FMO DATABASE

FMODB ID: R8M58

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1609851.115605
FMO2-HF: Nuclear repulsion	1546377.44384
FMO2-HF: Total energy	-63473.671764
FMO2-MP2: Total energy	-63655.696169

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.
2.949	4.228	0.009	-0.562	-0.726	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 : -0.039 / 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	-0.010	-0.003	3.746	-1.532	-0.253	0.009	-0.562	-0.726	0.001
4	A	2	PRO	0	-0.017	0.010	5.697	0.021	0.021	0.000	0.000	0.000	0.000
5	A	3	SER	0	-0.042	-0.027	8.782	-0.275	-0.275	0.000	0.000	0.000	0.000
6	A	4	TYR	0	0.021	-0.027	12.172	0.062	0.062	0.000	0.000	0.000	0.000
7	A	5	ARG	1	0.813	0.896	13.038	-0.701	-0.701	0.000	0.000	0.000	0.000
8	A	6	VAL	0	-0.014	-0.007	18.484	0.016	0.016	0.000	0.000	0.000	0.000
9	A	7	LYS	1	0.877	0.928	21.165	-0.370	-0.370	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.802	0.891	24.675	-0.144	-0.144	0.000	0.000	0.000	0.000
11	A	9	MET	0	-0.040	0.004	25.813	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.885	-0.956	28.932	0.233	0.233	0.000	0.000	0.000	0.000
13	A	11	ILE	0	0.101	0.064	24.945	0.002	0.002	0.000	0.000	0.000	0.000
14	A	12	ALA	0	-0.012	0.008	26.666	0.025	0.025	0.000	0.000	0.000	0.000
15	A	13	LYS	1	0.765	0.852	27.806	-0.212	-0.212	0.000	0.000	0.000	0.000
16	A	14	ASN	0	-0.027	-0.003	22.467	0.021	0.021	0.000	0.000	0.000	0.000
17	A	15	ASP	-1	-0.872	-0.928	20.149	0.342	0.342	0.000	0.000	0.000	0.000
18	A	16	GLU	-1	-0.735	-0.851	17.166	0.543	0.543	0.000	0.000	0.000	0.000
19	A	17	GLU	-1	-0.834	-0.914	14.235	1.214	1.214	0.000	0.000	0.000	0.000
20	A	18	CYS	0	-0.066	-0.013	18.189	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	19	VAL	0	-0.019	0.007	20.732	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	20	VAL	0	0.031	0.022	21.956	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	21	ASN	0	-0.007	-0.040	24.578	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	22	ALA	0	0.000	0.000	28.380	0.001	0.001	0.000	0.000	0.000	0.000
25	A	23	ALA	0	-0.008	0.005	30.603	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	24	ASN	0	0.000	-0.009	32.967	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	25	PRO	0	0.053	0.003	36.025	0.005	0.005	0.000	0.000	0.000	0.000
28	A	26	ARG	1	0.896	0.948	37.361	-0.152	-0.152	0.000	0.000	0.000	0.000
29	A	27	GLY	0	0.050	0.039	36.254	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.025	-0.011	37.273	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	29	PRO	0	0.041	0.012	37.863	0.008	0.008	0.000	0.000	0.000	0.000
32	A	30	GLY	0	0.030	0.028	37.562	0.007	0.007	0.000	0.000	0.000	0.000
33	A	31	ASP	-1	-0.903	-0.972	38.453	0.161	0.161	0.000	0.000	0.000	0.000
34	A	32	GLY	0	0.031	0.006	35.946	0.010	0.010	0.000	0.000	0.000	0.000
35	A	33	VAL	0	0.003	0.001	29.576	0.000	0.000	0.000	0.000	0.000	0.000
36	A	34	CYS	0	0.005	0.034	32.406	0.011	0.011	0.000	0.000	0.000	0.000
37	A	35	LYS	1	0.955	0.985	34.004	-0.148	-0.148	0.000	0.000	0.000	0.000
38	A	36	ALA	0	-0.031	-0.020	32.395	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	37	VAL	0	0.035	0.017	29.140	0.003	0.003	0.000	0.000	0.000	0.000
40	A	38	TYR	0	0.021	0.005	31.771	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	39	LYS	1	0.872	0.940	35.024	-0.201	-0.201	0.000	0.000	0.000	0.000
42	A	40	LYS	1	0.798	0.895	27.764	-0.310	-0.310	0.000	0.000	0.000	0.000
43	A	41	TRP	0	0.082	0.043	26.212	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	42	PRO	0	0.021	0.034	32.467	0.004	0.004	0.000	0.000	0.000	0.000
45	A	43	GLU	-1	-0.809	-0.918	32.063	0.261	0.261	0.000	0.000	0.000	0.000
46	A	44	SER	0	-0.006	-0.016	30.369	0.004	0.004	0.000	0.000	0.000	0.000
47	A	45	PHE	0	-0.006	-0.013	32.311	0.008	0.008	0.000	0.000	0.000	0.000
48	A	46	LYS	1	0.929	0.978	35.019	-0.228	-0.228	0.000	0.000	0.000	0.000
49	A	47	ASN	0	-0.021	-0.014	34.922	0.005	0.005	0.000	0.000	0.000	0.000
50	A	48	SER	0	0.020	0.015	32.564	0.001	0.001	0.000	0.000	0.000	0.000
51	A	49	ALA	0	-0.025	-0.003	33.613	0.007	0.007	0.000	0.000	0.000	0.000
52	A	50	THR	0	-0.005	0.005	31.563	0.000	0.000	0.000	0.000	0.000	0.000
53	A	51	PRO	0	0.005	-0.003	34.444	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	52	VAL	0	0.007	-0.006	34.043	0.011	0.011	0.000	0.000	0.000	0.000
55	A	53	GLY	0	0.018	0.028	31.654	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	54	THR	0	-0.045	-0.011	29.633	0.007	0.007	0.000	0.000	0.000	0.000
57	A	55	ALA	0	-0.023	-0.027	26.144	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	56	LYS	1	0.804	0.899	28.221	-0.263	-0.263	0.000	0.000	0.000	0.000
59	A	57	THR	0	-0.027	-0.041	24.117	0.006	0.006	0.000	0.000	0.000	0.000
60	A	58	VAL	0	-0.072	-0.024	26.636	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	59	MET	0	-0.004	0.010	23.065	0.020	0.020	0.000	0.000	0.000	0.000
62	A	60	CYS	0	-0.059	-0.026	27.275	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	61	GLY	0	-0.019	-0.011	27.452	0.008	0.008	0.000	0.000	0.000	0.000
64	A	62	THR	0	0.000	-0.015	22.493	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	63	TYR	0	0.013	0.020	21.820	0.032	0.032	0.000	0.000	0.000	0.000
66	A	64	PRO	0	0.024	0.001	20.608	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	65	VAL	0	0.012	0.004	23.737	0.008	0.008	0.000	0.000	0.000	0.000
68	A	66	ILE	0	0.019	0.002	20.770	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	67	HIS	0	-0.002	-0.003	25.435	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	68	ALA	0	0.040	0.014	26.617	0.006	0.006	0.000	0.000	0.000	0.000
71	A	69	VAL	0	-0.053	-0.006	28.759	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	70	GLY	0	0.046	0.026	31.745	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	71	PRO	0	0.004	0.011	32.356	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	72	ASN	0	0.045	0.048	35.839	0.000	0.000	0.000	0.000	0.000	0.000
75	A	73	PHE	0	0.020	-0.003	34.384	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	74	SER	0	-0.038	-0.027	39.747	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	75	ASN	0	-0.113	-0.064	41.900	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	76	TYR	0	-0.037	-0.024	37.754	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	77	SER	0	0.045	0.019	41.144	0.000	0.000	0.000	0.000	0.000	0.000
80	A	78	GLU	-1	-0.731	-0.852	38.601	0.145	0.145	0.000	0.000	0.000	0.000
81	A	79	SER	0	-0.038	-0.030	37.202	0.008	0.008	0.000	0.000	0.000	0.000
82	A	80	GLU	-1	-0.857	-0.919	36.523	0.154	0.154	0.000	0.000	0.000	0.000
83	A	81	GLY	0	0.033	0.010	36.113	0.011	0.011	0.000	0.000	0.000	0.000
84	A	82	ASP	-1	-0.830	-0.900	32.275	0.204	0.204	0.000	0.000	0.000	0.000
85	A	83	ARG	1	0.945	0.978	31.779	-0.159	-0.159	0.000	0.000	0.000	0.000
86	A	84	GLU	-1	-0.815	-0.905	31.605	0.219	0.219	0.000	0.000	0.000	0.000
87	A	85	LEU	0	-0.047	-0.025	29.374	0.017	0.017	0.000	0.000	0.000	0.000
88	A	86	ALA	0	0.008	0.003	27.471	0.023	0.023	0.000	0.000	0.000	0.000
89	A	87	ALA	0	-0.078	-0.039	26.779	0.026	0.026	0.000	0.000	0.000	0.000
90	A	88	ALA	0	0.048	0.025	27.170	0.024	0.024	0.000	0.000	0.000	0.000
91	A	89	TYR	0	0.028	-0.011	23.400	0.031	0.031	0.000	0.000	0.000	0.000
92	A	90	ARG	1	0.944	0.991	22.823	-0.264	-0.264	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.859	-0.935	22.606	0.365	0.365	0.000	0.000	0.000	0.000
94	A	92	VAL	0	-0.008	-0.001	20.997	0.030	0.030	0.000	0.000	0.000	0.000
95	A	93	ALA	0	0.069	0.038	18.418	0.048	0.048	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.920	0.982	18.307	-0.471	-0.471	0.000	0.000	0.000	0.000
97	A	95	GLU	-1	-0.770	-0.848	20.034	0.513	0.513	0.000	0.000	0.000	0.000
98	A	96	VAL	0	0.029	0.003	15.420	0.022	0.022	0.000	0.000	0.000	0.000
99	A	97	THR	0	-0.012	-0.020	14.820	0.111	0.111	0.000	0.000	0.000	0.000
100	A	98	ARG	1	0.725	0.841	16.324	-0.485	-0.485	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.057	-0.039	18.425	-0.030	-0.030	0.000	0.000	0.000	0.000
102	A	100	GLY	0	-0.008	0.014	14.090	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	101	VAL	0	-0.049	-0.015	13.408	0.142	0.142	0.000	0.000	0.000	0.000
104	A	102	ASN	0	0.009	-0.019	9.867	0.536	0.536	0.000	0.000	0.000	0.000
105	A	103	SER	0	-0.020	-0.005	11.648	-0.097	-0.097	0.000	0.000	0.000	0.000
106	A	104	VAL	0	0.012	-0.005	14.421	-0.057	-0.057	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.000	0.025	17.783	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	106	ILE	0	0.008	-0.008	20.437	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	107	PRO	0	-0.012	-0.003	22.794	-0.028	-0.028	0.000	0.000	0.000	0.000
110	A	108	LEU	0	0.048	0.020	25.520	0.007	0.007	0.000	0.000	0.000	0.000
111	A	109	LEU	0	0.017	0.031	26.511	-0.028	-0.028	0.000	0.000	0.000	0.000
112	A	110	SER	0	-0.005	-0.028	29.445	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	111	THR	0	-0.038	-0.031	30.839	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	112	GLY	0	0.003	0.019	33.484	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	113	VAL	0	0.033	0.007	35.809	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	114	TYR	0	-0.041	-0.016	35.532	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	115	SER	0	0.025	0.025	36.546	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	116	GLY	0	0.031	0.017	37.776	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	117	GLY	0	-0.027	-0.002	40.772	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	118	LYS	1	0.850	0.917	36.758	-0.144	-0.144	0.000	0.000	0.000	0.000
121	A	119	ASP	-1	-0.862	-0.938	34.284	0.152	0.152	0.000	0.000	0.000	0.000
122	A	120	ARG	1	0.774	0.850	33.292	-0.152	-0.152	0.000	0.000	0.000	0.000
123	A	121	LEU	0	-0.012	0.020	28.106	0.015	0.015	0.000	0.000	0.000	0.000
124	A	122	THR	0	0.033	0.000	28.822	0.016	0.016	0.000	0.000	0.000	0.000
125	A	123	GLN	0	-0.031	-0.020	28.601	0.003	0.003	0.000	0.000	0.000	0.000
126	A	124	SER	0	0.019	-0.012	28.576	0.021	0.021	0.000	0.000	0.000	0.000
127	A	125	LEU	0	0.001	0.005	22.753	0.021	0.021	0.000	0.000	0.000	0.000
128	A	126	ASN	0	0.027	0.014	23.821	0.026	0.026	0.000	0.000	0.000	0.000
129	A	127	HIS	0	-0.032	-0.014	24.186	0.034	0.034	0.000	0.000	0.000	0.000
130	A	128	LEU	0	-0.029	-0.006	20.127	0.027	0.027	0.000	0.000	0.000	0.000
131	A	129	PHE	0	-0.014	-0.019	19.350	0.037	0.037	0.000	0.000	0.000	0.000
132	A	130	THR	0	-0.033	-0.027	19.438	0.032	0.032	0.000	0.000	0.000	0.000
133	A	131	ALA	0	-0.050	-0.007	20.645	0.010	0.010	0.000	0.000	0.000	0.000
134	A	132	MET	0	0.007	0.002	16.199	0.035	0.035	0.000	0.000	0.000	0.000
135	A	133	ASP	-1	-0.732	-0.798	15.190	0.540	0.540	0.000	0.000	0.000	0.000
136	A	134	SER	0	-0.125	-0.050	14.196	0.055	0.055	0.000	0.000	0.000	0.000
137	A	135	THR	0	-0.088	-0.057	12.735	0.067	0.067	0.000	0.000	0.000	0.000
138	A	136	ASP	-1	-0.881	-0.955	7.546	2.571	2.571	0.000	0.000	0.000	0.000
139	A	137	ALA	0	0.016	0.018	8.974	0.179	0.179	0.000	0.000	0.000	0.000
140	A	138	ASP	-1	-0.785	-0.860	10.804	0.862	0.862	0.000	0.000	0.000	0.000
141	A	139	VAL	0	-0.008	0.000	12.604	-0.069	-0.069	0.000	0.000	0.000	0.000
142	A	140	VAL	0	-0.046	-0.023	16.072	-0.079	-0.079	0.000	0.000	0.000	0.000
143	A	141	ILE	0	0.040	0.011	18.966	-0.015	-0.015	0.000	0.000	0.000	0.000
144	A	142	TYR	0	-0.061	-0.068	21.577	-0.048	-0.048	0.000	0.000	0.000	0.000
145	A	143	CYS	0	-0.046	-0.005	25.534	-0.016	-0.016	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.931	0.945	28.841	-0.194	-0.194	0.000	0.000	0.000	0.000
147	A	145	ASP	-1	-0.752	-0.877	32.187	0.119	0.119	0.000	0.000	0.000	0.000
148	A	146	LYS	1	0.858	0.906	31.692	-0.092	-0.092	0.000	0.000	0.000	0.000
149	A	147	GLU	-1	-0.762	-0.849	31.774	0.096	0.096	0.000	0.000	0.000	0.000
150	A	148	TRP	0	-0.008	-0.017	30.539	0.006	0.006	0.000	0.000	0.000	0.000
151	A	149	GLU	-1	-0.760	-0.877	26.751	0.178	0.178	0.000	0.000	0.000	0.000
152	A	150	LYS	1	0.824	0.904	26.988	-0.087	-0.087	0.000	0.000	0.000	0.000
153	A	151	LYS	1	0.979	0.999	27.549	-0.125	-0.125	0.000	0.000	0.000	0.000
154	A	152	ILE	0	-0.009	-0.009	23.440	0.004	0.004	0.000	0.000	0.000	0.000
155	A	153	SER	0	0.000	0.001	23.026	0.015	0.015	0.000	0.000	0.000	0.000
156	A	154	GLU	-1	-0.922	-0.971	23.061	0.107	0.107	0.000	0.000	0.000	0.000
157	A	155	ALA	0	-0.003	-0.013	24.193	-0.005	-0.005	0.000	0.000	0.000	0.000
158	A	156	ILE	0	-0.018	-0.002	18.215	0.017	0.017	0.000	0.000	0.000	0.000
159	A	157	GLN	0	0.003	-0.004	18.328	0.023	0.023	0.000	0.000	0.000	0.000
160	A	158	MET	0	-0.036	-0.013	20.258	-0.018	-0.018	0.000	0.000	0.000	0.000
161	A	159	ARG	1	0.752	0.852	18.140	-0.345	-0.345	0.000	0.000	0.000	0.000
162	A	160	THR	0	-0.064	-0.013	14.826	-0.027	-0.027	0.000	0.000	0.000	0.000

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