FMO DATABASE

FMODB ID: 2LKQR

Calculation Name: 1VR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1071553.16461
FMO2-HF: Nuclear repulsion	1021423.428828
FMO2-HF: Total energy	-50129.735783
FMO2-MP2: Total energy	-50274.214767

3D Structure Molmil

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.
-15.273	-8.302	8.627	-5.016	-10.579	-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 : 0.032 / q_NPA : 0.032

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	VAL	0	0.075	0.029	2.687	-5.495	-2.176	0.552	-1.699	-2.172	-0.012
4	A	4	LYS	1	0.980	0.997	5.419	-1.207	-1.207	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.826	0.937	2.636	0.435	1.663	1.883	-0.665	-2.445	0.001
6	A	6	TRP	0	0.013	-0.024	2.026	0.057	-0.721	5.370	-1.396	-3.196	-0.009
7	A	7	VAL	0	-0.031	0.019	6.144	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.030	0.022	9.342	0.099	0.099	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.052	-0.076	12.635	0.027	0.027	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.925	-0.939	15.833	-0.228	-0.228	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.019	-0.013	16.486	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.021	0.014	18.732	0.040	0.040	0.000	0.000	0.000	0.000
13	A	13	MET	0	0.011	0.032	21.389	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.017	-0.041	23.213	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.814	-0.888	26.091	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.891	-0.967	28.433	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.131	-0.089	30.106	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.005	0.015	30.837	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.007	-0.013	32.810	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.045	0.012	33.550	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.826	0.906	33.783	0.044	0.044	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.904	-0.951	31.911	-0.050	-0.050	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.001	0.018	29.041	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.045	0.008	29.198	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.054	-0.029	30.546	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.966	0.985	25.913	0.089	0.089	0.000	0.000	0.000	0.000
27	A	27	MET	0	0.039	0.032	25.667	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.897	0.959	26.665	0.099	0.099	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.109	-0.049	26.674	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.017	-0.014	20.069	0.009	0.009	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.092	-0.033	23.178	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.004	0.010	21.968	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.036	-0.034	24.259	0.014	0.014	0.000	0.000	0.000	0.000
34	A	34	GLH	0	0.104	0.039	18.873	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	CYS	0	-0.082	-0.040	23.350	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.035	0.028	17.523	0.009	0.009	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.014	0.003	21.990	0.011	0.011	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.919	0.960	22.820	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.747	-0.882	24.764	0.059	0.059	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.907	0.925	27.286	-0.029	-0.029	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.976	-0.974	27.641	0.101	0.101	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.065	-0.027	24.107	0.017	0.017	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.051	-0.019	22.342	0.024	0.024	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.006	0.004	19.911	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.909	0.959	22.049	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.051	0.014	23.062	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.035	-0.014	20.802	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.023	0.004	23.923	0.012	0.012	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.051	0.025	24.814	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.926	0.940	27.502	0.172	0.172	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.977	-0.985	29.834	-0.135	-0.135	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.831	-0.907	30.689	-0.097	-0.097	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.115	-0.088	30.842	0.012	0.012	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.070	-0.016	34.544	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.918	-0.955	36.922	-0.074	-0.074	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.074	-0.031	35.799	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.848	-0.919	39.656	-0.048	-0.048	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.012	0.009	37.646	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.866	-0.932	38.417	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.091	-0.057	39.142	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.013	0.011	35.419	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.011	-0.011	30.320	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.016	0.015	32.137	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.064	-0.049	32.758	0.005	0.005	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.905	0.950	32.256	0.051	0.051	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.043	0.015	26.549	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.042	0.026	26.663	0.013	0.013	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.010	-0.009	22.136	0.003	0.003	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.032	0.005	22.667	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.929	-0.962	21.717	0.017	0.017	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.036	-0.014	16.907	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.018	-0.014	15.930	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.024	-0.007	10.323	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	74	HIS	0	0.052	0.019	12.545	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.935	-0.983	10.065	0.617	0.617	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.946	-0.979	8.484	2.039	2.039	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.818	-0.899	9.043	0.791	0.791	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.040	-0.035	4.464	1.053	1.225	-0.001	-0.032	-0.139	0.000
79	A	79	ILE	0	0.058	0.023	2.432	-1.332	0.232	0.813	-0.742	-1.634	-0.002
80	A	80	THR	0	-0.008	-0.028	3.857	0.327	0.598	-0.001	-0.028	-0.242	0.000
81	A	81	HIS	0	-0.007	-0.001	5.992	0.206	0.206	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.061	0.028	8.221	0.084	0.084	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.028	-0.003	9.090	0.054	0.054	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.026	-0.016	10.805	0.089	0.089	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.050	0.034	13.020	0.037	0.037	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.011	-0.006	10.944	0.019	0.019	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.068	-0.028	15.030	0.031	0.031	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.997	-0.990	16.906	-0.090	-0.090	0.000	0.000	0.000	0.000
89	A	89	HIS	0	0.019	0.005	18.421	0.018	0.018	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.070	-0.034	17.946	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.905	-0.952	18.490	-0.238	-0.238	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.015	-0.015	17.257	-0.071	-0.071	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.020	-0.016	15.291	-0.070	-0.070	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.046	0.052	11.313	0.058	0.058	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.019	-0.006	13.638	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.004	0.015	10.447	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.003	0.004	13.527	0.015	0.015	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.833	-0.927	14.450	0.369	0.369	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.915	-0.977	16.526	0.540	0.540	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.983	-0.982	18.807	0.301	0.301	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.022	-0.008	19.547	-0.049	-0.049	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.876	0.946	19.930	-0.223	-0.223	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.006	0.004	17.148	0.021	0.021	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.870	0.932	14.282	-0.301	-0.301	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.016	0.016	13.876	0.031	0.031	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.001	0.006	13.492	0.008	0.008	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.038	0.024	8.368	-0.024	-0.024	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.019	0.017	10.887	0.027	0.027	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.027	0.006	11.608	-0.183	-0.183	0.000	0.000	0.000	0.000
110	A	110	HIS	0	-0.076	-0.043	12.376	-0.080	-0.080	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.802	-0.916	8.977	-1.125	-1.125	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.033	-0.018	7.693	-0.478	-0.478	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.032	-0.024	8.022	-0.318	-0.318	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.929	-0.957	8.594	-1.536	-1.536	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.026	-0.018	3.972	-0.403	-0.290	-0.001	-0.015	-0.097	0.000
116	A	116	LEU	0	-0.035	-0.022	5.778	-0.322	-0.322	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.066	-0.024	7.782	0.288	0.288	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.947	-0.971	3.905	-9.924	-8.914	0.013	-0.435	-0.588	-0.003
119	A	119	ALA	0	-0.063	-0.018	4.775	0.219	0.291	-0.001	-0.004	-0.066	0.000
120	A	120	LEU	0	-0.069	-0.054	6.677	0.615	0.615	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.013	0.016	10.385	-0.054	-0.054	0.000	0.000	0.000	0.000

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