FMO DATABASE

FMODB ID: 173RZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-913069.558921
FMO2-HF: Nuclear repulsion	867832.664599
FMO2-HF: Total energy	-45236.894322
FMO2-MP2: Total energy	-45367.983519

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.
-82.725	-87.843	27.375	-12.846	-9.41	0.076

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 : -0.838 / q_NPA : -0.898

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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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	0.002	0.000	3.486	0.756	3.964	0.087	-1.683	-1.611	0.006
4	A	4	LEU	0	0.009	0.013	6.156	-4.688	-4.688	0.000	0.000	0.000	0.000
5	A	5	GLN	0	-0.011	-0.021	9.620	-0.207	-0.207	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.772	-0.877	12.431	21.625	21.625	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.019	0.002	15.801	-0.511	-0.511	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.027	0.008	18.899	-0.164	-0.164	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.023	0.018	21.772	-0.504	-0.504	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.013	-0.013	23.390	-0.119	-0.119	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.032	-0.008	26.221	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.010	-0.004	29.792	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.073	0.038	32.272	-0.100	-0.100	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.009	-0.011	35.317	0.167	0.167	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.030	-0.008	36.852	-0.200	-0.200	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.015	0.003	34.767	-0.055	-0.055	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.067	-0.058	32.118	0.104	0.104	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.024	0.011	26.670	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.917	0.963	23.288	-13.267	-13.267	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.007	0.033	20.810	0.270	0.270	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.040	-0.046	19.275	-0.573	-0.573	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.080	-0.031	14.069	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.060	0.028	13.706	-0.958	-0.958	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.061	0.038	8.524	1.354	1.354	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.000	-0.011	6.952	-1.108	-1.108	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.013	0.008	8.302	1.651	1.651	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.039	-0.021	10.860	-0.538	-0.538	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.003	0.008	5.321	-1.044	-1.044	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.007	0.001	6.591	1.401	1.401	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.044	-0.021	9.661	-0.495	-0.495	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.003	-0.014	11.758	1.755	1.755	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.839	-0.898	14.101	16.863	16.863	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.054	-0.036	15.943	-1.325	-1.325	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.014	0.011	15.312	1.525	1.525	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.014	-0.009	16.453	-1.478	-1.478	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.000	0.005	17.154	1.208	1.208	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.001	-0.008	17.625	-0.824	-0.824	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.785	0.876	20.528	-11.389	-11.389	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.007	-0.011	21.925	0.494	0.494	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.029	0.023	23.907	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.011	-0.026	27.153	0.122	0.122	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.024	0.029	28.392	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.907	0.959	28.120	-10.396	-10.396	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.052	0.024	25.725	0.129	0.129	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.914	0.976	15.692	-18.593	-18.593	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.817	-0.885	23.186	11.484	11.484	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.002	-0.005	22.187	0.589	0.589	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.024	-0.010	22.756	-0.627	-0.627	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.001	-0.014	22.759	-0.679	-0.679	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.009	-0.005	20.569	0.723	0.723	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.004	-0.002	19.918	-0.798	-0.798	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.050	0.031	20.013	0.918	0.918	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.069	0.037	18.959	-0.375	-0.375	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.001	0.003	21.367	-0.201	-0.201	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.014	-0.006	23.913	-0.498	-0.498	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.000	0.004	25.391	-0.204	-0.204	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.003	-0.013	24.759	0.500	0.500	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.024	-0.007	25.537	-0.838	-0.838	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.031	0.017	25.658	0.627	0.627	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.053	0.038	27.450	-0.323	-0.323	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.802	-0.912	29.039	9.567	9.567	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.007	0.010	30.291	-0.207	-0.207	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.007	-0.008	27.777	-0.090	-0.090	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.846	0.924	31.265	-9.865	-9.865	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.004	0.004	32.750	-0.252	-0.252	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.724	0.835	32.031	-10.046	-10.046	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.008	-0.005	26.909	0.144	0.144	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.049	-0.030	28.036	-0.343	-0.343	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.023	0.000	20.251	0.226	0.226	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.023	-0.015	23.108	-0.451	-0.451	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.879	0.921	19.169	-14.664	-14.664	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.777	-0.855	20.236	13.140	13.140	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.047	0.006	18.564	0.250	0.250	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.032	0.001	18.701	0.414	0.414	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.785	0.872	17.834	-13.805	-13.805	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.004	-0.003	14.101	0.376	0.376	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.007	0.017	14.989	1.236	1.236	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.012	-0.003	16.262	-0.794	-0.794	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.075	-0.070	18.726	0.365	0.365	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.012	-0.008	21.787	-0.130	-0.130	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.005	-0.005	23.878	0.157	0.157	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.036	-0.011	25.661	0.198	0.198	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.086	0.044	29.116	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	82	SER	0	0.026	0.005	32.930	0.026	0.026	0.000	0.000	0.000	0.000
85	A	82	LEU	0	-0.007	0.023	29.358	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	83	LYS	1	0.825	0.890	33.393	-9.177	-9.177	0.000	0.000	0.000	0.000
87	A	84	PRO	0	0.082	0.028	33.308	0.305	0.305	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.820	-0.897	32.800	9.230	9.230	0.000	0.000	0.000	0.000
89	A	86	ASP	-1	-0.762	-0.833	29.395	10.640	10.640	0.000	0.000	0.000	0.000
90	A	87	THR	0	-0.018	0.000	28.108	0.479	0.479	0.000	0.000	0.000	0.000
91	A	88	ALA	0	-0.006	-0.015	24.908	-0.131	-0.131	0.000	0.000	0.000	0.000
92	A	89	VAL	0	0.009	0.028	19.382	0.019	0.019	0.000	0.000	0.000	0.000
93	A	90	TYR	0	-0.016	-0.035	20.603	-0.060	-0.060	0.000	0.000	0.000	0.000
94	A	91	TYR	0	-0.005	-0.005	15.056	0.018	0.018	0.000	0.000	0.000	0.000
95	A	93	TYR	0	-0.062	-0.062	12.540	0.632	0.632	0.000	0.000	0.000	0.000
96	A	94	ALA	0	0.050	0.014	10.318	-1.752	-1.752	0.000	0.000	0.000	0.000
97	A	95	PRO	0	-0.004	0.008	10.452	2.882	2.882	0.000	0.000	0.000	0.000
98	A	96	MET	0	-0.053	-0.034	10.916	-0.598	-0.598	0.000	0.000	0.000	0.000
99	A	97	ILE	0	0.040	0.032	7.786	-1.319	-1.319	0.000	0.000	0.000	0.000
100	A	98	TYR	0	-0.037	-0.028	8.227	2.633	2.633	0.000	0.000	0.000	0.000
101	A	99	TYR	0	0.057	0.014	2.179	-3.618	-3.409	5.012	-2.341	-2.880	-0.007
102	A	100	GLY	0	-0.004	0.008	5.199	1.058	1.058	0.000	0.000	0.000	0.000
103	A	100	GLY	0	0.007	0.012	5.980	-0.989	-0.989	0.000	0.000	0.000	0.000
104	A	100	ARG	1	0.854	0.926	4.934	-51.275	-51.234	-0.001	-0.003	-0.037	0.000
105	A	100	TYR	0	0.061	0.021	7.516	1.942	1.942	0.000	0.000	0.000	0.000
106	A	100	SER	0	-0.047	-0.037	5.506	1.539	1.539	0.000	0.000	0.000	0.000
107	A	101	ASP	-1	-0.806	-0.856	7.431	24.060	24.060	0.000	0.000	0.000	0.000
108	A	102	TYR	0	-0.070	-0.057	1.576	-27.869	-36.445	22.277	-8.819	-4.882	0.077
109	A	103	TRP	0	0.008	-0.017	7.899	-6.047	-6.047	0.000	0.000	0.000	0.000
110	A	104	GLY	0	0.017	0.025	9.033	3.767	3.767	0.000	0.000	0.000	0.000
111	A	105	GLN	0	-0.037	-0.033	8.732	-2.939	-2.939	0.000	0.000	0.000	0.000
112	A	106	GLY	0	-0.013	-0.001	12.762	-1.476	-1.476	0.000	0.000	0.000	0.000
113	A	107	THR	0	-0.047	-0.030	16.174	-0.405	-0.405	0.000	0.000	0.000	0.000
114	A	108	GLN	0	0.016	0.009	19.251	-0.324	-0.324	0.000	0.000	0.000	0.000
115	A	109	VAL	0	0.019	0.012	22.846	-0.104	-0.104	0.000	0.000	0.000	0.000
116	A	110	THR	0	-0.037	-0.027	25.873	-0.092	-0.092	0.000	0.000	0.000	0.000
117	A	111	VAL	0	0.016	0.019	29.389	-0.108	-0.108	0.000	0.000	0.000	0.000
118	A	112	SER	0	-0.028	-0.016	32.728	-0.137	-0.137	0.000	0.000	0.000	0.000

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