FMO DATABASE

FMODB ID: QVMGY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1308477.381353
FMO2-HF: Nuclear repulsion	1251716.415331
FMO2-HF: Total energy	-56760.966022
FMO2-MP2: Total energy	-56927.89076

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.
-122.056	-125.206	26.976	-12.897	-10.931	0.024

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 : -0.810 / q_NPA : -0.903

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	0.850	0.923	3.321	-44.875	-42.038	0.141	-1.455	-1.523	0.017
4	A	12	GLU	-1	-0.851	-0.929	1.966	31.671	29.603	12.000	-5.273	-4.660	-0.059
5	A	13	GLN	0	-0.021	-0.025	1.760	-36.338	-40.257	14.835	-6.169	-4.748	0.066
6	A	14	ALA	0	-0.002	-0.002	6.074	-5.671	-5.671	0.000	0.000	0.000	0.000
7	A	15	ASN	0	-0.103	-0.051	7.812	-4.522	-4.522	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.026	0.013	8.554	-2.625	-2.625	0.000	0.000	0.000	0.000
9	A	17	GLU	-1	-0.703	-0.802	10.181	19.542	19.542	0.000	0.000	0.000	0.000
10	A	18	ARG	1	0.724	0.860	11.939	-18.790	-18.790	0.000	0.000	0.000	0.000
11	A	19	TRP	0	-0.057	-0.049	12.890	-2.442	-2.442	0.000	0.000	0.000	0.000
12	A	20	ASP	-1	-0.866	-0.921	11.749	26.579	26.579	0.000	0.000	0.000	0.000
13	A	21	GLY	0	-0.030	-0.006	14.748	-0.939	-0.939	0.000	0.000	0.000	0.000
14	A	22	GLY	0	-0.040	-0.034	17.885	-1.052	-1.052	0.000	0.000	0.000	0.000
15	A	23	SER	0	-0.038	-0.003	16.249	-0.459	-0.459	0.000	0.000	0.000	0.000
16	A	24	GLY	0	0.056	0.016	13.228	0.073	0.073	0.000	0.000	0.000	0.000
17	A	25	GLY	0	-0.032	-0.012	11.532	-0.965	-0.965	0.000	0.000	0.000	0.000
18	A	26	ILE	0	-0.031	0.000	6.261	0.058	0.058	0.000	0.000	0.000	0.000
19	A	27	THR	0	-0.032	-0.017	9.636	-3.056	-3.056	0.000	0.000	0.000	0.000
20	A	28	SER	0	0.040	-0.014	11.294	1.579	1.579	0.000	0.000	0.000	0.000
21	A	29	PRO	0	-0.019	-0.017	13.723	-1.172	-1.172	0.000	0.000	0.000	0.000
22	A	30	PHE	0	-0.076	-0.019	16.423	-1.376	-1.376	0.000	0.000	0.000	0.000
23	A	31	LYS	1	0.903	0.951	18.569	-12.773	-12.773	0.000	0.000	0.000	0.000
24	A	32	LEU	0	0.017	0.025	21.183	-0.642	-0.642	0.000	0.000	0.000	0.000
25	A	33	PRO	0	0.054	0.039	19.842	0.962	0.962	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.714	-0.827	18.785	15.119	15.119	0.000	0.000	0.000	0.000
27	A	35	GLU	-1	-0.731	-0.821	20.880	11.577	11.577	0.000	0.000	0.000	0.000
28	A	36	SER	0	-0.060	-0.061	20.922	-0.575	-0.575	0.000	0.000	0.000	0.000
29	A	37	PRO	0	-0.039	0.004	23.516	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	38	SER	0	0.025	0.013	25.146	0.261	0.261	0.000	0.000	0.000	0.000
31	A	39	TRP	0	0.063	0.011	25.648	-0.344	-0.344	0.000	0.000	0.000	0.000
32	A	40	THR	0	0.003	-0.013	27.253	-0.259	-0.259	0.000	0.000	0.000	0.000
33	A	41	GLU	-1	-0.763	-0.856	28.768	10.589	10.589	0.000	0.000	0.000	0.000
34	A	42	TRP	0	-0.009	-0.005	27.927	-0.209	-0.209	0.000	0.000	0.000	0.000
35	A	43	ARG	1	0.848	0.927	30.073	-9.937	-9.937	0.000	0.000	0.000	0.000
36	A	44	LEU	0	0.051	0.034	32.623	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	45	TYR	0	-0.002	-0.021	32.893	-0.128	-0.128	0.000	0.000	0.000	0.000
38	A	46	ASN	0	-0.094	-0.066	31.302	-0.177	-0.177	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.894	-0.929	35.248	7.997	7.997	0.000	0.000	0.000	0.000
40	A	48	GLU	-1	-0.938	-0.926	38.083	7.721	7.721	0.000	0.000	0.000	0.000
41	A	49	THR	0	-0.066	-0.058	38.912	0.119	0.119	0.000	0.000	0.000	0.000
42	A	50	ASN	0	0.022	-0.014	42.135	-0.256	-0.256	0.000	0.000	0.000	0.000
43	A	51	SER	0	0.013	0.013	42.509	0.203	0.203	0.000	0.000	0.000	0.000
44	A	52	ASN	0	-0.006	-0.006	40.058	0.186	0.186	0.000	0.000	0.000	0.000
45	A	53	GLN	0	-0.082	-0.057	38.483	0.030	0.030	0.000	0.000	0.000	0.000
46	A	54	ASP	-1	-0.816	-0.880	37.926	7.741	7.741	0.000	0.000	0.000	0.000
47	A	55	ASN	0	-0.047	-0.046	36.822	0.210	0.210	0.000	0.000	0.000	0.000
48	A	56	PRO	0	-0.053	-0.022	31.199	0.173	0.173	0.000	0.000	0.000	0.000
49	A	57	LEU	0	0.041	0.042	29.265	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	58	GLY	0	0.038	0.007	28.559	0.095	0.095	0.000	0.000	0.000	0.000
51	A	59	PHE	0	-0.068	-0.017	25.094	-0.147	-0.147	0.000	0.000	0.000	0.000
52	A	60	LYS	1	0.963	0.981	18.800	-14.187	-14.187	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.689	-0.794	21.016	13.287	13.287	0.000	0.000	0.000	0.000
54	A	62	SER	0	-0.100	-0.054	16.128	0.902	0.902	0.000	0.000	0.000	0.000
55	A	63	TRP	0	0.086	0.045	16.196	-0.710	-0.710	0.000	0.000	0.000	0.000
56	A	64	GLY	0	-0.028	-0.004	13.208	1.450	1.450	0.000	0.000	0.000	0.000
57	A	65	PHE	0	0.044	0.006	12.119	-1.809	-1.809	0.000	0.000	0.000	0.000
58	A	66	GLY	0	0.032	0.014	11.237	2.509	2.509	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.934	0.969	5.025	-34.907	-34.907	0.000	0.000	0.000	0.000
60	A	68	VAL	0	0.025	0.033	6.586	0.958	0.958	0.000	0.000	0.000	0.000
61	A	69	VAL	0	-0.034	-0.033	8.450	-3.207	-3.207	0.000	0.000	0.000	0.000
62	A	70	PHE	0	0.083	0.062	9.689	0.812	0.812	0.000	0.000	0.000	0.000
63	A	71	LYS	1	0.869	0.905	13.067	-19.566	-19.566	0.000	0.000	0.000	0.000
64	A	72	ARG	1	0.805	0.874	15.974	-18.141	-18.141	0.000	0.000	0.000	0.000
65	A	73	TYR	0	-0.046	-0.030	19.371	-0.348	-0.348	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.006	0.008	22.469	0.239	0.239	0.000	0.000	0.000	0.000
67	A	75	ARG	1	0.816	0.883	25.660	-11.469	-11.469	0.000	0.000	0.000	0.000
68	A	76	TYR	0	-0.050	-0.047	29.263	0.076	0.076	0.000	0.000	0.000	0.000
69	A	77	ASP	-1	-0.754	-0.833	31.773	9.120	9.120	0.000	0.000	0.000	0.000
70	A	78	ARG	1	0.840	0.921	34.810	-8.854	-8.854	0.000	0.000	0.000	0.000
71	A	79	THR	0	-0.025	-0.016	36.563	-0.157	-0.157	0.000	0.000	0.000	0.000
72	A	80	GLU	-1	-0.882	-0.951	36.759	8.038	8.038	0.000	0.000	0.000	0.000
73	A	81	ALA	0	-0.008	-0.006	36.775	0.234	0.234	0.000	0.000	0.000	0.000
74	A	82	SER	0	-0.031	-0.042	33.436	0.471	0.471	0.000	0.000	0.000	0.000
75	A	83	LEU	0	0.023	0.011	32.385	0.444	0.444	0.000	0.000	0.000	0.000
76	A	84	HIS	0	0.006	0.000	32.089	0.338	0.338	0.000	0.000	0.000	0.000
77	A	85	ARG	1	0.769	0.845	28.335	-10.745	-10.745	0.000	0.000	0.000	0.000
78	A	86	VAL	0	-0.012	-0.004	27.817	0.532	0.532	0.000	0.000	0.000	0.000
79	A	87	LEU	0	-0.027	-0.025	27.214	0.614	0.614	0.000	0.000	0.000	0.000
80	A	88	GLY	0	0.005	0.011	27.293	0.333	0.333	0.000	0.000	0.000	0.000
81	A	89	SER	0	-0.047	-0.039	23.121	0.653	0.653	0.000	0.000	0.000	0.000
82	A	90	TRP	0	-0.063	-0.047	21.051	0.918	0.918	0.000	0.000	0.000	0.000
83	A	91	THR	0	0.035	0.017	22.250	-0.836	-0.836	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.053	0.030	22.251	0.633	0.633	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.852	-0.918	22.081	13.379	13.379	0.000	0.000	0.000	0.000
86	A	94	SER	0	-0.018	-0.018	19.273	0.296	0.296	0.000	0.000	0.000	0.000
87	A	95	VAL	0	0.006	0.003	17.763	1.338	1.338	0.000	0.000	0.000	0.000
88	A	96	ASN	0	-0.029	-0.037	17.312	1.219	1.219	0.000	0.000	0.000	0.000
89	A	97	TYR	0	0.019	0.021	15.784	1.383	1.383	0.000	0.000	0.000	0.000
90	A	98	ALA	0	0.030	0.020	13.715	1.231	1.231	0.000	0.000	0.000	0.000
91	A	99	ALA	0	0.015	0.007	12.772	1.869	1.869	0.000	0.000	0.000	0.000
92	A	100	SER	0	-0.093	-0.069	13.616	1.082	1.082	0.000	0.000	0.000	0.000
93	A	101	ARG	1	0.900	0.950	10.103	-26.955	-26.955	0.000	0.000	0.000	0.000
94	A	102	PHE	0	-0.042	-0.022	6.915	3.641	3.641	0.000	0.000	0.000	0.000
95	A	103	LEU	0	-0.056	-0.016	9.984	0.124	0.124	0.000	0.000	0.000	0.000
96	A	104	GLY	0	0.053	0.021	12.655	1.067	1.067	0.000	0.000	0.000	0.000
97	A	105	ALA	0	-0.032	-0.017	14.480	-0.942	-0.942	0.000	0.000	0.000	0.000
98	A	106	ASN	0	0.000	0.014	15.148	-1.744	-1.744	0.000	0.000	0.000	0.000
99	A	107	GLN	0	0.000	0.000	17.055	0.152	0.152	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.024	0.009	13.520	0.216	0.216	0.000	0.000	0.000	0.000
101	A	109	GLY	0	0.010	0.014	16.305	-0.799	-0.799	0.000	0.000	0.000	0.000
102	A	110	CYS	0	-0.028	-0.002	15.477	1.793	1.793	0.000	0.000	0.000	0.000
103	A	111	THR	0	-0.037	-0.041	16.918	-1.136	-1.136	0.000	0.000	0.000	0.000
104	A	112	TYR	0	0.047	0.014	17.740	0.688	0.688	0.000	0.000	0.000	0.000
105	A	113	SER	0	-0.063	-0.048	19.332	-0.562	-0.562	0.000	0.000	0.000	0.000
106	A	114	ILE	0	0.033	0.023	20.900	0.520	0.520	0.000	0.000	0.000	0.000
107	A	115	ARG	1	0.829	0.900	23.648	-11.323	-11.323	0.000	0.000	0.000	0.000
108	A	116	PHE	0	0.071	0.024	25.578	0.207	0.207	0.000	0.000	0.000	0.000
109	A	117	ARG	1	0.890	0.937	28.981	-8.665	-8.665	0.000	0.000	0.000	0.000
110	A	118	GLY	0	0.017	0.026	30.117	-0.244	-0.244	0.000	0.000	0.000	0.000
111	A	119	VAL	0	0.038	0.024	29.858	0.155	0.155	0.000	0.000	0.000	0.000
112	A	120	SER	0	-0.004	-0.021	24.877	0.285	0.285	0.000	0.000	0.000	0.000
113	A	121	VAL	0	0.027	0.034	25.991	-0.271	-0.271	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.039	-0.028	21.175	0.725	0.725	0.000	0.000	0.000	0.000
115	A	123	ILE	0	0.009	0.032	22.831	-0.414	-0.414	0.000	0.000	0.000	0.000
116	A	124	SER	0	-0.004	-0.009	20.559	0.718	0.718	0.000	0.000	0.000	0.000
117	A	125	GLY	0	0.070	0.038	20.864	-0.747	-0.747	0.000	0.000	0.000	0.000
118	A	126	GLY	0	-0.007	0.005	20.227	0.831	0.831	0.000	0.000	0.000	0.000
119	A	127	SER	0	0.067	0.020	17.611	-0.803	-0.803	0.000	0.000	0.000	0.000
120	A	128	ARG	1	0.931	0.962	19.703	-12.517	-12.517	0.000	0.000	0.000	0.000
121	A	129	THR	0	-0.029	-0.025	22.931	-0.616	-0.616	0.000	0.000	0.000	0.000
122	A	130	LEU	0	0.026	0.011	18.379	-0.290	-0.290	0.000	0.000	0.000	0.000
123	A	131	GLN	0	0.068	0.048	22.347	0.361	0.361	0.000	0.000	0.000	0.000
124	A	132	HIS	0	0.003	-0.017	25.264	-0.182	-0.182	0.000	0.000	0.000	0.000
125	A	133	LEU	0	-0.050	-0.011	21.232	-0.132	-0.132	0.000	0.000	0.000	0.000
126	A	134	CYS	0	-0.029	-0.023	22.751	0.191	0.191	0.000	0.000	0.000	0.000
127	A	135	GLU	-1	-0.848	-0.909	24.906	10.733	10.733	0.000	0.000	0.000	0.000
128	A	136	MET	0	0.034	0.005	27.561	-0.382	-0.382	0.000	0.000	0.000	0.000
129	A	137	ALA	0	-0.022	0.011	24.156	-0.211	-0.211	0.000	0.000	0.000	0.000
130	A	138	ILE	0	0.017	0.002	26.157	-0.166	-0.166	0.000	0.000	0.000	0.000
131	A	139	ARG	1	0.832	0.922	28.369	-9.431	-9.431	0.000	0.000	0.000	0.000
132	A	140	SER	0	0.036	-0.005	27.685	-0.210	-0.210	0.000	0.000	0.000	0.000
133	A	141	LYS	1	0.762	0.883	24.723	-12.883	-12.883	0.000	0.000	0.000	0.000
134	A	142	GLN	0	-0.008	-0.014	28.691	-0.445	-0.445	0.000	0.000	0.000	0.000
135	A	143	GLU	-1	-0.816	-0.885	32.199	9.094	9.094	0.000	0.000	0.000	0.000
136	A	144	LEU	0	-0.026	-0.017	28.136	-0.224	-0.224	0.000	0.000	0.000	0.000
137	A	145	LEU	0	-0.063	-0.036	28.772	-0.139	-0.139	0.000	0.000	0.000	0.000
138	A	146	GLN	0	-0.014	-0.009	32.702	-0.316	-0.316	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.026	0.007	34.129	-0.268	-0.268	0.000	0.000	0.000	0.000
140	A	148	THR	0	0.048	0.017	37.475	0.053	0.053	0.000	0.000	0.000	0.000
141	A	149	PRO	0	0.048	0.046	39.706	0.140	0.140	0.000	0.000	0.000	0.000
142	A	150	VAL	0	-0.035	0.003	36.942	-0.122	-0.122	0.000	0.000	0.000	0.000
143	A	151	GLU	-1	-0.816	-0.914	40.158	7.674	7.674	0.000	0.000	0.000	0.000
144	A	152	VAL	0	-0.122	-0.059	43.043	-0.291	-0.291	0.000	0.000	0.000	0.000

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