FMO DATABASE

FMODB ID: 6YGVZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-935535.821183
FMO2-HF: Nuclear repulsion	890452.520596
FMO2-HF: Total energy	-45083.300587
FMO2-MP2: Total energy	-45213.927145

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.
-5.921	-2.088	2.005	-1.512	-4.324	0.003

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 : 0.005 / q_NPA : -0.002

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	0.069	0.014	3.811	-1.617	0.120	-0.017	-0.815	-0.904	0.004
4	A	145	LEU	0	0.042	0.029	6.494	0.105	0.105	0.000	0.000	0.000	0.000
5	A	146	THR	0	0.012	-0.002	3.281	-1.494	-0.987	0.031	-0.123	-0.415	0.000
6	A	147	LEU	0	-0.005	0.005	2.719	-1.876	-0.606	0.720	-0.278	-1.712	0.000
7	A	148	ILE	0	0.058	0.037	5.294	-0.159	-0.098	-0.001	-0.003	-0.057	0.000
8	A	149	LYS	1	0.984	0.996	8.496	-0.856	-0.856	0.000	0.000	0.000	0.000
9	A	150	THR	0	-0.066	-0.042	6.431	-0.107	-0.107	0.000	0.000	0.000	0.000
10	A	151	ALA	0	0.028	0.000	8.867	-0.125	-0.125	0.000	0.000	0.000	0.000
11	A	152	GLU	-1	-0.904	-0.955	10.525	0.362	0.362	0.000	0.000	0.000	0.000
12	A	153	HIS	0	-0.099	-0.044	12.288	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	154	TRP	0	-0.008	-0.032	11.127	-0.078	-0.078	0.000	0.000	0.000	0.000
14	A	155	ALA	0	0.014	0.027	14.289	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	156	ARG	1	0.947	0.984	16.045	-0.313	-0.313	0.000	0.000	0.000	0.000
16	A	157	GLN	0	-0.082	-0.030	16.789	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	158	ASP	-1	-0.876	-0.924	19.326	0.037	0.037	0.000	0.000	0.000	0.000
18	A	159	ILE	0	-0.004	-0.024	16.770	0.005	0.005	0.000	0.000	0.000	0.000
19	A	160	ARG	1	0.961	0.986	20.052	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	161	THR	0	-0.004	-0.009	23.203	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	162	ILE	0	-0.042	0.003	16.081	0.003	0.003	0.000	0.000	0.000	0.000
22	A	163	GLU	-1	-0.854	-0.933	18.286	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	164	ASP	-1	-0.824	-0.925	17.471	-0.071	-0.071	0.000	0.000	0.000	0.000
24	A	165	SER	0	-0.028	-0.011	15.078	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	166	LYS	1	0.960	0.977	13.131	-0.148	-0.148	0.000	0.000	0.000	0.000
26	A	167	LEU	0	0.041	0.021	12.769	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	168	ARG	1	0.864	0.936	11.046	0.342	0.342	0.000	0.000	0.000	0.000
28	A	169	ALA	0	0.000	0.000	8.825	-0.066	-0.066	0.000	0.000	0.000	0.000
29	A	170	LEU	0	-0.004	-0.007	8.445	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	171	LEU	0	0.025	0.029	10.391	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	172	THR	0	-0.023	-0.025	5.377	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	173	LEU	0	-0.058	-0.024	5.678	-0.113	-0.113	0.000	0.000	0.000	0.000
33	A	174	CYS	0	0.011	0.006	7.012	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	175	ALA	0	0.024	0.026	7.991	0.001	0.001	0.000	0.000	0.000	0.000
35	A	176	VAL	0	-0.082	-0.050	2.196	-0.461	-0.344	1.274	-0.272	-1.119	-0.001
36	A	177	MET	0	-0.028	-0.021	5.309	0.026	0.051	-0.001	0.000	-0.023	0.000
37	A	178	THR	0	0.037	0.026	7.641	0.050	0.050	0.000	0.000	0.000	0.000
38	A	179	ARG	1	0.880	0.944	5.669	0.701	0.701	0.000	0.000	0.000	0.000
39	A	180	LYS	1	0.830	0.931	3.869	0.774	0.890	-0.001	-0.021	-0.094	0.000
40	A	181	PHE	0	0.014	0.036	9.516	0.048	0.048	0.000	0.000	0.000	0.000
41	A	182	SER	0	0.066	0.031	13.126	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	183	LYS	1	0.998	0.966	15.629	0.193	0.193	0.000	0.000	0.000	0.000
43	A	184	SER	0	-0.033	-0.012	17.683	0.004	0.004	0.000	0.000	0.000	0.000
44	A	185	GLN	0	-0.003	0.012	17.125	0.012	0.012	0.000	0.000	0.000	0.000
45	A	186	LEU	0	0.003	0.005	14.796	0.008	0.008	0.000	0.000	0.000	0.000
46	A	187	SER	0	0.019	0.012	18.563	0.007	0.007	0.000	0.000	0.000	0.000
47	A	188	LEU	0	0.044	0.030	20.939	0.007	0.007	0.000	0.000	0.000	0.000
48	A	189	LEU	0	-0.011	0.009	14.559	0.011	0.011	0.000	0.000	0.000	0.000
49	A	190	CYS	0	0.004	0.003	19.176	0.006	0.006	0.000	0.000	0.000	0.000
50	A	191	GLU	-1	-0.841	-0.920	21.345	-0.041	-0.041	0.000	0.000	0.000	0.000
51	A	192	THR	0	-0.093	-0.064	21.063	0.012	0.012	0.000	0.000	0.000	0.000
52	A	193	HIS	0	0.018	0.048	18.794	0.006	0.006	0.000	0.000	0.000	0.000
53	A	194	LEU	0	0.011	0.003	21.889	0.006	0.006	0.000	0.000	0.000	0.000
54	A	195	ARG	1	0.935	0.965	25.417	0.019	0.019	0.000	0.000	0.000	0.000
55	A	196	ARG	1	0.833	0.929	21.658	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	197	GLU	-1	-0.892	-0.955	23.097	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	198	GLY	0	-0.023	0.010	26.046	0.000	0.000	0.000	0.000	0.000	0.000
58	A	199	LEU	0	-0.050	-0.018	24.970	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	200	GLY	0	0.040	0.020	29.043	0.001	0.001	0.000	0.000	0.000	0.000
60	A	201	GLN	0	-0.008	-0.034	29.047	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	202	ASP	-1	-0.914	-0.949	30.310	-0.045	-0.045	0.000	0.000	0.000	0.000
62	A	203	GLN	0	-0.028	-0.008	27.034	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	204	ALA	0	0.020	-0.003	25.922	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	205	GLU	-1	-0.938	-0.969	24.768	-0.079	-0.079	0.000	0.000	0.000	0.000
65	A	206	PRO	0	0.028	0.018	24.161	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	207	VAL	0	0.016	0.011	20.524	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	208	LEU	0	0.003	-0.012	19.924	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	209	GLU	-1	-0.855	-0.912	19.712	-0.152	-0.152	0.000	0.000	0.000	0.000
69	A	210	VAL	0	-0.017	-0.007	16.273	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	211	TYR	0	0.009	-0.044	14.527	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	212	GLN	0	-0.019	-0.020	14.951	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	213	ARG	1	0.843	0.911	16.047	0.153	0.153	0.000	0.000	0.000	0.000
73	A	214	LEU	0	0.020	0.019	11.461	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	215	HIS	0	-0.105	-0.048	11.316	-0.068	-0.068	0.000	0.000	0.000	0.000
75	A	216	SER	0	-0.075	-0.044	12.085	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	217	ASP	-1	-0.786	-0.882	11.162	-0.402	-0.402	0.000	0.000	0.000	0.000
77	A	218	LYS	1	0.881	0.924	11.588	0.346	0.346	0.000	0.000	0.000	0.000
78	A	219	GLY	0	-0.009	-0.009	11.506	0.038	0.038	0.000	0.000	0.000	0.000
79	A	220	GLY	0	0.008	0.014	11.440	0.007	0.007	0.000	0.000	0.000	0.000
80	A	221	SER	0	0.006	0.018	12.012	0.042	0.042	0.000	0.000	0.000	0.000
81	A	222	PHE	0	0.037	0.004	14.864	0.030	0.030	0.000	0.000	0.000	0.000
82	A	223	GLU	-1	-0.794	-0.890	9.526	-0.562	-0.562	0.000	0.000	0.000	0.000
83	A	224	ALA	0	-0.059	-0.039	13.756	0.029	0.029	0.000	0.000	0.000	0.000
84	A	225	ALA	0	0.018	0.012	15.898	0.027	0.027	0.000	0.000	0.000	0.000
85	A	226	LEU	0	0.010	0.004	15.036	0.020	0.020	0.000	0.000	0.000	0.000
86	A	227	TRP	0	-0.019	-0.021	15.690	0.014	0.014	0.000	0.000	0.000	0.000
87	A	228	GLN	0	-0.025	-0.003	17.755	0.011	0.011	0.000	0.000	0.000	0.000
88	A	229	GLN	0	-0.055	-0.037	20.930	0.018	0.018	0.000	0.000	0.000	0.000
89	A	230	TRP	0	-0.005	0.011	19.737	0.011	0.011	0.000	0.000	0.000	0.000
90	A	231	ASP	-1	-0.785	-0.852	22.436	-0.065	-0.065	0.000	0.000	0.000	0.000
91	A	232	ARG	1	0.887	0.911	20.636	0.023	0.023	0.000	0.000	0.000	0.000
92	A	233	GLN	0	-0.041	-0.023	21.636	0.005	0.005	0.000	0.000	0.000	0.000
93	A	234	SER	0	0.034	-0.016	22.882	0.008	0.008	0.000	0.000	0.000	0.000
94	A	235	LEU	0	-0.007	-0.003	16.910	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	236	ILE	0	-0.031	-0.010	18.069	0.002	0.002	0.000	0.000	0.000	0.000
96	A	237	MET	0	-0.001	0.007	19.393	0.015	0.015	0.000	0.000	0.000	0.000
97	A	238	PHE	0	0.028	0.020	15.875	0.007	0.007	0.000	0.000	0.000	0.000
98	A	239	ILE	0	0.024	-0.008	13.704	0.000	0.000	0.000	0.000	0.000	0.000
99	A	240	THR	0	-0.025	-0.020	15.649	0.020	0.020	0.000	0.000	0.000	0.000
100	A	241	ALA	0	0.013	0.023	17.937	0.017	0.017	0.000	0.000	0.000	0.000
101	A	242	PHE	0	0.026	-0.003	10.682	0.007	0.007	0.000	0.000	0.000	0.000
102	A	243	LEU	0	-0.004	-0.019	10.961	0.013	0.013	0.000	0.000	0.000	0.000
103	A	244	ASN	0	-0.122	-0.077	14.336	0.042	0.042	0.000	0.000	0.000	0.000
104	A	245	ILE	0	-0.024	0.004	16.974	0.009	0.009	0.000	0.000	0.000	0.000
105	A	246	ALA	0	-0.046	-0.015	12.535	0.001	0.001	0.000	0.000	0.000	0.000
106	A	247	LEU	0	-0.025	-0.032	11.116	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	248	GLN	0	-0.005	0.011	14.883	0.005	0.005	0.000	0.000	0.000	0.000
108	A	249	LEU	0	-0.032	0.004	17.387	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	250	PRO	0	0.019	0.008	17.180	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	251	CYS	0	0.009	0.000	13.102	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	252	GLU	-1	-0.967	-0.977	15.660	-0.146	-0.146	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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