FMO DATABASE

FMODB ID: LJYK9

Calculation Name: 3KF8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF8

Chain ID: B

ChEMBL ID:

UniProt ID: C5M4J8

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-964730.7888
FMO2-HF: Nuclear repulsion	917779.971246
FMO2-HF: Total energy	-46950.817554
FMO2-MP2: Total energy	-47087.345707

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(B:2:SER)

Summations of interaction energy for fragment #1(B:2: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.
-6.865	-2.938	-0.019	-1.87	-2.037	-0.002

Interaction energy analysis for fragmet #1(B:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.028

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	B	4	ILE	0	-0.060	-0.020	3.810	-0.701	1.669	-0.035	-1.295	-1.040	0.002
4	B	5	ILE	0	-0.001	-0.001	6.662	-0.010	-0.010	0.000	0.000	0.000	0.000
5	B	6	LEU	0	0.038	0.009	9.476	0.075	0.075	0.000	0.000	0.000	0.000
6	B	7	ILE	0	-0.002	-0.006	12.813	0.042	0.042	0.000	0.000	0.000	0.000
7	B	8	PRO	0	0.035	0.006	13.303	0.005	0.005	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.013	0.004	14.212	0.024	0.024	0.000	0.000	0.000	0.000
9	B	10	ASN	0	-0.029	-0.016	13.576	0.027	0.027	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.012	0.014	10.094	-0.016	-0.016	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.003	-0.003	10.923	0.023	0.023	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.025	-0.023	13.026	-0.013	-0.013	0.000	0.000	0.000	0.000
13	B	14	GLU	-1	-0.886	-0.921	8.241	-0.587	-0.587	0.000	0.000	0.000	0.000
14	B	15	PHE	0	-0.036	-0.029	4.096	-0.242	0.044	0.004	-0.076	-0.213	0.000
15	B	16	PRO	0	0.001	0.003	9.331	0.020	0.020	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.921	-0.972	10.916	-0.260	-0.260	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.055	0.006	9.298	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	19	SER	0	0.022	-0.014	10.758	0.002	0.002	0.000	0.000	0.000	0.000
19	B	20	ILE	0	0.020	-0.012	12.490	0.015	0.015	0.000	0.000	0.000	0.000
20	B	21	SER	0	-0.072	-0.035	14.572	0.021	0.021	0.000	0.000	0.000	0.000
21	B	22	ASN	0	-0.075	-0.032	10.142	-0.025	-0.025	0.000	0.000	0.000	0.000
22	B	23	PRO	0	0.003	0.020	9.592	-0.028	-0.028	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.882	-0.937	3.539	-2.534	-1.776	0.010	-0.377	-0.391	-0.003
24	B	25	ARG	1	0.759	0.861	4.400	-1.092	-0.960	-0.001	-0.013	-0.118	0.000
25	B	26	LEU	0	0.013	0.010	3.836	0.203	0.584	0.003	-0.109	-0.275	-0.001
26	B	27	ARG	1	0.887	0.939	5.593	-0.359	-0.359	0.000	0.000	0.000	0.000
27	B	28	ILE	0	-0.017	0.002	7.500	-0.199	-0.199	0.000	0.000	0.000	0.000
28	B	29	LEU	0	0.008	0.022	10.640	0.036	0.036	0.000	0.000	0.000	0.000
29	B	30	ALA	0	-0.006	-0.006	13.403	-0.032	-0.032	0.000	0.000	0.000	0.000
30	B	31	GLN	0	0.006	-0.001	16.502	0.006	0.006	0.000	0.000	0.000	0.000
31	B	32	VAL	0	0.000	0.008	20.224	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	33	LYS	1	0.813	0.908	22.009	0.006	0.006	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.873	-0.949	24.366	0.032	0.032	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.006	-0.005	24.597	0.009	0.009	0.000	0.000	0.000	0.000
35	B	36	ILE	0	0.025	0.019	26.339	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	37	PRO	0	0.015	-0.003	27.817	0.006	0.006	0.000	0.000	0.000	0.000
37	B	38	HIS	0	-0.080	-0.041	29.878	0.006	0.006	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.867	-0.940	27.227	0.049	0.049	0.000	0.000	0.000	0.000
39	B	40	SER	0	-0.033	-0.002	25.108	0.009	0.009	0.000	0.000	0.000	0.000
40	B	41	THR	0	0.006	-0.007	22.392	0.014	0.014	0.000	0.000	0.000	0.000
41	B	42	ILE	0	-0.019	0.015	18.324	-0.010	-0.010	0.000	0.000	0.000	0.000
42	B	43	VAL	0	-0.003	0.002	21.045	0.004	0.004	0.000	0.000	0.000	0.000
43	B	44	ILE	0	-0.006	-0.005	15.433	-0.004	-0.004	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.802	-0.912	18.935	-0.041	-0.041	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.904	0.954	17.009	0.104	0.104	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.017	-0.010	17.161	0.013	0.013	0.000	0.000	0.000	0.000
47	B	48	PRO	0	-0.014	-0.028	19.518	-0.016	-0.016	0.000	0.000	0.000	0.000
48	B	49	THR	0	-0.041	-0.026	22.277	-0.008	-0.008	0.000	0.000	0.000	0.000
49	B	50	ILE	0	-0.005	0.033	16.529	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	51	THR	0	0.069	0.035	18.080	-0.009	-0.009	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.032	-0.012	20.942	0.014	0.014	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.908	-0.948	17.484	-0.205	-0.205	0.000	0.000	0.000	0.000
53	B	54	GLN	0	-0.021	-0.012	21.377	0.013	0.013	0.000	0.000	0.000	0.000
54	B	55	SER	0	0.015	-0.006	19.333	-0.013	-0.013	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.037	-0.020	19.897	0.005	0.005	0.000	0.000	0.000	0.000
56	B	57	TYR	0	-0.013	-0.011	19.876	0.003	0.003	0.000	0.000	0.000	0.000
57	B	58	ILE	0	0.022	0.025	15.091	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	59	ASN	0	-0.013	-0.019	19.680	0.002	0.002	0.000	0.000	0.000	0.000
59	B	60	ILE	0	0.042	0.025	14.722	0.006	0.006	0.000	0.000	0.000	0.000
60	B	61	CYS	0	-0.009	0.014	18.897	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	62	ILE	0	0.016	-0.007	18.150	0.019	0.019	0.000	0.000	0.000	0.000
62	B	63	PHE	0	0.045	0.004	20.590	0.004	0.004	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.054	-0.026	20.533	-0.014	-0.014	0.000	0.000	0.000	0.000
64	B	65	LEU	0	0.012	0.000	16.514	0.014	0.014	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.033	-0.010	21.204	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	67	GLU	-1	-0.964	-0.971	24.526	0.137	0.137	0.000	0.000	0.000	0.000
67	B	68	ALA	0	-0.001	-0.002	21.697	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	69	CYS	0	-0.056	-0.012	20.939	0.006	0.006	0.000	0.000	0.000	0.000
69	B	70	SER	0	0.015	0.014	22.566	-0.017	-0.017	0.000	0.000	0.000	0.000
70	B	71	SER	0	0.052	-0.011	24.177	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	72	ARG	1	0.823	0.894	24.665	-0.067	-0.067	0.000	0.000	0.000	0.000
72	B	73	VAL	0	0.007	0.009	19.547	-0.011	-0.011	0.000	0.000	0.000	0.000
73	B	74	LEU	0	-0.002	0.009	22.175	0.000	0.000	0.000	0.000	0.000	0.000
74	B	75	VAL	0	-0.081	-0.029	24.800	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	76	PRO	0	0.040	0.027	25.518	0.001	0.001	0.000	0.000	0.000	0.000
76	B	77	GLY	0	-0.028	-0.020	25.051	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	78	THR	0	-0.084	-0.043	21.678	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	79	LEU	0	-0.020	0.002	19.507	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	80	VAL	0	0.013	-0.012	16.488	0.013	0.013	0.000	0.000	0.000	0.000
80	B	81	ASN	0	-0.035	-0.020	11.598	-0.059	-0.059	0.000	0.000	0.000	0.000
81	B	82	ILE	0	0.007	-0.014	12.329	0.020	0.020	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.784	-0.848	8.941	0.727	0.727	0.000	0.000	0.000	0.000
83	B	84	ALA	0	0.029	0.004	8.779	-0.071	-0.071	0.000	0.000	0.000	0.000
84	B	85	PHE	0	0.011	0.004	8.250	0.241	0.241	0.000	0.000	0.000	0.000
85	B	86	TYR	0	-0.005	0.019	8.955	-0.097	-0.097	0.000	0.000	0.000	0.000
86	B	87	ASP	-1	-0.766	-0.879	10.024	0.131	0.131	0.000	0.000	0.000	0.000
87	B	88	GLY	0	0.051	0.029	12.438	-0.040	-0.040	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-1.050	-1.006	13.688	0.012	0.012	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.079	-0.052	16.005	0.001	0.001	0.000	0.000	0.000	0.000
90	B	91	ILE	0	0.007	-0.016	12.177	0.027	0.027	0.000	0.000	0.000	0.000
91	B	92	ASN	0	-0.057	-0.028	13.225	-0.039	-0.039	0.000	0.000	0.000	0.000
92	B	93	PRO	0	-0.011	-0.005	12.882	0.076	0.076	0.000	0.000	0.000	0.000
93	B	94	VAL	0	-0.041	-0.041	11.393	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	95	ASP	-1	-0.871	-0.946	13.477	0.363	0.363	0.000	0.000	0.000	0.000
95	B	96	ILE	0	-0.045	-0.023	14.140	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	97	TYR	0	0.004	0.021	13.474	-0.036	-0.036	0.000	0.000	0.000	0.000
97	B	98	GLU	-1	-0.801	-0.883	17.571	0.061	0.061	0.000	0.000	0.000	0.000
98	B	99	VAL	0	-0.034	-0.008	15.724	0.011	0.011	0.000	0.000	0.000	0.000
99	B	100	ASN	0	-0.003	-0.011	19.162	-0.023	-0.023	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.097	0.030	20.610	-0.008	-0.008	0.000	0.000	0.000	0.000
101	B	102	ALA	0	-0.037	-0.020	22.448	-0.013	-0.013	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.030	-0.021	17.516	-0.006	-0.006	0.000	0.000	0.000	0.000
103	B	104	PHE	0	0.002	0.004	15.521	-0.020	-0.020	0.000	0.000	0.000	0.000
104	B	105	THR	0	-0.031	-0.016	19.670	0.000	0.000	0.000	0.000	0.000	0.000
105	B	106	MET	0	0.028	0.007	19.506	-0.024	-0.024	0.000	0.000	0.000	0.000
106	B	107	GLU	-1	-0.828	-0.915	19.374	-0.125	-0.125	0.000	0.000	0.000	0.000
107	B	108	ASN	0	-0.021	-0.016	15.983	-0.034	-0.034	0.000	0.000	0.000	0.000
108	B	109	ILE	0	-0.026	-0.004	14.703	-0.049	-0.049	0.000	0.000	0.000	0.000
109	B	110	GLN	0	-0.010	-0.013	14.779	-0.048	-0.048	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.035	0.020	12.431	-0.048	-0.048	0.000	0.000	0.000	0.000
111	B	112	ILE	0	-0.034	-0.035	9.692	-0.085	-0.085	0.000	0.000	0.000	0.000
112	B	113	ASP	-1	-0.926	-0.940	10.031	-0.784	-0.784	0.000	0.000	0.000	0.000
113	B	114	GLU	-1	-0.871	-0.934	10.929	-0.510	-0.510	0.000	0.000	0.000	0.000
114	B	115	MET	0	-0.094	-0.041	7.518	-0.044	-0.044	0.000	0.000	0.000	0.000
115	B	116	ASN	0	-0.050	-0.026	6.247	-1.220	-1.220	0.000	0.000	0.000	0.000
116	B	117	ASN	0	-0.043	-0.031	7.449	-0.003	-0.003	0.000	0.000	0.000	0.000
117	B	118	SER	0	-0.032	-0.002	9.164	0.121	0.121	0.000	0.000	0.000	0.000
118	B	119	ILE	0	-0.009	-0.008	7.131	0.182	0.182	0.000	0.000	0.000	0.000
119	B	120	GLY	0	0.027	0.018	8.977	-0.091	-0.091	0.000	0.000	0.000	0.000
120	B	121	LYS	1	0.903	0.958	11.213	0.227	0.227	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER)