FMO DATABASE

FMODB ID: N9YGQ

Calculation Name: 3HDU-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: 3HDU

Chain ID: A

ChEMBL ID:
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UniProt ID: Q2LUI2

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1436425.188704
FMO2-HF: Nuclear repulsion	1375633.474405
FMO2-HF: Total energy	-60791.714299
FMO2-MP2: Total energy	-60964.092232

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-37.405	-39.207	20.887	-10.297	-8.787	-0.084

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.031

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	7	ASN	0	-0.007	-0.026	3.083	-1.875	0.158	0.039	-0.946	-1.126	0.003
4	A	8	GLU	-1	-0.824	-0.892	1.668	-36.814	-41.135	20.838	-9.306	-7.211	-0.087
5	A	9	GLU	-1	-0.853	-0.920	3.571	-0.887	-0.401	0.010	-0.045	-0.450	0.000
6	A	10	VAL	0	-0.069	-0.027	5.749	1.019	1.019	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.016	0.000	6.983	0.523	0.523	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.040	0.018	7.743	0.493	0.493	0.000	0.000	0.000	0.000
9	A	13	SER	0	-0.008	-0.013	9.443	0.481	0.481	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.032	-0.012	11.441	0.226	0.226	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.009	-0.007	12.463	0.173	0.173	0.000	0.000	0.000	0.000
12	A	16	ASN	0	0.019	-0.012	12.263	0.134	0.134	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.767	-0.861	15.493	-0.338	-0.338	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.052	-0.018	16.516	0.085	0.085	0.000	0.000	0.000	0.000
15	A	19	PHE	0	0.002	-0.022	17.645	0.056	0.056	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.830	-0.891	17.567	-0.648	-0.648	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.913	-0.961	20.224	-0.372	-0.372	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.753	0.854	21.597	0.442	0.442	0.000	0.000	0.000	0.000
19	A	23	ILE	0	-0.011	0.025	22.657	0.037	0.037	0.000	0.000	0.000	0.000
20	A	24	PRO	0	0.022	0.005	25.641	0.011	0.011	0.000	0.000	0.000	0.000
21	A	25	PHE	0	-0.002	-0.024	28.630	0.020	0.020	0.000	0.000	0.000	0.000
22	A	26	ASN	0	0.076	0.051	23.985	0.007	0.007	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.917	0.957	28.101	0.210	0.210	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.045	-0.016	31.375	0.016	0.016	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.016	-0.018	28.419	0.009	0.009	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.008	0.011	26.705	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	31	LEU	0	0.010	0.005	20.814	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.827	0.901	19.458	0.503	0.503	0.000	0.000	0.000	0.000
29	A	33	VAL	0	0.024	0.002	14.383	0.021	0.021	0.000	0.000	0.000	0.000
30	A	34	ARG	1	0.844	0.930	15.400	0.585	0.585	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.027	0.005	10.965	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	36	ILE	0	-0.011	-0.009	9.240	0.210	0.210	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.030	0.005	9.658	-0.345	-0.345	0.000	0.000	0.000	0.000
34	A	38	PRO	0	0.001	-0.006	8.898	0.252	0.252	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.900	-0.946	11.990	-1.124	-1.124	0.000	0.000	0.000	0.000
36	A	40	GLN	0	-0.062	-0.033	14.003	0.173	0.173	0.000	0.000	0.000	0.000
37	A	41	VAL	0	-0.005	0.027	14.102	-0.199	-0.199	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.966	0.980	16.244	0.725	0.725	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.004	0.022	17.747	-0.072	-0.072	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.010	-0.008	20.356	0.033	0.033	0.000	0.000	0.000	0.000
41	A	45	PHE	0	-0.016	-0.022	22.779	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.763	-0.859	25.893	-0.261	-0.261	0.000	0.000	0.000	0.000
43	A	47	MET	0	-0.043	-0.012	28.624	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.820	0.895	26.899	0.300	0.300	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.837	-0.915	33.372	-0.155	-0.155	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.857	-0.930	35.788	-0.196	-0.196	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.016	0.003	37.591	0.003	0.003	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.010	-0.009	40.187	0.005	0.005	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.016	0.007	43.221	0.004	0.004	0.000	0.000	0.000	0.000
50	A	54	ASN	0	-0.020	0.004	43.927	0.007	0.007	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.038	0.002	45.979	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	56	ILE	0	-0.004	0.000	44.585	0.002	0.002	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.899	0.963	38.580	0.164	0.164	0.000	0.000	0.000	0.000
54	A	58	ARG	1	0.978	0.969	40.836	0.137	0.137	0.000	0.000	0.000	0.000
55	A	59	MET	0	0.014	0.016	40.328	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.015	0.006	39.251	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	61	TYR	0	-0.008	-0.022	35.452	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.028	0.031	35.333	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.050	0.030	35.155	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	64	VAL	0	0.001	0.014	31.743	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.024	0.000	30.964	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	66	SER	0	-0.053	-0.020	30.190	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	67	SER	0	0.017	-0.007	29.675	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	68	ALA	0	0.007	0.014	26.547	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.013	0.017	25.225	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.803	-0.891	25.211	-0.392	-0.392	0.000	0.000	0.000	0.000
67	A	71	MET	0	-0.006	0.003	22.530	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	72	THR	0	-0.008	-0.033	20.672	-0.067	-0.067	0.000	0.000	0.000	0.000
69	A	73	ALA	0	-0.002	-0.012	20.232	-0.067	-0.067	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.049	0.023	20.989	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.005	0.001	14.644	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	76	ALA	0	0.021	0.000	16.202	-0.105	-0.105	0.000	0.000	0.000	0.000
73	A	77	ALA	0	-0.025	-0.012	16.938	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	78	PHE	0	-0.005	-0.018	12.308	0.018	0.018	0.000	0.000	0.000	0.000
75	A	79	MET	0	0.009	0.015	11.021	-0.103	-0.103	0.000	0.000	0.000	0.000
76	A	80	GLY	0	0.059	0.038	12.898	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	81	PHE	0	-0.057	-0.060	15.312	0.056	0.056	0.000	0.000	0.000	0.000
78	A	82	GLN	0	0.001	-0.004	9.242	0.111	0.111	0.000	0.000	0.000	0.000
79	A	83	GLU	-1	-0.859	-0.919	9.601	-1.401	-1.401	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.838	0.922	12.079	0.564	0.564	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.105	-0.027	13.853	0.094	0.094	0.000	0.000	0.000	0.000
82	A	86	SER	0	0.009	-0.002	11.260	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.016	0.004	10.757	0.026	0.026	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.776	0.886	13.036	0.221	0.221	0.000	0.000	0.000	0.000
85	A	89	PRO	0	0.043	0.016	11.871	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	90	MET	0	0.027	0.001	9.209	-0.066	-0.066	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.882	-0.935	12.030	-0.414	-0.414	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.806	-0.900	15.784	-0.213	-0.213	0.000	0.000	0.000	0.000
89	A	93	LYS	1	0.826	0.920	9.753	0.914	0.914	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.040	0.009	12.371	-0.032	-0.032	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.006	0.010	15.749	0.032	0.032	0.000	0.000	0.000	0.000
92	A	96	MET	0	-0.131	-0.053	15.818	0.056	0.056	0.000	0.000	0.000	0.000
93	A	97	ILE	0	0.043	0.017	16.387	0.031	0.031	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.012	0.016	19.259	0.017	0.017	0.000	0.000	0.000	0.000
95	A	99	ARG	1	0.905	0.959	20.599	0.361	0.361	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.044	0.003	18.784	0.020	0.020	0.000	0.000	0.000	0.000
97	A	101	SER	0	0.030	0.018	23.401	0.010	0.010	0.000	0.000	0.000	0.000
98	A	102	THR	0	-0.013	-0.012	26.834	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	103	MET	0	-0.080	-0.035	28.243	0.018	0.018	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.015	-0.020	30.019	0.021	0.021	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.050	0.030	29.227	-0.023	-0.023	0.000	0.000	0.000	0.000
102	A	106	HIS	0	-0.067	-0.023	31.403	0.025	0.025	0.000	0.000	0.000	0.000
103	A	107	VAL	0	0.030	0.000	31.104	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.894	-0.931	33.450	-0.197	-0.197	0.000	0.000	0.000	0.000
105	A	109	TYR	0	-0.074	-0.061	34.388	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.021	-0.011	34.373	0.013	0.013	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.847	0.925	35.680	0.219	0.219	0.000	0.000	0.000	0.000
108	A	112	PRO	0	-0.060	-0.025	37.480	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	113	GLY	0	0.047	0.000	35.258	0.002	0.002	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.111	-0.060	35.892	0.002	0.002	0.000	0.000	0.000	0.000
111	A	115	GLY	0	0.091	0.067	34.277	0.010	0.010	0.000	0.000	0.000	0.000
112	A	116	ARG	1	0.824	0.907	31.839	0.216	0.216	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.935	-0.961	27.040	-0.317	-0.317	0.000	0.000	0.000	0.000
114	A	118	PHE	0	-0.027	-0.013	27.945	0.010	0.010	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.012	-0.011	22.339	-0.036	-0.036	0.000	0.000	0.000	0.000
116	A	120	CYS	0	-0.020	0.002	23.437	0.044	0.044	0.000	0.000	0.000	0.000
117	A	121	THR	0	0.001	0.008	19.402	-0.068	-0.068	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.008	0.000	19.877	0.066	0.066	0.000	0.000	0.000	0.000
119	A	123	TYR	0	-0.026	-0.037	18.826	-0.111	-0.111	0.000	0.000	0.000	0.000
120	A	124	ASN	0	-0.031	-0.009	17.513	0.132	0.132	0.000	0.000	0.000	0.000
121	A	125	VAL	0	0.001	0.013	19.430	0.006	0.006	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.976	0.983	21.362	0.301	0.301	0.000	0.000	0.000	0.000
123	A	127	THR	0	0.026	0.014	18.446	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.028	-0.015	20.973	0.023	0.023	0.000	0.000	0.000	0.000
125	A	129	ASN	0	-0.015	-0.030	22.000	-0.034	-0.034	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.999	0.982	22.969	0.223	0.223	0.000	0.000	0.000	0.000
127	A	131	VAL	0	0.013	0.021	25.008	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.021	0.022	20.982	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	133	VAL	0	-0.032	-0.013	22.837	0.017	0.017	0.000	0.000	0.000	0.000
130	A	134	ILE	0	-0.015	-0.008	20.903	-0.028	-0.028	0.000	0.000	0.000	0.000
131	A	135	ARG	1	0.859	0.931	23.276	0.384	0.384	0.000	0.000	0.000	0.000
132	A	136	THR	0	-0.011	-0.024	23.399	-0.040	-0.040	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.796	-0.865	24.811	-0.360	-0.360	0.000	0.000	0.000	0.000
134	A	138	LEU	0	0.021	0.004	25.570	-0.033	-0.033	0.000	0.000	0.000	0.000
135	A	139	MET	0	0.012	-0.008	24.674	0.035	0.035	0.000	0.000	0.000	0.000
136	A	140	ASN	0	-0.031	-0.022	28.490	-0.026	-0.026	0.000	0.000	0.000	0.000
137	A	141	ASP	-1	-0.815	-0.929	29.197	-0.266	-0.266	0.000	0.000	0.000	0.000
138	A	142	GLN	0	-0.130	-0.072	29.742	0.004	0.004	0.000	0.000	0.000	0.000
139	A	143	ASP	-1	-0.930	-0.944	27.006	-0.333	-0.333	0.000	0.000	0.000	0.000
140	A	144	GLU	-1	-0.825	-0.883	29.696	-0.192	-0.192	0.000	0.000	0.000	0.000
141	A	145	LEU	0	-0.014	-0.015	29.195	-0.009	-0.009	0.000	0.000	0.000	0.000
142	A	146	ILE	0	-0.020	-0.018	31.760	0.022	0.022	0.000	0.000	0.000	0.000
143	A	147	ALA	0	-0.004	0.002	31.731	0.016	0.016	0.000	0.000	0.000	0.000
144	A	148	VAL	0	0.005	0.013	29.586	-0.023	-0.023	0.000	0.000	0.000	0.000
145	A	149	GLY	0	0.034	0.019	28.683	0.020	0.020	0.000	0.000	0.000	0.000
146	A	150	SER	0	-0.051	-0.012	27.940	-0.023	-0.023	0.000	0.000	0.000	0.000
147	A	151	VAL	0	0.007	0.001	25.710	0.021	0.021	0.000	0.000	0.000	0.000
148	A	152	SER	0	-0.056	-0.017	25.969	-0.017	-0.017	0.000	0.000	0.000	0.000
149	A	153	TYR	0	0.020	0.001	23.245	0.003	0.003	0.000	0.000	0.000	0.000
150	A	154	ILE	0	-0.019	-0.024	24.898	0.003	0.003	0.000	0.000	0.000	0.000
151	A	155	LEU	0	-0.054	-0.009	20.612	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	156	VAL	0	-0.011	-0.012	24.731	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)