FMO DATABASE

FMODB ID: QVVMY

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	OptHSide
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	-916071.047169
FMO2-HF: Nuclear repulsion	869699.579719
FMO2-HF: Total energy	-46371.46745
FMO2-MP2: Total energy	-46502.704177

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.
-4.529	0.634	2.087	-2.95	-4.298	-0.014

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 : 0.004 / q_NPA : -0.007

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	0.046	0.003	3.822	-1.623	0.586	-0.020	-1.150	-1.039	0.004
4	B	6	GLN	0	0.058	0.008	6.419	0.325	0.325	0.000	0.000	0.000	0.000
5	B	7	ASP	-1	-0.818	-0.864	3.554	1.062	1.566	0.020	-0.211	-0.313	-0.001
6	B	8	PHE	0	0.014	0.016	4.264	0.266	0.413	-0.001	-0.011	-0.135	0.000
7	B	9	LEU	0	0.001	0.000	5.452	0.329	0.329	0.000	0.000	0.000	0.000
8	B	10	ARG	1	0.857	0.925	6.347	-0.755	-0.755	0.000	0.000	0.000	0.000
9	B	11	THR	0	-0.047	-0.045	6.296	0.052	0.052	0.000	0.000	0.000	0.000
10	B	12	HIS	1	0.871	0.934	6.261	0.386	0.386	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.032	0.047	9.945	-0.029	-0.029	0.000	0.000	0.000	0.000
12	B	14	ASP	-1	-0.809	-0.874	12.407	-0.023	-0.023	0.000	0.000	0.000	0.000
13	B	15	PHE	0	0.071	0.019	15.915	0.005	0.005	0.000	0.000	0.000	0.000
14	B	16	PRO	0	0.066	0.034	18.367	-0.014	-0.014	0.000	0.000	0.000	0.000
15	B	17	LYS	1	0.866	0.958	19.965	0.099	0.099	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.076	-0.049	19.502	0.015	0.015	0.000	0.000	0.000	0.000
17	B	19	SER	0	-0.002	-0.005	22.059	0.003	0.003	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.010	-0.014	21.575	0.014	0.014	0.000	0.000	0.000	0.000
19	B	21	PRO	0	0.027	0.014	26.314	-0.006	-0.006	0.000	0.000	0.000	0.000
20	B	22	ASN	0	0.041	0.024	27.421	0.001	0.001	0.000	0.000	0.000	0.000
21	B	23	ILE	0	0.055	0.027	22.052	0.004	0.004	0.000	0.000	0.000	0.000
22	B	24	ALA	0	0.055	0.036	22.873	0.005	0.005	0.000	0.000	0.000	0.000
23	B	25	ALA	0	-0.029	-0.016	23.211	0.014	0.014	0.000	0.000	0.000	0.000
24	B	26	TYR	0	-0.025	-0.038	17.797	0.011	0.011	0.000	0.000	0.000	0.000
25	B	27	CYS	0	-0.062	-0.025	16.120	0.015	0.015	0.000	0.000	0.000	0.000
26	B	28	ASN	0	0.046	0.006	18.623	0.028	0.028	0.000	0.000	0.000	0.000
27	B	29	VAL	0	0.004	0.007	20.036	0.023	0.023	0.000	0.000	0.000	0.000
28	B	30	MET	0	0.005	0.013	16.655	0.028	0.028	0.000	0.000	0.000	0.000
29	B	31	MET	0	-0.017	0.008	12.610	0.005	0.005	0.000	0.000	0.000	0.000
30	B	32	VAL	0	0.004	0.020	14.702	0.061	0.061	0.000	0.000	0.000	0.000
31	B	33	ARG	1	0.941	0.974	16.497	-0.025	-0.025	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.752	0.872	12.106	0.065	0.065	0.000	0.000	0.000	0.000
33	B	35	GLY	0	0.027	0.010	11.638	0.066	0.066	0.000	0.000	0.000	0.000
34	B	36	ILE	0	-0.081	-0.028	9.742	0.129	0.129	0.000	0.000	0.000	0.000
35	B	37	ASN	0	-0.008	-0.023	11.921	0.086	0.086	0.000	0.000	0.000	0.000
36	B	38	VAL	0	0.036	0.016	13.989	-0.046	-0.046	0.000	0.000	0.000	0.000
37	B	39	HIS	0	0.055	0.011	15.406	0.070	0.070	0.000	0.000	0.000	0.000
38	B	40	GLY	0	0.035	0.023	18.760	0.013	0.013	0.000	0.000	0.000	0.000
39	B	41	ARG	1	0.869	0.949	11.995	-0.774	-0.774	0.000	0.000	0.000	0.000
40	B	42	CYS	0	-0.003	0.003	16.792	-0.027	-0.027	0.000	0.000	0.000	0.000
41	B	43	LYS	1	0.899	0.953	8.163	-0.281	-0.281	0.000	0.000	0.000	0.000
42	B	44	SER	0	0.058	0.042	14.089	-0.042	-0.042	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.043	0.021	14.056	-0.039	-0.039	0.000	0.000	0.000	0.000
44	B	46	ASN	0	-0.036	-0.028	10.288	0.061	0.061	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.042	0.026	12.130	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	48	PHE	0	-0.019	-0.004	12.011	-0.035	-0.035	0.000	0.000	0.000	0.000
47	B	49	VAL	0	0.053	0.012	12.543	0.018	0.018	0.000	0.000	0.000	0.000
48	B	50	HIS	0	-0.044	0.001	14.904	0.003	0.003	0.000	0.000	0.000	0.000
49	B	51	THR	0	0.027	0.009	15.729	0.020	0.020	0.000	0.000	0.000	0.000
50	B	52	ASP	-1	-0.773	-0.866	16.611	-0.309	-0.309	0.000	0.000	0.000	0.000
51	B	53	PRO	0	0.052	0.017	12.910	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	54	ARG	1	0.918	0.948	14.269	0.200	0.200	0.000	0.000	0.000	0.000
53	B	55	ASN	0	-0.004	0.021	16.820	-0.023	-0.023	0.000	0.000	0.000	0.000
54	B	56	LEU	0	0.007	0.008	11.721	-0.012	-0.012	0.000	0.000	0.000	0.000
55	B	57	ASN	0	-0.145	-0.136	12.629	-0.120	-0.120	0.000	0.000	0.000	0.000
56	B	58	THR	0	0.130	0.248	13.880	0.014	0.014	0.000	0.000	0.000	0.000
57	B	59	LEU	0	-0.212	-0.184	16.733	-0.015	-0.015	0.000	0.000	0.000	0.000
58	B	60	DCY	-1	-0.695	-0.923	18.990	-0.304	-0.304	0.000	0.000	0.000	0.000
59	B	61	ILE	0	-0.061	-0.002	16.983	-0.050	-0.050	0.000	0.000	0.000	0.000
60	B	62	ASN	0	-0.007	-0.020	15.214	-0.122	-0.122	0.000	0.000	0.000	0.000
61	B	63	GLN	0	0.030	0.023	13.921	0.004	0.004	0.000	0.000	0.000	0.000
62	B	64	PRO	0	0.016	-0.006	13.882	-0.079	-0.079	0.000	0.000	0.000	0.000
63	B	65	ASN	0	-0.074	-0.024	10.043	-0.153	-0.153	0.000	0.000	0.000	0.000
64	B	66	ARG	1	0.970	0.976	7.757	0.905	0.905	0.000	0.000	0.000	0.000
65	B	67	ALA	0	-0.008	0.017	9.406	0.120	0.120	0.000	0.000	0.000	0.000
66	B	68	LEU	0	0.021	0.005	9.503	-0.160	-0.160	0.000	0.000	0.000	0.000
67	B	69	ARG	1	0.865	0.925	12.095	0.769	0.769	0.000	0.000	0.000	0.000
68	B	70	THR	0	-0.031	-0.035	13.733	-0.043	-0.043	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.027	-0.001	15.771	0.016	0.016	0.000	0.000	0.000	0.000
70	B	72	GLN	0	0.029	0.021	18.182	0.022	0.022	0.000	0.000	0.000	0.000
71	B	73	GLN	0	0.031	0.013	21.947	0.000	0.000	0.000	0.000	0.000	0.000
72	B	74	GLN	0	-0.026	0.001	20.512	-0.031	-0.031	0.000	0.000	0.000	0.000
73	B	75	LEU	0	0.008	0.000	16.822	0.015	0.015	0.000	0.000	0.000	0.000
74	B	76	PRO	0	0.043	0.020	20.289	0.010	0.010	0.000	0.000	0.000	0.000
75	B	77	VAL	0	-0.019	-0.009	16.274	-0.020	-0.020	0.000	0.000	0.000	0.000
76	B	78	THR	0	-0.025	-0.039	17.358	0.029	0.029	0.000	0.000	0.000	0.000
77	B	79	ASP	-1	-0.854	-0.917	16.365	-0.082	-0.082	0.000	0.000	0.000	0.000
78	B	81	LYS	1	0.917	0.938	16.891	0.037	0.037	0.000	0.000	0.000	0.000
79	B	82	LEU	0	-0.058	-0.020	18.340	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	83	ILE	0	-0.037	-0.027	20.154	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	84	ARG	1	0.936	0.973	23.486	-0.086	-0.086	0.000	0.000	0.000	0.000
82	B	85	SER	0	0.019	-0.007	21.656	0.001	0.001	0.000	0.000	0.000	0.000
83	B	86	HIS	0	0.047	0.053	23.058	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	87	PRO	0	0.021	-0.009	26.319	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	88	THR	0	-0.010	-0.009	24.223	0.018	0.018	0.000	0.000	0.000	0.000
86	B	90	SER	0	-0.026	0.000	21.997	-0.017	-0.017	0.000	0.000	0.000	0.000
87	B	91	TYR	0	-0.007	-0.028	16.217	0.012	0.012	0.000	0.000	0.000	0.000
88	B	92	THR	0	0.019	0.011	22.151	-0.011	-0.011	0.000	0.000	0.000	0.000
89	B	93	GLY	0	0.044	-0.003	21.415	0.007	0.007	0.000	0.000	0.000	0.000
90	B	94	ASN	0	-0.056	-0.014	21.429	0.004	0.004	0.000	0.000	0.000	0.000
91	B	95	GLN	0	0.042	0.027	21.309	-0.012	-0.012	0.000	0.000	0.000	0.000
92	B	96	PHE	0	0.003	-0.001	20.005	0.008	0.008	0.000	0.000	0.000	0.000
93	B	97	ASN	0	0.016	0.014	21.251	-0.018	-0.018	0.000	0.000	0.000	0.000
94	B	98	HIS	0	0.060	0.013	18.522	-0.010	-0.010	0.000	0.000	0.000	0.000
95	B	99	ARG	1	0.977	0.992	18.049	0.224	0.224	0.000	0.000	0.000	0.000
96	B	100	VAL	0	0.049	0.033	12.886	-0.007	-0.007	0.000	0.000	0.000	0.000
97	B	101	ARG	1	0.893	0.951	12.490	0.408	0.408	0.000	0.000	0.000	0.000
98	B	102	VAL	0	0.020	0.006	9.060	-0.031	-0.031	0.000	0.000	0.000	0.000
99	B	103	GLY	0	0.030	0.011	6.955	0.156	0.156	0.000	0.000	0.000	0.000
100	B	104	CYS	0	-0.064	-0.037	6.808	-0.316	-0.316	0.000	0.000	0.000	0.000
101	B	105	TRP	0	0.039	-0.005	5.874	-0.126	-0.126	0.000	0.000	0.000	0.000
102	B	106	GLY	0	0.023	0.026	7.835	-0.028	-0.028	0.000	0.000	0.000	0.000
103	B	107	GLY	0	0.027	0.020	10.895	0.072	0.072	0.000	0.000	0.000	0.000
104	B	108	LEU	0	-0.030	-0.011	9.124	0.102	0.102	0.000	0.000	0.000	0.000
105	B	109	PRO	0	-0.006	0.017	8.113	-0.289	-0.289	0.000	0.000	0.000	0.000
106	B	110	VAL	0	0.001	-0.016	2.957	-0.603	0.160	0.079	-0.194	-0.647	0.000
107	B	111	HIS	0	-0.043	-0.031	2.376	-3.981	-2.498	2.010	-1.371	-2.121	-0.017
108	B	112	LEU	0	-0.010	0.001	4.735	0.254	0.311	-0.001	-0.013	-0.043	0.000
109	B	113	ASP	-1	-0.844	-0.901	7.526	-0.511	-0.511	0.000	0.000	0.000	0.000
110	B	114	GLY	0	0.010	0.002	9.217	0.113	0.113	0.000	0.000	0.000	0.000
111	B	115	THR	0	-0.060	-0.033	12.804	0.011	0.011	0.000	0.000	0.000	0.000

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