FMO DATABASE

FMODB ID: 5347Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-596087.9716
FMO2-HF: Nuclear repulsion	558981.113402
FMO2-HF: Total energy	-37106.858197
FMO2-MP2: Total energy	-37215.408115

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.
17.76	23.208	0.943	-2.733	-3.659	0.013

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 : -0.914 / q_NPA : -0.961

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	-0.035	-0.018	3.414	-13.526	-10.276	0.028	-1.546	-1.732	0.011
4	B	7	GLN	0	0.001	-0.002	2.352	-4.756	-3.429	0.914	-0.875	-1.366	0.001
5	B	8	LEU	0	0.042	0.018	3.940	-7.701	-6.830	0.001	-0.312	-0.561	0.001
6	B	9	LYS	1	0.952	0.971	5.651	-37.996	-37.996	0.000	0.000	0.000	0.000
7	B	10	SER	0	0.023	0.007	7.773	-2.345	-2.345	0.000	0.000	0.000	0.000
8	B	11	GLN	0	0.017	0.010	6.417	-1.662	-1.662	0.000	0.000	0.000	0.000
9	B	12	ILE	0	0.028	0.021	9.217	-2.525	-2.525	0.000	0.000	0.000	0.000
10	B	13	GLN	0	-0.022	-0.018	11.455	-1.558	-1.558	0.000	0.000	0.000	0.000
11	B	14	GLN	0	-0.022	-0.011	11.500	-0.534	-0.534	0.000	0.000	0.000	0.000
12	B	15	TYR	0	0.087	0.049	13.324	-1.067	-1.067	0.000	0.000	0.000	0.000
13	B	16	LEU	0	-0.037	0.000	15.045	-1.359	-1.359	0.000	0.000	0.000	0.000
14	B	17	VAL	0	-0.078	-0.054	17.075	-1.225	-1.225	0.000	0.000	0.000	0.000
15	B	18	GLU	-1	-0.980	-0.985	16.493	18.063	18.063	0.000	0.000	0.000	0.000
16	B	19	SER	0	-0.032	-0.022	18.580	-0.722	-0.722	0.000	0.000	0.000	0.000
17	B	20	GLY	0	0.005	0.017	20.452	-0.677	-0.677	0.000	0.000	0.000	0.000
18	B	21	ASN	0	-0.005	-0.007	20.143	-0.600	-0.600	0.000	0.000	0.000	0.000
19	B	22	TYR	0	-0.003	-0.004	18.785	-0.468	-0.468	0.000	0.000	0.000	0.000
20	B	23	GLU	-1	-0.944	-0.986	21.429	11.348	11.348	0.000	0.000	0.000	0.000
21	B	24	LEU	0	0.003	0.006	24.881	-0.534	-0.534	0.000	0.000	0.000	0.000
22	B	25	ILE	0	0.020	0.020	20.355	-0.299	-0.299	0.000	0.000	0.000	0.000
23	B	26	SER	0	-0.030	-0.011	23.761	-0.582	-0.582	0.000	0.000	0.000	0.000
24	B	27	ASN	0	-0.004	-0.026	25.263	-0.511	-0.511	0.000	0.000	0.000	0.000
25	B	28	GLU	-1	-0.775	-0.855	27.738	10.791	10.791	0.000	0.000	0.000	0.000
26	B	29	LEU	0	0.019	0.013	24.188	-0.328	-0.328	0.000	0.000	0.000	0.000
27	B	30	LYS	1	0.915	0.949	27.961	-11.320	-11.320	0.000	0.000	0.000	0.000
28	B	31	ALA	0	-0.015	-0.001	30.395	-0.391	-0.391	0.000	0.000	0.000	0.000
29	B	32	ARG	1	0.843	0.909	29.939	-10.810	-10.810	0.000	0.000	0.000	0.000
30	B	33	LEU	0	0.004	0.000	28.205	-0.283	-0.283	0.000	0.000	0.000	0.000
31	B	34	LEU	0	-0.038	-0.025	32.617	-0.303	-0.303	0.000	0.000	0.000	0.000
32	B	35	GLN	0	-0.035	-0.017	35.222	-0.057	-0.057	0.000	0.000	0.000	0.000
33	B	36	GLU	-1	-0.841	-0.919	32.466	9.692	9.692	0.000	0.000	0.000	0.000
34	B	37	GLY	0	0.035	0.013	36.695	-0.144	-0.144	0.000	0.000	0.000	0.000
35	B	38	TRP	0	-0.031	-0.014	28.921	-0.191	-0.191	0.000	0.000	0.000	0.000
36	B	39	VAL	0	0.045	0.006	33.182	-0.034	-0.034	0.000	0.000	0.000	0.000
37	B	40	ASP	-1	-0.829	-0.908	35.197	7.933	7.933	0.000	0.000	0.000	0.000
38	B	41	LYS	1	0.889	0.963	35.748	-9.156	-9.156	0.000	0.000	0.000	0.000
39	B	42	VAL	0	0.037	0.019	32.028	-0.061	-0.061	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.811	0.911	35.200	-8.309	-8.309	0.000	0.000	0.000	0.000
41	B	44	ASP	-1	-0.894	-0.961	38.019	7.512	7.512	0.000	0.000	0.000	0.000
42	B	45	LEU	0	-0.031	-0.004	33.339	-0.130	-0.130	0.000	0.000	0.000	0.000
43	B	46	THR	0	0.002	-0.020	35.531	0.022	0.022	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.913	0.959	37.191	-7.609	-7.609	0.000	0.000	0.000	0.000
45	B	48	SER	0	0.020	0.017	39.691	-0.206	-0.206	0.000	0.000	0.000	0.000
46	B	49	GLU	-1	-0.800	-0.876	35.323	8.922	8.922	0.000	0.000	0.000	0.000
47	B	50	MET	0	-0.067	-0.030	38.329	-0.009	-0.009	0.000	0.000	0.000	0.000
48	B	51	ASN	0	-0.078	-0.040	40.013	-0.247	-0.247	0.000	0.000	0.000	0.000
49	B	52	ILE	0	-0.033	0.001	38.900	-0.120	-0.120	0.000	0.000	0.000	0.000
50	B	53	ASN	0	-0.086	-0.036	36.440	0.034	0.034	0.000	0.000	0.000	0.000
51	B	54	GLU	-1	-0.899	-0.945	40.258	7.303	7.303	0.000	0.000	0.000	0.000
52	B	55	SER	0	-0.038	-0.024	36.451	-0.086	-0.086	0.000	0.000	0.000	0.000
53	B	56	THR	0	0.056	0.021	39.070	0.051	0.051	0.000	0.000	0.000	0.000
54	B	57	ASN	0	-0.063	-0.022	35.435	-0.041	-0.041	0.000	0.000	0.000	0.000
55	B	58	PHE	0	0.056	0.012	29.532	0.065	0.065	0.000	0.000	0.000	0.000
56	B	59	THR	0	0.025	-0.001	28.385	0.098	0.098	0.000	0.000	0.000	0.000
57	B	60	GLN	0	0.007	0.006	30.135	0.148	0.148	0.000	0.000	0.000	0.000
58	B	61	ILE	0	0.047	0.045	32.338	0.154	0.154	0.000	0.000	0.000	0.000
59	B	62	LEU	0	-0.008	-0.001	27.245	0.005	0.005	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.057	-0.037	27.979	0.303	0.303	0.000	0.000	0.000	0.000
61	B	64	THR	0	-0.017	-0.035	28.761	0.267	0.267	0.000	0.000	0.000	0.000
62	B	65	VAL	0	0.004	0.010	31.370	0.015	0.015	0.000	0.000	0.000	0.000
63	B	66	GLU	-1	-0.916	-0.962	23.748	12.985	12.985	0.000	0.000	0.000	0.000
64	B	67	PRO	0	-0.006	-0.007	26.313	0.220	0.220	0.000	0.000	0.000	0.000
65	B	68	LYS	1	0.837	0.893	27.352	-9.391	-9.391	0.000	0.000	0.000	0.000
66	B	69	ALA	0	0.003	0.011	28.973	-0.105	-0.105	0.000	0.000	0.000	0.000
67	B	70	LEU	0	-0.013	-0.019	22.948	0.069	0.069	0.000	0.000	0.000	0.000
68	B	71	GLU	-1	-0.951	-0.980	26.772	11.652	11.652	0.000	0.000	0.000	0.000
69	B	72	MET	0	-0.073	-0.022	28.743	-0.240	-0.240	0.000	0.000	0.000	0.000
70	B	73	VAL	0	-0.103	-0.037	26.848	-0.239	-0.239	0.000	0.000	0.000	0.000
71	B	74	SER	0	0.028	0.027	29.706	0.066	0.066	0.000	0.000	0.000	0.000
72	B	75	ASP	-1	-0.843	-0.926	28.585	11.174	11.174	0.000	0.000	0.000	0.000
73	B	76	SER	0	-0.047	-0.035	28.132	0.315	0.315	0.000	0.000	0.000	0.000
74	B	77	THR	0	-0.013	-0.012	28.272	0.193	0.193	0.000	0.000	0.000	0.000
75	B	78	ARG	1	0.968	0.998	22.582	-12.963	-12.963	0.000	0.000	0.000	0.000
76	B	79	GLU	-1	-0.897	-0.955	23.802	14.395	14.395	0.000	0.000	0.000	0.000
77	B	80	THR	0	-0.081	-0.050	24.540	0.329	0.329	0.000	0.000	0.000	0.000
78	B	81	VAL	0	0.026	0.015	22.763	0.217	0.217	0.000	0.000	0.000	0.000
79	B	82	LEU	0	-0.002	0.006	18.592	0.789	0.789	0.000	0.000	0.000	0.000
80	B	83	LYS	1	0.776	0.863	20.099	-11.700	-11.700	0.000	0.000	0.000	0.000
81	B	84	GLN	0	0.029	0.008	21.913	0.452	0.452	0.000	0.000	0.000	0.000
82	B	85	ILE	0	-0.019	-0.011	16.716	0.440	0.440	0.000	0.000	0.000	0.000
83	B	86	ARG	1	0.907	0.956	17.114	-14.921	-14.921	0.000	0.000	0.000	0.000
84	B	87	GLU	-1	-0.779	-0.867	18.015	13.713	13.713	0.000	0.000	0.000	0.000
85	B	88	PHE	0	0.024	0.018	15.240	0.270	0.270	0.000	0.000	0.000	0.000
86	B	89	LEU	0	-0.060	-0.039	12.535	0.942	0.942	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.954	-0.996	15.169	17.079	17.079	0.000	0.000	0.000	0.000
88	B	91	GLU	-1	-0.894	-0.942	17.583	14.667	14.667	0.000	0.000	0.000	0.000
89	B	92	ILE	0	-0.060	-0.016	12.365	0.225	0.225	0.000	0.000	0.000	0.000
90	B	93	VAL	0	-0.130	-0.058	13.472	0.762	0.762	0.000	0.000	0.000	0.000
91	B	94	ASP	-1	-0.825	-0.878	16.169	14.998	14.998	0.000	0.000	0.000	0.000
92	B	95	THR	0	-0.157	-0.093	18.110	-0.877	-0.877	0.000	0.000	0.000	0.000

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