FMO DATABASE

FMODB ID: R9N38

Calculation Name: 5D5P-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: 5D5P

Chain ID: A

ChEMBL ID:
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UniProt ID: Q6LX55

Base Structure: X-ray

Registration Date: 2023-06-21

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1406476.749296
FMO2-HF: Nuclear repulsion	1347564.845474
FMO2-HF: Total energy	-58911.903822
FMO2-MP2: Total energy	-59085.31449

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:2:ASN)

Summations of interaction energy for fragment #1(A:2:ASN)

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.
-30.519	-33.519	24.972	-9.098	-12.873	0.062

Interaction energy analysis for fragmet #1(A:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.046

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	4	GLU	-1	-0.982	-0.988	2.416	-8.068	-4.512	4.191	-3.208	-4.539	0.023
4	A	5	ASN	0	-0.015	-0.007	1.733	-11.557	-19.268	20.686	-5.753	-7.221	0.037
5	A	6	THR	0	0.019	0.012	3.553	-4.188	-3.711	0.066	-0.020	-0.523	0.003
6	A	7	ILE	0	-0.042	-0.017	5.558	-1.031	-1.031	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.855	0.928	6.327	-2.206	-2.206	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.003	0.007	7.622	-0.665	-0.665	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.031	0.009	9.480	-0.362	-0.362	0.000	0.000	0.000	0.000
10	A	11	TYR	0	-0.055	-0.045	10.891	-0.209	-0.209	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.842	-0.918	11.599	1.007	1.007	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.869	-0.941	13.696	0.496	0.496	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.047	-0.033	15.490	-0.119	-0.119	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.049	-0.007	16.453	-0.079	-0.079	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.067	-0.020	18.347	-0.094	-0.094	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.066	-0.043	20.418	-0.046	-0.046	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.032	0.025	18.613	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.764	0.851	12.158	-0.623	-0.623	0.000	0.000	0.000	0.000
19	A	20	PHE	0	-0.029	-0.013	18.083	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.005	0.004	17.950	-0.037	-0.037	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.960	-0.973	13.297	0.421	0.421	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.937	0.969	10.602	-0.677	-0.677	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.036	0.018	10.691	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.834	-0.932	6.365	0.308	0.308	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.813	-0.877	5.861	0.347	0.347	0.000	0.000	0.000	0.000
26	A	27	ILE	0	0.005	0.008	7.515	-0.121	-0.121	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.873	-0.932	6.610	-0.128	-0.128	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.056	-0.034	3.397	-0.638	-0.275	0.032	-0.098	-0.297	-0.001
29	A	30	ILE	0	0.000	0.000	4.496	0.048	0.194	-0.001	-0.009	-0.136	0.000
30	A	31	GLN	0	-0.070	-0.051	7.228	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.029	-0.009	4.593	-0.139	-0.052	-0.001	-0.006	-0.080	0.000
32	A	33	THR	0	-0.020	-0.014	4.487	-0.095	-0.013	-0.001	-0.004	-0.077	0.000
33	A	34	ILE	0	-0.012	-0.009	6.365	0.032	0.032	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.932	0.957	9.655	0.129	0.129	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.082	-0.024	7.249	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.017	0.011	9.922	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.932	0.959	11.561	0.509	0.509	0.000	0.000	0.000	0.000
38	A	39	ASN	0	0.006	0.015	14.010	0.088	0.088	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.009	0.010	14.834	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.046	0.026	16.839	0.007	0.007	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.010	-0.007	18.960	0.018	0.018	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.025	0.012	21.560	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.106	-0.071	23.185	0.017	0.017	0.000	0.000	0.000	0.000
44	A	45	SER	0	0.123	0.060	26.722	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.093	-0.041	29.704	0.000	0.000	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.776	-0.907	29.682	-0.055	-0.055	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.867	0.954	30.325	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.924	0.943	27.600	0.002	0.002	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.033	0.025	23.401	0.004	0.004	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.900	0.939	25.616	0.046	0.046	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.026	-0.002	25.844	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.014	-0.016	20.927	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.057	0.026	21.960	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.841	-0.899	22.557	-0.070	-0.070	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.063	-0.029	19.968	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.018	-0.010	16.571	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.012	-0.001	18.080	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.830	0.916	20.378	0.051	0.051	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.080	-0.039	14.716	0.006	0.006	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.045	-0.018	13.816	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.922	-0.946	15.446	-0.204	-0.204	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.034	-0.021	15.711	-0.036	-0.036	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.029	-0.005	17.512	0.044	0.044	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.014	-0.006	18.965	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.014	0.001	20.896	0.011	0.011	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.050	-0.018	22.376	0.010	0.010	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.003	0.002	22.226	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.922	-0.956	24.570	-0.091	-0.091	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.028	-0.010	25.349	0.009	0.009	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.007	0.004	27.691	0.005	0.005	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.066	0.021	25.614	0.006	0.006	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.009	-0.008	28.601	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.038	0.023	29.939	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.061	0.030	27.094	0.006	0.006	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.950	-0.974	28.978	0.043	0.043	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.053	-0.018	31.766	0.002	0.002	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.017	-0.006	27.973	0.008	0.008	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.951	0.952	28.493	-0.108	-0.108	0.000	0.000	0.000	0.000
79	A	80	MET	0	0.012	0.009	23.741	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	PRO	0	-0.023	0.012	25.349	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.009	0.011	23.300	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	83	LEU	0	0.077	0.030	18.869	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	84	ASN	0	0.004	-0.019	21.161	0.002	0.002	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.861	0.942	23.487	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.018	0.004	19.597	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.026	0.007	17.573	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.013	0.026	19.895	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.014	0.003	19.352	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.053	-0.027	15.024	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.908	-0.951	17.200	0.012	0.012	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.126	-0.071	19.528	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.055	-0.032	18.739	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.879	-0.940	15.529	-0.300	-0.300	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.088	-0.028	14.970	-0.050	-0.050	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.821	-0.920	10.409	-0.582	-0.582	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.086	-0.052	10.586	0.030	0.030	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.013	0.019	13.102	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.016	0.003	16.128	0.032	0.032	0.000	0.000	0.000	0.000
99	A	100	THR	0	-0.015	-0.017	18.490	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.880	0.894	21.275	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.043	-0.030	24.242	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.865	0.945	27.102	-0.048	-0.048	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.058	0.034	25.418	0.005	0.005	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.044	0.014	27.140	0.012	0.012	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.019	0.014	29.862	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	107	PRO	0	0.019	0.008	33.535	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.027	0.016	35.406	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.066	-0.045	31.327	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.025	0.013	31.081	0.004	0.004	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.074	-0.034	27.692	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	LEU	0	0.023	0.011	21.558	0.004	0.004	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.027	-0.003	19.410	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.015	-0.016	17.519	0.017	0.017	0.000	0.000	0.000	0.000
114	A	115	ILE	0	0.032	0.016	12.993	-0.028	-0.028	0.000	0.000	0.000	0.000
115	A	116	MET	0	-0.031	-0.010	13.303	0.046	0.046	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.691	-0.838	7.924	0.406	0.406	0.000	0.000	0.000	0.000
117	A	118	LYS	1	1.040	1.016	6.714	0.642	0.642	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.873	0.944	7.782	-0.584	-0.584	0.000	0.000	0.000	0.000
119	A	120	GLY	0	0.063	0.039	11.897	0.046	0.046	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.776	0.874	5.796	-1.591	-1.591	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.002	-0.006	12.265	-0.091	-0.091	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.016	0.000	8.522	0.072	0.072	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.002	-0.026	11.781	0.006	0.006	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.012	-0.003	15.007	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.066	-0.044	18.660	0.001	0.001	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.026	0.010	22.205	0.000	0.000	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.050	-0.072	25.751	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	129	PRO	0	0.031	0.009	29.111	0.003	0.003	0.000	0.000	0.000	0.000
129	A	130	SER	0	0.047	0.024	32.650	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	131	SER	0	0.042	0.020	34.786	0.000	0.000	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.055	-0.043	36.996	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	133	ILE	0	-0.015	-0.001	36.806	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.039	0.022	34.432	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.893	0.959	36.752	-0.024	-0.024	0.000	0.000	0.000	0.000
135	A	136	ASN	0	0.026	-0.003	32.882	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.019	0.018	35.193	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.019	-0.016	31.333	0.001	0.001	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.768	-0.906	30.767	-0.013	-0.013	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.997	0.995	29.826	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	141	THR	0	-0.052	-0.021	29.262	0.004	0.004	0.000	0.000	0.000	0.000
141	A	142	VAL	0	-0.017	-0.012	25.399	0.004	0.004	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.896	-0.942	25.201	-0.010	-0.010	0.000	0.000	0.000	0.000
143	A	144	LEU	0	0.011	0.010	24.877	0.000	0.000	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.706	-0.773	23.707	0.037	0.037	0.000	0.000	0.000	0.000
145	A	146	LEU	0	0.027	0.034	18.633	0.010	0.010	0.000	0.000	0.000	0.000
146	A	147	ILE	0	0.037	0.015	19.981	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	148	THR	0	-0.006	-0.001	20.823	0.004	0.004	0.000	0.000	0.000	0.000
148	A	149	ALA	0	-0.044	-0.021	17.810	0.011	0.011	0.000	0.000	0.000	0.000
149	A	150	LEU	0	0.020	0.019	15.134	0.009	0.009	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.903	-0.956	16.310	0.025	0.025	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.844	0.933	16.493	-0.146	-0.146	0.000	0.000	0.000	0.000
152	A	153	ILE	0	-0.030	-0.002	12.071	0.023	0.023	0.000	0.000	0.000	0.000
153	A	154	GLY	0	0.030	0.021	13.066	-0.031	-0.031	0.000	0.000	0.000	0.000
154	A	155	ILE	0	-0.050	-0.018	11.936	-0.017	-0.017	0.000	0.000	0.000	0.000
155	A	156	VAL	0	0.014	0.002	16.003	0.009	0.009	0.000	0.000	0.000	0.000
156	A	157	VAL	0	0.020	0.011	19.214	-0.010	-0.010	0.000	0.000	0.000	0.000
157	A	158	LYS	1	0.990	1.012	21.622	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN)