FMO DATABASE

FMODB ID: R5VK8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1200935.048825
FMO2-HF: Nuclear repulsion	1146719.743758
FMO2-HF: Total energy	-54215.305067
FMO2-MP2: Total energy	-54369.686183

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.
-1.081	0.538	-0.019	-0.594	-1.006	0.002

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 : -0.014 / q_NPA : -0.024

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	-0.032	-0.008	3.801	-1.094	0.436	-0.018	-0.593	-0.919	0.002
4	A	4	GLU	-1	-0.741	-0.863	5.285	0.687	0.776	-0.001	-0.001	-0.087	0.000
5	A	5	ARG	1	0.781	0.886	8.040	0.226	0.226	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.879	-0.945	11.238	-1.072	-1.072	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.025	-0.023	12.875	0.129	0.129	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.082	0.026	15.121	0.017	0.017	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.914	0.962	14.534	0.847	0.847	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.898	0.944	12.608	0.344	0.344	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.841	-0.927	16.838	-0.144	-0.144	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.944	-0.966	20.067	-0.382	-0.382	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.857	-0.910	17.817	-0.464	-0.464	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.026	0.000	20.284	0.044	0.044	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.025	-0.027	22.146	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.005	-0.003	24.863	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.022	0.022	21.605	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.024	0.001	23.422	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.037	0.026	23.108	0.033	0.033	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.029	-0.002	23.996	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.057	-0.028	24.141	0.041	0.041	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.027	0.030	22.049	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.832	-0.911	25.383	0.250	0.250	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.928	-0.973	28.175	0.255	0.255	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.013	0.028	23.565	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.046	-0.015	26.788	-0.029	-0.029	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.007	-0.003	27.697	0.022	0.022	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.034	0.002	24.639	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.841	-0.901	24.910	0.132	0.132	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.018	-0.040	25.090	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.026	0.002	26.349	0.000	0.000	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.049	-0.031	22.272	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.042	-0.003	20.401	0.048	0.048	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.004	0.020	19.369	0.034	0.034	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.011	-0.045	18.196	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.026	0.008	22.570	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.048	-0.013	23.041	0.038	0.038	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.954	0.991	25.872	-0.226	-0.226	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.004	-0.015	24.396	0.029	0.029	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.883	0.932	27.637	-0.280	-0.280	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.006	-0.011	28.257	0.020	0.020	0.000	0.000	0.000	0.000
42	A	42	TRP	0	-0.055	-0.016	27.572	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.939	0.948	28.537	-0.104	-0.104	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.012	0.002	27.741	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.017	-0.012	23.252	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.862	0.919	24.064	0.125	0.125	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.083	0.055	27.712	0.016	0.016	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.931	0.966	29.772	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.891	-0.947	32.240	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.036	0.024	29.703	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.022	-0.014	29.957	0.008	0.008	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.104	-0.064	32.799	0.008	0.008	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.024	-0.013	36.274	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.951	-0.957	33.288	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.060	-0.022	31.328	0.007	0.007	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.042	-0.017	34.821	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.016	-0.016	33.373	0.011	0.011	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.867	-0.938	35.121	0.147	0.147	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.009	-0.018	36.141	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.034	-0.011	38.023	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.014	-0.011	33.765	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.876	0.951	31.669	-0.179	-0.179	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.022	0.020	27.910	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.006	0.010	28.093	0.025	0.025	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.026	-0.003	22.299	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.098	0.035	23.814	0.034	0.034	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.011	-0.009	20.641	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.027	-0.007	17.935	0.011	0.011	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.019	-0.022	15.907	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.855	-0.928	16.065	0.161	0.161	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.021	-0.007	13.029	0.071	0.071	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.039	-0.013	11.715	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.052	-0.005	11.855	-0.187	-0.187	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.851	-0.896	8.636	1.975	1.975	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.030	-0.019	10.626	-0.048	-0.048	0.000	0.000	0.000	0.000
76	A	77	GLN	0	0.051	0.049	13.800	-0.207	-0.207	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.035	-0.013	15.752	0.031	0.031	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.009	0.000	18.744	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	80	THR	0	0.003	-0.017	21.727	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	81	GLY	0	-0.027	-0.017	24.878	0.021	0.021	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.866	-0.917	19.362	0.777	0.777	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.038	-0.020	21.567	-0.059	-0.059	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.860	0.924	15.896	-0.757	-0.757	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.029	0.020	18.624	-0.058	-0.058	0.000	0.000	0.000	0.000
85	A	86	PHE	0	0.003	-0.027	18.474	0.044	0.044	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.042	0.026	17.842	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.007	-0.016	19.806	0.016	0.016	0.000	0.000	0.000	0.000
88	A	89	ASN	0	0.034	0.017	22.528	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.045	0.030	25.344	0.026	0.026	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.012	0.011	27.487	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	92	PRO	0	0.043	0.016	27.212	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.073	0.018	30.365	0.017	0.017	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.033	-0.010	26.912	0.012	0.012	0.000	0.000	0.000	0.000
94	A	95	MET	0	0.008	0.015	25.181	0.013	0.013	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.071	-0.008	30.346	0.023	0.023	0.000	0.000	0.000	0.000
96	A	97	PRO	0	-0.020	-0.040	33.523	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	98	ALA	0	0.001	-0.002	30.397	0.007	0.007	0.000	0.000	0.000	0.000
98	A	99	HIS	1	0.836	0.886	26.141	-0.144	-0.144	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.963	0.985	30.112	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.032	-0.011	33.157	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.807	-0.880	27.771	0.185	0.185	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.021	-0.007	25.809	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	104	MET	0	0.002	-0.010	22.934	0.036	0.036	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.004	-0.004	16.405	-0.034	-0.034	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.009	-0.005	18.440	-0.054	-0.054	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.008	-0.009	14.106	-0.088	-0.088	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.022	-0.045	10.150	0.191	0.191	0.000	0.000	0.000	0.000
108	A	109	LEU	0	-0.031	0.017	12.883	-0.111	-0.111	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.003	0.004	13.395	0.102	0.102	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.809	0.877	12.107	-1.361	-1.361	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.043	0.022	17.106	-0.079	-0.079	0.000	0.000	0.000	0.000
112	A	113	THR	0	-0.004	-0.002	17.909	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.075	0.017	20.804	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	115	ARG	1	1.009	1.019	16.319	-0.116	-0.116	0.000	0.000	0.000	0.000
115	A	116	ASN	0	-0.010	-0.008	15.539	-0.117	-0.117	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.047	-0.029	18.930	-0.042	-0.042	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.905	-0.953	22.370	-0.015	-0.015	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.947	-0.974	16.406	-0.203	-0.203	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.037	-0.024	18.789	-0.045	-0.045	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.946	-0.977	21.047	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	122	HIS	0	-0.033	-0.003	22.979	-0.022	-0.022	0.000	0.000	0.000	0.000
122	A	123	CYS	0	-0.009	-0.001	20.288	-0.042	-0.042	0.000	0.000	0.000	0.000
123	A	124	VAL	0	0.013	0.012	22.561	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.958	-0.992	24.977	-0.108	-0.108	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.857	-0.952	24.829	-0.247	-0.247	0.000	0.000	0.000	0.000
126	A	127	HIS	0	0.009	0.015	24.478	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.864	0.942	26.488	0.108	0.108	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.843	0.924	29.188	0.224	0.224	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.076	-0.013	26.752	0.001	0.001	0.000	0.000	0.000	0.000
130	A	131	LEU	0	-0.044	-0.009	31.089	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:1:ASN)