FMO DATABASE

FMODB ID: 6Y76Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1606801.402806
FMO2-HF: Nuclear repulsion	1543328.51727
FMO2-HF: Total energy	-63472.885536
FMO2-MP2: Total energy	-63654.916365

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.
2.835	4.03	0.001	-0.475	-0.721	0.002

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 : -0.035 / q_NPA : -0.037

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	-0.005	0.002	3.816	-1.046	0.149	0.001	-0.475	-0.721	0.002
4	A	2	PRO	0	0.022	0.028	5.537	0.142	0.142	0.000	0.000	0.000	0.000
5	A	3	SER	0	-0.068	-0.024	8.580	-0.175	-0.175	0.000	0.000	0.000	0.000
6	A	4	TYR	0	0.051	-0.010	12.039	0.048	0.048	0.000	0.000	0.000	0.000
7	A	5	ARG	1	0.930	0.964	14.482	-0.430	-0.430	0.000	0.000	0.000	0.000
8	A	6	VAL	0	0.002	0.011	18.277	0.016	0.016	0.000	0.000	0.000	0.000
9	A	7	LYS	1	0.905	0.961	21.187	-0.266	-0.266	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.867	0.938	24.201	-0.115	-0.115	0.000	0.000	0.000	0.000
11	A	9	MET	0	-0.044	-0.027	26.113	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.936	-0.989	28.544	0.171	0.171	0.000	0.000	0.000	0.000
13	A	11	ILE	0	0.092	0.060	24.386	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.001	0.000	26.328	0.015	0.015	0.000	0.000	0.000	0.000
15	A	13	LYS	1	0.755	0.851	27.610	-0.145	-0.145	0.000	0.000	0.000	0.000
16	A	14	ASN	0	-0.047	0.006	22.296	0.013	0.013	0.000	0.000	0.000	0.000
17	A	15	ASP	-1	-0.892	-0.943	20.083	0.230	0.230	0.000	0.000	0.000	0.000
18	A	16	GLU	-1	-0.746	-0.863	17.095	0.386	0.386	0.000	0.000	0.000	0.000
19	A	17	GLU	-1	-0.836	-0.923	14.353	0.814	0.814	0.000	0.000	0.000	0.000
20	A	18	CYS	0	-0.068	-0.020	18.214	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	19	VAL	0	-0.019	0.012	20.639	0.000	0.000	0.000	0.000	0.000	0.000
22	A	20	VAL	0	0.034	0.024	22.011	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	21	ASN	0	-0.003	-0.042	24.603	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	22	ALA	0	-0.007	-0.002	28.353	0.007	0.007	0.000	0.000	0.000	0.000
25	A	23	ALA	0	0.004	0.011	30.336	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	24	ASN	0	-0.011	-0.014	32.677	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	25	PRO	0	0.062	0.012	35.559	0.003	0.003	0.000	0.000	0.000	0.000
28	A	26	ARG	1	0.916	0.950	36.950	-0.118	-0.118	0.000	0.000	0.000	0.000
29	A	27	GLY	0	0.060	0.052	36.012	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.056	-0.031	37.023	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	29	PRO	0	0.056	0.020	37.529	0.007	0.007	0.000	0.000	0.000	0.000
32	A	30	GLY	0	0.008	0.014	37.477	0.005	0.005	0.000	0.000	0.000	0.000
33	A	31	ASP	-1	-0.892	-0.967	38.143	0.119	0.119	0.000	0.000	0.000	0.000
34	A	32	GLY	0	0.001	-0.006	36.013	0.007	0.007	0.000	0.000	0.000	0.000
35	A	33	VAL	0	0.019	0.001	29.361	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	34	CYS	0	0.030	0.049	32.454	0.006	0.006	0.000	0.000	0.000	0.000
37	A	35	LYS	1	0.957	0.994	33.793	-0.110	-0.110	0.000	0.000	0.000	0.000
38	A	36	ALA	0	-0.049	-0.030	32.525	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	37	VAL	0	0.028	0.010	29.207	0.001	0.001	0.000	0.000	0.000	0.000
40	A	38	TYR	0	-0.008	-0.004	31.832	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	39	LYS	1	0.924	0.967	34.063	-0.141	-0.141	0.000	0.000	0.000	0.000
42	A	40	LYS	1	0.821	0.919	29.205	-0.186	-0.186	0.000	0.000	0.000	0.000
43	A	41	TRP	0	0.092	0.047	26.470	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	42	PRO	0	0.033	0.039	32.345	0.006	0.006	0.000	0.000	0.000	0.000
45	A	43	GLU	-1	-0.872	-0.953	32.864	0.165	0.165	0.000	0.000	0.000	0.000
46	A	44	SER	0	-0.027	-0.030	30.123	0.005	0.005	0.000	0.000	0.000	0.000
47	A	45	PHE	0	-0.019	-0.015	32.158	0.008	0.008	0.000	0.000	0.000	0.000
48	A	46	LYS	1	0.941	0.977	34.851	-0.145	-0.145	0.000	0.000	0.000	0.000
49	A	47	ASN	0	-0.052	-0.034	34.773	0.002	0.002	0.000	0.000	0.000	0.000
50	A	48	SER	0	0.031	0.024	32.748	0.006	0.006	0.000	0.000	0.000	0.000
51	A	49	ALA	0	-0.028	0.003	33.608	0.006	0.006	0.000	0.000	0.000	0.000
52	A	50	THR	0	-0.014	-0.024	31.314	0.001	0.001	0.000	0.000	0.000	0.000
53	A	51	PRO	0	-0.018	-0.006	34.093	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	52	VAL	0	0.008	0.000	33.599	0.008	0.008	0.000	0.000	0.000	0.000
55	A	53	GLY	0	0.045	0.040	31.216	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	54	THR	0	-0.051	-0.007	29.360	0.008	0.008	0.000	0.000	0.000	0.000
57	A	55	ALA	0	-0.008	-0.022	25.900	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	56	LYS	1	0.832	0.921	27.954	-0.189	-0.189	0.000	0.000	0.000	0.000
59	A	57	THR	0	-0.019	-0.055	23.962	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	58	VAL	0	-0.072	-0.025	26.914	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	59	MET	0	-0.018	0.006	23.096	0.013	0.013	0.000	0.000	0.000	0.000
62	A	60	CYS	0	-0.037	-0.009	27.117	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	61	GLY	0	0.036	0.021	27.465	0.005	0.005	0.000	0.000	0.000	0.000
64	A	62	THR	0	-0.017	-0.026	22.432	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	63	TYR	0	0.012	0.019	21.670	0.023	0.023	0.000	0.000	0.000	0.000
66	A	64	PRO	0	0.049	0.014	20.629	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	65	VAL	0	0.001	0.008	23.678	0.009	0.009	0.000	0.000	0.000	0.000
68	A	66	ILE	0	0.009	-0.003	20.868	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	67	HIS	0	0.001	-0.011	25.488	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	68	ALA	0	0.042	0.024	26.305	0.001	0.001	0.000	0.000	0.000	0.000
71	A	69	VAL	0	-0.060	-0.016	28.397	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	70	GLY	0	0.052	0.028	31.675	0.003	0.003	0.000	0.000	0.000	0.000
73	A	71	PRO	0	-0.012	0.007	32.150	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	72	ASN	0	0.036	0.012	35.557	0.001	0.001	0.000	0.000	0.000	0.000
75	A	73	PHE	0	0.015	-0.010	34.213	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	74	SER	0	-0.026	-0.009	39.534	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	75	ASN	0	-0.063	-0.031	41.757	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	76	TYR	0	-0.013	0.008	38.520	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	77	SER	0	0.050	0.026	41.041	0.000	0.000	0.000	0.000	0.000	0.000
80	A	78	GLU	-1	-0.772	-0.889	38.436	0.136	0.136	0.000	0.000	0.000	0.000
81	A	79	SER	0	0.010	0.007	37.322	0.008	0.008	0.000	0.000	0.000	0.000
82	A	80	GLU	-1	-0.930	-0.971	36.722	0.145	0.145	0.000	0.000	0.000	0.000
83	A	81	GLY	0	0.016	0.005	36.124	0.008	0.008	0.000	0.000	0.000	0.000
84	A	82	ASP	-1	-0.833	-0.903	32.467	0.198	0.198	0.000	0.000	0.000	0.000
85	A	83	ARG	1	0.962	0.986	31.584	-0.168	-0.168	0.000	0.000	0.000	0.000
86	A	84	GLU	-1	-0.873	-0.949	31.411	0.190	0.190	0.000	0.000	0.000	0.000
87	A	85	LEU	0	-0.050	-0.030	29.188	0.012	0.012	0.000	0.000	0.000	0.000
88	A	86	ALA	0	-0.008	-0.002	27.349	0.018	0.018	0.000	0.000	0.000	0.000
89	A	87	ALA	0	-0.068	-0.030	26.504	0.025	0.025	0.000	0.000	0.000	0.000
90	A	88	ALA	0	0.049	0.028	27.129	0.016	0.016	0.000	0.000	0.000	0.000
91	A	89	TYR	0	0.035	-0.003	23.290	0.020	0.020	0.000	0.000	0.000	0.000
92	A	90	ARG	1	0.956	0.979	22.624	-0.250	-0.250	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.881	-0.943	22.567	0.294	0.294	0.000	0.000	0.000	0.000
94	A	92	VAL	0	-0.013	-0.008	20.584	0.017	0.017	0.000	0.000	0.000	0.000
95	A	93	ALA	0	0.052	0.033	18.269	0.031	0.031	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.920	0.966	18.153	-0.351	-0.351	0.000	0.000	0.000	0.000
97	A	95	GLU	-1	-0.767	-0.831	19.759	0.380	0.380	0.000	0.000	0.000	0.000
98	A	96	VAL	0	0.031	0.006	15.237	0.008	0.008	0.000	0.000	0.000	0.000
99	A	97	THR	0	-0.004	-0.009	14.477	0.083	0.083	0.000	0.000	0.000	0.000
100	A	98	ARG	1	0.733	0.855	15.925	-0.341	-0.341	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.084	-0.059	18.360	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	100	GLY	0	0.003	0.021	14.133	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	101	VAL	0	-0.065	-0.021	13.513	0.084	0.084	0.000	0.000	0.000	0.000
104	A	102	ASN	0	0.017	-0.002	10.019	0.378	0.378	0.000	0.000	0.000	0.000
105	A	103	SER	0	0.001	0.009	11.607	-0.043	-0.043	0.000	0.000	0.000	0.000
106	A	104	VAL	0	0.009	-0.003	14.374	-0.042	-0.042	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.003	0.025	17.729	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	106	ILE	0	0.005	-0.013	20.590	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	107	PRO	0	-0.013	0.003	22.704	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	108	LEU	0	0.041	0.014	25.208	0.009	0.009	0.000	0.000	0.000	0.000
111	A	109	LEU	0	0.002	0.017	26.550	-0.023	-0.023	0.000	0.000	0.000	0.000
112	A	110	SER	0	0.021	-0.012	29.439	0.000	0.000	0.000	0.000	0.000	0.000
113	A	111	THR	0	-0.014	-0.020	30.775	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	112	GLY	0	-0.013	0.007	33.477	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	113	VAL	0	0.026	0.002	35.821	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	114	TYR	0	-0.043	-0.009	35.070	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	115	SER	0	0.035	0.030	36.292	0.000	0.000	0.000	0.000	0.000	0.000
118	A	116	GLY	0	0.026	0.024	37.596	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	117	GLY	0	-0.015	0.000	40.733	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	118	LYS	1	0.951	0.987	37.438	-0.132	-0.132	0.000	0.000	0.000	0.000
121	A	119	ASP	-1	-0.894	-0.949	34.612	0.139	0.139	0.000	0.000	0.000	0.000
122	A	120	ARG	1	0.727	0.808	33.219	-0.139	-0.139	0.000	0.000	0.000	0.000
123	A	121	LEU	0	0.017	0.029	28.282	0.013	0.013	0.000	0.000	0.000	0.000
124	A	122	THR	0	0.021	-0.007	28.976	0.013	0.013	0.000	0.000	0.000	0.000
125	A	123	GLN	0	-0.010	0.003	28.547	0.005	0.005	0.000	0.000	0.000	0.000
126	A	124	SER	0	0.013	-0.008	28.404	0.020	0.020	0.000	0.000	0.000	0.000
127	A	125	LEU	0	0.013	0.011	22.638	0.015	0.015	0.000	0.000	0.000	0.000
128	A	126	ASN	0	0.011	0.005	23.830	0.029	0.029	0.000	0.000	0.000	0.000
129	A	127	HIS	0	-0.040	-0.043	24.143	0.035	0.035	0.000	0.000	0.000	0.000
130	A	128	LEU	0	-0.022	0.003	19.969	0.021	0.021	0.000	0.000	0.000	0.000
131	A	129	PHE	0	-0.007	-0.018	19.230	0.029	0.029	0.000	0.000	0.000	0.000
132	A	130	THR	0	-0.017	-0.004	19.364	0.032	0.032	0.000	0.000	0.000	0.000
133	A	131	ALA	0	-0.081	-0.027	20.489	0.020	0.020	0.000	0.000	0.000	0.000
134	A	132	MET	0	-0.018	-0.020	16.371	0.024	0.024	0.000	0.000	0.000	0.000
135	A	133	ASP	-1	-0.729	-0.794	15.193	0.524	0.524	0.000	0.000	0.000	0.000
136	A	134	SER	0	-0.093	-0.032	13.846	0.065	0.065	0.000	0.000	0.000	0.000
137	A	135	THR	0	-0.072	-0.043	12.978	0.069	0.069	0.000	0.000	0.000	0.000
138	A	136	ASP	-1	-0.895	-0.959	7.508	1.994	1.994	0.000	0.000	0.000	0.000
139	A	137	ALA	0	0.019	0.021	8.980	0.096	0.096	0.000	0.000	0.000	0.000
140	A	138	ASP	-1	-0.860	-0.926	10.250	0.737	0.737	0.000	0.000	0.000	0.000
141	A	139	VAL	0	-0.006	-0.006	12.392	-0.054	-0.054	0.000	0.000	0.000	0.000
142	A	140	VAL	0	-0.048	-0.023	15.917	-0.050	-0.050	0.000	0.000	0.000	0.000
143	A	141	ILE	0	0.021	0.003	18.760	-0.010	-0.010	0.000	0.000	0.000	0.000
144	A	142	TYR	0	-0.065	-0.063	21.493	-0.041	-0.041	0.000	0.000	0.000	0.000
145	A	143	CYS	0	-0.031	-0.002	25.180	-0.009	-0.009	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.932	0.941	28.510	-0.147	-0.147	0.000	0.000	0.000	0.000
147	A	145	ASP	-1	-0.785	-0.881	31.798	0.108	0.108	0.000	0.000	0.000	0.000
148	A	146	LYS	1	0.893	0.921	31.552	-0.085	-0.085	0.000	0.000	0.000	0.000
149	A	147	GLU	-1	-0.852	-0.921	31.699	0.095	0.095	0.000	0.000	0.000	0.000
150	A	148	TRP	0	-0.003	-0.019	30.237	0.008	0.008	0.000	0.000	0.000	0.000
151	A	149	GLU	-1	-0.843	-0.925	26.634	0.143	0.143	0.000	0.000	0.000	0.000
152	A	150	LYS	1	0.910	0.965	26.868	-0.086	-0.086	0.000	0.000	0.000	0.000
153	A	151	LYS	1	1.032	1.017	27.561	-0.116	-0.116	0.000	0.000	0.000	0.000
154	A	152	ILE	0	-0.007	-0.001	23.190	0.007	0.007	0.000	0.000	0.000	0.000
155	A	153	SER	0	-0.009	-0.011	22.958	0.017	0.017	0.000	0.000	0.000	0.000
156	A	154	GLU	-1	-0.941	-0.974	22.837	0.123	0.123	0.000	0.000	0.000	0.000
157	A	155	ALA	0	-0.016	-0.013	23.848	0.003	0.003	0.000	0.000	0.000	0.000
158	A	156	ILE	0	-0.014	-0.009	17.961	0.017	0.017	0.000	0.000	0.000	0.000
159	A	157	GLN	0	-0.031	-0.020	18.446	0.028	0.028	0.000	0.000	0.000	0.000
160	A	158	MET	0	-0.064	-0.022	19.971	-0.005	-0.005	0.000	0.000	0.000	0.000
161	A	159	ARG	1	0.752	0.851	17.877	-0.366	-0.366	0.000	0.000	0.000	0.000
162	A	160	THR	0	-0.027	0.008	14.624	0.009	0.009	0.000	0.000	0.000	0.000

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