FMO DATABASE

FMODB ID: R88M8

Calculation Name: 4PER-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PER

Chain ID: B

ChEMBL ID:

UniProt ID: P27043

Base Structure: X-ray

Registration Date: 2023-09-21

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	111
LigandCharge	DCY=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-916804.668892
FMO2-HF: Nuclear repulsion	870434.854694
FMO2-HF: Total energy	-46369.814198
FMO2-MP2: Total energy	-46501.20389

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(B:3:PRO)

Summations of interaction energy for fragment #1(B:3:PRO)

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.
-5.071	0.632	2.923	-3.665	-4.96	-0.017

Interaction energy analysis for fragmet #1(B:3:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.006

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	B	5	TYR	0	0.083	0.035	3.822	-1.649	0.768	-0.020	-1.273	-1.124	0.005
4	B	6	GLN	0	0.057	0.006	6.434	0.376	0.376	0.000	0.000	0.000	0.000
5	B	7	ASP	-1	-0.831	-0.908	3.463	0.605	1.701	0.046	-0.561	-0.580	-0.004
6	B	8	PHE	0	0.003	0.007	4.411	0.382	0.510	-0.001	-0.008	-0.119	0.000
7	B	9	LEU	0	-0.008	-0.005	5.570	0.347	0.347	0.000	0.000	0.000	0.000
8	B	10	ARG	1	0.861	0.930	6.436	-0.671	-0.671	0.000	0.000	0.000	0.000
9	B	11	THR	0	-0.055	-0.044	6.454	0.081	0.081	0.000	0.000	0.000	0.000
10	B	12	HIS	1	0.861	0.925	6.352	0.169	0.169	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.037	0.049	10.073	-0.035	-0.035	0.000	0.000	0.000	0.000
12	B	14	ASP	-1	-0.820	-0.893	12.524	-0.014	-0.014	0.000	0.000	0.000	0.000
13	B	15	PHE	0	0.069	0.022	16.048	0.003	0.003	0.000	0.000	0.000	0.000
14	B	16	PRO	0	0.014	0.018	18.486	-0.008	-0.008	0.000	0.000	0.000	0.000
15	B	17	LYS	1	0.865	0.950	20.104	0.080	0.080	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.059	-0.047	19.785	0.012	0.012	0.000	0.000	0.000	0.000
17	B	19	SER	0	-0.022	-0.011	22.212	0.007	0.007	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.014	-0.012	21.689	0.013	0.013	0.000	0.000	0.000	0.000
19	B	21	PRO	0	0.025	0.013	26.478	-0.006	-0.006	0.000	0.000	0.000	0.000
20	B	22	ASN	0	0.052	0.032	27.527	0.002	0.002	0.000	0.000	0.000	0.000
21	B	23	ILE	0	0.064	0.032	22.125	0.004	0.004	0.000	0.000	0.000	0.000
22	B	24	ALA	0	0.060	0.035	23.020	0.008	0.008	0.000	0.000	0.000	0.000
23	B	25	ALA	0	-0.043	-0.024	23.387	0.016	0.016	0.000	0.000	0.000	0.000
24	B	26	TYR	0	-0.017	-0.021	18.047	0.013	0.013	0.000	0.000	0.000	0.000
25	B	27	CYS	0	-0.051	-0.021	16.260	0.010	0.010	0.000	0.000	0.000	0.000
26	B	28	ASN	0	0.057	0.015	18.818	0.035	0.035	0.000	0.000	0.000	0.000
27	B	29	VAL	0	0.000	0.013	20.260	0.023	0.023	0.000	0.000	0.000	0.000
28	B	30	MET	0	0.005	0.003	16.628	0.022	0.022	0.000	0.000	0.000	0.000
29	B	31	MET	0	-0.019	0.004	12.910	0.011	0.011	0.000	0.000	0.000	0.000
30	B	32	VAL	0	0.015	0.025	14.950	0.066	0.066	0.000	0.000	0.000	0.000
31	B	33	ARG	1	0.950	0.977	16.584	-0.041	-0.041	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.811	0.905	12.312	0.018	0.018	0.000	0.000	0.000	0.000
33	B	35	GLY	0	0.027	0.021	11.701	0.073	0.073	0.000	0.000	0.000	0.000
34	B	36	ILE	0	-0.086	-0.027	9.885	0.142	0.142	0.000	0.000	0.000	0.000
35	B	37	ASN	0	-0.012	-0.027	12.176	0.105	0.105	0.000	0.000	0.000	0.000
36	B	38	VAL	0	0.027	0.021	14.018	-0.049	-0.049	0.000	0.000	0.000	0.000
37	B	39	HIS	0	0.038	-0.006	15.819	0.072	0.072	0.000	0.000	0.000	0.000
38	B	40	GLY	0	0.033	0.023	18.792	0.015	0.015	0.000	0.000	0.000	0.000
39	B	41	ARG	1	0.896	0.960	11.628	-0.871	-0.871	0.000	0.000	0.000	0.000
40	B	42	CYS	0	-0.004	0.006	16.978	-0.029	-0.029	0.000	0.000	0.000	0.000
41	B	43	LYS	1	0.890	0.958	8.202	-0.510	-0.510	0.000	0.000	0.000	0.000
42	B	44	SER	0	0.054	0.036	14.236	-0.049	-0.049	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.052	0.024	14.006	-0.050	-0.050	0.000	0.000	0.000	0.000
44	B	46	ASN	0	-0.022	-0.022	10.460	0.114	0.114	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.081	0.058	12.184	0.002	0.002	0.000	0.000	0.000	0.000
46	B	48	PHE	0	-0.023	-0.004	12.124	-0.021	-0.021	0.000	0.000	0.000	0.000
47	B	49	VAL	0	0.051	0.009	12.817	0.012	0.012	0.000	0.000	0.000	0.000
48	B	50	HIS	0	-0.063	-0.011	14.990	0.001	0.001	0.000	0.000	0.000	0.000
49	B	51	THR	0	0.042	0.008	15.912	0.019	0.019	0.000	0.000	0.000	0.000
50	B	52	ASP	-1	-0.858	-0.928	16.682	-0.275	-0.275	0.000	0.000	0.000	0.000
51	B	53	PRO	0	-0.004	-0.008	12.972	-0.028	-0.028	0.000	0.000	0.000	0.000
52	B	54	ARG	1	1.033	1.031	14.273	0.204	0.204	0.000	0.000	0.000	0.000
53	B	55	ASN	0	-0.016	0.021	16.793	-0.023	-0.023	0.000	0.000	0.000	0.000
54	B	56	LEU	0	-0.021	-0.011	11.691	-0.006	-0.006	0.000	0.000	0.000	0.000
55	B	57	ASN	0	-0.044	-0.073	12.911	-0.060	-0.060	0.000	0.000	0.000	0.000
56	B	58	THR	0	0.075	0.953	13.831	-0.010	-0.010	0.000	0.000	0.000	0.000
57	B	59	LEU	0	0.027	-1.271	14.867	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	60	DCY	-1	-0.853	-0.932	17.301	-0.303	-0.303	0.000	0.000	0.000	0.000
59	B	61	ILE	0	-0.239	0.270	16.661	-0.044	-0.044	0.000	0.000	0.000	0.000
60	B	62	ASN	0	-0.014	-0.004	14.803	-0.091	-0.091	0.000	0.000	0.000	0.000
61	B	63	GLN	0	0.039	0.022	13.958	0.028	0.028	0.000	0.000	0.000	0.000
62	B	64	PRO	0	0.010	-0.003	13.668	-0.083	-0.083	0.000	0.000	0.000	0.000
63	B	65	ASN	0	-0.064	-0.026	9.777	-0.141	-0.141	0.000	0.000	0.000	0.000
64	B	66	ARG	1	0.975	0.974	7.172	0.914	0.914	0.000	0.000	0.000	0.000
65	B	67	ALA	0	-0.016	0.012	9.257	0.136	0.136	0.000	0.000	0.000	0.000
66	B	68	LEU	0	0.019	0.003	9.226	-0.142	-0.142	0.000	0.000	0.000	0.000
67	B	69	ARG	1	0.915	0.947	12.055	0.730	0.730	0.000	0.000	0.000	0.000
68	B	70	THR	0	-0.012	-0.021	13.735	-0.033	-0.033	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.027	0.001	15.777	0.012	0.012	0.000	0.000	0.000	0.000
70	B	72	GLN	0	0.034	0.017	18.134	0.020	0.020	0.000	0.000	0.000	0.000
71	B	73	GLN	0	0.023	0.012	21.898	0.004	0.004	0.000	0.000	0.000	0.000
72	B	74	GLN	0	-0.022	0.003	20.510	-0.029	-0.029	0.000	0.000	0.000	0.000
73	B	75	LEU	0	0.008	-0.001	16.831	0.012	0.012	0.000	0.000	0.000	0.000
74	B	76	PRO	0	0.039	0.018	20.322	0.014	0.014	0.000	0.000	0.000	0.000
75	B	77	VAL	0	-0.023	-0.011	16.406	-0.020	-0.020	0.000	0.000	0.000	0.000
76	B	78	THR	0	-0.017	-0.032	17.460	0.023	0.023	0.000	0.000	0.000	0.000
77	B	79	ASP	-1	-0.940	-0.968	16.817	0.003	0.003	0.000	0.000	0.000	0.000
78	B	81	LYS	1	0.982	0.974	16.971	-0.027	-0.027	0.000	0.000	0.000	0.000
79	B	82	LEU	0	-0.055	-0.024	18.505	-0.006	-0.006	0.000	0.000	0.000	0.000
80	B	83	ILE	0	-0.052	-0.031	20.265	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	84	ARG	1	0.956	0.979	23.628	-0.112	-0.112	0.000	0.000	0.000	0.000
82	B	85	SER	0	0.021	-0.005	21.725	0.005	0.005	0.000	0.000	0.000	0.000
83	B	86	HIS	0	0.042	0.042	23.216	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	87	PRO	0	0.016	-0.007	26.494	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	88	THR	0	-0.004	-0.008	24.433	0.019	0.019	0.000	0.000	0.000	0.000
86	B	90	SER	0	-0.030	-0.003	22.187	-0.020	-0.020	0.000	0.000	0.000	0.000
87	B	91	TYR	0	-0.013	-0.024	16.443	0.015	0.015	0.000	0.000	0.000	0.000
88	B	92	THR	0	0.027	0.015	22.293	-0.016	-0.016	0.000	0.000	0.000	0.000
89	B	93	GLY	0	0.038	-0.011	21.521	0.012	0.012	0.000	0.000	0.000	0.000
90	B	94	ASN	0	-0.047	-0.007	21.491	0.004	0.004	0.000	0.000	0.000	0.000
91	B	95	GLN	0	0.042	0.022	21.406	-0.003	-0.003	0.000	0.000	0.000	0.000
92	B	96	PHE	0	0.015	0.005	20.321	0.005	0.005	0.000	0.000	0.000	0.000
93	B	97	ASN	0	0.002	0.006	21.312	-0.019	-0.019	0.000	0.000	0.000	0.000
94	B	98	HIS	0	0.050	0.007	18.547	-0.006	-0.006	0.000	0.000	0.000	0.000
95	B	99	ARG	1	0.980	0.994	18.026	0.189	0.189	0.000	0.000	0.000	0.000
96	B	100	VAL	0	0.029	0.026	12.907	0.003	0.003	0.000	0.000	0.000	0.000
97	B	101	ARG	1	0.942	0.998	12.105	0.330	0.330	0.000	0.000	0.000	0.000
98	B	102	VAL	0	0.038	0.012	8.996	-0.016	-0.016	0.000	0.000	0.000	0.000
99	B	103	GLY	0	0.028	0.005	6.948	0.143	0.143	0.000	0.000	0.000	0.000
100	B	104	CYS	0	-0.068	-0.038	6.732	-0.302	-0.302	0.000	0.000	0.000	0.000
101	B	105	TRP	0	0.048	0.002	5.655	-0.136	-0.136	0.000	0.000	0.000	0.000
102	B	106	GLY	0	0.021	0.028	7.593	-0.034	-0.034	0.000	0.000	0.000	0.000
103	B	107	GLY	0	0.008	0.011	10.635	0.073	0.073	0.000	0.000	0.000	0.000
104	B	108	LEU	0	-0.003	0.000	8.950	0.105	0.105	0.000	0.000	0.000	0.000
105	B	109	PRO	0	-0.016	0.011	8.032	-0.284	-0.284	0.000	0.000	0.000	0.000
106	B	110	VAL	0	0.000	-0.014	2.714	-0.725	0.155	0.212	-0.256	-0.835	0.000
107	B	111	HIS	0	-0.050	-0.037	2.293	-3.811	-2.688	2.687	-1.552	-2.258	-0.018
108	B	112	LEU	0	-0.029	-0.006	4.661	0.168	0.227	-0.001	-0.015	-0.044	0.000
109	B	113	ASP	-1	-0.874	-0.936	7.697	-0.349	-0.349	0.000	0.000	0.000	0.000
110	B	114	GLY	0	-0.038	-0.029	9.296	0.100	0.100	0.000	0.000	0.000	0.000
111	B	115	THR	0	-0.012	0.003	12.913	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:PRO)