FMO DATABASE

FMODB ID: 49N2N

Calculation Name: 1VC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VC1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1F5

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-887952.485584
FMO2-HF: Nuclear repulsion	845264.419399
FMO2-HF: Total energy	-42688.066185
FMO2-MP2: Total energy	-42814.066972

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:1:MET)

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

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.
-5.956	-0.656	8.91	-4.881	-9.329	-0.032

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : 0.001

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	3	ASN	0	-0.015	-0.008	3.830	-0.609	1.500	-0.020	-1.094	-0.996	0.006
4	A	4	LEU	0	0.060	0.030	6.750	0.397	0.397	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.851	0.935	8.603	0.150	0.150	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.007	0.015	11.888	0.091	0.091	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.869	-0.920	14.537	-0.199	-0.199	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.004	0.004	16.672	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.002	-0.002	20.398	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.820	-0.861	24.231	0.072	0.072	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.062	-0.043	26.568	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.834	-0.908	29.954	0.028	0.028	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.833	-0.904	31.915	0.062	0.062	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.822	0.902	27.378	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.020	0.000	23.288	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.004	0.014	22.487	0.021	0.021	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.005	-0.018	16.781	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.913	0.946	18.617	0.084	0.084	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.019	0.001	12.951	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.005	-0.009	14.109	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.047	0.006	10.819	-0.116	-0.116	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.841	-0.908	10.062	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.002	0.018	9.187	0.077	0.077	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.795	-0.910	6.185	0.800	0.800	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.008	-0.004	4.546	0.524	0.670	-0.001	-0.018	-0.127	0.000
26	A	26	TYR	0	-0.083	-0.036	2.220	-4.187	-1.753	5.735	-2.849	-5.319	-0.010
27	A	27	ASN	0	0.002	-0.034	2.477	-0.052	0.410	3.198	-0.898	-2.762	-0.028
28	A	28	SER	0	-0.018	-0.018	5.163	-0.480	-0.404	-0.001	-0.011	-0.064	0.000
29	A	29	SER	0	0.001	-0.010	5.378	-0.669	-0.596	-0.001	-0.011	-0.061	0.000
30	A	30	GLU	-1	-0.839	-0.911	5.563	-0.090	-0.090	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.006	0.011	7.497	-0.373	-0.373	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.879	0.930	10.183	-0.910	-0.910	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.800	-0.896	10.519	0.518	0.518	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.024	-0.019	9.252	-0.161	-0.161	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.003	-0.004	13.080	-0.082	-0.082	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.830	0.917	15.020	-0.528	-0.528	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.028	-0.025	14.609	-0.077	-0.077	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.057	0.045	17.309	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.001	0.000	18.749	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.081	-0.043	20.698	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.044	-0.029	21.220	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.033	-0.031	22.959	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.005	-0.021	25.050	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.819	0.918	26.758	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.899	0.925	28.065	-0.104	-0.104	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.796	0.896	27.200	-0.061	-0.061	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.001	0.003	20.401	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.012	-0.003	23.030	0.012	0.012	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.022	0.011	16.584	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.791	-0.870	20.292	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.008	-0.024	17.035	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.033	0.012	19.424	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.062	-0.036	16.866	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.034	0.011	13.992	-0.034	-0.034	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.019	0.000	15.204	0.016	0.016	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.026	-0.006	10.352	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	57	MET	0	0.001	0.000	12.511	0.034	0.034	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.771	-0.866	8.294	0.907	0.907	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.006	-0.012	11.895	0.041	0.041	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.030	0.026	8.025	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.020	0.014	9.996	0.079	0.079	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.007	-0.010	11.115	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.015	0.006	13.687	-0.048	-0.048	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.029	-0.028	10.699	0.013	0.013	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.013	0.001	13.257	-0.075	-0.075	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.005	0.009	16.074	-0.062	-0.062	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.034	-0.023	14.780	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.009	0.014	13.452	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.009	0.009	17.642	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.837	0.907	19.573	-0.466	-0.466	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.769	-0.879	18.144	0.450	0.450	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.003	0.007	21.221	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.947	0.981	22.922	-0.248	-0.248	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.029	-0.008	23.163	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.073	-0.041	22.861	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.008	0.016	26.140	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.766	0.898	24.702	-0.171	-0.171	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.827	-0.913	26.658	0.129	0.129	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.001	-0.017	18.049	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.042	-0.016	23.769	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.022	0.004	19.889	0.008	0.008	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.038	-0.001	22.843	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.006	-0.021	22.875	0.003	0.003	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.056	-0.018	21.777	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.887	0.952	18.208	0.098	0.098	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.796	-0.909	22.413	0.066	0.066	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.109	-0.057	18.977	0.011	0.011	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.018	0.005	16.749	0.030	0.030	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.026	-0.014	20.436	0.030	0.030	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.982	0.983	21.672	-0.071	-0.071	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.013	-0.005	16.962	0.008	0.008	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.020	0.019	19.377	0.022	0.022	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.885	0.940	21.977	-0.100	-0.100	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.050	-0.025	22.795	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.050	-0.044	18.970	0.010	0.010	0.000	0.000	0.000	0.000
96	A	96	HIS	0	0.000	0.001	22.406	0.014	0.014	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.048	0.020	18.834	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.822	-0.910	23.200	0.144	0.144	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.852	0.944	25.682	-0.172	-0.172	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.063	-0.028	23.311	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	PHE	0	-0.023	-0.023	18.599	0.005	0.005	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.876	0.946	24.652	-0.124	-0.124	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.027	-0.026	24.455	0.011	0.011	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.060	-0.031	27.037	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.910	-0.946	27.391	0.029	0.029	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.002	-0.037	27.750	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.037	0.016	24.944	0.015	0.015	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.895	-0.950	27.758	0.011	0.011	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.776	-0.850	31.359	0.046	0.046	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.080	-0.026	28.135	0.011	0.011	0.000	0.000	0.000	0.000

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