FMO DATABASE

FMODB ID: 82RMY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-817414.854482
FMO2-HF: Nuclear repulsion	774348.565017
FMO2-HF: Total energy	-43066.289465
FMO2-MP2: Total energy	-43193.745098

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.
-1.956	3.143	2.497	-3.169	-4.429	0.007

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 : 0.076 / q_NPA : 0.042

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	0.021	0.007	2.693	-2.248	1.643	0.315	-2.217	-1.988	0.008
4	A	57	VAL	0	0.039	0.035	4.335	0.410	0.618	0.000	-0.031	-0.178	0.000
5	A	58	PRO	0	0.047	0.019	6.578	0.432	0.432	0.000	0.000	0.000	0.000
6	A	59	TYR	0	-0.062	-0.006	7.180	0.230	0.230	0.000	0.000	0.000	0.000
7	A	60	TYR	0	0.065	0.012	5.021	0.187	0.187	0.000	0.000	0.000	0.000
8	A	61	GLU	-1	-0.881	-0.947	9.787	-0.921	-0.921	0.000	0.000	0.000	0.000
9	A	62	LYS	1	0.868	0.923	12.024	0.736	0.736	0.000	0.000	0.000	0.000
10	A	63	ALA	0	-0.008	0.009	12.710	0.061	0.061	0.000	0.000	0.000	0.000
11	A	64	ILE	0	0.008	-0.013	12.266	0.042	0.042	0.000	0.000	0.000	0.000
12	A	65	ALA	0	-0.074	-0.020	15.606	0.036	0.036	0.000	0.000	0.000	0.000
13	A	66	SER	0	-0.019	-0.016	17.727	0.022	0.022	0.000	0.000	0.000	0.000
14	A	67	GLY	0	-0.024	-0.010	19.565	0.005	0.005	0.000	0.000	0.000	0.000
15	A	68	LEU	0	-0.038	-0.004	16.073	0.013	0.013	0.000	0.000	0.000	0.000
16	A	69	GLN	0	-0.020	-0.027	20.375	0.005	0.005	0.000	0.000	0.000	0.000
17	A	70	GLY	0	0.005	-0.002	20.231	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	71	LYS	1	0.845	0.916	17.253	-0.036	-0.036	0.000	0.000	0.000	0.000
19	A	72	ASP	-1	-0.764	-0.895	16.749	-0.079	-0.079	0.000	0.000	0.000	0.000
20	A	73	LEU	0	0.042	0.025	15.482	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	74	ALA	0	0.014	0.013	15.469	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	75	GLU	-1	-0.832	-0.903	13.306	0.022	0.022	0.000	0.000	0.000	0.000
23	A	76	CYS	0	-0.049	-0.016	11.169	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	77	TYR	0	-0.013	-0.031	10.702	-0.101	-0.101	0.000	0.000	0.000	0.000
25	A	78	LEU	0	-0.005	-0.005	10.574	-0.052	-0.052	0.000	0.000	0.000	0.000
26	A	79	GLY	0	0.032	0.015	7.914	0.026	0.026	0.000	0.000	0.000	0.000
27	A	80	LEU	0	-0.012	0.015	6.539	-0.153	-0.153	0.000	0.000	0.000	0.000
28	A	81	GLY	0	0.031	0.009	7.596	-0.221	-0.221	0.000	0.000	0.000	0.000
29	A	82	SER	0	0.005	0.000	7.783	0.036	0.036	0.000	0.000	0.000	0.000
30	A	83	THR	0	-0.029	-0.024	2.363	-0.345	0.114	0.886	-0.353	-0.993	-0.003
31	A	84	PHE	0	0.011	-0.013	4.743	-0.366	-0.299	-0.001	-0.005	-0.061	0.000
32	A	85	ARG	1	0.912	0.949	6.974	-0.218	-0.218	0.000	0.000	0.000	0.000
33	A	86	THR	0	-0.058	-0.040	4.966	0.113	0.113	0.000	0.000	0.000	0.000
34	A	87	LEU	0	-0.050	-0.019	2.305	-0.352	0.122	1.297	-0.563	-1.209	0.002
35	A	88	GLY	0	0.025	0.027	5.448	0.018	0.018	0.000	0.000	0.000	0.000
36	A	89	GLU	-1	-0.826	-0.888	8.329	-0.748	-0.748	0.000	0.000	0.000	0.000
37	A	90	TYR	0	0.003	-0.018	10.099	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	91	ARG	1	1.004	0.998	12.548	0.204	0.204	0.000	0.000	0.000	0.000
39	A	92	LYS	1	0.836	0.913	10.841	0.820	0.820	0.000	0.000	0.000	0.000
40	A	93	ALA	0	0.004	0.004	10.347	0.001	0.001	0.000	0.000	0.000	0.000
41	A	94	GLU	-1	-0.766	-0.823	11.890	-0.079	-0.079	0.000	0.000	0.000	0.000
42	A	95	ALA	0	0.001	0.001	15.686	0.021	0.021	0.000	0.000	0.000	0.000
43	A	96	VAL	0	-0.017	-0.006	11.442	0.028	0.028	0.000	0.000	0.000	0.000
44	A	97	LEU	0	-0.012	0.003	11.905	0.038	0.038	0.000	0.000	0.000	0.000
45	A	98	ALA	0	0.019	0.019	15.314	0.033	0.033	0.000	0.000	0.000	0.000
46	A	99	ASN	0	-0.015	-0.004	17.686	0.035	0.035	0.000	0.000	0.000	0.000
47	A	100	GLY	0	0.033	0.012	16.922	0.012	0.012	0.000	0.000	0.000	0.000
48	A	101	VAL	0	-0.005	-0.013	17.847	0.019	0.019	0.000	0.000	0.000	0.000
49	A	102	LYS	1	0.896	0.945	20.530	0.164	0.164	0.000	0.000	0.000	0.000
50	A	103	GLN	0	-0.006	0.015	20.649	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	104	PHE	0	-0.021	-0.007	18.834	0.009	0.009	0.000	0.000	0.000	0.000
52	A	105	PRO	0	0.053	0.036	21.818	0.010	0.010	0.000	0.000	0.000	0.000
53	A	106	ASN	0	-0.001	-0.007	24.106	0.008	0.008	0.000	0.000	0.000	0.000
54	A	107	HIS	0	0.012	0.007	16.431	0.015	0.015	0.000	0.000	0.000	0.000
55	A	108	GLN	0	0.095	0.038	20.036	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	109	ALA	0	0.031	0.022	15.913	0.005	0.005	0.000	0.000	0.000	0.000
57	A	110	LEU	0	-0.017	-0.001	14.503	0.007	0.007	0.000	0.000	0.000	0.000
58	A	111	ARG	1	0.808	0.880	16.721	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	112	VAL	0	0.040	0.025	16.785	0.000	0.000	0.000	0.000	0.000	0.000
60	A	113	PHE	0	0.004	-0.023	10.987	0.014	0.014	0.000	0.000	0.000	0.000
61	A	114	TYR	0	-0.040	-0.044	14.715	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	115	ALA	0	0.052	0.028	16.844	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	116	MET	0	-0.043	-0.010	13.783	0.025	0.025	0.000	0.000	0.000	0.000
64	A	117	VAL	0	-0.027	-0.017	12.721	0.002	0.002	0.000	0.000	0.000	0.000
65	A	118	LEU	0	-0.021	-0.002	15.160	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	119	TYR	0	0.001	0.004	16.484	0.003	0.003	0.000	0.000	0.000	0.000
67	A	120	ASN	0	-0.036	-0.025	13.497	0.029	0.029	0.000	0.000	0.000	0.000
68	A	121	LEU	0	-0.069	-0.028	16.063	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	122	GLY	0	0.011	0.014	18.287	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	123	ARG	1	0.745	0.842	20.589	0.076	0.076	0.000	0.000	0.000	0.000
71	A	124	TYR	0	0.002	-0.017	20.704	0.000	0.000	0.000	0.000	0.000	0.000
72	A	125	GLU	-1	-0.848	-0.908	24.087	0.012	0.012	0.000	0.000	0.000	0.000
73	A	126	GLN	0	0.107	0.055	23.657	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	127	GLY	0	-0.002	-0.011	22.013	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	128	VAL	0	-0.003	-0.014	22.684	0.011	0.011	0.000	0.000	0.000	0.000
76	A	129	GLU	-1	-0.809	-0.891	25.397	0.001	0.001	0.000	0.000	0.000	0.000
77	A	130	LEU	0	-0.048	-0.022	21.222	0.001	0.001	0.000	0.000	0.000	0.000
78	A	131	LEU	0	0.007	-0.008	20.255	0.006	0.006	0.000	0.000	0.000	0.000
79	A	132	LEU	0	0.013	0.013	24.170	0.005	0.005	0.000	0.000	0.000	0.000
80	A	133	LYS	1	0.801	0.908	26.875	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	134	ILE	0	0.020	0.012	21.578	0.001	0.001	0.000	0.000	0.000	0.000
82	A	135	ILE	0	-0.001	0.016	25.110	0.002	0.002	0.000	0.000	0.000	0.000
83	A	136	ALA	0	0.031	0.025	27.483	0.000	0.000	0.000	0.000	0.000	0.000
84	A	137	GLU	-1	-0.861	-0.931	27.747	0.016	0.016	0.000	0.000	0.000	0.000
85	A	138	THR	0	-0.114	-0.089	25.733	0.000	0.000	0.000	0.000	0.000	0.000
86	A	139	SER	0	0.020	0.032	28.507	0.007	0.007	0.000	0.000	0.000	0.000
87	A	140	ASP	-1	-0.898	-0.948	28.765	0.075	0.075	0.000	0.000	0.000	0.000
88	A	141	ASP	-1	-0.839	-0.892	31.381	0.067	0.067	0.000	0.000	0.000	0.000
89	A	142	GLU	-1	-0.889	-0.942	33.315	0.048	0.048	0.000	0.000	0.000	0.000
90	A	143	THR	0	-0.106	-0.072	35.008	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	144	ILE	0	0.011	-0.013	30.137	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	145	GLN	0	-0.068	-0.045	33.382	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	146	SER	0	-0.041	-0.018	35.964	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	147	TYR	0	-0.033	-0.014	36.431	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	148	LYS	1	0.865	0.949	32.661	-0.037	-0.037	0.000	0.000	0.000	0.000
96	A	149	GLN	0	0.037	0.001	35.284	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	150	ALA	0	0.004	0.013	37.737	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	151	ILE	0	-0.006	-0.002	31.371	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	152	LEU	0	-0.017	-0.019	31.539	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	153	PHE	0	-0.053	-0.011	33.951	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	154	TYR	0	0.046	0.003	35.028	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	155	ALA	0	-0.024	0.003	30.052	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	156	ASP	-1	-0.873	-0.925	30.668	0.005	0.005	0.000	0.000	0.000	0.000
104	A	157	LYS	1	0.790	0.870	32.566	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	158	LEU	0	-0.033	-0.011	29.499	0.003	0.003	0.000	0.000	0.000	0.000
106	A	159	ASP	-1	-0.892	-0.932	33.136	0.021	0.021	0.000	0.000	0.000	0.000
107	A	160	GLU	-1	-0.987	-0.983	35.418	0.004	0.004	0.000	0.000	0.000	0.000
108	A	161	THR	0	-0.058	-0.036	38.789	0.003	0.003	0.000	0.000	0.000	0.000
109	A	162	TRP	0	0.025	0.012	41.848	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	163	LYS	1	0.906	0.960	45.277	-0.010	-0.010	0.000	0.000	0.000	0.000

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