FMO DATABASE

FMODB ID: ZVN5N

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:

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	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-936551.83583
FMO2-HF: Nuclear repulsion	891468.130722
FMO2-HF: Total energy	-45083.705108
FMO2-MP2: Total energy	-45214.366332

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.
-3.691	-0.443	2.776	-1.584	-4.438	0.006

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 : -0.002 / q_NPA : -0.010

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	0.060	0.009	3.811	-1.546	0.159	-0.018	-0.820	-0.867	0.004
4	A	145	LEU	0	0.056	0.037	6.343	0.067	0.067	0.000	0.000	0.000	0.000
5	A	146	THR	0	0.016	-0.001	3.162	0.306	0.780	0.042	-0.115	-0.401	0.000
6	A	147	LEU	0	-0.003	0.012	2.328	-1.680	-0.726	1.265	-0.346	-1.873	0.002
7	A	148	ILE	0	0.061	0.038	5.505	-0.116	-0.116	0.000	0.000	0.000	0.000
8	A	149	LYS	1	0.842	0.913	8.494	-0.685	-0.685	0.000	0.000	0.000	0.000
9	A	150	THR	0	-0.040	-0.036	6.393	-0.113	-0.113	0.000	0.000	0.000	0.000
10	A	151	ALA	0	0.030	0.000	8.895	-0.127	-0.127	0.000	0.000	0.000	0.000
11	A	152	GLU	-1	-0.811	-0.895	10.566	0.406	0.406	0.000	0.000	0.000	0.000
12	A	153	HIS	0	-0.079	-0.035	12.242	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	154	TRP	0	-0.002	-0.028	10.988	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	155	ALA	0	0.014	0.026	14.123	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	156	ARG	1	0.930	0.976	15.975	-0.319	-0.319	0.000	0.000	0.000	0.000
16	A	157	GLN	0	-0.073	-0.025	16.610	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	158	ASP	-1	-0.849	-0.916	19.062	0.041	0.041	0.000	0.000	0.000	0.000
18	A	159	ILE	0	-0.019	-0.029	16.429	0.004	0.004	0.000	0.000	0.000	0.000
19	A	160	ARG	1	0.935	0.947	19.746	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	161	THR	0	0.002	-0.005	22.976	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	162	ILE	0	-0.039	0.009	15.925	0.002	0.002	0.000	0.000	0.000	0.000
22	A	163	GLU	-1	-0.764	-0.845	18.187	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	164	ASP	-1	-0.800	-0.907	17.470	-0.060	-0.060	0.000	0.000	0.000	0.000
24	A	165	SER	0	-0.051	-0.048	14.918	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	166	LYS	1	0.892	0.931	13.109	-0.085	-0.085	0.000	0.000	0.000	0.000
26	A	167	LEU	0	0.044	0.022	12.797	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	168	ARG	1	0.822	0.897	10.685	0.337	0.337	0.000	0.000	0.000	0.000
28	A	169	ALA	0	0.002	0.007	8.871	-0.062	-0.062	0.000	0.000	0.000	0.000
29	A	170	LEU	0	0.001	-0.002	8.567	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	171	LEU	0	0.034	0.035	10.410	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	172	THR	0	-0.023	-0.025	5.478	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	173	LEU	0	-0.057	-0.020	5.550	-0.081	-0.081	0.000	0.000	0.000	0.000
33	A	174	CYS	0	0.002	-0.003	6.980	0.021	0.021	0.000	0.000	0.000	0.000
34	A	175	ALA	0	0.017	0.028	7.784	0.005	0.005	0.000	0.000	0.000	0.000
35	A	176	VAL	0	-0.080	-0.050	2.203	-0.355	-0.362	1.489	-0.287	-1.195	0.000
36	A	177	MET	0	-0.028	-0.016	5.261	0.036	0.057	-0.001	-0.001	-0.018	0.000
37	A	178	THR	0	0.023	0.014	7.690	0.033	0.033	0.000	0.000	0.000	0.000
38	A	179	ARG	1	0.860	0.932	5.962	0.572	0.572	0.000	0.000	0.000	0.000
39	A	180	LYS	1	0.829	0.935	3.973	0.495	0.596	-0.001	-0.015	-0.084	0.000
40	A	181	PHE	0	0.024	0.038	9.737	0.039	0.039	0.000	0.000	0.000	0.000
41	A	182	SER	0	0.062	0.031	13.364	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	183	LYS	1	1.003	0.969	15.906	0.176	0.176	0.000	0.000	0.000	0.000
43	A	184	SER	0	-0.023	-0.004	17.899	0.003	0.003	0.000	0.000	0.000	0.000
44	A	185	GLN	0	-0.025	-0.003	17.340	0.008	0.008	0.000	0.000	0.000	0.000
45	A	186	LEU	0	-0.001	0.003	14.886	0.008	0.008	0.000	0.000	0.000	0.000
46	A	187	SER	0	0.049	0.023	18.683	0.004	0.004	0.000	0.000	0.000	0.000
47	A	188	LEU	0	0.002	0.011	21.135	0.006	0.006	0.000	0.000	0.000	0.000
48	A	189	LEU	0	-0.016	0.006	14.781	0.010	0.010	0.000	0.000	0.000	0.000
49	A	190	CYS	0	0.001	0.006	19.242	0.005	0.005	0.000	0.000	0.000	0.000
50	A	191	GLU	-1	-0.816	-0.904	21.354	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	192	THR	0	-0.078	-0.060	21.116	0.010	0.010	0.000	0.000	0.000	0.000
52	A	193	HIS	0	0.019	0.044	18.905	0.007	0.007	0.000	0.000	0.000	0.000
53	A	194	LEU	0	-0.006	-0.002	21.838	0.005	0.005	0.000	0.000	0.000	0.000
54	A	195	ARG	1	0.911	0.957	24.757	0.005	0.005	0.000	0.000	0.000	0.000
55	A	196	ARG	1	0.779	0.885	21.633	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	197	GLU	-1	-0.856	-0.925	22.991	0.014	0.014	0.000	0.000	0.000	0.000
57	A	198	GLY	0	-0.019	0.010	25.918	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	199	LEU	0	-0.057	-0.020	24.827	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	200	GLY	0	0.044	0.023	28.927	0.001	0.001	0.000	0.000	0.000	0.000
60	A	201	GLN	0	-0.024	-0.050	28.885	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	202	ASP	-1	-0.884	-0.921	30.259	-0.035	-0.035	0.000	0.000	0.000	0.000
62	A	203	GLN	0	-0.047	-0.034	26.899	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	204	ALA	0	0.016	-0.005	25.863	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	205	GLU	-1	-0.929	-0.963	24.723	-0.066	-0.066	0.000	0.000	0.000	0.000
65	A	206	PRO	0	0.027	0.015	24.028	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	207	VAL	0	0.010	0.008	20.517	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	208	LEU	0	0.011	-0.013	19.854	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	209	GLU	-1	-0.858	-0.907	19.696	-0.134	-0.134	0.000	0.000	0.000	0.000
69	A	210	VAL	0	-0.013	-0.008	16.164	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	211	TYR	0	0.019	-0.032	14.504	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	212	GLN	0	-0.025	-0.021	14.962	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	213	ARG	1	0.856	0.919	16.082	0.137	0.137	0.000	0.000	0.000	0.000
73	A	214	LEU	0	0.000	0.007	11.306	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	215	HIS	0	-0.087	-0.035	11.300	-0.064	-0.064	0.000	0.000	0.000	0.000
75	A	216	SER	0	-0.017	-0.023	12.197	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	217	ASP	-1	-0.841	-0.904	11.142	-0.370	-0.370	0.000	0.000	0.000	0.000
77	A	218	LYS	1	0.885	0.927	11.599	0.310	0.310	0.000	0.000	0.000	0.000
78	A	219	GLY	0	0.001	-0.003	11.630	0.035	0.035	0.000	0.000	0.000	0.000
79	A	220	GLY	0	-0.002	0.008	11.232	0.003	0.003	0.000	0.000	0.000	0.000
80	A	221	SER	0	0.007	0.021	11.789	0.042	0.042	0.000	0.000	0.000	0.000
81	A	222	PHE	0	0.037	0.002	14.763	0.027	0.027	0.000	0.000	0.000	0.000
82	A	223	GLU	-1	-0.747	-0.867	9.033	-0.518	-0.518	0.000	0.000	0.000	0.000
83	A	224	ALA	0	-0.052	-0.033	13.490	0.027	0.027	0.000	0.000	0.000	0.000
84	A	225	ALA	0	0.015	0.009	15.637	0.025	0.025	0.000	0.000	0.000	0.000
85	A	226	LEU	0	0.009	0.007	14.772	0.020	0.020	0.000	0.000	0.000	0.000
86	A	227	TRP	0	-0.018	-0.021	15.616	0.013	0.013	0.000	0.000	0.000	0.000
87	A	228	GLN	0	-0.036	-0.007	17.711	0.013	0.013	0.000	0.000	0.000	0.000
88	A	229	GLN	0	-0.048	-0.032	20.812	0.018	0.018	0.000	0.000	0.000	0.000
89	A	230	TRP	0	-0.012	0.010	19.974	0.012	0.012	0.000	0.000	0.000	0.000
90	A	231	ASP	-1	-0.785	-0.857	22.442	-0.053	-0.053	0.000	0.000	0.000	0.000
91	A	232	ARG	1	0.862	0.885	20.580	0.020	0.020	0.000	0.000	0.000	0.000
92	A	233	GLN	0	-0.028	-0.012	21.775	0.009	0.009	0.000	0.000	0.000	0.000
93	A	234	SER	0	0.022	-0.020	22.622	0.008	0.008	0.000	0.000	0.000	0.000
94	A	235	LEU	0	-0.015	-0.007	16.868	0.000	0.000	0.000	0.000	0.000	0.000
95	A	236	ILE	0	-0.019	-0.008	18.029	0.005	0.005	0.000	0.000	0.000	0.000
96	A	237	MET	0	0.010	0.042	19.252	0.017	0.017	0.000	0.000	0.000	0.000
97	A	238	PHE	0	0.024	0.017	15.939	0.008	0.008	0.000	0.000	0.000	0.000
98	A	239	ILE	0	0.024	-0.006	13.602	0.003	0.003	0.000	0.000	0.000	0.000
99	A	240	THR	0	-0.037	-0.028	15.489	0.022	0.022	0.000	0.000	0.000	0.000
100	A	241	ALA	0	0.016	0.024	17.778	0.017	0.017	0.000	0.000	0.000	0.000
101	A	242	PHE	0	0.033	0.000	10.579	0.009	0.009	0.000	0.000	0.000	0.000
102	A	243	LEU	0	-0.007	-0.021	10.805	0.018	0.018	0.000	0.000	0.000	0.000
103	A	244	ASN	0	-0.101	-0.051	14.358	0.033	0.033	0.000	0.000	0.000	0.000
104	A	245	ILE	0	-0.007	0.008	17.064	0.007	0.007	0.000	0.000	0.000	0.000
105	A	246	ALA	0	-0.044	-0.016	12.561	0.001	0.001	0.000	0.000	0.000	0.000
106	A	247	LEU	0	-0.037	-0.036	11.522	0.000	0.000	0.000	0.000	0.000	0.000
107	A	248	GLN	0	-0.015	0.002	15.083	0.003	0.003	0.000	0.000	0.000	0.000
108	A	249	LEU	0	-0.019	0.009	17.486	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	250	PRO	0	0.016	0.004	17.097	0.001	0.001	0.000	0.000	0.000	0.000
110	A	251	CYS	0	0.030	0.018	13.705	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	252	GLU	-1	-0.975	-0.982	15.768	-0.108	-0.108	0.000	0.000	0.000	0.000

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