FMO DATABASE

FMODB ID: QY1ZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-649228.091905
FMO2-HF: Nuclear repulsion	611742.032601
FMO2-HF: Total energy	-37486.059303
FMO2-MP2: Total energy	-37594.062773

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.
-4.32	-2.961	-0.009	-0.571	-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 : 0.030 / q_NPA : 0.003

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	0.005	0.000	3.857	-1.062	0.297	-0.009	-0.571	-0.778	0.003
4	A	0	HIS	0	0.022	0.020	6.515	-0.143	-0.143	0.000	0.000	0.000	0.000
5	A	1	MET	0	0.027	0.005	7.878	1.007	1.007	0.000	0.000	0.000	0.000
6	A	2	ASN	0	-0.008	-0.008	8.977	-0.472	-0.472	0.000	0.000	0.000	0.000
7	A	3	SER	0	0.004	0.003	9.154	0.657	0.657	0.000	0.000	0.000	0.000
8	A	4	CYS	0	-0.020	-0.003	11.398	-0.389	-0.389	0.000	0.000	0.000	0.000
9	A	5	ILE	0	0.030	0.018	13.637	0.017	0.017	0.000	0.000	0.000	0.000
10	A	6	LEU	0	-0.023	-0.012	16.197	-0.109	-0.109	0.000	0.000	0.000	0.000
11	A	7	GLN	0	-0.008	-0.007	19.590	0.014	0.014	0.000	0.000	0.000	0.000
12	A	8	ALA	0	-0.023	-0.013	22.721	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	9	THR	0	0.049	0.037	24.516	0.007	0.007	0.000	0.000	0.000	0.000
14	A	10	VAL	0	0.011	-0.001	23.701	0.001	0.001	0.000	0.000	0.000	0.000
15	A	11	VAL	0	-0.051	-0.029	26.202	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	12	GLU	-1	-0.877	-0.923	26.103	0.194	0.194	0.000	0.000	0.000	0.000
17	A	13	ALA	0	0.016	0.000	25.227	0.027	0.027	0.000	0.000	0.000	0.000
18	A	14	PRO	0	-0.005	0.000	21.453	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	15	GLN	0	-0.029	-0.008	22.081	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	16	LEU	0	-0.025	0.000	18.552	0.002	0.002	0.000	0.000	0.000	0.000
21	A	17	ARG	1	0.895	0.956	17.508	0.083	0.083	0.000	0.000	0.000	0.000
22	A	18	TYR	0	0.053	0.028	17.435	0.016	0.016	0.000	0.000	0.000	0.000
23	A	19	ALA	0	-0.009	-0.003	14.386	0.025	0.025	0.000	0.000	0.000	0.000
24	A	20	GLN	0	0.018	0.003	15.970	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	21	ASP	-1	-0.796	-0.881	13.821	-0.737	-0.737	0.000	0.000	0.000	0.000
26	A	22	ASN	0	-0.080	-0.049	16.367	0.062	0.062	0.000	0.000	0.000	0.000
27	A	23	GLN	0	-0.047	-0.020	14.603	0.004	0.004	0.000	0.000	0.000	0.000
28	A	24	THR	0	-0.045	-0.034	10.799	0.012	0.012	0.000	0.000	0.000	0.000
29	A	25	PRO	0	-0.008	0.001	13.954	0.017	0.017	0.000	0.000	0.000	0.000
30	A	26	VAL	0	-0.028	-0.026	13.729	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	27	ALA	0	0.008	0.013	15.341	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	28	GLU	-1	-0.870	-0.935	16.826	0.181	0.181	0.000	0.000	0.000	0.000
33	A	29	MET	0	0.031	0.027	19.261	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	30	VAL	0	-0.020	0.004	21.327	0.031	0.031	0.000	0.000	0.000	0.000
35	A	31	VAL	0	0.014	0.010	21.530	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	32	GLN	0	0.025	0.000	24.482	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	33	PHE	0	0.018	0.015	22.921	0.023	0.023	0.000	0.000	0.000	0.000
38	A	34	PRO	0	0.032	0.000	26.851	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	35	GLY	0	0.006	0.023	28.119	0.026	0.026	0.000	0.000	0.000	0.000
40	A	36	LEU	0	0.035	-0.003	26.760	0.006	0.006	0.000	0.000	0.000	0.000
41	A	37	SER	0	-0.042	-0.018	29.735	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	38	SER	0	0.017	0.019	28.748	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	39	LYS	1	0.788	0.886	28.672	-0.300	-0.300	0.000	0.000	0.000	0.000
44	A	40	ASP	-1	-0.788	-0.883	31.735	0.250	0.250	0.000	0.000	0.000	0.000
45	A	41	ALA	0	-0.016	-0.005	34.292	0.009	0.009	0.000	0.000	0.000	0.000
46	A	42	PRO	0	-0.011	-0.025	30.412	0.014	0.014	0.000	0.000	0.000	0.000
47	A	43	ALA	0	0.005	0.026	26.206	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	44	ARG	1	0.846	0.891	26.216	-0.253	-0.253	0.000	0.000	0.000	0.000
49	A	45	LEU	0	-0.028	-0.004	18.875	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.845	0.935	17.651	-0.193	-0.193	0.000	0.000	0.000	0.000
51	A	47	VAL	0	-0.019	-0.016	17.145	0.093	0.093	0.000	0.000	0.000	0.000
52	A	48	VAL	0	0.019	0.007	13.779	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	49	GLY	0	0.024	0.026	12.566	0.212	0.212	0.000	0.000	0.000	0.000
54	A	50	TRP	0	0.022	-0.010	9.488	-0.313	-0.313	0.000	0.000	0.000	0.000
55	A	51	GLY	0	0.027	0.009	11.052	0.153	0.153	0.000	0.000	0.000	0.000
56	A	52	ALA	0	0.016	-0.003	11.980	0.036	0.036	0.000	0.000	0.000	0.000
57	A	53	VAL	0	0.024	0.017	11.566	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	54	ALA	0	-0.024	0.003	13.825	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	55	GLN	0	-0.012	-0.028	15.541	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	56	GLU	-1	-0.911	-0.953	16.564	0.791	0.791	0.000	0.000	0.000	0.000
61	A	57	LEU	0	-0.006	-0.024	16.021	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	58	GLN	0	-0.013	-0.016	19.372	-0.049	-0.049	0.000	0.000	0.000	0.000
63	A	59	ASP	-1	-0.865	-0.918	21.591	0.210	0.210	0.000	0.000	0.000	0.000
64	A	60	ARG	1	0.842	0.920	21.641	-0.461	-0.461	0.000	0.000	0.000	0.000
65	A	61	CYS	0	-0.014	0.022	21.704	0.027	0.027	0.000	0.000	0.000	0.000
66	A	62	ARG	1	0.849	0.908	24.516	-0.284	-0.284	0.000	0.000	0.000	0.000
67	A	63	LEU	0	-0.016	-0.012	27.640	0.023	0.023	0.000	0.000	0.000	0.000
68	A	64	ASN	0	-0.036	-0.027	29.606	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	65	ASP	-1	-0.809	-0.885	26.603	0.346	0.346	0.000	0.000	0.000	0.000
70	A	66	GLU	-1	-0.943	-0.970	26.617	0.409	0.409	0.000	0.000	0.000	0.000
71	A	67	VAL	0	-0.040	-0.011	21.697	0.006	0.006	0.000	0.000	0.000	0.000
72	A	68	VAL	0	-0.004	-0.005	18.454	0.011	0.011	0.000	0.000	0.000	0.000
73	A	69	LEU	0	-0.007	-0.008	16.890	0.013	0.013	0.000	0.000	0.000	0.000
74	A	70	GLU	-1	-0.803	-0.888	10.328	2.654	2.654	0.000	0.000	0.000	0.000
75	A	71	GLY	0	0.054	0.020	10.728	0.007	0.007	0.000	0.000	0.000	0.000
76	A	72	ARG	1	0.783	0.908	5.980	-4.486	-4.486	0.000	0.000	0.000	0.000
77	A	73	LEU	0	0.023	0.002	10.617	-0.342	-0.342	0.000	0.000	0.000	0.000
78	A	74	ARG	1	0.837	0.909	12.045	-0.154	-0.154	0.000	0.000	0.000	0.000
79	A	75	ILE	0	0.017	0.000	14.881	-0.048	-0.048	0.000	0.000	0.000	0.000
80	A	76	ASN	0	-0.070	-0.028	16.684	-0.108	-0.108	0.000	0.000	0.000	0.000
81	A	77	SER	0	0.063	0.051	18.653	0.011	0.011	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.814	-0.910	25.358	0.057	0.057	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.782	0.873	22.032	-0.067	-0.067	0.000	0.000	0.000	0.000
84	A	88	GLN	0	0.062	0.042	20.468	0.017	0.017	0.000	0.000	0.000	0.000
85	A	89	THR	0	-0.001	-0.016	19.459	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	90	GLU	-1	-0.776	-0.884	14.637	0.319	0.319	0.000	0.000	0.000	0.000
87	A	91	LEU	0	-0.003	0.008	13.907	0.095	0.095	0.000	0.000	0.000	0.000
88	A	92	THR	0	-0.016	-0.011	9.519	-0.144	-0.144	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.005	-0.008	11.052	0.498	0.498	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.099	-0.058	7.393	0.468	0.468	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.864	0.909	8.024	-2.726	-2.726	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.013	0.010	13.143	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	97	HIS	0	0.023	0.018	16.962	0.002	0.002	0.000	0.000	0.000	0.000
94	A	98	HIS	0	-0.021	-0.007	19.905	-0.058	-0.058	0.000	0.000	0.000	0.000

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