FMO DATABASE

FMODB ID: R89K8

Calculation Name: 2VSW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VSW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BY84

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1202519.96164
FMO2-HF: Nuclear repulsion	1149546.338729
FMO2-HF: Total energy	-52973.62291
FMO2-MP2: Total energy	-53125.481918

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:5:MET)

Summations of interaction energy for fragment #1(A:5: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.
-26.232	-17.245	12.818	-5.858	-15.95	-0.064

Interaction energy analysis for fragmet #1(A:5:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.107 / q_NPA : -0.044

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	7	GLY	0	0.029	0.006	3.369	0.621	3.753	1.420	-1.905	-2.647	0.000
4	A	8	THR	0	-0.033	-0.016	3.692	0.060	-1.256	0.144	1.489	-0.317	-0.001
5	A	9	GLN	0	0.035	0.010	7.318	0.441	0.441	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.020	0.004	10.044	-0.107	-0.107	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.042	0.017	13.464	0.033	0.033	0.000	0.000	0.000	0.000
8	A	12	THR	0	0.083	0.027	16.458	0.000	0.000	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.894	-0.950	19.030	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.904	0.946	17.777	0.082	0.082	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.023	0.020	16.481	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	16	VAL	0	0.036	0.017	18.556	0.001	0.001	0.000	0.000	0.000	0.000
13	A	17	ALA	0	-0.010	-0.001	21.895	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.069	-0.032	16.534	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	19	LEU	0	-0.027	-0.026	19.905	0.002	0.002	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.946	-0.969	22.337	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.084	-0.001	22.987	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.014	0.005	24.389	0.003	0.003	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.064	-0.053	22.499	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.822	-0.913	18.659	-0.113	-0.113	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.901	0.968	19.556	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.010	-0.001	16.073	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.016	0.001	13.531	0.015	0.015	0.000	0.000	0.000	0.000
24	A	28	LEU	0	0.024	0.014	14.522	0.010	0.010	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.013	-0.007	11.407	0.007	0.007	0.000	0.000	0.000	0.000
26	A	30	ASP	-1	-0.715	-0.820	13.554	0.115	0.115	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.049	-0.046	11.123	0.009	0.009	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.803	0.882	13.035	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	33	PRO	0	-0.016	-0.016	15.727	0.007	0.007	0.000	0.000	0.000	0.000
30	A	34	PHE	0	0.046	0.008	18.646	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	35	VAL	0	0.010	0.019	21.348	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.843	-0.916	19.066	0.063	0.063	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.036	-0.024	19.587	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	38	ASN	0	-0.054	-0.043	21.420	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	39	THR	0	-0.058	-0.026	24.741	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.024	-0.025	24.101	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	41	HIS	1	0.782	0.895	20.557	-0.053	-0.053	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.036	0.031	17.941	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.002	-0.002	21.602	0.007	0.007	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.959	-0.981	22.365	0.036	0.036	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.016	0.020	18.101	0.005	0.005	0.000	0.000	0.000	0.000
42	A	46	ILE	0	-0.044	-0.028	17.133	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.016	-0.003	16.711	0.010	0.010	0.000	0.000	0.000	0.000
44	A	48	ILE	0	-0.009	-0.007	12.720	0.007	0.007	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.003	-0.016	14.460	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	50	CYS	0	0.052	0.040	13.202	0.024	0.024	0.000	0.000	0.000	0.000
47	A	51	SER	0	-0.051	-0.020	14.276	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	52	LYN	0	0.098	0.033	12.479	0.033	0.033	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.008	0.001	15.564	0.026	0.026	0.000	0.000	0.000	0.000
50	A	54	MET	0	0.017	0.006	14.400	0.029	0.029	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.849	0.933	9.755	-0.206	-0.206	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.940	0.983	12.080	-0.220	-0.220	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.966	0.968	14.634	-0.206	-0.206	0.000	0.000	0.000	0.000
54	A	58	LEU	0	0.034	0.030	10.369	0.023	0.023	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.013	-0.010	10.357	0.035	0.035	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.039	-0.007	11.309	0.018	0.018	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.798	-0.867	11.507	1.013	1.013	0.000	0.000	0.000	0.000
58	A	62	LYS	1	0.769	0.858	13.993	-0.493	-0.493	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.007	0.011	15.039	-0.051	-0.051	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.037	0.024	13.631	0.082	0.082	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.030	0.012	9.489	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.052	0.015	12.273	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.879	-0.939	14.926	0.240	0.240	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.010	-0.019	13.209	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.015	0.005	12.264	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	70	GLN	0	-0.001	-0.032	16.297	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	71	HIS	0	-0.063	-0.019	19.476	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.045	-0.020	17.881	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	73	ALA	0	-0.057	-0.006	20.168	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.889	0.943	21.943	-0.101	-0.101	0.000	0.000	0.000	0.000
71	A	75	HIS	0	0.065	0.034	21.890	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.983	0.986	24.471	-0.070	-0.070	0.000	0.000	0.000	0.000
73	A	77	VAL	0	-0.024	0.006	18.579	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.873	-0.928	21.190	0.059	0.059	0.000	0.000	0.000	0.000
75	A	79	ILE	0	-0.056	-0.022	16.823	0.005	0.005	0.000	0.000	0.000	0.000
76	A	80	ASP	-1	-0.735	-0.857	16.884	0.012	0.012	0.000	0.000	0.000	0.000
77	A	81	CYS	0	-0.035	-0.011	13.615	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.038	-0.039	13.787	-0.058	-0.058	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.025	-0.030	15.557	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.801	0.905	13.228	0.113	0.113	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.023	0.016	10.158	0.040	0.040	0.000	0.000	0.000	0.000
82	A	86	VAL	0	-0.016	-0.003	10.632	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	87	VAL	0	-0.007	-0.004	8.214	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	88	TYR	0	0.007	-0.029	11.001	0.013	0.013	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.774	-0.846	11.229	0.108	0.108	0.000	0.000	0.000	0.000
86	A	90	GLN	0	0.095	0.029	13.079	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.034	-0.025	14.130	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	92	SER	0	-0.019	-0.023	9.397	-0.038	-0.038	0.000	0.000	0.000	0.000
89	A	93	GLN	0	-0.044	-0.024	11.542	0.018	0.018	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.866	-0.940	9.145	-0.093	-0.093	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.047	0.009	2.686	-0.983	-0.337	1.171	-0.365	-1.452	0.000
92	A	96	ALA	0	-0.034	-0.003	4.939	-0.401	-0.372	-0.001	-0.002	-0.027	0.000
93	A	97	SER	0	-0.090	-0.039	7.001	-0.046	-0.046	0.000	0.000	0.000	0.000
94	A	98	LEU	0	0.001	0.012	4.010	-0.040	0.084	-0.001	-0.013	-0.111	0.000
95	A	99	SER	0	0.013	-0.002	6.935	-0.067	-0.067	0.000	0.000	0.000	0.000
96	A	100	SER	0	0.041	0.000	5.651	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.860	-0.937	6.144	0.440	0.440	0.000	0.000	0.000	0.000
98	A	102	CYS	0	-0.059	0.016	6.628	0.102	0.102	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.043	-0.004	7.168	0.036	0.036	0.000	0.000	0.000	0.000
100	A	104	LEU	0	0.091	0.048	6.061	0.033	0.033	0.000	0.000	0.000	0.000
101	A	105	THR	0	0.060	0.012	2.480	-0.521	-0.130	1.121	-0.275	-1.237	0.000
102	A	106	VAL	0	-0.029	-0.019	2.751	-1.884	-0.675	0.504	-0.668	-1.045	-0.011
103	A	107	LEU	0	-0.065	-0.031	5.517	0.238	0.238	0.000	0.000	0.000	0.000
104	A	108	LEU	0	0.068	0.022	2.465	-1.718	-0.393	1.300	-0.537	-2.088	0.001
105	A	109	GLY	0	0.022	0.025	2.314	-2.484	-1.072	2.091	-1.320	-2.183	-0.003
106	A	110	LYS	1	0.756	0.851	2.924	0.492	-0.969	0.079	1.785	-0.404	0.000
107	A	111	LEU	0	0.025	0.010	5.845	-0.069	-0.069	0.000	0.000	0.000	0.000
108	A	112	GLU	-1	-0.740	-0.868	2.314	-14.038	-10.714	4.991	-4.023	-4.292	-0.050
109	A	113	LYS	1	0.879	0.950	4.611	-6.079	-5.907	-0.001	-0.024	-0.147	0.000
110	A	114	SER	0	-0.057	-0.017	7.340	-0.081	-0.081	0.000	0.000	0.000	0.000
111	A	115	PHE	0	-0.044	-0.032	9.007	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	116	ASN	0	-0.023	-0.010	8.589	-0.144	-0.144	0.000	0.000	0.000	0.000
113	A	117	SER	0	-0.046	-0.020	9.350	-0.159	-0.159	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.005	0.006	5.786	0.161	0.161	0.000	0.000	0.000	0.000
115	A	119	HIS	0	0.014	0.020	6.907	-0.025	-0.025	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.003	0.003	6.560	0.042	0.042	0.000	0.000	0.000	0.000
117	A	121	LEU	0	-0.018	-0.016	8.982	-0.105	-0.105	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.010	-0.006	12.268	0.012	0.012	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.045	0.019	13.225	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	124	GLY	0	-0.024	-0.005	14.034	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	125	PHE	0	0.016	-0.008	14.846	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	126	ALA	0	-0.015	0.023	17.883	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	127	GLU	-1	-0.879	-0.917	18.158	-0.022	-0.022	0.000	0.000	0.000	0.000
124	A	128	PHE	0	0.073	0.018	18.687	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	129	SER	0	-0.020	-0.041	20.526	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	130	ARG	1	0.818	0.906	21.642	0.008	0.008	0.000	0.000	0.000	0.000
127	A	131	CYS	0	-0.105	-0.046	22.751	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	132	PHE	0	0.022	0.002	23.646	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	133	PRO	0	0.077	0.029	25.609	0.005	0.005	0.000	0.000	0.000	0.000
130	A	134	GLY	0	-0.044	-0.020	27.723	0.003	0.003	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.011	0.002	24.855	0.000	0.000	0.000	0.000	0.000	0.000
132	A	136	CYS	0	-0.056	-0.018	24.142	0.007	0.007	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.837	-0.903	25.135	0.043	0.043	0.000	0.000	0.000	0.000
134	A	138	GLY	0	-0.016	-0.009	25.958	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:MET)