FMO DATABASE

FMODB ID: MV8YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-838387.682249
FMO2-HF: Nuclear repulsion	796024.3215
FMO2-HF: Total energy	-42363.360749
FMO2-MP2: Total energy	-42488.594253

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.
-29.881	-26.024	7.698	-5.152	-6.405	0.043

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 : 0.018

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	0.030	0.022	3.197	-0.337	1.472	0.020	-0.749	-1.081	0.000
4	A	22	LYS	1	1.026	1.011	1.899	-23.666	-22.999	7.656	-3.748	-4.575	0.047
5	A	23	LEU	0	-0.020	-0.018	4.329	1.111	1.309	-0.001	-0.034	-0.163	0.000
6	A	24	ILE	0	0.037	0.040	6.417	0.168	0.168	0.000	0.000	0.000	0.000
7	A	25	GLU	-1	-0.788	-0.870	7.782	-0.424	-0.424	0.000	0.000	0.000	0.000
8	A	26	MET	0	-0.021	-0.010	7.631	0.365	0.365	0.000	0.000	0.000	0.000
9	A	27	LEU	0	-0.050	-0.020	10.069	0.031	0.031	0.000	0.000	0.000	0.000
10	A	28	TYR	0	0.051	0.015	12.009	0.011	0.011	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.851	-0.929	12.781	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	30	GLY	0	-0.070	-0.041	14.106	0.024	0.024	0.000	0.000	0.000	0.000
13	A	31	ILE	0	0.026	0.012	15.995	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	32	LEU	0	0.009	0.011	17.125	0.003	0.003	0.000	0.000	0.000	0.000
15	A	33	ARG	1	0.888	0.950	13.725	-0.172	-0.172	0.000	0.000	0.000	0.000
16	A	34	PHE	0	0.007	-0.002	17.966	0.000	0.000	0.000	0.000	0.000	0.000
17	A	35	SER	0	0.031	0.016	21.519	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	36	SER	0	0.007	0.009	23.274	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	37	GLN	0	-0.031	-0.006	24.138	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	38	ALA	0	0.034	-0.006	25.847	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.784	0.887	27.502	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.942	0.975	29.057	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	41	CYS	0	-0.083	-0.029	29.699	0.002	0.002	0.000	0.000	0.000	0.000
24	A	42	ILE	0	-0.011	0.007	31.308	0.000	0.000	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.914	-0.965	33.070	0.018	0.018	0.000	0.000	0.000	0.000
26	A	44	ASN	0	-0.091	-0.058	34.336	0.001	0.001	0.000	0.000	0.000	0.000
27	A	45	GLU	-1	-0.943	-0.953	36.401	0.028	0.028	0.000	0.000	0.000	0.000
28	A	46	ASP	-1	-0.862	-0.906	34.344	0.064	0.064	0.000	0.000	0.000	0.000
29	A	47	ILE	0	0.041	-0.010	34.132	0.003	0.003	0.000	0.000	0.000	0.000
30	A	48	GLU	-1	-0.881	-0.942	33.590	0.068	0.068	0.000	0.000	0.000	0.000
31	A	49	LYS	1	0.870	0.927	29.916	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	50	LYS	1	0.869	0.936	29.326	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	51	ILE	0	-0.026	-0.015	29.303	0.000	0.000	0.000	0.000	0.000	0.000
34	A	52	TYR	0	-0.020	0.000	23.357	0.010	0.010	0.000	0.000	0.000	0.000
35	A	53	TYR	0	0.001	-0.029	24.316	0.009	0.009	0.000	0.000	0.000	0.000
36	A	54	ILE	0	0.010	0.007	24.345	0.002	0.002	0.000	0.000	0.000	0.000
37	A	55	ASN	0	0.021	0.004	24.740	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.872	0.952	17.592	-0.219	-0.219	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.034	-0.027	20.472	0.012	0.012	0.000	0.000	0.000	0.000
40	A	58	THR	0	0.033	-0.003	20.493	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	59	ASP	-1	-0.872	-0.896	19.202	0.152	0.152	0.000	0.000	0.000	0.000
42	A	60	ILE	0	-0.001	0.010	14.713	0.005	0.005	0.000	0.000	0.000	0.000
43	A	61	PHE	0	0.018	0.001	16.327	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	62	THR	0	-0.027	-0.024	18.608	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	63	GLU	-1	-0.963	-0.978	12.587	0.378	0.378	0.000	0.000	0.000	0.000
46	A	64	LEU	0	-0.011	-0.022	12.330	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.041	-0.013	14.616	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	66	ASN	0	-0.076	-0.052	15.515	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	67	ILE	0	-0.036	0.003	9.861	0.007	0.007	0.000	0.000	0.000	0.000
50	A	68	LEU	0	-0.068	-0.020	12.584	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	69	ASP	-1	-0.728	-0.856	13.807	0.034	0.034	0.000	0.000	0.000	0.000
52	A	70	TYR	0	-0.060	-0.048	15.890	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	71	GLU	-1	-0.974	-1.009	17.544	0.027	0.027	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.797	0.899	13.373	-0.028	-0.028	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.003	0.019	17.066	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	74	GLY	0	0.020	-0.005	17.800	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.913	-0.934	21.287	-0.089	-0.089	0.000	0.000	0.000	0.000
58	A	76	VAL	0	0.037	0.012	16.591	0.003	0.003	0.000	0.000	0.000	0.000
59	A	77	ALA	0	0.007	0.018	18.107	0.003	0.003	0.000	0.000	0.000	0.000
60	A	78	VAL	0	0.043	0.015	19.078	0.009	0.009	0.000	0.000	0.000	0.000
61	A	79	TYR	0	-0.002	0.005	20.634	0.012	0.012	0.000	0.000	0.000	0.000
62	A	80	LEU	0	0.017	-0.005	15.792	0.004	0.004	0.000	0.000	0.000	0.000
63	A	81	THR	0	0.020	0.012	19.896	0.015	0.015	0.000	0.000	0.000	0.000
64	A	82	GLY	0	-0.011	0.015	21.493	0.010	0.010	0.000	0.000	0.000	0.000
65	A	83	LEU	0	0.002	0.004	20.210	0.009	0.009	0.000	0.000	0.000	0.000
66	A	84	TYR	0	0.059	0.017	15.506	0.005	0.005	0.000	0.000	0.000	0.000
67	A	85	THR	0	-0.031	-0.029	21.466	0.012	0.012	0.000	0.000	0.000	0.000
68	A	86	HIS	0	-0.023	-0.006	24.571	0.010	0.010	0.000	0.000	0.000	0.000
69	A	87	GLN	0	0.005	-0.014	22.290	0.005	0.005	0.000	0.000	0.000	0.000
70	A	88	ILE	0	0.034	0.018	22.198	0.007	0.007	0.000	0.000	0.000	0.000
71	A	89	LYS	1	0.940	0.974	25.765	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	90	VAL	0	-0.010	-0.002	27.806	0.002	0.002	0.000	0.000	0.000	0.000
73	A	91	LEU	0	0.027	0.011	23.597	0.003	0.003	0.000	0.000	0.000	0.000
74	A	92	THR	0	-0.050	-0.021	28.284	0.005	0.005	0.000	0.000	0.000	0.000
75	A	93	GLN	0	-0.014	-0.013	31.125	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	94	ALA	0	0.017	0.020	30.612	0.000	0.000	0.000	0.000	0.000	0.000
77	A	95	ASN	0	0.016	0.020	31.496	0.002	0.002	0.000	0.000	0.000	0.000
78	A	96	VAL	0	-0.040	-0.028	33.381	0.001	0.001	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.917	-0.943	36.369	0.005	0.005	0.000	0.000	0.000	0.000
80	A	98	ASN	0	-0.010	0.000	35.487	0.002	0.002	0.000	0.000	0.000	0.000
81	A	99	ASP	-1	-0.739	-0.831	34.722	0.000	0.000	0.000	0.000	0.000	0.000
82	A	100	ALA	0	0.035	-0.005	32.399	0.000	0.000	0.000	0.000	0.000	0.000
83	A	101	SER	0	-0.047	-0.048	31.406	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	102	LYS	1	0.847	0.886	31.508	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	103	ILE	0	0.048	0.020	26.784	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	104	ASP	-1	-0.832	-0.897	26.732	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	105	LEU	0	-0.048	-0.017	26.913	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	106	VAL	0	0.005	0.011	22.933	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	107	LEU	0	-0.028	-0.030	22.531	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	108	ASN	0	0.001	0.011	22.317	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	109	VAL	0	0.029	0.029	21.552	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	110	ALA	0	-0.026	-0.004	19.054	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.902	0.920	18.166	0.043	0.043	0.000	0.000	0.000	0.000
94	A	112	GLY	0	0.019	0.016	19.038	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	113	LEU	0	-0.039	-0.023	16.238	-0.022	-0.022	0.000	0.000	0.000	0.000
96	A	114	LEU	0	-0.029	-0.011	13.010	-0.056	-0.056	0.000	0.000	0.000	0.000
97	A	115	GLU	-1	-0.949	-0.983	14.395	-0.230	-0.230	0.000	0.000	0.000	0.000
98	A	116	ALA	0	0.033	0.036	16.446	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	117	TRP	0	-0.049	-0.041	7.155	0.059	0.059	0.000	0.000	0.000	0.000
100	A	118	ARG	1	0.755	0.839	11.162	0.174	0.174	0.000	0.000	0.000	0.000
101	A	119	GLU	-1	-0.919	-0.939	12.810	-0.323	-0.323	0.000	0.000	0.000	0.000
102	A	120	ILE	0	-0.080	-0.043	11.349	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	121	HIS	1	0.821	0.903	6.096	1.464	1.464	0.000	0.000	0.000	0.000
104	A	122	SER	0	0.004	0.004	9.183	-0.117	-0.117	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.969	-0.968	8.307	-1.150	-1.150	0.000	0.000	0.000	0.000
106	A	124	GLU	-1	-0.916	-0.948	3.432	-6.960	-5.777	0.023	-0.621	-0.586	-0.004

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