FMO DATABASE

FMODB ID: R8MG8

Calculation Name: 1RPU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RPU

Chain ID: A

ChEMBL ID:

UniProt ID: Q66104

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1307841.310711
FMO2-HF: Nuclear repulsion	1251080.748487
FMO2-HF: Total energy	-56760.562224
FMO2-MP2: Total energy	-56927.489849

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:9:ASP)

Summations of interaction energy for fragment #1(A:9: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.
-117.932	-117.943	23.313	-12.406	-10.896	0.003

Interaction energy analysis for fragmet #1(A:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.859 / q_NPA : -0.949

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	11	ARG	1	0.851	0.925	2.841	-45.475	-41.922	0.169	-1.814	-1.908	0.015
4	A	12	GLU	-1	-0.847	-0.929	1.847	31.320	29.153	12.791	-5.915	-4.709	-0.069
5	A	13	GLN	0	-0.013	-0.006	1.880	-34.518	-35.915	10.353	-4.677	-4.279	0.057
6	A	14	ALA	0	0.027	0.014	6.381	-5.370	-5.370	0.000	0.000	0.000	0.000
7	A	15	ASN	0	-0.107	-0.048	7.656	-4.165	-4.165	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.033	0.011	8.714	-2.713	-2.713	0.000	0.000	0.000	0.000
9	A	17	GLU	-1	-0.720	-0.786	10.332	19.617	19.617	0.000	0.000	0.000	0.000
10	A	18	ARG	1	0.732	0.864	12.102	-18.641	-18.641	0.000	0.000	0.000	0.000
11	A	19	TRP	0	-0.095	-0.075	13.421	-2.233	-2.233	0.000	0.000	0.000	0.000
12	A	20	ASP	-1	-0.867	-0.921	12.277	25.385	25.385	0.000	0.000	0.000	0.000
13	A	21	GLY	0	-0.073	-0.034	15.506	-0.821	-0.821	0.000	0.000	0.000	0.000
14	A	22	GLY	0	-0.026	-0.012	18.857	0.066	0.066	0.000	0.000	0.000	0.000
15	A	23	SER	0	-0.021	-0.003	16.946	0.058	0.058	0.000	0.000	0.000	0.000
16	A	24	GLY	0	0.116	0.052	13.550	0.315	0.315	0.000	0.000	0.000	0.000
17	A	25	GLY	0	-0.036	-0.021	12.176	-1.130	-1.130	0.000	0.000	0.000	0.000
18	A	26	ILE	0	-0.060	-0.018	6.923	0.089	0.089	0.000	0.000	0.000	0.000
19	A	27	THR	0	-0.012	-0.008	10.453	-1.901	-1.901	0.000	0.000	0.000	0.000
20	A	28	SER	0	0.028	-0.022	11.840	1.514	1.514	0.000	0.000	0.000	0.000
21	A	29	PRO	0	-0.012	-0.006	14.236	-1.187	-1.187	0.000	0.000	0.000	0.000
22	A	30	PHE	0	-0.056	-0.021	16.375	-1.330	-1.330	0.000	0.000	0.000	0.000
23	A	31	LYS	1	0.911	0.958	19.019	-12.659	-12.659	0.000	0.000	0.000	0.000
24	A	32	LEU	0	0.009	0.015	21.715	-0.546	-0.546	0.000	0.000	0.000	0.000
25	A	33	PRO	0	0.020	0.025	20.320	0.652	0.652	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.686	-0.814	18.923	14.859	14.859	0.000	0.000	0.000	0.000
27	A	35	GLU	-1	-0.735	-0.823	21.040	11.496	11.496	0.000	0.000	0.000	0.000
28	A	36	SER	0	-0.071	-0.066	20.846	-0.581	-0.581	0.000	0.000	0.000	0.000
29	A	37	PRO	0	-0.024	0.015	23.398	0.082	0.082	0.000	0.000	0.000	0.000
30	A	38	SER	0	0.018	0.015	25.013	0.252	0.252	0.000	0.000	0.000	0.000
31	A	39	TRP	0	0.067	0.001	25.802	-0.279	-0.279	0.000	0.000	0.000	0.000
32	A	40	THR	0	-0.011	-0.026	27.226	-0.274	-0.274	0.000	0.000	0.000	0.000
33	A	41	GLU	-1	-0.755	-0.842	29.231	10.366	10.366	0.000	0.000	0.000	0.000
34	A	42	TRP	0	-0.009	-0.002	28.095	-0.169	-0.169	0.000	0.000	0.000	0.000
35	A	43	ARG	1	0.897	0.956	30.236	-9.920	-9.920	0.000	0.000	0.000	0.000
36	A	44	LEU	0	0.020	0.026	32.711	-0.159	-0.159	0.000	0.000	0.000	0.000
37	A	45	TYR	0	0.003	-0.015	32.953	-0.124	-0.124	0.000	0.000	0.000	0.000
38	A	46	ASN	0	-0.104	-0.066	31.406	-0.171	-0.171	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.890	-0.934	35.407	8.009	8.009	0.000	0.000	0.000	0.000
40	A	48	GLU	-1	-0.948	-0.927	38.402	7.754	7.754	0.000	0.000	0.000	0.000
41	A	49	THR	0	-0.071	-0.062	39.100	0.106	0.106	0.000	0.000	0.000	0.000
42	A	50	ASN	0	0.012	-0.026	42.431	-0.223	-0.223	0.000	0.000	0.000	0.000
43	A	51	SER	0	0.013	0.016	42.890	0.186	0.186	0.000	0.000	0.000	0.000
44	A	52	ASN	0	0.007	0.005	40.355	0.171	0.171	0.000	0.000	0.000	0.000
45	A	53	GLN	0	-0.076	-0.062	38.935	0.008	0.008	0.000	0.000	0.000	0.000
46	A	54	ASP	-1	-0.828	-0.879	38.455	7.605	7.605	0.000	0.000	0.000	0.000
47	A	55	ASN	0	-0.066	-0.062	36.920	0.211	0.211	0.000	0.000	0.000	0.000
48	A	56	PRO	0	-0.036	-0.011	31.362	0.132	0.132	0.000	0.000	0.000	0.000
49	A	57	LEU	0	0.032	0.037	28.822	0.001	0.001	0.000	0.000	0.000	0.000
50	A	58	GLY	0	0.061	0.014	28.416	0.024	0.024	0.000	0.000	0.000	0.000
51	A	59	PHE	0	-0.073	-0.012	24.684	-0.125	-0.125	0.000	0.000	0.000	0.000
52	A	60	LYS	1	0.950	0.975	18.301	-14.343	-14.343	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.718	-0.814	20.768	12.991	12.991	0.000	0.000	0.000	0.000
54	A	62	SER	0	-0.099	-0.058	15.803	0.811	0.811	0.000	0.000	0.000	0.000
55	A	63	TRP	0	0.101	0.051	15.922	-0.614	-0.614	0.000	0.000	0.000	0.000
56	A	64	GLY	0	-0.034	-0.007	12.964	1.348	1.348	0.000	0.000	0.000	0.000
57	A	65	PHE	0	0.040	0.022	12.255	-1.500	-1.500	0.000	0.000	0.000	0.000
58	A	66	GLY	0	0.043	0.017	11.252	2.305	2.305	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.915	0.952	5.412	-32.127	-32.127	0.000	0.000	0.000	0.000
60	A	68	VAL	0	0.030	0.020	6.758	0.899	0.899	0.000	0.000	0.000	0.000
61	A	69	VAL	0	-0.035	-0.022	8.470	-2.686	-2.686	0.000	0.000	0.000	0.000
62	A	70	PHE	0	0.078	0.050	10.525	1.103	1.103	0.000	0.000	0.000	0.000
63	A	71	LYS	1	0.876	0.910	13.137	-19.290	-19.290	0.000	0.000	0.000	0.000
64	A	72	ARG	1	0.826	0.886	15.966	-17.993	-17.993	0.000	0.000	0.000	0.000
65	A	73	TYR	0	-0.034	-0.021	19.367	-0.421	-0.421	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.009	0.002	22.397	0.163	0.163	0.000	0.000	0.000	0.000
67	A	75	ARG	1	0.802	0.860	25.495	-11.373	-11.373	0.000	0.000	0.000	0.000
68	A	76	TYR	0	-0.051	-0.047	29.004	0.109	0.109	0.000	0.000	0.000	0.000
69	A	77	ASP	-1	-0.766	-0.839	31.519	8.936	8.936	0.000	0.000	0.000	0.000
70	A	78	ARG	1	0.851	0.920	34.555	-8.739	-8.739	0.000	0.000	0.000	0.000
71	A	79	THR	0	-0.018	-0.011	36.360	-0.181	-0.181	0.000	0.000	0.000	0.000
72	A	80	GLU	-1	-0.879	-0.947	36.914	7.896	7.896	0.000	0.000	0.000	0.000
73	A	81	ALA	0	-0.015	-0.007	37.062	0.233	0.233	0.000	0.000	0.000	0.000
74	A	82	SER	0	-0.026	-0.044	33.765	0.454	0.454	0.000	0.000	0.000	0.000
75	A	83	LEU	0	-0.008	-0.004	32.479	0.433	0.433	0.000	0.000	0.000	0.000
76	A	84	HIS	0	0.006	-0.010	32.300	0.314	0.314	0.000	0.000	0.000	0.000
77	A	85	ARG	1	0.790	0.864	28.322	-10.780	-10.780	0.000	0.000	0.000	0.000
78	A	86	VAL	0	0.013	0.005	27.827	0.499	0.499	0.000	0.000	0.000	0.000
79	A	87	LEU	0	-0.033	-0.022	27.368	0.571	0.571	0.000	0.000	0.000	0.000
80	A	88	GLY	0	0.003	0.015	27.968	0.170	0.170	0.000	0.000	0.000	0.000
81	A	89	SER	0	-0.071	-0.059	23.109	0.657	0.657	0.000	0.000	0.000	0.000
82	A	90	TRP	0	-0.069	-0.042	21.631	0.918	0.918	0.000	0.000	0.000	0.000
83	A	91	THR	0	0.041	0.016	22.939	-0.742	-0.742	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.095	0.042	23.007	0.581	0.581	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.868	-0.926	22.760	13.117	13.117	0.000	0.000	0.000	0.000
86	A	94	SER	0	-0.057	-0.033	20.229	0.345	0.345	0.000	0.000	0.000	0.000
87	A	95	VAL	0	0.017	0.002	18.630	1.211	1.211	0.000	0.000	0.000	0.000
88	A	96	ASN	0	-0.032	-0.032	18.085	1.107	1.107	0.000	0.000	0.000	0.000
89	A	97	TYR	0	0.003	0.003	16.138	1.348	1.348	0.000	0.000	0.000	0.000
90	A	98	ALA	0	0.026	0.007	14.261	1.043	1.043	0.000	0.000	0.000	0.000
91	A	99	ALA	0	0.001	0.007	13.423	1.767	1.767	0.000	0.000	0.000	0.000
92	A	100	SER	0	-0.055	-0.042	14.234	1.111	1.111	0.000	0.000	0.000	0.000
93	A	101	ARG	1	0.918	0.967	10.026	-26.361	-26.361	0.000	0.000	0.000	0.000
94	A	102	PHE	0	-0.025	-0.014	7.558	3.115	3.115	0.000	0.000	0.000	0.000
95	A	103	LEU	0	-0.065	-0.018	10.645	0.121	0.121	0.000	0.000	0.000	0.000
96	A	104	GLY	0	0.027	0.021	13.753	-0.051	-0.051	0.000	0.000	0.000	0.000
97	A	105	ALA	0	0.006	0.002	14.412	-0.958	-0.958	0.000	0.000	0.000	0.000
98	A	106	ASN	0	-0.015	-0.007	15.185	-1.813	-1.813	0.000	0.000	0.000	0.000
99	A	107	GLN	0	-0.001	0.001	17.333	-0.122	-0.122	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.020	0.002	13.053	0.162	0.162	0.000	0.000	0.000	0.000
101	A	109	GLY	0	0.002	0.003	15.522	-0.826	-0.826	0.000	0.000	0.000	0.000
102	A	110	CYS	0	-0.021	0.000	15.014	1.638	1.638	0.000	0.000	0.000	0.000
103	A	111	THR	0	-0.049	-0.045	16.609	-1.000	-1.000	0.000	0.000	0.000	0.000
104	A	112	TYR	0	0.050	0.018	17.575	0.627	0.627	0.000	0.000	0.000	0.000
105	A	113	SER	0	-0.071	-0.044	19.728	-0.606	-0.606	0.000	0.000	0.000	0.000
106	A	114	ILE	0	0.036	0.029	21.171	0.476	0.476	0.000	0.000	0.000	0.000
107	A	115	ARG	1	0.888	0.949	23.831	-11.296	-11.296	0.000	0.000	0.000	0.000
108	A	116	PHE	0	0.045	0.003	25.793	0.162	0.162	0.000	0.000	0.000	0.000
109	A	117	ARG	1	0.890	0.933	29.103	-8.653	-8.653	0.000	0.000	0.000	0.000
110	A	118	GLY	0	0.003	0.013	30.203	-0.231	-0.231	0.000	0.000	0.000	0.000
111	A	119	VAL	0	0.032	0.025	29.521	0.233	0.233	0.000	0.000	0.000	0.000
112	A	120	SER	0	-0.012	-0.029	24.357	0.332	0.332	0.000	0.000	0.000	0.000
113	A	121	VAL	0	0.010	0.017	26.140	-0.168	-0.168	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.003	-0.004	21.032	0.685	0.685	0.000	0.000	0.000	0.000
115	A	123	ILE	0	0.001	0.020	22.795	-0.342	-0.342	0.000	0.000	0.000	0.000
116	A	124	SER	0	-0.026	-0.028	20.459	0.717	0.717	0.000	0.000	0.000	0.000
117	A	125	GLY	0	0.086	0.045	20.614	-0.704	-0.704	0.000	0.000	0.000	0.000
118	A	126	GLY	0	-0.015	-0.001	19.809	0.801	0.801	0.000	0.000	0.000	0.000
119	A	127	SER	0	0.067	0.013	17.575	-0.706	-0.706	0.000	0.000	0.000	0.000
120	A	128	ARG	1	0.949	0.983	19.692	-12.390	-12.390	0.000	0.000	0.000	0.000
121	A	129	THR	0	-0.036	-0.019	23.162	-0.496	-0.496	0.000	0.000	0.000	0.000
122	A	130	LEU	0	0.046	0.022	19.096	-0.269	-0.269	0.000	0.000	0.000	0.000
123	A	131	GLN	0	0.061	0.037	22.765	0.190	0.190	0.000	0.000	0.000	0.000
124	A	132	HIS	0	-0.014	-0.028	25.940	-0.242	-0.242	0.000	0.000	0.000	0.000
125	A	133	LEU	0	-0.065	-0.021	21.016	-0.141	-0.141	0.000	0.000	0.000	0.000
126	A	134	CYS	0	-0.016	-0.021	23.337	0.152	0.152	0.000	0.000	0.000	0.000
127	A	135	GLU	-1	-0.847	-0.897	25.311	10.488	10.488	0.000	0.000	0.000	0.000
128	A	136	MET	0	0.023	0.000	27.336	-0.356	-0.356	0.000	0.000	0.000	0.000
129	A	137	ALA	0	-0.020	0.005	24.217	-0.217	-0.217	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.009	0.004	26.224	-0.138	-0.138	0.000	0.000	0.000	0.000
131	A	139	ARG	1	0.890	0.936	28.347	-9.229	-9.229	0.000	0.000	0.000	0.000
132	A	140	SER	0	0.006	-0.009	27.893	-0.222	-0.222	0.000	0.000	0.000	0.000
133	A	141	LYS	1	0.799	0.909	24.736	-12.617	-12.617	0.000	0.000	0.000	0.000
134	A	142	GLN	0	0.014	0.000	28.832	-0.382	-0.382	0.000	0.000	0.000	0.000
135	A	143	GLU	-1	-0.833	-0.899	32.392	8.914	8.914	0.000	0.000	0.000	0.000
136	A	144	LEU	0	-0.033	-0.018	28.121	-0.187	-0.187	0.000	0.000	0.000	0.000
137	A	145	LEU	0	-0.071	-0.045	28.905	-0.097	-0.097	0.000	0.000	0.000	0.000
138	A	146	GLN	0	-0.013	-0.009	32.768	-0.288	-0.288	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.029	0.010	34.123	-0.260	-0.260	0.000	0.000	0.000	0.000
140	A	148	THR	0	0.040	0.017	37.471	0.033	0.033	0.000	0.000	0.000	0.000
141	A	149	PRO	0	0.048	0.043	39.720	0.131	0.131	0.000	0.000	0.000	0.000
142	A	150	VAL	0	-0.026	-0.008	37.032	-0.083	-0.083	0.000	0.000	0.000	0.000
143	A	151	GLU	-1	-0.866	-0.932	40.100	7.555	7.555	0.000	0.000	0.000	0.000
144	A	152	VAL	0	-0.074	-0.028	43.110	-0.228	-0.228	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASP)