FMO DATABASE

FMODB ID: LZG89

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1471930.936292
FMO2-HF: Nuclear repulsion	1411525.73886
FMO2-HF: Total energy	-60405.197432
FMO2-MP2: Total energy	-60583.852639

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.
-8.748	-5.135	10.259	-6.312	-7.561	-0.054

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 : -0.048 / 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	4	THR	0	0.025	0.017	3.880	1.132	2.491	-0.009	-0.648	-0.703	0.001
4	A	5	VAL	0	-0.059	-0.026	6.451	-0.382	-0.382	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.027	-0.006	9.689	0.031	0.031	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.092	-0.042	12.831	-0.098	-0.098	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.839	-0.876	15.718	0.146	0.146	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.072	-0.028	19.377	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.001	-0.013	22.241	0.014	0.014	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.749	0.834	23.534	0.020	0.020	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.787	-0.860	28.277	0.018	0.018	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.027	-0.020	30.862	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.917	-0.960	34.138	0.002	0.002	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.005	0.006	33.448	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	16	PRO	0	-0.028	-0.003	37.875	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.062	0.025	40.204	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.005	-0.012	41.889	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.034	-0.043	39.223	0.000	0.000	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.849	-0.925	40.015	0.018	0.018	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.767	-0.845	39.999	0.004	0.004	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.029	-0.018	35.907	0.000	0.000	0.000	0.000	0.000	0.000
22	A	23	PHE	0	0.006	-0.013	35.545	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.822	-0.908	35.244	0.023	0.023	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.063	-0.022	33.163	0.001	0.001	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.049	-0.034	30.243	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.021	0.003	30.800	0.005	0.005	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.856	-0.926	31.970	0.022	0.022	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.002	0.010	25.902	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.020	0.002	27.935	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.865	0.946	29.192	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.031	0.032	28.395	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.003	-0.012	25.078	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.090	-0.051	26.421	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	35	HIS	0	0.012	-0.001	28.826	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.036	-0.024	19.790	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	37	PRO	0	-0.032	-0.006	22.111	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.874	0.926	19.125	0.157	0.157	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.019	0.012	19.495	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.965	-0.969	19.060	-0.072	-0.072	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.830	0.886	19.605	0.014	0.014	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.008	0.009	21.048	0.005	0.005	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.059	-0.027	21.761	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.797	-0.892	24.130	0.057	0.057	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.058	-0.030	22.051	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.028	0.025	26.746	0.003	0.003	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.055	-0.044	28.827	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	ASN	0	0.014	0.014	29.365	0.003	0.003	0.000	0.000	0.000	0.000
48	A	49	ALA	0	-0.003	-0.001	24.697	0.007	0.007	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.010	-0.020	23.654	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.764	0.848	16.804	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	52	TRP	0	0.015	0.010	18.044	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.788	-0.881	16.409	0.043	0.043	0.000	0.000	0.000	0.000
53	A	54	MET	0	0.009	0.023	15.259	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.849	-0.938	16.527	-0.129	-0.129	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.906	0.956	13.920	0.164	0.164	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.010	0.003	12.343	0.021	0.021	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.074	0.017	12.455	-0.091	-0.091	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.075	-0.023	14.317	0.042	0.042	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.775	-0.891	14.339	-0.241	-0.241	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.816	0.890	12.445	0.174	0.174	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.004	0.009	9.908	-0.117	-0.117	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.099	-0.031	10.359	-0.078	-0.078	0.000	0.000	0.000	0.000
63	A	64	ILE	0	0.004	0.006	7.046	-0.061	-0.061	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.004	-0.023	9.700	0.066	0.066	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.017	0.002	9.983	0.013	0.013	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.037	0.023	11.697	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	68	TYR	0	0.043	0.022	12.597	0.079	0.079	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.042	0.027	15.105	-0.041	-0.041	0.000	0.000	0.000	0.000
69	A	70	CYS	0	-0.078	-0.024	18.545	0.030	0.030	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.008	-0.006	21.196	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	72	TYR	0	0.024	0.010	23.183	0.007	0.007	0.000	0.000	0.000	0.000
72	A	73	HIS	0	0.009	-0.002	27.453	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.002	-0.008	30.778	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.861	-0.919	33.547	0.043	0.043	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.805	0.882	36.686	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.945	-0.948	39.199	0.029	0.029	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.031	-0.025	37.390	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.019	0.033	37.669	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.810	0.891	29.916	-0.052	-0.052	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.036	0.030	29.420	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.031	-0.021	27.565	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.012	0.018	21.469	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.010	-0.004	21.882	0.010	0.010	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.051	0.032	17.471	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.022	-0.013	18.796	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.885	0.930	17.089	-0.189	-0.189	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.025	0.007	14.102	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.853	-0.900	14.505	0.162	0.162	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.003	0.001	12.679	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	91	ASN	0	-0.084	-0.059	7.257	0.100	0.100	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.014	0.010	8.562	0.103	0.103	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.031	-0.020	11.291	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.014	0.010	14.031	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.046	-0.033	16.907	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.066	0.024	20.457	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	97	SER	0	-0.084	-0.035	23.372	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	TRP	0	0.094	0.047	27.052	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.005	-0.021	29.938	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.000	0.018	33.262	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	SER	0	0.033	0.010	36.412	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.052	0.034	40.052	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.783	0.889	40.871	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.056	0.034	44.456	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.912	-0.971	46.052	0.006	0.006	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.050	-0.033	45.689	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.011	0.024	42.442	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.013	-0.003	37.985	0.003	0.003	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.011	0.005	37.776	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.008	-0.016	31.879	0.003	0.003	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.800	0.884	31.597	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.046	0.018	22.804	0.005	0.005	0.000	0.000	0.000	0.000
112	A	113	GLN	0	-0.005	-0.021	22.434	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.017	-0.016	18.992	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.013	-0.026	18.731	-0.021	-0.021	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.007	-0.009	14.924	0.016	0.016	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.805	-0.863	10.901	0.363	0.363	0.000	0.000	0.000	0.000
117	A	118	LEU	0	-0.003	0.001	9.343	0.007	0.007	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.007	-0.015	3.782	-0.517	-0.211	0.023	-0.125	-0.204	0.001
119	A	120	VAL	0	0.031	0.013	3.687	-0.639	-0.113	0.000	-0.228	-0.299	0.000
120	A	121	PRO	0	0.014	0.015	2.001	-8.602	-8.977	7.309	-3.745	-3.189	-0.037
121	A	122	LEU	0	0.029	0.012	2.636	0.925	1.587	0.568	-0.063	-1.166	-0.005
122	A	123	PRO	0	0.031	-0.003	2.520	-1.748	-1.471	2.222	-1.186	-1.313	-0.013
123	A	124	SER	0	0.050	0.030	2.806	-0.709	0.016	0.143	-0.287	-0.581	-0.001
124	A	125	LEU	0	-0.011	-0.002	4.090	0.223	0.356	0.003	-0.030	-0.106	0.000
125	A	126	LEU	0	0.022	0.006	6.843	0.159	0.159	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.996	1.004	6.992	0.401	0.401	0.000	0.000	0.000	0.000
127	A	128	LEU	0	-0.001	-0.003	8.394	0.123	0.123	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.009	0.017	11.522	0.072	0.072	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.022	0.003	7.415	0.055	0.055	0.000	0.000	0.000	0.000
130	A	131	SER	0	-0.009	-0.022	10.156	0.076	0.076	0.000	0.000	0.000	0.000
131	A	132	PRO	0	-0.015	-0.012	11.607	0.069	0.069	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.034	0.024	13.705	0.043	0.043	0.000	0.000	0.000	0.000
133	A	134	ILE	0	0.008	0.009	9.539	0.035	0.035	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.900	0.937	12.995	0.086	0.086	0.000	0.000	0.000	0.000
135	A	136	HIS	0	-0.010	0.015	15.486	0.036	0.036	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.785	-0.886	15.759	-0.143	-0.143	0.000	0.000	0.000	0.000
137	A	138	PHE	0	0.000	-0.002	15.329	0.025	0.025	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.007	-0.010	17.379	0.035	0.035	0.000	0.000	0.000	0.000
139	A	140	SER	0	-0.003	0.003	20.594	0.017	0.017	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.014	0.008	17.613	0.011	0.011	0.000	0.000	0.000	0.000
141	A	142	VAL	0	0.025	0.010	20.610	0.013	0.013	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.812	-0.882	23.039	-0.039	-0.039	0.000	0.000	0.000	0.000
143	A	144	THR	0	-0.043	-0.030	24.788	0.004	0.004	0.000	0.000	0.000	0.000
144	A	145	TYR	0	-0.033	-0.013	24.688	0.006	0.006	0.000	0.000	0.000	0.000
145	A	146	MET	0	-0.027	-0.004	25.988	0.007	0.007	0.000	0.000	0.000	0.000
146	A	147	ALA	0	-0.011	-0.008	29.203	0.003	0.003	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.047	-0.025	28.284	0.000	0.000	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.038	0.022	29.064	0.002	0.002	0.000	0.000	0.000	0.000
149	A	150	LYS	1	0.867	0.923	32.480	0.014	0.014	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.868	0.924	32.721	0.030	0.030	0.000	0.000	0.000	0.000
151	A	152	ALA	0	0.029	0.038	34.200	0.000	0.000	0.000	0.000	0.000	0.000
152	A	153	PHE	0	-0.050	-0.051	35.856	0.003	0.003	0.000	0.000	0.000	0.000
153	A	154	LEU	0	-0.011	0.011	39.298	0.001	0.001	0.000	0.000	0.000	0.000
154	A	155	GLU	-1	-0.961	-0.975	37.322	-0.017	-0.017	0.000	0.000	0.000	0.000
155	A	156	HIS	0	0.002	-0.004	41.229	0.001	0.001	0.000	0.000	0.000	0.000
156	A	157	HIS	0	0.003	-0.010	39.227	0.003	0.003	0.000	0.000	0.000	0.000
157	A	158	HIS	1	0.869	0.949	37.371	0.000	0.000	0.000	0.000	0.000	0.000
158	A	159	HIS	0	0.071	0.041	32.830	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)