FMO DATABASE

FMODB ID: KGRG3

Calculation Name: 3FKC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FKC

Chain ID: A

ChEMBL ID:

UniProt ID: Q86T24

Base Structure: X-ray

Registration Date: 2023-09-20

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-863274.690674
FMO2-HF: Nuclear repulsion	819693.607392
FMO2-HF: Total energy	-43581.083282
FMO2-MP2: Total energy	-43711.328009

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:4:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
3.444	5.056	-0.012	-0.755	-0.846	0.001

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.010 / q_NPA : 0.990

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	6	LEU	0	0.043	0.029	3.786	1.927	3.539	-0.012	-0.755	-0.846	0.001
4	A	7	ILE	0	0.008	-0.003	6.391	-0.512	-0.512	0.000	0.000	0.000	0.000
5	A	8	SER	0	-0.020	-0.015	9.713	0.961	0.961	0.000	0.000	0.000	0.000
6	A	9	ALA	0	0.017	0.014	13.268	-0.257	-0.257	0.000	0.000	0.000	0.000
7	A	10	THR	0	-0.021	-0.025	16.802	0.155	0.155	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.825	-0.903	20.400	-11.409	-11.409	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.016	-0.019	23.348	0.245	0.245	0.000	0.000	0.000	0.000
10	A	13	GLN	0	0.012	0.011	26.461	0.637	0.637	0.000	0.000	0.000	0.000
11	A	14	TYR	0	0.001	0.015	25.410	0.407	0.407	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.004	0.000	27.524	0.335	0.335	0.000	0.000	0.000	0.000
13	A	16	GLY	0	0.052	0.026	29.569	0.308	0.308	0.000	0.000	0.000	0.000
14	A	17	SER	0	0.044	0.014	30.392	0.320	0.320	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.028	0.004	28.839	0.273	0.273	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.019	-0.002	31.921	0.236	0.236	0.000	0.000	0.000	0.000
17	A	20	ASN	0	-0.022	-0.019	34.874	0.369	0.369	0.000	0.000	0.000	0.000
18	A	21	SER	0	0.003	-0.013	33.882	0.196	0.196	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.039	-0.017	33.736	0.183	0.183	0.000	0.000	0.000	0.000
20	A	23	ASN	0	0.026	0.021	37.261	0.326	0.326	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.885	-0.935	38.763	-7.395	-7.395	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.054	-0.033	35.070	0.198	0.198	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.845	0.902	40.621	6.945	6.945	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.036	-0.005	43.110	0.155	0.155	0.000	0.000	0.000	0.000
25	A	28	HIS	0	-0.002	0.002	42.704	0.241	0.241	0.000	0.000	0.000	0.000
26	A	29	GLY	0	0.002	-0.001	44.980	0.091	0.091	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.022	-0.010	40.483	0.020	0.020	0.000	0.000	0.000	0.000
28	A	31	PHE	0	-0.003	-0.022	37.427	-0.120	-0.120	0.000	0.000	0.000	0.000
29	A	32	CYS	0	-0.076	0.001	40.455	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	33	ASP	-1	-0.759	-0.864	41.325	-6.913	-6.913	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.050	-0.018	43.358	0.099	0.099	0.000	0.000	0.000	0.000
32	A	35	THR	0	-0.031	-0.012	45.967	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.003	-0.002	47.708	0.016	0.016	0.000	0.000	0.000	0.000
34	A	37	ILE	0	-0.039	-0.025	50.517	0.014	0.014	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.034	0.007	52.675	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.822	-0.911	55.671	-5.201	-5.201	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.895	-0.940	59.439	-5.135	-5.135	0.000	0.000	0.000	0.000
38	A	41	ARG	1	0.892	0.960	53.761	5.530	5.530	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.940	0.962	53.460	5.311	5.311	0.000	0.000	0.000	0.000
40	A	43	PHE	0	0.004	0.006	48.941	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.850	0.934	45.284	6.334	6.334	0.000	0.000	0.000	0.000
42	A	45	ALA	0	0.050	0.013	43.352	-0.055	-0.055	0.000	0.000	0.000	0.000
43	A	46	HIS	0	0.030	0.034	38.779	0.066	0.066	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.856	0.918	40.277	6.665	6.665	0.000	0.000	0.000	0.000
45	A	48	ASN	0	0.019	0.009	33.870	0.146	0.146	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.027	0.016	34.801	-0.139	-0.139	0.000	0.000	0.000	0.000
47	A	50	LEU	0	0.017	0.025	37.512	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.013	0.005	38.101	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.002	0.009	34.707	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	53	SER	0	-0.034	-0.027	36.484	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	54	SER	0	-0.058	-0.046	39.010	0.090	0.090	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.040	0.004	40.744	-0.056	-0.056	0.000	0.000	0.000	0.000
53	A	56	TYR	0	0.021	0.034	42.625	0.025	0.025	0.000	0.000	0.000	0.000
54	A	57	PHE	0	0.045	-0.005	43.182	0.066	0.066	0.000	0.000	0.000	0.000
55	A	58	HIS	0	-0.074	-0.026	36.411	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	59	GLN	0	-0.025	-0.012	41.513	0.016	0.016	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.016	0.013	44.408	0.046	0.046	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.007	-0.026	42.106	0.085	0.085	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.039	-0.017	42.015	-0.096	-0.096	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.032	-0.007	43.017	0.030	0.030	0.000	0.000	0.000	0.000
61	A	64	ALA	0	-0.004	-0.002	45.384	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	65	GLY	0	0.052	0.016	46.331	0.144	0.144	0.000	0.000	0.000	0.000
63	A	66	GLN	0	-0.031	-0.030	46.547	-0.054	-0.054	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.008	-0.006	48.415	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	68	VAL	0	-0.017	0.004	48.665	0.019	0.019	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.863	-0.944	51.702	-5.369	-5.369	0.000	0.000	0.000	0.000
67	A	70	LEU	0	-0.042	-0.013	50.031	-0.090	-0.090	0.000	0.000	0.000	0.000
68	A	71	SER	0	0.047	0.023	54.512	0.057	0.057	0.000	0.000	0.000	0.000
69	A	72	PHE	0	-0.059	-0.047	56.032	-0.078	-0.078	0.000	0.000	0.000	0.000
70	A	73	ILE	0	0.012	0.020	51.570	-0.057	-0.057	0.000	0.000	0.000	0.000
71	A	74	ARG	1	0.791	0.855	55.737	5.325	5.325	0.000	0.000	0.000	0.000
72	A	75	ALA	0	0.007	-0.005	54.925	-0.134	-0.134	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.835	-0.918	54.074	-5.440	-5.440	0.000	0.000	0.000	0.000
74	A	77	ILE	0	0.013	0.021	52.190	-0.122	-0.122	0.000	0.000	0.000	0.000
75	A	78	PHE	0	0.031	-0.001	47.714	-0.170	-0.170	0.000	0.000	0.000	0.000
76	A	79	ALA	0	-0.012	0.001	49.075	-0.136	-0.136	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.832	-0.907	48.234	-6.424	-6.424	0.000	0.000	0.000	0.000
78	A	81	ILE	0	-0.034	-0.008	45.857	-0.184	-0.184	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.024	-0.011	44.600	-0.208	-0.208	0.000	0.000	0.000	0.000
80	A	83	ASN	0	0.015	-0.008	43.542	-0.225	-0.225	0.000	0.000	0.000	0.000
81	A	84	TYR	0	-0.016	0.028	39.383	-0.196	-0.196	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.054	-0.033	39.887	-0.227	-0.227	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.012	-0.032	38.936	-0.160	-0.160	0.000	0.000	0.000	0.000
84	A	87	SER	0	-0.018	-0.038	38.858	-0.041	-0.041	0.000	0.000	0.000	0.000
85	A	88	SER	0	-0.084	-0.039	36.667	-0.211	-0.211	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.920	0.962	38.745	7.809	7.809	0.000	0.000	0.000	0.000
87	A	90	ILE	0	0.067	0.032	42.137	0.076	0.076	0.000	0.000	0.000	0.000
88	A	91	VAL	0	-0.002	-0.013	45.369	-0.047	-0.047	0.000	0.000	0.000	0.000
89	A	92	ARG	1	0.925	0.954	47.997	6.001	6.001	0.000	0.000	0.000	0.000
90	A	93	VAL	0	0.040	0.038	50.527	0.111	0.111	0.000	0.000	0.000	0.000
91	A	94	ARG	1	0.840	0.901	52.872	5.321	5.321	0.000	0.000	0.000	0.000
92	A	95	SER	0	0.038	0.009	56.062	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	96	ASP	-1	-0.843	-0.908	57.076	-5.323	-5.323	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.002	0.011	55.690	0.035	0.035	0.000	0.000	0.000	0.000
95	A	98	LEU	0	-0.022	-0.003	51.365	-0.088	-0.088	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.851	-0.929	53.642	-5.678	-5.678	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.791	-0.869	55.222	-5.398	-5.398	0.000	0.000	0.000	0.000
98	A	101	LEU	0	-0.001	0.001	48.901	-0.071	-0.071	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.024	0.022	50.269	-0.110	-0.110	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.909	0.961	50.811	5.715	5.715	0.000	0.000	0.000	0.000
101	A	104	SER	0	0.041	-0.010	51.769	0.002	0.002	0.000	0.000	0.000	0.000
102	A	105	GLY	0	0.010	0.002	47.744	-0.082	-0.082	0.000	0.000	0.000	0.000
103	A	106	GLN	0	-0.040	-0.030	47.362	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.045	-0.007	48.990	-0.060	-0.060	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.039	0.025	46.574	-0.037	-0.037	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.065	0.054	45.043	-0.157	-0.157	0.000	0.000	0.000	0.000
107	A	110	VAL	0	-0.049	-0.024	42.376	-0.241	-0.241	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.841	0.893	38.975	7.722	7.722	0.000	0.000	0.000	0.000
109	A	112	PHE	0	0.032	0.026	40.671	0.077	0.077	0.000	0.000	0.000	0.000
110	A	113	ILE	0	0.051	0.020	42.666	0.084	0.084	0.000	0.000	0.000	0.000
111	A	114	ALA	0	-0.048	-0.020	45.798	0.143	0.143	0.000	0.000	0.000	0.000
112	A	115	ALA	0	0.006	0.011	44.964	0.106	0.106	0.000	0.000	0.000	0.000
113	A	116	LEU	0	-0.066	-0.019	45.426	0.142	0.142	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)