FMO DATABASE

FMODB ID: 4352N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-596015.988961
FMO2-HF: Nuclear repulsion	558909.877384
FMO2-HF: Total energy	-37106.111577
FMO2-MP2: Total energy	-37214.696141

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.
18.372	24.094	0.627	-2.58	-3.768	0.01

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 : -0.910 / q_NPA : -0.956

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	-0.033	-0.018	3.407	-12.527	-9.502	0.017	-1.449	-1.593	0.009
4	B	7	GLN	0	0.015	-0.002	2.513	-1.635	-0.061	0.609	-0.742	-1.441	-0.001
5	B	8	LEU	0	0.054	0.024	3.897	-7.845	-6.833	0.002	-0.386	-0.628	0.002
6	B	9	LYS	1	0.954	0.971	5.555	-37.296	-37.185	-0.001	-0.003	-0.106	0.000
7	B	10	SER	0	0.013	0.002	7.723	-3.796	-3.796	0.000	0.000	0.000	0.000
8	B	11	GLN	0	-0.004	0.000	6.256	-4.380	-4.380	0.000	0.000	0.000	0.000
9	B	12	ILE	0	0.028	0.025	9.014	-2.494	-2.494	0.000	0.000	0.000	0.000
10	B	13	GLN	0	-0.022	-0.019	11.186	-1.867	-1.867	0.000	0.000	0.000	0.000
11	B	14	GLN	0	-0.015	-0.006	11.998	-1.248	-1.248	0.000	0.000	0.000	0.000
12	B	15	TYR	0	0.101	0.051	13.053	-1.127	-1.127	0.000	0.000	0.000	0.000
13	B	16	LEU	0	-0.042	-0.005	14.747	-1.378	-1.378	0.000	0.000	0.000	0.000
14	B	17	VAL	0	-0.082	-0.058	16.847	-1.264	-1.264	0.000	0.000	0.000	0.000
15	B	18	GLU	-1	-0.985	-0.985	16.545	17.906	17.906	0.000	0.000	0.000	0.000
16	B	19	SER	0	-0.048	-0.020	18.394	-0.998	-0.998	0.000	0.000	0.000	0.000
17	B	20	GLY	0	0.032	0.027	20.174	-0.681	-0.681	0.000	0.000	0.000	0.000
18	B	21	ASN	0	0.054	0.020	19.908	-0.032	-0.032	0.000	0.000	0.000	0.000
19	B	22	TYR	0	0.001	-0.007	18.886	-0.486	-0.486	0.000	0.000	0.000	0.000
20	B	23	GLU	-1	-0.939	-0.982	21.355	11.562	11.562	0.000	0.000	0.000	0.000
21	B	24	LEU	0	0.004	0.008	24.654	-0.499	-0.499	0.000	0.000	0.000	0.000
22	B	25	ILE	0	0.007	0.021	19.975	-0.301	-0.301	0.000	0.000	0.000	0.000
23	B	26	SER	0	-0.054	-0.025	23.768	-0.538	-0.538	0.000	0.000	0.000	0.000
24	B	27	ASN	0	-0.005	-0.022	25.254	-0.416	-0.416	0.000	0.000	0.000	0.000
25	B	28	GLU	-1	-0.844	-0.912	27.483	10.861	10.861	0.000	0.000	0.000	0.000
26	B	29	LEU	0	0.012	0.007	24.117	-0.331	-0.331	0.000	0.000	0.000	0.000
27	B	30	LYS	1	0.952	0.963	27.953	-11.325	-11.325	0.000	0.000	0.000	0.000
28	B	31	ALA	0	-0.011	0.002	30.389	-0.394	-0.394	0.000	0.000	0.000	0.000
29	B	32	ARG	1	0.874	0.933	29.885	-10.852	-10.852	0.000	0.000	0.000	0.000
30	B	33	LEU	0	0.025	0.012	28.245	-0.281	-0.281	0.000	0.000	0.000	0.000
31	B	34	LEU	0	-0.049	-0.029	32.611	-0.311	-0.311	0.000	0.000	0.000	0.000
32	B	35	GLN	0	-0.058	-0.027	35.037	-0.020	-0.020	0.000	0.000	0.000	0.000
33	B	36	GLU	-1	-0.835	-0.902	32.887	9.874	9.874	0.000	0.000	0.000	0.000
34	B	37	GLY	0	0.002	0.007	36.713	-0.143	-0.143	0.000	0.000	0.000	0.000
35	B	38	TRP	0	-0.022	-0.008	29.212	-0.182	-0.182	0.000	0.000	0.000	0.000
36	B	39	VAL	0	0.013	-0.013	33.176	-0.041	-0.041	0.000	0.000	0.000	0.000
37	B	40	ASP	-1	-0.943	-0.974	35.195	7.814	7.814	0.000	0.000	0.000	0.000
38	B	41	LYS	1	1.016	1.015	36.144	-8.894	-8.894	0.000	0.000	0.000	0.000
39	B	42	VAL	0	0.015	0.012	32.309	-0.047	-0.047	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.896	0.957	35.200	-8.448	-8.448	0.000	0.000	0.000	0.000
41	B	44	ASP	-1	-0.908	-0.949	38.019	7.596	7.596	0.000	0.000	0.000	0.000
42	B	45	LEU	0	-0.042	-0.016	33.293	-0.117	-0.117	0.000	0.000	0.000	0.000
43	B	46	THR	0	0.002	-0.019	35.539	0.028	0.028	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.944	0.951	37.191	-7.539	-7.539	0.000	0.000	0.000	0.000
45	B	48	SER	0	-0.006	0.002	39.668	-0.209	-0.209	0.000	0.000	0.000	0.000
46	B	49	GLU	-1	-0.882	-0.963	35.227	8.708	8.708	0.000	0.000	0.000	0.000
47	B	50	MET	0	-0.105	-0.040	38.329	-0.018	-0.018	0.000	0.000	0.000	0.000
48	B	51	ASN	0	-0.040	-0.016	40.013	-0.175	-0.175	0.000	0.000	0.000	0.000
49	B	52	ILE	0	-0.046	0.000	38.899	-0.147	-0.147	0.000	0.000	0.000	0.000
50	B	53	ASN	0	-0.037	-0.009	35.820	-0.073	-0.073	0.000	0.000	0.000	0.000
51	B	54	GLU	-1	-0.907	-0.947	40.258	7.333	7.333	0.000	0.000	0.000	0.000
52	B	55	SER	0	-0.054	-0.035	36.432	-0.075	-0.075	0.000	0.000	0.000	0.000
53	B	56	THR	0	0.035	0.014	39.070	0.111	0.111	0.000	0.000	0.000	0.000
54	B	57	ASN	0	-0.016	0.000	35.323	-0.037	-0.037	0.000	0.000	0.000	0.000
55	B	58	PHE	0	0.045	0.008	29.328	0.065	0.065	0.000	0.000	0.000	0.000
56	B	59	THR	0	0.021	-0.003	28.402	0.109	0.109	0.000	0.000	0.000	0.000
57	B	60	GLN	0	0.004	0.004	30.135	0.078	0.078	0.000	0.000	0.000	0.000
58	B	61	ILE	0	0.051	0.061	32.338	0.164	0.164	0.000	0.000	0.000	0.000
59	B	62	LEU	0	-0.007	-0.004	26.962	0.007	0.007	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.057	-0.047	27.977	0.282	0.282	0.000	0.000	0.000	0.000
61	B	64	THR	0	-0.007	-0.008	28.761	0.287	0.287	0.000	0.000	0.000	0.000
62	B	65	VAL	0	-0.002	-0.005	31.199	0.029	0.029	0.000	0.000	0.000	0.000
63	B	66	GLU	-1	-0.921	-0.964	23.625	13.031	13.031	0.000	0.000	0.000	0.000
64	B	67	PRO	0	-0.019	-0.013	26.307	0.222	0.222	0.000	0.000	0.000	0.000
65	B	68	LYS	1	0.940	0.971	27.356	-9.488	-9.488	0.000	0.000	0.000	0.000
66	B	69	ALA	0	0.000	0.011	28.936	-0.104	-0.104	0.000	0.000	0.000	0.000
67	B	70	LEU	0	-0.020	-0.022	22.807	0.084	0.084	0.000	0.000	0.000	0.000
68	B	71	GLU	-1	-0.954	-0.980	26.772	11.437	11.437	0.000	0.000	0.000	0.000
69	B	72	MET	0	-0.061	-0.016	28.743	-0.294	-0.294	0.000	0.000	0.000	0.000
70	B	73	VAL	0	-0.102	-0.037	26.971	-0.228	-0.228	0.000	0.000	0.000	0.000
71	B	74	SER	0	0.026	0.026	29.802	0.079	0.079	0.000	0.000	0.000	0.000
72	B	75	ASP	-1	-0.834	-0.921	28.658	11.167	11.167	0.000	0.000	0.000	0.000
73	B	76	SER	0	-0.050	-0.035	28.172	0.312	0.312	0.000	0.000	0.000	0.000
74	B	77	THR	0	-0.024	-0.023	28.043	0.240	0.240	0.000	0.000	0.000	0.000
75	B	78	ARG	1	0.967	0.990	22.013	-13.315	-13.315	0.000	0.000	0.000	0.000
76	B	79	GLU	-1	-0.921	-0.963	23.927	14.226	14.226	0.000	0.000	0.000	0.000
77	B	80	THR	0	-0.082	-0.055	24.498	0.349	0.349	0.000	0.000	0.000	0.000
78	B	81	VAL	0	0.035	0.020	22.610	0.228	0.228	0.000	0.000	0.000	0.000
79	B	82	LEU	0	-0.003	0.001	18.736	0.806	0.806	0.000	0.000	0.000	0.000
80	B	83	LYS	1	0.872	0.946	20.016	-11.320	-11.320	0.000	0.000	0.000	0.000
81	B	84	GLN	0	0.081	0.042	21.771	0.423	0.423	0.000	0.000	0.000	0.000
82	B	85	ILE	0	-0.034	-0.018	16.472	0.478	0.478	0.000	0.000	0.000	0.000
83	B	86	ARG	1	0.927	0.954	16.966	-15.038	-15.038	0.000	0.000	0.000	0.000
84	B	87	GLU	-1	-0.875	-0.945	17.814	13.945	13.945	0.000	0.000	0.000	0.000
85	B	88	PHE	0	0.011	0.017	15.154	0.353	0.353	0.000	0.000	0.000	0.000
86	B	89	LEU	0	-0.074	-0.045	12.586	0.979	0.979	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.961	-0.996	15.056	16.985	16.985	0.000	0.000	0.000	0.000
88	B	91	GLU	-1	-0.944	-0.973	17.462	14.786	14.786	0.000	0.000	0.000	0.000
89	B	92	ILE	0	-0.078	-0.015	12.132	0.317	0.317	0.000	0.000	0.000	0.000
90	B	93	VAL	0	-0.139	-0.060	13.533	0.851	0.851	0.000	0.000	0.000	0.000
91	B	94	ASP	-1	-0.804	-0.873	16.085	15.436	15.436	0.000	0.000	0.000	0.000
92	B	95	THR	0	-0.172	-0.101	18.246	-0.922	-0.922	0.000	0.000	0.000	0.000

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