FMO DATABASE

FMODB ID: QY13Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-722067.416925
FMO2-HF: Nuclear repulsion	680499.233717
FMO2-HF: Total energy	-41568.183208
FMO2-MP2: Total energy	-41687.143324

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.
-0.328	1.412	-0.012	-0.895	-0.833	0.001

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 : 0.947 / q_NPA : 0.960

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	2	PHE	0	0.027	0.007	3.823	-0.269	1.471	-0.012	-0.895	-0.833	0.001
4	A	3	ASN	0	-0.022	-0.014	6.410	2.601	2.601	0.000	0.000	0.000	0.000
5	A	4	GLN	0	-0.029	-0.009	10.157	1.414	1.414	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.011	0.015	12.853	0.187	0.187	0.000	0.000	0.000	0.000
7	A	6	MET	0	-0.012	-0.013	16.523	0.289	0.289	0.000	0.000	0.000	0.000
8	A	7	LEU	0	0.002	0.003	19.556	0.133	0.133	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.016	-0.007	23.101	0.160	0.160	0.000	0.000	0.000	0.000
10	A	9	GLY	0	0.018	0.022	26.802	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.840	0.905	29.498	8.822	8.822	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.024	0.004	30.487	-0.167	-0.167	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.012	-0.024	32.532	0.371	0.371	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.860	0.913	34.273	8.658	8.658	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.798	-0.893	34.329	-8.453	-8.453	0.000	0.000	0.000	0.000
16	A	15	PRO	0	-0.007	0.005	31.351	-0.091	-0.091	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.797	-0.858	30.985	-9.509	-9.509	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.041	-0.025	31.202	-0.308	-0.308	0.000	0.000	0.000	0.000
19	A	18	ARG	1	0.802	0.873	30.569	9.865	9.865	0.000	0.000	0.000	0.000
20	A	19	TYR	0	-0.012	-0.038	30.284	-0.175	-0.175	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.002	0.000	25.953	0.211	0.211	0.000	0.000	0.000	0.000
22	A	21	SER	0	0.034	0.009	29.446	0.104	0.104	0.000	0.000	0.000	0.000
23	A	22	ALA	0	-0.013	0.000	27.473	0.181	0.181	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.016	0.011	29.583	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	24	ALA	0	-0.072	-0.033	25.725	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.042	0.031	27.858	0.008	0.008	0.000	0.000	0.000	0.000
27	A	26	VAL	0	-0.041	-0.025	24.793	-0.551	-0.551	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.026	0.016	26.564	0.486	0.486	0.000	0.000	0.000	0.000
29	A	28	HIS	0	0.027	0.028	24.734	-0.793	-0.793	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.030	0.013	27.489	0.512	0.512	0.000	0.000	0.000	0.000
31	A	30	THR	0	0.018	0.009	27.751	-0.421	-0.421	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.017	0.024	25.798	0.451	0.451	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.020	0.012	28.970	-0.199	-0.199	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.016	-0.016	25.902	0.116	0.116	0.000	0.000	0.000	0.000
35	A	34	ASN	0	-0.010	-0.012	29.167	-0.117	-0.117	0.000	0.000	0.000	0.000
36	A	35	ARG	1	0.797	0.865	29.212	10.119	10.119	0.000	0.000	0.000	0.000
37	A	36	SER	0	-0.027	-0.021	29.020	0.163	0.163	0.000	0.000	0.000	0.000
38	A	37	PHE	0	-0.018	-0.008	28.820	0.155	0.155	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.817	0.913	33.611	7.760	7.760	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.009	-0.010	36.306	0.099	0.099	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.025	-0.002	37.352	0.160	0.160	0.000	0.000	0.000	0.000
42	A	41	SER	0	-0.044	-0.012	40.168	0.224	0.224	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.010	0.018	41.135	0.162	0.162	0.000	0.000	0.000	0.000
44	A	43	GLU	-1	-0.829	-0.937	39.990	-7.630	-7.630	0.000	0.000	0.000	0.000
45	A	44	ILE	0	-0.044	-0.014	34.696	-0.190	-0.190	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.807	-0.865	33.675	-9.141	-9.141	0.000	0.000	0.000	0.000
47	A	46	ALA	0	-0.016	-0.021	31.627	-0.117	-0.117	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.820	-0.863	27.210	-11.098	-11.098	0.000	0.000	0.000	0.000
49	A	48	TYR	0	0.007	-0.012	28.759	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	49	VAL	0	0.022	0.016	22.969	-0.270	-0.270	0.000	0.000	0.000	0.000
51	A	50	ASN	0	0.027	0.013	25.124	0.500	0.500	0.000	0.000	0.000	0.000
52	A	51	CYS	0	-0.054	-0.027	23.114	-0.794	-0.794	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.001	-0.004	21.603	0.394	0.394	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.013	0.001	22.213	-0.598	-0.598	0.000	0.000	0.000	0.000
55	A	54	TRP	0	0.060	0.010	20.770	0.428	0.428	0.000	0.000	0.000	0.000
56	A	55	ARG	1	0.963	0.970	23.889	11.980	11.980	0.000	0.000	0.000	0.000
57	A	56	LYS	1	1.037	1.013	26.575	10.235	10.235	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.021	0.033	23.694	0.489	0.489	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.008	0.021	26.743	0.169	0.169	0.000	0.000	0.000	0.000
60	A	59	GLU	-1	-0.857	-0.916	28.329	-9.731	-9.731	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.045	-0.049	30.603	0.523	0.523	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.003	-0.023	28.537	0.207	0.207	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.010	-0.009	31.519	0.232	0.232	0.000	0.000	0.000	0.000
64	A	63	LEU	0	-0.052	-0.005	34.064	0.257	0.257	0.000	0.000	0.000	0.000
65	A	64	TYR	0	-0.040	-0.016	33.902	0.325	0.325	0.000	0.000	0.000	0.000
66	A	65	CYS	0	-0.053	-0.011	33.347	-0.048	-0.048	0.000	0.000	0.000	0.000
67	A	66	GLN	0	0.042	0.017	35.459	0.020	0.020	0.000	0.000	0.000	0.000
68	A	67	LYS	1	0.888	0.931	36.499	7.668	7.668	0.000	0.000	0.000	0.000
69	A	68	GLY	0	0.012	0.015	36.529	0.314	0.314	0.000	0.000	0.000	0.000
70	A	69	SER	0	-0.006	-0.006	34.424	0.045	0.045	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.077	-0.036	31.847	-0.248	-0.248	0.000	0.000	0.000	0.000
72	A	71	VAL	0	0.010	-0.002	27.700	0.030	0.030	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.041	0.022	26.322	-0.144	-0.144	0.000	0.000	0.000	0.000
74	A	73	VAL	0	-0.017	-0.023	21.430	0.076	0.076	0.000	0.000	0.000	0.000
75	A	74	SER	0	-0.034	-0.018	18.228	-0.325	-0.325	0.000	0.000	0.000	0.000
76	A	75	GLY	0	0.035	0.027	16.746	0.497	0.497	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.922	0.981	12.289	20.115	20.115	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.051	0.022	14.656	1.136	1.136	0.000	0.000	0.000	0.000
79	A	78	GLN	0	-0.076	-0.052	14.100	-2.645	-2.645	0.000	0.000	0.000	0.000
80	A	79	THR	0	0.007	-0.001	14.980	0.729	0.729	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.858	0.914	16.866	13.473	13.473	0.000	0.000	0.000	0.000
82	A	81	SER	0	0.033	0.016	19.290	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	82	TYR	0	-0.072	-0.028	21.839	-0.291	-0.291	0.000	0.000	0.000	0.000
84	A	83	GLU	-1	-0.811	-0.902	25.154	-10.851	-10.851	0.000	0.000	0.000	0.000
85	A	84	ASN	0	-0.117	-0.069	28.527	0.025	0.025	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.874	-0.927	31.270	-8.320	-8.320	0.000	0.000	0.000	0.000
87	A	86	GLU	-1	-0.951	-0.972	32.020	-9.321	-9.321	0.000	0.000	0.000	0.000
88	A	87	GLY	0	-0.029	-0.011	31.232	0.252	0.252	0.000	0.000	0.000	0.000
89	A	88	VAL	0	-0.058	-0.025	31.007	0.102	0.102	0.000	0.000	0.000	0.000
90	A	89	ASN	0	-0.007	-0.003	24.933	0.147	0.147	0.000	0.000	0.000	0.000
91	A	90	VAL	0	-0.027	-0.007	26.214	0.003	0.003	0.000	0.000	0.000	0.000
92	A	91	TYR	0	-0.017	-0.021	20.433	-0.381	-0.381	0.000	0.000	0.000	0.000
93	A	92	VAL	0	-0.010	-0.002	21.490	0.452	0.452	0.000	0.000	0.000	0.000
94	A	93	THR	0	-0.013	-0.022	19.273	-0.890	-0.890	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.814	-0.876	19.421	-13.597	-13.597	0.000	0.000	0.000	0.000
96	A	95	VAL	0	0.022	-0.002	18.792	-1.093	-1.093	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.043	-0.004	16.646	0.810	0.810	0.000	0.000	0.000	0.000
98	A	97	ALA	0	0.000	-0.005	18.224	-0.765	-0.765	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.877	-0.947	16.176	-18.323	-18.323	0.000	0.000	0.000	0.000
100	A	99	THR	0	-0.078	-0.042	19.465	0.815	0.815	0.000	0.000	0.000	0.000
101	A	100	VAL	0	0.036	0.002	22.223	-0.144	-0.144	0.000	0.000	0.000	0.000
102	A	101	ARG	1	0.898	0.966	25.285	10.592	10.592	0.000	0.000	0.000	0.000
103	A	102	PHE	0	0.083	0.023	27.988	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	103	MET	0	-0.071	-0.035	29.083	-0.139	-0.139	0.000	0.000	0.000	0.000
105	A	104	ASP	-1	-0.782	-0.846	32.849	-8.482	-8.482	0.000	0.000	0.000	0.000

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