FMO DATABASE

FMODB ID: Q1QMY

Calculation Name: 3V33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V33

Chain ID: A

ChEMBL ID:

UniProt ID: Q5D1E8

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:

Apendix: None

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1738571.160616
FMO2-HF: Nuclear repulsion	1672183.264284
FMO2-HF: Total energy	-66387.896332
FMO2-MP2: Total energy	-66582.818753

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:134:ASP)

Summations of interaction energy for fragment #1(A:134: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.
-184.087	-192.911	37.69	-16.132	-12.735	0.173

Interaction energy analysis for fragmet #1(A:134:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.827 / q_NPA : -0.877

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	136	ARG	1	0.821	0.918	3.816	-33.355	-31.669	-0.013	-0.817	-0.856	0.004
4	A	137	PRO	0	0.036	0.025	6.440	0.270	0.270	0.000	0.000	0.000	0.000
5	A	138	VAL	0	-0.031	0.000	8.190	-1.471	-1.471	0.000	0.000	0.000	0.000
6	A	139	VAL	0	0.005	0.002	11.352	-1.020	-1.020	0.000	0.000	0.000	0.000
7	A	140	ILE	0	-0.002	-0.010	14.781	-0.354	-0.354	0.000	0.000	0.000	0.000
8	A	141	ASP	-1	-0.767	-0.859	17.755	12.153	12.153	0.000	0.000	0.000	0.000
9	A	142	GLY	0	0.047	0.004	21.374	-0.175	-0.175	0.000	0.000	0.000	0.000
10	A	143	SER	0	-0.006	-0.016	22.878	-0.419	-0.419	0.000	0.000	0.000	0.000
11	A	144	ASN	0	0.007	0.031	24.052	-0.056	-0.056	0.000	0.000	0.000	0.000
12	A	145	VAL	0	0.027	0.009	20.977	-0.255	-0.255	0.000	0.000	0.000	0.000
13	A	146	ALA	0	-0.017	-0.020	24.446	-0.223	-0.223	0.000	0.000	0.000	0.000
14	A	147	MET	0	-0.063	-0.013	27.072	-0.352	-0.352	0.000	0.000	0.000	0.000
15	A	148	SER	0	-0.002	0.023	26.722	-0.392	-0.392	0.000	0.000	0.000	0.000
16	A	149	HIS	0	-0.033	-0.005	26.620	-0.304	-0.304	0.000	0.000	0.000	0.000
17	A	150	GLY	0	0.002	0.010	28.601	-0.277	-0.277	0.000	0.000	0.000	0.000
18	A	151	ASN	0	-0.043	-0.061	31.950	0.071	0.071	0.000	0.000	0.000	0.000
19	A	152	LYS	1	0.965	0.989	30.597	-10.241	-10.241	0.000	0.000	0.000	0.000
20	A	153	GLU	-1	-0.899	-0.916	34.286	8.069	8.069	0.000	0.000	0.000	0.000
21	A	154	VAL	0	-0.065	-0.045	34.018	-0.170	-0.170	0.000	0.000	0.000	0.000
22	A	155	PHE	0	0.034	0.005	27.251	0.293	0.293	0.000	0.000	0.000	0.000
23	A	156	SER	0	-0.007	-0.014	29.815	-0.237	-0.237	0.000	0.000	0.000	0.000
24	A	157	CYS	0	-0.010	-0.009	27.256	0.425	0.425	0.000	0.000	0.000	0.000
25	A	158	ARG	1	0.847	0.888	25.741	-10.410	-10.410	0.000	0.000	0.000	0.000
26	A	159	GLY	0	0.038	0.031	24.630	0.479	0.479	0.000	0.000	0.000	0.000
27	A	160	ILE	0	0.007	-0.003	21.194	0.635	0.635	0.000	0.000	0.000	0.000
28	A	161	LEU	0	-0.009	0.000	20.681	0.701	0.701	0.000	0.000	0.000	0.000
29	A	162	LEU	0	-0.033	-0.010	20.144	0.717	0.717	0.000	0.000	0.000	0.000
30	A	163	ALA	0	0.000	0.007	18.953	0.646	0.646	0.000	0.000	0.000	0.000
31	A	164	VAL	0	-0.013	-0.014	15.965	1.141	1.141	0.000	0.000	0.000	0.000
32	A	165	ASN	0	-0.006	-0.026	15.314	1.345	1.345	0.000	0.000	0.000	0.000
33	A	166	TRP	0	0.042	0.037	12.928	1.248	1.248	0.000	0.000	0.000	0.000
34	A	167	PHE	0	0.015	-0.015	11.352	1.035	1.035	0.000	0.000	0.000	0.000
35	A	168	LEU	0	-0.036	-0.007	10.940	2.046	2.046	0.000	0.000	0.000	0.000
36	A	169	GLU	-1	-0.962	-0.977	11.840	18.579	18.579	0.000	0.000	0.000	0.000
37	A	170	ARG	1	0.789	0.890	8.957	-28.061	-28.061	0.000	0.000	0.000	0.000
38	A	171	GLY	0	-0.009	0.001	7.772	4.084	4.084	0.000	0.000	0.000	0.000
39	A	172	HIS	0	-0.015	-0.004	6.827	2.526	2.526	0.000	0.000	0.000	0.000
40	A	173	THR	0	-0.044	-0.037	6.964	-2.080	-2.080	0.000	0.000	0.000	0.000
41	A	174	ASP	-1	-0.944	-0.957	6.962	24.871	24.871	0.000	0.000	0.000	0.000
42	A	175	ILE	0	0.012	0.000	8.695	0.474	0.474	0.000	0.000	0.000	0.000
43	A	176	THR	0	0.004	0.010	12.022	-1.327	-1.327	0.000	0.000	0.000	0.000
44	A	177	VAL	0	-0.024	-0.005	15.081	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	178	PHE	0	0.028	0.018	18.213	-0.476	-0.476	0.000	0.000	0.000	0.000
46	A	179	VAL	0	0.015	0.001	21.299	-0.189	-0.189	0.000	0.000	0.000	0.000
47	A	180	PRO	0	0.062	0.052	24.908	-0.132	-0.132	0.000	0.000	0.000	0.000
48	A	181	SER	0	-0.026	-0.034	28.056	-0.238	-0.238	0.000	0.000	0.000	0.000
49	A	182	TRP	0	-0.010	-0.012	29.571	-0.201	-0.201	0.000	0.000	0.000	0.000
50	A	183	ARG	1	0.945	0.993	29.370	-9.825	-9.825	0.000	0.000	0.000	0.000
51	A	184	LYS	1	0.772	0.899	27.427	-10.583	-10.583	0.000	0.000	0.000	0.000
52	A	185	GLU	-1	-0.858	-0.900	32.037	7.968	7.968	0.000	0.000	0.000	0.000
53	A	186	GLN	0	0.046	0.022	35.724	0.172	0.172	0.000	0.000	0.000	0.000
54	A	187	PRO	0	-0.016	0.006	36.707	-0.092	-0.092	0.000	0.000	0.000	0.000
55	A	188	ARG	1	0.864	0.913	38.404	-7.360	-7.360	0.000	0.000	0.000	0.000
56	A	189	PRO	0	0.034	0.001	40.387	0.153	0.153	0.000	0.000	0.000	0.000
57	A	190	ASP	-1	-0.830	-0.895	40.880	7.549	7.549	0.000	0.000	0.000	0.000
58	A	191	VAL	0	-0.095	-0.047	36.194	0.198	0.198	0.000	0.000	0.000	0.000
59	A	192	PRO	0	0.019	0.031	36.826	0.112	0.112	0.000	0.000	0.000	0.000
60	A	193	ILE	0	-0.024	-0.026	30.856	0.247	0.247	0.000	0.000	0.000	0.000
61	A	194	THR	0	0.021	0.009	32.293	-0.259	-0.259	0.000	0.000	0.000	0.000
62	A	195	ASP	-1	-0.842	-0.945	30.064	10.244	10.244	0.000	0.000	0.000	0.000
63	A	196	GLN	0	-0.007	-0.026	29.864	0.171	0.171	0.000	0.000	0.000	0.000
64	A	197	HIS	0	-0.018	-0.008	29.417	0.011	0.011	0.000	0.000	0.000	0.000
65	A	198	ILE	0	0.034	0.015	24.724	0.219	0.219	0.000	0.000	0.000	0.000
66	A	199	LEU	0	0.012	0.011	24.983	0.458	0.458	0.000	0.000	0.000	0.000
67	A	200	ARG	1	0.985	0.981	24.700	-9.232	-9.232	0.000	0.000	0.000	0.000
68	A	201	GLU	-1	-0.896	-0.923	24.454	12.355	12.355	0.000	0.000	0.000	0.000
69	A	202	LEU	0	0.039	0.002	19.587	0.386	0.386	0.000	0.000	0.000	0.000
70	A	203	GLU	-1	-0.782	-0.875	20.352	11.588	11.588	0.000	0.000	0.000	0.000
71	A	204	LYS	1	0.918	0.963	21.403	-11.160	-11.160	0.000	0.000	0.000	0.000
72	A	205	LYS	1	0.817	0.894	18.577	-13.489	-13.489	0.000	0.000	0.000	0.000
73	A	206	LYS	1	0.893	0.946	16.507	-14.193	-14.193	0.000	0.000	0.000	0.000
74	A	207	ILE	0	0.050	0.044	15.235	0.567	0.567	0.000	0.000	0.000	0.000
75	A	208	LEU	0	-0.043	-0.006	16.990	0.218	0.218	0.000	0.000	0.000	0.000
76	A	209	VAL	0	0.013	-0.005	18.536	-0.412	-0.412	0.000	0.000	0.000	0.000
77	A	210	PHE	0	-0.007	-0.031	21.339	-0.201	-0.201	0.000	0.000	0.000	0.000
78	A	211	THR	0	0.008	0.012	23.688	-0.158	-0.158	0.000	0.000	0.000	0.000
79	A	212	PRO	0	0.026	0.008	25.907	-0.383	-0.383	0.000	0.000	0.000	0.000
80	A	213	SER	0	-0.022	-0.016	29.353	-0.068	-0.068	0.000	0.000	0.000	0.000
81	A	214	ARG	1	0.972	0.994	32.680	-7.964	-7.964	0.000	0.000	0.000	0.000
82	A	215	ARG	1	0.872	0.928	36.126	-7.647	-7.647	0.000	0.000	0.000	0.000
83	A	216	VAL	0	0.006	0.000	39.416	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	217	GLY	0	0.064	0.033	42.091	-0.046	-0.046	0.000	0.000	0.000	0.000
85	A	218	GLY	0	-0.006	-0.004	44.379	-0.082	-0.082	0.000	0.000	0.000	0.000
86	A	219	LYS	1	0.943	0.973	42.593	-6.637	-6.637	0.000	0.000	0.000	0.000
87	A	220	ARG	1	0.882	0.936	35.563	-8.262	-8.262	0.000	0.000	0.000	0.000
88	A	221	VAL	0	0.017	0.010	36.121	-0.054	-0.054	0.000	0.000	0.000	0.000
89	A	222	VAL	0	-0.010	-0.029	31.769	0.093	0.093	0.000	0.000	0.000	0.000
90	A	223	CYS	0	-0.035	-0.002	29.406	-0.153	-0.153	0.000	0.000	0.000	0.000
91	A	224	TYR	0	0.002	-0.008	28.592	0.067	0.067	0.000	0.000	0.000	0.000
92	A	225	ASP	-1	-0.769	-0.896	25.461	11.976	11.976	0.000	0.000	0.000	0.000
93	A	226	ASP	-1	-0.806	-0.907	23.945	11.600	11.600	0.000	0.000	0.000	0.000
94	A	227	ARG	1	0.824	0.876	23.068	-10.131	-10.131	0.000	0.000	0.000	0.000
95	A	228	PHE	0	-0.049	-0.026	21.592	0.260	0.260	0.000	0.000	0.000	0.000
96	A	229	ILE	0	0.005	0.011	18.967	0.692	0.692	0.000	0.000	0.000	0.000
97	A	230	VAL	0	0.051	0.018	18.173	0.874	0.874	0.000	0.000	0.000	0.000
98	A	231	LYS	1	0.878	0.962	18.373	-12.103	-12.103	0.000	0.000	0.000	0.000
99	A	232	LEU	0	0.033	0.018	14.432	0.313	0.313	0.000	0.000	0.000	0.000
100	A	233	ALA	0	0.036	0.033	13.805	1.088	1.088	0.000	0.000	0.000	0.000
101	A	234	TYR	0	0.007	-0.008	13.608	1.290	1.290	0.000	0.000	0.000	0.000
102	A	235	GLU	-1	-0.934	-0.975	14.597	15.253	15.253	0.000	0.000	0.000	0.000
103	A	236	SER	0	-0.079	-0.046	10.497	0.772	0.772	0.000	0.000	0.000	0.000
104	A	237	ASP	-1	-0.825	-0.910	9.692	28.804	28.804	0.000	0.000	0.000	0.000
105	A	238	GLY	0	0.003	-0.007	9.511	3.196	3.196	0.000	0.000	0.000	0.000
106	A	239	ILE	0	-0.064	-0.035	10.482	-0.836	-0.836	0.000	0.000	0.000	0.000
107	A	240	VAL	0	0.015	0.013	13.057	-0.390	-0.390	0.000	0.000	0.000	0.000
108	A	241	VAL	0	-0.016	-0.006	15.353	-0.216	-0.216	0.000	0.000	0.000	0.000
109	A	242	SER	0	-0.010	-0.025	17.961	-0.843	-0.843	0.000	0.000	0.000	0.000
110	A	243	ASN	0	-0.007	-0.010	21.713	0.709	0.709	0.000	0.000	0.000	0.000
111	A	244	ASP	-1	-0.861	-0.918	24.562	10.751	10.751	0.000	0.000	0.000	0.000
112	A	245	THR	0	-0.009	-0.016	24.270	0.359	0.359	0.000	0.000	0.000	0.000
113	A	246	TYR	0	-0.003	-0.037	21.684	0.313	0.313	0.000	0.000	0.000	0.000
114	A	247	ARG	1	0.973	0.979	26.682	-10.117	-10.117	0.000	0.000	0.000	0.000
115	A	248	ASP	-1	-0.885	-0.946	29.371	9.577	9.577	0.000	0.000	0.000	0.000
116	A	249	LEU	0	-0.013	-0.007	24.663	-0.076	-0.076	0.000	0.000	0.000	0.000
117	A	250	GLN	0	-0.068	-0.045	25.415	-0.099	-0.099	0.000	0.000	0.000	0.000
118	A	251	GLY	0	-0.070	-0.028	27.168	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	252	GLU	-1	-0.803	-0.840	28.180	10.144	10.144	0.000	0.000	0.000	0.000
120	A	253	ARG	1	0.871	0.956	24.614	-11.433	-11.433	0.000	0.000	0.000	0.000
121	A	254	GLN	0	0.023	-0.019	25.958	0.213	0.213	0.000	0.000	0.000	0.000
122	A	255	GLU	-1	-0.845	-0.933	21.493	12.405	12.405	0.000	0.000	0.000	0.000
123	A	256	TRP	0	-0.003	-0.004	20.943	0.444	0.444	0.000	0.000	0.000	0.000
124	A	257	LYS	1	0.914	0.978	21.985	-10.553	-10.553	0.000	0.000	0.000	0.000
125	A	258	ARG	1	0.864	0.921	21.315	-12.556	-12.556	0.000	0.000	0.000	0.000
126	A	259	PHE	0	0.040	0.026	14.040	0.204	0.204	0.000	0.000	0.000	0.000
127	A	260	ILE	0	-0.033	-0.037	18.344	0.716	0.716	0.000	0.000	0.000	0.000
128	A	261	GLU	-1	-0.883	-0.932	20.713	12.662	12.662	0.000	0.000	0.000	0.000
129	A	262	GLU	-1	-0.954	-0.971	16.934	17.098	17.098	0.000	0.000	0.000	0.000
130	A	263	ARG	1	0.768	0.875	10.895	-22.175	-22.175	0.000	0.000	0.000	0.000
131	A	264	LEU	0	-0.049	-0.004	16.024	0.598	0.598	0.000	0.000	0.000	0.000
132	A	265	LEU	0	-0.032	-0.011	14.617	0.262	0.262	0.000	0.000	0.000	0.000
133	A	266	MET	0	0.002	0.000	17.938	-0.451	-0.451	0.000	0.000	0.000	0.000
134	A	267	TYR	0	-0.031	-0.044	20.165	0.604	0.604	0.000	0.000	0.000	0.000
135	A	268	SER	0	-0.016	0.004	22.197	-0.917	-0.917	0.000	0.000	0.000	0.000
136	A	269	PHE	0	0.003	0.001	23.321	0.537	0.537	0.000	0.000	0.000	0.000
137	A	270	VAL	0	-0.040	-0.023	26.046	-0.475	-0.475	0.000	0.000	0.000	0.000
138	A	271	ASN	0	0.002	0.001	27.861	0.013	0.013	0.000	0.000	0.000	0.000
139	A	272	ASP	-1	-0.753	-0.846	26.393	11.186	11.186	0.000	0.000	0.000	0.000
140	A	273	LYS	1	0.897	0.925	22.006	-13.478	-13.478	0.000	0.000	0.000	0.000
141	A	274	PHE	0	0.023	0.013	17.061	-0.357	-0.357	0.000	0.000	0.000	0.000
142	A	275	MET	0	-0.004	0.009	20.429	0.261	0.261	0.000	0.000	0.000	0.000
143	A	276	PRO	0	0.052	0.039	16.394	-0.672	-0.672	0.000	0.000	0.000	0.000
144	A	277	PRO	0	0.010	0.015	19.197	-0.057	-0.057	0.000	0.000	0.000	0.000
145	A	278	ASP	-1	-0.850	-0.948	17.254	18.694	18.694	0.000	0.000	0.000	0.000
146	A	279	ASP	-1	-0.988	-0.999	17.426	15.663	15.663	0.000	0.000	0.000	0.000
147	A	280	PRO	0	-0.040	-0.012	15.520	-0.787	-0.787	0.000	0.000	0.000	0.000
148	A	281	LEU	0	-0.026	-0.001	17.231	-0.594	-0.594	0.000	0.000	0.000	0.000
149	A	282	GLY	0	0.025	0.025	20.599	-0.621	-0.621	0.000	0.000	0.000	0.000
150	A	283	ARG	1	0.942	0.953	21.709	-13.623	-13.623	0.000	0.000	0.000	0.000
151	A	284	HIS	0	-0.022	-0.017	22.620	0.476	0.476	0.000	0.000	0.000	0.000
152	A	285	GLY	0	0.019	0.029	19.343	0.246	0.246	0.000	0.000	0.000	0.000
153	A	286	PRO	0	-0.042	-0.017	13.853	-0.022	-0.022	0.000	0.000	0.000	0.000
154	A	287	SER	0	0.075	0.030	13.311	-0.206	-0.206	0.000	0.000	0.000	0.000
155	A	288	LEU	0	0.069	0.032	13.040	1.658	1.658	0.000	0.000	0.000	0.000
156	A	289	ASP	-1	-0.860	-0.925	9.624	28.569	28.569	0.000	0.000	0.000	0.000
157	A	290	ASN	0	-0.050	-0.041	8.605	6.840	6.840	0.000	0.000	0.000	0.000
158	A	291	PHE	0	-0.019	0.011	9.695	2.219	2.219	0.000	0.000	0.000	0.000
159	A	292	LEU	0	0.016	0.006	8.753	0.712	0.712	0.000	0.000	0.000	0.000
160	A	293	ARG	1	0.812	0.898	1.755	-120.517	-127.106	24.210	-9.994	-7.627	0.124
161	A	294	LYS	1	0.896	0.926	1.938	-81.498	-85.419	13.493	-5.321	-4.252	0.045
162	A	295	LYS	1	0.920	0.943	5.166	-39.635	-39.635	0.000	0.000	0.000	0.000
163	A	296	PRO	0	0.035	0.045	5.785	7.288	7.288	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:134:ASP)