FMO DATABASE

FMODB ID: Z63ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1487657.646446
FMO2-HF: Nuclear repulsion	1427316.911012
FMO2-HF: Total energy	-60340.735434
FMO2-MP2: Total energy	-60520.562107

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.
-1.867	2.116	2.915	-2.162	-4.735	-0.006

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 : -0.022 / q_NPA : -0.024

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	0.952	0.983	3.119	0.303	3.177	0.001	-1.258	-1.617	0.002
4	A	4	VAL	0	-0.021	-0.007	4.022	-0.934	-0.770	0.001	-0.075	-0.090	0.000
5	A	5	TYR	0	0.002	-0.002	2.419	-2.224	-1.279	2.913	-0.829	-3.028	-0.008
6	A	6	LEU	0	0.010	0.021	6.191	0.244	0.244	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.030	0.001	9.632	0.077	0.077	0.000	0.000	0.000	0.000
8	A	8	TRP	0	0.141	0.037	11.288	0.018	0.018	0.000	0.000	0.000	0.000
9	A	9	TRP	0	0.061	0.026	14.629	0.027	0.027	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.035	-0.005	11.053	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.053	0.028	14.179	0.021	0.021	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.851	-0.914	16.748	-0.204	-0.204	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.848	0.926	15.898	0.276	0.276	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.010	0.001	18.002	0.019	0.019	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.038	0.015	19.995	0.017	0.017	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.002	-0.012	22.539	0.019	0.019	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.033	-0.007	23.110	0.016	0.016	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.002	-0.006	22.001	0.014	0.014	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.002	0.011	25.784	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.877	-0.924	28.439	-0.103	-0.103	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.951	0.981	28.494	0.141	0.141	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.002	0.006	27.859	0.008	0.008	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.880	0.918	30.910	0.126	0.126	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.969	-0.981	33.649	-0.101	-0.101	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.065	-0.040	33.711	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.883	0.958	35.871	0.087	0.087	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.006	0.004	32.688	0.004	0.004	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.802	-0.903	35.754	-0.082	-0.082	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.067	-0.048	35.001	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.013	0.021	28.993	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.011	-0.012	30.169	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.040	0.010	26.995	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.032	-0.016	24.802	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.048	0.042	23.711	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.948	0.938	20.522	0.199	0.199	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.082	0.018	18.450	0.009	0.009	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.098	0.034	19.399	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.044	-0.042	22.092	0.018	0.018	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.017	0.017	18.616	0.017	0.017	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.003	-0.018	19.792	0.015	0.015	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.002	0.017	22.457	0.019	0.019	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.024	0.008	25.217	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.876	0.927	22.551	0.209	0.209	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.000	-0.009	25.453	0.012	0.012	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.035	-0.009	27.781	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.036	-0.005	28.147	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.047	-0.032	26.012	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.104	-0.054	30.386	0.007	0.007	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.001	0.002	32.885	0.005	0.005	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.881	-0.940	34.175	-0.098	-0.098	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.039	0.008	32.550	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.022	-0.013	34.281	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.026	0.008	28.977	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.854	0.937	32.649	0.100	0.100	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.020	0.001	28.791	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.022	0.020	29.087	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.884	-0.945	26.610	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.025	0.010	27.259	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.887	0.950	25.433	0.136	0.136	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.014	-0.008	25.176	0.016	0.016	0.000	0.000	0.000	0.000
61	A	61	TYR	0	0.037	0.024	25.690	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.921	0.905	25.820	0.056	0.056	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.060	-0.007	27.749	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.025	0.094	29.200	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.837	-0.935	29.256	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-1.071	-1.009	31.146	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.921	0.953	30.542	0.080	0.080	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.011	-0.006	31.934	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.933	-0.952	32.892	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.939	0.944	31.876	0.079	0.079	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.068	-0.029	30.309	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.055	0.040	30.869	0.006	0.006	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.005	-0.004	31.151	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.067	-0.023	29.467	0.004	0.004	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.010	0.000	28.976	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.013	0.010	32.680	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.004	0.013	33.530	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.053	0.016	36.262	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.050	-0.030	39.693	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.873	-0.944	41.097	-0.070	-0.070	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.037	-0.035	37.114	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.979	1.002	41.421	0.060	0.060	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.941	-0.987	44.637	-0.061	-0.061	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.906	0.955	39.978	0.078	0.078	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.847	0.934	37.652	0.085	0.085	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.015	0.011	33.664	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.019	0.013	29.298	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.035	-0.023	27.538	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.003	-0.002	23.897	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.846	-0.942	21.957	-0.268	-0.268	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.816	-0.917	17.038	-0.390	-0.390	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.064	-0.046	15.878	-0.033	-0.033	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.050	0.040	18.572	0.022	0.022	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.823	-0.908	16.439	-0.361	-0.361	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.041	-0.002	19.158	0.018	0.018	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.086	0.053	22.060	0.014	0.014	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.939	0.977	24.536	0.139	0.139	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.027	-0.008	24.111	0.015	0.015	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.053	0.029	24.212	0.011	0.011	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.870	-0.924	27.555	-0.112	-0.112	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.021	-0.009	29.965	0.009	0.009	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.004	0.002	28.338	0.007	0.007	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.008	-0.009	30.029	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.955	-0.979	33.196	-0.080	-0.080	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.902	-0.968	34.516	-0.085	-0.085	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.001	-0.003	33.871	0.004	0.004	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.974	0.996	36.750	0.097	0.097	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.876	0.970	39.110	0.083	0.083	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.040	-0.038	37.868	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	GLY	0	-0.016	-0.014	41.452	0.002	0.002	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.062	-0.021	38.431	0.001	0.001	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.901	0.989	40.367	0.074	0.074	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.930	-0.970	37.964	-0.089	-0.089	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.026	-0.017	33.290	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.934	0.987	31.532	0.113	0.113	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.002	0.006	26.221	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.027	-0.018	25.642	0.000	0.000	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.007	0.004	20.756	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.021	0.007	16.623	0.007	0.007	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.023	-0.016	15.775	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	121	MET	0	-0.035	0.008	17.646	0.027	0.027	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.856	0.939	13.439	0.484	0.484	0.000	0.000	0.000	0.000
123	A	123	PRO	0	-0.080	-0.063	17.009	0.037	0.037	0.000	0.000	0.000	0.000
124	A	124	TRP	0	-0.027	-0.027	14.495	0.024	0.024	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.038	0.010	21.455	0.026	0.026	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.044	-0.022	22.962	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.022	-0.012	25.430	0.012	0.012	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.004	-0.006	24.895	-0.021	-0.021	0.000	0.000	0.000	0.000
129	A	129	PRO	0	-0.022	-0.010	22.704	0.010	0.010	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.825	-0.899	26.031	-0.138	-0.138	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.022	-0.025	26.274	0.006	0.006	0.000	0.000	0.000	0.000
132	A	132	TYR	0	0.025	-0.009	20.109	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.035	-0.004	18.078	0.016	0.016	0.000	0.000	0.000	0.000
134	A	134	PHE	0	-0.038	-0.025	14.665	-0.009	-0.009	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.979	0.992	16.196	0.282	0.282	0.000	0.000	0.000	0.000
136	A	136	THR	0	-0.049	-0.022	11.399	-0.092	-0.092	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.831	-0.940	12.268	-0.518	-0.518	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.918	0.979	5.899	1.992	1.992	0.000	0.000	0.000	0.000
139	A	139	TRP	0	0.009	-0.005	8.701	0.148	0.148	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.001	-0.012	8.355	-0.327	-0.327	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.037	0.000	6.751	0.075	0.075	0.000	0.000	0.000	0.000
142	A	142	PHE	0	0.005	-0.019	9.034	-0.082	-0.082	0.000	0.000	0.000	0.000
143	A	143	PRO	0	-0.061	-0.041	11.119	-0.035	-0.035	0.000	0.000	0.000	0.000
144	A	144	TRP	0	-0.051	-0.031	12.110	0.018	0.018	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.864	-0.903	11.579	-0.637	-0.637	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.907	-0.945	11.112	-0.496	-0.496	0.000	0.000	0.000	0.000
147	A	147	PHE	0	-0.056	-0.042	6.499	-0.263	-0.263	0.000	0.000	0.000	0.000
148	A	148	PRO	0	-0.020	-0.011	8.089	0.116	0.116	0.000	0.000	0.000	0.000
149	A	149	VAL	0	0.030	0.014	9.117	-0.071	-0.071	0.000	0.000	0.000	0.000
150	A	150	ILE	0	-0.041	-0.019	8.250	0.019	0.019	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.936	-0.964	11.422	0.055	0.055	0.000	0.000	0.000	0.000
152	A	152	LYS	1	0.870	0.927	15.023	-0.182	-0.182	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.900	-0.940	16.902	0.075	0.075	0.000	0.000	0.000	0.000

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