FMO DATABASE

FMODB ID: Z6YQN

Calculation Name: 3VDY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VDY

Chain ID: A

ChEMBL ID:

UniProt ID: C0SPB6

Base Structure: X-ray

Registration Date: 2023-06-21

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-723103.018944
FMO2-HF: Nuclear repulsion	681535.987957
FMO2-HF: Total energy	-41567.030987
FMO2-MP2: Total energy	-41686.034526

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
3.533	5.435	-0.025	-0.986	-0.891	0

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.938 / q_NPA : 0.955

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].
3	A	2	PHE	0	0.022	0.001	3.847	-1.008	0.894	-0.025	-0.986	-0.891
4	A	3	ASN	0	-0.021	-0.010	6.450	2.751	2.751	0.000	0.000	0.000
5	A	4	GLN	0	0.002	0.001	10.170	1.366	1.366	0.000	0.000	0.000
6	A	5	VAL	0	0.017	0.023	12.997	0.230	0.230	0.000	0.000	0.000
7	A	6	MET	0	-0.011	-0.016	16.599	0.193	0.193	0.000	0.000	0.000
8	A	7	LEU	0	-0.010	-0.002	19.637	0.176	0.176	0.000	0.000	0.000
9	A	8	VAL	0	0.032	0.017	23.162	0.112	0.112	0.000	0.000	0.000
10	A	9	GLY	0	0.012	0.005	26.734	0.078	0.078	0.000	0.000	0.000
11	A	10	ARG	1	0.908	0.945	29.366	8.801	8.801	0.000	0.000	0.000
12	A	11	LEU	0	0.009	0.035	30.295	-0.187	-0.187	0.000	0.000	0.000
13	A	12	THR	0	0.000	-0.002	32.782	0.423	0.423	0.000	0.000	0.000
14	A	13	LYS	1	0.886	0.928	34.650	8.590	8.590	0.000	0.000	0.000
15	A	14	ASP	-1	-0.829	-0.920	34.978	-8.390	-8.390	0.000	0.000	0.000
16	A	15	PRO	0	-0.033	-0.010	31.920	-0.138	-0.138	0.000	0.000	0.000
17	A	16	ASP	-1	-0.914	-0.943	31.748	-9.216	-9.216	0.000	0.000	0.000
18	A	17	LEU	0	-0.006	-0.011	30.913	-0.395	-0.395	0.000	0.000	0.000
19	A	18	ARG	1	0.915	0.966	30.810	9.935	9.935	0.000	0.000	0.000
20	A	19	TYR	0	0.001	-0.045	30.646	-0.198	-0.198	0.000	0.000	0.000
21	A	20	THR	0	0.004	0.010	26.179	0.226	0.226	0.000	0.000	0.000
22	A	21	SER	0	0.023	0.009	29.601	0.039	0.039	0.000	0.000	0.000
23	A	22	ALA	0	-0.011	-0.007	27.653	0.145	0.145	0.000	0.000	0.000
24	A	23	GLY	0	0.021	0.008	29.616	0.124	0.124	0.000	0.000	0.000
25	A	24	ALA	0	-0.102	-0.043	26.101	-0.014	-0.014	0.000	0.000	0.000
26	A	25	ALA	0	0.049	0.033	28.171	0.047	0.047	0.000	0.000	0.000
27	A	26	VAL	0	-0.045	-0.036	25.476	-0.538	-0.538	0.000	0.000	0.000
28	A	27	ALA	0	0.010	0.014	26.897	0.432	0.432	0.000	0.000	0.000
29	A	28	HIS	0	-0.007	0.005	25.747	-0.629	-0.629	0.000	0.000	0.000
30	A	29	VAL	0	0.038	0.020	27.607	0.484	0.484	0.000	0.000	0.000
31	A	30	THR	0	0.007	0.003	28.175	-0.323	-0.323	0.000	0.000	0.000
32	A	31	LEU	0	0.023	-0.003	25.867	0.383	0.383	0.000	0.000	0.000
33	A	32	ALA	0	0.009	0.009	28.888	-0.189	-0.189	0.000	0.000	0.000
34	A	33	VAL	0	-0.021	-0.021	25.860	0.118	0.118	0.000	0.000	0.000
35	A	34	ASN	0	-0.011	-0.009	29.139	0.015	0.015	0.000	0.000	0.000
36	A	35	ARG	1	0.850	0.926	28.744	10.217	10.217	0.000	0.000	0.000
37	A	36	SER	0	-0.010	-0.009	28.985	0.191	0.191	0.000	0.000	0.000
38	A	37	PHE	0	-0.031	-0.007	28.944	0.290	0.290	0.000	0.000	0.000
39	A	38	LYS	1	0.975	0.985	33.451	7.942	7.942	0.000	0.000	0.000
40	A	39	ASN	0	0.067	0.048	35.913	0.052	0.052	0.000	0.000	0.000
41	A	40	ALA	0	0.003	-0.014	37.529	0.102	0.102	0.000	0.000	0.000
42	A	41	SER	0	-0.026	-0.023	40.465	0.192	0.192	0.000	0.000	0.000
43	A	42	GLY	0	-0.040	0.007	40.770	0.156	0.156	0.000	0.000	0.000
44	A	43	GLU	-1	-0.914	-0.963	40.063	-7.442	-7.442	0.000	0.000	0.000
45	A	44	ILE	0	-0.048	-0.035	34.531	-0.176	-0.176	0.000	0.000	0.000
46	A	45	GLU	-1	-0.930	-0.958	34.008	-8.976	-8.976	0.000	0.000	0.000
47	A	46	ALA	0	-0.004	-0.018	31.686	-0.190	-0.190	0.000	0.000	0.000
48	A	47	ASP	-1	-0.843	-0.900	27.098	-11.256	-11.256	0.000	0.000	0.000
49	A	48	TYR	0	-0.006	-0.017	29.002	0.076	0.076	0.000	0.000	0.000
50	A	49	VAL	0	0.018	0.020	23.005	-0.282	-0.282	0.000	0.000	0.000
51	A	50	ASN	0	0.024	0.011	25.532	0.629	0.629	0.000	0.000	0.000
52	A	51	CYS	0	-0.032	-0.017	23.562	-0.771	-0.771	0.000	0.000	0.000
53	A	52	THR	0	0.032	0.026	22.141	0.429	0.429	0.000	0.000	0.000
54	A	53	LEU	0	-0.028	-0.011	22.566	-0.590	-0.590	0.000	0.000	0.000
55	A	54	TRP	0	0.084	0.028	21.295	0.485	0.485	0.000	0.000	0.000
56	A	55	ARG	1	0.957	0.972	23.900	12.069	12.069	0.000	0.000	0.000
57	A	56	LYS	1	1.034	0.994	26.333	10.756	10.756	0.000	0.000	0.000
58	A	57	THR	0	-0.011	0.020	24.223	0.454	0.454	0.000	0.000	0.000
59	A	58	ALA	0	0.013	0.006	27.015	0.213	0.213	0.000	0.000	0.000
60	A	59	GLU	-1	-0.858	-0.897	28.460	-9.431	-9.431	0.000	0.000	0.000
61	A	60	ASN	0	0.000	-0.010	29.906	0.521	0.521	0.000	0.000	0.000
62	A	61	THR	0	-0.027	-0.013	28.386	0.281	0.281	0.000	0.000	0.000
63	A	62	ALA	0	0.002	-0.002	31.609	0.214	0.214	0.000	0.000	0.000
64	A	63	LEU	0	-0.050	-0.017	33.950	0.235	0.235	0.000	0.000	0.000
65	A	64	TYR	0	-0.056	-0.038	34.028	0.291	0.291	0.000	0.000	0.000
66	A	65	CYS	0	-0.047	-0.008	32.868	-0.057	-0.057	0.000	0.000	0.000
67	A	66	GLN	0	0.059	0.030	35.375	-0.058	-0.058	0.000	0.000	0.000
68	A	67	LYS	1	0.933	0.959	36.415	7.644	7.644	0.000	0.000	0.000
69	A	68	GLY	0	-0.054	-0.025	36.420	0.211	0.211	0.000	0.000	0.000
70	A	69	SER	0	0.012	0.010	34.229	0.001	0.001	0.000	0.000	0.000
71	A	70	LEU	0	-0.074	-0.020	31.508	-0.240	-0.240	0.000	0.000	0.000
72	A	71	VAL	0	0.023	0.004	27.509	0.018	0.018	0.000	0.000	0.000
73	A	72	GLY	0	0.004	0.002	26.219	-0.115	-0.115	0.000	0.000	0.000
74	A	73	VAL	0	0.001	-0.004	21.432	0.015	0.015	0.000	0.000	0.000
75	A	74	SER	0	-0.026	-0.003	18.223	-0.358	-0.358	0.000	0.000	0.000
76	A	75	GLY	0	0.093	0.047	16.931	0.452	0.452	0.000	0.000	0.000
77	A	76	ARG	1	0.942	0.989	12.434	20.959	20.959	0.000	0.000	0.000
78	A	77	ILE	0	0.033	0.030	14.673	1.041	1.041	0.000	0.000	0.000
79	A	78	GLN	0	-0.059	-0.039	14.838	-1.926	-1.926	0.000	0.000	0.000
80	A	79	THR	0	0.014	0.005	15.848	0.805	0.805	0.000	0.000	0.000
81	A	80	ARG	1	0.881	0.950	17.181	13.076	13.076	0.000	0.000	0.000
82	A	81	SER	0	0.023	0.006	19.836	0.084	0.084	0.000	0.000	0.000
83	A	82	TYR	0	-0.081	-0.033	22.253	-0.310	-0.310	0.000	0.000	0.000
84	A	83	GLU	-1	-0.816	-0.927	25.417	-10.491	-10.491	0.000	0.000	0.000
85	A	84	ASN	0	-0.120	-0.078	28.791	0.026	0.026	0.000	0.000	0.000
86	A	85	GLU	-1	-0.886	-0.928	31.603	-8.264	-8.264	0.000	0.000	0.000
87	A	86	GLU	-1	-0.903	-0.941	32.741	-9.034	-9.034	0.000	0.000	0.000
88	A	87	GLY	0	-0.069	-0.022	31.997	0.209	0.209	0.000	0.000	0.000
89	A	88	VAL	0	-0.052	-0.031	31.200	0.148	0.148	0.000	0.000	0.000
90	A	89	ASN	0	-0.009	0.007	25.221	0.194	0.194	0.000	0.000	0.000
91	A	90	VAL	0	-0.013	0.004	26.844	-0.088	-0.088	0.000	0.000	0.000
92	A	91	TYR	0	-0.006	-0.009	21.053	-0.351	-0.351	0.000	0.000	0.000
93	A	92	VAL	0	-0.010	-0.003	22.426	0.346	0.346	0.000	0.000	0.000
94	A	93	THR	0	-0.024	-0.033	19.576	-0.884	-0.884	0.000	0.000	0.000
95	A	94	GLU	-1	-0.888	-0.939	20.219	-13.237	-13.237	0.000	0.000	0.000
96	A	95	VAL	0	0.012	0.004	19.014	-1.131	-1.131	0.000	0.000	0.000
97	A	96	LEU	0	-0.047	-0.031	16.295	0.721	0.721	0.000	0.000	0.000
98	A	97	ALA	0	-0.010	-0.021	18.489	-0.687	-0.687	0.000	0.000	0.000
99	A	98	ASP	-1	-0.913	-0.938	16.330	-18.292	-18.292	0.000	0.000	0.000
100	A	99	THR	0	-0.064	-0.048	19.886	0.762	0.762	0.000	0.000	0.000
101	A	100	VAL	0	0.031	-0.008	22.593	-0.115	-0.115	0.000	0.000	0.000
102	A	101	ARG	1	0.906	0.964	25.534	10.836	10.836	0.000	0.000	0.000
103	A	102	PHE	0	0.027	-0.008	27.850	0.002	0.002	0.000	0.000	0.000
104	A	103	MET	0	-0.063	-0.039	29.299	-0.028	-0.028	0.000	0.000	0.000
105	A	104	ASP	-1	-0.830	-0.889	32.738	-8.475	-8.475	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)