FMO DATABASE

FMODB ID: YZYK2

Calculation Name: 3W6J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W6J

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0E0

Base Structure: X-ray

Registration Date: 2023-06-21

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1252703.50141
FMO2-HF: Nuclear repulsion	1190959.201528
FMO2-HF: Total energy	-61744.299882
FMO2-MP2: Total energy	-61922.69611

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-13.352	-7.493	5.875	-3.674	-8.059	-0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.007

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	3	VAL	0	-0.056	-0.032	2.151	-1.806	1.872	1.514	-1.955	-3.237	0.002
4	A	4	GLN	0	0.025	0.011	2.551	-3.121	-2.064	1.317	-0.984	-1.390	-0.014
5	A	5	LEU	0	-0.016	-0.008	2.413	-1.142	-0.881	3.016	-0.598	-2.679	0.005
6	A	6	PRO	0	-0.009	-0.005	5.785	-0.968	-0.953	-0.001	-0.011	-0.003	0.000
7	A	7	TYR	0	0.028	0.002	5.740	0.185	0.185	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.042	-0.017	11.190	-0.077	-0.077	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.001	0.008	14.239	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.926	0.964	13.161	0.210	0.210	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.077	0.019	12.310	0.041	0.041	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.865	-0.914	14.535	-0.124	-0.124	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.073	-0.034	17.514	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.057	-0.021	13.859	0.036	0.036	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.924	-0.962	18.917	0.019	0.019	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.010	0.001	19.122	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.006	-0.013	16.689	0.024	0.024	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.011	-0.007	17.448	0.033	0.033	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.743	-0.847	19.620	0.174	0.174	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.009	0.018	11.890	0.025	0.025	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.000	-0.023	14.671	0.053	0.053	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.018	-0.010	16.478	0.030	0.030	0.000	0.000	0.000	0.000
23	A	23	HIS	0	0.002	0.012	14.016	-0.024	-0.024	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.024	-0.010	11.024	0.039	0.039	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.016	-0.023	14.763	0.034	0.034	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.023	-0.001	17.829	-0.026	-0.026	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.898	0.954	13.215	-0.707	-0.707	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.091	-0.072	9.390	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.959	-0.966	16.188	0.381	0.381	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.070	-0.017	15.781	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.816	-0.913	19.674	0.240	0.240	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.046	-0.033	22.348	0.008	0.008	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.051	-0.041	23.372	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.853	-0.910	24.194	0.295	0.295	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.001	0.017	18.363	0.032	0.032	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.041	0.033	16.874	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.025	0.003	16.241	0.063	0.063	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.005	0.018	14.318	0.038	0.038	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.080	0.042	12.178	0.136	0.136	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.035	0.022	11.202	0.103	0.103	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.016	-0.032	11.313	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.845	-0.929	7.642	1.143	1.143	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.049	-0.011	6.705	0.286	0.286	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.040	-0.047	7.694	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.014	-0.011	7.149	-0.159	-0.159	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.015	0.022	3.168	-0.483	-0.153	0.034	-0.082	-0.282	0.000
47	A	47	TYR	0	-0.033	-0.037	4.191	-0.499	-0.396	-0.001	-0.006	-0.095	0.000
48	A	48	ILE	0	0.000	-0.003	6.952	-0.245	-0.245	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.006	-0.010	4.105	-0.035	0.149	-0.001	-0.012	-0.171	0.000
50	A	50	ALA	0	0.027	0.020	4.326	-0.632	-0.515	-0.001	-0.012	-0.104	0.000
51	A	51	MET	0	-0.043	-0.013	5.325	-0.178	-0.164	-0.001	-0.001	-0.012	0.000
52	A	52	GLN	0	-0.003	-0.012	8.255	0.062	0.062	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.939	-0.955	4.565	-5.027	-4.927	-0.001	-0.013	-0.086	0.000
54	A	54	LEU	0	-0.106	-0.051	7.729	0.093	0.093	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.967	-0.979	10.934	-0.598	-0.598	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.051	-0.015	11.777	0.140	0.140	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.904	-0.949	14.400	-0.228	-0.228	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.090	-0.046	11.353	0.065	0.065	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.025	0.009	15.160	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.034	0.011	17.285	0.018	0.018	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.872	-0.965	18.603	0.056	0.056	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.012	0.015	13.998	0.048	0.048	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.068	0.036	13.174	0.063	0.063	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.001	0.007	15.461	0.042	0.042	0.000	0.000	0.000	0.000
65	A	65	MET	0	-0.024	0.009	15.845	0.031	0.031	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.041	0.019	12.669	0.041	0.041	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.006	0.000	14.199	0.047	0.047	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.040	-0.034	16.831	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.005	-0.004	13.661	0.001	0.001	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.026	0.010	11.439	0.024	0.024	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.013	0.004	15.478	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.025	-0.015	19.076	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.865	0.925	11.958	-0.906	-0.906	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.031	-0.025	17.808	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.924	0.964	19.597	-0.236	-0.236	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.030	-0.005	20.086	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.031	0.007	18.082	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.032	-0.029	20.105	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.006	-0.015	23.393	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.000	0.026	26.127	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.786	-0.889	25.139	0.267	0.267	0.000	0.000	0.000	0.000
82	A	98	PRO	0	-0.041	-0.024	24.200	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	99	ARG	1	0.773	0.846	21.763	-0.305	-0.305	0.000	0.000	0.000	0.000
84	A	100	GLU	-1	-0.833	-0.900	24.025	0.207	0.207	0.000	0.000	0.000	0.000
85	A	101	GLU	-1	-0.847	-0.907	26.009	0.152	0.152	0.000	0.000	0.000	0.000
86	A	102	LEU	0	0.011	-0.010	18.890	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	103	THR	0	0.044	0.018	23.535	0.006	0.006	0.000	0.000	0.000	0.000
88	A	104	GLN	0	-0.034	-0.036	24.649	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	105	ARG	1	0.789	0.893	24.325	-0.156	-0.156	0.000	0.000	0.000	0.000
90	A	106	LEU	0	0.001	0.003	19.982	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	107	LEU	0	0.006	0.011	24.045	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	108	GLU	-1	-0.785	-0.872	27.177	0.105	0.105	0.000	0.000	0.000	0.000
93	A	109	TYR	0	-0.017	-0.016	22.785	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.982	0.992	24.929	-0.208	-0.208	0.000	0.000	0.000	0.000
95	A	111	LYS	1	0.804	0.895	26.547	-0.121	-0.121	0.000	0.000	0.000	0.000
96	A	112	PHE	0	-0.013	-0.026	29.714	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	113	LYS	1	0.881	0.941	22.524	-0.146	-0.146	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.894	-0.943	27.871	0.143	0.143	0.000	0.000	0.000	0.000
99	A	115	ALA	0	0.005	-0.004	30.211	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.018	0.009	29.963	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	117	ARG	1	0.855	0.913	25.423	-0.148	-0.148	0.000	0.000	0.000	0.000
102	A	118	GLU	-1	-0.813	-0.876	31.635	0.066	0.066	0.000	0.000	0.000	0.000
103	A	119	LEU	0	-0.002	-0.008	34.857	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	120	LYS	1	0.902	0.952	30.252	-0.047	-0.047	0.000	0.000	0.000	0.000
105	A	121	ARG	1	0.942	0.964	32.756	-0.090	-0.090	0.000	0.000	0.000	0.000
106	A	122	ARG	1	0.854	0.928	36.635	-0.060	-0.060	0.000	0.000	0.000	0.000
107	A	123	GLU	-1	-0.973	-0.983	34.997	0.020	0.020	0.000	0.000	0.000	0.000
108	A	124	GLU	-1	-0.878	-0.937	34.121	0.037	0.037	0.000	0.000	0.000	0.000
109	A	125	GLU	-1	-0.891	-0.959	38.917	0.043	0.043	0.000	0.000	0.000	0.000
110	A	126	ARG	1	0.846	0.919	42.004	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	127	ALA	0	-0.025	0.003	40.847	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	128	LEU	0	0.012	0.015	42.052	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	129	LEU	0	-0.014	0.008	44.835	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	130	PHE	0	0.005	-0.014	46.253	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	131	THR	0	0.013	0.009	49.743	0.002	0.002	0.000	0.000	0.000	0.000
116	A	132	LYS	1	0.905	0.948	52.026	0.000	0.000	0.000	0.000	0.000	0.000
117	A	133	PRO	0	-0.002	-0.006	53.047	0.001	0.001	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.030	0.012	54.745	0.001	0.001	0.000	0.000	0.000	0.000
119	A	135	SER	0	-0.018	-0.015	57.921	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	136	ASP	-1	-0.815	-0.880	61.272	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	137	LEU	0	-0.054	-0.036	62.798	0.000	0.000	0.000	0.000	0.000	0.000
122	A	138	SER	0	0.012	-0.021	64.323	0.001	0.001	0.000	0.000	0.000	0.000
123	A	139	ALA	0	-0.017	-0.002	66.698	0.000	0.000	0.000	0.000	0.000	0.000
124	A	140	TYR	0	-0.032	-0.010	68.220	0.000	0.000	0.000	0.000	0.000	0.000
125	A	141	ALA	0	-0.035	-0.001	68.758	0.001	0.001	0.000	0.000	0.000	0.000
126	A	149	LEU	0	-0.008	-0.007	60.142	0.000	0.000	0.000	0.000	0.000	0.000
127	A	150	ASP	-1	-0.964	-0.977	60.555	0.003	0.003	0.000	0.000	0.000	0.000
128	A	151	VAL	0	-0.017	-0.009	55.865	0.001	0.001	0.000	0.000	0.000	0.000
129	A	152	ASN	0	0.021	0.009	52.544	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	153	VAL	0	0.057	-0.001	47.962	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	154	TYR	0	-0.003	0.002	46.601	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	155	ASP	-1	-0.802	-0.903	49.066	0.004	0.004	0.000	0.000	0.000	0.000
133	A	156	MET	0	-0.024	-0.005	50.370	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	157	LEU	0	0.022	0.012	44.290	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	158	GLY	0	0.021	0.011	46.556	0.000	0.000	0.000	0.000	0.000	0.000
136	A	159	ALA	0	-0.045	-0.029	48.290	0.000	0.000	0.000	0.000	0.000	0.000
137	A	160	LEU	0	0.008	0.009	45.837	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	161	SER	0	0.023	0.009	43.848	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	162	LYS	1	0.923	0.955	45.370	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	163	LEU	0	-0.044	-0.030	47.987	0.000	0.000	0.000	0.000	0.000	0.000
141	A	164	LEU	0	0.004	-0.003	42.925	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	165	ARG	1	0.965	0.991	42.820	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	166	ARG	1	0.854	0.949	44.714	0.009	0.009	0.000	0.000	0.000	0.000
144	A	167	LYS	1	0.904	0.964	43.818	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	168	LYS	1	0.933	0.958	46.784	0.027	0.027	0.000	0.000	0.000	0.000
146	A	169	LEU	0	0.026	0.016	48.404	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	170	GLN	0	0.009	0.003	50.908	0.000	0.000	0.000	0.000	0.000	0.000
148	A	171	LYS	1	0.951	0.975	52.375	0.025	0.025	0.000	0.000	0.000	0.000
149	A	172	PRO	0	0.028	0.015	55.841	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	173	MET	0	0.021	0.018	58.186	0.000	0.000	0.000	0.000	0.000	0.000

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