FMO DATABASE

FMODB ID: 3QL1L

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	OptH
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	-964080.787604
FMO2-HF: Nuclear repulsion	917130.524525
FMO2-HF: Total energy	-46950.263079
FMO2-MP2: Total energy	-47086.838364

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.
-7.719	-4.712	-0.018	-1.303	-1.686	-0.001

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 : -0.024 / 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

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	B	4	ILE	0	-0.034	-0.004	3.810	-0.349	1.623	-0.032	-1.047	-0.894	0.000
4	B	5	ILE	0	0.006	0.002	6.272	0.108	0.108	0.000	0.000	0.000	0.000
5	B	6	LEU	0	0.032	0.003	9.512	0.201	0.201	0.000	0.000	0.000	0.000
6	B	7	ILE	0	0.002	-0.001	12.562	0.114	0.114	0.000	0.000	0.000	0.000
7	B	8	PRO	0	0.029	0.000	13.007	-0.070	-0.070	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.019	0.004	13.524	-0.026	-0.026	0.000	0.000	0.000	0.000
9	B	10	ASN	0	-0.010	-0.005	12.477	0.077	0.077	0.000	0.000	0.000	0.000
10	B	11	ILE	0	-0.005	0.007	9.108	-0.068	-0.068	0.000	0.000	0.000	0.000
11	B	12	PRO	0	-0.006	-0.009	9.923	-0.086	-0.086	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.030	-0.023	12.076	0.000	0.000	0.000	0.000	0.000	0.000
13	B	14	GLU	-1	-0.959	-0.971	7.328	-1.048	-1.048	0.000	0.000	0.000	0.000
14	B	15	PHE	0	-0.056	-0.039	3.249	-0.612	-0.312	0.011	-0.086	-0.224	0.000
15	B	16	PRO	0	0.005	0.003	8.428	0.074	0.074	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.925	-0.973	10.460	-0.258	-0.258	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.047	0.014	8.866	0.027	0.027	0.000	0.000	0.000	0.000
18	B	19	SER	0	0.017	-0.017	10.475	0.112	0.112	0.000	0.000	0.000	0.000
19	B	20	ILE	0	0.035	-0.004	12.655	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	21	SER	0	-0.078	-0.041	14.715	0.036	0.036	0.000	0.000	0.000	0.000
21	B	22	ASN	0	-0.075	-0.033	10.212	0.096	0.096	0.000	0.000	0.000	0.000
22	B	23	PRO	0	0.006	0.026	9.762	-0.102	-0.102	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.877	-0.939	3.672	-2.314	-2.072	0.001	-0.048	-0.195	0.000
24	B	25	ARG	1	0.782	0.888	4.353	-0.497	-0.338	-0.001	-0.014	-0.144	0.000
25	B	26	LEU	0	-0.003	0.003	3.887	-1.037	-0.703	0.003	-0.108	-0.229	-0.001
26	B	27	ARG	1	0.909	0.963	5.631	0.627	0.627	0.000	0.000	0.000	0.000
27	B	28	ILE	0	-0.023	0.002	7.512	-0.302	-0.302	0.000	0.000	0.000	0.000
28	B	29	LEU	0	0.005	0.021	10.664	0.146	0.146	0.000	0.000	0.000	0.000
29	B	30	ALA	0	-0.001	-0.007	13.416	-0.040	-0.040	0.000	0.000	0.000	0.000
30	B	31	GLN	0	0.012	0.006	16.525	0.038	0.038	0.000	0.000	0.000	0.000
31	B	32	VAL	0	0.004	0.017	20.247	-0.015	-0.015	0.000	0.000	0.000	0.000
32	B	33	LYS	1	0.829	0.904	22.036	0.191	0.191	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.868	-0.936	24.402	-0.088	-0.088	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.010	-0.013	24.632	-0.007	-0.007	0.000	0.000	0.000	0.000
35	B	36	ILE	0	0.025	0.014	26.376	0.008	0.008	0.000	0.000	0.000	0.000
36	B	37	PRO	0	0.009	-0.007	27.855	0.002	0.002	0.000	0.000	0.000	0.000
37	B	38	HIS	0	-0.028	-0.014	29.911	0.007	0.007	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.911	-0.960	27.385	-0.085	-0.085	0.000	0.000	0.000	0.000
39	B	40	SER	0	-0.048	-0.005	25.145	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	41	THR	0	0.005	-0.005	22.361	-0.008	-0.008	0.000	0.000	0.000	0.000
41	B	42	ILE	0	-0.026	0.009	18.278	0.009	0.009	0.000	0.000	0.000	0.000
42	B	43	VAL	0	0.003	0.004	21.086	-0.021	-0.021	0.000	0.000	0.000	0.000
43	B	44	ILE	0	-0.017	-0.009	15.508	0.011	0.011	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.819	-0.933	18.874	-0.286	-0.286	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.943	0.994	17.036	0.269	0.269	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.017	-0.007	17.013	0.044	0.044	0.000	0.000	0.000	0.000
47	B	48	PRO	0	-0.014	-0.031	19.539	-0.008	-0.008	0.000	0.000	0.000	0.000
48	B	49	THR	0	-0.045	-0.030	22.301	-0.014	-0.014	0.000	0.000	0.000	0.000
49	B	50	ILE	0	-0.006	0.033	16.497	0.011	0.011	0.000	0.000	0.000	0.000
50	B	51	THR	0	0.071	0.045	17.988	0.013	0.013	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.044	-0.027	20.922	0.010	0.010	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.905	-0.945	16.774	-0.420	-0.420	0.000	0.000	0.000	0.000
53	B	54	GLN	0	-0.035	-0.025	20.830	-0.004	-0.004	0.000	0.000	0.000	0.000
54	B	55	SER	0	0.005	-0.011	18.814	-0.047	-0.047	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.035	-0.017	19.232	0.044	0.044	0.000	0.000	0.000	0.000
56	B	57	TYR	0	-0.024	-0.010	19.350	-0.021	-0.021	0.000	0.000	0.000	0.000
57	B	58	ILE	0	0.029	0.028	15.065	0.002	0.002	0.000	0.000	0.000	0.000
58	B	59	ASN	0	-0.019	-0.025	19.316	0.014	0.014	0.000	0.000	0.000	0.000
59	B	60	ILE	0	0.037	0.027	14.970	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	61	CYS	0	0.006	0.020	18.943	0.025	0.025	0.000	0.000	0.000	0.000
61	B	62	ILE	0	0.017	-0.006	18.130	0.002	0.002	0.000	0.000	0.000	0.000
62	B	63	PHE	0	0.051	0.003	20.619	0.019	0.019	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.064	-0.031	20.645	0.014	0.014	0.000	0.000	0.000	0.000
64	B	65	LEU	0	0.014	-0.003	16.618	0.015	0.015	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.038	-0.022	21.217	0.007	0.007	0.000	0.000	0.000	0.000
66	B	67	GLU	-1	-0.959	-0.967	24.538	0.047	0.047	0.000	0.000	0.000	0.000
67	B	68	ALA	0	0.002	0.000	21.670	0.004	0.004	0.000	0.000	0.000	0.000
68	B	69	CYS	0	-0.061	-0.006	20.919	0.004	0.004	0.000	0.000	0.000	0.000
69	B	70	SER	0	0.032	0.029	22.566	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	71	SER	0	0.054	-0.013	24.179	-0.009	-0.009	0.000	0.000	0.000	0.000
71	B	72	ARG	1	0.925	0.977	24.785	0.044	0.044	0.000	0.000	0.000	0.000
72	B	73	VAL	0	0.013	0.013	19.654	-0.012	-0.012	0.000	0.000	0.000	0.000
73	B	74	LEU	0	-0.007	0.005	22.190	-0.015	-0.015	0.000	0.000	0.000	0.000
74	B	75	VAL	0	-0.089	-0.033	24.817	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	76	PRO	0	0.039	0.024	25.534	-0.007	-0.007	0.000	0.000	0.000	0.000
76	B	77	GLY	0	-0.031	-0.023	25.075	0.009	0.009	0.000	0.000	0.000	0.000
77	B	78	THR	0	-0.074	-0.036	21.662	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	79	LEU	0	-0.017	0.007	19.457	-0.018	-0.018	0.000	0.000	0.000	0.000
79	B	80	VAL	0	0.012	-0.013	16.505	0.030	0.030	0.000	0.000	0.000	0.000
80	B	81	ASN	0	0.003	0.007	11.539	-0.120	-0.120	0.000	0.000	0.000	0.000
81	B	82	ILE	0	-0.002	-0.020	12.347	0.067	0.067	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.822	-0.887	9.016	0.124	0.124	0.000	0.000	0.000	0.000
83	B	84	ALA	0	0.016	-0.006	8.798	0.044	0.044	0.000	0.000	0.000	0.000
84	B	85	PHE	0	-0.004	0.002	8.284	0.054	0.054	0.000	0.000	0.000	0.000
85	B	86	TYR	0	0.006	0.024	8.486	0.056	0.056	0.000	0.000	0.000	0.000
86	B	87	ASP	-1	-0.783	-0.901	9.802	-0.326	-0.326	0.000	0.000	0.000	0.000
87	B	88	GLY	0	0.040	0.026	11.955	0.033	0.033	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-1.045	-0.999	13.180	-0.166	-0.166	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.049	-0.033	15.605	0.016	0.016	0.000	0.000	0.000	0.000
90	B	91	ILE	0	-0.014	-0.027	12.453	-0.050	-0.050	0.000	0.000	0.000	0.000
91	B	92	ASN	0	-0.054	-0.023	13.208	0.071	0.071	0.000	0.000	0.000	0.000
92	B	93	PRO	0	-0.015	-0.010	12.914	0.018	0.018	0.000	0.000	0.000	0.000
93	B	94	VAL	0	-0.046	-0.038	11.444	0.039	0.039	0.000	0.000	0.000	0.000
94	B	95	ASP	-1	-0.886	-0.958	13.440	0.186	0.186	0.000	0.000	0.000	0.000
95	B	96	ILE	0	-0.025	-0.010	14.145	-0.054	-0.054	0.000	0.000	0.000	0.000
96	B	97	TYR	0	-0.024	-0.005	13.211	-0.009	-0.009	0.000	0.000	0.000	0.000
97	B	98	GLU	-1	-0.894	-0.961	17.565	-0.079	-0.079	0.000	0.000	0.000	0.000
98	B	99	VAL	0	-0.032	-0.003	15.729	0.021	0.021	0.000	0.000	0.000	0.000
99	B	100	ASN	0	0.002	-0.011	19.149	-0.017	-0.017	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.091	0.019	20.604	-0.017	-0.017	0.000	0.000	0.000	0.000
101	B	102	ALA	0	-0.029	-0.012	22.463	-0.014	-0.014	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.031	-0.019	17.540	0.012	0.012	0.000	0.000	0.000	0.000
103	B	104	PHE	0	-0.001	0.004	15.775	-0.022	-0.022	0.000	0.000	0.000	0.000
104	B	105	THR	0	0.008	0.026	19.669	0.001	0.001	0.000	0.000	0.000	0.000
105	B	106	MET	0	0.034	0.007	19.470	-0.034	-0.034	0.000	0.000	0.000	0.000
106	B	107	GLU	-1	-0.866	-0.955	19.312	-0.160	-0.160	0.000	0.000	0.000	0.000
107	B	108	ASN	0	-0.023	-0.019	15.900	-0.007	-0.007	0.000	0.000	0.000	0.000
108	B	109	ILE	0	-0.019	-0.002	14.657	-0.058	-0.058	0.000	0.000	0.000	0.000
109	B	110	GLN	0	-0.011	-0.014	14.710	-0.046	-0.046	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.029	0.019	12.054	-0.024	-0.024	0.000	0.000	0.000	0.000
111	B	112	ILE	0	-0.045	-0.039	9.653	-0.043	-0.043	0.000	0.000	0.000	0.000
112	B	113	ASP	-1	-0.972	-0.970	9.941	-0.729	-0.729	0.000	0.000	0.000	0.000
113	B	114	GLU	-1	-0.854	-0.921	10.865	-0.291	-0.291	0.000	0.000	0.000	0.000
114	B	115	MET	0	-0.106	-0.045	7.522	0.088	0.088	0.000	0.000	0.000	0.000
115	B	116	ASN	0	-0.019	0.003	6.299	-1.120	-1.120	0.000	0.000	0.000	0.000
116	B	117	ASN	0	-0.009	-0.023	7.379	0.092	0.092	0.000	0.000	0.000	0.000
117	B	118	SER	0	-0.081	-0.031	9.069	0.160	0.160	0.000	0.000	0.000	0.000
118	B	119	ILE	0	0.010	-0.002	7.254	0.082	0.082	0.000	0.000	0.000	0.000
119	B	120	GLY	0	0.003	0.004	8.921	0.046	0.046	0.000	0.000	0.000	0.000
120	B	121	LYS	1	0.933	0.978	11.172	-0.142	-0.142	0.000	0.000	0.000	0.000

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