.099	0.000	0.000	0.000	0.000
67	B	70	LEU	0	-0.006	-0.007	22.855	0.068	0.068	0.000	0.000	0.000	0.000
68	B	71	GLU	-1	-0.929	-0.950	26.611	11.964	11.964	0.000	0.000	0.000	0.000
69	B	72	MET	0	-0.082	-0.036	28.541	-0.155	-0.155	0.000	0.000	0.000	0.000
70	B	73	VAL	0	-0.062	-0.015	27.077	-0.309	-0.309	0.000	0.000	0.000	0.000
71	B	74	SER	0	0.020	0.019	29.203	0.173	0.173	0.000	0.000	0.000	0.000
72	B	75	ASP	-1	-0.841	-0.935	28.157	11.159	11.159	0.000	0.000	0.000	0.000
73	B	76	SER	0	-0.038	-0.017	28.136	0.276	0.276	0.000	0.000	0.000	0.000
74	B	77	THR	0	-0.022	-0.025	28.299	0.139	0.139	0.000	0.000	0.000	0.000
75	B	78	ARG	1	0.870	0.941	23.542	-12.393	-12.393	0.000	0.000	0.000	0.000
76	B	79	GLU	-1	-0.851	-0.942	23.484	14.430	14.430	0.000	0.000	0.000	0.000
77	B	80	THR	0	-0.091	-0.057	24.774	0.271	0.271	0.000	0.000	0.000	0.000
78	B	81	VAL	0	0.029	0.014	22.854	0.233	0.233	0.000	0.000	0.000	0.000
79	B	82	LEU	0	-0.014	-0.008	18.799	0.752	0.752	0.000	0.000	0.000	0.000
80	B	83	LYS	1	0.781	0.883	20.291	-11.840	-11.840	0.000	0.000	0.000	0.000
81	B	84	GLN	0	0.007	-0.010	21.869	0.544	0.544	0.000	0.000	0.000	0.000
82	B	85	ILE	0	-0.005	-0.004	16.974	0.420	0.420	0.000	0.000	0.000	0.000
83	B	86	ARG	1	0.794	0.889	17.039	-14.676	-14.676	0.000	0.000	0.000	0.000
84	B	87	GLU	-1	-0.749	-0.864	18.052	13.918	13.918	0.000	0.000	0.000	0.000
85	B	88	PHE	0	0.016	0.016	15.435	0.237	0.237	0.000	0.000	0.000	0.000
86	B	89	LEU	0	-0.049	-0.038	12.594	0.943	0.943	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.881	-0.947	15.160	16.878	16.878	0.000	0.000	0.000	0.000
88	B	91	GLU	-1	-0.876	-0.923	17.655	14.622	14.622	0.000	0.000	0.000	0.000
89	B	92	ILE	0	-0.077	-0.025	12.828	0.065	0.065	0.000	0.000	0.000	0.000
90	B	93	VAL	0	-0.085	-0.050	13.903	1.053	1.053	0.000	0.000	0.000	0.000
91	B	94	ASP	-1	-0.871	-0.903	16.641	14.738	14.738	0.000	0.000	0.000	0.000
92	B	95	THR	0	-0.138	-0.076	18.382	-0.859	-0.859	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:ASP)