FMO DATABASE

FMODB ID: R8YG8

Calculation Name: 5VAP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VAP

Chain ID: A

ChEMBL ID:

UniProt ID: O72142

Base Structure: X-ray

Registration Date: 2023-09-22

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-938852.740915
FMO2-HF: Nuclear repulsion	893768.880651
FMO2-HF: Total energy	-45083.860265
FMO2-MP2: Total energy	-45214.504092

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:142:ILE)

Summations of interaction energy for fragment #1(A:142:ILE)

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.
-3.894	1.095	3.781	-2.916	-5.852	-0.004

Interaction energy analysis for fragmet #1(A:142:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.034

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	144	LEU	0	0.065	0.015	3.875	-1.076	0.396	0.001	-0.741	-0.732	0.003
4	A	145	LEU	0	0.049	0.030	6.408	0.275	0.275	0.000	0.000	0.000	0.000
5	A	146	THR	0	0.011	-0.008	2.228	-2.973	-0.779	1.543	-1.556	-2.181	-0.011
6	A	147	LEU	0	-0.010	0.009	2.380	-0.265	0.658	1.205	-0.355	-1.772	0.002
7	A	148	ILE	0	0.063	0.033	5.252	0.205	0.277	-0.001	-0.003	-0.069	0.000
8	A	149	LYS	1	0.835	0.903	7.937	0.237	0.237	0.000	0.000	0.000	0.000
9	A	150	THR	0	-0.026	-0.024	6.228	0.243	0.243	0.000	0.000	0.000	0.000
10	A	151	ALA	0	0.027	-0.001	8.754	0.018	0.018	0.000	0.000	0.000	0.000
11	A	152	GLU	-1	-0.807	-0.897	10.792	-0.079	-0.079	0.000	0.000	0.000	0.000
12	A	153	HIS	0	-0.084	-0.033	12.004	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	154	TRP	0	0.001	-0.023	11.104	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	155	ALA	0	0.016	0.022	14.296	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	156	ARG	1	0.892	0.962	15.737	-0.136	-0.136	0.000	0.000	0.000	0.000
16	A	157	GLN	0	-0.035	-0.011	16.530	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	158	ASP	-1	-0.839	-0.917	19.441	0.120	0.120	0.000	0.000	0.000	0.000
18	A	159	ILE	0	-0.040	-0.026	16.294	0.020	0.020	0.000	0.000	0.000	0.000
19	A	160	ARG	1	0.913	0.932	19.577	-0.096	-0.096	0.000	0.000	0.000	0.000
20	A	161	THR	0	0.018	0.006	22.566	0.003	0.003	0.000	0.000	0.000	0.000
21	A	162	ILE	0	-0.032	0.012	15.695	0.008	0.008	0.000	0.000	0.000	0.000
22	A	163	GLU	-1	-0.732	-0.826	17.622	0.352	0.352	0.000	0.000	0.000	0.000
23	A	164	ASP	-1	-0.795	-0.899	16.931	0.235	0.235	0.000	0.000	0.000	0.000
24	A	165	SER	0	-0.053	-0.052	14.549	0.031	0.031	0.000	0.000	0.000	0.000
25	A	166	LYS	1	0.855	0.913	12.414	-0.384	-0.384	0.000	0.000	0.000	0.000
26	A	167	LEU	0	0.048	0.035	12.354	0.036	0.036	0.000	0.000	0.000	0.000
27	A	168	ARG	1	0.834	0.905	10.187	-0.272	-0.272	0.000	0.000	0.000	0.000
28	A	169	ALA	0	-0.004	0.001	8.439	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	170	LEU	0	0.007	0.000	8.270	0.046	0.046	0.000	0.000	0.000	0.000
30	A	171	LEU	0	0.041	0.039	10.523	-0.058	-0.058	0.000	0.000	0.000	0.000
31	A	172	THR	0	-0.020	-0.023	5.064	-0.039	-0.039	0.000	0.000	0.000	0.000
32	A	173	LEU	0	-0.068	-0.022	5.998	-0.062	-0.062	0.000	0.000	0.000	0.000
33	A	174	CYS	0	0.002	-0.001	7.032	-0.139	-0.139	0.000	0.000	0.000	0.000
34	A	175	ALA	0	0.013	0.028	8.109	-0.072	-0.072	0.000	0.000	0.000	0.000
35	A	176	VAL	0	-0.064	-0.046	2.328	-0.577	-0.325	1.034	-0.256	-1.029	0.002
36	A	177	MET	0	-0.022	-0.014	5.576	-0.098	-0.098	0.000	0.000	0.000	0.000
37	A	178	THR	0	0.036	0.019	7.952	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	179	ARG	1	0.788	0.897	6.340	0.046	0.046	0.000	0.000	0.000	0.000
39	A	180	LYS	1	0.838	0.931	4.484	0.597	0.673	-0.001	-0.005	-0.069	0.000
40	A	181	PHE	0	0.019	0.035	9.941	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	182	SER	0	0.044	0.027	13.678	0.001	0.001	0.000	0.000	0.000	0.000
42	A	183	LYS	1	0.968	0.956	16.510	0.115	0.115	0.000	0.000	0.000	0.000
43	A	184	SER	0	-0.020	-0.006	18.514	0.009	0.009	0.000	0.000	0.000	0.000
44	A	185	GLN	0	-0.006	0.009	17.604	0.017	0.017	0.000	0.000	0.000	0.000
45	A	186	LEU	0	-0.011	-0.003	15.039	0.010	0.010	0.000	0.000	0.000	0.000
46	A	187	SER	0	0.051	0.026	18.822	0.012	0.012	0.000	0.000	0.000	0.000
47	A	188	LEU	0	-0.002	0.006	21.186	0.008	0.008	0.000	0.000	0.000	0.000
48	A	189	LEU	0	-0.018	0.005	15.071	0.007	0.007	0.000	0.000	0.000	0.000
49	A	190	CYS	0	-0.019	0.004	19.525	0.013	0.013	0.000	0.000	0.000	0.000
50	A	191	GLU	-1	-0.758	-0.886	21.679	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	192	THR	0	-0.080	-0.062	21.341	0.003	0.003	0.000	0.000	0.000	0.000
52	A	193	HIS	0	0.022	0.044	18.839	0.000	0.000	0.000	0.000	0.000	0.000
53	A	194	LEU	0	-0.034	-0.015	22.090	0.008	0.008	0.000	0.000	0.000	0.000
54	A	195	ARG	1	0.902	0.951	24.761	0.030	0.030	0.000	0.000	0.000	0.000
55	A	196	ARG	1	0.768	0.879	21.643	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	197	GLU	-1	-0.850	-0.923	22.837	0.046	0.046	0.000	0.000	0.000	0.000
57	A	198	GLY	0	-0.012	0.004	25.933	0.003	0.003	0.000	0.000	0.000	0.000
58	A	199	LEU	0	-0.056	-0.019	24.977	0.001	0.001	0.000	0.000	0.000	0.000
59	A	200	GLY	0	0.052	0.026	29.026	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	201	GLN	0	-0.046	-0.055	29.293	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	202	ASP	-1	-0.865	-0.915	30.377	0.008	0.008	0.000	0.000	0.000	0.000
62	A	203	GLN	0	-0.047	-0.038	26.728	0.004	0.004	0.000	0.000	0.000	0.000
63	A	204	ALA	0	0.021	0.001	25.835	0.001	0.001	0.000	0.000	0.000	0.000
64	A	205	GLU	-1	-0.924	-0.957	24.879	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	206	PRO	0	0.036	0.021	24.061	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	207	VAL	0	0.001	-0.001	20.794	0.002	0.002	0.000	0.000	0.000	0.000
67	A	208	LEU	0	0.002	-0.013	20.045	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	209	GLU	-1	-0.872	-0.918	20.018	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	210	VAL	0	-0.006	-0.005	16.540	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	211	TYR	0	0.021	-0.030	14.695	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	212	GLN	0	-0.020	-0.014	15.368	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	213	ARG	1	0.869	0.934	16.620	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	214	LEU	0	0.014	0.008	11.533	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	215	HIS	0	-0.053	-0.031	11.575	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	216	SER	0	-0.083	-0.047	12.691	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	217	ASP	-1	-0.790	-0.876	11.421	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	218	LYS	1	0.827	0.885	12.059	0.101	0.101	0.000	0.000	0.000	0.000
78	A	219	GLY	0	0.015	0.007	11.781	0.018	0.018	0.000	0.000	0.000	0.000
79	A	220	GLY	0	0.004	0.019	10.916	0.026	0.026	0.000	0.000	0.000	0.000
80	A	221	SER	0	-0.002	0.014	11.384	0.027	0.027	0.000	0.000	0.000	0.000
81	A	222	PHE	0	0.040	-0.005	14.703	0.012	0.012	0.000	0.000	0.000	0.000
82	A	223	GLU	-1	-0.744	-0.863	8.604	0.183	0.183	0.000	0.000	0.000	0.000
83	A	224	ALA	0	-0.045	-0.028	13.084	0.026	0.026	0.000	0.000	0.000	0.000
84	A	225	ALA	0	0.007	0.007	15.243	0.007	0.007	0.000	0.000	0.000	0.000
85	A	226	LEU	0	0.022	0.006	15.020	0.002	0.002	0.000	0.000	0.000	0.000
86	A	227	TRP	0	-0.012	-0.019	15.458	0.015	0.015	0.000	0.000	0.000	0.000
87	A	228	GLN	0	-0.038	-0.003	17.522	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	229	GLN	0	-0.049	-0.029	20.646	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	230	TRP	0	-0.011	0.007	19.380	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	231	ASP	-1	-0.782	-0.855	22.233	0.092	0.092	0.000	0.000	0.000	0.000
91	A	232	ARG	1	0.837	0.866	20.168	-0.182	-0.182	0.000	0.000	0.000	0.000
92	A	233	GLN	0	0.005	0.004	21.375	0.010	0.010	0.000	0.000	0.000	0.000
93	A	234	SER	0	0.003	-0.034	22.612	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	235	LEU	0	-0.012	-0.007	16.644	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	236	ILE	0	-0.016	-0.002	17.940	0.005	0.005	0.000	0.000	0.000	0.000
96	A	237	MET	0	0.007	0.041	19.411	0.004	0.004	0.000	0.000	0.000	0.000
97	A	238	PHE	0	0.024	0.015	16.008	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	239	ILE	0	0.018	-0.007	13.700	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	240	THR	0	-0.039	-0.036	15.734	0.001	0.001	0.000	0.000	0.000	0.000
100	A	241	ALA	0	0.011	0.018	18.203	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	242	PHE	0	0.033	0.008	10.718	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	243	LEU	0	-0.007	-0.015	11.252	-0.021	-0.021	0.000	0.000	0.000	0.000
103	A	244	ASN	0	-0.080	-0.037	14.589	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	245	ILE	0	-0.007	0.001	16.958	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	246	ALA	0	-0.016	-0.003	12.376	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	247	LEU	0	-0.036	-0.026	11.314	-0.040	-0.040	0.000	0.000	0.000	0.000
107	A	248	GLN	0	-0.060	-0.029	14.749	0.002	0.002	0.000	0.000	0.000	0.000
108	A	249	LEU	0	0.011	0.020	17.187	0.007	0.007	0.000	0.000	0.000	0.000
109	A	250	PRO	0	0.003	-0.005	17.044	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	251	CYS	0	0.036	0.026	13.886	0.008	0.008	0.000	0.000	0.000	0.000
111	A	252	GLU	-1	-0.948	-0.971	15.823	-0.224	-0.224	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:142:ILE)