FMO DATABASE

FMODB ID: 9GZ12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-964608.967726
FMO2-HF: Nuclear repulsion	917657.806312
FMO2-HF: Total energy	-46951.161414
FMO2-MP2: Total energy	-47087.639163

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.
-25.507	-19.563	9.338	-7.598	-7.684	-0.056

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 : -0.063 / q_NPA : -0.036

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	-0.048	-0.023	3.862	-0.998	0.990	-0.025	-1.097	-0.866	0.003
4	B	5	ILE	0	0.011	0.007	6.198	0.051	0.051	0.000	0.000	0.000	0.000
5	B	6	LEU	0	0.038	0.010	9.296	0.010	0.010	0.000	0.000	0.000	0.000
6	B	7	ILE	0	-0.002	-0.009	12.752	0.007	0.007	0.000	0.000	0.000	0.000
7	B	8	PRO	0	-0.008	-0.004	13.128	0.007	0.007	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.011	-0.003	13.938	0.005	0.005	0.000	0.000	0.000	0.000
9	B	10	ASN	0	-0.009	0.003	13.055	-0.005	-0.005	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.014	0.018	9.098	0.003	0.003	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.008	0.004	10.010	0.003	0.003	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.019	-0.025	12.293	-0.030	-0.030	0.000	0.000	0.000	0.000
13	B	14	GLU	-1	-0.866	-0.924	7.866	-0.061	-0.061	0.000	0.000	0.000	0.000
14	B	15	PHE	0	-0.039	-0.029	3.054	-1.343	-0.197	0.379	-0.542	-0.983	0.005
15	B	16	PRO	0	0.025	0.022	8.360	-0.072	-0.072	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.924	-0.968	10.039	-0.442	-0.442	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.043	0.002	8.130	-0.066	-0.066	0.000	0.000	0.000	0.000
18	B	19	SER	0	0.010	-0.006	9.582	0.150	0.150	0.000	0.000	0.000	0.000
19	B	20	ILE	0	0.022	0.002	11.503	-0.054	-0.054	0.000	0.000	0.000	0.000
20	B	21	SER	0	-0.074	-0.038	13.650	0.028	0.028	0.000	0.000	0.000	0.000
21	B	22	ASN	0	-0.091	-0.044	9.410	0.057	0.057	0.000	0.000	0.000	0.000
22	B	23	PRO	0	0.012	0.025	8.601	-0.148	-0.148	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.819	-0.905	1.944	-20.574	-20.039	8.222	-4.713	-4.044	-0.053
24	B	25	ARG	1	0.734	0.844	3.345	0.771	1.351	0.008	-0.187	-0.401	0.000
25	B	26	LEU	0	0.024	0.014	2.659	-1.617	0.036	0.755	-1.058	-1.350	-0.011
26	B	27	ARG	1	0.869	0.935	5.125	-0.198	-0.156	-0.001	-0.001	-0.040	0.000
27	B	28	ILE	0	-0.001	0.008	7.149	-0.081	-0.081	0.000	0.000	0.000	0.000
28	B	29	LEU	0	-0.016	-0.004	10.247	0.018	0.018	0.000	0.000	0.000	0.000
29	B	30	ALA	0	0.006	0.000	13.217	-0.013	-0.013	0.000	0.000	0.000	0.000
30	B	31	GLN	0	-0.011	-0.008	16.262	0.003	0.003	0.000	0.000	0.000	0.000
31	B	32	VAL	0	0.023	0.019	20.038	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	33	LYS	1	0.753	0.877	21.725	0.018	0.018	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.878	-0.948	24.315	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.016	-0.019	24.310	0.003	0.003	0.000	0.000	0.000	0.000
35	B	36	ILE	0	0.064	0.046	25.904	0.000	0.000	0.000	0.000	0.000	0.000
36	B	37	PRO	0	-0.012	-0.004	27.229	0.001	0.001	0.000	0.000	0.000	0.000
37	B	38	HIS	0	-0.062	-0.051	29.098	0.005	0.005	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.853	-0.921	26.352	-0.014	-0.014	0.000	0.000	0.000	0.000
39	B	40	SER	0	-0.039	-0.008	24.970	0.001	0.001	0.000	0.000	0.000	0.000
40	B	41	THR	0	0.001	-0.013	21.811	0.002	0.002	0.000	0.000	0.000	0.000
41	B	42	ILE	0	-0.022	0.010	17.731	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	43	VAL	0	0.014	0.014	20.855	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	44	ILE	0	-0.013	-0.008	15.139	0.004	0.004	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.784	-0.880	18.683	-0.039	-0.039	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.915	0.945	16.859	0.059	0.059	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.003	0.003	17.211	0.006	0.006	0.000	0.000	0.000	0.000
47	B	48	PRO	0	-0.032	-0.027	19.553	-0.007	-0.007	0.000	0.000	0.000	0.000
48	B	49	THR	0	-0.026	-0.024	22.732	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	50	ILE	0	0.000	0.025	16.184	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	51	THR	0	0.064	0.033	18.352	-0.006	-0.006	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.034	-0.010	21.161	0.005	0.005	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.907	-0.953	17.084	-0.102	-0.102	0.000	0.000	0.000	0.000
53	B	54	GLN	0	-0.029	-0.017	21.357	0.004	0.004	0.000	0.000	0.000	0.000
54	B	55	SER	0	0.029	-0.004	19.228	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.066	-0.043	19.592	0.000	0.000	0.000	0.000	0.000	0.000
56	B	57	TYR	0	-0.001	-0.003	19.628	0.001	0.001	0.000	0.000	0.000	0.000
57	B	58	ILE	0	0.016	0.020	14.790	-0.004	-0.004	0.000	0.000	0.000	0.000
58	B	59	ASN	0	0.016	0.000	19.441	0.008	0.008	0.000	0.000	0.000	0.000
59	B	60	ILE	0	0.021	0.008	14.248	-0.005	-0.005	0.000	0.000	0.000	0.000
60	B	61	CYS	0	-0.022	0.005	18.461	0.009	0.009	0.000	0.000	0.000	0.000
61	B	62	ILE	0	0.023	-0.002	17.902	0.003	0.003	0.000	0.000	0.000	0.000
62	B	63	PHE	0	0.027	-0.002	20.213	0.009	0.009	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.028	-0.024	19.853	0.004	0.004	0.000	0.000	0.000	0.000
64	B	65	LEU	0	0.029	0.019	16.084	0.011	0.011	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.024	-0.005	20.784	0.005	0.005	0.000	0.000	0.000	0.000
66	B	67	GLU	-1	-0.983	-0.982	24.160	0.065	0.065	0.000	0.000	0.000	0.000
67	B	68	ALA	0	-0.008	0.000	21.311	0.003	0.003	0.000	0.000	0.000	0.000
68	B	69	CYS	0	-0.070	-0.024	21.008	0.005	0.005	0.000	0.000	0.000	0.000
69	B	70	SER	0	0.020	0.012	22.569	-0.010	-0.010	0.000	0.000	0.000	0.000
70	B	71	SER	0	0.053	0.003	23.986	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	72	ARG	1	0.808	0.881	24.548	-0.034	-0.034	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.004	-0.002	19.228	-0.006	-0.006	0.000	0.000	0.000	0.000
73	B	74	LEU	0	0.005	0.011	21.642	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	75	VAL	0	-0.077	-0.024	24.233	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	76	PRO	0	0.031	0.018	25.101	0.000	0.000	0.000	0.000	0.000	0.000
76	B	77	GLY	0	-0.026	-0.022	25.138	0.001	0.001	0.000	0.000	0.000	0.000
77	B	78	THR	0	-0.075	-0.039	21.558	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	79	LEU	0	-0.011	0.007	19.689	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	80	VAL	0	0.016	-0.009	16.433	0.009	0.009	0.000	0.000	0.000	0.000
80	B	81	ASN	0	-0.027	-0.019	11.504	-0.035	-0.035	0.000	0.000	0.000	0.000
81	B	82	ILE	0	0.010	-0.006	12.065	0.011	0.011	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.796	-0.856	8.849	0.391	0.391	0.000	0.000	0.000	0.000
83	B	84	ALA	0	0.040	0.006	8.232	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	85	PHE	0	0.014	0.005	7.406	0.092	0.092	0.000	0.000	0.000	0.000
85	B	86	TYR	0	-0.046	-0.028	7.516	0.103	0.103	0.000	0.000	0.000	0.000
86	B	87	ASP	-1	-0.751	-0.850	8.624	-0.376	-0.376	0.000	0.000	0.000	0.000
87	B	88	GLY	0	0.049	0.038	11.238	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-1.023	-0.998	12.660	-0.082	-0.082	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.086	-0.067	14.503	0.038	0.038	0.000	0.000	0.000	0.000
90	B	91	ILE	0	0.015	-0.009	11.173	-0.033	-0.033	0.000	0.000	0.000	0.000
91	B	92	ASN	0	-0.056	-0.030	12.135	0.049	0.049	0.000	0.000	0.000	0.000
92	B	93	PRO	0	-0.013	-0.009	12.107	0.022	0.022	0.000	0.000	0.000	0.000
93	B	94	VAL	0	-0.046	-0.042	10.993	0.001	0.001	0.000	0.000	0.000	0.000
94	B	95	ASP	-1	-0.861	-0.935	13.172	0.217	0.217	0.000	0.000	0.000	0.000
95	B	96	ILE	0	-0.051	-0.026	13.639	-0.012	-0.012	0.000	0.000	0.000	0.000
96	B	97	TYR	0	0.005	0.020	13.282	-0.016	-0.016	0.000	0.000	0.000	0.000
97	B	98	GLU	-1	-0.801	-0.870	17.413	0.030	0.030	0.000	0.000	0.000	0.000
98	B	99	VAL	0	-0.029	-0.011	15.793	0.011	0.011	0.000	0.000	0.000	0.000
99	B	100	ASN	0	0.000	-0.001	19.186	-0.015	-0.015	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.088	0.033	21.033	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	102	ALA	0	-0.024	-0.022	22.475	-0.007	-0.007	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.029	-0.019	17.939	0.002	0.002	0.000	0.000	0.000	0.000
103	B	104	PHE	0	-0.004	0.006	15.556	-0.009	-0.009	0.000	0.000	0.000	0.000
104	B	105	THR	0	-0.043	-0.030	19.952	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	106	MET	0	0.017	0.009	20.263	-0.011	-0.011	0.000	0.000	0.000	0.000
106	B	107	GLU	-1	-0.806	-0.902	20.014	-0.047	-0.047	0.000	0.000	0.000	0.000
107	B	108	ASN	0	-0.023	-0.010	17.093	-0.014	-0.014	0.000	0.000	0.000	0.000
108	B	109	ILE	0	-0.040	-0.014	15.657	-0.023	-0.023	0.000	0.000	0.000	0.000
109	B	110	GLN	0	-0.011	-0.011	15.309	-0.023	-0.023	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.050	0.024	13.580	-0.024	-0.024	0.000	0.000	0.000	0.000
111	B	112	ILE	0	-0.036	-0.032	10.419	-0.040	-0.040	0.000	0.000	0.000	0.000
112	B	113	ASP	-1	-0.918	-0.938	10.801	-0.363	-0.363	0.000	0.000	0.000	0.000
113	B	114	GLU	-1	-0.877	-0.943	11.636	-0.223	-0.223	0.000	0.000	0.000	0.000
114	B	115	MET	0	-0.097	-0.035	8.495	-0.012	-0.012	0.000	0.000	0.000	0.000
115	B	116	ASN	0	-0.030	-0.005	6.642	-0.615	-0.615	0.000	0.000	0.000	0.000
116	B	117	ASN	0	-0.057	-0.034	7.969	-0.061	-0.061	0.000	0.000	0.000	0.000
117	B	118	SER	0	-0.041	-0.025	9.957	0.063	0.063	0.000	0.000	0.000	0.000
118	B	119	ILE	0	-0.038	-0.018	7.968	0.125	0.125	0.000	0.000	0.000	0.000
119	B	120	GLY	0	0.069	0.021	9.186	-0.026	-0.026	0.000	0.000	0.000	0.000
120	B	121	LYS	1	0.874	0.953	11.783	0.035	0.035	0.000	0.000	0.000	0.000

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