FMO DATABASE

FMODB ID: V5YN1

Calculation Name: 5C8O-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: 5C8O

Chain ID: A

ChEMBL ID:
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UniProt ID: G4N991

Base Structure: X-ray

Registration Date: 2023-06-22

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1396813.087303
FMO2-HF: Nuclear repulsion	1336768.188387
FMO2-HF: Total energy	-60044.898916
FMO2-MP2: Total energy	-60220.222941

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:GLY)

Summations of interaction energy for fragment #1(A:1:GLY)

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.
-0.768	0.661	-0.006	-0.868	-0.555	0.004

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.018

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	TYR	0	-0.042	-0.043	3.853	-1.311	0.118	-0.006	-0.868	-0.555	0.004
4	A	4	ALA	0	-0.006	-0.001	6.687	0.254	0.254	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.036	0.028	8.173	0.359	0.359	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.061	-0.038	10.258	0.080	0.080	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.043	0.021	12.240	0.145	0.145	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.051	-0.039	14.956	0.093	0.093	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.005	0.007	14.212	0.071	0.071	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.073	-0.022	15.257	0.076	0.076	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.004	-0.022	17.991	0.060	0.060	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.794	0.895	20.770	0.224	0.224	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.835	-0.925	23.492	-0.243	-0.243	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.022	0.009	19.833	0.007	0.007	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.052	-0.029	24.188	0.016	0.016	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.017	0.003	24.467	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.844	-0.901	27.681	-0.176	-0.176	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.036	0.024	30.238	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.012	0.001	26.577	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.901	0.955	25.598	0.182	0.182	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.025	0.031	20.199	0.010	0.010	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.838	0.884	24.495	0.223	0.223	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.028	0.015	22.892	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.786	-0.862	24.873	-0.198	-0.198	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.045	-0.015	21.142	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.910	0.955	20.780	0.268	0.268	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.828	0.901	22.083	0.166	0.166	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.003	-0.015	22.780	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.847	-0.902	23.580	-0.164	-0.164	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.019	-0.006	25.745	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.002	0.006	26.695	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.007	-0.013	23.633	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.021	-0.020	26.483	0.022	0.022	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.000	-0.003	26.510	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.052	-0.031	24.346	0.009	0.009	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.046	-0.045	25.808	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.019	0.009	20.116	0.008	0.008	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.863	-0.945	24.258	-0.260	-0.260	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.040	0.015	20.138	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.008	0.006	22.778	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.943	0.999	24.016	0.261	0.261	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.029	-0.032	19.007	0.016	0.016	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.011	0.016	17.562	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.019	0.012	20.891	0.023	0.023	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.005	-0.039	22.309	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.788	-0.877	22.314	-0.187	-0.187	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.021	-0.003	24.382	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.029	0.023	26.547	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.070	-0.038	21.026	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.036	0.009	19.166	0.008	0.008	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.850	0.918	17.534	0.266	0.266	0.000	0.000	0.000	0.000
52	A	52	TRP	0	-0.057	-0.031	13.329	0.041	0.041	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.007	0.016	16.865	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.005	-0.019	19.059	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.079	-0.038	21.068	0.017	0.017	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.016	-0.005	23.932	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.021	-0.009	25.966	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.016	-0.001	25.934	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.004	-0.002	29.061	0.002	0.002	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.007	0.009	31.062	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.031	-0.027	30.355	0.011	0.011	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.014	-0.010	33.487	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.006	-0.001	35.289	0.005	0.005	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.795	-0.843	30.963	-0.056	-0.056	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.020	-0.018	33.076	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.058	0.008	32.229	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.843	0.881	29.994	0.057	0.057	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.815	-0.844	28.393	-0.053	-0.053	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.000	0.006	27.352	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.037	0.008	26.216	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.804	0.869	23.877	0.042	0.042	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.772	0.864	22.742	0.061	0.061	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.012	-0.020	21.771	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.868	-0.931	17.552	-0.307	-0.307	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.042	-0.024	20.990	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.799	-0.875	24.069	-0.109	-0.109	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.013	0.002	27.094	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	HIS	1	0.845	0.903	30.289	0.113	0.113	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.807	-0.859	27.634	-0.157	-0.157	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.001	-0.005	27.020	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.002	0.010	30.861	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.771	0.837	30.853	0.151	0.151	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.796	0.899	27.722	0.174	0.174	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.051	-0.035	31.673	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.062	-0.025	35.629	0.004	0.004	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.007	0.025	35.642	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.074	-0.061	38.122	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.041	-0.044	35.800	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.813	-0.885	36.065	-0.066	-0.066	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.791	-0.857	38.752	-0.058	-0.058	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.043	-0.024	38.266	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.044	-0.012	33.771	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.021	0.004	38.229	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.017	-0.008	36.658	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.007	-0.005	36.084	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	GLN	0	0.027	0.019	36.520	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.025	-0.015	32.859	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.007	-0.001	31.396	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.014	0.007	29.964	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.012	0.004	25.106	0.005	0.005	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.112	0.045	23.630	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.016	0.009	23.097	0.018	0.018	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.086	-0.086	24.639	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.039	0.017	24.114	0.011	0.011	0.000	0.000	0.000	0.000
105	A	105	TRP	0	0.008	0.001	26.270	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.800	-0.874	29.000	-0.160	-0.160	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.077	-0.024	29.265	0.011	0.011	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.008	0.014	27.848	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.816	0.886	29.757	0.158	0.158	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.896	-0.960	29.731	-0.175	-0.175	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.054	-0.011	25.967	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.860	0.915	26.242	0.243	0.243	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.008	0.012	21.823	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.005	0.001	20.837	0.033	0.033	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.828	-0.918	18.431	-0.463	-0.463	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.004	-0.002	19.216	-0.049	-0.049	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.020	0.009	21.159	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.911	0.939	14.859	0.606	0.606	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.053	-0.013	16.332	-0.089	-0.089	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.017	0.031	18.568	0.055	0.055	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.783	-0.884	20.557	-0.295	-0.295	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.017	0.014	23.323	0.013	0.013	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.831	-0.882	26.038	-0.162	-0.162	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.042	-0.014	23.504	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.939	0.976	28.062	0.138	0.138	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.030	0.017	29.129	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	127	SER	0	-0.038	-0.045	30.737	0.008	0.008	0.000	0.000	0.000	0.000
128	A	128	GLY	0	-0.015	0.006	33.476	0.009	0.009	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.020	-0.001	34.368	0.005	0.005	0.000	0.000	0.000	0.000
130	A	130	TRP	0	0.002	-0.004	31.158	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	131	ASN	0	0.015	0.001	24.856	0.017	0.017	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.884	0.947	22.833	0.248	0.248	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.002	0.009	21.504	-0.017	-0.017	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.881	0.906	16.294	0.496	0.496	0.000	0.000	0.000	0.000
135	A	135	ILE	0	0.001	0.012	15.101	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	136	TYR	0	0.049	0.027	12.529	0.092	0.092	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.043	0.024	13.576	-0.100	-0.100	0.000	0.000	0.000	0.000
138	A	138	ASP	-1	-0.775	-0.867	11.650	-0.938	-0.938	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.821	-0.887	9.488	-1.366	-1.366	0.000	0.000	0.000	0.000
140	A	140	HIS	1	0.839	0.907	10.120	0.866	0.866	0.000	0.000	0.000	0.000
141	A	141	ILE	0	0.016	0.032	12.868	0.089	0.089	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.058	0.014	14.404	-0.122	-0.122	0.000	0.000	0.000	0.000
143	A	143	ASN	0	-0.052	-0.035	15.296	0.113	0.113	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.848	0.919	17.343	0.301	0.301	0.000	0.000	0.000	0.000
145	A	145	ASN	0	0.008	-0.008	19.445	0.037	0.037	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.079	0.042	21.794	0.033	0.033	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.853	-0.896	22.217	-0.274	-0.274	0.000	0.000	0.000	0.000
148	A	148	LEU	0	0.024	0.007	19.877	-0.042	-0.042	0.000	0.000	0.000	0.000
149	A	149	ILE	0	-0.047	-0.017	16.197	0.039	0.039	0.000	0.000	0.000	0.000
150	A	150	HIS	0	0.042	0.012	16.242	-0.092	-0.092	0.000	0.000	0.000	0.000
151	A	151	CYS	0	-0.047	-0.014	10.881	0.065	0.065	0.000	0.000	0.000	0.000

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