FMO DATABASE

FMODB ID: 6G32Z

Calculation Name: 1VR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VR9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZZ4

Base Structure: X-ray

Registration Date: 2023-09-26

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1073089.116081
FMO2-HF: Nuclear repulsion	1022958.484626
FMO2-HF: Total energy	-50130.631454
FMO2-MP2: Total energy	-50275.184467

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.
-15.571	-6.365	7.599	-5.817	-10.986	-0.025

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 : 0.020 / q_NPA : 0.020

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

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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	VAL	0	0.060	0.020	2.938	-4.562	-1.112	0.218	-1.735	-1.932	-0.007
4	A	4	LYS	1	0.842	0.900	5.502	-1.143	-1.143	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.746	0.892	2.616	2.097	2.830	3.604	-1.076	-3.261	-0.001
6	A	6	TRP	0	0.006	0.003	2.131	-0.859	-0.319	2.912	-0.964	-2.488	-0.004
7	A	7	VAL	0	-0.045	0.008	6.298	-0.175	-0.175	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.040	0.022	9.559	0.098	0.098	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.031	-0.060	12.835	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.931	-0.929	16.011	-0.165	-0.165	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.008	-0.008	16.568	-0.055	-0.055	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.024	0.012	18.783	0.035	0.035	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.002	0.010	21.475	0.008	0.008	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.027	-0.044	23.285	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.761	-0.850	26.177	0.030	0.030	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.769	-0.884	28.550	0.028	0.028	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.108	-0.079	30.168	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.003	0.009	30.930	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.005	-0.039	32.876	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.030	0.004	33.555	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.759	0.840	33.739	0.027	0.027	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.864	-0.905	31.925	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.019	0.008	28.310	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.049	0.012	29.157	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.016	-0.004	30.482	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.973	0.983	26.018	0.048	0.048	0.000	0.000	0.000	0.000
27	A	27	MET	0	0.050	0.036	25.585	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.850	0.932	26.537	0.072	0.072	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.107	-0.050	26.695	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.010	-0.023	20.267	0.006	0.006	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.100	-0.037	23.067	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.014	0.016	21.804	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.038	-0.042	24.058	0.011	0.011	0.000	0.000	0.000	0.000
34	A	34	GLH	0	0.085	0.035	18.726	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	CYS	0	-0.080	-0.035	23.245	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.042	0.034	17.545	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.015	0.004	21.966	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.949	0.983	23.063	-0.060	-0.060	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.762	-0.885	24.877	0.084	0.084	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.786	0.850	27.477	-0.043	-0.043	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.964	-0.964	28.005	0.117	0.117	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.064	-0.022	24.376	0.018	0.018	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.030	-0.021	22.562	0.030	0.030	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.006	0.003	19.989	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.819	0.906	22.133	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.069	0.027	22.972	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.044	-0.018	20.611	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.018	0.004	23.807	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.030	0.001	24.329	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.922	0.943	27.292	0.152	0.152	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.960	-0.976	28.854	-0.134	-0.134	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.797	-0.892	30.998	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.058	-0.047	30.870	0.011	0.011	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.059	-0.010	34.376	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.930	-0.965	36.717	-0.066	-0.066	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.056	-0.017	35.664	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.866	-0.929	39.520	-0.036	-0.036	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.019	0.002	37.665	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.803	-0.873	38.401	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.081	-0.034	38.969	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.000	-0.002	35.549	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.011	-0.004	30.262	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.024	0.007	32.082	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.058	-0.047	32.716	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.813	0.904	32.098	0.054	0.054	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.055	-0.002	26.535	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.029	0.018	26.692	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.016	-0.008	21.922	0.005	0.005	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.026	0.007	22.507	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.913	-0.959	21.724	0.022	0.022	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.033	-0.014	16.539	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.025	-0.018	15.801	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.021	-0.002	10.151	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	74	HIS	0	0.043	0.012	12.545	0.004	0.004	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.847	-0.931	10.308	0.741	0.741	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.868	-0.931	8.772	2.114	2.114	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.813	-0.885	8.973	0.872	0.872	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.028	-0.022	4.319	1.009	1.215	-0.001	-0.036	-0.169	0.000
79	A	79	ILE	0	0.061	0.024	2.454	-1.350	0.105	0.761	-0.672	-1.544	-0.002
80	A	80	THR	0	-0.008	-0.028	4.111	0.288	0.540	-0.001	-0.022	-0.229	0.000
81	A	81	HIS	0	-0.013	-0.002	6.243	0.197	0.197	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.065	0.029	8.553	0.084	0.084	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.024	0.001	9.464	0.053	0.053	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.033	-0.019	11.196	0.090	0.090	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.056	0.037	13.352	0.041	0.041	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.005	-0.005	10.603	0.021	0.021	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.072	-0.024	15.318	0.031	0.031	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.978	-0.985	17.223	-0.094	-0.094	0.000	0.000	0.000	0.000
89	A	89	HIS	0	0.010	-0.001	18.542	0.021	0.021	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.087	-0.042	17.998	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.858	-0.917	18.174	-0.207	-0.207	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.030	-0.027	17.000	-0.064	-0.064	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.014	-0.008	15.117	-0.063	-0.063	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.044	0.046	11.047	0.048	0.048	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.011	-0.003	13.565	0.011	0.011	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.002	0.011	10.557	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.018	0.015	13.609	0.017	0.017	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.780	-0.898	14.645	0.428	0.428	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.916	-0.977	16.789	0.563	0.563	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.919	-0.937	19.039	0.257	0.257	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.018	-0.006	19.346	-0.046	-0.046	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.782	0.888	20.071	-0.265	-0.265	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.002	-0.007	17.388	0.027	0.027	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.766	0.880	14.352	-0.389	-0.389	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.023	0.017	14.107	0.040	0.040	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.015	-0.001	13.524	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.030	0.021	8.060	0.007	0.007	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.010	-0.029	10.805	0.005	0.005	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.017	0.000	11.340	-0.175	-0.175	0.000	0.000	0.000	0.000
110	A	110	HIS	0	-0.065	-0.043	12.380	-0.115	-0.115	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.771	-0.866	9.049	-0.892	-0.892	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.016	-0.009	7.715	-0.485	-0.485	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.028	-0.022	8.160	-0.359	-0.359	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.914	-0.952	8.257	-1.452	-1.452	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.022	-0.021	4.215	-0.500	-0.378	-0.001	-0.015	-0.106	0.000
116	A	116	LEU	0	-0.037	-0.028	5.716	-0.417	-0.417	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.067	-0.025	7.687	0.260	0.260	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.884	-0.937	3.110	-11.927	-9.556	0.108	-1.292	-1.187	-0.011
119	A	119	ALA	0	-0.060	-0.020	4.712	0.162	0.239	-0.001	-0.005	-0.070	0.000
120	A	120	LEU	0	-0.043	-0.041	6.791	0.543	0.543	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.015	0.015	10.599	-0.044	-0.044	0.000	0.000	0.000	0.000

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