FMO DATABASE

FMODB ID: ZVLYN

Calculation Name: 3GPG-A-Xray372

Preferred Name: Polyprotein P1234

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3GPG

Chain ID: A

ChEMBL ID: CHEMBL4295622

UniProt ID: Q8JUX6

Base Structure: X-ray

Registration Date: 2023-09-22

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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1608011.809391
FMO2-HF: Nuclear repulsion	1544538.300961
FMO2-HF: Total energy	-63473.50843
FMO2-MP2: Total energy	-63655.565685

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:HIS)

Summations of interaction energy for fragment #1(A:-1:HIS)

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.
3.141	4.327	0.001	-0.465	-0.722	0.001

Interaction energy analysis for fragmet #1(A:-1:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.035

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	A	1	ALA	0	-0.002	0.004	3.816	-1.050	0.136	0.001	-0.465	-0.722	0.001
4	A	2	PRO	0	0.012	0.025	5.660	0.146	0.146	0.000	0.000	0.000	0.000
5	A	3	SER	0	-0.062	-0.041	8.588	-0.237	-0.237	0.000	0.000	0.000	0.000
6	A	4	TYR	0	0.031	-0.023	12.049	0.063	0.063	0.000	0.000	0.000	0.000
7	A	5	ARG	1	0.847	0.917	13.103	-0.614	-0.614	0.000	0.000	0.000	0.000
8	A	6	VAL	0	-0.012	0.001	18.283	0.017	0.017	0.000	0.000	0.000	0.000
9	A	7	LYS	1	0.885	0.942	21.032	-0.332	-0.332	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.808	0.905	24.202	-0.136	-0.136	0.000	0.000	0.000	0.000
11	A	9	MET	0	-0.038	-0.009	25.869	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.896	-0.956	28.540	0.209	0.209	0.000	0.000	0.000	0.000
13	A	11	ILE	0	0.099	0.059	24.426	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.002	0.013	26.317	0.021	0.021	0.000	0.000	0.000	0.000
15	A	13	LYS	1	0.753	0.844	27.598	-0.183	-0.183	0.000	0.000	0.000	0.000
16	A	14	ASN	0	-0.048	-0.006	22.337	0.023	0.023	0.000	0.000	0.000	0.000
17	A	15	ASP	-1	-0.873	-0.933	19.997	0.304	0.304	0.000	0.000	0.000	0.000
18	A	16	GLU	-1	-0.738	-0.843	17.051	0.482	0.482	0.000	0.000	0.000	0.000
19	A	17	GLU	-1	-0.833	-0.898	14.183	1.048	1.048	0.000	0.000	0.000	0.000
20	A	18	CYS	0	-0.069	-0.013	18.132	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	19	VAL	0	-0.017	0.005	20.625	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	20	VAL	0	0.030	0.024	21.933	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	21	ASN	0	-0.010	-0.043	24.594	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	22	ALA	0	-0.001	-0.002	28.344	0.005	0.005	0.000	0.000	0.000	0.000
25	A	23	ALA	0	-0.004	0.007	30.331	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	24	ASN	0	-0.016	-0.021	32.669	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	25	PRO	0	0.071	0.014	35.551	0.004	0.004	0.000	0.000	0.000	0.000
28	A	26	ARG	1	0.918	0.956	36.942	-0.134	-0.134	0.000	0.000	0.000	0.000
29	A	27	GLY	0	0.050	0.047	36.001	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.048	-0.028	37.010	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	29	PRO	0	0.059	0.025	37.518	0.007	0.007	0.000	0.000	0.000	0.000
32	A	30	GLY	0	0.009	0.017	37.467	0.006	0.006	0.000	0.000	0.000	0.000
33	A	31	ASP	-1	-0.901	-0.971	38.094	0.138	0.138	0.000	0.000	0.000	0.000
34	A	32	GLY	0	0.042	0.008	36.012	0.008	0.008	0.000	0.000	0.000	0.000
35	A	33	VAL	0	0.007	-0.005	29.425	0.000	0.000	0.000	0.000	0.000	0.000
36	A	34	CYS	0	0.022	0.044	32.445	0.008	0.008	0.000	0.000	0.000	0.000
37	A	35	LYS	1	0.954	0.992	33.784	-0.130	-0.130	0.000	0.000	0.000	0.000
38	A	36	ALA	0	-0.052	-0.029	32.546	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	37	VAL	0	0.039	0.014	29.181	0.003	0.003	0.000	0.000	0.000	0.000
40	A	38	TYR	0	-0.002	0.000	31.820	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	39	LYS	1	0.893	0.947	34.848	-0.175	-0.175	0.000	0.000	0.000	0.000
42	A	40	LYS	1	0.782	0.888	28.276	-0.260	-0.260	0.000	0.000	0.000	0.000
43	A	41	TRP	0	0.103	0.056	26.317	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	42	PRO	0	0.028	0.044	32.326	0.005	0.005	0.000	0.000	0.000	0.000
45	A	43	GLU	-1	-0.819	-0.917	32.151	0.218	0.218	0.000	0.000	0.000	0.000
46	A	44	SER	0	-0.002	-0.028	30.183	0.004	0.004	0.000	0.000	0.000	0.000
47	A	45	PHE	0	-0.038	-0.030	32.139	0.008	0.008	0.000	0.000	0.000	0.000
48	A	46	LYS	1	0.937	0.981	34.834	-0.188	-0.188	0.000	0.000	0.000	0.000
49	A	47	ASN	0	-0.046	-0.031	34.755	0.003	0.003	0.000	0.000	0.000	0.000
50	A	48	SER	0	0.045	0.030	32.585	0.003	0.003	0.000	0.000	0.000	0.000
51	A	49	ALA	0	-0.033	-0.001	33.595	0.006	0.006	0.000	0.000	0.000	0.000
52	A	50	THR	0	-0.016	-0.016	31.266	0.003	0.003	0.000	0.000	0.000	0.000
53	A	51	PRO	0	-0.023	-0.012	33.878	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	52	VAL	0	0.011	-0.007	33.593	0.009	0.009	0.000	0.000	0.000	0.000
55	A	53	GLY	0	0.019	0.026	31.214	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	54	THR	0	-0.016	0.004	29.325	0.003	0.003	0.000	0.000	0.000	0.000
57	A	55	ALA	0	-0.008	-0.017	25.884	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	56	LYS	1	0.832	0.923	27.946	-0.221	-0.221	0.000	0.000	0.000	0.000
59	A	57	THR	0	-0.015	-0.041	23.918	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	58	VAL	0	-0.082	-0.030	26.898	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	59	MET	0	-0.020	0.007	23.086	0.015	0.015	0.000	0.000	0.000	0.000
62	A	60	CYS	0	-0.071	-0.037	27.107	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	61	GLY	0	0.022	0.013	27.465	0.008	0.008	0.000	0.000	0.000	0.000
64	A	62	THR	0	-0.013	-0.024	22.427	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	63	TYR	0	0.020	0.015	21.981	0.029	0.029	0.000	0.000	0.000	0.000
66	A	64	PRO	0	0.042	0.014	20.591	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	65	VAL	0	0.001	0.007	23.660	0.010	0.010	0.000	0.000	0.000	0.000
68	A	66	ILE	0	0.012	-0.003	20.799	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	67	HIS	0	-0.003	-0.011	25.475	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	68	ALA	0	0.041	0.021	26.278	0.000	0.000	0.000	0.000	0.000	0.000
71	A	69	VAL	0	-0.057	-0.014	28.391	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	70	GLY	0	0.056	0.031	31.678	0.001	0.001	0.000	0.000	0.000	0.000
73	A	71	PRO	0	-0.005	0.008	32.150	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	72	ASN	0	0.046	0.033	35.559	0.000	0.000	0.000	0.000	0.000	0.000
75	A	73	PHE	0	0.013	-0.013	34.198	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	74	SER	0	-0.039	-0.022	39.539	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	75	ASN	0	-0.081	-0.041	41.733	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	76	TYR	0	-0.057	-0.034	37.679	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	77	SER	0	0.050	0.026	41.046	0.000	0.000	0.000	0.000	0.000	0.000
80	A	78	GLU	-1	-0.733	-0.857	38.725	0.139	0.139	0.000	0.000	0.000	0.000
81	A	79	SER	0	-0.042	-0.029	37.332	0.008	0.008	0.000	0.000	0.000	0.000
82	A	80	GLU	-1	-0.866	-0.926	36.731	0.146	0.146	0.000	0.000	0.000	0.000
83	A	81	GLY	0	0.022	0.005	36.130	0.010	0.010	0.000	0.000	0.000	0.000
84	A	82	ASP	-1	-0.820	-0.896	32.333	0.198	0.198	0.000	0.000	0.000	0.000
85	A	83	ARG	1	0.963	0.988	31.734	-0.162	-0.162	0.000	0.000	0.000	0.000
86	A	84	GLU	-1	-0.824	-0.907	31.417	0.200	0.200	0.000	0.000	0.000	0.000
87	A	85	LEU	0	-0.050	-0.029	29.219	0.015	0.015	0.000	0.000	0.000	0.000
88	A	86	ALA	0	0.006	0.004	27.354	0.020	0.020	0.000	0.000	0.000	0.000
89	A	87	ALA	0	-0.070	-0.038	26.508	0.027	0.027	0.000	0.000	0.000	0.000
90	A	88	ALA	0	0.057	0.031	27.129	0.019	0.019	0.000	0.000	0.000	0.000
91	A	89	TYR	0	0.040	0.002	23.348	0.025	0.025	0.000	0.000	0.000	0.000
92	A	90	ARG	1	0.937	0.979	22.624	-0.252	-0.252	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.861	-0.933	22.566	0.326	0.326	0.000	0.000	0.000	0.000
94	A	92	VAL	0	-0.014	-0.008	20.601	0.023	0.023	0.000	0.000	0.000	0.000
95	A	93	ALA	0	0.052	0.035	18.344	0.041	0.041	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.912	0.970	18.147	-0.403	-0.403	0.000	0.000	0.000	0.000
97	A	95	GLU	-1	-0.752	-0.818	19.749	0.449	0.449	0.000	0.000	0.000	0.000
98	A	96	VAL	0	0.027	0.004	15.240	0.018	0.018	0.000	0.000	0.000	0.000
99	A	97	THR	0	-0.012	-0.017	14.332	0.094	0.094	0.000	0.000	0.000	0.000
100	A	98	ARG	1	0.730	0.833	15.910	-0.406	-0.406	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.083	-0.056	18.351	-0.020	-0.020	0.000	0.000	0.000	0.000
102	A	100	GLY	0	0.004	0.020	14.113	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	101	VAL	0	-0.060	-0.022	13.488	0.110	0.110	0.000	0.000	0.000	0.000
104	A	102	ASN	0	0.006	-0.023	10.073	0.451	0.451	0.000	0.000	0.000	0.000
105	A	103	SER	0	-0.002	0.005	11.593	-0.052	-0.052	0.000	0.000	0.000	0.000
106	A	104	VAL	0	0.006	-0.005	14.361	-0.050	-0.050	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.001	0.024	17.719	-0.024	-0.024	0.000	0.000	0.000	0.000
108	A	106	ILE	0	0.009	-0.012	20.386	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	107	PRO	0	-0.012	0.004	22.700	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	108	LEU	0	0.043	0.016	25.314	0.008	0.008	0.000	0.000	0.000	0.000
111	A	109	LEU	0	0.000	0.018	26.598	-0.025	-0.025	0.000	0.000	0.000	0.000
112	A	110	SER	0	0.015	-0.016	29.440	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	111	THR	0	-0.030	-0.032	30.701	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	112	GLY	0	0.009	0.023	33.481	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	113	VAL	0	0.012	0.003	35.822	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	114	TYR	0	-0.048	-0.016	35.327	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	115	SER	0	0.027	0.020	36.441	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	116	GLY	0	0.030	0.021	37.601	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	117	GLY	0	-0.023	-0.005	40.738	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	118	LYS	1	0.860	0.932	37.069	-0.136	-0.136	0.000	0.000	0.000	0.000
121	A	119	ASP	-1	-0.884	-0.946	34.532	0.143	0.143	0.000	0.000	0.000	0.000
122	A	120	ARG	1	0.762	0.835	33.266	-0.144	-0.144	0.000	0.000	0.000	0.000
123	A	121	LEU	0	0.003	0.021	28.210	0.013	0.013	0.000	0.000	0.000	0.000
124	A	122	THR	0	0.023	-0.005	28.987	0.014	0.014	0.000	0.000	0.000	0.000
125	A	123	GLN	0	-0.023	-0.013	28.561	0.004	0.004	0.000	0.000	0.000	0.000
126	A	124	SER	0	0.026	-0.009	28.497	0.020	0.020	0.000	0.000	0.000	0.000
127	A	125	LEU	0	0.005	0.008	22.669	0.018	0.018	0.000	0.000	0.000	0.000
128	A	126	ASN	0	0.012	0.008	23.842	0.026	0.026	0.000	0.000	0.000	0.000
129	A	127	HIS	0	-0.038	-0.028	24.157	0.034	0.034	0.000	0.000	0.000	0.000
130	A	128	LEU	0	-0.025	0.000	20.073	0.023	0.023	0.000	0.000	0.000	0.000
131	A	129	PHE	0	-0.004	-0.017	19.238	0.031	0.031	0.000	0.000	0.000	0.000
132	A	130	THR	0	-0.023	-0.017	19.377	0.028	0.028	0.000	0.000	0.000	0.000
133	A	131	ALA	0	-0.079	-0.028	20.501	0.019	0.019	0.000	0.000	0.000	0.000
134	A	132	MET	0	-0.013	-0.016	16.276	0.029	0.029	0.000	0.000	0.000	0.000
135	A	133	ASP	-1	-0.732	-0.786	15.201	0.512	0.512	0.000	0.000	0.000	0.000
136	A	134	SER	0	-0.094	-0.034	13.860	0.059	0.059	0.000	0.000	0.000	0.000
137	A	135	THR	0	-0.078	-0.050	12.977	0.076	0.076	0.000	0.000	0.000	0.000
138	A	136	ASP	-1	-0.885	-0.953	7.543	2.250	2.250	0.000	0.000	0.000	0.000
139	A	137	ALA	0	0.012	0.017	8.976	0.146	0.146	0.000	0.000	0.000	0.000
140	A	138	ASP	-1	-0.795	-0.878	10.610	0.780	0.780	0.000	0.000	0.000	0.000
141	A	139	VAL	0	-0.010	-0.006	12.389	-0.056	-0.056	0.000	0.000	0.000	0.000
142	A	140	VAL	0	-0.039	-0.018	15.916	-0.060	-0.060	0.000	0.000	0.000	0.000
143	A	141	ILE	0	0.020	0.001	18.758	-0.011	-0.011	0.000	0.000	0.000	0.000
144	A	142	TYR	0	-0.067	-0.075	21.398	-0.046	-0.046	0.000	0.000	0.000	0.000
145	A	143	CYS	0	-0.044	-0.010	25.179	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.943	0.946	28.512	-0.172	-0.172	0.000	0.000	0.000	0.000
147	A	145	ASP	-1	-0.770	-0.885	31.799	0.116	0.116	0.000	0.000	0.000	0.000
148	A	146	LYS	1	0.879	0.909	31.558	-0.088	-0.088	0.000	0.000	0.000	0.000
149	A	147	GLU	-1	-0.758	-0.840	31.708	0.096	0.096	0.000	0.000	0.000	0.000
150	A	148	TRP	0	0.002	-0.018	30.248	0.007	0.007	0.000	0.000	0.000	0.000
151	A	149	GLU	-1	-0.779	-0.884	26.582	0.162	0.162	0.000	0.000	0.000	0.000
152	A	150	LYS	1	0.829	0.904	26.879	-0.087	-0.087	0.000	0.000	0.000	0.000
153	A	151	LYS	1	1.018	1.017	27.621	-0.122	-0.122	0.000	0.000	0.000	0.000
154	A	152	ILE	0	-0.016	-0.011	23.288	0.005	0.005	0.000	0.000	0.000	0.000
155	A	153	SER	0	-0.006	-0.007	22.974	0.015	0.015	0.000	0.000	0.000	0.000
156	A	154	GLU	-1	-0.923	-0.969	22.900	0.113	0.113	0.000	0.000	0.000	0.000
157	A	155	ALA	0	-0.019	-0.017	23.904	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	156	ILE	0	-0.014	-0.010	18.006	0.012	0.012	0.000	0.000	0.000	0.000
159	A	157	GLN	0	-0.014	-0.010	18.486	0.023	0.023	0.000	0.000	0.000	0.000
160	A	158	MET	0	-0.054	-0.016	20.031	-0.013	-0.013	0.000	0.000	0.000	0.000
161	A	159	ARG	1	0.760	0.852	18.121	-0.342	-0.342	0.000	0.000	0.000	0.000
162	A	160	THR	0	-0.048	-0.003	14.473	-0.013	-0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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