FMO DATABASE

FMODB ID: V5R11

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1256170.596685
FMO2-HF: Nuclear repulsion	1194425.790669
FMO2-HF: Total energy	-61744.806016
FMO2-MP2: Total energy	-61923.164755

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.
-12.135	-5.243	5.739	-4.184	-8.446	-0.006

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 : 0.010 / q_NPA : 0.006

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	-0.053	-0.029	2.047	-0.859	3.088	1.170	-2.181	-2.935	0.005
4	A	4	GLN	0	0.024	0.012	2.595	-1.976	-0.533	1.057	-1.015	-1.485	-0.015
5	A	5	LEU	0	-0.005	-0.002	2.445	-1.114	-1.075	3.420	-0.642	-2.817	0.005
6	A	6	PRO	0	-0.024	-0.013	5.865	-0.830	-0.809	-0.001	-0.009	-0.012	0.000
7	A	7	TYR	0	0.043	0.011	5.662	0.233	0.233	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.055	-0.027	11.207	-0.075	-0.075	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.006	0.007	13.730	-0.055	-0.055	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.880	0.933	12.955	0.279	0.279	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.088	0.025	12.106	0.046	0.046	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.822	-0.889	14.431	-0.154	-0.154	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.077	-0.029	17.197	0.014	0.014	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.033	-0.010	13.768	0.036	0.036	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.900	-0.942	18.763	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.024	0.007	19.394	0.011	0.011	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.002	-0.016	16.371	0.019	0.019	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.001	-0.011	16.970	0.035	0.035	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.770	-0.859	19.295	0.135	0.135	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.011	0.025	11.565	0.022	0.022	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.012	-0.010	14.308	0.054	0.054	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.010	-0.002	16.187	0.028	0.028	0.000	0.000	0.000	0.000
23	A	23	HIS	0	-0.008	0.007	13.639	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.021	-0.013	10.647	0.038	0.038	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.009	-0.017	14.564	0.036	0.036	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.053	-0.029	17.777	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.897	0.951	13.162	-0.640	-0.640	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.096	-0.063	9.780	0.024	0.024	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.954	-0.965	16.590	0.323	0.323	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.053	-0.012	16.268	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.819	-0.912	20.025	0.209	0.209	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.054	-0.038	22.365	0.011	0.011	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.026	-0.033	23.380	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.839	-0.891	24.261	0.267	0.267	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.007	0.018	18.316	0.030	0.030	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.036	0.029	17.113	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.002	-0.017	16.259	0.062	0.062	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.002	0.017	14.116	0.032	0.032	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.074	0.045	12.184	0.153	0.153	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.027	0.015	11.100	0.102	0.102	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.006	-0.026	10.934	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.802	-0.894	7.821	0.992	0.992	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.027	-0.002	6.428	0.220	0.220	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.021	-0.032	7.448	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.022	-0.013	6.783	-0.158	-0.158	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.009	0.017	2.972	-0.655	-0.253	0.083	-0.127	-0.357	0.000
47	A	47	TYR	0	-0.023	-0.033	3.847	-0.471	-0.318	0.000	-0.004	-0.150	0.000
48	A	48	ILE	0	-0.006	-0.012	6.768	-0.261	-0.261	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.021	-0.024	3.517	-0.083	0.245	0.011	-0.045	-0.294	0.000
50	A	50	ALA	0	0.022	0.017	4.205	-0.824	-0.642	-0.001	-0.026	-0.155	0.000
51	A	51	MET	0	-0.068	-0.017	5.025	-0.108	-0.085	-0.001	-0.002	-0.020	0.000
52	A	52	GLN	0	-0.006	-0.007	7.520	0.071	0.071	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.942	-0.963	3.867	-5.757	-5.403	0.001	-0.133	-0.221	-0.001
54	A	54	LEU	0	-0.084	-0.037	7.305	0.125	0.125	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.971	-0.983	10.746	-0.590	-0.590	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.041	-0.015	11.646	0.155	0.155	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.899	-0.954	13.962	-0.242	-0.242	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.079	-0.039	10.861	0.069	0.069	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.012	0.012	14.621	0.018	0.018	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.002	-0.026	16.827	0.024	0.024	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.830	-0.913	18.135	0.039	0.039	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.011	0.007	13.597	0.049	0.049	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.038	0.030	12.916	0.054	0.054	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.004	0.003	15.264	0.043	0.043	0.000	0.000	0.000	0.000
65	A	65	MET	0	-0.013	0.012	15.494	0.031	0.031	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.030	0.017	12.192	0.041	0.041	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.004	0.000	13.708	0.052	0.052	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.042	-0.032	16.477	0.011	0.011	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.008	-0.007	13.070	0.004	0.004	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.038	0.021	11.244	0.025	0.025	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.018	0.005	15.251	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.031	-0.019	18.884	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.829	0.899	11.706	-0.850	-0.850	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.028	-0.028	17.514	0.008	0.008	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.925	0.952	19.346	-0.240	-0.240	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.046	-0.006	20.059	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.018	0.003	17.860	0.012	0.012	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.029	-0.013	20.021	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.007	-0.006	23.363	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	80	PRO	0	-0.020	0.011	25.863	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.775	-0.873	25.301	0.243	0.243	0.000	0.000	0.000	0.000
82	A	98	PRO	0	-0.026	-0.024	23.904	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	99	ARG	1	0.755	0.840	21.604	-0.277	-0.277	0.000	0.000	0.000	0.000
84	A	100	GLU	-1	-0.851	-0.904	23.441	0.180	0.180	0.000	0.000	0.000	0.000
85	A	101	GLU	-1	-0.823	-0.875	25.546	0.138	0.138	0.000	0.000	0.000	0.000
86	A	102	LEU	0	0.014	0.000	18.422	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	103	THR	0	0.021	0.006	23.116	0.004	0.004	0.000	0.000	0.000	0.000
88	A	104	GLN	0	-0.018	-0.033	24.424	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	105	ARG	1	0.772	0.854	23.897	-0.142	-0.142	0.000	0.000	0.000	0.000
90	A	106	LEU	0	-0.004	0.000	19.562	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	107	LEU	0	0.009	0.012	23.609	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	108	GLU	-1	-0.801	-0.882	26.903	0.090	0.090	0.000	0.000	0.000	0.000
93	A	109	TYR	0	-0.053	-0.041	22.458	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.979	0.996	24.851	-0.176	-0.176	0.000	0.000	0.000	0.000
95	A	111	LYS	1	0.794	0.885	26.325	-0.107	-0.107	0.000	0.000	0.000	0.000
96	A	112	PHE	0	0.006	-0.006	29.372	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	113	LYS	1	0.884	0.936	22.538	-0.108	-0.108	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.847	-0.917	27.738	0.118	0.118	0.000	0.000	0.000	0.000
99	A	115	ALA	0	-0.016	-0.008	30.159	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.012	0.005	29.498	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	117	ARG	1	0.842	0.899	25.243	-0.124	-0.124	0.000	0.000	0.000	0.000
102	A	118	GLU	-1	-0.823	-0.885	31.332	0.049	0.049	0.000	0.000	0.000	0.000
103	A	119	LEU	0	-0.007	-0.018	34.616	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	120	LYS	1	0.828	0.894	30.811	-0.023	-0.023	0.000	0.000	0.000	0.000
105	A	121	ARG	1	0.939	0.968	33.181	-0.070	-0.070	0.000	0.000	0.000	0.000
106	A	122	ARG	1	0.803	0.884	36.832	-0.045	-0.045	0.000	0.000	0.000	0.000
107	A	123	GLU	-1	-0.916	-0.942	34.661	0.006	0.006	0.000	0.000	0.000	0.000
108	A	124	GLU	-1	-0.856	-0.915	34.010	0.019	0.019	0.000	0.000	0.000	0.000
109	A	125	GLU	-1	-0.849	-0.924	38.745	0.030	0.030	0.000	0.000	0.000	0.000
110	A	126	ARG	1	0.844	0.921	41.971	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	127	ALA	0	-0.009	0.004	40.360	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	128	LEU	0	0.023	0.024	41.892	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	129	LEU	0	-0.003	0.012	44.303	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	130	PHE	0	0.009	-0.013	46.432	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	131	THR	0	0.005	-0.003	49.586	0.002	0.002	0.000	0.000	0.000	0.000
116	A	132	LYS	1	0.883	0.944	51.537	0.005	0.005	0.000	0.000	0.000	0.000
117	A	133	PRO	0	0.034	0.011	52.697	0.001	0.001	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.020	0.009	54.224	0.001	0.001	0.000	0.000	0.000	0.000
119	A	135	SER	0	-0.011	-0.010	57.415	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	136	ASP	-1	-0.811	-0.876	60.756	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	137	LEU	0	-0.010	-0.016	62.506	0.001	0.001	0.000	0.000	0.000	0.000
122	A	138	SER	0	-0.005	-0.022	64.225	0.001	0.001	0.000	0.000	0.000	0.000
123	A	139	ALA	0	-0.034	-0.015	66.670	0.000	0.000	0.000	0.000	0.000	0.000
124	A	140	TYR	0	-0.024	-0.002	68.040	0.000	0.000	0.000	0.000	0.000	0.000
125	A	141	ALA	0	-0.056	-0.014	68.380	0.001	0.001	0.000	0.000	0.000	0.000
126	A	149	LEU	0	-0.007	-0.006	59.625	0.000	0.000	0.000	0.000	0.000	0.000
127	A	150	ASP	-1	-0.954	-0.975	60.110	0.000	0.000	0.000	0.000	0.000	0.000
128	A	151	VAL	0	-0.025	-0.013	55.423	0.000	0.000	0.000	0.000	0.000	0.000
129	A	152	ASN	0	0.020	0.011	51.933	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	153	VAL	0	0.054	-0.001	47.459	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	154	TYR	0	-0.013	0.002	46.579	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	155	ASP	-1	-0.785	-0.898	48.532	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	156	MET	0	-0.025	0.000	49.904	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	157	LEU	0	0.041	0.023	43.885	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	158	GLY	0	0.021	0.024	46.271	0.000	0.000	0.000	0.000	0.000	0.000
136	A	159	ALA	0	-0.039	-0.029	48.187	0.000	0.000	0.000	0.000	0.000	0.000
137	A	160	LEU	0	0.017	0.009	45.086	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	161	SER	0	-0.001	-0.014	43.864	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	162	LYS	1	0.925	0.956	45.234	0.001	0.001	0.000	0.000	0.000	0.000
140	A	163	LEU	0	-0.036	-0.008	48.054	0.000	0.000	0.000	0.000	0.000	0.000
141	A	164	LEU	0	0.026	-0.003	42.412	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	165	ARG	1	0.941	0.981	42.505	0.001	0.001	0.000	0.000	0.000	0.000
143	A	166	ARG	1	0.839	0.929	44.583	0.016	0.016	0.000	0.000	0.000	0.000
144	A	167	LYS	1	0.861	0.925	44.071	0.002	0.002	0.000	0.000	0.000	0.000
145	A	168	LYS	1	0.938	0.970	46.678	0.033	0.033	0.000	0.000	0.000	0.000
146	A	169	LEU	0	0.030	0.018	48.374	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	170	GLN	0	0.014	0.012	50.673	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	171	LYS	1	0.947	0.972	52.275	0.030	0.030	0.000	0.000	0.000	0.000
149	A	172	PRO	0	0.030	0.019	55.738	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	173	MET	0	0.011	0.011	58.239	-0.001	-0.001	0.000	0.000	0.000	0.000

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