FMO DATABASE

FMODB ID: ZY45N

Calculation Name: 3VOQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VOQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BPZ7

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	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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-998396.476454
FMO2-HF: Nuclear repulsion	949601.521759
FMO2-HF: Total energy	-48794.954695
FMO2-MP2: Total energy	-48936.41053

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:369:GLY)

Summations of interaction energy for fragment #1(A:369:GLY)

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.
-1.346	1.14	0.405	-1.096	-1.794	0.004

Interaction energy analysis for fragmet #1(A:369:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.020

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

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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	371	MET	0	0.025	0.006	3.789	-0.070	0.947	-0.001	-0.426	-0.589	0.002
4	A	372	ALA	0	0.012	0.012	2.554	-0.848	-0.081	0.404	-0.440	-0.731	0.002
5	A	373	THR	0	0.014	0.006	3.235	-0.075	0.518	0.003	-0.223	-0.373	0.000
6	A	374	VAL	0	0.026	-0.001	5.311	0.498	0.607	-0.001	-0.007	-0.101	0.000
7	A	375	GLN	0	-0.038	-0.016	7.497	0.120	0.120	0.000	0.000	0.000	0.000
8	A	376	ASP	-1	-0.882	-0.959	7.577	-0.586	-0.586	0.000	0.000	0.000	0.000
9	A	377	MET	0	0.000	0.009	9.418	0.082	0.082	0.000	0.000	0.000	0.000
10	A	378	LEU	0	-0.042	-0.007	11.519	0.102	0.102	0.000	0.000	0.000	0.000
11	A	379	SER	0	-0.039	-0.016	12.601	0.066	0.066	0.000	0.000	0.000	0.000
12	A	380	SER	0	0.006	0.005	13.773	0.038	0.038	0.000	0.000	0.000	0.000
13	A	381	HIS	0	0.043	0.046	15.048	0.035	0.035	0.000	0.000	0.000	0.000
14	A	382	HIS	0	0.017	0.030	16.776	0.013	0.013	0.000	0.000	0.000	0.000
15	A	383	TYR	0	0.023	0.000	18.779	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	384	LYS	1	0.803	0.890	13.814	0.197	0.197	0.000	0.000	0.000	0.000
17	A	385	SER	0	-0.057	-0.017	19.452	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	386	PHE	0	0.048	0.026	15.610	0.009	0.009	0.000	0.000	0.000	0.000
19	A	387	LYS	1	0.821	0.899	21.009	0.058	0.058	0.000	0.000	0.000	0.000
20	A	388	VAL	0	0.054	0.034	21.582	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	389	SER	0	0.000	0.006	24.281	0.011	0.011	0.000	0.000	0.000	0.000
22	A	390	MET	0	0.027	0.033	26.896	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	391	ILE	0	0.064	0.022	27.991	0.010	0.010	0.000	0.000	0.000	0.000
24	A	392	HIS	1	0.792	0.883	31.195	0.067	0.067	0.000	0.000	0.000	0.000
25	A	393	ARG	1	0.945	0.944	34.896	0.060	0.060	0.000	0.000	0.000	0.000
26	A	394	LEU	0	0.037	0.017	32.449	0.004	0.004	0.000	0.000	0.000	0.000
27	A	395	ARG	1	0.915	0.971	34.753	0.060	0.060	0.000	0.000	0.000	0.000
28	A	396	PHE	0	0.034	0.028	34.908	0.002	0.002	0.000	0.000	0.000	0.000
29	A	397	THR	0	0.048	0.029	29.635	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	398	THR	0	-0.053	-0.021	31.881	0.006	0.006	0.000	0.000	0.000	0.000
31	A	399	ASP	-1	-0.874	-0.924	29.310	-0.066	-0.066	0.000	0.000	0.000	0.000
32	A	400	VAL	0	-0.057	-0.037	26.836	0.006	0.006	0.000	0.000	0.000	0.000
33	A	401	GLN	0	0.019	0.022	25.157	0.003	0.003	0.000	0.000	0.000	0.000
34	A	402	LEU	0	0.011	0.014	22.080	0.005	0.005	0.000	0.000	0.000	0.000
35	A	403	GLY	0	0.015	-0.005	22.791	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	404	ILE	0	0.002	0.002	19.571	0.000	0.000	0.000	0.000	0.000	0.000
37	A	405	SER	0	-0.015	-0.032	20.751	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	406	GLY	0	0.035	0.002	21.606	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	407	ASP	-1	-0.887	-0.883	22.635	-0.088	-0.088	0.000	0.000	0.000	0.000
40	A	408	LYS	1	0.862	0.919	25.318	0.075	0.075	0.000	0.000	0.000	0.000
41	A	409	VAL	0	0.010	0.020	23.636	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	410	GLU	-1	-0.864	-0.910	26.078	-0.059	-0.059	0.000	0.000	0.000	0.000
43	A	411	ILE	0	0.009	0.000	26.931	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	412	ASP	-1	-0.869	-0.930	29.208	-0.050	-0.050	0.000	0.000	0.000	0.000
45	A	413	PRO	0	-0.080	-0.036	30.318	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	414	VAL	0	0.041	0.012	29.511	0.004	0.004	0.000	0.000	0.000	0.000
47	A	415	THR	0	-0.046	-0.034	31.991	0.001	0.001	0.000	0.000	0.000	0.000
48	A	416	ASN	0	0.060	0.039	33.868	0.004	0.004	0.000	0.000	0.000	0.000
49	A	417	GLN	0	0.073	0.039	35.940	0.001	0.001	0.000	0.000	0.000	0.000
50	A	418	LYS	1	0.831	0.902	38.244	0.029	0.029	0.000	0.000	0.000	0.000
51	A	419	ALA	0	0.028	0.018	41.481	0.002	0.002	0.000	0.000	0.000	0.000
52	A	420	SER	0	0.012	0.005	44.482	0.002	0.002	0.000	0.000	0.000	0.000
53	A	421	THR	0	0.005	-0.003	44.136	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	422	LYS	1	0.961	0.999	46.596	0.022	0.022	0.000	0.000	0.000	0.000
55	A	423	PHE	0	-0.024	-0.027	49.045	0.000	0.000	0.000	0.000	0.000	0.000
56	A	424	TRP	0	0.077	0.046	38.717	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	425	ILE	0	0.026	0.004	41.439	0.000	0.000	0.000	0.000	0.000	0.000
58	A	426	LYS	1	0.997	1.009	40.164	0.036	0.036	0.000	0.000	0.000	0.000
59	A	427	GLN	0	-0.042	-0.020	35.941	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	428	LYS	1	0.851	0.909	37.584	0.050	0.050	0.000	0.000	0.000	0.000
61	A	429	PRO	0	0.065	0.036	33.935	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	430	ILE	0	-0.036	-0.005	31.605	0.002	0.002	0.000	0.000	0.000	0.000
63	A	431	SER	0	-0.042	-0.042	30.996	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	432	ILE	0	-0.046	-0.021	28.564	0.004	0.004	0.000	0.000	0.000	0.000
65	A	433	ASP	-1	-0.839	-0.913	28.829	-0.098	-0.098	0.000	0.000	0.000	0.000
66	A	434	SER	0	0.022	-0.020	24.975	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	435	ASP	-1	-0.829	-0.917	26.986	-0.131	-0.131	0.000	0.000	0.000	0.000
68	A	436	LEU	0	-0.092	-0.038	29.136	0.003	0.003	0.000	0.000	0.000	0.000
69	A	437	LEU	0	-0.032	-0.008	24.066	0.002	0.002	0.000	0.000	0.000	0.000
70	A	438	CYS	0	-0.087	-0.034	27.671	0.003	0.003	0.000	0.000	0.000	0.000
71	A	439	ALA	0	0.057	0.025	24.480	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	440	CYS	0	0.015	0.014	20.630	0.015	0.015	0.000	0.000	0.000	0.000
73	A	441	ASP	-1	-0.833	-0.892	21.093	-0.215	-0.215	0.000	0.000	0.000	0.000
74	A	442	LEU	0	0.021	0.008	18.060	0.018	0.018	0.000	0.000	0.000	0.000
75	A	443	ALA	0	-0.088	-0.062	21.160	0.010	0.010	0.000	0.000	0.000	0.000
76	A	444	GLU	-1	-0.931	-0.974	23.800	-0.113	-0.113	0.000	0.000	0.000	0.000
77	A	445	GLU	-1	-0.893	-0.956	17.362	-0.293	-0.293	0.000	0.000	0.000	0.000
78	A	446	LYS	1	0.875	0.956	21.913	0.106	0.106	0.000	0.000	0.000	0.000
79	A	447	SER	0	-0.008	-0.016	22.430	0.006	0.006	0.000	0.000	0.000	0.000
80	A	448	PRO	0	0.071	0.016	17.762	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	449	SER	0	-0.051	-0.026	19.139	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	450	HIS	0	0.022	0.031	21.836	0.006	0.006	0.000	0.000	0.000	0.000
83	A	451	ALA	0	0.033	0.028	19.955	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	452	ILE	0	0.041	0.007	21.980	0.010	0.010	0.000	0.000	0.000	0.000
85	A	453	PHE	0	0.051	0.037	21.000	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	454	LYS	1	0.828	0.908	23.137	0.169	0.169	0.000	0.000	0.000	0.000
87	A	455	LEU	0	0.030	0.019	23.525	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	456	THR	0	-0.027	-0.032	26.031	0.012	0.012	0.000	0.000	0.000	0.000
89	A	457	TYR	0	0.034	0.010	27.972	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	458	LEU	0	0.008	0.013	30.455	0.006	0.006	0.000	0.000	0.000	0.000
91	A	459	SER	0	-0.009	-0.017	33.861	0.003	0.003	0.000	0.000	0.000	0.000
92	A	460	ASN	0	-0.046	-0.035	36.332	0.003	0.003	0.000	0.000	0.000	0.000
93	A	461	HIS	0	0.044	0.023	38.729	0.000	0.000	0.000	0.000	0.000	0.000
94	A	462	ASP	-1	-0.818	-0.890	38.484	-0.066	-0.066	0.000	0.000	0.000	0.000
95	A	463	TYR	0	-0.029	-0.022	32.906	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	464	LYS	1	0.782	0.895	33.603	0.077	0.077	0.000	0.000	0.000	0.000
97	A	465	HIS	0	0.055	0.027	30.598	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	466	LEU	0	-0.055	-0.022	28.534	0.010	0.010	0.000	0.000	0.000	0.000
99	A	467	TYR	0	0.025	0.011	27.374	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	468	PHE	0	-0.009	-0.008	24.134	0.015	0.015	0.000	0.000	0.000	0.000
101	A	469	GLU	-1	-0.918	-0.962	23.753	-0.109	-0.109	0.000	0.000	0.000	0.000
102	A	470	SER	0	0.002	-0.008	20.138	0.017	0.017	0.000	0.000	0.000	0.000
103	A	471	ASP	-1	-0.780	-0.853	16.985	-0.182	-0.182	0.000	0.000	0.000	0.000
104	A	472	ALA	0	0.051	0.004	16.791	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	473	ALA	0	-0.024	0.005	12.864	-0.046	-0.046	0.000	0.000	0.000	0.000
106	A	474	THR	0	-0.044	-0.052	13.650	-0.050	-0.050	0.000	0.000	0.000	0.000
107	A	475	VAL	0	-0.041	-0.012	16.150	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	476	ASN	0	-0.062	-0.055	12.879	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	477	GLU	-1	-0.769	-0.849	11.258	-0.316	-0.316	0.000	0.000	0.000	0.000
110	A	478	ILE	0	-0.029	-0.013	13.170	0.003	0.003	0.000	0.000	0.000	0.000
111	A	479	VAL	0	0.000	-0.014	16.593	0.011	0.011	0.000	0.000	0.000	0.000
112	A	480	LEU	0	-0.013	0.005	9.721	0.006	0.006	0.000	0.000	0.000	0.000
113	A	481	LYS	1	0.852	0.921	14.238	0.238	0.238	0.000	0.000	0.000	0.000
114	A	482	VAL	0	-0.002	-0.021	15.376	0.028	0.028	0.000	0.000	0.000	0.000
115	A	483	ASN	0	-0.069	-0.053	17.061	0.044	0.044	0.000	0.000	0.000	0.000
116	A	484	TYR	0	0.028	0.017	9.470	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	485	ILE	0	-0.049	-0.030	16.650	0.028	0.028	0.000	0.000	0.000	0.000
118	A	486	LEU	0	-0.090	-0.049	19.828	0.021	0.021	0.000	0.000	0.000	0.000
119	A	487	GLU	-1	-0.971	-0.985	16.600	-0.395	-0.395	0.000	0.000	0.000	0.000
120	A	488	SER	0	-0.058	-0.036	19.593	0.014	0.014	0.000	0.000	0.000	0.000
121	A	489	ARG	1	0.831	0.918	21.150	0.170	0.170	0.000	0.000	0.000	0.000
122	A	490	ALA	0	-0.032	-0.013	24.119	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:369:GLY)