FMO DATABASE

FMODB ID: 661ZZ

Calculation Name: 3RBW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RBW

Chain ID: A

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1542637.308461
FMO2-HF: Nuclear repulsion	1479458.474933
FMO2-HF: Total energy	-63178.833528
FMO2-MP2: Total energy	-63357.777454

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:38:ASP)

Summations of interaction energy for fragment #1(A: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.
-108.126	-111.285	30.7	-15.117	-12.421	0.141

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.811 / q_NPA : -0.886

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	40	LEU	0	0.014	0.022	3.750	-4.076	-1.890	-0.010	-1.225	-0.951	0.002
4	A	41	SER	0	-0.085	-0.079	6.108	-0.794	-0.794	0.000	0.000	0.000	0.000
5	A	42	LEU	0	0.036	0.009	9.810	-0.085	-0.085	0.000	0.000	0.000	0.000
6	A	43	GLU	-1	-0.791	-0.890	12.604	14.357	14.357	0.000	0.000	0.000	0.000
7	A	44	GLU	-1	-0.850	-0.887	7.848	24.116	24.116	0.000	0.000	0.000	0.000
8	A	45	ILE	0	0.007	0.004	9.054	-0.551	-0.551	0.000	0.000	0.000	0.000
9	A	46	LEU	0	-0.014	0.000	11.736	-0.660	-0.660	0.000	0.000	0.000	0.000
10	A	47	ARG	1	0.844	0.916	14.239	-15.801	-15.801	0.000	0.000	0.000	0.000
11	A	48	LEU	0	-0.045	-0.021	9.729	-0.596	-0.596	0.000	0.000	0.000	0.000
12	A	49	TYR	0	0.008	0.000	13.359	-0.684	-0.684	0.000	0.000	0.000	0.000
13	A	50	ASN	0	-0.047	0.001	16.403	-0.680	-0.680	0.000	0.000	0.000	0.000
14	A	51	GLN	0	-0.050	-0.028	18.808	-0.962	-0.962	0.000	0.000	0.000	0.000
15	A	52	PRO	0	0.009	0.022	19.062	0.725	0.725	0.000	0.000	0.000	0.000
16	A	53	ILE	0	-0.016	0.002	16.373	0.248	0.248	0.000	0.000	0.000	0.000
17	A	54	ASN	0	0.052	0.016	19.221	-0.815	-0.815	0.000	0.000	0.000	0.000
18	A	55	GLU	-1	-0.746	-0.861	21.083	11.409	11.409	0.000	0.000	0.000	0.000
19	A	56	GLU	-1	-0.784	-0.852	20.986	13.361	13.361	0.000	0.000	0.000	0.000
20	A	57	GLN	0	0.051	0.012	16.548	0.055	0.055	0.000	0.000	0.000	0.000
21	A	58	ALA	0	0.044	0.031	18.003	0.736	0.736	0.000	0.000	0.000	0.000
22	A	59	TRP	0	0.025	0.004	20.362	0.323	0.323	0.000	0.000	0.000	0.000
23	A	60	ALA	0	-0.017	-0.013	16.883	0.158	0.158	0.000	0.000	0.000	0.000
24	A	61	VAL	0	0.021	0.004	14.523	0.717	0.717	0.000	0.000	0.000	0.000
25	A	62	CYS	0	0.002	0.012	16.851	0.216	0.216	0.000	0.000	0.000	0.000
26	A	63	TYR	0	0.020	0.011	17.953	-0.398	-0.398	0.000	0.000	0.000	0.000
27	A	64	GLN	0	0.000	-0.024	12.766	-1.318	-1.318	0.000	0.000	0.000	0.000
28	A	65	CYS	0	-0.016	0.011	15.384	0.580	0.580	0.000	0.000	0.000	0.000
29	A	66	CYS	0	-0.035	-0.013	16.320	-0.497	-0.497	0.000	0.000	0.000	0.000
30	A	67	GLY	0	0.014	-0.017	17.511	-0.522	-0.522	0.000	0.000	0.000	0.000
31	A	68	SER	0	-0.015	-0.033	13.229	-0.160	-0.160	0.000	0.000	0.000	0.000
32	A	69	LEU	0	-0.010	0.002	15.744	-0.381	-0.381	0.000	0.000	0.000	0.000
33	A	70	ARG	1	0.850	0.903	18.806	-13.806	-13.806	0.000	0.000	0.000	0.000
34	A	71	ALA	0	-0.074	-0.043	16.749	-0.667	-0.667	0.000	0.000	0.000	0.000
35	A	72	ALA	0	0.038	0.022	17.297	-0.285	-0.285	0.000	0.000	0.000	0.000
36	A	73	ALA	0	0.059	0.031	18.970	-0.576	-0.576	0.000	0.000	0.000	0.000
37	A	74	ARG	1	0.872	0.944	19.608	-15.198	-15.198	0.000	0.000	0.000	0.000
38	A	75	ARG	1	0.894	0.927	19.111	-14.353	-14.353	0.000	0.000	0.000	0.000
39	A	76	ARG	1	0.901	0.956	21.969	-10.995	-10.995	0.000	0.000	0.000	0.000
40	A	77	GLN	0	0.066	0.044	18.102	-0.567	-0.567	0.000	0.000	0.000	0.000
41	A	78	PRO	0	-0.024	-0.003	20.562	-0.420	-0.420	0.000	0.000	0.000	0.000
42	A	79	ARG	1	0.840	0.911	20.987	-10.838	-10.838	0.000	0.000	0.000	0.000
43	A	80	HIS	0	0.049	0.031	18.822	-0.583	-0.583	0.000	0.000	0.000	0.000
44	A	81	ARG	1	0.874	0.903	21.190	-10.799	-10.799	0.000	0.000	0.000	0.000
45	A	82	VAL	0	-0.029	-0.009	18.655	0.488	0.488	0.000	0.000	0.000	0.000
46	A	83	ARG	1	0.845	0.897	20.307	-12.358	-12.358	0.000	0.000	0.000	0.000
47	A	84	SER	0	0.017	-0.006	17.667	-0.323	-0.323	0.000	0.000	0.000	0.000
48	A	85	ALA	0	0.078	0.029	15.695	0.537	0.537	0.000	0.000	0.000	0.000
49	A	86	ALA	0	0.007	0.008	13.313	1.206	1.206	0.000	0.000	0.000	0.000
50	A	87	GLN	0	-0.066	-0.044	12.540	0.625	0.625	0.000	0.000	0.000	0.000
51	A	88	ILE	0	0.008	0.013	13.217	0.999	0.999	0.000	0.000	0.000	0.000
52	A	89	ARG	1	0.943	0.980	8.035	-22.940	-22.940	0.000	0.000	0.000	0.000
53	A	90	VAL	0	0.030	0.013	8.419	-1.001	-1.001	0.000	0.000	0.000	0.000
54	A	91	TRP	0	-0.022	-0.027	3.316	0.548	1.827	0.043	-0.533	-0.788	0.004
55	A	92	ARG	1	0.883	0.921	1.723	-139.087	-146.621	30.414	-13.030	-9.849	0.136
56	A	93	ASP	-1	-0.840	-0.927	5.088	30.529	30.676	-0.001	-0.005	-0.141	0.000
57	A	94	GLY	0	0.037	0.031	7.380	-4.913	-4.913	0.000	0.000	0.000	0.000
58	A	95	ALA	0	-0.018	0.003	8.304	-3.799	-3.799	0.000	0.000	0.000	0.000
59	A	96	VAL	0	0.023	0.000	9.505	1.330	1.330	0.000	0.000	0.000	0.000
60	A	97	THR	0	-0.046	-0.006	10.122	-0.576	-0.576	0.000	0.000	0.000	0.000
61	A	98	LEU	0	0.009	0.015	12.088	0.513	0.513	0.000	0.000	0.000	0.000
62	A	99	ALA	0	-0.025	-0.002	11.611	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	100	PRO	0	0.012	-0.003	13.547	-0.996	-0.996	0.000	0.000	0.000	0.000
64	A	101	ALA	0	0.025	0.022	15.905	0.607	0.607	0.000	0.000	0.000	0.000
65	A	102	ALA	0	-0.005	-0.001	18.376	0.208	0.208	0.000	0.000	0.000	0.000
66	A	103	ASP	-1	-0.875	-0.911	19.388	11.985	11.985	0.000	0.000	0.000	0.000
67	A	119	GLN	0	0.034	0.019	29.580	0.055	0.055	0.000	0.000	0.000	0.000
68	A	120	CYS	0	-0.035	-0.023	26.484	0.120	0.120	0.000	0.000	0.000	0.000
69	A	121	MET	0	-0.010	0.002	27.907	0.194	0.194	0.000	0.000	0.000	0.000
70	A	122	GLU	-1	-0.844	-0.937	25.624	12.066	12.066	0.000	0.000	0.000	0.000
71	A	123	THR	0	0.040	0.006	26.595	0.314	0.314	0.000	0.000	0.000	0.000
72	A	124	GLU	-1	-0.690	-0.813	28.025	10.146	10.146	0.000	0.000	0.000	0.000
73	A	125	VAL	0	-0.054	-0.006	21.694	0.276	0.276	0.000	0.000	0.000	0.000
74	A	126	ILE	0	-0.045	-0.019	23.495	0.490	0.490	0.000	0.000	0.000	0.000
75	A	127	GLU	-1	-0.864	-0.921	25.353	10.737	10.737	0.000	0.000	0.000	0.000
76	A	128	SER	0	-0.005	-0.023	24.033	0.353	0.353	0.000	0.000	0.000	0.000
77	A	129	LEU	0	-0.035	-0.030	18.981	0.380	0.380	0.000	0.000	0.000	0.000
78	A	130	GLY	0	0.037	0.018	22.223	0.285	0.285	0.000	0.000	0.000	0.000
79	A	131	ILE	0	0.040	0.022	24.791	0.018	0.018	0.000	0.000	0.000	0.000
80	A	132	ILE	0	-0.063	-0.031	18.631	0.073	0.073	0.000	0.000	0.000	0.000
81	A	133	ILE	0	-0.018	-0.022	18.588	0.438	0.438	0.000	0.000	0.000	0.000
82	A	134	TYR	0	-0.007	-0.016	21.477	0.340	0.340	0.000	0.000	0.000	0.000
83	A	135	LYS	1	0.968	0.969	22.169	-11.161	-11.161	0.000	0.000	0.000	0.000
84	A	136	ALA	0	-0.040	-0.020	18.351	0.092	0.092	0.000	0.000	0.000	0.000
85	A	137	LEU	0	-0.045	-0.019	20.140	0.236	0.236	0.000	0.000	0.000	0.000
86	A	138	ASP	-1	-0.844	-0.920	22.939	10.364	10.364	0.000	0.000	0.000	0.000
87	A	139	TYR	0	-0.067	-0.037	18.984	-0.103	-0.103	0.000	0.000	0.000	0.000
88	A	140	GLY	0	0.026	0.009	22.679	0.108	0.108	0.000	0.000	0.000	0.000
89	A	141	LEU	0	-0.032	0.020	25.099	-0.351	-0.351	0.000	0.000	0.000	0.000
90	A	142	LYS	1	0.732	0.843	28.468	-9.506	-9.506	0.000	0.000	0.000	0.000
91	A	143	GLU	-1	-0.887	-0.954	31.429	8.481	8.481	0.000	0.000	0.000	0.000
92	A	144	ASN	0	-0.127	-0.063	33.654	-0.097	-0.097	0.000	0.000	0.000	0.000
93	A	145	GLU	-1	-0.851	-0.911	31.453	8.896	8.896	0.000	0.000	0.000	0.000
94	A	146	GLU	-1	-0.817	-0.889	30.991	9.230	9.230	0.000	0.000	0.000	0.000
95	A	147	ARG	1	0.783	0.873	23.125	-11.900	-11.900	0.000	0.000	0.000	0.000
96	A	148	GLU	-1	-0.919	-0.947	30.127	8.640	8.640	0.000	0.000	0.000	0.000
97	A	149	LEU	0	-0.035	-0.016	26.837	0.453	0.453	0.000	0.000	0.000	0.000
98	A	150	SER	0	-0.033	-0.048	28.934	-0.355	-0.355	0.000	0.000	0.000	0.000
99	A	151	PRO	0	0.069	0.020	31.133	0.194	0.194	0.000	0.000	0.000	0.000
100	A	152	PRO	0	-0.056	-0.029	30.718	0.006	0.006	0.000	0.000	0.000	0.000
101	A	153	LEU	0	-0.015	-0.014	24.829	0.253	0.253	0.000	0.000	0.000	0.000
102	A	154	GLU	-1	-0.884	-0.940	28.841	9.340	9.340	0.000	0.000	0.000	0.000
103	A	155	GLN	0	0.046	0.022	31.045	0.119	0.119	0.000	0.000	0.000	0.000
104	A	156	LEU	0	-0.058	-0.025	25.378	0.026	0.026	0.000	0.000	0.000	0.000
105	A	157	ILE	0	-0.006	-0.019	24.630	0.190	0.190	0.000	0.000	0.000	0.000
106	A	158	ASP	-1	-0.837	-0.905	28.497	9.299	9.299	0.000	0.000	0.000	0.000
107	A	159	HIS	0	-0.050	-0.034	31.634	-0.125	-0.125	0.000	0.000	0.000	0.000
108	A	160	MET	0	-0.132	-0.068	23.535	0.068	0.068	0.000	0.000	0.000	0.000
109	A	161	ALA	0	-0.012	-0.007	28.717	0.041	0.041	0.000	0.000	0.000	0.000
110	A	162	ASN	0	-0.122	-0.056	30.299	-0.360	-0.360	0.000	0.000	0.000	0.000
111	A	163	THR	0	-0.011	-0.004	33.359	-0.286	-0.286	0.000	0.000	0.000	0.000
112	A	164	VAL	0	-0.001	-0.001	35.237	0.056	0.056	0.000	0.000	0.000	0.000
113	A	165	GLU	-1	-0.988	-0.982	37.777	7.064	7.064	0.000	0.000	0.000	0.000
114	A	192	ALA	0	0.064	0.034	35.094	-0.115	-0.115	0.000	0.000	0.000	0.000
115	A	193	ILE	0	-0.056	-0.034	28.658	0.171	0.171	0.000	0.000	0.000	0.000
116	A	194	ARG	1	0.847	0.891	31.017	-9.575	-9.575	0.000	0.000	0.000	0.000
117	A	195	SER	0	-0.030	-0.026	27.889	0.045	0.045	0.000	0.000	0.000	0.000
118	A	196	TYR	0	0.086	0.021	22.408	0.007	0.007	0.000	0.000	0.000	0.000
119	A	197	ARG	1	0.844	0.910	24.270	-10.216	-10.216	0.000	0.000	0.000	0.000
120	A	198	ASP	-1	-0.742	-0.828	25.878	10.288	10.288	0.000	0.000	0.000	0.000
121	A	199	VAL	0	0.096	0.050	23.798	-0.155	-0.155	0.000	0.000	0.000	0.000
122	A	200	MET	0	0.029	0.071	19.665	-0.073	-0.073	0.000	0.000	0.000	0.000
123	A	201	LYS	1	0.916	0.969	23.907	-10.013	-10.013	0.000	0.000	0.000	0.000
124	A	202	LEU	0	0.051	0.025	27.250	-0.147	-0.147	0.000	0.000	0.000	0.000
125	A	203	CYS	0	-0.013	0.005	23.013	0.063	0.063	0.000	0.000	0.000	0.000
126	A	204	ALA	0	-0.035	-0.007	24.841	0.157	0.157	0.000	0.000	0.000	0.000
127	A	205	ALA	0	0.002	-0.006	25.695	-0.077	-0.077	0.000	0.000	0.000	0.000
128	A	206	HIS	1	0.814	0.906	24.854	-12.256	-12.256	0.000	0.000	0.000	0.000
129	A	207	LEU	0	-0.024	-0.002	23.367	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	208	PRO	0	-0.013	-0.011	27.956	-0.282	-0.282	0.000	0.000	0.000	0.000
131	A	209	THR	0	0.000	-0.025	27.973	-0.498	-0.498	0.000	0.000	0.000	0.000
132	A	210	GLU	-1	-0.934	-0.963	27.202	10.957	10.957	0.000	0.000	0.000	0.000
133	A	211	SER	0	-0.044	-0.054	26.041	0.260	0.260	0.000	0.000	0.000	0.000
134	A	212	ASP	-1	-0.815	-0.871	23.708	12.698	12.698	0.000	0.000	0.000	0.000
135	A	213	ALA	0	0.002	0.010	21.695	0.798	0.798	0.000	0.000	0.000	0.000
136	A	214	PRO	0	-0.054	-0.029	18.468	0.735	0.735	0.000	0.000	0.000	0.000
137	A	215	ASN	0	-0.004	-0.003	17.020	1.689	1.689	0.000	0.000	0.000	0.000
138	A	216	HIS	0	-0.027	-0.024	17.330	1.368	1.368	0.000	0.000	0.000	0.000
139	A	217	TYR	0	0.021	-0.019	17.631	0.698	0.698	0.000	0.000	0.000	0.000
140	A	218	GLN	0	0.004	0.019	10.753	-0.507	-0.507	0.000	0.000	0.000	0.000
141	A	219	ALA	0	-0.014	-0.009	13.163	1.767	1.767	0.000	0.000	0.000	0.000
142	A	220	VAL	0	0.012	0.008	14.376	0.765	0.765	0.000	0.000	0.000	0.000
143	A	221	CYS	0	-0.058	-0.015	11.795	-0.053	-0.053	0.000	0.000	0.000	0.000
144	A	222	ARG	1	0.868	0.909	9.594	-24.818	-24.818	0.000	0.000	0.000	0.000
145	A	223	ALA	0	-0.026	0.000	10.148	1.523	1.523	0.000	0.000	0.000	0.000
146	A	224	LEU	0	0.068	0.041	11.874	0.491	0.491	0.000	0.000	0.000	0.000
147	A	225	PHE	0	-0.020	0.006	2.749	1.374	2.038	0.254	-0.289	-0.628	-0.001
148	A	226	ALA	0	-0.004	-0.007	8.259	0.970	0.970	0.000	0.000	0.000	0.000
149	A	227	GLU	-1	-0.874	-0.947	9.468	18.367	18.367	0.000	0.000	0.000	0.000
150	A	228	THR	0	0.000	-0.021	8.888	-1.383	-1.383	0.000	0.000	0.000	0.000
151	A	229	MET	0	-0.047	-0.024	4.819	2.130	2.229	0.000	-0.035	-0.064	0.000
152	A	230	GLU	-1	-0.993	-0.984	8.400	19.784	19.784	0.000	0.000	0.000	0.000
153	A	231	LEU	0	-0.009	0.011	12.115	-1.255	-1.255	0.000	0.000	0.000	0.000
154	A	232	HIS	1	0.772	0.889	9.447	-21.508	-21.508	0.000	0.000	0.000	0.000

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