FMO DATABASE

FMODB ID: R9568

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

Total energy (hartree)

FMO2-HF: Electronic energy	-649088.653896
FMO2-HF: Nuclear repulsion	611602.832435
FMO2-HF: Total energy	-37485.821461
FMO2-MP2: Total energy	-37593.814759

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.
-4.194	-2.778	0.003	-0.616	-0.804	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 : 0.014 / q_NPA : 0.000

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

Sort

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	0.011	0.000	3.808	-1.589	-0.173	0.003	-0.616	-0.804	0.003
4	A	0	HIS	0	0.043	0.033	6.384	0.330	0.330	0.000	0.000	0.000	0.000
5	A	1	MET	0	0.031	0.007	7.760	0.974	0.974	0.000	0.000	0.000	0.000
6	A	2	ASN	0	-0.006	-0.012	9.212	-0.424	-0.424	0.000	0.000	0.000	0.000
7	A	3	SER	0	-0.012	-0.001	9.828	0.375	0.375	0.000	0.000	0.000	0.000
8	A	4	CYS	0	-0.010	0.015	11.677	-0.379	-0.379	0.000	0.000	0.000	0.000
9	A	5	ILE	0	0.036	0.006	13.677	0.096	0.096	0.000	0.000	0.000	0.000
10	A	6	LEU	0	-0.030	-0.008	16.486	-0.113	-0.113	0.000	0.000	0.000	0.000
11	A	7	GLN	0	-0.004	0.008	19.854	0.018	0.018	0.000	0.000	0.000	0.000
12	A	8	ALA	0	-0.043	-0.028	22.748	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	9	THR	0	0.054	0.031	24.427	0.010	0.010	0.000	0.000	0.000	0.000
14	A	10	VAL	0	0.003	0.004	24.162	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	11	VAL	0	-0.040	-0.027	26.525	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	12	GLU	-1	-0.884	-0.931	26.433	0.189	0.189	0.000	0.000	0.000	0.000
17	A	13	ALA	0	-0.017	-0.015	25.571	0.029	0.029	0.000	0.000	0.000	0.000
18	A	14	PRO	0	-0.003	0.003	21.773	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	15	GLN	0	-0.025	0.008	22.445	-0.056	-0.056	0.000	0.000	0.000	0.000
20	A	16	LEU	0	0.005	0.009	18.633	0.010	0.010	0.000	0.000	0.000	0.000
21	A	17	ARG	1	0.933	0.975	18.150	0.051	0.051	0.000	0.000	0.000	0.000
22	A	18	TYR	0	0.036	0.017	17.836	0.024	0.024	0.000	0.000	0.000	0.000
23	A	19	ALA	0	-0.024	-0.019	14.741	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	20	GLN	0	0.073	0.040	15.760	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	21	ASP	-1	-0.822	-0.882	13.414	-0.653	-0.653	0.000	0.000	0.000	0.000
26	A	22	ASN	0	-0.058	-0.053	16.057	0.065	0.065	0.000	0.000	0.000	0.000
27	A	23	GLN	0	-0.084	-0.038	14.305	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	24	THR	0	-0.046	-0.040	10.844	0.060	0.060	0.000	0.000	0.000	0.000
29	A	25	PRO	0	-0.013	0.007	14.001	0.003	0.003	0.000	0.000	0.000	0.000
30	A	26	VAL	0	-0.017	-0.017	14.046	0.026	0.026	0.000	0.000	0.000	0.000
31	A	27	ALA	0	0.013	0.013	15.762	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	28	GLU	-1	-0.874	-0.936	17.207	0.213	0.213	0.000	0.000	0.000	0.000
33	A	29	MET	0	0.032	0.025	19.631	-0.037	-0.037	0.000	0.000	0.000	0.000
34	A	30	VAL	0	-0.018	0.000	21.801	0.026	0.026	0.000	0.000	0.000	0.000
35	A	31	VAL	0	0.003	0.007	21.695	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	32	GLN	0	0.007	-0.012	24.634	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	33	PHE	0	0.016	0.013	23.259	0.026	0.026	0.000	0.000	0.000	0.000
38	A	34	PRO	0	0.028	0.002	26.713	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	35	GLY	0	0.013	0.025	27.868	0.028	0.028	0.000	0.000	0.000	0.000
40	A	36	LEU	0	0.042	0.000	27.034	0.005	0.005	0.000	0.000	0.000	0.000
41	A	37	SER	0	-0.042	-0.020	29.961	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	38	SER	0	0.017	0.020	29.258	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	39	LYS	1	0.791	0.888	28.864	-0.276	-0.276	0.000	0.000	0.000	0.000
44	A	40	ASP	-1	-0.764	-0.869	31.889	0.233	0.233	0.000	0.000	0.000	0.000
45	A	41	ALA	0	-0.050	-0.023	34.222	0.008	0.008	0.000	0.000	0.000	0.000
46	A	42	PRO	0	-0.010	-0.018	30.803	0.016	0.016	0.000	0.000	0.000	0.000
47	A	43	ALA	0	-0.006	0.013	26.480	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	44	ARG	1	0.889	0.927	26.600	-0.235	-0.235	0.000	0.000	0.000	0.000
49	A	45	LEU	0	-0.029	-0.016	19.158	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.837	0.927	18.293	-0.201	-0.201	0.000	0.000	0.000	0.000
51	A	47	VAL	0	-0.022	-0.020	17.190	0.080	0.080	0.000	0.000	0.000	0.000
52	A	48	VAL	0	0.019	0.008	14.158	-0.086	-0.086	0.000	0.000	0.000	0.000
53	A	49	GLY	0	0.022	0.024	12.946	0.223	0.223	0.000	0.000	0.000	0.000
54	A	50	TRP	0	0.019	-0.010	9.699	-0.300	-0.300	0.000	0.000	0.000	0.000
55	A	51	GLY	0	0.026	0.007	10.986	0.175	0.175	0.000	0.000	0.000	0.000
56	A	52	ALA	0	0.015	-0.004	11.753	0.021	0.021	0.000	0.000	0.000	0.000
57	A	53	VAL	0	0.028	0.021	11.839	-0.049	-0.049	0.000	0.000	0.000	0.000
58	A	54	ALA	0	-0.027	0.002	13.875	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	55	GLN	0	-0.031	-0.041	15.633	-0.072	-0.072	0.000	0.000	0.000	0.000
60	A	56	GLU	-1	-0.915	-0.948	16.601	0.851	0.851	0.000	0.000	0.000	0.000
61	A	57	LEU	0	-0.016	-0.032	16.359	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	58	GLN	0	-0.019	-0.025	19.620	-0.032	-0.032	0.000	0.000	0.000	0.000
63	A	59	ASP	-1	-0.892	-0.934	21.506	0.276	0.276	0.000	0.000	0.000	0.000
64	A	60	ARG	1	0.825	0.914	21.902	-0.489	-0.489	0.000	0.000	0.000	0.000
65	A	61	CYS	0	-0.037	0.009	21.851	0.015	0.015	0.000	0.000	0.000	0.000
66	A	62	ARG	1	0.912	0.946	24.554	-0.300	-0.300	0.000	0.000	0.000	0.000
67	A	63	LEU	0	-0.005	-0.016	27.928	0.019	0.019	0.000	0.000	0.000	0.000
68	A	64	ASN	0	-0.053	-0.034	29.932	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	65	ASP	-1	-0.776	-0.858	26.641	0.372	0.372	0.000	0.000	0.000	0.000
70	A	66	GLU	-1	-0.971	-0.983	26.670	0.397	0.397	0.000	0.000	0.000	0.000
71	A	67	VAL	0	-0.031	-0.020	21.577	0.012	0.012	0.000	0.000	0.000	0.000
72	A	68	VAL	0	-0.001	-0.007	18.483	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	69	LEU	0	-0.008	-0.002	16.781	0.035	0.035	0.000	0.000	0.000	0.000
74	A	70	GLU	-1	-0.796	-0.885	10.274	2.671	2.671	0.000	0.000	0.000	0.000
75	A	71	GLY	0	0.029	0.004	10.775	0.084	0.084	0.000	0.000	0.000	0.000
76	A	72	ARG	1	0.811	0.926	6.292	-4.168	-4.168	0.000	0.000	0.000	0.000
77	A	73	LEU	0	0.008	-0.009	11.031	-0.296	-0.296	0.000	0.000	0.000	0.000
78	A	74	ARG	1	0.841	0.910	12.465	-0.178	-0.178	0.000	0.000	0.000	0.000
79	A	75	ILE	0	0.023	0.009	15.193	-0.035	-0.035	0.000	0.000	0.000	0.000
80	A	76	ASN	0	-0.040	-0.008	17.202	-0.081	-0.081	0.000	0.000	0.000	0.000
81	A	77	SER	0	0.046	0.031	19.072	0.011	0.011	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.830	-0.924	25.851	0.013	0.013	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.815	0.901	22.740	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	88	GLN	0	0.040	0.022	21.498	0.001	0.001	0.000	0.000	0.000	0.000
85	A	89	THR	0	-0.029	-0.023	19.572	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	90	GLU	-1	-0.777	-0.881	15.107	0.326	0.326	0.000	0.000	0.000	0.000
87	A	91	LEU	0	0.009	0.018	14.007	0.080	0.080	0.000	0.000	0.000	0.000
88	A	92	THR	0	-0.027	-0.017	10.166	-0.118	-0.118	0.000	0.000	0.000	0.000
89	A	93	VAL	0	0.005	-0.013	11.446	0.437	0.437	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.082	-0.045	7.676	0.449	0.449	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.869	0.905	7.796	-2.934	-2.934	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.018	0.010	13.142	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	97	HIS	0	0.014	0.022	16.893	0.002	0.002	0.000	0.000	0.000	0.000
94	A	98	HIS	0	0.006	0.004	19.680	-0.059	-0.059	0.000	0.000	0.000	0.000

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