FMO DATABASE

FMODB ID: V56M1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-909567.415989
FMO2-HF: Nuclear repulsion	864330.729379
FMO2-HF: Total energy	-45236.686611
FMO2-MP2: Total energy	-45367.705957

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.
-81.083	-79.861	23.624	-13.882	-10.963	0.081

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 : -0.865 / q_NPA : -0.932

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	0.041	0.012	3.675	1.270	5.071	0.026	-1.955	-1.872	0.007
4	A	4	LEU	0	-0.015	0.000	6.379	-5.287	-5.287	0.000	0.000	0.000	0.000
5	A	5	GLN	0	-0.004	-0.016	9.462	-0.976	-0.976	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.774	-0.892	12.687	21.415	21.415	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.014	-0.014	16.029	0.131	0.131	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.002	0.008	19.284	-0.209	-0.209	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.004	0.008	22.179	-0.511	-0.511	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.001	-0.005	23.746	-0.283	-0.283	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.039	-0.018	26.339	-0.069	-0.069	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.003	0.003	30.003	-0.075	-0.075	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.034	0.016	32.418	-0.066	-0.066	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.018	-0.006	35.257	0.177	0.177	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.020	0.003	36.421	-0.221	-0.221	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.042	-0.012	34.652	-0.053	-0.053	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.054	-0.062	31.864	0.096	0.096	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.023	0.019	26.689	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.932	0.972	23.721	-12.960	-12.960	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.013	0.020	20.678	0.264	0.264	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.007	-0.015	19.012	-0.496	-0.496	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.063	-0.028	13.708	-0.046	-0.046	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.031	0.013	13.466	-0.655	-0.655	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.066	0.040	8.083	1.278	1.278	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.006	0.005	6.917	-1.407	-1.407	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.016	-0.001	7.822	1.937	1.937	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.056	-0.028	10.159	-0.260	-0.260	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.008	0.010	4.658	-1.167	-1.095	-0.001	-0.012	-0.058	0.000
29	A	29	VAL	0	0.007	0.010	6.417	1.158	1.158	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.045	-0.011	9.282	-0.371	-0.371	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.023	-0.012	11.554	1.199	1.199	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.860	-0.931	13.991	16.935	16.935	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.054	-0.039	16.096	-1.316	-1.316	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.009	0.010	15.432	1.454	1.454	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.004	-0.007	16.451	-1.449	-1.449	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.002	0.012	17.117	1.113	1.113	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.006	-0.002	17.342	-0.868	-0.868	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.816	0.903	20.147	-11.308	-11.308	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.013	-0.001	21.448	0.446	0.446	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.020	0.011	23.473	-0.043	-0.043	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.007	-0.005	26.510	0.190	0.190	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.031	0.020	28.041	0.140	0.140	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.899	0.953	28.221	-10.150	-10.150	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.045	0.026	25.572	0.083	0.083	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.914	0.977	15.574	-18.251	-18.251	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.828	-0.894	22.934	11.352	11.352	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.003	-0.008	22.007	0.523	0.523	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.019	-0.006	22.484	-0.628	-0.628	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.015	-0.024	22.496	-0.662	-0.662	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.008	-0.004	20.756	0.685	0.685	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.005	0.005	20.310	-0.799	-0.799	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.025	0.019	20.257	0.849	0.849	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.080	0.034	18.855	-0.245	-0.245	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.011	0.000	21.383	-0.232	-0.232	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.027	0.018	24.300	-0.386	-0.386	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.034	-0.011	25.660	-0.224	-0.224	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.013	-0.008	25.155	0.448	0.448	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.035	-0.008	25.677	-0.848	-0.848	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.026	0.014	25.873	0.592	0.592	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.061	0.034	27.324	-0.302	-0.302	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.821	-0.927	28.984	9.482	9.482	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.038	-0.007	30.644	-0.190	-0.190	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.006	-0.005	27.745	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.889	0.957	31.200	-9.759	-9.759	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.011	0.001	32.738	-0.276	-0.276	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.724	0.832	31.729	-9.950	-9.950	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.006	-0.013	26.570	0.171	0.171	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.037	-0.017	27.850	-0.328	-0.328	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.011	0.006	20.353	0.287	0.287	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.032	-0.017	22.991	-0.465	-0.465	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.908	0.932	19.405	-14.358	-14.358	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.836	-0.890	20.343	13.110	13.110	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.030	-0.006	18.727	0.474	0.474	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.008	0.010	18.317	0.533	0.533	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.815	0.899	17.145	-13.504	-13.504	0.000	0.000	0.000	0.000
76	A	76	ASN	0	0.003	0.004	13.374	0.216	0.216	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.007	0.006	14.542	1.014	1.014	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.018	0.002	16.381	-0.952	-0.952	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.048	-0.045	18.661	0.306	0.306	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.007	-0.009	21.624	-0.208	-0.208	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.018	-0.011	23.531	0.204	0.204	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.024	-0.006	25.464	0.056	0.056	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.077	0.038	28.833	-0.045	-0.045	0.000	0.000	0.000	0.000
84	A	82	SER	0	0.022	0.007	32.641	-0.081	-0.081	0.000	0.000	0.000	0.000
85	A	82	LEU	0	-0.005	0.018	29.400	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	83	LYS	1	0.864	0.916	33.284	-9.133	-9.133	0.000	0.000	0.000	0.000
87	A	84	PRO	0	0.059	0.024	33.124	0.317	0.317	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.853	-0.915	32.721	9.101	9.101	0.000	0.000	0.000	0.000
89	A	86	ASP	-1	-0.777	-0.854	29.196	10.572	10.572	0.000	0.000	0.000	0.000
90	A	87	THR	0	-0.006	0.020	27.985	0.492	0.492	0.000	0.000	0.000	0.000
91	A	88	ALA	0	-0.021	-0.020	24.684	-0.103	-0.103	0.000	0.000	0.000	0.000
92	A	89	VAL	0	-0.006	0.009	19.339	0.068	0.068	0.000	0.000	0.000	0.000
93	A	90	TYR	0	-0.031	-0.047	20.314	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	91	TYR	0	-0.002	-0.003	14.966	0.067	0.067	0.000	0.000	0.000	0.000
95	A	93	TYR	0	-0.060	-0.054	12.445	0.820	0.820	0.000	0.000	0.000	0.000
96	A	94	ALA	0	0.042	0.004	10.492	-1.834	-1.834	0.000	0.000	0.000	0.000
97	A	95	PRO	0	-0.016	0.001	10.462	2.806	2.806	0.000	0.000	0.000	0.000
98	A	96	MET	0	-0.055	-0.031	11.203	-0.697	-0.697	0.000	0.000	0.000	0.000
99	A	97	ILE	0	0.047	0.020	7.323	-1.383	-1.383	0.000	0.000	0.000	0.000
100	A	98	TYR	0	-0.028	-0.016	7.715	3.023	3.023	0.000	0.000	0.000	0.000
101	A	99	TYR	0	0.053	0.009	2.412	-5.223	-4.484	7.141	-4.274	-3.606	-0.007
102	A	100	GLY	0	0.008	0.024	5.668	1.299	1.299	0.000	0.000	0.000	0.000
103	A	100	GLY	0	-0.008	-0.007	6.632	-0.324	-0.324	0.000	0.000	0.000	0.000
104	A	100	ARG	1	0.903	0.944	6.217	-45.660	-45.660	0.000	0.000	0.000	0.000
105	A	100	TYR	0	0.044	0.013	7.242	2.532	2.532	0.000	0.000	0.000	0.000
106	A	100	SER	0	-0.051	-0.019	5.963	0.604	0.604	0.000	0.000	0.000	0.000
107	A	101	ASP	-1	-0.804	-0.857	8.045	24.569	24.569	0.000	0.000	0.000	0.000
108	A	102	TYR	0	-0.071	-0.055	1.681	-30.822	-34.212	16.458	-7.641	-5.427	0.081
109	A	103	TRP	0	-0.009	-0.026	7.753	-5.835	-5.835	0.000	0.000	0.000	0.000
110	A	104	GLY	0	0.027	0.034	8.891	3.274	3.274	0.000	0.000	0.000	0.000
111	A	105	GLN	0	-0.034	-0.031	8.960	-3.135	-3.135	0.000	0.000	0.000	0.000
112	A	106	GLY	0	-0.004	0.007	13.049	-1.506	-1.506	0.000	0.000	0.000	0.000
113	A	107	THR	0	-0.054	-0.026	16.330	-0.390	-0.390	0.000	0.000	0.000	0.000
114	A	108	GLN	0	0.010	0.006	19.390	-0.620	-0.620	0.000	0.000	0.000	0.000
115	A	109	VAL	0	0.019	0.017	22.951	-0.103	-0.103	0.000	0.000	0.000	0.000
116	A	110	THR	0	-0.023	-0.023	25.802	-0.165	-0.165	0.000	0.000	0.000	0.000
117	A	111	VAL	0	0.028	0.019	29.370	-0.133	-0.133	0.000	0.000	0.000	0.000
118	A	112	SER	0	0.011	0.008	32.651	-0.141	-0.141	0.000	0.000	0.000	0.000

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