FMO DATABASE

FMODB ID: KGG83

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

Total energy (hartree)

FMO2-HF: Electronic energy	-916039.489057
FMO2-HF: Nuclear repulsion	869666.541288
FMO2-HF: Total energy	-46372.947769
FMO2-MP2: Total energy	-46504.003578

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.
-4.318	1.4	1.505	-2.917	-4.303	-0.016

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 : 0.012 / q_NPA : -0.002

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	0.022	-0.010	3.691	-1.358	0.544	-0.006	-1.015	-0.879	0.002
4	B	6	GLN	0	0.048	0.013	6.301	0.365	0.365	0.000	0.000	0.000	0.000
5	B	7	ASP	-1	-0.784	-0.858	3.083	0.159	1.107	0.108	-0.438	-0.618	-0.002
6	B	8	PHE	0	0.012	0.022	4.287	0.306	0.481	-0.001	-0.018	-0.156	0.000
7	B	9	LEU	0	0.011	-0.001	5.259	0.373	0.407	-0.001	-0.001	-0.032	0.000
8	B	10	ARG	1	0.821	0.906	6.021	-0.563	-0.563	0.000	0.000	0.000	0.000
9	B	11	THR	0	-0.038	-0.042	5.862	0.115	0.115	0.000	0.000	0.000	0.000
10	B	12	HIS	1	0.865	0.937	6.185	0.594	0.594	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.024	0.032	9.814	0.007	0.007	0.000	0.000	0.000	0.000
12	B	14	ASP	-1	-0.763	-0.852	12.223	-0.093	-0.093	0.000	0.000	0.000	0.000
13	B	15	PHE	0	0.078	0.035	15.568	0.026	0.026	0.000	0.000	0.000	0.000
14	B	16	PRO	0	0.053	0.014	18.204	-0.013	-0.013	0.000	0.000	0.000	0.000
15	B	17	LYS	1	0.850	0.947	19.884	0.140	0.140	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.076	-0.045	18.659	0.018	0.018	0.000	0.000	0.000	0.000
17	B	19	SER	0	0.000	-0.007	21.339	0.006	0.006	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.006	-0.019	21.140	0.012	0.012	0.000	0.000	0.000	0.000
19	B	21	PRO	0	0.028	0.016	25.983	-0.005	-0.005	0.000	0.000	0.000	0.000
20	B	22	ASN	0	0.036	0.024	27.129	0.001	0.001	0.000	0.000	0.000	0.000
21	B	23	ILE	0	0.054	0.028	21.683	0.002	0.002	0.000	0.000	0.000	0.000
22	B	24	ALA	0	0.053	0.036	22.640	0.003	0.003	0.000	0.000	0.000	0.000
23	B	25	ALA	0	-0.030	-0.019	23.196	0.011	0.011	0.000	0.000	0.000	0.000
24	B	26	TYR	0	-0.025	-0.039	17.231	0.009	0.009	0.000	0.000	0.000	0.000
25	B	27	CYS	0	-0.063	-0.019	16.101	0.018	0.018	0.000	0.000	0.000	0.000
26	B	28	ASN	0	0.043	0.011	18.496	0.024	0.024	0.000	0.000	0.000	0.000
27	B	29	VAL	0	0.009	0.015	19.985	0.021	0.021	0.000	0.000	0.000	0.000
28	B	30	MET	0	-0.011	0.003	16.305	0.026	0.026	0.000	0.000	0.000	0.000
29	B	31	MET	0	-0.001	0.015	12.545	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	32	VAL	0	0.012	0.021	14.314	0.054	0.054	0.000	0.000	0.000	0.000
31	B	33	ARG	1	0.934	0.964	15.817	0.021	0.021	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.759	0.876	11.502	0.165	0.165	0.000	0.000	0.000	0.000
33	B	35	GLY	0	0.021	0.021	11.129	0.045	0.045	0.000	0.000	0.000	0.000
34	B	36	ILE	0	-0.066	-0.035	9.430	0.135	0.135	0.000	0.000	0.000	0.000
35	B	37	ASN	0	-0.007	-0.019	11.582	0.079	0.079	0.000	0.000	0.000	0.000
36	B	38	VAL	0	0.039	0.015	13.371	-0.037	-0.037	0.000	0.000	0.000	0.000
37	B	39	HIS	0	0.046	0.011	15.212	0.074	0.074	0.000	0.000	0.000	0.000
38	B	40	GLY	0	0.048	0.034	18.295	0.008	0.008	0.000	0.000	0.000	0.000
39	B	41	ARG	1	0.857	0.933	11.908	-0.702	-0.702	0.000	0.000	0.000	0.000
40	B	42	CYS	0	0.009	0.010	16.667	-0.028	-0.028	0.000	0.000	0.000	0.000
41	B	43	LYS	1	0.902	0.956	8.375	-0.136	-0.136	0.000	0.000	0.000	0.000
42	B	44	SER	0	0.058	0.036	14.190	-0.039	-0.039	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.042	0.019	13.860	-0.032	-0.032	0.000	0.000	0.000	0.000
44	B	46	ASN	0	-0.061	-0.051	10.100	0.049	0.049	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.036	0.014	12.501	0.003	0.003	0.000	0.000	0.000	0.000
46	B	48	PHE	0	-0.033	-0.005	11.870	-0.040	-0.040	0.000	0.000	0.000	0.000
47	B	49	VAL	0	0.054	0.020	12.741	0.027	0.027	0.000	0.000	0.000	0.000
48	B	50	HIS	0	-0.047	0.001	15.105	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	51	THR	0	0.027	0.003	15.549	0.021	0.021	0.000	0.000	0.000	0.000
50	B	52	ASP	-1	-0.760	-0.842	16.837	-0.353	-0.353	0.000	0.000	0.000	0.000
51	B	53	PRO	0	0.045	0.008	13.076	-0.027	-0.027	0.000	0.000	0.000	0.000
52	B	54	ARG	1	0.921	0.948	14.284	0.229	0.229	0.000	0.000	0.000	0.000
53	B	55	ASN	0	-0.040	0.000	16.891	-0.015	-0.015	0.000	0.000	0.000	0.000
54	B	56	LEU	0	-0.021	-0.009	11.605	-0.011	-0.011	0.000	0.000	0.000	0.000
55	B	57	ASN	0	0.025	0.018	12.400	-0.083	-0.083	0.000	0.000	0.000	0.000
56	B	58	THR	0	-0.095	-0.066	14.020	-0.017	-0.017	0.000	0.000	0.000	0.000
57	B	59	LEU	0	-0.028	-0.044	17.027	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	60	DCY	-1	-0.771	-0.859	19.277	-0.315	-0.315	0.000	0.000	0.000	0.000
59	B	61	ILE	0	-0.066	-0.014	17.299	-0.056	-0.056	0.000	0.000	0.000	0.000
60	B	62	ASN	0	0.008	-0.009	15.197	-0.141	-0.141	0.000	0.000	0.000	0.000
61	B	63	GLN	0	0.035	0.026	13.927	-0.009	-0.009	0.000	0.000	0.000	0.000
62	B	64	PRO	0	0.030	0.020	14.227	-0.078	-0.078	0.000	0.000	0.000	0.000
63	B	65	ASN	0	-0.036	-0.034	10.396	-0.107	-0.107	0.000	0.000	0.000	0.000
64	B	66	ARG	1	0.944	0.976	8.505	0.721	0.721	0.000	0.000	0.000	0.000
65	B	67	ALA	0	-0.002	0.013	9.785	0.061	0.061	0.000	0.000	0.000	0.000
66	B	68	LEU	0	0.006	0.003	9.630	-0.158	-0.158	0.000	0.000	0.000	0.000
67	B	69	ARG	1	0.881	0.936	12.141	0.813	0.813	0.000	0.000	0.000	0.000
68	B	70	THR	0	-0.032	-0.031	13.422	-0.040	-0.040	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.036	-0.017	15.776	0.007	0.007	0.000	0.000	0.000	0.000
70	B	72	GLN	0	0.022	0.025	18.169	0.025	0.025	0.000	0.000	0.000	0.000
71	B	73	GLN	0	0.023	0.005	21.934	0.002	0.002	0.000	0.000	0.000	0.000
72	B	74	GLN	0	-0.023	0.006	20.567	-0.036	-0.036	0.000	0.000	0.000	0.000
73	B	75	LEU	0	0.017	0.012	16.574	0.020	0.020	0.000	0.000	0.000	0.000
74	B	76	PRO	0	0.053	0.024	19.949	0.007	0.007	0.000	0.000	0.000	0.000
75	B	77	VAL	0	-0.035	-0.018	16.411	-0.026	-0.026	0.000	0.000	0.000	0.000
76	B	78	THR	0	-0.042	-0.054	17.302	0.037	0.037	0.000	0.000	0.000	0.000
77	B	79	ASP	-1	-0.840	-0.901	15.973	-0.150	-0.150	0.000	0.000	0.000	0.000
78	B	81	LYS	1	0.899	0.928	16.887	0.075	0.075	0.000	0.000	0.000	0.000
79	B	82	LEU	0	-0.054	-0.015	18.310	0.000	0.000	0.000	0.000	0.000	0.000
80	B	83	ILE	0	-0.016	-0.018	20.153	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	84	ARG	1	0.928	0.960	23.106	-0.063	-0.063	0.000	0.000	0.000	0.000
82	B	85	SER	0	0.007	-0.013	21.453	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	86	HIS	0	0.068	0.055	22.766	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	87	PRO	0	0.032	-0.001	26.006	-0.010	-0.010	0.000	0.000	0.000	0.000
85	B	88	THR	0	-0.021	-0.009	23.798	0.015	0.015	0.000	0.000	0.000	0.000
86	B	90	SER	0	-0.031	0.005	21.744	-0.016	-0.016	0.000	0.000	0.000	0.000
87	B	91	TYR	0	-0.013	-0.028	16.174	0.011	0.011	0.000	0.000	0.000	0.000
88	B	92	THR	0	0.015	0.010	22.252	-0.008	-0.008	0.000	0.000	0.000	0.000
89	B	93	GLY	0	0.037	0.003	21.308	0.003	0.003	0.000	0.000	0.000	0.000
90	B	94	ASN	0	-0.040	-0.006	21.204	0.005	0.005	0.000	0.000	0.000	0.000
91	B	95	GLN	0	0.051	0.024	21.219	-0.015	-0.015	0.000	0.000	0.000	0.000
92	B	96	PHE	0	-0.008	0.000	19.895	0.010	0.010	0.000	0.000	0.000	0.000
93	B	97	ASN	0	0.035	0.017	21.699	-0.017	-0.017	0.000	0.000	0.000	0.000
94	B	98	HIS	0	0.047	0.022	18.788	-0.010	-0.010	0.000	0.000	0.000	0.000
95	B	99	ARG	1	0.985	0.991	17.938	0.235	0.235	0.000	0.000	0.000	0.000
96	B	100	VAL	0	0.029	0.024	13.058	-0.021	-0.021	0.000	0.000	0.000	0.000
97	B	101	ARG	1	0.897	0.950	12.426	0.453	0.453	0.000	0.000	0.000	0.000
98	B	102	VAL	0	0.007	-0.008	9.226	-0.040	-0.040	0.000	0.000	0.000	0.000
99	B	103	GLY	0	0.017	0.012	6.945	0.148	0.148	0.000	0.000	0.000	0.000
100	B	104	CYS	0	-0.055	-0.016	6.645	-0.413	-0.413	0.000	0.000	0.000	0.000
101	B	105	TRP	0	0.033	-0.017	6.444	-0.026	-0.026	0.000	0.000	0.000	0.000
102	B	106	GLY	0	0.009	0.014	8.352	-0.056	-0.056	0.000	0.000	0.000	0.000
103	B	107	GLY	0	0.052	0.034	11.334	0.057	0.057	0.000	0.000	0.000	0.000
104	B	108	LEU	0	-0.045	-0.015	9.043	0.087	0.087	0.000	0.000	0.000	0.000
105	B	109	PRO	0	-0.011	0.009	8.090	-0.263	-0.263	0.000	0.000	0.000	0.000
106	B	110	VAL	0	0.008	-0.023	3.160	-0.595	0.094	0.041	-0.163	-0.567	0.000
107	B	111	HIS	0	-0.040	-0.035	2.591	-3.826	-1.908	1.365	-1.272	-2.010	-0.016
108	B	112	LEU	0	-0.035	-0.018	4.732	0.232	0.284	-0.001	-0.010	-0.041	0.000
109	B	113	ASP	-1	-0.837	-0.899	7.801	-0.525	-0.525	0.000	0.000	0.000	0.000
110	B	114	GLY	0	0.039	0.022	9.533	0.109	0.109	0.000	0.000	0.000	0.000
111	B	115	THR	0	-0.044	-0.036	12.809	-0.007	-0.007	0.000	0.000	0.000	0.000

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