FMO DATABASE

FMODB ID: K3MZ3

Calculation Name: 1PXU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PXU

Chain ID: A

ChEMBL ID:

UniProt ID: P31696

Base Structure: X-ray

Registration Date: 2023-06-19

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208852.131421
FMO2-HF: Nuclear repulsion	1154636.12316
FMO2-HF: Total energy	-54216.00826
FMO2-MP2: Total energy	-54370.435397

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:ASN)

Summations of interaction energy for fragment #1(A:1: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.
-0.925	0.468	-0.011	-0.529	-0.854	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / 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

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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	PRO	0	-0.018	0.004	3.843	-1.283	0.110	-0.011	-0.529	-0.854	0.003
4	A	4	GLU	-1	-0.708	-0.836	5.509	0.675	0.675	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.731	0.829	8.422	0.080	0.080	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.895	-0.958	11.464	-0.655	-0.655	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.026	-0.022	13.061	0.073	0.073	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.029	0.010	15.542	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.896	0.932	15.246	0.564	0.564	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.831	0.899	12.499	0.044	0.044	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.796	-0.905	16.934	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.927	-0.960	20.273	-0.259	-0.259	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.812	-0.879	17.242	-0.343	-0.343	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.030	-0.002	20.174	0.029	0.029	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.019	-0.027	22.153	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.009	-0.004	24.839	0.006	0.006	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.021	0.018	21.322	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.001	0.010	23.355	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.027	0.007	22.931	0.032	0.032	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.041	0.009	24.040	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.059	-0.026	24.230	0.027	0.027	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.041	0.031	22.180	-0.037	-0.037	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.819	-0.886	25.445	0.241	0.241	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.843	-0.931	28.085	0.219	0.219	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.022	0.011	23.809	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.052	-0.018	26.617	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.037	-0.013	27.521	0.016	0.016	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.043	0.007	24.575	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.783	-0.854	24.807	0.109	0.109	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.011	-0.024	25.044	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.043	-0.017	26.876	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.060	-0.056	22.793	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.046	-0.006	20.684	0.043	0.043	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.011	0.008	18.961	0.038	0.038	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.039	-0.043	18.449	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.012	-0.033	22.501	0.007	0.007	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.070	-0.018	23.540	0.036	0.036	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.887	0.963	25.708	-0.218	-0.218	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.022	-0.019	24.099	0.030	0.030	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.863	0.935	27.368	-0.294	-0.294	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.002	-0.002	28.178	0.023	0.023	0.000	0.000	0.000	0.000
42	A	42	TRP	0	-0.050	-0.027	27.104	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.926	0.958	28.174	-0.158	-0.158	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.039	0.014	27.374	0.018	0.018	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.027	-0.012	23.071	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.815	0.904	24.061	0.028	0.028	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.094	0.055	27.656	0.014	0.014	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.932	0.964	29.781	-0.082	-0.082	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.908	-0.943	31.953	0.029	0.029	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.052	0.028	29.568	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.007	-0.004	29.458	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.096	-0.070	32.529	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.035	-0.011	35.896	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.944	-0.965	32.684	0.016	0.016	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.094	-0.040	31.172	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.021	-0.010	34.587	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.007	0.000	33.272	0.010	0.010	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.842	-0.927	34.484	0.152	0.152	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.029	-0.031	35.788	0.006	0.006	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.025	0.000	37.948	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.050	-0.037	33.236	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.846	0.909	31.496	-0.185	-0.185	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.033	0.026	27.778	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.018	0.008	27.707	0.019	0.019	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.026	-0.003	22.027	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.100	0.043	23.706	0.026	0.026	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.004	-0.007	20.367	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.017	-0.008	17.853	0.021	0.021	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.000	-0.015	16.124	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.821	-0.906	15.810	0.131	0.131	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.030	-0.017	12.918	0.060	0.060	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.058	-0.016	11.765	-0.082	-0.082	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.050	-0.012	11.717	-0.122	-0.122	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.837	-0.887	8.513	1.966	1.966	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.065	0.019	10.744	-0.081	-0.081	0.000	0.000	0.000	0.000
76	A	77	GLN	0	0.030	0.019	13.850	-0.164	-0.164	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.008	0.012	15.878	0.030	0.030	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.010	-0.013	18.915	0.008	0.008	0.000	0.000	0.000	0.000
79	A	80	THR	0	0.010	-0.007	22.114	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	81	GLY	0	-0.019	-0.005	25.426	0.017	0.017	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.804	-0.866	19.105	0.747	0.747	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.048	-0.028	21.086	-0.055	-0.055	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.740	0.846	15.637	-0.704	-0.704	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.016	0.006	18.530	-0.060	-0.060	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.018	-0.017	18.292	0.048	0.048	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.034	0.009	16.957	-0.034	-0.034	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.009	-0.010	19.494	0.008	0.008	0.000	0.000	0.000	0.000
88	A	89	ASN	0	0.013	0.007	22.284	-0.036	-0.036	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.056	0.028	25.172	0.022	0.022	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.011	0.018	27.525	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	92	PRO	0	0.039	0.018	27.339	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.037	0.004	30.390	0.012	0.012	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.012	-0.003	26.466	0.005	0.005	0.000	0.000	0.000	0.000
94	A	95	MET	0	0.002	0.015	24.713	0.009	0.009	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.035	-0.005	30.320	0.017	0.017	0.000	0.000	0.000	0.000
96	A	97	PRO	0	0.003	-0.025	33.578	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.018	-0.012	30.410	0.007	0.007	0.000	0.000	0.000	0.000
98	A	99	HIS	1	0.859	0.899	25.786	-0.134	-0.134	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.908	0.951	29.930	-0.063	-0.063	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.040	-0.018	32.970	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.742	-0.817	27.004	0.189	0.189	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.032	-0.017	25.609	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	104	MET	0	0.003	0.004	22.477	0.033	0.033	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.015	-0.010	16.095	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	106	ASN	0	0.010	0.013	18.188	-0.043	-0.043	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.027	0.018	14.402	-0.070	-0.070	0.000	0.000	0.000	0.000
107	A	108	SER	0	0.007	-0.027	10.420	0.137	0.137	0.000	0.000	0.000	0.000
108	A	109	LEU	0	-0.038	-0.006	12.579	-0.063	-0.063	0.000	0.000	0.000	0.000
109	A	110	MET	0	0.015	0.036	13.660	0.118	0.118	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.828	0.892	12.132	-1.341	-1.341	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.042	0.028	16.906	-0.062	-0.062	0.000	0.000	0.000	0.000
112	A	113	THR	0	-0.028	-0.015	17.925	0.008	0.008	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.032	0.013	20.871	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	115	ARG	1	1.022	1.029	17.299	-0.305	-0.305	0.000	0.000	0.000	0.000
115	A	116	ASN	0	-0.040	-0.031	15.622	-0.045	-0.045	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.015	-0.010	19.001	-0.034	-0.034	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.904	-0.954	22.532	0.142	0.142	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.892	-0.962	17.438	0.143	0.143	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.034	-0.013	18.985	-0.043	-0.043	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.949	-0.987	21.317	0.085	0.085	0.000	0.000	0.000	0.000
121	A	122	HIS	0	-0.072	-0.036	23.445	-0.015	-0.015	0.000	0.000	0.000	0.000
122	A	123	CYS	0	-0.008	0.002	20.558	-0.039	-0.039	0.000	0.000	0.000	0.000
123	A	124	VAL	0	-0.018	-0.010	22.634	-0.021	-0.021	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.877	-0.917	25.152	-0.029	-0.029	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.838	-0.908	24.621	-0.109	-0.109	0.000	0.000	0.000	0.000
126	A	127	HIS	0	0.010	0.010	24.417	-0.013	-0.013	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.851	0.912	26.563	0.002	0.002	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.809	0.884	29.008	0.084	0.084	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.041	0.002	26.492	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	131	LEU	0	-0.087	-0.026	30.993	0.001	0.001	0.000	0.000	0.000	0.000

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