FMO DATABASE

FMODB ID: ZVL5N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1307711.72912
FMO2-HF: Nuclear repulsion	1250952.034357
FMO2-HF: Total energy	-56759.694763
FMO2-MP2: Total energy	-56926.728923

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.
-104.811	-93.263	5.241	-8.414	-8.376	0.013

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 : -0.857 / q_NPA : -0.934

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	0.826	0.888	3.063	-45.284	-41.686	0.107	-1.870	-1.835	0.015
4	A	12	GLU	-1	-0.911	-0.961	2.269	36.293	40.637	3.460	-4.001	-3.804	-0.036
5	A	13	GLN	0	0.018	0.016	2.407	-28.646	-25.040	1.674	-2.543	-2.737	0.034
6	A	14	ALA	0	0.023	0.015	6.382	-5.072	-5.072	0.000	0.000	0.000	0.000
7	A	15	ASN	0	-0.117	-0.051	7.954	-3.906	-3.906	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.040	0.010	8.734	-2.715	-2.715	0.000	0.000	0.000	0.000
9	A	17	GLU	-1	-0.723	-0.829	10.331	19.713	19.713	0.000	0.000	0.000	0.000
10	A	18	ARG	1	0.744	0.872	12.193	-18.659	-18.659	0.000	0.000	0.000	0.000
11	A	19	TRP	0	-0.090	-0.072	13.385	-2.275	-2.275	0.000	0.000	0.000	0.000
12	A	20	ASP	-1	-0.850	-0.912	12.469	25.223	25.223	0.000	0.000	0.000	0.000
13	A	21	GLY	0	-0.070	-0.035	15.567	-0.812	-0.812	0.000	0.000	0.000	0.000
14	A	22	GLY	0	-0.027	-0.012	18.995	0.039	0.039	0.000	0.000	0.000	0.000
15	A	23	SER	0	-0.021	-0.003	17.077	0.077	0.077	0.000	0.000	0.000	0.000
16	A	24	GLY	0	0.107	0.047	13.715	0.346	0.346	0.000	0.000	0.000	0.000
17	A	25	GLY	0	-0.028	-0.018	12.402	-1.106	-1.106	0.000	0.000	0.000	0.000
18	A	26	ILE	0	-0.050	-0.013	7.741	0.257	0.257	0.000	0.000	0.000	0.000
19	A	27	THR	0	-0.010	-0.009	10.706	-1.677	-1.677	0.000	0.000	0.000	0.000
20	A	28	SER	0	0.036	0.014	12.314	1.390	1.390	0.000	0.000	0.000	0.000
21	A	29	PRO	0	-0.006	-0.002	14.526	-1.148	-1.148	0.000	0.000	0.000	0.000
22	A	30	PHE	0	-0.047	-0.006	17.044	-1.263	-1.263	0.000	0.000	0.000	0.000
23	A	31	LYS	1	0.945	0.973	19.448	-12.611	-12.611	0.000	0.000	0.000	0.000
24	A	32	LEU	0	0.006	0.011	21.929	-0.559	-0.559	0.000	0.000	0.000	0.000
25	A	33	PRO	0	0.014	0.028	20.459	0.663	0.663	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.689	-0.811	18.973	14.788	14.788	0.000	0.000	0.000	0.000
27	A	35	GLU	-1	-0.761	-0.863	21.057	11.545	11.545	0.000	0.000	0.000	0.000
28	A	36	SER	0	-0.084	-0.089	20.872	-0.534	-0.534	0.000	0.000	0.000	0.000
29	A	37	PRO	0	-0.019	0.022	23.495	0.067	0.067	0.000	0.000	0.000	0.000
30	A	38	SER	0	0.032	0.022	25.045	0.265	0.265	0.000	0.000	0.000	0.000
31	A	39	TRP	0	0.046	-0.009	25.848	-0.232	-0.232	0.000	0.000	0.000	0.000
32	A	40	THR	0	-0.029	-0.034	27.272	-0.238	-0.238	0.000	0.000	0.000	0.000
33	A	41	GLU	-1	-0.792	-0.878	29.581	10.253	10.253	0.000	0.000	0.000	0.000
34	A	42	TRP	0	-0.043	-0.010	28.329	-0.201	-0.201	0.000	0.000	0.000	0.000
35	A	43	ARG	1	0.939	0.956	30.460	-9.832	-9.832	0.000	0.000	0.000	0.000
36	A	44	LEU	0	0.015	0.022	32.908	-0.163	-0.163	0.000	0.000	0.000	0.000
37	A	45	TYR	0	0.017	-0.037	33.201	-0.139	-0.139	0.000	0.000	0.000	0.000
38	A	46	ASN	0	-0.075	-0.041	31.483	-0.220	-0.220	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.890	-0.926	35.647	8.091	8.091	0.000	0.000	0.000	0.000
40	A	48	GLU	-1	-0.951	-0.941	38.645	7.840	7.840	0.000	0.000	0.000	0.000
41	A	49	THR	0	-0.073	-0.060	39.373	0.083	0.083	0.000	0.000	0.000	0.000
42	A	50	ASN	0	-0.001	-0.037	42.740	-0.204	-0.204	0.000	0.000	0.000	0.000
43	A	51	SER	0	0.005	0.004	43.440	0.166	0.166	0.000	0.000	0.000	0.000
44	A	52	ASN	0	0.036	0.022	40.811	0.136	0.136	0.000	0.000	0.000	0.000
45	A	53	GLN	0	-0.073	-0.039	39.480	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	54	ASP	-1	-0.805	-0.863	38.923	7.593	7.593	0.000	0.000	0.000	0.000
47	A	55	ASN	0	-0.098	-0.072	37.266	0.188	0.188	0.000	0.000	0.000	0.000
48	A	56	PRO	0	-0.018	0.013	31.827	0.137	0.137	0.000	0.000	0.000	0.000
49	A	57	LEU	0	0.036	0.048	28.901	0.055	0.055	0.000	0.000	0.000	0.000
50	A	58	GLY	0	0.041	0.001	28.765	0.029	0.029	0.000	0.000	0.000	0.000
51	A	59	PHE	0	-0.048	0.003	24.976	-0.138	-0.138	0.000	0.000	0.000	0.000
52	A	60	LYS	1	0.927	0.968	17.860	-14.770	-14.770	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.737	-0.851	21.056	12.987	12.987	0.000	0.000	0.000	0.000
54	A	62	SER	0	-0.106	-0.059	16.219	0.862	0.862	0.000	0.000	0.000	0.000
55	A	63	TRP	0	0.115	0.053	16.337	-0.622	-0.622	0.000	0.000	0.000	0.000
56	A	64	GLY	0	-0.038	-0.011	13.388	1.372	1.372	0.000	0.000	0.000	0.000
57	A	65	PHE	0	0.035	0.021	12.449	-1.465	-1.465	0.000	0.000	0.000	0.000
58	A	66	GLY	0	0.045	0.020	11.347	2.207	2.207	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.925	0.961	6.101	-30.834	-30.834	0.000	0.000	0.000	0.000
60	A	68	VAL	0	0.027	0.030	7.053	1.460	1.460	0.000	0.000	0.000	0.000
61	A	69	VAL	0	-0.022	-0.011	8.809	-2.611	-2.611	0.000	0.000	0.000	0.000
62	A	70	PHE	0	0.078	0.044	10.939	1.178	1.178	0.000	0.000	0.000	0.000
63	A	71	LYS	1	0.891	0.919	13.558	-19.318	-19.318	0.000	0.000	0.000	0.000
64	A	72	ARG	1	0.825	0.895	16.000	-17.781	-17.781	0.000	0.000	0.000	0.000
65	A	73	TYR	0	-0.031	-0.014	19.742	-0.357	-0.357	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.004	0.005	22.747	0.137	0.137	0.000	0.000	0.000	0.000
67	A	75	ARG	1	0.814	0.878	25.851	-11.393	-11.393	0.000	0.000	0.000	0.000
68	A	76	TYR	0	-0.063	-0.058	29.305	0.093	0.093	0.000	0.000	0.000	0.000
69	A	77	ASP	-1	-0.780	-0.871	31.891	8.728	8.728	0.000	0.000	0.000	0.000
70	A	78	ARG	1	0.843	0.917	34.944	-8.690	-8.690	0.000	0.000	0.000	0.000
71	A	79	THR	0	-0.026	-0.006	36.746	-0.172	-0.172	0.000	0.000	0.000	0.000
72	A	80	GLU	-1	-0.863	-0.948	37.302	7.866	7.866	0.000	0.000	0.000	0.000
73	A	81	ALA	0	-0.025	-0.005	37.316	0.228	0.228	0.000	0.000	0.000	0.000
74	A	82	SER	0	-0.010	-0.002	33.798	0.416	0.416	0.000	0.000	0.000	0.000
75	A	83	LEU	0	0.006	0.002	32.916	0.436	0.436	0.000	0.000	0.000	0.000
76	A	84	HIS	0	0.015	-0.006	32.597	0.348	0.348	0.000	0.000	0.000	0.000
77	A	85	ARG	1	0.809	0.898	28.112	-10.742	-10.742	0.000	0.000	0.000	0.000
78	A	86	VAL	0	0.000	0.005	28.179	0.490	0.490	0.000	0.000	0.000	0.000
79	A	87	LEU	0	-0.025	-0.024	27.632	0.558	0.558	0.000	0.000	0.000	0.000
80	A	88	GLY	0	0.001	0.016	28.210	0.163	0.163	0.000	0.000	0.000	0.000
81	A	89	SER	0	-0.085	-0.063	23.581	0.624	0.624	0.000	0.000	0.000	0.000
82	A	90	TRP	0	-0.060	-0.026	21.782	0.915	0.915	0.000	0.000	0.000	0.000
83	A	91	THR	0	0.024	0.015	23.450	-0.692	-0.692	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.109	0.042	23.600	0.560	0.560	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.874	-0.922	23.381	12.960	12.960	0.000	0.000	0.000	0.000
86	A	94	SER	0	-0.090	-0.068	20.912	0.370	0.370	0.000	0.000	0.000	0.000
87	A	95	VAL	0	0.028	0.006	19.197	1.184	1.184	0.000	0.000	0.000	0.000
88	A	96	ASN	0	-0.019	-0.029	18.729	1.030	1.030	0.000	0.000	0.000	0.000
89	A	97	TYR	0	-0.007	-0.001	16.404	1.196	1.196	0.000	0.000	0.000	0.000
90	A	98	ALA	0	0.025	0.011	14.796	0.987	0.987	0.000	0.000	0.000	0.000
91	A	99	ALA	0	-0.001	0.006	14.049	1.680	1.680	0.000	0.000	0.000	0.000
92	A	100	SER	0	-0.051	-0.044	14.780	1.053	1.053	0.000	0.000	0.000	0.000
93	A	101	ARG	1	0.939	0.974	9.768	-26.648	-26.648	0.000	0.000	0.000	0.000
94	A	102	PHE	0	-0.034	-0.014	8.193	3.037	3.037	0.000	0.000	0.000	0.000
95	A	103	LEU	0	-0.076	-0.025	11.129	0.153	0.153	0.000	0.000	0.000	0.000
96	A	104	GLY	0	0.031	0.024	13.697	-0.064	-0.064	0.000	0.000	0.000	0.000
97	A	105	ALA	0	0.008	0.004	14.367	-0.902	-0.902	0.000	0.000	0.000	0.000
98	A	106	ASN	0	-0.007	-0.004	15.328	-1.758	-1.758	0.000	0.000	0.000	0.000
99	A	107	GLN	0	0.004	-0.003	17.235	0.072	0.072	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.001	-0.004	13.079	0.196	0.196	0.000	0.000	0.000	0.000
101	A	109	GLY	0	0.001	-0.001	15.622	-0.808	-0.808	0.000	0.000	0.000	0.000
102	A	110	CYS	0	-0.013	0.004	15.225	1.577	1.577	0.000	0.000	0.000	0.000
103	A	111	THR	0	-0.052	-0.044	17.055	-0.857	-0.857	0.000	0.000	0.000	0.000
104	A	112	TYR	0	0.052	0.024	18.007	0.604	0.604	0.000	0.000	0.000	0.000
105	A	113	SER	0	-0.069	-0.028	19.992	-0.534	-0.534	0.000	0.000	0.000	0.000
106	A	114	ILE	0	0.055	0.035	21.579	0.474	0.474	0.000	0.000	0.000	0.000
107	A	115	ARG	1	0.893	0.953	24.232	-11.299	-11.299	0.000	0.000	0.000	0.000
108	A	116	PHE	0	0.049	0.003	26.165	0.163	0.163	0.000	0.000	0.000	0.000
109	A	117	ARG	1	0.869	0.916	29.471	-8.599	-8.599	0.000	0.000	0.000	0.000
110	A	118	GLY	0	-0.014	0.005	30.527	-0.228	-0.228	0.000	0.000	0.000	0.000
111	A	119	VAL	0	0.037	0.025	29.854	0.226	0.226	0.000	0.000	0.000	0.000
112	A	120	SER	0	-0.056	-0.040	24.801	0.356	0.356	0.000	0.000	0.000	0.000
113	A	121	VAL	0	0.058	0.035	26.479	-0.193	-0.193	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.015	-0.023	21.530	0.699	0.699	0.000	0.000	0.000	0.000
115	A	123	ILE	0	-0.001	0.016	23.203	-0.348	-0.348	0.000	0.000	0.000	0.000
116	A	124	SER	0	-0.021	-0.035	21.003	0.685	0.685	0.000	0.000	0.000	0.000
117	A	125	GLY	0	0.069	0.041	20.907	-0.692	-0.692	0.000	0.000	0.000	0.000
118	A	126	GLY	0	-0.023	-0.005	19.883	0.778	0.778	0.000	0.000	0.000	0.000
119	A	127	SER	0	0.077	0.018	17.583	-0.616	-0.616	0.000	0.000	0.000	0.000
120	A	128	ARG	1	0.956	0.992	19.692	-12.286	-12.286	0.000	0.000	0.000	0.000
121	A	129	THR	0	-0.044	-0.024	23.157	-0.484	-0.484	0.000	0.000	0.000	0.000
122	A	130	LEU	0	0.055	0.023	19.618	-0.255	-0.255	0.000	0.000	0.000	0.000
123	A	131	GLN	0	0.028	0.022	22.818	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	132	HIS	0	0.027	0.005	26.068	-0.294	-0.294	0.000	0.000	0.000	0.000
125	A	133	LEU	0	-0.052	-0.012	21.166	-0.130	-0.130	0.000	0.000	0.000	0.000
126	A	134	CYS	0	-0.007	-0.013	23.321	0.138	0.138	0.000	0.000	0.000	0.000
127	A	135	GLU	-1	-0.873	-0.927	25.537	10.318	10.318	0.000	0.000	0.000	0.000
128	A	136	MET	0	0.012	-0.003	27.638	-0.353	-0.353	0.000	0.000	0.000	0.000
129	A	137	ALA	0	-0.015	0.001	24.590	-0.203	-0.203	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.002	0.006	26.632	-0.109	-0.109	0.000	0.000	0.000	0.000
131	A	139	ARG	1	0.972	0.984	28.731	-9.248	-9.248	0.000	0.000	0.000	0.000
132	A	140	SER	0	0.029	0.005	28.354	-0.213	-0.213	0.000	0.000	0.000	0.000
133	A	141	LYS	1	0.792	0.921	25.168	-12.510	-12.510	0.000	0.000	0.000	0.000
134	A	142	GLN	0	0.002	-0.009	29.263	-0.321	-0.321	0.000	0.000	0.000	0.000
135	A	143	GLU	-1	-0.931	-0.960	32.825	8.788	8.788	0.000	0.000	0.000	0.000
136	A	144	LEU	0	-0.036	-0.019	28.575	-0.174	-0.174	0.000	0.000	0.000	0.000
137	A	145	LEU	0	-0.082	-0.049	29.333	-0.091	-0.091	0.000	0.000	0.000	0.000
138	A	146	GLN	0	-0.013	0.000	33.177	-0.314	-0.314	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.017	0.013	34.770	-0.255	-0.255	0.000	0.000	0.000	0.000
140	A	148	THR	0	0.034	0.025	37.873	0.039	0.039	0.000	0.000	0.000	0.000
141	A	149	PRO	0	0.033	0.046	40.133	0.140	0.140	0.000	0.000	0.000	0.000
142	A	150	VAL	0	-0.019	-0.027	37.298	-0.060	-0.060	0.000	0.000	0.000	0.000
143	A	151	GLU	-1	-0.883	-0.948	40.463	7.573	7.573	0.000	0.000	0.000	0.000
144	A	152	VAL	0	-0.035	-0.001	43.806	-0.191	-0.191	0.000	0.000	0.000	0.000

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