FMO DATABASE

FMODB ID: R9RL8

Calculation Name: 1VDM-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1VDM

Chain ID: A

ChEMBL ID:
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UniProt ID: O57827

Base Structure: X-ray

Registration Date: 2023-09-20

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1486034.149024
FMO2-HF: Nuclear repulsion	1425692.264742
FMO2-HF: Total energy	-60341.884282
FMO2-MP2: Total energy	-60521.615794

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.
-0.167	5.033	1.949	-2.582	-4.566	0

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 : 0.011 / q_NPA : 0.003

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	LYS	1	0.964	0.986	3.133	0.243	4.161	0.002	-1.899	-2.021	0.006
4	A	4	VAL	0	-0.025	-0.010	4.059	-0.691	-0.538	0.000	-0.063	-0.089	0.000
5	A	5	TYR	0	0.012	0.004	2.578	-1.788	-0.659	1.947	-0.620	-2.456	-0.006
6	A	6	LEU	0	-0.021	0.010	6.257	0.267	0.267	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.030	-0.014	9.679	0.099	0.099	0.000	0.000	0.000	0.000
8	A	8	TRP	0	0.135	0.038	11.344	-0.024	-0.024	0.000	0.000	0.000	0.000
9	A	9	TRP	0	0.058	0.023	14.675	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.006	0.027	10.802	0.021	0.021	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.055	0.027	14.269	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.821	-0.905	16.796	-0.136	-0.136	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.867	0.929	15.794	0.183	0.183	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.013	0.001	18.040	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.037	0.013	20.044	0.005	0.005	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.023	-0.018	22.592	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.030	-0.005	23.120	0.011	0.011	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.003	-0.001	22.057	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.003	0.008	25.846	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.869	-0.924	28.493	-0.105	-0.105	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.808	0.892	28.559	0.157	0.157	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.017	0.013	28.129	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.874	0.925	31.541	0.118	0.118	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.857	-0.911	33.485	-0.131	-0.131	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.045	-0.033	33.688	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.851	0.936	35.929	0.107	0.107	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.027	0.020	32.978	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.772	-0.875	35.830	-0.094	-0.094	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.054	-0.037	35.294	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.010	0.020	29.025	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.017	-0.013	30.402	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.043	0.013	27.084	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.028	-0.013	24.888	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.059	0.032	23.807	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.923	0.913	20.405	0.184	0.184	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.094	0.025	18.514	0.021	0.021	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.091	0.030	19.488	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.058	-0.047	22.182	0.021	0.021	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.014	0.015	18.722	0.020	0.020	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.013	-0.010	19.876	0.020	0.020	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.012	0.018	22.528	0.018	0.018	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.014	0.003	25.356	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.866	0.924	22.686	0.152	0.152	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.001	-0.009	25.397	0.012	0.012	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.038	-0.012	27.843	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.055	-0.028	28.442	0.006	0.006	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.044	-0.029	25.986	0.007	0.007	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.100	-0.048	30.139	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.004	0.001	32.941	0.002	0.002	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.854	-0.917	34.097	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.021	0.014	32.851	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.010	-0.010	34.350	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.010	0.005	29.016	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.844	0.922	32.729	0.112	0.112	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.012	-0.003	28.750	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.023	0.020	29.325	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.828	-0.903	26.639	-0.203	-0.203	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.025	0.012	27.258	0.012	0.012	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.820	0.895	25.264	0.170	0.170	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.009	-0.007	25.207	0.014	0.014	0.000	0.000	0.000	0.000
61	A	61	TYR	0	0.058	0.040	25.702	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.948	0.935	25.941	0.169	0.169	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.060	0.025	27.767	0.009	0.009	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.040	0.029	29.202	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.865	-0.927	29.771	-0.083	-0.083	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-1.087	-1.014	31.389	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.898	0.936	30.916	0.107	0.107	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.004	0.002	31.942	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.954	-0.971	32.900	-0.114	-0.114	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.943	0.953	31.903	0.147	0.147	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.052	-0.024	30.205	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.052	0.041	30.887	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.003	-0.005	31.134	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.079	-0.020	29.446	0.006	0.006	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.047	0.025	29.250	0.009	0.009	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.010	0.010	32.650	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.022	0.019	33.705	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.047	0.010	36.359	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.022	-0.001	39.785	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.813	-0.907	41.191	-0.089	-0.089	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.004	-0.011	37.336	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.870	0.927	41.515	0.082	0.082	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.897	-0.946	44.625	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.834	0.902	40.279	0.092	0.092	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.790	0.890	37.695	0.100	0.100	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.014	0.010	33.835	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.024	0.022	29.399	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.041	-0.020	27.660	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.003	-0.004	24.082	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.850	-0.937	21.836	-0.331	-0.331	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.857	-0.941	17.217	-0.460	-0.460	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.027	-0.020	15.764	-0.042	-0.042	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.034	0.030	18.675	0.020	0.020	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.833	-0.912	16.248	-0.701	-0.701	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.055	0.001	19.170	0.020	0.020	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.074	0.049	22.072	0.020	0.020	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.950	0.983	24.539	0.291	0.291	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.026	-0.005	23.934	0.022	0.022	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.056	0.026	24.296	0.021	0.021	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.854	-0.897	27.557	-0.231	-0.231	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.023	-0.013	29.959	0.017	0.017	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.008	-0.003	28.470	0.014	0.014	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.006	-0.002	29.969	0.015	0.015	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.836	-0.912	33.271	-0.142	-0.142	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.813	-0.902	34.595	-0.119	-0.119	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.005	0.001	33.793	0.009	0.009	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.860	0.931	36.673	0.163	0.163	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.768	0.890	39.113	0.128	0.128	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.038	-0.033	38.090	0.007	0.007	0.000	0.000	0.000	0.000
110	A	110	GLY	0	-0.015	-0.014	41.554	0.005	0.005	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.056	-0.020	38.493	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.917	0.992	40.464	0.091	0.091	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.882	-0.937	38.031	-0.130	-0.130	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.021	-0.017	33.379	0.000	0.000	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.888	0.955	31.902	0.153	0.153	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.009	0.001	26.340	0.000	0.000	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.012	-0.010	25.788	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.007	0.000	20.968	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.012	0.011	16.871	0.009	0.009	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.029	-0.019	15.857	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	121	MET	0	-0.022	0.008	17.669	0.022	0.022	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.891	0.953	13.329	0.873	0.873	0.000	0.000	0.000	0.000
123	A	123	PRO	0	-0.083	-0.068	17.141	0.063	0.063	0.000	0.000	0.000	0.000
124	A	124	TRP	0	-0.044	-0.033	14.396	0.026	0.026	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.050	0.003	21.489	0.039	0.039	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.043	-0.035	22.989	0.005	0.005	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.028	-0.020	25.456	0.027	0.027	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.004	0.000	24.924	-0.027	-0.027	0.000	0.000	0.000	0.000
129	A	129	PRO	0	-0.018	-0.012	22.753	0.019	0.019	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.827	-0.898	26.061	-0.204	-0.204	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.030	-0.030	26.354	0.007	0.007	0.000	0.000	0.000	0.000
132	A	132	TYR	0	0.022	-0.009	20.201	-0.024	-0.024	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.039	-0.011	18.430	0.019	0.019	0.000	0.000	0.000	0.000
134	A	134	PHE	0	-0.033	-0.018	14.734	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.981	0.988	16.257	0.514	0.514	0.000	0.000	0.000	0.000
136	A	136	THR	0	-0.039	-0.021	11.432	-0.111	-0.111	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.815	-0.928	11.529	-1.324	-1.324	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.919	0.979	6.313	3.063	3.063	0.000	0.000	0.000	0.000
139	A	139	TRP	0	-0.014	-0.011	8.718	0.259	0.259	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.007	-0.012	8.358	-0.339	-0.339	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.035	-0.002	6.691	0.093	0.093	0.000	0.000	0.000	0.000
142	A	142	PHE	0	0.012	-0.015	9.113	-0.022	-0.022	0.000	0.000	0.000	0.000
143	A	143	PRO	0	-0.050	-0.038	11.181	0.002	0.002	0.000	0.000	0.000	0.000
144	A	144	TRP	0	-0.078	-0.040	12.177	0.058	0.058	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.849	-0.907	11.350	-0.617	-0.617	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.899	-0.938	11.059	-0.251	-0.251	0.000	0.000	0.000	0.000
147	A	147	PHE	0	-0.053	-0.045	5.931	-0.240	-0.240	0.000	0.000	0.000	0.000
148	A	148	PRO	0	-0.015	-0.006	8.118	0.096	0.096	0.000	0.000	0.000	0.000
149	A	149	VAL	0	0.021	0.011	9.108	0.079	0.079	0.000	0.000	0.000	0.000
150	A	150	ILE	0	-0.041	-0.021	8.199	-0.075	-0.075	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.929	-0.959	11.328	0.316	0.316	0.000	0.000	0.000	0.000
152	A	152	LYS	1	0.870	0.926	14.926	-0.430	-0.430	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.907	-0.942	16.798	0.069	0.069	0.000	0.000	0.000	0.000

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