FMO DATABASE

FMODB ID: 72N7K

Calculation Name: 3K1I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1I

Chain ID: A

ChEMBL ID:

UniProt ID: O25709

Base Structure: X-ray

Registration Date: 2023-06-22

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-839955.33702
FMO2-HF: Nuclear repulsion	797591.458056
FMO2-HF: Total energy	-42363.878964
FMO2-MP2: Total energy	-42489.093535

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:19:SER)

Summations of interaction energy for fragment #1(A:19: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.
-39.157	-33.943	10.57	-7.718	-8.064	0.024

Interaction energy analysis for fragmet #1(A:19:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.024

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	21	ALA	0	0.027	0.029	3.240	0.158	1.702	0.007	-0.682	-0.869	0.001
4	A	22	LYS	1	1.027	1.008	1.842	-24.439	-25.250	9.425	-4.089	-4.525	0.053
5	A	23	LEU	0	-0.024	-0.006	4.613	1.182	1.313	-0.001	-0.021	-0.108	0.000
6	A	24	ILE	0	0.044	0.020	6.586	0.310	0.310	0.000	0.000	0.000	0.000
7	A	25	GLU	-1	-0.806	-0.878	7.505	-0.783	-0.783	0.000	0.000	0.000	0.000
8	A	26	MET	0	-0.037	-0.026	7.908	0.368	0.368	0.000	0.000	0.000	0.000
9	A	27	LEU	0	-0.019	0.001	10.253	0.087	0.087	0.000	0.000	0.000	0.000
10	A	28	TYR	0	0.036	0.003	12.265	0.035	0.035	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.786	-0.888	13.157	-0.101	-0.101	0.000	0.000	0.000	0.000
12	A	30	GLY	0	-0.043	-0.015	14.331	0.049	0.049	0.000	0.000	0.000	0.000
13	A	31	ILE	0	0.016	0.010	16.135	0.019	0.019	0.000	0.000	0.000	0.000
14	A	32	LEU	0	-0.011	0.004	17.078	0.018	0.018	0.000	0.000	0.000	0.000
15	A	33	ARG	1	0.862	0.921	13.173	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	34	PHE	0	-0.010	-0.008	18.203	0.012	0.012	0.000	0.000	0.000	0.000
17	A	35	SER	0	0.040	0.004	21.902	0.003	0.003	0.000	0.000	0.000	0.000
18	A	36	SER	0	-0.003	0.002	23.343	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	37	GLN	0	-0.035	-0.010	24.625	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	38	ALA	0	0.025	0.010	26.101	0.002	0.002	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.804	0.895	27.760	0.035	0.035	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.895	0.945	29.199	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	41	CYS	0	-0.078	-0.030	29.904	0.005	0.005	0.000	0.000	0.000	0.000
24	A	42	ILE	0	-0.010	0.002	31.585	0.001	0.001	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.887	-0.948	32.653	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	44	ASN	0	-0.108	-0.056	34.720	0.003	0.003	0.000	0.000	0.000	0.000
27	A	45	GLU	-1	-0.916	-0.949	36.797	0.014	0.014	0.000	0.000	0.000	0.000
28	A	46	ASP	-1	-0.819	-0.883	34.130	0.047	0.047	0.000	0.000	0.000	0.000
29	A	47	ILE	0	0.028	-0.015	34.181	0.002	0.002	0.000	0.000	0.000	0.000
30	A	48	GLU	-1	-0.908	-0.945	34.175	0.053	0.053	0.000	0.000	0.000	0.000
31	A	49	LYS	1	0.862	0.911	30.412	-0.046	-0.046	0.000	0.000	0.000	0.000
32	A	50	LYS	1	0.830	0.920	29.503	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	51	ILE	0	0.004	0.002	29.545	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	52	TYR	0	-0.021	0.000	23.903	0.007	0.007	0.000	0.000	0.000	0.000
35	A	53	TYR	0	0.004	-0.021	24.450	0.006	0.006	0.000	0.000	0.000	0.000
36	A	54	ILE	0	-0.003	-0.001	24.651	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	55	ASN	0	0.006	0.005	25.248	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.877	0.939	17.937	-0.173	-0.173	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.009	0.000	20.596	0.005	0.005	0.000	0.000	0.000	0.000
40	A	58	THR	0	-0.040	-0.038	20.697	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	59	ASP	-1	-0.833	-0.888	20.112	0.111	0.111	0.000	0.000	0.000	0.000
42	A	60	ILE	0	0.008	0.011	15.110	0.005	0.005	0.000	0.000	0.000	0.000
43	A	61	PHE	0	0.021	-0.003	16.734	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	62	THR	0	-0.030	-0.022	18.751	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	63	GLU	-1	-0.947	-0.970	13.700	0.260	0.260	0.000	0.000	0.000	0.000
46	A	64	LEU	0	-0.013	-0.018	12.549	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.037	-0.022	14.927	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	66	ASN	0	-0.078	-0.050	16.245	0.013	0.013	0.000	0.000	0.000	0.000
49	A	67	ILE	0	-0.030	-0.001	10.235	0.027	0.027	0.000	0.000	0.000	0.000
50	A	68	LEU	0	-0.056	-0.010	12.982	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	69	ASP	-1	-0.739	-0.866	14.279	0.069	0.069	0.000	0.000	0.000	0.000
52	A	70	TYR	0	-0.042	-0.051	16.340	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	71	GLU	-1	-0.946	-0.949	18.115	0.062	0.062	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.755	0.850	14.351	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.032	0.030	16.706	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	74	GLY	0	-0.002	-0.005	17.266	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.925	-0.955	21.060	-0.135	-0.135	0.000	0.000	0.000	0.000
58	A	76	VAL	0	0.041	0.015	16.828	0.003	0.003	0.000	0.000	0.000	0.000
59	A	77	ALA	0	0.001	0.006	17.826	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	78	VAL	0	0.011	-0.002	19.014	0.012	0.012	0.000	0.000	0.000	0.000
61	A	79	TYR	0	-0.005	-0.003	20.423	0.015	0.015	0.000	0.000	0.000	0.000
62	A	80	LEU	0	0.007	0.001	15.930	0.004	0.004	0.000	0.000	0.000	0.000
63	A	81	THR	0	0.046	0.031	20.052	0.010	0.010	0.000	0.000	0.000	0.000
64	A	82	GLY	0	-0.002	0.027	22.003	0.012	0.012	0.000	0.000	0.000	0.000
65	A	83	LEU	0	-0.014	-0.001	20.065	0.009	0.009	0.000	0.000	0.000	0.000
66	A	84	TYR	0	0.076	0.023	15.770	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	85	THR	0	-0.023	-0.027	21.868	0.016	0.016	0.000	0.000	0.000	0.000
68	A	86	HIS	0	0.001	0.002	24.992	0.014	0.014	0.000	0.000	0.000	0.000
69	A	87	GLN	0	-0.010	-0.013	22.347	0.006	0.006	0.000	0.000	0.000	0.000
70	A	88	ILE	0	0.044	0.022	22.590	0.009	0.009	0.000	0.000	0.000	0.000
71	A	89	LYS	1	0.923	0.981	26.030	0.029	0.029	0.000	0.000	0.000	0.000
72	A	90	VAL	0	0.009	-0.001	28.009	0.005	0.005	0.000	0.000	0.000	0.000
73	A	91	LEU	0	0.031	0.015	23.686	0.004	0.004	0.000	0.000	0.000	0.000
74	A	92	THR	0	-0.037	-0.026	28.377	0.009	0.009	0.000	0.000	0.000	0.000
75	A	93	GLN	0	-0.085	-0.049	31.205	0.000	0.000	0.000	0.000	0.000	0.000
76	A	94	ALA	0	0.012	0.004	30.427	0.002	0.002	0.000	0.000	0.000	0.000
77	A	95	ASN	0	-0.006	-0.001	31.441	0.004	0.004	0.000	0.000	0.000	0.000
78	A	96	VAL	0	-0.025	-0.007	33.268	0.003	0.003	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.820	-0.909	36.339	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	98	ASN	0	-0.019	0.001	35.635	0.002	0.002	0.000	0.000	0.000	0.000
81	A	99	ASP	-1	-0.738	-0.825	34.984	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	100	ALA	0	0.054	0.009	32.387	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	101	SER	0	-0.039	-0.038	31.416	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	102	LYS	1	0.794	0.867	31.216	0.020	0.020	0.000	0.000	0.000	0.000
85	A	103	ILE	0	0.040	0.012	26.848	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	104	ASP	-1	-0.806	-0.885	26.739	-0.056	-0.056	0.000	0.000	0.000	0.000
87	A	105	LEU	0	-0.068	-0.027	26.915	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	106	VAL	0	0.025	0.018	23.088	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	107	LEU	0	-0.026	-0.010	22.491	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	108	ASN	0	0.000	0.001	22.144	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	109	VAL	0	-0.005	0.009	21.451	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	110	ALA	0	-0.004	-0.003	18.678	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.883	0.934	17.639	0.107	0.107	0.000	0.000	0.000	0.000
94	A	112	GLY	0	0.051	0.034	18.235	-0.036	-0.036	0.000	0.000	0.000	0.000
95	A	113	LEU	0	-0.053	-0.027	16.045	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	114	LEU	0	-0.017	-0.003	12.474	-0.080	-0.080	0.000	0.000	0.000	0.000
97	A	115	GLU	-1	-0.947	-0.983	13.827	-0.349	-0.349	0.000	0.000	0.000	0.000
98	A	116	ALA	0	0.033	0.021	15.925	-0.039	-0.039	0.000	0.000	0.000	0.000
99	A	117	TRP	0	-0.065	-0.042	7.110	0.019	0.019	0.000	0.000	0.000	0.000
100	A	118	ARG	1	0.767	0.841	10.976	0.341	0.341	0.000	0.000	0.000	0.000
101	A	119	GLU	-1	-0.913	-0.935	12.364	-0.489	-0.489	0.000	0.000	0.000	0.000
102	A	120	ILE	0	-0.091	-0.043	10.933	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	121	HIS	1	0.813	0.897	5.613	2.291	2.291	0.000	0.000	0.000	0.000
104	A	122	SER	0	-0.013	-0.003	9.223	-0.104	-0.104	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.917	-0.948	7.664	-1.840	-1.840	0.000	0.000	0.000	0.000
106	A	124	GLU	-1	-0.942	-0.973	2.732	-15.857	-11.507	1.139	-2.926	-2.562	-0.030

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:19:SER)