FMO DATABASE

FMODB ID: QYQLY

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	OptAll
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	-1487383.38383
FMO2-HF: Nuclear repulsion	1427040.408925
FMO2-HF: Total energy	-60342.974905
FMO2-MP2: Total energy	-60522.633064

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.
-0.282	4.347	2.799	-2.572	-4.855	-0.002

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 : 0.019 / q_NPA : 0.007

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	0.831	0.904	3.223	1.036	4.637	-0.006	-1.824	-1.771	0.005
4	A	4	VAL	0	-0.018	-0.011	4.039	-0.745	-0.542	0.001	-0.070	-0.134	0.000
5	A	5	TYR	0	0.032	0.020	2.629	-1.654	-0.829	2.804	-0.678	-2.950	-0.007
6	A	6	LEU	0	-0.054	-0.014	5.922	0.293	0.293	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.024	-0.016	9.259	0.088	0.088	0.000	0.000	0.000	0.000
8	A	8	TRP	0	0.101	0.026	10.955	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	TRP	0	0.063	0.026	14.396	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.000	0.037	9.996	0.038	0.038	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.059	0.028	13.805	0.001	0.001	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.812	-0.896	16.371	-0.128	-0.128	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.867	0.925	15.844	0.138	0.138	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.007	0.013	17.848	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.032	0.013	19.847	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.005	-0.012	22.301	0.013	0.013	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.028	-0.009	22.638	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.022	-0.011	21.633	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.010	0.005	25.396	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.862	-0.917	28.102	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.831	0.890	28.225	0.152	0.152	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.000	0.009	27.733	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.849	0.899	31.262	0.110	0.110	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.852	-0.899	32.990	-0.127	-0.127	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.062	-0.038	33.032	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.873	0.934	35.221	0.106	0.106	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.018	0.023	32.360	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.783	-0.875	35.540	-0.093	-0.093	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.061	-0.035	35.127	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.012	0.021	28.863	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.023	-0.017	30.325	0.009	0.009	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.043	0.021	26.697	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.030	-0.017	24.217	0.015	0.015	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.042	-0.008	23.614	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.817	0.881	19.889	0.209	0.209	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.119	0.039	18.128	0.023	0.023	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.049	0.017	19.085	0.017	0.017	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.014	-0.011	21.611	0.023	0.023	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.004	0.015	18.723	0.024	0.024	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.011	-0.023	19.655	0.021	0.021	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.011	0.018	22.338	0.020	0.020	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.028	0.010	25.265	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.849	0.911	22.433	0.141	0.141	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.005	-0.006	25.154	0.013	0.013	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.034	-0.022	27.512	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.033	-0.029	28.077	0.004	0.004	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.053	-0.023	25.589	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.071	-0.032	29.916	0.004	0.004	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.022	0.000	32.603	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.867	-0.924	33.802	-0.074	-0.074	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.018	0.013	32.704	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.014	0.002	34.027	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.021	0.008	28.587	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.830	0.919	32.815	0.115	0.115	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.015	-0.002	28.553	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.005	0.008	28.714	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.761	-0.851	26.399	-0.222	-0.222	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.037	0.022	27.114	0.015	0.015	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.825	0.883	25.220	0.191	0.191	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.012	0.006	25.263	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	TYR	0	0.056	0.037	26.170	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.957	0.969	26.309	0.187	0.187	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.021	0.051	28.595	0.007	0.007	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.025	-0.036	28.327	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.865	-0.925	30.007	-0.106	-0.106	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.961	-0.994	32.001	-0.094	-0.094	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.871	0.920	30.572	0.119	0.119	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.029	-0.016	32.205	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.874	-0.919	33.202	-0.129	-0.129	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.883	0.921	31.854	0.141	0.141	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.033	-0.008	29.873	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.033	0.020	31.095	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.007	-0.001	30.995	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.077	-0.024	29.250	0.006	0.006	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.031	0.014	29.301	0.009	0.009	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.000	0.002	32.479	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.031	0.019	33.358	0.005	0.005	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.050	0.018	35.950	0.006	0.006	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.004	0.004	39.350	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.852	-0.936	40.539	-0.092	-0.092	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.005	-0.013	36.901	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.879	0.942	41.011	0.081	0.081	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.874	-0.941	44.389	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.813	0.915	39.929	0.093	0.093	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.789	0.878	37.402	0.098	0.098	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.023	0.006	33.374	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.007	0.008	28.873	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.001	0.003	27.213	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.028	-0.014	23.977	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.833	-0.922	21.735	-0.341	-0.341	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.844	-0.933	16.908	-0.459	-0.459	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.028	-0.029	15.313	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.038	0.024	18.054	0.011	0.011	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.837	-0.921	15.883	-0.740	-0.740	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.053	-0.007	18.731	0.023	0.023	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.025	0.039	21.891	0.027	0.027	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.952	0.976	24.659	0.303	0.303	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.017	-0.007	23.382	0.023	0.023	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.047	0.022	24.053	0.024	0.024	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.848	-0.891	27.512	-0.239	-0.239	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.020	-0.010	29.946	0.017	0.017	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.009	-0.001	28.247	0.015	0.015	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.018	0.006	30.107	0.014	0.014	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.792	-0.884	33.288	-0.146	-0.146	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.811	-0.898	34.397	-0.123	-0.123	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.005	-0.007	33.462	0.010	0.010	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.814	0.886	36.490	0.165	0.165	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.775	0.885	38.946	0.132	0.132	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.023	-0.003	38.031	0.007	0.007	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.007	-0.006	41.314	0.005	0.005	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.030	-0.015	38.219	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.900	0.979	40.219	0.089	0.089	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.870	-0.933	37.452	-0.128	-0.128	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.010	-0.007	32.959	0.000	0.000	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.865	0.948	31.095	0.153	0.153	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.028	-0.014	25.869	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.007	-0.001	25.334	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.022	0.001	20.481	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.000	0.009	16.191	0.008	0.008	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.016	-0.014	15.367	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	121	MET	0	-0.026	0.010	17.446	0.025	0.025	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.857	0.943	12.830	0.928	0.928	0.000	0.000	0.000	0.000
123	A	123	PRO	0	-0.091	-0.071	16.976	0.064	0.064	0.000	0.000	0.000	0.000
124	A	124	TRP	0	-0.026	-0.011	14.590	0.022	0.022	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.056	-0.018	21.472	0.033	0.033	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.027	-0.043	22.960	0.008	0.008	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.033	-0.014	25.418	0.024	0.024	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.008	0.008	24.557	-0.026	-0.026	0.000	0.000	0.000	0.000
129	A	129	PRO	0	-0.015	-0.010	22.745	0.019	0.019	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.826	-0.906	26.063	-0.202	-0.202	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.029	-0.023	25.873	0.006	0.006	0.000	0.000	0.000	0.000
132	A	132	TYR	0	0.012	-0.005	19.976	-0.027	-0.027	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.023	-0.002	18.194	0.023	0.023	0.000	0.000	0.000	0.000
134	A	134	PHE	0	-0.029	-0.015	14.244	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.968	0.970	15.528	0.510	0.510	0.000	0.000	0.000	0.000
136	A	136	THR	0	-0.047	-0.019	11.001	-0.107	-0.107	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.742	-0.867	10.998	-1.477	-1.477	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.848	0.916	6.491	2.385	2.385	0.000	0.000	0.000	0.000
139	A	139	TRP	0	0.009	0.005	8.834	0.261	0.261	0.000	0.000	0.000	0.000
140	A	140	ILE	0	0.000	-0.003	8.230	-0.374	-0.374	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.019	0.005	6.702	0.061	0.061	0.000	0.000	0.000	0.000
142	A	142	PHE	0	0.026	-0.004	8.890	-0.027	-0.027	0.000	0.000	0.000	0.000
143	A	143	PRO	0	-0.051	-0.037	11.117	0.002	0.002	0.000	0.000	0.000	0.000
144	A	144	TRP	0	-0.085	-0.043	12.258	0.082	0.082	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.809	-0.897	11.303	-0.637	-0.637	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.900	-0.944	10.656	-0.319	-0.319	0.000	0.000	0.000	0.000
147	A	147	PHE	0	-0.039	-0.033	5.318	-0.252	-0.252	0.000	0.000	0.000	0.000
148	A	148	PRO	0	-0.015	-0.012	8.293	0.131	0.131	0.000	0.000	0.000	0.000
149	A	149	VAL	0	0.019	0.020	9.099	0.053	0.053	0.000	0.000	0.000	0.000
150	A	150	ILE	0	-0.038	-0.016	8.398	-0.072	-0.072	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.922	-0.961	11.574	0.262	0.262	0.000	0.000	0.000	0.000
152	A	152	LYS	1	0.891	0.931	15.056	-0.367	-0.367	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.946	-0.953	17.130	-0.006	-0.006	0.000	0.000	0.000	0.000

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