FMO DATABASE

FMODB ID: 4JL1N

Calculation Name: 1VHF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0E6

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	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	101
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-812138.693508
FMO2-HF: Nuclear repulsion	770272.00362
FMO2-HF: Total energy	-41866.689889
FMO2-MP2: Total energy	-41991.056624

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-43.499	-49.298	33.974	-16.885	-11.291	-0.12

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.062

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	2	ILE	0	0.023	0.016	3.809	-0.281	2.846	-0.011	-1.672	-1.444	0.008
4	A	3	LEU	0	-0.003	-0.007	6.102	0.104	0.104	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.004	0.012	9.705	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	5	TYR	0	0.009	-0.001	12.402	0.110	0.110	0.000	0.000	0.000	0.000
7	A	6	SER	0	-0.025	-0.031	15.720	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.059	-0.043	19.192	0.024	0.024	0.000	0.000	0.000	0.000
9	A	8	PHE	0	-0.018	-0.022	19.924	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.056	0.035	25.552	0.013	0.013	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.040	-0.040	28.354	0.003	0.003	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.869	-0.933	27.330	-0.082	-0.082	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.852	-0.927	26.879	-0.103	-0.103	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.847	0.909	25.754	0.168	0.168	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.052	0.034	22.961	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.016	-0.012	22.257	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.913	-0.924	23.271	-0.185	-0.185	0.000	0.000	0.000	0.000
18	A	17	ILE	0	0.011	-0.003	19.700	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	18	GLY	0	0.047	0.024	18.602	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.840	0.913	18.855	0.114	0.114	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.923	0.961	20.652	0.191	0.191	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.002	-0.002	15.661	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.012	-0.001	15.542	-0.033	-0.033	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.904	-0.945	17.327	-0.161	-0.161	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.769	0.861	17.457	0.358	0.358	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.920	0.968	14.397	0.143	0.143	0.000	0.000	0.000	0.000
27	A	26	LEU	0	0.005	0.004	12.362	-0.062	-0.062	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.040	-0.002	10.886	-0.233	-0.233	0.000	0.000	0.000	0.000
29	A	28	ALA	0	0.019	0.010	10.252	0.101	0.101	0.000	0.000	0.000	0.000
30	A	29	CYM	-1	-0.770	-0.806	12.132	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	30	PHE	0	0.000	0.005	13.870	-0.090	-0.090	0.000	0.000	0.000	0.000
32	A	31	ASN	0	-0.013	0.006	16.324	0.040	0.040	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.015	0.004	18.256	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	33	PHE	0	-0.031	-0.019	18.974	0.026	0.026	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.818	-0.890	24.011	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.061	-0.034	23.854	0.012	0.012	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.835	0.915	27.203	0.049	0.049	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.049	-0.057	27.395	0.003	0.003	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.028	0.006	29.143	0.008	0.008	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.093	-0.058	29.295	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	40	TRP	0	-0.011	0.001	31.282	0.008	0.008	0.000	0.000	0.000	0.000
42	A	41	TRP	0	0.028	-0.006	32.953	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.937	0.972	35.408	0.109	0.109	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.000	0.003	37.730	0.005	0.005	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.932	-0.955	38.529	-0.064	-0.064	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.031	-0.013	34.719	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	46	VAL	0	-0.022	-0.009	33.820	0.006	0.006	0.000	0.000	0.000	0.000
48	A	47	GLN	0	-0.026	-0.021	33.823	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.842	-0.905	31.179	-0.106	-0.106	0.000	0.000	0.000	0.000
50	A	49	LYN	0	-0.037	-0.010	31.207	0.009	0.009	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.746	-0.806	26.636	-0.164	-0.164	0.000	0.000	0.000	0.000
52	A	51	TRP	0	0.008	0.001	24.678	0.012	0.012	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.009	0.010	20.740	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	53	ALA	0	-0.002	-0.015	19.049	0.023	0.023	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.023	0.003	13.785	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.002	-0.022	13.312	0.071	0.071	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.764	0.812	9.689	-0.036	-0.036	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.014	-0.029	7.375	0.134	0.134	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.001	-0.013	3.134	-0.207	0.174	0.014	-0.154	-0.241	0.000
60	A	59	GLU	-1	-0.804	-0.872	1.648	-40.790	-51.933	33.233	-14.043	-8.047	-0.124
61	A	60	GLU	-1	-0.883	-0.933	3.127	-2.869	-1.831	0.058	-0.483	-0.614	-0.004
62	A	61	LYS	1	0.823	0.909	6.190	1.634	1.634	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.844	-0.882	7.537	-1.605	-1.605	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.880	0.920	9.228	1.103	1.103	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.822	-0.911	11.878	-0.696	-0.696	0.000	0.000	0.000	0.000
66	A	65	LEU	0	0.018	0.020	10.931	0.167	0.167	0.000	0.000	0.000	0.000
67	A	66	TYR	0	0.003	-0.039	11.975	0.240	0.240	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.870	-0.905	15.150	-0.438	-0.438	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.830	-0.907	16.782	-0.295	-0.295	0.000	0.000	0.000	0.000
70	A	69	LEU	0	0.015	0.008	16.475	0.065	0.065	0.000	0.000	0.000	0.000
71	A	70	ARG	1	0.873	0.923	18.648	0.400	0.400	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.839	0.910	20.590	0.473	0.473	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.049	-0.011	20.358	0.040	0.040	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.016	0.015	21.300	0.039	0.039	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.030	-0.008	24.279	0.012	0.012	0.000	0.000	0.000	0.000
76	A	75	TYR	0	-0.049	-0.066	25.400	0.016	0.016	0.000	0.000	0.000	0.000
77	A	76	GLU	-1	-0.916	-0.955	26.391	-0.212	-0.212	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.042	-0.030	24.966	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	78	PRO	0	-0.023	0.002	21.837	0.012	0.012	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.039	0.033	20.689	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	80	ILE	0	-0.015	-0.008	15.547	0.000	0.000	0.000	0.000	0.000	0.000
82	A	81	PHE	0	-0.016	-0.003	14.323	0.001	0.001	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.007	-0.021	8.153	0.135	0.135	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.059	-0.007	10.046	0.073	0.073	0.000	0.000	0.000	0.000
85	A	84	LYN	0	0.055	0.029	5.208	-0.264	-0.264	0.000	0.000	0.000	0.000
86	A	85	VAL	0	-0.051	-0.027	4.905	-0.484	-0.415	-0.001	-0.007	-0.061	0.000
87	A	86	GLU	-1	-0.888	-0.948	5.157	1.885	1.915	-0.001	-0.001	-0.028	0.000
88	A	87	ASN	0	-0.076	-0.047	6.405	0.067	0.067	0.000	0.000	0.000	0.000
89	A	88	VAL	0	0.017	0.004	4.442	-0.191	-0.140	-0.001	-0.010	-0.040	0.000
90	A	89	LEU	0	-0.016	0.008	7.249	0.060	0.060	0.000	0.000	0.000	0.000
91	A	90	THR	0	0.050	0.020	8.964	0.115	0.115	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.859	-0.949	9.442	0.758	0.758	0.000	0.000	0.000	0.000
93	A	92	TYR	0	-0.024	-0.010	9.671	-0.065	-0.065	0.000	0.000	0.000	0.000
94	A	93	MET	0	0.023	0.010	3.346	0.266	0.857	0.684	-0.507	-0.768	0.000
95	A	94	ASN	0	-0.016	-0.017	6.720	0.195	0.195	0.000	0.000	0.000	0.000
96	A	95	TRP	0	0.020	0.016	9.065	-0.120	-0.120	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.018	-0.006	6.475	-0.099	-0.099	0.000	0.000	0.000	0.000
98	A	97	ARG	1	0.928	0.960	4.430	-2.977	-2.920	-0.001	-0.008	-0.048	0.000
99	A	98	GLU	-1	-0.973	-0.985	7.596	0.293	0.293	0.000	0.000	0.000	0.000
100	A	99	SER	0	-0.095	-0.035	11.090	-0.081	-0.081	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.074	-0.026	7.471	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)