FMO DATABASE

FMODB ID: VR931

Calculation Name: 3KIK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIK

Chain ID: A

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-621227.009606
FMO2-HF: Nuclear repulsion	582946.819547
FMO2-HF: Total energy	-38280.190059
FMO2-MP2: Total energy	-38391.249951

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:3:MET)

Summations of interaction energy for fragment #1(A:3: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.
-2.012	-0.713	2.297	-1.279	-2.316	0.002

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.038

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	A	5	THR	0	0.030	0.014	2.030	-1.914	-0.779	2.298	-1.262	-2.171	0.002
4	A	6	ALA	0	-0.028	-0.008	4.669	-0.255	-0.091	-0.001	-0.017	-0.145	0.000
5	A	7	GLN	0	0.050	0.017	8.102	-0.022	-0.022	0.000	0.000	0.000	0.000
6	A	8	LEU	0	0.011	0.003	6.385	0.051	0.051	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.858	0.923	8.645	-0.551	-0.551	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.032	-0.017	10.240	0.041	0.041	0.000	0.000	0.000	0.000
9	A	11	GLN	0	0.055	0.016	13.213	0.025	0.025	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.014	0.008	11.349	0.004	0.004	0.000	0.000	0.000	0.000
11	A	13	GLN	0	0.017	-0.009	14.050	0.109	0.109	0.000	0.000	0.000	0.000
12	A	14	GLN	0	0.079	0.033	16.178	0.008	0.008	0.000	0.000	0.000	0.000
13	A	15	TYR	0	0.059	0.040	16.178	0.003	0.003	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.059	-0.036	16.323	0.016	0.016	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.046	-0.025	19.938	0.017	0.017	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.898	-0.942	22.198	-0.101	-0.101	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.115	-0.053	23.199	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.014	0.013	24.879	0.000	0.000	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.051	-0.009	20.090	0.025	0.025	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.063	0.014	22.910	0.016	0.016	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.905	-0.952	24.499	0.105	0.105	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.037	-0.013	17.106	0.036	0.036	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.037	0.020	19.729	0.047	0.047	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.023	-0.009	21.284	0.032	0.032	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.031	-0.042	21.113	0.032	0.032	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.852	-0.916	14.617	0.628	0.628	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.004	0.001	17.899	0.070	0.070	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.941	0.964	20.294	-0.231	-0.231	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.023	0.007	16.648	0.020	0.020	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.935	0.980	12.968	-0.564	-0.564	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.033	0.023	17.135	0.033	0.033	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.054	-0.029	19.694	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	35	GLN	0	-0.011	0.006	13.198	-0.067	-0.067	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.841	-0.894	17.082	0.590	0.590	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.021	0.012	18.411	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	38	TRP	0	-0.052	-0.027	21.865	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	39	VAL	0	0.002	-0.014	23.918	-0.035	-0.035	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.946	-0.984	25.349	0.317	0.317	0.000	0.000	0.000	0.000
39	A	41	LYS	1	1.008	1.015	23.365	-0.455	-0.455	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.010	0.017	28.064	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.912	0.970	28.322	-0.316	-0.316	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.878	-0.940	30.779	0.258	0.258	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.027	-0.013	32.355	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	46	THR	0	-0.009	-0.015	34.135	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.941	0.961	35.445	-0.204	-0.204	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.042	-0.023	36.047	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.876	-0.944	37.957	0.148	0.148	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.080	-0.043	40.410	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.003	-0.006	40.926	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	52	ILE	0	-0.034	0.013	41.141	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	53	ASN	0	-0.048	-0.034	44.591	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.920	-0.953	45.905	0.110	0.110	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.053	-0.009	47.441	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.018	-0.025	44.606	0.003	0.003	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.025	-0.010	44.948	0.005	0.005	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.075	0.031	38.426	0.003	0.003	0.000	0.000	0.000	0.000
57	A	59	THR	0	0.032	0.016	41.845	0.004	0.004	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.032	-0.005	42.711	0.005	0.005	0.000	0.000	0.000	0.000
59	A	61	ILE	0	-0.006	0.008	39.497	0.003	0.003	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.006	-0.001	36.549	0.009	0.009	0.000	0.000	0.000	0.000
61	A	63	SER	0	-0.019	-0.009	38.451	0.004	0.004	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.045	-0.019	39.198	0.003	0.003	0.000	0.000	0.000	0.000
63	A	65	VAL	0	0.033	0.006	34.185	0.008	0.008	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.935	-0.962	33.972	0.156	0.156	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.013	-0.014	33.249	0.010	0.010	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.958	0.979	32.867	-0.157	-0.157	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.004	0.004	30.044	0.018	0.018	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.027	-0.016	28.420	0.025	0.025	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.896	-0.943	27.980	0.201	0.201	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.099	-0.041	26.823	0.013	0.013	0.000	0.000	0.000	0.000
71	A	73	VAL	0	-0.112	-0.038	22.091	0.037	0.037	0.000	0.000	0.000	0.000
72	A	74	SER	0	-0.004	-0.011	18.894	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.831	-0.933	20.436	0.331	0.331	0.000	0.000	0.000	0.000
74	A	76	SER	0	-0.004	0.013	15.305	0.017	0.017	0.000	0.000	0.000	0.000
75	A	77	THR	0	-0.037	-0.038	17.233	0.007	0.007	0.000	0.000	0.000	0.000
76	A	78	ARG	1	0.946	0.973	18.247	-0.276	-0.276	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.913	-0.960	18.699	0.279	0.279	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.104	-0.072	14.386	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.022	0.009	17.303	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.018	-0.007	19.731	-0.040	-0.040	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.865	0.936	17.102	-0.039	-0.039	0.000	0.000	0.000	0.000
82	A	84	GLN	0	0.013	0.009	15.926	-0.056	-0.056	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.020	-0.002	20.295	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	86	ARG	1	0.915	0.961	22.419	-0.084	-0.084	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.860	-0.945	20.050	-0.066	-0.066	0.000	0.000	0.000	0.000
86	A	88	PHE	0	-0.011	0.003	23.358	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	89	LEU	0	0.005	-0.032	24.844	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.965	-0.977	25.846	-0.038	-0.038	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.919	-0.944	25.633	-0.087	-0.087	0.000	0.000	0.000	0.000
90	A	92	ILE	0	-0.149	-0.048	28.640	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.096	-0.051	31.563	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.896	-0.939	32.450	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	95	THR	0	0.022	-0.004	30.484	0.003	0.003	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.097	-0.034	31.647	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)