FMO DATABASE

FMODB ID: R5628

Calculation Name: 3K63-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K63

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PRA0

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	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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1023166.970102
FMO2-HF: Nuclear repulsion	974876.090004
FMO2-HF: Total energy	-48290.880098
FMO2-MP2: Total energy	-48433.99848

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:132:MET)

Summations of interaction energy for fragment #1(A:132:MET)

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.
-25.228	-24.862	18.993	-7.555	-11.802	0.041

Interaction energy analysis for fragmet #1(A:132:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / 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

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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	134	ASP	-1	-0.945	-0.977	2.419	-4.541	-2.194	3.039	-2.232	-3.154	-0.017
4	A	135	PHE	0	0.103	0.043	3.618	-0.135	0.164	0.002	-0.031	-0.270	0.000
5	A	136	LYS	1	0.931	0.945	5.064	0.152	0.201	-0.001	-0.001	-0.046	0.000
6	A	137	LYS	1	0.929	0.971	7.235	2.099	2.099	0.000	0.000	0.000	0.000
7	A	138	ILE	0	0.043	0.038	5.861	0.264	0.264	0.000	0.000	0.000	0.000
8	A	139	VAL	0	0.021	0.016	8.712	0.306	0.306	0.000	0.000	0.000	0.000
9	A	140	ASN	0	-0.078	-0.040	10.836	0.249	0.249	0.000	0.000	0.000	0.000
10	A	141	ASN	0	0.000	-0.010	12.246	0.221	0.221	0.000	0.000	0.000	0.000
11	A	142	ILE	0	-0.026	0.023	11.619	0.013	0.013	0.000	0.000	0.000	0.000
12	A	143	ARG	1	0.887	0.924	14.831	0.845	0.845	0.000	0.000	0.000	0.000
13	A	144	LEU	0	0.013	0.009	18.254	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	145	LYS	1	0.909	0.970	20.505	0.366	0.366	0.000	0.000	0.000	0.000
15	A	146	ASP	-1	-0.802	-0.878	16.419	-1.016	-1.016	0.000	0.000	0.000	0.000
16	A	147	THR	0	-0.057	-0.030	12.674	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	148	PHE	0	-0.001	-0.013	15.132	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	149	ASP	-1	-0.733	-0.806	17.403	-0.437	-0.437	0.000	0.000	0.000	0.000
19	A	150	PHE	0	0.004	-0.005	20.422	0.001	0.001	0.000	0.000	0.000	0.000
20	A	151	LYS	1	0.874	0.939	22.843	0.196	0.196	0.000	0.000	0.000	0.000
21	A	152	LEU	0	0.004	0.003	25.871	0.005	0.005	0.000	0.000	0.000	0.000
22	A	153	ALA	0	-0.004	-0.004	28.381	0.003	0.003	0.000	0.000	0.000	0.000
23	A	154	ALA	0	-0.006	0.008	30.043	0.008	0.008	0.000	0.000	0.000	0.000
24	A	155	PHE	0	-0.038	-0.029	31.848	0.005	0.005	0.000	0.000	0.000	0.000
25	A	156	PRO	0	-0.006	0.002	30.505	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	157	ASN	0	-0.049	-0.032	30.835	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	158	GLN	0	0.013	0.013	32.275	0.010	0.010	0.000	0.000	0.000	0.000
28	A	159	ASN	0	0.005	0.013	30.307	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	160	TYR	0	0.004	-0.054	23.447	0.019	0.019	0.000	0.000	0.000	0.000
30	A	161	ASP	-1	-0.858	-0.932	30.235	-0.211	-0.211	0.000	0.000	0.000	0.000
31	A	162	GLN	0	-0.037	-0.016	33.304	0.017	0.017	0.000	0.000	0.000	0.000
32	A	163	LEU	0	-0.068	-0.031	31.254	0.014	0.014	0.000	0.000	0.000	0.000
33	A	164	LEU	0	0.007	0.002	33.824	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	165	PRO	0	0.010	0.006	32.485	0.002	0.002	0.000	0.000	0.000	0.000
35	A	166	SER	0	0.008	-0.015	33.147	0.000	0.000	0.000	0.000	0.000	0.000
36	A	167	GLN	0	0.013	0.023	35.301	0.001	0.001	0.000	0.000	0.000	0.000
37	A	168	ILE	0	0.043	0.026	28.736	0.006	0.006	0.000	0.000	0.000	0.000
38	A	169	TYR	0	-0.025	-0.019	31.088	0.008	0.008	0.000	0.000	0.000	0.000
39	A	170	LYS	1	0.802	0.882	32.112	0.099	0.099	0.000	0.000	0.000	0.000
40	A	171	ASN	0	-0.012	-0.026	33.008	0.015	0.015	0.000	0.000	0.000	0.000
41	A	172	TYR	0	0.031	0.026	26.934	0.000	0.000	0.000	0.000	0.000	0.000
42	A	173	TYR	0	-0.031	-0.001	28.502	0.004	0.004	0.000	0.000	0.000	0.000
43	A	174	GLN	0	-0.002	-0.001	30.598	0.009	0.009	0.000	0.000	0.000	0.000
44	A	175	GLY	0	0.001	0.005	27.059	0.008	0.008	0.000	0.000	0.000	0.000
45	A	176	ILE	0	-0.041	-0.022	22.787	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	177	GLU	-1	-0.827	-0.879	22.778	-0.182	-0.182	0.000	0.000	0.000	0.000
47	A	178	ILE	0	-0.020	-0.025	16.970	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	179	GLN	0	-0.034	-0.031	18.952	0.000	0.000	0.000	0.000	0.000	0.000
49	A	180	GLN	0	-0.044	-0.051	10.172	0.128	0.128	0.000	0.000	0.000	0.000
50	A	181	HIS	0	-0.022	-0.016	15.099	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	182	LYS	1	0.811	0.890	11.587	1.115	1.115	0.000	0.000	0.000	0.000
52	A	183	TYR	0	0.037	0.005	7.323	0.446	0.446	0.000	0.000	0.000	0.000
53	A	184	GLN	0	-0.007	0.014	7.799	0.037	0.037	0.000	0.000	0.000	0.000
54	A	185	ASN	0	-0.004	0.010	5.299	0.716	0.716	0.000	0.000	0.000	0.000
55	A	186	GLU	-1	-0.867	-0.949	2.465	-5.823	-4.348	0.559	-0.480	-1.554	-0.004
56	A	187	LEU	0	-0.030	-0.018	4.386	0.370	0.463	-0.001	-0.005	-0.086	0.000
57	A	188	ASP	-1	-0.877	-0.910	7.517	-0.102	-0.102	0.000	0.000	0.000	0.000
58	A	189	ILE	0	0.017	0.007	10.856	0.015	0.015	0.000	0.000	0.000	0.000
59	A	190	LYS	1	0.877	0.931	13.883	0.254	0.254	0.000	0.000	0.000	0.000
60	A	191	ILE	0	0.024	0.016	17.167	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	192	ILE	0	-0.033	-0.021	19.479	0.026	0.026	0.000	0.000	0.000	0.000
62	A	193	ASN	0	-0.026	-0.023	22.097	0.024	0.024	0.000	0.000	0.000	0.000
63	A	194	PHE	0	0.041	0.032	24.576	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	195	LEU	0	-0.022	-0.020	26.793	0.020	0.020	0.000	0.000	0.000	0.000
65	A	196	TYR	0	0.045	0.025	29.284	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	197	PRO	0	-0.025	-0.019	30.032	0.006	0.006	0.000	0.000	0.000	0.000
67	A	198	ASP	-1	-0.786	-0.879	31.245	-0.153	-0.153	0.000	0.000	0.000	0.000
68	A	199	GLY	0	-0.025	0.000	33.676	0.010	0.010	0.000	0.000	0.000	0.000
69	A	200	ASP	-1	-0.864	-0.945	35.088	-0.098	-0.098	0.000	0.000	0.000	0.000
70	A	201	PHE	0	0.020	-0.002	36.716	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	202	GLY	0	0.030	0.022	37.759	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	203	SER	0	-0.070	-0.064	36.802	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	204	ALA	0	-0.005	-0.003	33.799	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	205	ASN	0	0.009	-0.024	35.431	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	206	LYS	1	0.910	0.973	37.649	0.112	0.112	0.000	0.000	0.000	0.000
76	A	207	ASN	0	-0.012	-0.001	34.385	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	208	GLY	0	0.042	0.057	33.965	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	209	THR	0	-0.104	-0.078	29.408	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	210	LEU	0	-0.026	-0.004	27.931	0.020	0.020	0.000	0.000	0.000	0.000
80	A	211	LYS	1	0.822	0.937	25.756	0.175	0.175	0.000	0.000	0.000	0.000
81	A	212	LEU	0	0.005	-0.004	21.726	0.021	0.021	0.000	0.000	0.000	0.000
82	A	213	SER	0	-0.003	0.006	21.847	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	214	LEU	0	0.004	-0.013	16.720	0.002	0.002	0.000	0.000	0.000	0.000
84	A	215	MET	0	-0.011	-0.003	15.230	0.042	0.042	0.000	0.000	0.000	0.000
85	A	216	LEU	0	-0.046	-0.028	11.231	-0.041	-0.041	0.000	0.000	0.000	0.000
86	A	217	THR	0	0.031	0.015	9.354	0.113	0.113	0.000	0.000	0.000	0.000
87	A	218	ASP	-1	-0.823	-0.912	4.383	-0.374	-0.260	-0.001	-0.015	-0.098	0.000
88	A	219	LYS	1	0.895	0.928	4.998	1.028	1.028	0.000	0.000	0.000	0.000
89	A	220	LYS	1	0.866	0.946	2.075	-20.811	-25.031	15.394	-4.709	-6.466	0.062
90	A	221	ASN	0	-0.094	-0.080	4.102	-0.304	-0.095	0.002	-0.082	-0.128	0.000
91	A	222	ASN	0	-0.005	0.008	7.074	-0.132	-0.132	0.000	0.000	0.000	0.000
92	A	223	GLN	0	-0.021	-0.004	8.734	-0.118	-0.118	0.000	0.000	0.000	0.000
93	A	224	VAL	0	0.022	0.010	10.053	-0.158	-0.158	0.000	0.000	0.000	0.000
94	A	225	TYR	0	-0.039	-0.019	9.031	0.025	0.025	0.000	0.000	0.000	0.000
95	A	226	TYR	0	0.053	0.023	13.812	-0.042	-0.042	0.000	0.000	0.000	0.000
96	A	227	LYS	1	0.915	0.953	15.084	0.513	0.513	0.000	0.000	0.000	0.000
97	A	228	LEU	0	0.031	0.035	18.135	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	229	LEU	0	-0.046	-0.027	18.516	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	230	GLU	-1	-0.857	-0.945	21.624	-0.217	-0.217	0.000	0.000	0.000	0.000
100	A	231	VAL	0	-0.035	-0.009	22.723	-0.030	-0.030	0.000	0.000	0.000	0.000
101	A	232	SER	0	0.064	0.026	25.883	0.020	0.020	0.000	0.000	0.000	0.000
102	A	233	GLY	0	-0.023	-0.016	28.198	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	234	PHE	0	-0.059	-0.020	26.578	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	235	LYS	1	0.962	0.995	32.044	0.143	0.143	0.000	0.000	0.000	0.000
105	A	236	SER	0	0.035	-0.006	35.741	0.001	0.001	0.000	0.000	0.000	0.000
106	A	237	ASN	0	-0.059	-0.043	38.151	0.008	0.008	0.000	0.000	0.000	0.000
107	A	238	PRO	0	0.045	0.012	41.825	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	239	TYR	0	0.011	0.006	43.754	0.001	0.001	0.000	0.000	0.000	0.000
109	A	240	GLY	0	-0.019	-0.007	41.189	0.004	0.004	0.000	0.000	0.000	0.000
110	A	241	VAL	0	0.017	0.011	41.935	0.001	0.001	0.000	0.000	0.000	0.000
111	A	242	ASP	-1	-0.839	-0.900	40.555	-0.096	-0.096	0.000	0.000	0.000	0.000
112	A	243	GLU	-1	-0.786	-0.889	39.354	-0.100	-0.100	0.000	0.000	0.000	0.000
113	A	244	ASN	0	-0.090	-0.040	42.125	0.006	0.006	0.000	0.000	0.000	0.000
114	A	245	GLY	0	0.002	0.002	45.041	0.005	0.005	0.000	0.000	0.000	0.000
115	A	246	THR	0	0.002	0.005	44.467	0.004	0.004	0.000	0.000	0.000	0.000
116	A	247	ILE	0	0.029	0.002	45.386	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	248	PRO	0	-0.041	-0.021	42.976	0.003	0.003	0.000	0.000	0.000	0.000
118	A	249	GLY	0	-0.016	-0.004	45.148	0.000	0.000	0.000	0.000	0.000	0.000
119	A	250	LEU	0	-0.054	-0.005	47.411	0.004	0.004	0.000	0.000	0.000	0.000
120	A	251	GLU	-1	-0.958	-0.972	49.693	-0.053	-0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:132:MET)