FMO DATABASE

FMODB ID: V5RR1

Calculation Name: 2VW9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VW9

Chain ID: A

ChEMBL ID:

UniProt ID: O25841

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-766333.459422
FMO2-HF: Nuclear repulsion	723478.368696
FMO2-HF: Total energy	-42855.090726
FMO2-MP2: Total energy	-42978.308892

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:1001:MET)

Summations of interaction energy for fragment #1(A:1001: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.
0.456	1.888	-0.01	-0.516	-0.906	0.003

Interaction energy analysis for fragmet #1(A:1001:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.016

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	1003	ASN	0	0.016	0.013	3.787	-0.974	0.458	-0.010	-0.516	-0.906	0.003
4	A	1004	LYS	1	0.859	0.919	5.968	0.925	0.925	0.000	0.000	0.000	0.000
5	A	1005	VAL	0	0.007	0.010	9.577	0.039	0.039	0.000	0.000	0.000	0.000
6	A	1006	ILE	0	0.020	-0.003	12.819	0.041	0.041	0.000	0.000	0.000	0.000
7	A	1007	MET	0	-0.036	-0.013	16.213	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	1008	VAL	0	0.039	0.036	19.207	0.016	0.016	0.000	0.000	0.000	0.000
9	A	1009	GLY	0	0.006	0.002	22.938	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	1010	ARG	1	0.928	0.967	24.964	0.126	0.126	0.000	0.000	0.000	0.000
11	A	1011	LEU	0	0.002	0.000	26.016	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	1012	THR	0	-0.012	-0.007	27.274	0.010	0.010	0.000	0.000	0.000	0.000
13	A	1013	ARG	1	0.829	0.906	25.012	0.131	0.131	0.000	0.000	0.000	0.000
14	A	1014	ASN	0	0.016	0.000	30.130	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	1015	VAL	0	0.015	0.022	27.032	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	1016	GLU	-1	-0.888	-0.934	27.325	-0.090	-0.090	0.000	0.000	0.000	0.000
17	A	1017	LEU	0	-0.035	-0.026	26.708	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	1018	LYS	1	0.936	0.976	24.965	0.077	0.077	0.000	0.000	0.000	0.000
19	A	1019	TYR	0	0.017	0.001	27.189	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	1020	LEU	0	-0.037	-0.026	21.720	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	1021	PRO	0	0.023	0.003	26.246	0.004	0.004	0.000	0.000	0.000	0.000
22	A	1022	SER	0	-0.007	-0.006	23.447	0.002	0.002	0.000	0.000	0.000	0.000
23	A	1023	GLY	0	0.065	0.039	26.523	0.005	0.005	0.000	0.000	0.000	0.000
24	A	1024	SER	0	-0.056	-0.025	22.487	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	1025	ALA	0	0.053	0.046	24.587	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	1026	ALA	0	-0.023	-0.027	22.392	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	1027	ALA	0	0.020	0.018	22.393	0.010	0.010	0.000	0.000	0.000	0.000
28	A	1028	THR	0	-0.035	-0.008	21.961	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	1029	ILE	0	0.009	0.019	22.058	0.015	0.015	0.000	0.000	0.000	0.000
30	A	1030	GLY	0	0.041	0.021	23.028	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	1031	LEU	0	-0.026	-0.009	21.064	0.010	0.010	0.000	0.000	0.000	0.000
32	A	1032	ALA	0	0.023	0.016	24.331	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	1033	THR	0	-0.006	-0.014	22.020	0.003	0.003	0.000	0.000	0.000	0.000
34	A	1034	SER	0	-0.030	0.002	24.525	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	1035	ARG	1	0.930	0.977	22.505	0.211	0.211	0.000	0.000	0.000	0.000
36	A	1036	ARG	1	0.974	0.982	26.333	0.136	0.136	0.000	0.000	0.000	0.000
37	A	1037	PHE	0	-0.011	-0.007	27.403	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	1038	LYS	1	0.920	0.958	29.489	0.109	0.109	0.000	0.000	0.000	0.000
39	A	1039	LYS	1	0.940	0.963	31.119	0.100	0.100	0.000	0.000	0.000	0.000
40	A	1040	GLN	0	0.023	0.004	32.693	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	1041	ASP	-1	-0.816	-0.890	34.049	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	1042	GLY	0	-0.023	-0.042	37.240	0.001	0.001	0.000	0.000	0.000	0.000
43	A	1043	THR	0	-0.006	0.012	36.073	0.001	0.001	0.000	0.000	0.000	0.000
44	A	1044	LEU	0	0.045	0.043	32.632	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	1045	GLY	0	-0.120	-0.070	32.045	0.006	0.006	0.000	0.000	0.000	0.000
46	A	1046	GLU	-1	-0.948	-0.998	29.620	-0.124	-0.124	0.000	0.000	0.000	0.000
47	A	1047	GLU	-1	-0.898	-0.922	23.831	-0.203	-0.203	0.000	0.000	0.000	0.000
48	A	1048	VAL	0	0.018	-0.006	26.384	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	1049	CYS	0	-0.039	-0.013	19.612	0.000	0.000	0.000	0.000	0.000	0.000
50	A	1050	PHE	0	0.015	0.001	23.308	0.005	0.005	0.000	0.000	0.000	0.000
51	A	1051	ILE	0	0.026	0.006	16.699	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	1052	ASP	-1	-0.813	-0.890	20.276	-0.141	-0.141	0.000	0.000	0.000	0.000
53	A	1053	ALA	0	-0.005	-0.008	18.190	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	1054	ARG	1	0.745	0.833	16.868	0.195	0.195	0.000	0.000	0.000	0.000
55	A	1055	LEU	0	0.029	0.014	17.588	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	1056	PHE	0	0.029	-0.007	15.892	0.015	0.015	0.000	0.000	0.000	0.000
57	A	1057	GLY	0	0.034	0.024	19.923	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	1058	ARG	1	1.020	0.991	22.062	0.047	0.047	0.000	0.000	0.000	0.000
59	A	1059	THR	0	0.044	0.025	18.938	0.010	0.010	0.000	0.000	0.000	0.000
60	A	1060	ALA	0	-0.013	-0.004	21.999	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	1061	GLU	-1	-0.887	-0.956	23.611	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	1062	ILE	0	-0.047	-0.012	24.003	0.003	0.003	0.000	0.000	0.000	0.000
63	A	1063	ALA	0	0.024	-0.004	24.258	0.001	0.001	0.000	0.000	0.000	0.000
64	A	1064	ASN	0	0.001	-0.015	26.327	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	1065	GLN	0	-0.037	0.003	29.211	0.003	0.003	0.000	0.000	0.000	0.000
66	A	1066	TYR	0	-0.058	-0.037	29.073	0.005	0.005	0.000	0.000	0.000	0.000
67	A	1067	LEU	0	-0.030	0.005	25.587	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	1068	SER	0	0.035	0.017	30.181	0.006	0.006	0.000	0.000	0.000	0.000
69	A	1069	LYS	1	0.966	0.976	31.567	0.076	0.076	0.000	0.000	0.000	0.000
70	A	1070	GLY	0	-0.048	-0.018	31.599	0.005	0.005	0.000	0.000	0.000	0.000
71	A	1071	SER	0	-0.012	-0.020	29.998	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1072	SER	0	-0.051	-0.019	28.241	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	1073	VAL	0	-0.053	-0.033	23.690	0.008	0.008	0.000	0.000	0.000	0.000
74	A	1074	LEU	0	0.039	0.012	19.706	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	1075	ILE	0	-0.028	0.001	16.661	0.013	0.013	0.000	0.000	0.000	0.000
76	A	1076	GLU	-1	-0.813	-0.895	14.535	-0.339	-0.339	0.000	0.000	0.000	0.000
77	A	1077	GLY	0	0.019	0.005	12.889	0.056	0.056	0.000	0.000	0.000	0.000
78	A	1078	ARG	1	0.966	1.002	7.931	0.528	0.528	0.000	0.000	0.000	0.000
79	A	1079	LEU	0	0.009	-0.011	9.253	0.183	0.183	0.000	0.000	0.000	0.000
80	A	1080	THR	0	-0.053	-0.046	9.156	-0.142	-0.142	0.000	0.000	0.000	0.000
81	A	1081	TYR	0	0.033	0.021	11.088	0.039	0.039	0.000	0.000	0.000	0.000
82	A	1082	GLU	-1	-0.803	-0.884	12.623	-0.144	-0.144	0.000	0.000	0.000	0.000
83	A	1083	SER	0	0.035	0.006	15.799	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	1084	TRP	0	-0.058	-0.026	17.642	0.007	0.007	0.000	0.000	0.000	0.000
85	A	1085	MET	0	0.037	0.026	21.089	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	1086	ASP	-1	-0.827	-0.915	24.760	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	1087	GLN	0	0.018	-0.010	27.236	0.005	0.005	0.000	0.000	0.000	0.000
88	A	1088	THR	0	-0.016	0.014	30.358	0.004	0.004	0.000	0.000	0.000	0.000
89	A	1089	GLY	0	-0.015	-0.001	29.252	0.004	0.004	0.000	0.000	0.000	0.000
90	A	1090	LYS	1	0.894	0.929	27.243	0.053	0.053	0.000	0.000	0.000	0.000
91	A	1091	LYS	1	0.952	0.974	22.534	0.007	0.007	0.000	0.000	0.000	0.000
92	A	1092	ASN	0	-0.038	-0.016	22.542	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	1093	SER	0	0.004	0.008	17.397	0.004	0.004	0.000	0.000	0.000	0.000
94	A	1094	ARG	1	0.885	0.922	17.290	0.146	0.146	0.000	0.000	0.000	0.000
95	A	1095	HIS	0	0.047	0.044	12.848	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	1096	THR	0	-0.085	-0.044	14.640	0.008	0.008	0.000	0.000	0.000	0.000
97	A	1097	ILE	0	0.071	0.043	13.885	-0.056	-0.056	0.000	0.000	0.000	0.000
98	A	1098	THR	0	-0.058	0.004	12.417	0.064	0.064	0.000	0.000	0.000	0.000
99	A	1099	ALA	0	0.001	-0.022	13.448	-0.070	-0.070	0.000	0.000	0.000	0.000
100	A	1100	ASP	-1	-0.905	-0.949	12.190	-0.409	-0.409	0.000	0.000	0.000	0.000
101	A	1101	SER	0	-0.061	-0.033	15.406	0.053	0.053	0.000	0.000	0.000	0.000
102	A	1102	LEU	0	0.010	-0.013	18.618	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	1103	GLN	0	0.007	0.011	21.710	0.020	0.020	0.000	0.000	0.000	0.000
104	A	1104	PHE	0	0.012	0.001	24.063	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	1105	MET	0	-0.003	-0.001	26.625	0.000	0.000	0.000	0.000	0.000	0.000
106	A	1106	ASP	-1	-0.723	-0.841	29.562	-0.095	-0.095	0.000	0.000	0.000	0.000
107	A	1107	LYS	1	0.948	0.987	32.799	0.063	0.063	0.000	0.000	0.000	0.000
108	A	1108	LYS	1	0.867	0.930	32.192	0.090	0.090	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1001:MET)