FMO DATABASE

FMODB ID: 14MKZ

Calculation Name: 3K9I-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3K9I

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9KFK0

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-815288.06525
FMO2-HF: Nuclear repulsion	772222.797936
FMO2-HF: Total energy	-43065.267314
FMO2-MP2: Total energy	-43192.80395

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:54:ALA)

Summations of interaction energy for fragment #1(A:54:ALA)

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.
2.983	2.008	7.464	-2.241	-4.246	-0.003

Interaction energy analysis for fragmet #1(A:54:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.005

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	56	ALA	0	0.028	0.007	2.289	1.146	1.690	2.830	-1.353	-2.020	0.000
4	A	57	VAL	0	0.046	0.024	3.624	0.451	0.559	0.002	0.113	-0.223	0.000
5	A	58	PRO	0	0.034	0.020	5.784	0.323	0.323	0.000	0.000	0.000	0.000
6	A	59	TYR	0	-0.083	-0.025	6.684	0.169	0.169	0.000	0.000	0.000	0.000
7	A	60	TYR	0	0.078	0.018	4.963	0.139	0.139	0.000	0.000	0.000	0.000
8	A	61	GLU	-1	-0.928	-0.963	8.900	-0.535	-0.535	0.000	0.000	0.000	0.000
9	A	62	LYS	1	0.918	0.952	11.189	0.366	0.366	0.000	0.000	0.000	0.000
10	A	63	ALA	0	-0.018	0.006	11.849	0.037	0.037	0.000	0.000	0.000	0.000
11	A	64	ILE	0	0.012	0.005	12.059	0.031	0.031	0.000	0.000	0.000	0.000
12	A	65	ALA	0	-0.043	-0.004	14.854	0.027	0.027	0.000	0.000	0.000	0.000
13	A	66	SER	0	-0.044	-0.047	17.045	0.019	0.019	0.000	0.000	0.000	0.000
14	A	67	GLY	0	-0.043	-0.001	19.045	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	68	LEU	0	0.016	-0.014	15.421	0.000	0.000	0.000	0.000	0.000	0.000
16	A	69	GLN	0	0.032	0.022	19.794	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	70	GLY	0	0.007	-0.002	19.807	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	71	LYS	1	0.954	0.994	17.248	0.053	0.053	0.000	0.000	0.000	0.000
19	A	72	ASP	-1	-0.863	-0.940	17.106	-0.107	-0.107	0.000	0.000	0.000	0.000
20	A	73	LEU	0	0.034	0.019	15.420	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	74	ALA	0	0.002	0.013	14.973	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	75	GLU	-1	-0.908	-0.974	13.070	-0.133	-0.133	0.000	0.000	0.000	0.000
23	A	76	CYS	0	-0.053	-0.016	10.647	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	77	TYR	0	0.008	0.008	10.206	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	78	LEU	0	-0.014	-0.011	10.628	-0.059	-0.059	0.000	0.000	0.000	0.000
26	A	79	GLY	0	0.020	0.004	8.100	-0.054	-0.054	0.000	0.000	0.000	0.000
27	A	80	LEU	0	-0.011	0.012	6.587	-0.128	-0.128	0.000	0.000	0.000	0.000
28	A	81	GLY	0	0.037	0.009	7.236	-0.169	-0.169	0.000	0.000	0.000	0.000
29	A	82	SER	0	0.012	-0.002	7.002	-0.106	-0.106	0.000	0.000	0.000	0.000
30	A	83	THR	0	-0.036	-0.039	2.205	1.031	-1.108	4.624	-0.896	-1.590	-0.003
31	A	84	PHE	0	0.029	0.000	4.598	-0.623	-0.588	-0.001	-0.005	-0.029	0.000
32	A	85	ARG	1	0.922	0.967	7.515	0.497	0.497	0.000	0.000	0.000	0.000
33	A	86	THR	0	-0.082	-0.045	4.775	0.172	0.240	-0.001	-0.001	-0.065	0.000
34	A	87	LEU	0	-0.053	-0.025	3.345	-0.279	0.130	0.010	-0.099	-0.319	0.000
35	A	88	GLY	0	0.012	0.020	5.780	0.293	0.293	0.000	0.000	0.000	0.000
36	A	89	GLU	-1	-0.955	-0.975	8.978	-0.391	-0.391	0.000	0.000	0.000	0.000
37	A	90	TYR	0	0.029	-0.001	10.702	0.002	0.002	0.000	0.000	0.000	0.000
38	A	91	ARG	1	1.024	1.001	13.281	0.224	0.224	0.000	0.000	0.000	0.000
39	A	92	LYS	1	0.944	0.991	10.616	0.653	0.653	0.000	0.000	0.000	0.000
40	A	93	ALA	0	-0.001	-0.003	10.622	0.009	0.009	0.000	0.000	0.000	0.000
41	A	94	GLU	-1	-0.913	-0.961	12.011	-0.188	-0.188	0.000	0.000	0.000	0.000
42	A	95	ALA	0	0.017	0.017	15.361	0.027	0.027	0.000	0.000	0.000	0.000
43	A	96	VAL	0	-0.011	-0.013	11.109	0.031	0.031	0.000	0.000	0.000	0.000
44	A	97	LEU	0	-0.011	-0.003	12.148	0.031	0.031	0.000	0.000	0.000	0.000
45	A	98	ALA	0	0.029	0.029	15.063	0.033	0.033	0.000	0.000	0.000	0.000
46	A	99	ASN	0	-0.068	-0.034	17.052	0.034	0.034	0.000	0.000	0.000	0.000
47	A	100	GLY	0	0.070	0.038	16.751	0.017	0.017	0.000	0.000	0.000	0.000
48	A	101	VAL	0	-0.018	-0.013	17.645	0.022	0.022	0.000	0.000	0.000	0.000
49	A	102	LYS	1	0.945	0.966	20.310	0.162	0.162	0.000	0.000	0.000	0.000
50	A	103	GLN	0	-0.026	-0.018	19.861	0.001	0.001	0.000	0.000	0.000	0.000
51	A	104	PHE	0	-0.036	-0.006	18.465	0.012	0.012	0.000	0.000	0.000	0.000
52	A	105	PRO	0	0.038	0.027	21.872	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	106	ASN	0	-0.006	-0.013	24.229	0.001	0.001	0.000	0.000	0.000	0.000
54	A	107	HIS	0	0.013	0.012	16.552	0.004	0.004	0.000	0.000	0.000	0.000
55	A	108	GLN	0	0.089	0.034	20.103	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	109	ALA	0	0.032	0.031	15.959	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	110	LEU	0	0.017	0.007	14.450	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	111	ARG	1	0.883	0.953	16.652	0.086	0.086	0.000	0.000	0.000	0.000
59	A	112	VAL	0	0.039	0.028	16.092	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	113	PHE	0	-0.005	-0.026	10.340	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	114	TYR	0	-0.025	-0.011	14.436	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	115	ALA	0	0.053	0.027	16.515	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	116	MET	0	-0.063	-0.026	13.119	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	117	VAL	0	-0.015	-0.011	12.872	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	118	LEU	0	-0.026	-0.005	15.097	0.008	0.008	0.000	0.000	0.000	0.000
66	A	119	TYR	0	0.011	0.006	16.684	0.012	0.012	0.000	0.000	0.000	0.000
67	A	120	ASN	0	-0.034	-0.018	13.504	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	121	LEU	0	-0.068	-0.041	16.733	0.007	0.007	0.000	0.000	0.000	0.000
69	A	122	GLY	0	0.016	0.021	18.905	0.014	0.014	0.000	0.000	0.000	0.000
70	A	123	ARG	1	0.851	0.941	21.272	0.178	0.178	0.000	0.000	0.000	0.000
71	A	124	TYR	0	0.020	-0.008	21.596	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	125	GLU	-1	-0.858	-0.912	24.176	-0.078	-0.078	0.000	0.000	0.000	0.000
73	A	126	GLN	0	0.069	0.028	23.838	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	127	GLY	0	-0.006	-0.009	21.755	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	128	VAL	0	0.024	-0.007	22.419	0.000	0.000	0.000	0.000	0.000	0.000
76	A	129	GLU	-1	-0.845	-0.912	24.935	-0.082	-0.082	0.000	0.000	0.000	0.000
77	A	130	LEU	0	-0.047	-0.028	20.932	0.003	0.003	0.000	0.000	0.000	0.000
78	A	131	LEU	0	-0.010	-0.020	19.608	0.001	0.001	0.000	0.000	0.000	0.000
79	A	132	LEU	0	0.022	0.018	23.625	0.007	0.007	0.000	0.000	0.000	0.000
80	A	133	LYS	1	0.894	0.949	26.795	0.081	0.081	0.000	0.000	0.000	0.000
81	A	134	ILE	0	-0.005	0.005	21.035	0.002	0.002	0.000	0.000	0.000	0.000
82	A	135	ILE	0	-0.015	0.009	25.192	0.005	0.005	0.000	0.000	0.000	0.000
83	A	136	ALA	0	0.010	0.005	27.104	0.005	0.005	0.000	0.000	0.000	0.000
84	A	137	GLU	-1	-0.986	-1.016	28.181	-0.072	-0.072	0.000	0.000	0.000	0.000
85	A	138	THR	0	-0.117	-0.068	25.177	0.001	0.001	0.000	0.000	0.000	0.000
86	A	139	SER	0	0.007	0.019	28.003	0.002	0.002	0.000	0.000	0.000	0.000
87	A	140	ASP	-1	-0.899	-0.943	29.159	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	141	ASP	-1	-0.869	-0.887	31.020	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	142	GLU	-1	-0.875	-0.941	32.979	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	143	THR	0	-0.076	-0.074	34.671	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	144	ILE	0	0.007	-0.022	29.853	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	145	GLN	0	-0.047	-0.039	33.035	0.000	0.000	0.000	0.000	0.000	0.000
93	A	146	SER	0	-0.026	-0.003	35.701	0.000	0.000	0.000	0.000	0.000	0.000
94	A	147	TYR	0	-0.066	-0.030	36.091	0.001	0.001	0.000	0.000	0.000	0.000
95	A	148	LYS	1	0.971	1.003	33.322	0.045	0.045	0.000	0.000	0.000	0.000
96	A	149	GLN	0	-0.002	-0.018	35.140	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	150	ALA	0	0.034	0.024	37.293	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	151	ILE	0	-0.012	0.001	30.866	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	152	LEU	0	-0.016	-0.028	31.427	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	153	PHE	0	-0.071	-0.017	33.683	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	154	TYR	0	0.012	-0.018	34.681	0.001	0.001	0.000	0.000	0.000	0.000
102	A	155	ALA	0	-0.036	-0.020	29.923	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	156	ASP	-1	-0.926	-0.953	30.592	-0.066	-0.066	0.000	0.000	0.000	0.000
104	A	157	LYS	1	0.886	0.948	32.472	0.053	0.053	0.000	0.000	0.000	0.000
105	A	158	LEU	0	-0.022	-0.007	29.608	0.003	0.003	0.000	0.000	0.000	0.000
106	A	159	ASP	-1	-0.903	-0.937	32.829	-0.058	-0.058	0.000	0.000	0.000	0.000
107	A	160	GLU	-1	-1.012	-0.994	35.297	-0.043	-0.043	0.000	0.000	0.000	0.000
108	A	161	THR	0	-0.039	-0.028	38.691	0.002	0.002	0.000	0.000	0.000	0.000
109	A	162	TRP	0	0.008	-0.001	41.582	0.000	0.000	0.000	0.000	0.000	0.000
110	A	163	LYS	1	0.935	0.975	45.181	0.029	0.029	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:54:ALA)