FMO DATABASE

FMODB ID: 94792

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

Total energy (hartree)

FMO2-HF: Electronic energy	-838716.034463
FMO2-HF: Nuclear repulsion	796353.696559
FMO2-HF: Total energy	-42362.337904
FMO2-MP2: Total energy	-42487.594785

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.
-8.23	-3.881	3.501	-3.269	-4.58	0.006

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 : 0.035 / q_NPA : 0.010

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	0.028	0.024	3.238	-0.777	0.919	0.023	-0.686	-1.031	0.000
4	A	22	LYS	1	1.072	1.039	2.030	-3.904	-2.124	3.474	-2.246	-3.008	0.008
5	A	23	LEU	0	-0.019	-0.020	3.992	1.514	1.777	-0.001	-0.046	-0.216	0.000
6	A	24	ILE	0	0.030	0.040	5.583	0.867	0.867	0.000	0.000	0.000	0.000
7	A	25	GLU	-1	-0.822	-0.890	7.862	-1.026	-1.026	0.000	0.000	0.000	0.000
8	A	26	MET	0	0.011	-0.001	7.515	0.334	0.334	0.000	0.000	0.000	0.000
9	A	27	LEU	0	-0.052	-0.025	9.074	0.298	0.298	0.000	0.000	0.000	0.000
10	A	28	TYR	0	0.052	0.011	11.519	0.168	0.168	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.902	-0.974	11.974	-0.635	-0.635	0.000	0.000	0.000	0.000
12	A	30	GLY	0	-0.076	-0.046	13.730	0.100	0.100	0.000	0.000	0.000	0.000
13	A	31	ILE	0	0.015	0.010	15.462	0.073	0.073	0.000	0.000	0.000	0.000
14	A	32	LEU	0	0.000	-0.007	17.136	0.060	0.060	0.000	0.000	0.000	0.000
15	A	33	ARG	1	0.902	0.957	13.887	0.439	0.439	0.000	0.000	0.000	0.000
16	A	34	PHE	0	0.003	-0.004	17.124	0.039	0.039	0.000	0.000	0.000	0.000
17	A	35	SER	0	0.048	0.035	21.110	0.033	0.033	0.000	0.000	0.000	0.000
18	A	36	SER	0	-0.003	0.007	22.989	0.027	0.027	0.000	0.000	0.000	0.000
19	A	37	GLN	0	-0.044	-0.012	23.575	0.020	0.020	0.000	0.000	0.000	0.000
20	A	38	ALA	0	0.025	-0.015	25.257	0.016	0.016	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.878	0.946	27.046	0.159	0.159	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.952	0.980	28.697	0.120	0.120	0.000	0.000	0.000	0.000
23	A	41	CYS	0	-0.095	-0.027	29.184	0.011	0.011	0.000	0.000	0.000	0.000
24	A	42	ILE	0	-0.007	0.012	30.699	0.007	0.007	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.937	-0.973	33.231	-0.105	-0.105	0.000	0.000	0.000	0.000
26	A	44	ASN	0	-0.070	-0.045	34.067	0.001	0.001	0.000	0.000	0.000	0.000
27	A	45	GLU	-1	-0.948	-0.957	35.860	-0.053	-0.053	0.000	0.000	0.000	0.000
28	A	46	ASP	-1	-0.917	-0.945	33.484	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	47	ILE	0	0.036	-0.014	33.244	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	48	GLU	-1	-0.871	-0.939	32.525	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	49	LYS	1	0.927	0.973	29.107	0.072	0.072	0.000	0.000	0.000	0.000
32	A	50	LYS	1	0.903	0.961	28.331	0.064	0.064	0.000	0.000	0.000	0.000
33	A	51	ILE	0	-0.015	-0.005	28.300	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	52	TYR	0	-0.024	-0.006	22.360	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	53	TYR	0	-0.002	-0.030	23.355	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	54	ILE	0	0.017	0.009	23.323	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	55	ASN	0	0.045	-0.011	23.586	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.928	0.992	16.803	0.127	0.127	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.033	-0.021	19.223	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	58	THR	0	-0.024	-0.011	19.383	-0.020	-0.020	0.000	0.000	0.000	0.000
41	A	59	ASP	-1	-0.888	-0.922	17.773	-0.094	-0.094	0.000	0.000	0.000	0.000
42	A	60	ILE	0	-0.032	0.001	13.632	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	61	PHE	0	-0.008	-0.017	15.011	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	62	THR	0	-0.023	-0.010	17.554	0.017	0.017	0.000	0.000	0.000	0.000
45	A	63	GLU	-1	-0.978	-0.995	11.243	-0.275	-0.275	0.000	0.000	0.000	0.000
46	A	64	LEU	0	-0.030	-0.029	11.579	0.004	0.004	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.046	-0.020	13.705	0.020	0.020	0.000	0.000	0.000	0.000
48	A	66	ASN	0	-0.019	-0.008	15.015	0.045	0.045	0.000	0.000	0.000	0.000
49	A	67	ILE	0	-0.065	-0.010	8.869	0.032	0.032	0.000	0.000	0.000	0.000
50	A	68	LEU	0	-0.076	-0.029	12.528	0.046	0.046	0.000	0.000	0.000	0.000
51	A	69	ASP	-1	-0.834	-0.913	13.973	0.286	0.286	0.000	0.000	0.000	0.000
52	A	70	TYR	0	-0.083	-0.042	16.056	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	71	GLU	-1	-0.968	-1.000	17.804	0.211	0.211	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.926	0.968	12.743	-0.381	-0.381	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.008	0.016	17.078	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	74	GLY	0	0.030	0.002	17.873	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.906	-0.932	21.291	-0.083	-0.083	0.000	0.000	0.000	0.000
58	A	76	VAL	0	0.033	0.008	16.611	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	77	ALA	0	0.007	0.021	18.226	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	78	VAL	0	0.035	0.024	19.124	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	79	TYR	0	-0.008	0.004	20.794	0.000	0.000	0.000	0.000	0.000	0.000
62	A	80	LEU	0	0.019	-0.007	15.841	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	81	THR	0	0.019	-0.020	19.931	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	82	GLY	0	-0.009	0.008	21.298	0.002	0.002	0.000	0.000	0.000	0.000
65	A	83	LEU	0	0.008	0.005	20.433	0.003	0.003	0.000	0.000	0.000	0.000
66	A	84	TYR	0	0.053	0.017	14.595	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	85	THR	0	-0.030	-0.021	20.870	0.010	0.010	0.000	0.000	0.000	0.000
68	A	86	HIS	0	-0.029	-0.007	23.848	0.014	0.014	0.000	0.000	0.000	0.000
69	A	87	GLN	0	0.038	0.002	21.743	0.011	0.011	0.000	0.000	0.000	0.000
70	A	88	ILE	0	0.035	0.021	21.133	0.007	0.007	0.000	0.000	0.000	0.000
71	A	89	LYS	1	0.937	0.965	24.678	0.085	0.085	0.000	0.000	0.000	0.000
72	A	90	VAL	0	-0.018	-0.004	27.088	0.010	0.010	0.000	0.000	0.000	0.000
73	A	91	LEU	0	0.027	0.009	22.802	0.007	0.007	0.000	0.000	0.000	0.000
74	A	92	THR	0	-0.038	-0.010	27.396	0.011	0.011	0.000	0.000	0.000	0.000
75	A	93	GLN	0	-0.014	-0.017	30.053	0.002	0.002	0.000	0.000	0.000	0.000
76	A	94	ALA	0	0.037	0.025	29.929	0.005	0.005	0.000	0.000	0.000	0.000
77	A	95	ASN	0	-0.020	0.003	30.477	0.006	0.006	0.000	0.000	0.000	0.000
78	A	96	VAL	0	-0.055	-0.035	32.434	0.005	0.005	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.944	-0.973	35.507	-0.071	-0.071	0.000	0.000	0.000	0.000
80	A	98	ASN	0	-0.016	-0.016	34.744	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	99	ASP	-1	-0.795	-0.889	33.979	-0.095	-0.095	0.000	0.000	0.000	0.000
82	A	100	ALA	0	0.028	-0.007	31.988	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	101	SER	0	-0.043	-0.022	31.125	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	102	LYS	1	0.930	0.959	30.959	0.084	0.084	0.000	0.000	0.000	0.000
85	A	103	ILE	0	0.054	0.023	26.383	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	104	ASP	-1	-0.876	-0.942	26.420	-0.172	-0.172	0.000	0.000	0.000	0.000
87	A	105	LEU	0	-0.061	-0.026	26.860	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	106	VAL	0	0.010	0.016	22.556	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	107	LEU	0	-0.054	-0.041	22.446	-0.033	-0.033	0.000	0.000	0.000	0.000
90	A	108	ASN	0	-0.008	-0.002	22.400	-0.039	-0.039	0.000	0.000	0.000	0.000
91	A	109	VAL	0	0.020	0.026	21.193	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	110	ALA	0	-0.021	-0.008	18.938	-0.033	-0.033	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.933	0.943	18.283	0.222	0.222	0.000	0.000	0.000	0.000
94	A	112	GLY	0	0.014	0.015	19.135	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	113	LEU	0	-0.038	-0.022	16.301	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	114	LEU	0	-0.023	-0.007	13.076	-0.069	-0.069	0.000	0.000	0.000	0.000
97	A	115	GLU	-1	-0.974	-0.997	14.475	-0.456	-0.456	0.000	0.000	0.000	0.000
98	A	116	ALA	0	0.049	0.052	16.451	0.017	0.017	0.000	0.000	0.000	0.000
99	A	117	TRP	0	-0.041	-0.043	7.193	0.224	0.224	0.000	0.000	0.000	0.000
100	A	118	ARG	1	0.849	0.904	11.163	0.636	0.636	0.000	0.000	0.000	0.000
101	A	119	GLU	-1	-0.922	-0.950	12.795	-0.422	-0.422	0.000	0.000	0.000	0.000
102	A	120	ILE	0	-0.098	-0.046	11.566	0.037	0.037	0.000	0.000	0.000	0.000
103	A	121	HIS	1	0.825	0.915	7.465	1.194	1.194	0.000	0.000	0.000	0.000
104	A	122	SER	0	0.030	0.029	9.162	-0.176	-0.176	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.954	-0.954	8.598	-0.940	-0.940	0.000	0.000	0.000	0.000
106	A	124	GLU	-1	-0.975	-0.994	3.701	-5.670	-5.060	0.005	-0.291	-0.325	-0.002

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