FMO DATABASE

FMODB ID: YZM32

Calculation Name: 5HM1-A-Xray372

Preferred Name: Envelope polyprotein GP160

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5HM1

Chain ID: A

ChEMBL ID: CHEMBL3520

UniProt ID: P04578

Base Structure: X-ray

Registration Date: 2023-06-26

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-908814.698976
FMO2-HF: Nuclear repulsion	863578.550748
FMO2-HF: Total energy	-45236.148228
FMO2-MP2: Total energy	-45367.180531

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:ASP)

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

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.
-42.961	-37.291	7.369	-6.85	-6.19	0.009

Interaction energy analysis for fragmet #1(A:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.917 / q_NPA : -0.972

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

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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	3	GLN	0	0.035	0.007	3.631	2.871	6.559	0.030	-1.926	-1.793	0.007
4	A	4	LEU	0	-0.039	-0.012	6.249	-5.215	-5.215	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.002	-0.016	9.451	-0.933	-0.933	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.778	-0.898	12.497	21.027	21.027	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.022	-0.019	15.866	0.222	0.222	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.004	0.007	19.119	-0.260	-0.260	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.009	0.000	21.983	-0.501	-0.501	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.003	-0.003	23.475	-0.263	-0.263	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.034	-0.016	26.129	-0.083	-0.083	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.001	0.002	29.769	-0.077	-0.077	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.026	0.010	32.137	-0.101	-0.101	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.030	-0.001	35.064	0.165	0.165	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.030	0.001	36.309	-0.215	-0.215	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.038	-0.011	34.510	-0.053	-0.053	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.057	-0.054	31.712	0.063	0.063	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.034	0.021	26.483	0.035	0.035	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.935	0.974	24.236	-12.706	-12.706	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.022	0.015	20.664	0.269	0.269	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.014	-0.003	18.670	-0.503	-0.503	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.068	-0.028	13.717	-0.169	-0.169	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.041	0.014	13.422	-0.711	-0.711	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.069	0.044	8.098	1.269	1.269	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.001	0.002	6.978	-1.275	-1.275	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.013	-0.002	7.827	2.077	2.077	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.054	-0.034	10.168	-0.197	-0.197	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.001	0.006	4.478	-1.102	-1.027	-0.001	-0.011	-0.063	0.000
29	A	29	VAL	0	0.001	0.007	6.500	0.989	0.989	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.004	0.004	9.302	-0.240	-0.240	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.019	-0.008	11.338	0.988	0.988	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.900	-0.947	13.869	16.455	16.455	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.072	-0.056	15.940	-1.215	-1.215	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.006	0.010	15.442	1.307	1.307	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.012	-0.008	16.948	-1.347	-1.347	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.004	0.018	17.466	1.073	1.073	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.009	-0.003	17.481	-0.844	-0.844	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.860	0.939	20.282	-11.082	-11.082	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.010	-0.001	21.495	0.392	0.392	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.018	0.009	23.305	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.012	-0.005	26.225	0.215	0.215	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.034	0.018	27.656	0.146	0.146	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.893	0.951	27.949	-10.178	-10.178	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.066	0.030	25.470	0.154	0.154	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.919	0.982	15.958	-17.410	-17.410	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.859	-0.926	22.909	11.171	11.171	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.006	-0.011	22.260	0.509	0.509	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.015	0.003	22.753	-0.582	-0.582	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.016	-0.031	22.818	-0.641	-0.641	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.010	0.001	21.446	0.623	0.623	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.001	0.004	20.300	-0.754	-0.754	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.021	0.014	20.368	0.779	0.779	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.077	0.029	18.806	-0.254	-0.254	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.010	-0.003	21.313	-0.209	-0.209	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.003	0.004	24.181	-0.342	-0.342	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.023	-0.004	25.508	-0.194	-0.194	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.008	-0.003	25.316	0.444	0.444	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.043	-0.018	26.060	-0.932	-0.932	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.014	-0.005	26.363	0.541	0.541	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.074	0.044	27.667	-0.271	-0.271	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.845	-0.954	29.318	9.320	9.320	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.039	-0.011	30.964	-0.164	-0.164	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.003	-0.004	28.131	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.937	0.988	31.421	-9.474	-9.474	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.017	0.003	33.071	-0.267	-0.267	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.722	0.845	31.792	-9.832	-9.832	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.015	-0.007	26.646	0.154	0.154	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.038	-0.017	28.130	-0.316	-0.316	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.012	0.010	20.674	0.275	0.275	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.040	-0.022	23.093	-0.442	-0.442	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.976	0.982	19.602	-13.698	-13.698	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.881	-0.939	20.336	12.857	12.857	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.005	-0.024	18.877	1.288	1.288	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.021	0.026	18.348	0.478	0.478	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.861	0.937	17.198	-13.469	-13.469	0.000	0.000	0.000	0.000
76	A	76	ASN	0	0.006	0.027	12.661	-0.094	-0.094	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.018	-0.001	14.571	0.918	0.918	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.019	0.000	16.327	-0.951	-0.951	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.057	-0.044	18.610	0.358	0.358	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.005	-0.009	21.725	-0.234	-0.234	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.013	-0.006	23.749	0.266	0.266	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.025	-0.003	25.724	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.089	0.033	28.925	0.005	0.005	0.000	0.000	0.000	0.000
84	A	82	SER	0	0.006	-0.005	32.728	-0.096	-0.096	0.000	0.000	0.000	0.000
85	A	82	LEU	0	-0.011	0.013	29.283	-0.048	-0.048	0.000	0.000	0.000	0.000
86	A	83	LYS	1	0.990	1.000	33.206	-9.040	-9.040	0.000	0.000	0.000	0.000
87	A	84	PRO	0	0.047	0.022	32.998	0.307	0.307	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.931	-0.976	32.513	9.092	9.092	0.000	0.000	0.000	0.000
89	A	86	ASP	-1	-0.810	-0.887	29.172	10.431	10.431	0.000	0.000	0.000	0.000
90	A	87	THR	0	-0.032	-0.004	27.837	0.454	0.454	0.000	0.000	0.000	0.000
91	A	88	ALA	0	-0.017	-0.022	24.476	-0.108	-0.108	0.000	0.000	0.000	0.000
92	A	89	VAL	0	-0.001	0.014	19.036	0.084	0.084	0.000	0.000	0.000	0.000
93	A	90	TYR	0	-0.039	-0.038	20.185	-0.065	-0.065	0.000	0.000	0.000	0.000
94	A	91	TYR	0	0.014	-0.001	14.847	0.124	0.124	0.000	0.000	0.000	0.000
95	A	93	TYR	0	-0.060	-0.052	12.903	0.886	0.886	0.000	0.000	0.000	0.000
96	A	94	ALA	0	0.044	0.003	10.735	-1.693	-1.693	0.000	0.000	0.000	0.000
97	A	95	PRO	0	-0.025	-0.001	10.873	2.356	2.356	0.000	0.000	0.000	0.000
98	A	96	MET	0	-0.043	-0.026	11.290	-0.613	-0.613	0.000	0.000	0.000	0.000
99	A	97	ILE	0	0.046	0.024	7.148	-1.033	-1.033	0.000	0.000	0.000	0.000
100	A	98	TYR	0	-0.027	-0.014	7.840	2.433	2.433	0.000	0.000	0.000	0.000
101	A	99	TYR	0	0.047	0.003	2.313	1.506	1.332	7.234	-3.969	-3.091	-0.004
102	A	100	GLY	0	0.002	0.022	5.817	1.005	1.005	0.000	0.000	0.000	0.000
103	A	100	GLY	0	-0.013	-0.008	6.564	-0.348	-0.348	0.000	0.000	0.000	0.000
104	A	100	ARG	1	0.932	0.961	6.032	-42.350	-42.350	0.000	0.000	0.000	0.000
105	A	100	TYR	0	0.036	0.009	7.619	2.102	2.102	0.000	0.000	0.000	0.000
106	A	100	SER	0	-0.052	-0.029	6.209	0.918	0.918	0.000	0.000	0.000	0.000
107	A	101	ASP	-1	-0.811	-0.861	8.354	23.037	23.037	0.000	0.000	0.000	0.000
108	A	102	TYR	0	-0.017	-0.009	2.863	-4.338	-2.257	0.106	-0.944	-1.243	0.006
109	A	103	TRP	0	-0.006	-0.023	8.108	-4.998	-4.998	0.000	0.000	0.000	0.000
110	A	104	GLY	0	0.035	0.038	8.778	3.163	3.163	0.000	0.000	0.000	0.000
111	A	105	GLN	0	-0.018	-0.025	9.281	-2.864	-2.864	0.000	0.000	0.000	0.000
112	A	106	GLY	0	-0.010	0.014	12.583	-1.476	-1.476	0.000	0.000	0.000	0.000
113	A	107	THR	0	-0.050	-0.023	15.986	-0.226	-0.226	0.000	0.000	0.000	0.000
114	A	108	GLN	0	0.015	0.005	19.031	-0.814	-0.814	0.000	0.000	0.000	0.000
115	A	109	VAL	0	0.026	0.020	22.561	-0.109	-0.109	0.000	0.000	0.000	0.000
116	A	110	THR	0	-0.011	-0.015	25.502	-0.142	-0.142	0.000	0.000	0.000	0.000
117	A	111	VAL	0	0.026	0.020	29.023	-0.128	-0.128	0.000	0.000	0.000	0.000
118	A	112	SER	0	0.004	0.004	32.368	-0.166	-0.166	0.000	0.000	0.000	0.000

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