FMO DATABASE

FMODB ID: N1YZQ

Calculation Name: 3RBW-C-Xray372

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: 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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1492042.902765
FMO2-HF: Nuclear repulsion	1429928.02355
FMO2-HF: Total energy	-62114.879216
FMO2-MP2: Total energy	-62290.833255

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:37:ARG)

Summations of interaction energy for fragment #1(C:37:ARG)

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.
-128.379	-132.707	30.054	-13.451	-12.275	-0.091

Interaction energy analysis for fragmet #1(C:37:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.918 / q_NPA : 0.954

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	C	39	ALA	0	-0.061	-0.030	2.471	2.227	7.584	0.176	-2.934	-2.599	0.003
4	C	40	LEU	0	0.062	0.034	2.866	-17.337	-14.703	0.340	-1.150	-1.824	-0.010
5	C	41	SER	0	-0.095	-0.005	5.408	9.639	9.639	0.000	0.000	0.000	0.000
6	C	42	LEU	0	0.057	0.015	7.644	-1.648	-1.648	0.000	0.000	0.000	0.000
7	C	43	GLU	-1	-0.953	-0.986	8.149	-24.701	-24.701	0.000	0.000	0.000	0.000
8	C	44	GLU	-1	-0.876	-0.959	1.635	-102.197	-118.163	29.027	-7.856	-5.205	-0.070
9	C	45	ILE	0	0.013	0.012	6.343	0.325	0.325	0.000	0.000	0.000	0.000
10	C	46	LEU	0	-0.002	0.015	9.039	1.686	1.686	0.000	0.000	0.000	0.000
11	C	47	ARG	1	0.908	0.957	8.028	28.987	28.987	0.000	0.000	0.000	0.000
12	C	48	LEU	0	-0.029	-0.002	4.849	2.025	2.025	0.000	0.000	0.000	0.000
13	C	49	TYR	0	0.038	0.015	9.244	1.643	1.643	0.000	0.000	0.000	0.000
14	C	50	ASN	0	-0.039	-0.011	12.244	1.182	1.182	0.000	0.000	0.000	0.000
15	C	51	GLN	0	-0.059	-0.034	14.204	1.480	1.480	0.000	0.000	0.000	0.000
16	C	52	PRO	0	-0.021	0.005	15.391	-1.401	-1.401	0.000	0.000	0.000	0.000
17	C	53	ILE	0	0.006	0.023	14.961	-0.184	-0.184	0.000	0.000	0.000	0.000
18	C	54	ASN	0	0.077	0.020	17.411	0.895	0.895	0.000	0.000	0.000	0.000
19	C	55	GLU	-1	-0.776	-0.895	20.633	-12.454	-12.454	0.000	0.000	0.000	0.000
20	C	56	GLU	-1	-0.861	-0.939	21.766	-13.342	-13.342	0.000	0.000	0.000	0.000
21	C	57	GLN	0	0.042	0.004	15.901	-0.262	-0.262	0.000	0.000	0.000	0.000
22	C	58	ALA	0	-0.005	0.005	18.401	-0.682	-0.682	0.000	0.000	0.000	0.000
23	C	59	TRP	0	0.003	0.003	20.560	-0.011	-0.011	0.000	0.000	0.000	0.000
24	C	60	ALA	0	-0.004	-0.006	18.202	-0.111	-0.111	0.000	0.000	0.000	0.000
25	C	61	VAL	0	0.039	0.007	14.762	-0.235	-0.235	0.000	0.000	0.000	0.000
26	C	62	CYS	0	0.025	0.011	17.244	-0.045	-0.045	0.000	0.000	0.000	0.000
27	C	63	TYR	0	0.017	0.003	20.176	0.770	0.770	0.000	0.000	0.000	0.000
28	C	64	GLN	0	-0.017	-0.028	15.618	1.156	1.156	0.000	0.000	0.000	0.000
29	C	65	CYS	0	-0.006	0.016	16.994	-0.272	-0.272	0.000	0.000	0.000	0.000
30	C	66	CYS	0	-0.052	-0.026	17.884	0.442	0.442	0.000	0.000	0.000	0.000
31	C	67	GLY	0	0.012	0.002	20.486	0.661	0.661	0.000	0.000	0.000	0.000
32	C	68	SER	0	-0.042	-0.047	16.024	0.435	0.435	0.000	0.000	0.000	0.000
33	C	69	LEU	0	-0.013	0.008	18.451	0.376	0.376	0.000	0.000	0.000	0.000
34	C	70	ARG	1	0.908	0.902	21.063	11.726	11.726	0.000	0.000	0.000	0.000
35	C	71	ALA	0	-0.056	-0.026	20.521	0.477	0.477	0.000	0.000	0.000	0.000
36	C	72	ALA	0	-0.007	-0.005	20.161	0.098	0.098	0.000	0.000	0.000	0.000
37	C	73	ALA	0	0.013	0.010	22.272	0.355	0.355	0.000	0.000	0.000	0.000
38	C	74	ARG	0	0.029	0.039	25.645	0.557	0.557	0.000	0.000	0.000	0.000
39	C	75	ARG	1	0.929	0.976	20.481	13.959	13.959	0.000	0.000	0.000	0.000
40	C	76	ARG	1	0.900	0.960	25.455	9.965	9.965	0.000	0.000	0.000	0.000
41	C	77	GLN	0	0.016	0.016	20.609	0.605	0.605	0.000	0.000	0.000	0.000
42	C	78	PRO	0	-0.010	-0.009	22.792	0.128	0.128	0.000	0.000	0.000	0.000
43	C	79	ARG	1	0.912	0.966	22.756	10.568	10.568	0.000	0.000	0.000	0.000
44	C	80	HIS	0	0.028	0.016	18.989	0.355	0.355	0.000	0.000	0.000	0.000
45	C	81	ARG	1	0.936	0.970	21.187	12.197	12.197	0.000	0.000	0.000	0.000
46	C	82	VAL	0	0.003	-0.003	16.680	-0.648	-0.648	0.000	0.000	0.000	0.000
47	C	83	ARG	1	0.916	0.968	17.121	14.719	14.719	0.000	0.000	0.000	0.000
48	C	84	SER	0	0.087	0.031	14.004	0.498	0.498	0.000	0.000	0.000	0.000
49	C	85	ALA	0	0.066	0.032	12.760	-0.382	-0.382	0.000	0.000	0.000	0.000
50	C	86	ALA	0	0.063	0.037	9.743	-2.013	-2.013	0.000	0.000	0.000	0.000
51	C	87	GLN	0	-0.059	-0.054	9.607	-2.335	-2.335	0.000	0.000	0.000	0.000
52	C	88	ILE	0	0.022	0.026	12.230	0.199	0.199	0.000	0.000	0.000	0.000
53	C	89	ARG	1	0.840	0.914	7.912	29.807	29.807	0.000	0.000	0.000	0.000
54	C	90	VAL	0	0.047	0.011	8.695	2.933	2.933	0.000	0.000	0.000	0.000
55	C	91	TRP	0	-0.015	-0.049	6.836	-4.999	-4.999	0.000	0.000	0.000	0.000
56	C	92	ARG	1	0.957	0.986	3.465	42.335	42.760	0.003	-0.099	-0.329	0.000
57	C	93	ASP	-1	-0.921	-0.968	7.800	-21.553	-21.553	0.000	0.000	0.000	0.000
58	C	94	GLY	0	0.040	0.019	10.779	1.915	1.915	0.000	0.000	0.000	0.000
59	C	95	ALA	0	-0.042	0.003	11.494	1.473	1.473	0.000	0.000	0.000	0.000
60	C	96	VAL	0	0.045	0.027	11.349	-1.974	-1.974	0.000	0.000	0.000	0.000
61	C	97	THR	0	0.001	0.041	11.994	1.123	1.123	0.000	0.000	0.000	0.000
62	C	98	LEU	0	0.002	-0.007	13.310	-1.041	-1.041	0.000	0.000	0.000	0.000
63	C	99	ALA	0	-0.030	0.000	11.630	1.010	1.010	0.000	0.000	0.000	0.000
64	C	100	PRO	0	0.030	0.021	13.772	0.937	0.937	0.000	0.000	0.000	0.000
65	C	101	ALA	0	-0.007	-0.013	14.272	-1.154	-1.154	0.000	0.000	0.000	0.000
66	C	102	ALA	0	0.006	0.015	13.952	0.469	0.469	0.000	0.000	0.000	0.000
67	C	119	GLN	0	-0.003	-0.012	28.960	-0.012	-0.012	0.000	0.000	0.000	0.000
68	C	120	CYS	0	0.042	0.007	26.936	-0.186	-0.186	0.000	0.000	0.000	0.000
69	C	121	MET	0	-0.037	0.006	29.071	0.042	0.042	0.000	0.000	0.000	0.000
70	C	122	GLU	-1	-0.893	-0.969	27.758	-11.183	-11.183	0.000	0.000	0.000	0.000
71	C	123	THR	0	0.056	0.007	27.726	-0.348	-0.348	0.000	0.000	0.000	0.000
72	C	124	GLU	-1	-0.871	-0.946	27.583	-10.803	-10.803	0.000	0.000	0.000	0.000
73	C	125	VAL	0	-0.075	-0.015	22.237	-0.387	-0.387	0.000	0.000	0.000	0.000
74	C	126	ILE	0	0.017	0.011	23.576	-0.541	-0.541	0.000	0.000	0.000	0.000
75	C	127	GLU	-1	-0.913	-0.939	24.797	-12.216	-12.216	0.000	0.000	0.000	0.000
76	C	128	SER	0	-0.017	-0.019	21.884	-0.497	-0.497	0.000	0.000	0.000	0.000
77	C	129	LEU	0	-0.021	-0.033	18.554	-0.639	-0.639	0.000	0.000	0.000	0.000
78	C	130	GLY	0	0.074	0.056	21.176	-0.499	-0.499	0.000	0.000	0.000	0.000
79	C	131	ILE	0	0.054	0.031	21.818	-0.447	-0.447	0.000	0.000	0.000	0.000
80	C	132	ILE	0	-0.096	-0.054	16.387	-0.447	-0.447	0.000	0.000	0.000	0.000
81	C	133	ILE	0	0.006	-0.009	18.120	-0.931	-0.931	0.000	0.000	0.000	0.000
82	C	134	TYR	0	0.070	0.046	20.008	-0.231	-0.231	0.000	0.000	0.000	0.000
83	C	135	LYS	1	0.944	0.964	18.530	15.168	15.168	0.000	0.000	0.000	0.000
84	C	136	ALA	0	-0.054	-0.020	16.310	-0.492	-0.492	0.000	0.000	0.000	0.000
85	C	137	LEU	0	-0.038	-0.030	17.475	-0.519	-0.519	0.000	0.000	0.000	0.000
86	C	138	ASP	-1	-0.906	-0.960	20.438	-13.190	-13.190	0.000	0.000	0.000	0.000
87	C	139	TYR	0	-0.036	0.006	13.727	-0.383	-0.383	0.000	0.000	0.000	0.000
88	C	140	GLY	0	-0.019	-0.028	18.782	0.159	0.159	0.000	0.000	0.000	0.000
89	C	141	LEU	0	-0.002	0.021	20.065	0.390	0.390	0.000	0.000	0.000	0.000
90	C	142	LYS	1	0.822	0.901	23.446	12.151	12.151	0.000	0.000	0.000	0.000
91	C	143	GLU	-1	-0.925	-0.959	26.001	-10.799	-10.799	0.000	0.000	0.000	0.000
92	C	144	ASN	0	-0.055	-0.042	28.444	-0.114	-0.114	0.000	0.000	0.000	0.000
93	C	145	GLU	-1	-0.919	-0.941	26.502	-11.391	-11.391	0.000	0.000	0.000	0.000
94	C	146	GLU	-1	-0.882	-0.932	27.844	-10.408	-10.408	0.000	0.000	0.000	0.000
95	C	147	ARG	1	0.800	0.885	20.895	14.327	14.327	0.000	0.000	0.000	0.000
96	C	148	GLU	-1	-0.932	-0.956	27.577	-9.706	-9.706	0.000	0.000	0.000	0.000
97	C	149	LEU	0	-0.032	-0.024	25.426	-0.440	-0.440	0.000	0.000	0.000	0.000
98	C	150	SER	0	0.013	-0.001	29.194	0.426	0.426	0.000	0.000	0.000	0.000
99	C	151	PRO	0	0.064	0.012	31.579	-0.098	-0.098	0.000	0.000	0.000	0.000
100	C	152	PRO	0	-0.060	-0.034	31.014	-0.003	-0.003	0.000	0.000	0.000	0.000
101	C	153	LEU	0	-0.014	-0.019	24.917	-0.164	-0.164	0.000	0.000	0.000	0.000
102	C	154	GLU	-1	-0.909	-0.948	28.629	-10.101	-10.101	0.000	0.000	0.000	0.000
103	C	155	GLN	0	0.003	0.003	30.617	0.038	0.038	0.000	0.000	0.000	0.000
104	C	156	LEU	0	-0.028	-0.006	25.631	-0.011	-0.011	0.000	0.000	0.000	0.000
105	C	157	ILE	0	0.022	0.003	24.065	-0.280	-0.280	0.000	0.000	0.000	0.000
106	C	158	ASP	-1	-0.882	-0.931	27.824	-10.244	-10.244	0.000	0.000	0.000	0.000
107	C	159	HIS	0	-0.049	-0.048	31.093	0.080	0.080	0.000	0.000	0.000	0.000
108	C	160	MET	0	-0.146	-0.064	23.456	0.056	0.056	0.000	0.000	0.000	0.000
109	C	161	ALA	0	0.062	0.032	27.440	-0.426	-0.426	0.000	0.000	0.000	0.000
110	C	162	ASN	0	-0.072	-0.022	29.737	0.149	0.149	0.000	0.000	0.000	0.000
111	C	192	ALA	0	-0.006	-0.014	36.309	-0.050	-0.050	0.000	0.000	0.000	0.000
112	C	193	ILE	0	0.009	0.015	29.698	0.049	0.049	0.000	0.000	0.000	0.000
113	C	194	ARG	1	0.901	0.937	32.030	8.703	8.703	0.000	0.000	0.000	0.000
114	C	195	SER	0	0.005	0.012	29.843	-0.022	-0.022	0.000	0.000	0.000	0.000
115	C	196	TYR	0	0.075	0.020	24.376	0.069	0.069	0.000	0.000	0.000	0.000
116	C	197	ARG	1	0.907	0.946	26.274	9.661	9.661	0.000	0.000	0.000	0.000
117	C	198	ASP	-1	-0.860	-0.917	28.416	-9.688	-9.688	0.000	0.000	0.000	0.000
118	C	199	VAL	0	0.107	0.048	25.132	0.150	0.150	0.000	0.000	0.000	0.000
119	C	200	MET	0	-0.050	-0.031	23.727	-0.126	-0.126	0.000	0.000	0.000	0.000
120	C	201	LYS	1	0.911	0.953	26.133	9.701	9.701	0.000	0.000	0.000	0.000
121	C	202	LEU	0	0.065	0.045	28.972	0.238	0.238	0.000	0.000	0.000	0.000
122	C	203	CYS	0	-0.037	0.000	24.468	-0.125	-0.125	0.000	0.000	0.000	0.000
123	C	204	ALA	0	-0.029	-0.012	26.544	-0.174	-0.174	0.000	0.000	0.000	0.000
124	C	205	ALA	0	0.056	0.036	27.886	0.125	0.125	0.000	0.000	0.000	0.000
125	C	206	HIS	1	0.806	0.925	25.963	12.266	12.266	0.000	0.000	0.000	0.000
126	C	207	LEU	0	-0.013	0.001	25.643	-0.151	-0.151	0.000	0.000	0.000	0.000
127	C	208	PRO	0	-0.001	-0.003	29.769	0.294	0.294	0.000	0.000	0.000	0.000
128	C	209	THR	0	-0.015	-0.001	31.202	0.478	0.478	0.000	0.000	0.000	0.000
129	C	210	GLU	-1	-0.908	-0.950	30.249	-9.935	-9.935	0.000	0.000	0.000	0.000
130	C	211	SER	0	-0.035	-0.038	29.461	-0.234	-0.234	0.000	0.000	0.000	0.000
131	C	212	ASP	-1	-0.928	-0.961	26.544	-11.261	-11.261	0.000	0.000	0.000	0.000
132	C	213	ALA	0	0.074	0.037	24.725	-0.471	-0.471	0.000	0.000	0.000	0.000
133	C	214	PRO	0	-0.077	-0.034	21.959	-0.651	-0.651	0.000	0.000	0.000	0.000
134	C	215	ASN	0	0.004	-0.017	20.590	-1.056	-1.056	0.000	0.000	0.000	0.000
135	C	216	HIS	0	0.001	0.017	20.834	-0.626	-0.626	0.000	0.000	0.000	0.000
136	C	217	TYR	0	0.031	-0.017	19.446	-0.760	-0.760	0.000	0.000	0.000	0.000
137	C	218	GLN	0	-0.016	-0.002	15.081	-0.839	-0.839	0.000	0.000	0.000	0.000
138	C	219	ALA	0	0.004	-0.008	15.680	-1.386	-1.386	0.000	0.000	0.000	0.000
139	C	220	VAL	0	0.004	0.025	16.550	-0.734	-0.734	0.000	0.000	0.000	0.000
140	C	221	CYS	0	-0.053	-0.016	13.225	-0.900	-0.900	0.000	0.000	0.000	0.000
141	C	222	ARG	1	0.929	0.963	12.044	16.966	16.966	0.000	0.000	0.000	0.000
142	C	223	ALA	0	-0.036	0.006	11.913	-1.412	-1.412	0.000	0.000	0.000	0.000
143	C	224	LEU	0	0.055	0.027	11.201	-1.227	-1.227	0.000	0.000	0.000	0.000
144	C	225	PHE	0	-0.057	-0.013	4.249	-3.830	-3.576	-0.001	-0.025	-0.228	0.000
145	C	226	ALA	0	0.024	-0.004	7.896	-3.157	-3.157	0.000	0.000	0.000	0.000
146	C	227	GLU	-1	-0.914	-0.963	9.873	-21.253	-21.253	0.000	0.000	0.000	0.000
147	C	228	THR	0	-0.003	-0.021	6.561	0.324	0.324	0.000	0.000	0.000	0.000
148	C	229	MET	0	-0.092	-0.049	2.521	-9.538	-8.080	0.308	-0.576	-1.189	-0.005
149	C	230	GLU	-1	-0.988	-0.963	6.835	-23.972	-23.972	0.000	0.000	0.000	0.000
150	C	231	LEU	0	-0.061	-0.022	8.173	1.002	1.002	0.000	0.000	0.000	0.000
151	C	232	HIS	0	-0.031	-0.010	2.814	-11.033	-9.523	0.201	-0.811	-0.901	-0.009

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Interactive mode: IFIE and PIEDA for fragment #1(C:37:ARG)