FMO DATABASE

FMODB ID: K3J43

Calculation Name: 3KF6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF6

Chain ID: A

ChEMBL ID:

UniProt ID: Q0E7J7

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	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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1361025.827026
FMO2-HF: Nuclear repulsion	1302993.586715
FMO2-HF: Total energy	-58032.240311
FMO2-MP2: Total energy	-58199.375621

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:16:SER)

Summations of interaction energy for fragment #1(A:16:SER)

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.
-2.062	0.578	-0.018	-1.202	-1.418	0.005

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / 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

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	18	TRP	0	0.039	0.010	3.821	0.536	2.121	-0.022	-0.966	-0.597	0.004
4	A	19	ASN	0	-0.041	-0.020	3.503	-0.440	-0.195	0.002	-0.037	-0.210	0.000
5	A	20	PRO	0	0.016	0.035	7.202	0.053	0.053	0.000	0.000	0.000	0.000
6	A	21	MET	0	-0.024	-0.019	10.012	0.056	0.056	0.000	0.000	0.000	0.000
7	A	22	PHE	0	0.037	0.021	12.744	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.043	0.006	15.656	0.034	0.034	0.000	0.000	0.000	0.000
9	A	24	SER	0	0.002	0.005	17.636	0.023	0.023	0.000	0.000	0.000	0.000
10	A	25	ASP	-1	-0.812	-0.899	14.351	0.168	0.168	0.000	0.000	0.000	0.000
11	A	26	VAL	0	0.015	0.010	12.725	0.037	0.037	0.000	0.000	0.000	0.000
12	A	27	HIS	0	-0.021	-0.023	14.509	0.030	0.030	0.000	0.000	0.000	0.000
13	A	28	LYS	1	0.802	0.903	16.220	-0.155	-0.155	0.000	0.000	0.000	0.000
14	A	29	ILE	0	-0.100	-0.028	10.376	0.029	0.029	0.000	0.000	0.000	0.000
15	A	30	SER	0	-0.026	0.000	13.534	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	31	PHE	0	0.066	0.010	11.974	0.041	0.041	0.000	0.000	0.000	0.000
17	A	32	HIS	0	0.074	0.020	14.656	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	33	PRO	0	0.040	0.013	16.160	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	34	HIS	0	0.014	0.025	17.073	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	35	LEU	0	0.008	-0.025	14.330	0.014	0.014	0.000	0.000	0.000	0.000
21	A	36	GLN	0	0.026	0.035	11.116	0.030	0.030	0.000	0.000	0.000	0.000
22	A	37	ARG	1	0.925	0.986	12.593	-0.100	-0.100	0.000	0.000	0.000	0.000
23	A	38	TYR	0	-0.027	-0.014	9.756	0.000	0.000	0.000	0.000	0.000	0.000
24	A	39	ILE	0	-0.044	-0.028	6.033	0.096	0.096	0.000	0.000	0.000	0.000
25	A	40	GLY	0	0.080	0.048	8.395	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	41	PHE	0	-0.027	-0.015	8.330	0.080	0.080	0.000	0.000	0.000	0.000
27	A	42	TRP	0	0.046	0.011	9.203	-0.092	-0.092	0.000	0.000	0.000	0.000
28	A	43	MET	0	-0.030	-0.017	10.297	0.055	0.055	0.000	0.000	0.000	0.000
29	A	44	GLY	0	0.055	0.037	11.667	0.007	0.007	0.000	0.000	0.000	0.000
30	A	45	PHE	0	-0.013	-0.008	6.602	0.083	0.083	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.032	0.035	3.723	-0.376	-0.184	0.001	-0.047	-0.145	0.000
32	A	47	ILE	0	-0.054	-0.040	4.317	-0.100	0.070	-0.001	-0.020	-0.148	0.000
33	A	48	ARG	1	0.949	0.958	5.296	-0.643	-0.545	-0.001	-0.002	-0.095	0.000
34	A	49	TRP	0	-0.003	-0.002	3.768	-1.109	-0.759	0.003	-0.130	-0.223	0.001
35	A	50	ILE	0	0.010	-0.001	6.471	0.075	0.075	0.000	0.000	0.000	0.000
36	A	51	GLN	0	0.080	0.057	9.237	-0.071	-0.071	0.000	0.000	0.000	0.000
37	A	52	ILE	0	-0.040	0.003	12.077	0.018	0.018	0.000	0.000	0.000	0.000
38	A	53	VAL	0	0.003	-0.025	15.378	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	54	GLY	0	0.040	0.035	18.728	0.012	0.012	0.000	0.000	0.000	0.000
40	A	55	TYR	0	-0.029	-0.028	22.131	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	56	ILE	0	-0.030	-0.014	25.098	0.008	0.008	0.000	0.000	0.000	0.000
42	A	57	ALA	0	0.023	0.007	26.677	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	58	ALA	0	0.000	-0.008	27.883	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	59	ILE	0	0.003	0.000	27.826	0.001	0.001	0.000	0.000	0.000	0.000
45	A	60	ASP	-1	-0.804	-0.868	28.480	0.022	0.022	0.000	0.000	0.000	0.000
46	A	61	ILE	0	-0.017	-0.020	28.582	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	62	TYR	0	-0.032	-0.019	27.844	0.004	0.004	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.924	-0.962	29.954	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	64	GLY	0	0.013	0.008	27.522	0.002	0.002	0.000	0.000	0.000	0.000
50	A	65	LYS	1	0.848	0.917	22.423	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	66	HIS	0	0.068	0.047	24.727	0.005	0.005	0.000	0.000	0.000	0.000
52	A	67	VAL	0	-0.037	-0.034	23.325	0.003	0.003	0.000	0.000	0.000	0.000
53	A	68	LEU	0	0.022	0.027	22.990	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	69	THR	0	0.011	0.007	23.107	0.011	0.011	0.000	0.000	0.000	0.000
55	A	70	VAL	0	-0.030	-0.014	20.853	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	71	ASP	-1	-0.755	-0.869	22.612	0.048	0.048	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.725	-0.833	18.981	0.060	0.060	0.000	0.000	0.000	0.000
58	A	73	CYS	0	-0.047	-0.017	22.331	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.104	-0.076	20.582	0.008	0.008	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.010	-0.003	22.544	0.009	0.009	0.000	0.000	0.000	0.000
61	A	76	MET	0	-0.047	-0.020	21.426	0.000	0.000	0.000	0.000	0.000	0.000
62	A	77	VAL	0	0.057	0.042	22.496	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	78	LEU	0	-0.019	-0.012	16.077	0.014	0.014	0.000	0.000	0.000	0.000
64	A	79	ARG	1	0.877	0.938	20.743	-0.054	-0.054	0.000	0.000	0.000	0.000
65	A	80	VAL	0	-0.012	-0.011	18.193	0.016	0.016	0.000	0.000	0.000	0.000
66	A	81	VAL	0	-0.027	-0.018	19.225	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.024	-0.007	19.073	0.000	0.000	0.000	0.000	0.000	0.000
68	A	83	ILE	0	-0.006	-0.001	18.697	0.003	0.003	0.000	0.000	0.000	0.000
69	A	84	ILE	0	0.027	0.011	21.839	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	85	GLN	0	-0.026	-0.018	23.110	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	86	ASP	-1	-0.921	-0.959	18.612	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.835	-0.925	19.657	-0.119	-0.119	0.000	0.000	0.000	0.000
73	A	88	PHE	0	0.028	0.027	21.737	0.006	0.006	0.000	0.000	0.000	0.000
74	A	89	SER	0	-0.017	-0.003	23.703	0.008	0.008	0.000	0.000	0.000	0.000
75	A	90	MET	0	-0.024	0.004	17.546	0.004	0.004	0.000	0.000	0.000	0.000
76	A	91	SER	0	0.016	-0.011	22.678	0.011	0.011	0.000	0.000	0.000	0.000
77	A	92	LYS	1	0.953	0.979	24.399	0.054	0.054	0.000	0.000	0.000	0.000
78	A	93	ARG	1	0.854	0.916	20.830	0.094	0.094	0.000	0.000	0.000	0.000
79	A	94	ALA	0	0.012	0.022	23.449	0.003	0.003	0.000	0.000	0.000	0.000
80	A	95	ILE	0	-0.017	-0.008	25.377	0.004	0.004	0.000	0.000	0.000	0.000
81	A	96	SER	0	-0.101	-0.047	28.481	0.000	0.000	0.000	0.000	0.000	0.000
82	A	97	MET	0	-0.048	-0.014	25.845	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	98	SER	0	0.021	0.007	29.306	0.004	0.004	0.000	0.000	0.000	0.000
84	A	99	PRO	0	0.004	-0.009	30.206	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	100	GLY	0	-0.008	0.005	29.650	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	101	ASN	0	-0.025	-0.011	27.863	0.000	0.000	0.000	0.000	0.000	0.000
87	A	102	VAL	0	0.052	0.031	23.278	0.005	0.005	0.000	0.000	0.000	0.000
88	A	103	VAL	0	-0.008	0.002	21.302	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	104	CYS	0	-0.087	-0.039	17.015	0.012	0.012	0.000	0.000	0.000	0.000
90	A	105	VAL	0	0.022	-0.001	15.838	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	106	PHE	0	-0.012	-0.004	7.179	0.030	0.030	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.084	0.027	11.577	-0.040	-0.040	0.000	0.000	0.000	0.000
93	A	108	LYS	1	0.894	0.968	9.799	0.064	0.064	0.000	0.000	0.000	0.000
94	A	109	ILE	0	-0.011	0.004	9.657	-0.085	-0.085	0.000	0.000	0.000	0.000
95	A	110	ASN	0	-0.078	-0.054	12.738	0.010	0.010	0.000	0.000	0.000	0.000
96	A	111	SER	0	0.008	-0.002	14.901	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	112	PHE	0	-0.027	0.000	17.271	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	113	ARG	1	0.945	0.972	20.265	-0.069	-0.069	0.000	0.000	0.000	0.000
99	A	114	SER	0	0.041	0.011	21.114	0.009	0.009	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.978	-0.968	21.803	0.085	0.085	0.000	0.000	0.000	0.000
101	A	116	VAL	0	-0.049	-0.022	15.078	0.000	0.000	0.000	0.000	0.000	0.000
102	A	117	GLU	-1	-0.796	-0.898	17.565	0.058	0.058	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.021	-0.019	12.682	0.036	0.036	0.000	0.000	0.000	0.000
104	A	119	ILE	0	-0.033	-0.013	14.674	-0.030	-0.030	0.000	0.000	0.000	0.000
105	A	120	ALA	0	0.001	0.000	14.209	0.020	0.020	0.000	0.000	0.000	0.000
106	A	121	GLN	0	-0.064	-0.034	10.035	-0.025	-0.025	0.000	0.000	0.000	0.000
107	A	122	SER	0	0.011	-0.023	14.067	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	123	PHE	0	0.007	-0.002	16.001	0.018	0.018	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.880	-0.912	18.420	-0.169	-0.169	0.000	0.000	0.000	0.000
110	A	125	GLU	-1	-0.778	-0.885	21.094	-0.040	-0.040	0.000	0.000	0.000	0.000
111	A	126	LEU	0	-0.064	-0.030	20.456	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	127	ARG	1	0.905	0.926	24.666	0.072	0.072	0.000	0.000	0.000	0.000
113	A	128	ASP	-1	-0.749	-0.849	26.687	-0.061	-0.061	0.000	0.000	0.000	0.000
114	A	129	PRO	0	0.026	0.000	26.899	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	130	ASN	0	-0.073	-0.050	27.110	0.008	0.008	0.000	0.000	0.000	0.000
116	A	131	ASP	-1	-0.824	-0.911	22.566	-0.092	-0.092	0.000	0.000	0.000	0.000
117	A	132	GLU	-1	-0.868	-0.943	21.893	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	133	TRP	0	0.027	0.018	22.063	0.002	0.002	0.000	0.000	0.000	0.000
119	A	134	LYS	1	0.789	0.894	20.901	0.086	0.086	0.000	0.000	0.000	0.000
120	A	135	ALA	0	-0.033	-0.014	17.989	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	136	TRP	0	0.079	0.028	17.552	0.008	0.008	0.000	0.000	0.000	0.000
122	A	137	GLN	0	-0.005	-0.001	18.951	0.004	0.004	0.000	0.000	0.000	0.000
123	A	138	LYS	1	0.902	0.945	13.462	0.201	0.201	0.000	0.000	0.000	0.000
124	A	139	ARG	1	0.803	0.883	13.915	0.009	0.009	0.000	0.000	0.000	0.000
125	A	140	MET	0	0.009	0.012	15.042	0.032	0.032	0.000	0.000	0.000	0.000
126	A	141	ARG	1	0.918	0.961	15.623	0.090	0.090	0.000	0.000	0.000	0.000
127	A	142	TYR	0	-0.014	-0.024	5.771	-0.125	-0.125	0.000	0.000	0.000	0.000
128	A	143	LYS	1	0.916	0.945	12.255	-0.109	-0.109	0.000	0.000	0.000	0.000
129	A	144	LYS	1	0.938	0.982	13.872	-0.020	-0.020	0.000	0.000	0.000	0.000
130	A	145	ASN	0	-0.026	-0.023	12.579	0.027	0.027	0.000	0.000	0.000	0.000
131	A	146	LEU	0	0.040	0.028	7.600	0.022	0.022	0.000	0.000	0.000	0.000
132	A	147	THR	0	0.001	-0.021	11.665	0.044	0.044	0.000	0.000	0.000	0.000
133	A	148	LYS	1	0.906	0.954	15.089	-0.086	-0.086	0.000	0.000	0.000	0.000
134	A	149	ILE	0	0.021	0.014	10.069	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	150	SER	0	-0.012	-0.010	13.027	0.000	0.000	0.000	0.000	0.000	0.000
136	A	151	LYS	1	0.938	0.956	14.104	-0.182	-0.182	0.000	0.000	0.000	0.000
137	A	152	ASN	0	-0.043	-0.017	16.170	-0.030	-0.030	0.000	0.000	0.000	0.000
138	A	153	HIS	0	-0.023	0.005	13.861	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	154	HIS	0	-0.031	0.007	13.265	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)