FMO DATABASE

FMODB ID: ZYK8N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1021982.550593
FMO2-HF: Nuclear repulsion	973692.534481
FMO2-HF: Total energy	-48290.016111
FMO2-MP2: Total energy	-48433.168934

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.
-14.255	-10.037	8.625	-4.171	-8.674	0.005

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 : -0.021 / q_NPA : -0.022

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	134	ASP	-1	-0.940	-0.975	2.514	-4.466	-1.958	1.677	-1.756	-2.429	-0.016
4	A	135	PHE	0	0.118	0.041	3.826	-0.031	0.240	0.000	-0.033	-0.239	0.000
5	A	136	LYS	1	0.923	0.941	5.133	0.056	0.107	-0.001	-0.001	-0.048	0.000
6	A	137	LYS	1	0.930	0.965	7.426	1.850	1.850	0.000	0.000	0.000	0.000
7	A	138	ILE	0	0.051	0.048	5.450	0.245	0.245	0.000	0.000	0.000	0.000
8	A	139	VAL	0	0.013	0.014	8.680	0.282	0.282	0.000	0.000	0.000	0.000
9	A	140	ASN	0	-0.048	-0.030	10.768	0.225	0.225	0.000	0.000	0.000	0.000
10	A	141	ASN	0	-0.028	-0.017	12.244	0.097	0.097	0.000	0.000	0.000	0.000
11	A	142	ILE	0	-0.004	0.030	11.458	0.012	0.012	0.000	0.000	0.000	0.000
12	A	143	ARG	1	0.881	0.921	14.671	0.706	0.706	0.000	0.000	0.000	0.000
13	A	144	LEU	0	0.023	0.014	18.009	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	145	LYS	1	0.925	0.965	20.234	0.291	0.291	0.000	0.000	0.000	0.000
15	A	146	ASP	-1	-0.926	-0.944	17.030	-0.828	-0.828	0.000	0.000	0.000	0.000
16	A	147	THR	0	-0.066	-0.041	12.426	-0.047	-0.047	0.000	0.000	0.000	0.000
17	A	148	PHE	0	0.018	-0.012	14.769	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	149	ASP	-1	-0.765	-0.844	17.031	-0.360	-0.360	0.000	0.000	0.000	0.000
19	A	150	PHE	0	0.006	-0.005	19.994	0.011	0.011	0.000	0.000	0.000	0.000
20	A	151	LYS	1	0.970	1.001	22.419	0.128	0.128	0.000	0.000	0.000	0.000
21	A	152	LEU	0	0.003	0.002	25.387	0.010	0.010	0.000	0.000	0.000	0.000
22	A	153	ALA	0	-0.004	-0.001	27.904	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	154	ALA	0	-0.011	0.002	29.537	0.005	0.005	0.000	0.000	0.000	0.000
24	A	155	PHE	0	-0.032	-0.021	31.365	0.002	0.002	0.000	0.000	0.000	0.000
25	A	156	PRO	0	-0.015	-0.001	30.027	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	157	ASN	0	-0.042	-0.044	30.364	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	158	GLN	0	0.027	0.021	31.840	0.008	0.008	0.000	0.000	0.000	0.000
28	A	159	ASN	0	0.038	0.029	29.912	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	160	TYR	0	0.015	-0.016	23.112	0.016	0.016	0.000	0.000	0.000	0.000
30	A	161	ASP	-1	-0.874	-0.932	29.884	-0.169	-0.169	0.000	0.000	0.000	0.000
31	A	162	GLN	0	-0.061	-0.029	32.980	0.013	0.013	0.000	0.000	0.000	0.000
32	A	163	LEU	0	-0.061	-0.031	30.844	0.012	0.012	0.000	0.000	0.000	0.000
33	A	164	LEU	0	0.000	-0.010	33.492	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	165	PRO	0	0.008	0.007	32.148	0.004	0.004	0.000	0.000	0.000	0.000
35	A	166	SER	0	0.000	-0.018	32.789	0.002	0.002	0.000	0.000	0.000	0.000
36	A	167	GLN	0	0.044	0.054	34.873	0.000	0.000	0.000	0.000	0.000	0.000
37	A	168	ILE	0	0.036	0.033	28.348	0.007	0.007	0.000	0.000	0.000	0.000
38	A	169	TYR	0	-0.053	-0.032	30.711	0.009	0.009	0.000	0.000	0.000	0.000
39	A	170	LYS	1	0.931	0.962	31.736	0.059	0.059	0.000	0.000	0.000	0.000
40	A	171	ASN	0	-0.006	-0.025	32.614	0.013	0.013	0.000	0.000	0.000	0.000
41	A	172	TYR	0	0.035	0.033	26.824	0.004	0.004	0.000	0.000	0.000	0.000
42	A	173	TYR	0	-0.028	0.001	28.044	0.008	0.008	0.000	0.000	0.000	0.000
43	A	174	GLN	0	-0.006	-0.006	30.147	0.008	0.008	0.000	0.000	0.000	0.000
44	A	175	GLY	0	-0.003	0.005	26.566	0.007	0.007	0.000	0.000	0.000	0.000
45	A	176	ILE	0	-0.039	-0.021	22.096	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	177	GLU	-1	-0.913	-0.942	22.096	-0.105	-0.105	0.000	0.000	0.000	0.000
47	A	178	ILE	0	-0.032	-0.029	16.558	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	179	GLN	0	-0.042	-0.030	18.485	0.002	0.002	0.000	0.000	0.000	0.000
49	A	180	GLN	0	-0.045	-0.050	9.688	0.103	0.103	0.000	0.000	0.000	0.000
50	A	181	HIS	0	-0.029	-0.018	14.625	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	182	LYS	1	0.889	0.942	11.688	0.969	0.969	0.000	0.000	0.000	0.000
52	A	183	TYR	0	0.025	0.008	7.109	0.374	0.374	0.000	0.000	0.000	0.000
53	A	184	GLN	0	0.026	0.020	7.346	0.089	0.089	0.000	0.000	0.000	0.000
54	A	185	ASN	0	-0.024	0.000	4.947	0.705	0.705	0.000	0.000	0.000	0.000
55	A	186	GLU	-1	-0.853	-0.944	2.459	-4.196	-3.023	0.927	-0.385	-1.716	-0.002
56	A	187	LEU	0	-0.018	-0.018	3.891	0.230	0.358	-0.001	0.016	-0.143	0.000
57	A	188	ASP	-1	-0.877	-0.916	7.073	0.087	0.087	0.000	0.000	0.000	0.000
58	A	189	ILE	0	0.010	0.007	10.378	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	190	LYS	1	0.902	0.958	13.460	0.021	0.021	0.000	0.000	0.000	0.000
60	A	191	ILE	0	0.015	0.012	16.738	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	192	ILE	0	-0.044	-0.027	19.045	0.022	0.022	0.000	0.000	0.000	0.000
62	A	193	ASN	0	-0.032	-0.026	21.717	0.021	0.021	0.000	0.000	0.000	0.000
63	A	194	PHE	0	0.042	0.033	24.245	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	195	LEU	0	-0.024	-0.025	26.456	0.016	0.016	0.000	0.000	0.000	0.000
65	A	196	TYR	0	0.053	0.033	28.997	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	197	PRO	0	-0.009	-0.021	29.703	0.007	0.007	0.000	0.000	0.000	0.000
67	A	198	ASP	-1	-0.797	-0.882	31.082	-0.107	-0.107	0.000	0.000	0.000	0.000
68	A	199	GLY	0	-0.045	-0.012	33.447	0.008	0.008	0.000	0.000	0.000	0.000
69	A	200	ASP	-1	-0.909	-0.974	34.861	-0.066	-0.066	0.000	0.000	0.000	0.000
70	A	201	PHE	0	0.034	-0.003	36.421	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	202	GLY	0	0.023	0.033	37.466	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	203	SER	0	-0.078	-0.057	36.842	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	204	ALA	0	-0.010	-0.007	33.507	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	205	ASN	0	0.003	-0.022	35.171	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	206	LYS	1	0.911	0.967	37.364	0.082	0.082	0.000	0.000	0.000	0.000
76	A	207	ASN	0	0.024	0.019	34.269	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	208	GLY	0	0.028	0.049	33.758	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	209	THR	0	-0.101	-0.076	29.213	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	210	LEU	0	-0.026	-0.010	27.638	0.018	0.018	0.000	0.000	0.000	0.000
80	A	211	LYS	1	0.932	0.990	25.409	0.106	0.106	0.000	0.000	0.000	0.000
81	A	212	LEU	0	0.010	-0.007	21.081	0.020	0.020	0.000	0.000	0.000	0.000
82	A	213	SER	0	-0.016	0.000	21.591	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	214	LEU	0	0.011	-0.014	16.415	0.007	0.007	0.000	0.000	0.000	0.000
84	A	215	MET	0	-0.009	-0.004	14.871	0.030	0.030	0.000	0.000	0.000	0.000
85	A	216	LEU	0	-0.049	-0.027	10.917	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	217	THR	0	0.026	0.017	8.672	0.093	0.093	0.000	0.000	0.000	0.000
87	A	218	ASP	-1	-0.841	-0.905	4.212	0.152	0.287	-0.001	-0.022	-0.113	0.000
88	A	219	LYS	1	0.927	0.938	4.493	0.278	0.391	-0.001	-0.006	-0.106	0.000
89	A	220	LYS	1	0.913	0.982	2.199	-10.150	-10.516	6.020	-1.907	-3.748	0.023
90	A	221	ASN	0	-0.106	-0.082	3.972	-0.489	-0.284	0.005	-0.077	-0.132	0.000
91	A	222	ASN	0	0.030	0.023	6.910	-0.214	-0.214	0.000	0.000	0.000	0.000
92	A	223	GLN	0	-0.049	-0.021	8.593	-0.210	-0.210	0.000	0.000	0.000	0.000
93	A	224	VAL	0	0.020	0.013	9.862	-0.109	-0.109	0.000	0.000	0.000	0.000
94	A	225	TYR	0	-0.028	-0.018	8.978	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	226	TYR	0	0.041	0.019	13.669	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	227	LYS	1	0.919	0.955	15.260	0.369	0.369	0.000	0.000	0.000	0.000
97	A	228	LEU	0	0.015	0.029	17.977	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	229	LEU	0	-0.036	-0.023	18.621	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	230	GLU	-1	-0.921	-0.961	21.464	-0.167	-0.167	0.000	0.000	0.000	0.000
100	A	231	VAL	0	-0.032	-0.006	22.689	-0.028	-0.028	0.000	0.000	0.000	0.000
101	A	232	SER	0	0.058	0.020	25.680	0.019	0.019	0.000	0.000	0.000	0.000
102	A	233	GLY	0	-0.029	-0.019	27.959	-0.018	-0.018	0.000	0.000	0.000	0.000
103	A	234	PHE	0	-0.060	-0.020	26.300	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	235	LYS	1	0.972	0.995	31.753	0.108	0.108	0.000	0.000	0.000	0.000
105	A	236	SER	0	0.026	-0.009	35.437	0.002	0.002	0.000	0.000	0.000	0.000
106	A	237	ASN	0	-0.036	-0.028	37.880	0.006	0.006	0.000	0.000	0.000	0.000
107	A	238	PRO	0	0.031	0.016	41.580	0.000	0.000	0.000	0.000	0.000	0.000
108	A	239	TYR	0	0.016	0.003	43.528	0.001	0.001	0.000	0.000	0.000	0.000
109	A	240	GLY	0	-0.003	-0.014	40.906	0.004	0.004	0.000	0.000	0.000	0.000
110	A	241	VAL	0	-0.032	-0.004	41.629	0.001	0.001	0.000	0.000	0.000	0.000
111	A	242	ASP	-1	-0.887	-0.941	40.253	-0.064	-0.064	0.000	0.000	0.000	0.000
112	A	243	GLU	-1	-0.826	-0.940	38.707	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	244	ASN	0	-0.071	-0.029	41.824	0.002	0.002	0.000	0.000	0.000	0.000
114	A	245	GLY	0	-0.011	-0.006	44.647	0.004	0.004	0.000	0.000	0.000	0.000
115	A	246	THR	0	0.018	0.024	44.126	0.003	0.003	0.000	0.000	0.000	0.000
116	A	247	ILE	0	0.020	0.005	45.056	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	248	PRO	0	-0.061	-0.038	42.804	0.003	0.003	0.000	0.000	0.000	0.000
118	A	249	GLY	0	-0.013	-0.006	44.868	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	250	LEU	0	-0.053	-0.008	47.147	0.002	0.002	0.000	0.000	0.000	0.000
120	A	251	GLU	-1	-0.953	-0.967	49.546	-0.033	-0.033	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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