FMO DATABASE

FMODB ID: 39ZYL

Calculation Name: 3P9V-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: 3P9V

Chain ID: A

ChEMBL ID:
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UniProt ID: A1U5H9

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	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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1471402.557186
FMO2-HF: Nuclear repulsion	1410997.642411
FMO2-HF: Total energy	-60404.914776
FMO2-MP2: Total energy	-60583.54744

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:ALA)

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

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.
-7.468	-1.745	7.121	-5.726	-7.118	-0.045

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.028

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	THR	0	0.024	0.019	3.825	0.527	2.215	-0.022	-0.849	-0.817	0.001
4	A	5	VAL	0	-0.053	-0.019	6.482	-0.411	-0.411	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.016	-0.007	9.641	0.063	0.063	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.088	-0.050	12.942	-0.095	-0.095	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.837	-0.889	15.907	0.169	0.169	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.071	-0.023	19.532	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	10	ASN	0	0.027	-0.003	22.291	0.013	0.013	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.775	0.866	23.274	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.872	-0.929	28.342	0.030	0.030	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.039	-0.024	30.962	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.918	-0.956	34.275	0.011	0.011	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.006	-0.005	33.408	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	16	PRO	0	-0.026	0.001	37.780	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.070	0.025	40.251	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.019	0.011	41.651	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.003	-0.016	39.166	0.001	0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.871	-0.933	40.232	0.024	0.024	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.797	-0.889	40.597	0.011	0.011	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.030	-0.020	35.894	0.001	0.001	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.003	-0.015	35.567	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.841	-0.916	35.667	0.029	0.029	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.041	-0.005	33.371	0.001	0.001	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.050	-0.034	30.612	0.001	0.001	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.038	-0.014	30.857	0.006	0.006	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.876	-0.919	32.400	0.031	0.031	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.000	-0.003	25.848	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.041	0.012	28.249	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.887	0.959	29.536	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.037	0.029	28.792	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.010	-0.002	25.318	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.090	-0.046	26.373	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.015	-0.023	28.787	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.047	-0.038	19.811	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	PRO	0	-0.030	-0.010	22.314	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.887	0.936	19.343	0.124	0.124	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.005	0.004	19.851	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.964	-0.975	19.411	-0.055	-0.055	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.812	0.877	20.222	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.019	0.016	21.299	0.007	0.007	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.076	-0.037	21.925	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.783	-0.892	24.449	0.061	0.061	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.082	-0.040	22.131	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.030	0.026	26.818	0.002	0.002	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.054	-0.047	28.853	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	ASN	0	0.022	0.021	29.491	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.006	0.012	24.623	0.008	0.008	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.015	-0.012	23.823	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.764	0.862	17.116	-0.083	-0.083	0.000	0.000	0.000	0.000
51	A	52	TRP	0	0.003	0.004	18.158	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.776	-0.875	16.562	0.053	0.053	0.000	0.000	0.000	0.000
53	A	54	MET	0	0.027	0.028	15.234	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.843	-0.928	16.554	-0.100	-0.100	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.900	0.955	14.251	0.147	0.147	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.016	0.017	12.472	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.088	0.020	12.511	-0.079	-0.079	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.075	-0.032	14.529	0.039	0.039	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.810	-0.908	14.528	-0.247	-0.247	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.848	0.907	12.514	0.186	0.186	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.012	0.006	10.058	-0.114	-0.114	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.094	-0.025	10.264	-0.081	-0.081	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.005	-0.010	7.204	-0.075	-0.075	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.003	-0.028	9.849	0.052	0.052	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.026	0.006	10.568	0.058	0.058	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.038	0.015	11.814	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	68	TYR	0	0.041	0.019	12.942	0.079	0.079	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.057	0.031	15.463	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	70	CYS	0	-0.067	-0.012	18.877	0.028	0.028	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.011	0.002	21.453	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	72	TYR	0	0.008	-0.008	23.247	0.007	0.007	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.008	-0.004	27.565	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.014	0.009	30.709	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.869	-0.930	33.539	0.050	0.050	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.818	0.875	36.568	-0.028	-0.028	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.973	-0.967	38.954	0.036	0.036	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.009	-0.004	37.342	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.018	0.028	37.497	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.858	0.920	29.967	-0.070	-0.070	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.037	0.035	29.324	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.035	-0.027	27.388	0.001	0.001	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.007	0.014	21.559	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.023	-0.009	22.108	0.011	0.011	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.052	0.029	17.576	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.048	-0.025	18.894	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.926	0.944	16.807	-0.194	-0.194	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.006	-0.004	14.389	-0.032	-0.032	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.838	-0.897	15.272	0.151	0.151	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.025	-0.006	12.670	0.013	0.013	0.000	0.000	0.000	0.000
90	A	91	ASN	0	-0.057	-0.038	7.227	0.061	0.061	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.024	0.014	8.838	0.150	0.150	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.039	-0.019	11.547	-0.037	-0.037	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.020	0.004	14.195	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.035	-0.019	17.123	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.064	0.023	20.639	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	97	SER	0	-0.096	-0.050	23.464	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	TRP	0	0.090	0.042	27.189	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.058	-0.037	30.102	0.004	0.004	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.011	0.009	33.209	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	SER	0	0.014	0.003	36.277	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.063	0.032	39.920	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.809	0.906	40.834	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.046	0.027	44.134	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.910	-0.970	46.277	0.012	0.012	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.059	-0.039	45.602	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.015	0.023	42.289	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.001	0.006	37.728	0.003	0.003	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.034	-0.007	37.766	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.003	-0.011	31.785	0.004	0.004	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.941	0.976	31.241	-0.039	-0.039	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.014	0.005	22.944	0.005	0.005	0.000	0.000	0.000	0.000
112	A	113	GLN	0	-0.010	-0.020	22.220	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.024	-0.020	18.916	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.016	-0.017	18.562	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.016	-0.017	14.624	0.010	0.010	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.834	-0.876	11.035	0.447	0.447	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.002	0.003	9.297	0.027	0.027	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.012	-0.012	3.781	-0.525	-0.183	0.029	-0.145	-0.226	0.001
119	A	120	VAL	0	0.026	0.005	4.195	-0.517	-0.249	-0.001	-0.078	-0.188	0.000
120	A	121	PRO	0	0.007	0.003	2.322	-6.855	-4.565	2.628	-2.621	-2.298	-0.025
121	A	122	LEU	0	0.032	0.015	2.970	0.848	1.517	0.182	-0.020	-0.832	-0.003
122	A	123	PRO	0	0.039	0.002	2.427	-1.372	-1.895	3.850	-1.579	-1.748	-0.017
123	A	124	SER	0	0.079	0.044	2.549	-1.020	-0.171	0.445	-0.414	-0.879	-0.002
124	A	125	LEU	0	-0.029	-0.011	3.792	0.276	0.416	0.010	-0.020	-0.130	0.000
125	A	126	LEU	0	-0.002	-0.010	6.297	0.180	0.180	0.000	0.000	0.000	0.000
126	A	127	LYS	1	1.007	1.009	6.694	0.307	0.307	0.000	0.000	0.000	0.000
127	A	128	LEU	0	-0.005	-0.009	8.003	0.125	0.125	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.013	0.015	11.220	0.059	0.059	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.030	0.014	7.842	0.064	0.064	0.000	0.000	0.000	0.000
130	A	131	SER	0	-0.011	-0.022	9.793	0.076	0.076	0.000	0.000	0.000	0.000
131	A	132	PRO	0	-0.001	-0.003	11.398	0.072	0.072	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.033	0.020	13.889	0.042	0.042	0.000	0.000	0.000	0.000
133	A	134	ILE	0	0.017	0.016	9.612	0.030	0.030	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.901	0.941	13.047	0.036	0.036	0.000	0.000	0.000	0.000
135	A	136	HIS	0	-0.010	0.010	15.317	0.032	0.032	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.839	-0.921	15.700	-0.116	-0.116	0.000	0.000	0.000	0.000
137	A	138	PHE	0	0.003	-0.002	15.370	0.022	0.022	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.007	-0.023	17.406	0.027	0.027	0.000	0.000	0.000	0.000
139	A	140	SER	0	0.030	0.037	20.441	0.012	0.012	0.000	0.000	0.000	0.000
140	A	141	LEU	0	-0.001	-0.002	17.645	0.009	0.009	0.000	0.000	0.000	0.000
141	A	142	VAL	0	0.022	0.007	20.652	0.009	0.009	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.838	-0.900	23.163	-0.020	-0.020	0.000	0.000	0.000	0.000
143	A	144	THR	0	-0.048	-0.030	25.028	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	TYR	0	-0.023	-0.007	24.786	0.005	0.005	0.000	0.000	0.000	0.000
145	A	146	MET	0	-0.029	-0.005	26.037	0.005	0.005	0.000	0.000	0.000	0.000
146	A	147	ALA	0	-0.008	-0.007	29.222	0.001	0.001	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.044	-0.032	28.414	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.035	0.024	29.107	0.001	0.001	0.000	0.000	0.000	0.000
149	A	150	LYS	1	0.854	0.927	32.526	0.003	0.003	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.855	0.922	32.909	0.019	0.019	0.000	0.000	0.000	0.000
151	A	152	ALA	0	0.047	0.038	34.500	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	153	PHE	0	-0.041	-0.038	36.168	0.001	0.001	0.000	0.000	0.000	0.000
153	A	154	LEU	0	-0.049	0.005	39.397	0.000	0.000	0.000	0.000	0.000	0.000
154	A	155	GLU	-1	-0.918	-0.965	37.836	-0.009	-0.009	0.000	0.000	0.000	0.000
155	A	156	HIS	0	-0.025	-0.019	42.042	0.002	0.002	0.000	0.000	0.000	0.000
156	A	157	HIS	0	-0.019	-0.011	39.291	0.003	0.003	0.000	0.000	0.000	0.000
157	A	158	HIS	1	0.900	0.956	37.400	-0.007	-0.007	0.000	0.000	0.000	0.000
158	A	159	HIS	0	0.090	0.066	33.277	0.004	0.004	0.000	0.000	0.000	0.000

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