FMO DATABASE

FMODB ID: YY6N2

Calculation Name: 3RBW-C-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RBW

Chain ID: C

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	157
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1513498.430498
FMO2-HF: Nuclear repulsion	1450870.662601
FMO2-HF: Total energy	-62627.767897
FMO2-MP2: Total energy	-62805.349445

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(C:36:ACE )

Summations of interaction energy for fragment #1(C:36: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.
0.288	1.124	-0.004	-0.317	-0.514	0

Interaction energy analysis for fragmet #1(C:36:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.001

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].
3	C	38	ASP	-1	-0.850	-0.931	3.852	0.422	1.258	-0.004	-0.317	-0.514
4	C	39	ALA	0	-0.055	-0.024	6.642	0.365	0.365	0.000	0.000	0.000
5	C	40	LEU	0	0.061	0.033	9.481	-0.190	-0.190	0.000	0.000	0.000
6	C	41	SER	0	-0.097	-0.007	12.275	0.101	0.101	0.000	0.000	0.000
7	C	42	LEU	0	0.060	0.016	15.764	-0.004	-0.004	0.000	0.000	0.000
8	C	43	GLU	-1	-0.954	-0.985	18.266	-0.207	-0.207	0.000	0.000	0.000
9	C	44	GLU	-1	-0.873	-0.957	12.352	-0.668	-0.668	0.000	0.000	0.000
10	C	45	ILE	0	0.007	0.011	15.686	0.012	0.012	0.000	0.000	0.000
11	C	46	LEU	0	0.001	0.016	17.471	0.023	0.023	0.000	0.000	0.000
12	C	47	ARG	1	0.910	0.958	18.544	0.232	0.232	0.000	0.000	0.000
13	C	48	LEU	0	-0.029	-0.002	13.839	0.020	0.020	0.000	0.000	0.000
14	C	49	TYR	0	0.035	0.014	17.736	0.017	0.017	0.000	0.000	0.000
15	C	50	ASN	0	-0.036	-0.009	20.869	0.010	0.010	0.000	0.000	0.000
16	C	51	GLN	0	-0.060	-0.034	23.520	0.017	0.017	0.000	0.000	0.000
17	C	52	PRO	0	-0.021	0.003	23.918	-0.014	-0.014	0.000	0.000	0.000
18	C	53	ILE	0	0.006	0.022	22.035	0.001	0.001	0.000	0.000	0.000
19	C	54	ASN	0	0.077	0.021	24.607	0.007	0.007	0.000	0.000	0.000
20	C	55	GLU	-1	-0.776	-0.895	26.733	-0.064	-0.064	0.000	0.000	0.000
21	C	56	GLU	-1	-0.863	-0.939	26.484	-0.061	-0.061	0.000	0.000	0.000
22	C	57	GLN	0	0.048	0.006	21.459	-0.004	-0.004	0.000	0.000	0.000
23	C	58	ALA	0	-0.010	0.003	24.125	-0.011	-0.011	0.000	0.000	0.000
24	C	59	TRP	0	0.008	0.005	26.584	-0.002	-0.002	0.000	0.000	0.000
25	C	60	ALA	0	-0.005	-0.007	22.877	-0.003	-0.003	0.000	0.000	0.000
26	C	61	VAL	0	0.037	0.008	20.446	-0.005	-0.005	0.000	0.000	0.000
27	C	62	CYS	0	0.025	0.010	22.713	-0.005	-0.005	0.000	0.000	0.000
28	C	63	TYR	0	0.017	0.002	24.331	0.007	0.007	0.000	0.000	0.000
29	C	64	GLN	0	-0.024	-0.030	19.344	0.012	0.012	0.000	0.000	0.000
30	C	65	CYS	0	0.002	0.020	21.942	-0.007	-0.007	0.000	0.000	0.000
31	C	66	CYS	0	-0.054	-0.027	22.880	0.002	0.002	0.000	0.000	0.000
32	C	67	GLY	0	0.012	0.002	24.224	0.008	0.008	0.000	0.000	0.000
33	C	68	SER	0	-0.042	-0.047	20.264	0.007	0.007	0.000	0.000	0.000
34	C	69	LEU	0	-0.015	0.006	22.268	0.004	0.004	0.000	0.000	0.000
35	C	70	ARG	1	0.914	0.903	25.291	0.057	0.057	0.000	0.000	0.000
36	C	71	ALA	0	-0.061	-0.026	23.572	0.006	0.006	0.000	0.000	0.000
37	C	72	ALA	0	-0.007	-0.005	23.364	0.003	0.003	0.000	0.000	0.000
38	C	73	ALA	0	0.013	0.009	25.350	0.004	0.004	0.000	0.000	0.000
39	C	74	ARG	0	0.031	0.040	28.687	0.006	0.006	0.000	0.000	0.000
40	C	75	ARG	1	0.930	0.976	22.579	0.077	0.077	0.000	0.000	0.000
41	C	76	ARG	1	0.900	0.960	27.726	0.047	0.047	0.000	0.000	0.000
42	C	77	GLN	0	0.017	0.017	23.279	0.009	0.009	0.000	0.000	0.000
43	C	78	PRO	0	-0.012	-0.011	26.262	0.001	0.001	0.000	0.000	0.000
44	C	79	ARG	1	0.901	0.962	26.898	0.060	0.060	0.000	0.000	0.000
45	C	80	HIS	0	0.033	0.017	23.753	0.003	0.003	0.000	0.000	0.000
46	C	81	ARG	1	0.938	0.971	27.151	0.086	0.086	0.000	0.000	0.000
47	C	82	VAL	0	0.003	-0.003	24.199	-0.010	-0.010	0.000	0.000	0.000
48	C	83	ARG	1	0.913	0.967	25.759	0.118	0.118	0.000	0.000	0.000
49	C	84	SER	0	0.091	0.031	23.530	0.006	0.006	0.000	0.000	0.000
50	C	85	ALA	0	0.063	0.030	21.700	-0.009	-0.009	0.000	0.000	0.000
51	C	86	ALA	0	0.066	0.039	19.006	-0.025	-0.025	0.000	0.000	0.000
52	C	87	GLN	0	-0.061	-0.055	18.011	-0.035	-0.035	0.000	0.000	0.000
53	C	88	ILE	0	0.022	0.026	19.100	-0.006	-0.006	0.000	0.000	0.000
54	C	89	ARG	1	0.837	0.913	13.969	0.363	0.363	0.000	0.000	0.000
55	C	90	VAL	0	0.049	0.012	14.771	0.041	0.041	0.000	0.000	0.000
56	C	91	TRP	0	-0.009	-0.047	9.512	-0.101	-0.101	0.000	0.000	0.000
57	C	92	ARG	1	0.952	0.986	5.687	0.469	0.469	0.000	0.000	0.000
58	C	93	ASP	-1	-0.921	-0.969	10.421	-0.074	-0.074	0.000	0.000	0.000
59	C	94	GLY	0	0.041	0.019	13.428	0.031	0.031	0.000	0.000	0.000
60	C	95	ALA	0	-0.044	0.003	14.875	0.016	0.016	0.000	0.000	0.000
61	C	96	VAL	0	0.052	0.029	15.776	-0.039	-0.039	0.000	0.000	0.000
62	C	97	THR	0	-0.004	0.041	15.947	0.013	0.013	0.000	0.000	0.000
63	C	98	LEU	0	0.006	-0.005	18.313	-0.015	-0.015	0.000	0.000	0.000
64	C	99	ALA	0	-0.035	-0.003	17.488	0.013	0.013	0.000	0.000	0.000
65	C	100	PRO	0	0.036	0.024	19.133	0.020	0.020	0.000	0.000	0.000
66	C	101	ALA	0	-0.011	-0.020	21.153	-0.018	-0.018	0.000	0.000	0.000
67	C	102	ALA	0	0.014	0.010	22.562	-0.003	-0.003	0.000	0.000	0.000
68	C	103	NME	0	-0.011	0.007	23.647	0.008	0.008	0.000	0.000	0.000
69	C	118	ACE	0	-0.009	-0.019	32.982	-0.001	-0.001	0.000	0.000	0.000
70	C	119	GLN	0	0.013	-0.001	33.802	0.004	0.004	0.000	0.000	0.000
71	C	120	CYS	0	0.039	0.016	32.853	-0.003	-0.003	0.000	0.000	0.000
72	C	121	MET	0	-0.037	0.007	34.525	0.001	0.001	0.000	0.000	0.000
73	C	122	GLU	-1	-0.895	-0.969	32.362	-0.065	-0.065	0.000	0.000	0.000
74	C	123	THR	0	0.057	0.008	33.226	-0.004	-0.004	0.000	0.000	0.000
75	C	124	GLU	-1	-0.867	-0.944	34.654	-0.069	-0.069	0.000	0.000	0.000
76	C	125	VAL	0	-0.079	-0.017	28.305	-0.005	-0.005	0.000	0.000	0.000
77	C	126	ILE	0	0.019	0.012	30.378	-0.006	-0.006	0.000	0.000	0.000
78	C	127	GLU	-1	-0.907	-0.937	31.505	-0.082	-0.082	0.000	0.000	0.000
79	C	128	SER	0	-0.022	-0.021	29.653	-0.006	-0.006	0.000	0.000	0.000
80	C	129	LEU	0	-0.019	-0.033	24.949	-0.007	-0.007	0.000	0.000	0.000
81	C	130	GLY	0	0.074	0.054	28.559	-0.004	-0.004	0.000	0.000	0.000
82	C	131	ILE	0	0.052	0.031	30.867	-0.004	-0.004	0.000	0.000	0.000
83	C	132	ILE	0	-0.096	-0.052	24.791	-0.004	-0.004	0.000	0.000	0.000
84	C	133	ILE	0	0.010	-0.008	25.105	-0.009	-0.009	0.000	0.000	0.000
85	C	134	TYR	0	0.065	0.044	27.835	0.000	0.000	0.000	0.000	0.000
86	C	135	LYS	1	0.943	0.965	28.245	0.111	0.111	0.000	0.000	0.000
87	C	136	ALA	0	-0.054	-0.020	24.627	-0.004	-0.004	0.000	0.000	0.000
88	C	137	LEU	0	-0.038	-0.030	26.328	-0.002	-0.002	0.000	0.000	0.000
89	C	138	ASP	-1	-0.908	-0.960	28.829	-0.079	-0.079	0.000	0.000	0.000
90	C	139	TYR	0	-0.033	0.008	24.124	-0.006	-0.006	0.000	0.000	0.000
91	C	140	GLY	0	-0.020	-0.029	28.436	0.004	0.004	0.000	0.000	0.000
92	C	141	LEU	0	-0.003	0.021	29.953	0.005	0.005	0.000	0.000	0.000
93	C	142	LYS	1	0.823	0.901	33.452	0.067	0.067	0.000	0.000	0.000
94	C	143	GLU	-1	-0.923	-0.958	36.267	-0.062	-0.062	0.000	0.000	0.000
95	C	144	ASN	0	-0.056	-0.042	38.809	-0.001	-0.001	0.000	0.000	0.000
96	C	145	GLU	-1	-0.918	-0.940	36.137	-0.059	-0.059	0.000	0.000	0.000
97	C	146	GLU	-1	-0.882	-0.932	37.141	-0.055	-0.055	0.000	0.000	0.000
98	C	147	ARG	1	0.798	0.884	28.604	0.084	0.084	0.000	0.000	0.000
99	C	148	GLU	-1	-0.930	-0.955	36.066	-0.043	-0.043	0.000	0.000	0.000
100	C	149	LEU	0	-0.034	-0.024	32.829	-0.003	-0.003	0.000	0.000	0.000
101	C	150	SER	0	0.013	-0.002	35.119	0.004	0.004	0.000	0.000	0.000
102	C	151	PRO	0	0.066	0.013	37.898	-0.001	-0.001	0.000	0.000	0.000
103	C	152	PRO	0	-0.058	-0.033	36.437	-0.001	-0.001	0.000	0.000	0.000
104	C	153	LEU	0	-0.015	-0.020	31.265	-0.002	-0.002	0.000	0.000	0.000
105	C	154	GLU	-1	-0.899	-0.943	35.148	-0.051	-0.051	0.000	0.000	0.000
106	C	155	GLN	0	0.011	0.003	37.585	-0.001	-0.001	0.000	0.000	0.000
107	C	156	LEU	0	-0.046	-0.015	31.195	-0.001	-0.001	0.000	0.000	0.000
108	C	157	ILE	0	0.035	0.009	31.569	-0.004	-0.004	0.000	0.000	0.000
109	C	158	ASP	-1	-0.877	-0.928	35.044	-0.056	-0.056	0.000	0.000	0.000
110	C	159	HIS	0	-0.068	-0.048	37.311	0.003	0.003	0.000	0.000	0.000
111	C	160	MET	0	-0.134	-0.055	29.889	0.000	0.000	0.000	0.000	0.000
112	C	161	ALA	0	0.090	0.039	34.796	-0.005	-0.005	0.000	0.000	0.000
113	C	162	ASN	0	-0.093	-0.027	37.373	0.000	0.000	0.000	0.000	0.000
114	C	163	NME	0	-0.012	-0.006	40.509	0.003	0.003	0.000	0.000	0.000
115	C	191	ACE	0	0.060	0.012	42.700	0.000	0.000	0.000	0.000	0.000
116	C	192	ALA	0	-0.057	-0.037	41.422	0.000	0.000	0.000	0.000	0.000
117	C	193	ILE	0	-0.009	0.015	34.988	0.001	0.001	0.000	0.000	0.000
118	C	194	ARG	1	0.902	0.938	37.199	0.038	0.038	0.000	0.000	0.000
119	C	195	SER	0	0.003	0.009	34.448	0.000	0.000	0.000	0.000	0.000
120	C	196	TYR	0	0.076	0.019	28.990	0.001	0.001	0.000	0.000	0.000
121	C	197	ARG	1	0.903	0.945	30.778	0.043	0.043	0.000	0.000	0.000
122	C	198	ASP	-1	-0.856	-0.914	32.561	-0.044	-0.044	0.000	0.000	0.000
123	C	199	VAL	0	0.101	0.045	30.165	0.002	0.002	0.000	0.000	0.000
124	C	200	MET	0	-0.050	-0.030	27.690	0.000	0.000	0.000	0.000	0.000
125	C	201	LYS	1	0.917	0.956	30.584	0.039	0.039	0.000	0.000	0.000
126	C	202	LEU	0	0.063	0.043	33.561	0.003	0.003	0.000	0.000	0.000
127	C	203	CYS	0	-0.039	-0.001	29.155	-0.001	-0.001	0.000	0.000	0.000
128	C	204	ALA	0	-0.027	-0.011	31.139	0.000	0.000	0.000	0.000	0.000
129	C	205	ALA	0	0.058	0.037	31.971	0.003	0.003	0.000	0.000	0.000
130	C	206	HIS	1	0.805	0.924	30.784	0.055	0.055	0.000	0.000	0.000
131	C	207	LEU	0	-0.014	0.001	29.432	-0.001	-0.001	0.000	0.000	0.000
132	C	208	PRO	0	-0.001	-0.004	33.588	0.002	0.002	0.000	0.000	0.000
133	C	209	THR	0	-0.010	0.002	34.112	0.003	0.003	0.000	0.000	0.000
134	C	210	GLU	-1	-0.911	-0.951	33.548	-0.034	-0.034	0.000	0.000	0.000
135	C	211	SER	0	-0.036	-0.037	32.761	-0.002	-0.002	0.000	0.000	0.000
136	C	212	ASP	-1	-0.927	-0.962	28.916	-0.025	-0.025	0.000	0.000	0.000
137	C	213	ALA	0	0.077	0.037	27.892	-0.003	-0.003	0.000	0.000	0.000
138	C	214	PRO	0	-0.080	-0.034	24.997	-0.006	-0.006	0.000	0.000	0.000
139	C	215	ASN	0	0.003	-0.018	23.348	-0.003	-0.003	0.000	0.000	0.000
140	C	216	HIS	0	0.004	0.018	23.314	0.001	0.001	0.000	0.000	0.000
141	C	217	TYR	0	0.031	-0.018	23.574	-0.007	-0.007	0.000	0.000	0.000
142	C	218	GLN	0	-0.019	-0.003	17.165	-0.002	-0.002	0.000	0.000	0.000
143	C	219	ALA	0	0.003	-0.008	18.860	-0.015	-0.015	0.000	0.000	0.000
144	C	220	VAL	0	-0.002	0.022	19.684	-0.006	-0.006	0.000	0.000	0.000
145	C	221	CYS	0	-0.044	-0.013	17.804	-0.013	-0.013	0.000	0.000	0.000
146	C	222	ARG	1	0.922	0.960	14.360	0.025	0.025	0.000	0.000	0.000
147	C	223	ALA	0	-0.028	0.008	14.952	-0.009	-0.009	0.000	0.000	0.000
148	C	224	LEU	0	0.052	0.026	16.138	-0.014	-0.014	0.000	0.000	0.000
149	C	225	PHE	0	-0.055	-0.012	7.867	-0.061	-0.061	0.000	0.000	0.000
150	C	226	ALA	0	0.020	-0.006	12.168	-0.040	-0.040	0.000	0.000	0.000
151	C	227	GLU	-1	-0.909	-0.961	13.235	-0.106	-0.106	0.000	0.000	0.000
152	C	228	THR	0	-0.005	-0.022	13.360	0.008	0.008	0.000	0.000	0.000
153	C	229	MET	0	-0.105	-0.055	8.231	-0.184	-0.184	0.000	0.000	0.000
154	C	230	GLU	-1	-0.977	-0.959	10.945	-0.040	-0.040	0.000	0.000	0.000
155	C	231	LEU	0	-0.051	-0.018	13.261	0.020	0.020	0.000	0.000	0.000
156	C	232	HIS	0	-0.046	-0.027	9.599	-0.132	-0.132	0.000	0.000	0.000
157	C	233	NME	0	0.004	0.013	8.825	0.067	0.067	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:36:ACE )