FMO DATABASE

FMODB ID: Z6YKN

Calculation Name: 3KOJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KOJ

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-06-21

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	-648534.557028
FMO2-HF: Nuclear repulsion	611049.273213
FMO2-HF: Total energy	-37485.283815
FMO2-MP2: Total energy	-37593.328952

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:HIS)

Summations of interaction energy for fragment #1(A:-3:HIS)

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.
-3.429	-2.06	0.003	-0.595	-0.778	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.001

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	-1	SER	0	0.021	0.013	3.808	-1.426	-0.057	0.003	-0.595	-0.778	0.003
4	A	0	HIS	0	0.026	0.016	6.370	0.403	0.403	0.000	0.000	0.000	0.000
5	A	1	MET	0	0.026	0.001	7.764	0.893	0.893	0.000	0.000	0.000	0.000
6	A	2	ASN	0	-0.015	-0.007	9.225	-0.392	-0.392	0.000	0.000	0.000	0.000
7	A	3	SER	0	0.006	0.003	9.828	0.439	0.439	0.000	0.000	0.000	0.000
8	A	4	CYS	0	-0.011	0.012	11.677	-0.353	-0.353	0.000	0.000	0.000	0.000
9	A	5	ILE	0	0.045	0.011	13.542	0.083	0.083	0.000	0.000	0.000	0.000
10	A	6	LEU	0	-0.027	-0.011	16.459	-0.104	-0.104	0.000	0.000	0.000	0.000
11	A	7	GLN	0	-0.002	0.011	19.854	0.013	0.013	0.000	0.000	0.000	0.000
12	A	8	ALA	0	-0.051	-0.032	22.787	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	9	THR	0	0.061	0.033	24.427	0.012	0.012	0.000	0.000	0.000	0.000
14	A	10	VAL	0	-0.002	0.004	24.267	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	11	VAL	0	-0.048	-0.033	26.548	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	12	GLU	-1	-0.940	-0.984	26.315	0.131	0.131	0.000	0.000	0.000	0.000
17	A	13	ALA	0	-0.030	-0.019	25.590	0.025	0.025	0.000	0.000	0.000	0.000
18	A	14	PRO	0	-0.016	-0.001	21.845	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	15	GLN	0	-0.009	0.012	22.466	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	16	LEU	0	-0.007	0.005	18.547	0.004	0.004	0.000	0.000	0.000	0.000
21	A	17	ARG	1	0.928	0.970	18.249	0.140	0.140	0.000	0.000	0.000	0.000
22	A	18	TYR	0	0.037	0.016	17.813	0.022	0.022	0.000	0.000	0.000	0.000
23	A	19	ALA	0	-0.032	-0.027	14.763	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	20	GLN	0	0.075	0.039	15.732	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	21	ASP	-1	-0.820	-0.899	13.097	-0.719	-0.719	0.000	0.000	0.000	0.000
26	A	22	ASN	0	-0.034	-0.038	16.072	0.070	0.070	0.000	0.000	0.000	0.000
27	A	23	GLN	0	-0.113	-0.050	13.868	-0.054	-0.054	0.000	0.000	0.000	0.000
28	A	24	THR	0	-0.047	-0.024	10.806	0.074	0.074	0.000	0.000	0.000	0.000
29	A	25	PRO	0	-0.011	0.012	13.860	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	26	VAL	0	-0.002	-0.009	14.004	0.012	0.012	0.000	0.000	0.000	0.000
31	A	27	ALA	0	0.012	0.008	15.757	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	28	GLU	-1	-0.953	-0.979	17.227	0.104	0.104	0.000	0.000	0.000	0.000
33	A	29	MET	0	0.043	0.025	19.592	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	30	VAL	0	-0.028	-0.001	21.808	0.018	0.018	0.000	0.000	0.000	0.000
35	A	31	VAL	0	0.007	0.009	21.750	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	32	GLN	0	0.013	-0.009	24.667	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	33	PHE	0	0.006	0.004	23.280	0.025	0.025	0.000	0.000	0.000	0.000
38	A	34	PRO	0	0.021	-0.002	26.713	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	35	GLY	0	0.024	0.029	27.868	0.023	0.023	0.000	0.000	0.000	0.000
40	A	36	LEU	0	0.047	0.000	27.202	0.006	0.006	0.000	0.000	0.000	0.000
41	A	37	SER	0	-0.050	-0.019	29.844	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	38	SER	0	0.021	0.019	28.905	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	39	LYS	1	0.793	0.899	29.428	-0.228	-0.228	0.000	0.000	0.000	0.000
44	A	40	ASP	-1	-0.775	-0.884	31.916	0.193	0.193	0.000	0.000	0.000	0.000
45	A	41	ALA	0	-0.053	-0.023	34.180	0.008	0.008	0.000	0.000	0.000	0.000
46	A	42	PRO	0	-0.011	-0.018	30.803	0.014	0.014	0.000	0.000	0.000	0.000
47	A	43	ALA	0	-0.001	0.016	26.499	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	44	ARG	1	0.953	0.972	26.639	-0.184	-0.184	0.000	0.000	0.000	0.000
49	A	45	LEU	0	-0.023	-0.008	19.090	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.967	0.999	19.281	-0.092	-0.092	0.000	0.000	0.000	0.000
51	A	47	VAL	0	-0.014	-0.015	17.151	0.065	0.065	0.000	0.000	0.000	0.000
52	A	48	VAL	0	0.015	0.012	14.202	-0.078	-0.078	0.000	0.000	0.000	0.000
53	A	49	GLY	0	0.017	0.021	12.949	0.198	0.198	0.000	0.000	0.000	0.000
54	A	50	TRP	0	0.026	-0.006	9.657	-0.280	-0.280	0.000	0.000	0.000	0.000
55	A	51	GLY	0	0.022	0.002	10.865	0.169	0.169	0.000	0.000	0.000	0.000
56	A	52	ALA	0	0.016	-0.004	11.594	0.025	0.025	0.000	0.000	0.000	0.000
57	A	53	VAL	0	0.035	0.024	11.860	-0.041	-0.041	0.000	0.000	0.000	0.000
58	A	54	ALA	0	-0.024	-0.001	13.787	-0.032	-0.032	0.000	0.000	0.000	0.000
59	A	55	GLN	0	-0.030	-0.028	15.561	-0.070	-0.070	0.000	0.000	0.000	0.000
60	A	56	GLU	-1	-0.921	-0.952	16.736	0.804	0.804	0.000	0.000	0.000	0.000
61	A	57	LEU	0	-0.020	-0.033	16.394	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	58	GLN	0	0.028	0.005	19.541	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	59	ASP	-1	-0.923	-0.953	21.396	0.262	0.262	0.000	0.000	0.000	0.000
64	A	60	ARG	1	0.826	0.911	21.973	-0.464	-0.464	0.000	0.000	0.000	0.000
65	A	61	CYS	0	-0.043	0.004	21.358	0.009	0.009	0.000	0.000	0.000	0.000
66	A	62	ARG	1	0.927	0.957	24.485	-0.265	-0.265	0.000	0.000	0.000	0.000
67	A	63	LEU	0	0.005	-0.010	27.875	0.016	0.016	0.000	0.000	0.000	0.000
68	A	64	ASN	0	-0.034	-0.026	29.957	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	65	ASP	-1	-0.793	-0.870	26.584	0.337	0.337	0.000	0.000	0.000	0.000
70	A	66	GLU	-1	-0.984	-0.987	26.660	0.355	0.355	0.000	0.000	0.000	0.000
71	A	67	VAL	0	-0.022	-0.015	21.539	0.016	0.016	0.000	0.000	0.000	0.000
72	A	68	VAL	0	-0.003	-0.006	17.960	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	69	LEU	0	-0.023	-0.013	16.739	0.033	0.033	0.000	0.000	0.000	0.000
74	A	70	GLU	-1	-0.817	-0.912	10.417	2.449	2.449	0.000	0.000	0.000	0.000
75	A	71	GLY	0	0.015	0.000	10.807	0.081	0.081	0.000	0.000	0.000	0.000
76	A	72	ARG	1	0.830	0.938	6.371	-3.597	-3.597	0.000	0.000	0.000	0.000
77	A	73	LEU	0	0.014	-0.007	11.041	-0.273	-0.273	0.000	0.000	0.000	0.000
78	A	74	ARG	1	0.885	0.949	13.016	0.009	0.009	0.000	0.000	0.000	0.000
79	A	75	ILE	0	0.017	0.008	15.253	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	76	ASN	0	-0.010	0.000	17.440	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	77	SER	0	0.021	0.015	19.295	0.011	0.011	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.837	-0.927	25.701	-0.067	-0.067	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.821	0.908	22.791	0.056	0.056	0.000	0.000	0.000	0.000
84	A	88	GLN	0	0.019	0.008	21.962	0.003	0.003	0.000	0.000	0.000	0.000
85	A	89	THR	0	-0.041	-0.019	19.399	0.003	0.003	0.000	0.000	0.000	0.000
86	A	90	GLU	-1	-0.822	-0.930	14.863	0.209	0.209	0.000	0.000	0.000	0.000
87	A	91	LEU	0	0.000	0.013	14.198	0.061	0.061	0.000	0.000	0.000	0.000
88	A	92	THR	0	-0.034	-0.021	10.100	-0.119	-0.119	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.009	-0.022	11.482	0.404	0.404	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.078	-0.039	7.717	0.408	0.408	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.889	0.927	7.644	-2.837	-2.837	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.022	0.013	13.132	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	97	HIS	0	0.018	0.027	16.881	0.020	0.020	0.000	0.000	0.000	0.000
94	A	98	HIS	0	0.006	0.006	19.663	-0.051	-0.051	0.000	0.000	0.000	0.000

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