FMO DATABASE

FMODB ID: VR8K1

Calculation Name: 3RBW-B-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	160
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1557969.076094
FMO2-HF: Nuclear repulsion	1494280.175264
FMO2-HF: Total energy	-63688.90083
FMO2-MP2: Total energy	-63869.617836

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:37:ACE )

Summations of interaction energy for fragment #1(B:37:ACE )

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.
3.598	6.024	0.008	-1.209	-1.225	-0.004

Interaction energy analysis for fragmet #1(B:37:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.008

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	39	ALA	0	0.017	0.004	3.880	-0.640	1.239	-0.003	-1.004	-0.871	-0.003
4	B	40	LEU	0	0.004	0.025	4.373	0.372	0.508	0.000	-0.014	-0.122	0.000
5	B	41	SER	0	-0.057	-0.038	6.750	-0.174	-0.174	0.000	0.000	0.000	0.000
6	B	42	LEU	0	0.043	0.005	10.117	0.023	0.023	0.000	0.000	0.000	0.000
7	B	43	GLU	-1	-0.976	-0.994	12.887	0.242	0.242	0.000	0.000	0.000	0.000
8	B	44	GLU	-1	-0.859	-0.918	7.188	0.921	0.921	0.000	0.000	0.000	0.000
9	B	45	ILE	0	0.005	0.001	9.766	-0.001	-0.001	0.000	0.000	0.000	0.000
10	B	46	LEU	0	-0.032	-0.011	11.631	-0.013	-0.013	0.000	0.000	0.000	0.000
11	B	47	ARG	1	0.923	0.967	13.267	-0.237	-0.237	0.000	0.000	0.000	0.000
12	B	48	LEU	0	-0.040	-0.017	9.318	-0.009	-0.009	0.000	0.000	0.000	0.000
13	B	49	TYR	0	0.004	-0.003	12.488	-0.019	-0.019	0.000	0.000	0.000	0.000
14	B	50	ASN	0	-0.031	-0.002	15.889	-0.012	-0.012	0.000	0.000	0.000	0.000
15	B	51	GLN	0	-0.058	-0.033	18.190	-0.022	-0.022	0.000	0.000	0.000	0.000
16	B	52	PRO	0	-0.003	0.005	18.776	0.005	0.005	0.000	0.000	0.000	0.000
17	B	53	ILE	0	-0.015	0.014	16.941	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	54	ASN	0	0.022	0.002	19.489	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	55	GLU	-1	-0.738	-0.870	21.942	-0.016	-0.016	0.000	0.000	0.000	0.000
20	B	56	GLU	-1	-0.810	-0.881	22.179	-0.055	-0.055	0.000	0.000	0.000	0.000
21	B	57	GLN	0	0.055	0.009	17.005	0.005	0.005	0.000	0.000	0.000	0.000
22	B	58	ALA	0	0.053	0.039	19.488	-0.008	-0.008	0.000	0.000	0.000	0.000
23	B	59	TRP	0	0.025	0.016	21.656	-0.009	-0.009	0.000	0.000	0.000	0.000
24	B	60	ALA	0	-0.001	-0.024	18.959	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	61	VAL	0	0.013	-0.005	16.172	-0.011	-0.011	0.000	0.000	0.000	0.000
26	B	62	CYS	0	-0.019	-0.006	18.699	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	63	TYR	0	0.012	0.000	21.830	0.002	0.002	0.000	0.000	0.000	0.000
28	B	64	GLN	0	-0.018	-0.022	16.942	0.019	0.019	0.000	0.000	0.000	0.000
29	B	65	CYS	0	-0.032	0.012	18.484	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	66	CYS	0	0.005	0.004	19.508	0.005	0.005	0.000	0.000	0.000	0.000
31	B	67	GLY	0	-0.006	-0.015	22.390	0.001	0.001	0.000	0.000	0.000	0.000
32	B	68	SER	0	-0.018	-0.016	17.632	-0.010	-0.010	0.000	0.000	0.000	0.000
33	B	69	LEU	0	-0.003	0.002	20.408	0.004	0.004	0.000	0.000	0.000	0.000
34	B	70	ARG	1	0.869	0.925	22.725	0.075	0.075	0.000	0.000	0.000	0.000
35	B	71	ALA	0	-0.091	-0.060	22.337	0.006	0.006	0.000	0.000	0.000	0.000
36	B	72	ALA	0	0.047	0.039	21.415	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	73	ALA	0	0.042	0.020	23.443	0.007	0.007	0.000	0.000	0.000	0.000
38	B	74	ARG	1	0.897	0.945	25.777	0.093	0.093	0.000	0.000	0.000	0.000
39	B	75	ARG	1	0.913	0.958	24.155	0.090	0.090	0.000	0.000	0.000	0.000
40	B	76	ARG	1	0.889	0.950	26.936	0.043	0.043	0.000	0.000	0.000	0.000
41	B	77	GLN	0	0.043	0.030	21.581	0.006	0.006	0.000	0.000	0.000	0.000
42	B	78	PRO	0	-0.004	-0.007	23.794	0.003	0.003	0.000	0.000	0.000	0.000
43	B	79	ARG	1	0.921	0.975	24.035	0.023	0.023	0.000	0.000	0.000	0.000
44	B	80	HIS	0	0.049	0.024	20.626	0.013	0.013	0.000	0.000	0.000	0.000
45	B	81	ARG	1	0.888	0.916	23.480	-0.013	-0.013	0.000	0.000	0.000	0.000
46	B	82	VAL	0	-0.003	-0.011	19.824	0.005	0.005	0.000	0.000	0.000	0.000
47	B	83	ARG	1	0.930	0.974	21.083	-0.032	-0.032	0.000	0.000	0.000	0.000
48	B	84	SER	0	0.079	0.029	18.788	0.001	0.001	0.000	0.000	0.000	0.000
49	B	85	ALA	0	0.052	0.015	16.447	-0.005	-0.005	0.000	0.000	0.000	0.000
50	B	86	ALA	0	0.062	0.036	13.943	0.004	0.004	0.000	0.000	0.000	0.000
51	B	87	GLN	0	-0.087	-0.061	13.193	0.013	0.013	0.000	0.000	0.000	0.000
52	B	88	ILE	0	0.043	0.036	14.213	-0.032	-0.032	0.000	0.000	0.000	0.000
53	B	89	ARG	1	0.946	0.978	9.409	-0.105	-0.105	0.000	0.000	0.000	0.000
54	B	90	VAL	0	0.031	0.013	9.900	-0.035	-0.035	0.000	0.000	0.000	0.000
55	B	91	TRP	0	-0.028	-0.031	8.351	-0.083	-0.083	0.000	0.000	0.000	0.000
56	B	92	ARG	1	0.901	0.960	3.919	3.079	3.216	0.002	-0.086	-0.053	0.000
57	B	93	ASP	-1	-0.958	-0.990	8.763	-0.300	-0.300	0.000	0.000	0.000	0.000
58	B	94	GLY	0	0.066	0.029	11.743	0.085	0.085	0.000	0.000	0.000	0.000
59	B	95	ALA	0	0.007	0.021	13.034	0.074	0.074	0.000	0.000	0.000	0.000
60	B	96	VAL	0	0.035	0.009	13.019	-0.017	-0.017	0.000	0.000	0.000	0.000
61	B	97	THR	0	-0.021	0.012	13.308	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	98	LEU	0	-0.001	0.003	14.467	0.011	0.011	0.000	0.000	0.000	0.000
63	B	99	ALA	0	-0.051	-0.022	13.573	-0.009	-0.009	0.000	0.000	0.000	0.000
64	B	100	PRO	0	0.011	0.003	15.652	0.005	0.005	0.000	0.000	0.000	0.000
65	B	101	ALA	0	-0.009	-0.017	17.071	0.015	0.015	0.000	0.000	0.000	0.000
66	B	102	ALA	0	-0.014	-0.014	18.827	0.002	0.002	0.000	0.000	0.000	0.000
67	B	103	ASP	-1	-0.928	-0.944	19.714	0.058	0.058	0.000	0.000	0.000	0.000
68	B	104	NME	0	-0.035	-0.017	20.230	-0.011	-0.011	0.000	0.000	0.000	0.000
69	B	118	ACE	0	0.030	0.006	35.621	0.000	0.000	0.000	0.000	0.000	0.000
70	B	119	GLN	0	-0.023	-0.015	32.483	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	120	CYS	0	-0.038	-0.015	27.646	0.003	0.003	0.000	0.000	0.000	0.000
72	B	121	MET	0	-0.002	0.002	30.749	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	122	GLU	-1	-0.866	-0.950	28.980	-0.037	-0.037	0.000	0.000	0.000	0.000
74	B	123	THR	0	0.055	0.006	29.287	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	124	GLU	-1	-0.741	-0.844	29.524	0.001	0.001	0.000	0.000	0.000	0.000
76	B	125	VAL	0	-0.079	-0.023	23.996	0.002	0.002	0.000	0.000	0.000	0.000
77	B	126	ILE	0	-0.002	-0.005	25.746	0.000	0.000	0.000	0.000	0.000	0.000
78	B	127	GLU	-1	-0.837	-0.897	26.716	0.005	0.005	0.000	0.000	0.000	0.000
79	B	128	SER	0	-0.084	-0.024	25.032	0.003	0.003	0.000	0.000	0.000	0.000
80	B	129	LEU	0	-0.008	-0.030	20.566	0.005	0.005	0.000	0.000	0.000	0.000
81	B	130	GLY	0	0.049	0.018	23.216	0.003	0.003	0.000	0.000	0.000	0.000
82	B	131	ILE	0	0.051	0.035	25.501	0.004	0.004	0.000	0.000	0.000	0.000
83	B	132	ILE	0	-0.094	-0.026	18.980	0.008	0.008	0.000	0.000	0.000	0.000
84	B	133	ILE	0	0.001	-0.005	20.334	0.005	0.005	0.000	0.000	0.000	0.000
85	B	134	TYR	0	0.034	0.020	22.314	0.004	0.004	0.000	0.000	0.000	0.000
86	B	135	LYS	1	0.983	0.963	22.777	-0.042	-0.042	0.000	0.000	0.000	0.000
87	B	136	ALA	0	-0.016	-0.009	18.872	0.008	0.008	0.000	0.000	0.000	0.000
88	B	137	LEU	0	-0.056	-0.036	20.639	0.003	0.003	0.000	0.000	0.000	0.000
89	B	138	ASP	-1	-0.948	-0.963	23.156	0.042	0.042	0.000	0.000	0.000	0.000
90	B	139	TYR	0	-0.035	-0.013	18.488	0.010	0.010	0.000	0.000	0.000	0.000
91	B	140	GLY	0	-0.016	-0.017	22.526	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	141	LEU	0	0.017	0.041	24.534	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	142	LYS	1	0.816	0.896	27.995	-0.055	-0.055	0.000	0.000	0.000	0.000
94	B	143	GLU	-1	-0.931	-0.964	30.762	0.041	0.041	0.000	0.000	0.000	0.000
95	B	144	ASN	0	-0.054	-0.040	33.228	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	145	GLU	-1	-0.918	-0.938	30.767	0.038	0.038	0.000	0.000	0.000	0.000
97	B	146	GLU	-1	-0.868	-0.939	31.227	0.019	0.019	0.000	0.000	0.000	0.000
98	B	147	ARG	1	0.849	0.915	24.168	-0.018	-0.018	0.000	0.000	0.000	0.000
99	B	148	GLU	-1	-0.917	-0.955	30.580	0.004	0.004	0.000	0.000	0.000	0.000
100	B	149	LEU	0	-0.042	-0.016	27.431	-0.002	-0.002	0.000	0.000	0.000	0.000
101	B	150	SER	0	-0.046	-0.042	30.267	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	151	PRO	0	0.077	0.026	32.137	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	152	PRO	0	-0.052	-0.026	32.089	0.000	0.000	0.000	0.000	0.000	0.000
104	B	153	LEU	0	-0.027	-0.024	26.172	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	154	GLU	-1	-0.856	-0.918	30.302	0.003	0.003	0.000	0.000	0.000	0.000
106	B	155	GLN	0	0.011	0.001	32.132	-0.002	-0.002	0.000	0.000	0.000	0.000
107	B	156	LEU	0	-0.021	-0.013	26.814	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	157	ILE	0	-0.017	-0.029	26.082	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	158	ASP	-1	-0.808	-0.907	29.646	0.002	0.002	0.000	0.000	0.000	0.000
110	B	159	HIS	0	-0.101	-0.051	32.947	0.001	0.001	0.000	0.000	0.000	0.000
111	B	160	MET	0	-0.159	-0.088	25.043	-0.002	-0.002	0.000	0.000	0.000	0.000
112	B	161	ALA	0	-0.004	-0.015	29.582	0.001	0.001	0.000	0.000	0.000	0.000
113	B	162	ASN	0	-0.079	-0.010	31.383	0.003	0.003	0.000	0.000	0.000	0.000
114	B	163	THR	0	-0.024	-0.015	34.208	0.003	0.003	0.000	0.000	0.000	0.000
115	B	164	VAL	0	0.005	0.001	36.217	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	165	GLU	-1	-0.899	-0.959	38.995	0.004	0.004	0.000	0.000	0.000	0.000
117	B	166	NME	0	-0.082	-0.014	41.504	0.000	0.000	0.000	0.000	0.000	0.000
118	B	191	ACE	0	0.007	-0.005	39.791	0.000	0.000	0.000	0.000	0.000	0.000
119	B	192	ALA	0	0.005	-0.001	37.912	0.002	0.002	0.000	0.000	0.000	0.000
120	B	193	ILE	0	0.001	-0.001	31.361	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	194	ARG	1	0.915	0.959	33.765	0.027	0.027	0.000	0.000	0.000	0.000
122	B	195	SER	0	-0.025	-0.024	31.566	-0.002	-0.002	0.000	0.000	0.000	0.000
123	B	196	TYR	0	0.075	0.026	26.140	-0.004	-0.004	0.000	0.000	0.000	0.000
124	B	197	ARG	1	0.893	0.941	28.468	0.040	0.040	0.000	0.000	0.000	0.000
125	B	198	ASP	-1	-0.868	-0.932	30.223	-0.034	-0.034	0.000	0.000	0.000	0.000
126	B	199	VAL	0	0.100	0.046	26.253	0.000	0.000	0.000	0.000	0.000	0.000
127	B	200	MET	0	-0.020	0.018	24.131	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	201	LYS	1	0.946	0.963	27.887	0.039	0.039	0.000	0.000	0.000	0.000
129	B	202	LEU	0	0.074	0.043	30.740	0.001	0.001	0.000	0.000	0.000	0.000
130	B	203	CYS	0	-0.025	0.018	25.712	0.000	0.000	0.000	0.000	0.000	0.000
131	B	204	ALA	0	-0.038	0.002	27.752	-0.002	-0.002	0.000	0.000	0.000	0.000
132	B	205	ALA	0	0.020	0.023	29.074	0.000	0.000	0.000	0.000	0.000	0.000
133	B	206	HIS	1	0.804	0.894	26.889	0.044	0.044	0.000	0.000	0.000	0.000
134	B	207	LEU	0	-0.018	0.002	26.383	0.000	0.000	0.000	0.000	0.000	0.000
135	B	208	PRO	0	-0.006	-0.004	30.552	0.002	0.002	0.000	0.000	0.000	0.000
136	B	209	THR	0	-0.002	0.008	31.893	0.004	0.004	0.000	0.000	0.000	0.000
137	B	210	GLU	-1	-0.902	-0.947	31.077	-0.051	-0.051	0.000	0.000	0.000	0.000
138	B	211	SER	0	-0.054	-0.049	30.415	-0.003	-0.003	0.000	0.000	0.000	0.000
139	B	212	ASP	-1	-0.858	-0.926	27.654	-0.081	-0.081	0.000	0.000	0.000	0.000
140	B	213	ALA	0	-0.002	-0.006	25.891	-0.009	-0.009	0.000	0.000	0.000	0.000
141	B	214	PRO	0	-0.074	-0.041	23.379	-0.009	-0.009	0.000	0.000	0.000	0.000
142	B	215	ASN	0	0.025	0.013	21.882	-0.030	-0.030	0.000	0.000	0.000	0.000
143	B	216	HIS	0	-0.056	-0.009	21.398	-0.020	-0.020	0.000	0.000	0.000	0.000
144	B	217	TYR	0	0.024	-0.055	20.692	-0.006	-0.006	0.000	0.000	0.000	0.000
145	B	218	GLN	0	-0.014	0.021	16.703	-0.017	-0.017	0.000	0.000	0.000	0.000
146	B	219	ALA	0	-0.026	-0.012	16.899	-0.016	-0.016	0.000	0.000	0.000	0.000
147	B	220	VAL	0	0.035	0.018	16.647	-0.014	-0.014	0.000	0.000	0.000	0.000
148	B	221	CYS	0	-0.006	-0.002	14.202	0.014	0.014	0.000	0.000	0.000	0.000
149	B	222	ARG	1	0.949	0.968	12.709	0.236	0.236	0.000	0.000	0.000	0.000
150	B	223	ALA	0	-0.036	-0.008	12.117	-0.047	-0.047	0.000	0.000	0.000	0.000
151	B	224	LEU	0	0.083	0.046	12.423	0.005	0.005	0.000	0.000	0.000	0.000
152	B	225	PHE	0	-0.041	0.031	4.325	-0.065	0.021	0.000	-0.018	-0.068	0.000
153	B	226	ALA	0	-0.023	-0.026	9.073	0.022	0.022	0.000	0.000	0.000	0.000
154	B	227	GLU	-1	-0.883	-0.958	10.407	-0.032	-0.032	0.000	0.000	0.000	0.000
155	B	228	THR	0	-0.081	-0.072	8.800	0.062	0.062	0.000	0.000	0.000	0.000
156	B	229	MET	0	-0.094	-0.050	4.497	-0.172	0.016	0.009	-0.087	-0.111	-0.001
157	B	230	GLU	-1	-0.915	-0.950	7.788	-0.002	-0.002	0.000	0.000	0.000	0.000
158	B	231	LEU	0	-0.081	-0.019	10.943	0.029	0.029	0.000	0.000	0.000	0.000
159	B	232	HIS	0	-0.095	-0.051	7.743	0.300	0.300	0.000	0.000	0.000	0.000
160	B	233	NME	0	0.009	0.015	10.447	-0.054	-0.054	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:37:ACE )