FMO DATABASE

FMODB ID: LJKQ9

Calculation Name: 3RBW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RBW

Chain ID: B

ChEMBL ID:

UniProt ID: Q08AE8

Base Structure: X-ray

Registration Date: 2023-06-20

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	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1536720.421182
FMO2-HF: Nuclear repulsion	1473544.406386
FMO2-HF: Total energy	-63176.014796
FMO2-MP2: Total energy	-63355.114243

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(B:38:ASP)

Summations of interaction energy for fragment #1(B:38:ASP)

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.
-61.424	-56.767	19.821	-13.198	-11.281	0.111

Interaction energy analysis for fragmet #1(B:38:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.960

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	B	40	LEU	0	0.002	0.027	3.873	-2.271	-0.538	-0.017	-0.895	-0.821	0.002
4	B	41	SER	0	-0.053	-0.037	6.073	-1.636	-1.636	0.000	0.000	0.000	0.000
5	B	42	LEU	0	0.039	0.002	9.590	-0.495	-0.495	0.000	0.000	0.000	0.000
6	B	43	GLU	-1	-0.974	-0.995	12.317	16.270	16.270	0.000	0.000	0.000	0.000
7	B	44	GLU	-1	-0.859	-0.917	7.792	27.462	27.462	0.000	0.000	0.000	0.000
8	B	45	ILE	0	0.008	0.002	9.296	-0.716	-0.716	0.000	0.000	0.000	0.000
9	B	46	LEU	0	-0.035	-0.012	11.660	-0.894	-0.894	0.000	0.000	0.000	0.000
10	B	47	ARG	1	0.920	0.966	14.014	-16.404	-16.404	0.000	0.000	0.000	0.000
11	B	48	LEU	0	-0.039	-0.016	10.132	-0.711	-0.711	0.000	0.000	0.000	0.000
12	B	49	TYR	0	0.008	-0.002	12.485	-0.989	-0.989	0.000	0.000	0.000	0.000
13	B	50	ASN	0	-0.034	-0.004	16.352	-0.760	-0.760	0.000	0.000	0.000	0.000
14	B	51	GLN	0	-0.057	-0.033	18.469	-0.487	-0.487	0.000	0.000	0.000	0.000
15	B	52	PRO	0	-0.002	0.006	18.804	0.719	0.719	0.000	0.000	0.000	0.000
16	B	53	ILE	0	-0.015	0.014	16.337	0.249	0.249	0.000	0.000	0.000	0.000
17	B	54	ASN	0	0.021	0.002	18.961	-0.631	-0.631	0.000	0.000	0.000	0.000
18	B	55	GLU	-1	-0.739	-0.870	21.065	11.484	11.484	0.000	0.000	0.000	0.000
19	B	56	GLU	-1	-0.810	-0.882	20.783	13.579	13.579	0.000	0.000	0.000	0.000
20	B	57	GLN	0	0.053	0.008	15.969	-0.045	-0.045	0.000	0.000	0.000	0.000
21	B	58	ALA	0	0.053	0.040	18.068	0.805	0.805	0.000	0.000	0.000	0.000
22	B	59	TRP	0	0.024	0.014	20.300	0.457	0.457	0.000	0.000	0.000	0.000
23	B	60	ALA	0	-0.001	-0.022	16.717	0.172	0.172	0.000	0.000	0.000	0.000
24	B	61	VAL	0	0.012	-0.007	14.678	0.541	0.541	0.000	0.000	0.000	0.000
25	B	62	CYS	0	-0.016	-0.004	16.865	0.254	0.254	0.000	0.000	0.000	0.000
26	B	63	TYR	0	0.013	0.000	18.359	-0.537	-0.537	0.000	0.000	0.000	0.000
27	B	64	GLN	0	-0.015	-0.021	13.247	-1.387	-1.387	0.000	0.000	0.000	0.000
28	B	65	CYS	0	-0.034	0.011	15.474	0.658	0.658	0.000	0.000	0.000	0.000
29	B	66	CYS	0	0.011	0.006	16.463	-0.375	-0.375	0.000	0.000	0.000	0.000
30	B	67	GLY	0	-0.008	-0.017	17.889	-0.382	-0.382	0.000	0.000	0.000	0.000
31	B	68	SER	0	-0.019	-0.016	13.252	0.259	0.259	0.000	0.000	0.000	0.000
32	B	69	LEU	0	-0.004	0.002	15.771	-0.305	-0.305	0.000	0.000	0.000	0.000
33	B	70	ARG	1	0.866	0.924	18.652	-14.099	-14.099	0.000	0.000	0.000	0.000
34	B	71	ALA	0	-0.087	-0.060	16.937	-0.796	-0.796	0.000	0.000	0.000	0.000
35	B	72	ALA	0	0.045	0.040	16.859	0.157	0.157	0.000	0.000	0.000	0.000
36	B	73	ALA	0	0.040	0.019	18.667	-0.537	-0.537	0.000	0.000	0.000	0.000
37	B	74	ARG	1	0.898	0.945	19.892	-15.423	-15.423	0.000	0.000	0.000	0.000
38	B	75	ARG	1	0.914	0.959	18.588	-15.355	-15.355	0.000	0.000	0.000	0.000
39	B	76	ARG	1	0.890	0.950	21.721	-11.353	-11.353	0.000	0.000	0.000	0.000
40	B	77	GLN	0	0.042	0.031	17.560	-0.852	-0.852	0.000	0.000	0.000	0.000
41	B	78	PRO	0	-0.005	-0.008	20.890	-0.323	-0.323	0.000	0.000	0.000	0.000
42	B	79	ARG	1	0.922	0.975	21.113	-11.162	-11.162	0.000	0.000	0.000	0.000
43	B	80	HIS	0	0.043	0.021	18.125	-0.774	-0.774	0.000	0.000	0.000	0.000
44	B	81	ARG	1	0.889	0.917	21.431	-11.143	-11.143	0.000	0.000	0.000	0.000
45	B	82	VAL	0	-0.003	-0.011	18.663	0.579	0.579	0.000	0.000	0.000	0.000
46	B	83	ARG	1	0.934	0.975	20.535	-12.832	-12.832	0.000	0.000	0.000	0.000
47	B	84	SER	0	0.076	0.029	18.804	-0.338	-0.338	0.000	0.000	0.000	0.000
48	B	85	ALA	0	0.054	0.017	15.988	0.585	0.585	0.000	0.000	0.000	0.000
49	B	86	ALA	0	0.063	0.035	13.727	1.093	1.093	0.000	0.000	0.000	0.000
50	B	87	GLN	0	-0.087	-0.061	12.905	0.997	0.997	0.000	0.000	0.000	0.000
51	B	88	ILE	0	0.041	0.035	12.899	0.761	0.761	0.000	0.000	0.000	0.000
52	B	89	ARG	1	0.951	0.980	7.939	-25.414	-25.414	0.000	0.000	0.000	0.000
53	B	90	VAL	0	0.031	0.013	8.529	-0.974	-0.974	0.000	0.000	0.000	0.000
54	B	91	TRP	0	-0.034	-0.032	3.099	-0.154	1.516	0.096	-0.751	-1.015	0.007
55	B	92	ARG	1	0.911	0.961	1.771	-118.800	-118.578	19.611	-11.210	-8.623	0.103
56	B	93	ASP	-1	-0.956	-0.990	5.039	32.592	32.764	-0.001	-0.005	-0.166	0.000
57	B	94	GLY	0	0.064	0.029	7.667	-4.777	-4.777	0.000	0.000	0.000	0.000
58	B	95	ALA	0	0.011	0.022	8.626	-3.926	-3.926	0.000	0.000	0.000	0.000
59	B	96	VAL	0	0.033	0.008	9.820	1.301	1.301	0.000	0.000	0.000	0.000
60	B	97	THR	0	-0.021	0.012	10.041	-0.680	-0.680	0.000	0.000	0.000	0.000
61	B	98	LEU	0	0.001	0.004	12.139	0.744	0.744	0.000	0.000	0.000	0.000
62	B	99	ALA	0	-0.048	-0.020	11.898	0.257	0.257	0.000	0.000	0.000	0.000
63	B	100	PRO	0	0.006	0.000	13.768	-1.128	-1.128	0.000	0.000	0.000	0.000
64	B	101	ALA	0	-0.015	-0.020	16.054	0.570	0.570	0.000	0.000	0.000	0.000
65	B	102	ALA	0	-0.018	-0.011	18.455	0.285	0.285	0.000	0.000	0.000	0.000
66	B	103	ASP	-1	-0.949	-0.958	19.741	12.240	12.240	0.000	0.000	0.000	0.000
67	B	119	GLN	0	0.049	0.030	29.794	-0.164	-0.164	0.000	0.000	0.000	0.000
68	B	120	CYS	0	-0.076	-0.052	25.576	0.056	0.056	0.000	0.000	0.000	0.000
69	B	121	MET	0	-0.012	-0.002	28.274	0.183	0.183	0.000	0.000	0.000	0.000
70	B	122	GLU	-1	-0.866	-0.948	25.642	12.235	12.235	0.000	0.000	0.000	0.000
71	B	123	THR	0	0.062	0.008	26.633	0.433	0.433	0.000	0.000	0.000	0.000
72	B	124	GLU	-1	-0.747	-0.846	27.753	10.446	10.446	0.000	0.000	0.000	0.000
73	B	125	VAL	0	-0.078	-0.023	21.585	0.256	0.256	0.000	0.000	0.000	0.000
74	B	126	ILE	0	0.001	-0.004	23.905	0.460	0.460	0.000	0.000	0.000	0.000
75	B	127	GLU	-1	-0.842	-0.899	25.070	10.773	10.773	0.000	0.000	0.000	0.000
76	B	128	SER	0	-0.080	-0.023	23.618	0.372	0.372	0.000	0.000	0.000	0.000
77	B	129	LEU	0	-0.011	-0.031	18.927	0.470	0.470	0.000	0.000	0.000	0.000
78	B	130	GLY	0	0.046	0.017	22.107	0.320	0.320	0.000	0.000	0.000	0.000
79	B	131	ILE	0	0.052	0.035	24.566	0.037	0.037	0.000	0.000	0.000	0.000
80	B	132	ILE	0	-0.089	-0.025	18.239	0.111	0.111	0.000	0.000	0.000	0.000
81	B	133	ILE	0	-0.005	-0.007	19.064	0.284	0.284	0.000	0.000	0.000	0.000
82	B	134	TYR	0	0.036	0.020	21.429	0.215	0.215	0.000	0.000	0.000	0.000
83	B	135	LYS	1	0.983	0.963	22.440	-11.680	-11.680	0.000	0.000	0.000	0.000
84	B	136	ALA	0	-0.013	-0.007	18.338	0.039	0.039	0.000	0.000	0.000	0.000
85	B	137	LEU	0	-0.056	-0.037	20.200	0.159	0.159	0.000	0.000	0.000	0.000
86	B	138	ASP	-1	-0.946	-0.963	22.614	10.721	10.721	0.000	0.000	0.000	0.000
87	B	139	TYR	0	-0.040	-0.015	18.763	-0.024	-0.024	0.000	0.000	0.000	0.000
88	B	140	GLY	0	-0.015	-0.016	22.549	-0.072	-0.072	0.000	0.000	0.000	0.000
89	B	141	LEU	0	0.018	0.042	24.839	-0.283	-0.283	0.000	0.000	0.000	0.000
90	B	142	LYS	1	0.815	0.896	28.164	-9.352	-9.352	0.000	0.000	0.000	0.000
91	B	143	GLU	-1	-0.932	-0.964	31.026	8.693	8.693	0.000	0.000	0.000	0.000
92	B	144	ASN	0	-0.053	-0.040	33.354	0.111	0.111	0.000	0.000	0.000	0.000
93	B	145	GLU	-1	-0.918	-0.939	30.984	9.141	9.141	0.000	0.000	0.000	0.000
94	B	146	GLU	-1	-0.869	-0.939	31.008	9.285	9.285	0.000	0.000	0.000	0.000
95	B	147	ARG	1	0.851	0.916	23.688	-11.945	-11.945	0.000	0.000	0.000	0.000
96	B	148	GLU	-1	-0.918	-0.955	30.204	8.546	8.546	0.000	0.000	0.000	0.000
97	B	149	LEU	0	-0.040	-0.016	26.701	0.418	0.418	0.000	0.000	0.000	0.000
98	B	150	SER	0	-0.046	-0.041	29.164	-0.427	-0.427	0.000	0.000	0.000	0.000
99	B	151	PRO	0	0.075	0.024	31.074	0.219	0.219	0.000	0.000	0.000	0.000
100	B	152	PRO	0	-0.054	-0.027	30.599	0.032	0.032	0.000	0.000	0.000	0.000
101	B	153	LEU	0	-0.025	-0.022	25.172	0.294	0.294	0.000	0.000	0.000	0.000
102	B	154	GLU	-1	-0.856	-0.918	29.038	9.538	9.538	0.000	0.000	0.000	0.000
103	B	155	GLN	0	0.013	0.001	31.124	0.220	0.220	0.000	0.000	0.000	0.000
104	B	156	LEU	0	-0.023	-0.013	25.083	0.049	0.049	0.000	0.000	0.000	0.000
105	B	157	ILE	0	-0.017	-0.029	25.037	0.189	0.189	0.000	0.000	0.000	0.000
106	B	158	ASP	-1	-0.808	-0.906	28.462	9.478	9.478	0.000	0.000	0.000	0.000
107	B	159	HIS	0	-0.102	-0.052	31.513	-0.117	-0.117	0.000	0.000	0.000	0.000
108	B	160	MET	0	-0.158	-0.087	23.344	0.118	0.118	0.000	0.000	0.000	0.000
109	B	161	ALA	0	-0.006	-0.017	28.522	0.120	0.120	0.000	0.000	0.000	0.000
110	B	162	ASN	0	-0.079	-0.010	30.168	-0.060	-0.060	0.000	0.000	0.000	0.000
111	B	163	THR	0	-0.026	-0.016	33.323	-0.105	-0.105	0.000	0.000	0.000	0.000
112	B	164	VAL	0	0.013	0.008	35.260	0.062	0.062	0.000	0.000	0.000	0.000
113	B	165	GLU	-1	-0.981	-0.975	37.869	7.390	7.390	0.000	0.000	0.000	0.000
114	B	192	ALA	0	0.053	0.028	35.483	-0.122	-0.122	0.000	0.000	0.000	0.000
115	B	193	ILE	0	-0.038	-0.034	28.860	0.171	0.171	0.000	0.000	0.000	0.000
116	B	194	ARG	1	0.910	0.955	31.071	-9.461	-9.461	0.000	0.000	0.000	0.000
117	B	195	SER	0	-0.024	-0.022	27.962	0.139	0.139	0.000	0.000	0.000	0.000
118	B	196	TYR	0	0.071	0.026	22.680	0.081	0.081	0.000	0.000	0.000	0.000
119	B	197	ARG	1	0.895	0.940	24.748	-10.785	-10.785	0.000	0.000	0.000	0.000
120	B	198	ASP	-1	-0.869	-0.933	26.023	10.501	10.501	0.000	0.000	0.000	0.000
121	B	199	VAL	0	0.102	0.047	23.701	-0.165	-0.165	0.000	0.000	0.000	0.000
122	B	200	MET	0	-0.014	0.020	19.988	0.006	0.006	0.000	0.000	0.000	0.000
123	B	201	LYS	1	0.939	0.960	24.428	-10.110	-10.110	0.000	0.000	0.000	0.000
124	B	202	LEU	0	0.075	0.043	27.728	-0.231	-0.231	0.000	0.000	0.000	0.000
125	B	203	CYS	0	-0.024	0.019	23.203	0.085	0.085	0.000	0.000	0.000	0.000
126	B	204	ALA	0	-0.038	0.002	25.067	0.127	0.127	0.000	0.000	0.000	0.000
127	B	205	ALA	0	0.020	0.023	26.012	-0.144	-0.144	0.000	0.000	0.000	0.000
128	B	206	HIS	1	0.802	0.892	24.751	-12.371	-12.371	0.000	0.000	0.000	0.000
129	B	207	LEU	0	-0.017	0.003	23.681	0.077	0.077	0.000	0.000	0.000	0.000
130	B	208	PRO	0	-0.006	-0.004	27.953	-0.288	-0.288	0.000	0.000	0.000	0.000
131	B	209	THR	0	-0.003	0.008	28.714	-0.552	-0.552	0.000	0.000	0.000	0.000
132	B	210	GLU	-1	-0.902	-0.947	27.938	11.005	11.005	0.000	0.000	0.000	0.000
133	B	211	SER	0	-0.055	-0.050	26.719	0.321	0.321	0.000	0.000	0.000	0.000
134	B	212	ASP	-1	-0.857	-0.926	24.455	12.822	12.822	0.000	0.000	0.000	0.000
135	B	213	ALA	0	-0.003	-0.005	22.473	0.754	0.754	0.000	0.000	0.000	0.000
136	B	214	PRO	0	-0.074	-0.042	19.238	0.762	0.762	0.000	0.000	0.000	0.000
137	B	215	ASN	0	0.026	0.014	17.693	2.060	2.060	0.000	0.000	0.000	0.000
138	B	216	HIS	0	-0.059	-0.010	18.033	1.180	1.180	0.000	0.000	0.000	0.000
139	B	217	TYR	0	0.027	-0.054	17.991	0.608	0.608	0.000	0.000	0.000	0.000
140	B	218	GLN	0	-0.013	0.022	12.821	1.103	1.103	0.000	0.000	0.000	0.000
141	B	219	ALA	0	-0.024	-0.011	13.922	1.140	1.140	0.000	0.000	0.000	0.000
142	B	220	VAL	0	0.032	0.017	14.064	0.990	0.990	0.000	0.000	0.000	0.000
143	B	221	CYS	0	-0.007	-0.002	11.712	-0.216	-0.216	0.000	0.000	0.000	0.000
144	B	222	ARG	1	0.950	0.968	9.771	-22.781	-22.781	0.000	0.000	0.000	0.000
145	B	223	ALA	0	-0.038	-0.009	9.860	1.918	1.918	0.000	0.000	0.000	0.000
146	B	224	LEU	0	0.086	0.048	11.563	0.151	0.151	0.000	0.000	0.000	0.000
147	B	225	PHE	0	-0.040	0.031	2.981	1.156	1.954	0.133	-0.306	-0.625	-0.001
148	B	226	ALA	0	-0.025	-0.027	8.445	0.239	0.239	0.000	0.000	0.000	0.000
149	B	227	GLU	-1	-0.886	-0.959	9.528	17.970	17.970	0.000	0.000	0.000	0.000
150	B	228	THR	0	-0.078	-0.071	8.897	-1.569	-1.569	0.000	0.000	0.000	0.000
151	B	229	MET	0	-0.089	-0.048	5.060	1.242	1.304	-0.001	-0.031	-0.031	0.000
152	B	230	GLU	-1	-0.921	-0.953	8.121	19.508	19.508	0.000	0.000	0.000	0.000
153	B	231	LEU	0	-0.085	-0.019	11.502	-1.332	-1.332	0.000	0.000	0.000	0.000
154	B	232	HIS	0	-0.078	-0.034	9.367	0.138	0.138	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:38:ASP)