FMO DATABASE

FMODB ID: YVML2

Calculation Name: 2II7-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2II7

Chain ID: F

ChEMBL ID:

UniProt ID: Q8YSC3

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-622957.433929
FMO2-HF: Nuclear repulsion	587571.764391
FMO2-HF: Total energy	-35385.669538
FMO2-MP2: Total energy	-35489.77496

3D Structure Molmil

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(F:2:LEU)

Summations of interaction energy for fragment #1(F:2:LEU)

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.
-5.339	-1.451	0.921	-1.868	-2.939	-0.014

Interaction energy analysis for fragmet #1(F:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.014

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	F	4	ILE	0	0.001	-0.009	3.872	1.168	2.665	-0.018	-0.721	-0.758	0.002
4	F	5	GLY	0	0.014	0.013	6.796	-0.371	-0.371	0.000	0.000	0.000	0.000
5	F	6	ARG	1	0.859	0.925	10.316	-0.045	-0.045	0.000	0.000	0.000	0.000
6	F	7	THR	0	0.054	0.031	11.148	-0.075	-0.075	0.000	0.000	0.000	0.000
7	F	8	CYS	0	0.001	0.013	13.362	-0.072	-0.072	0.000	0.000	0.000	0.000
8	F	9	TRP	0	-0.054	-0.034	13.408	0.083	0.083	0.000	0.000	0.000	0.000
9	F	10	ALA	0	0.037	0.015	19.143	-0.021	-0.021	0.000	0.000	0.000	0.000
10	F	11	ILE	0	-0.048	-0.015	22.567	0.014	0.014	0.000	0.000	0.000	0.000
11	F	12	ALA	0	-0.039	-0.023	25.358	-0.008	-0.008	0.000	0.000	0.000	0.000
12	F	13	GLU	-1	-0.883	-0.938	28.615	0.024	0.024	0.000	0.000	0.000	0.000
13	F	14	GLY	0	0.001	-0.008	29.133	-0.004	-0.004	0.000	0.000	0.000	0.000
14	F	15	TYR	0	-0.009	-0.032	31.391	0.001	0.001	0.000	0.000	0.000	0.000
15	F	16	ILE	0	-0.025	-0.001	32.246	-0.004	-0.004	0.000	0.000	0.000	0.000
16	F	17	PRO	0	0.019	0.003	35.197	0.001	0.001	0.000	0.000	0.000	0.000
17	F	18	PRO	0	-0.060	-0.011	38.414	-0.005	-0.005	0.000	0.000	0.000	0.000
18	F	31	GLU	-1	-0.789	-0.880	28.413	-0.014	-0.014	0.000	0.000	0.000	0.000
19	F	32	THR	0	-0.057	-0.053	22.806	-0.016	-0.016	0.000	0.000	0.000	0.000
20	F	33	VAL	0	0.031	0.030	20.053	0.014	0.014	0.000	0.000	0.000	0.000
21	F	34	CYS	0	-0.028	-0.009	18.644	-0.030	-0.030	0.000	0.000	0.000	0.000
22	F	35	ILE	0	0.030	0.012	14.310	0.027	0.027	0.000	0.000	0.000	0.000
23	F	36	LEU	0	-0.018	-0.008	9.795	-0.038	-0.038	0.000	0.000	0.000	0.000
24	F	37	ASN	0	-0.014	-0.010	8.657	-0.120	-0.120	0.000	0.000	0.000	0.000
25	F	38	ALA	0	-0.019	-0.024	5.374	-0.066	-0.066	0.000	0.000	0.000	0.000
26	F	39	GLY	0	0.055	0.034	4.035	-1.089	-0.873	0.000	-0.053	-0.162	0.000
27	F	40	ASP	-1	-0.842	-0.929	2.536	-7.304	-5.321	0.941	-1.087	-1.837	-0.016
28	F	41	GLU	-1	-0.895	-0.933	5.378	-0.340	-0.271	-0.001	-0.001	-0.066	0.000
29	F	42	ASP	-1	-0.855	-0.930	8.803	-0.803	-0.803	0.000	0.000	0.000	0.000
30	F	43	ALA	0	0.014	0.025	11.597	0.068	0.068	0.000	0.000	0.000	0.000
31	F	44	HIS	0	0.024	0.002	13.006	0.079	0.079	0.000	0.000	0.000	0.000
32	F	45	VAL	0	-0.029	-0.010	15.977	0.043	0.043	0.000	0.000	0.000	0.000
33	F	46	GLU	-1	-0.823	-0.885	18.057	-0.119	-0.119	0.000	0.000	0.000	0.000
34	F	47	ILE	0	-0.006	-0.015	21.019	0.021	0.021	0.000	0.000	0.000	0.000
35	F	48	THR	0	-0.073	-0.021	23.484	-0.002	-0.002	0.000	0.000	0.000	0.000
36	F	49	ILE	0	0.018	0.011	26.655	0.009	0.009	0.000	0.000	0.000	0.000
37	F	50	TYR	0	-0.004	-0.007	26.901	0.000	0.000	0.000	0.000	0.000	0.000
38	F	51	TYR	0	0.040	0.008	31.909	-0.002	-0.002	0.000	0.000	0.000	0.000
39	F	52	SER	0	0.015	0.011	35.454	0.003	0.003	0.000	0.000	0.000	0.000
40	F	53	ASP	-1	-0.821	-0.894	38.240	0.000	0.000	0.000	0.000	0.000	0.000
41	F	54	LYS	1	0.769	0.870	37.615	0.007	0.007	0.000	0.000	0.000	0.000
42	F	55	GLU	-1	-0.889	-0.952	35.536	0.009	0.009	0.000	0.000	0.000	0.000
43	F	56	PRO	0	-0.036	-0.018	30.699	-0.004	-0.004	0.000	0.000	0.000	0.000
44	F	57	VAL	0	-0.025	0.004	31.584	-0.003	-0.003	0.000	0.000	0.000	0.000
45	F	58	GLY	0	0.013	-0.008	29.436	0.000	0.000	0.000	0.000	0.000	0.000
46	F	59	PRO	0	-0.027	-0.033	24.829	-0.003	-0.003	0.000	0.000	0.000	0.000
47	F	60	TYR	0	0.054	0.028	25.852	-0.008	-0.008	0.000	0.000	0.000	0.000
48	F	61	ARG	1	0.814	0.882	22.822	0.115	0.115	0.000	0.000	0.000	0.000
49	F	62	LEU	0	-0.024	-0.018	18.907	-0.006	-0.006	0.000	0.000	0.000	0.000
50	F	63	THR	0	0.018	0.014	15.787	0.009	0.009	0.000	0.000	0.000	0.000
51	F	64	VAL	0	-0.042	-0.026	13.168	0.033	0.033	0.000	0.000	0.000	0.000
52	F	65	PRO	0	0.025	0.002	12.968	-0.086	-0.086	0.000	0.000	0.000	0.000
53	F	66	ALA	0	0.020	0.019	7.721	-0.023	-0.023	0.000	0.000	0.000	0.000
54	F	67	ARG	1	0.755	0.875	4.606	2.439	2.562	-0.001	-0.006	-0.116	0.000
55	F	68	ARG	1	0.889	0.953	8.101	1.021	1.021	0.000	0.000	0.000	0.000
56	F	69	THR	0	-0.017	-0.013	11.580	0.004	0.004	0.000	0.000	0.000	0.000
57	F	70	LYS	1	0.877	0.926	14.051	0.289	0.289	0.000	0.000	0.000	0.000
58	F	71	HIS	0	0.035	0.020	17.436	0.005	0.005	0.000	0.000	0.000	0.000
59	F	72	VAL	0	-0.008	-0.008	20.197	-0.011	-0.011	0.000	0.000	0.000	0.000
60	F	73	ARG	1	0.869	0.929	22.954	0.109	0.109	0.000	0.000	0.000	0.000
61	F	74	PHE	0	0.040	0.005	25.779	-0.008	-0.008	0.000	0.000	0.000	0.000
62	F	75	ASN	0	-0.066	-0.022	28.578	-0.003	-0.003	0.000	0.000	0.000	0.000
63	F	76	ASP	-1	-0.792	-0.884	28.021	-0.100	-0.100	0.000	0.000	0.000	0.000
64	F	77	LEU	0	-0.059	-0.012	25.318	-0.010	-0.010	0.000	0.000	0.000	0.000
65	F	78	ASN	0	-0.053	-0.052	29.322	0.009	0.009	0.000	0.000	0.000	0.000
66	F	79	ASP	-1	-0.886	-0.926	29.245	-0.102	-0.102	0.000	0.000	0.000	0.000
67	F	80	PRO	0	-0.009	-0.015	29.063	-0.006	-0.006	0.000	0.000	0.000	0.000
68	F	81	ALA	0	0.002	-0.003	32.205	0.004	0.004	0.000	0.000	0.000	0.000
69	F	82	PRO	0	-0.018	0.000	33.128	-0.001	-0.001	0.000	0.000	0.000	0.000
70	F	83	ILE	0	0.003	0.027	30.142	0.004	0.004	0.000	0.000	0.000	0.000
71	F	84	PRO	0	-0.042	-0.020	34.280	-0.001	-0.001	0.000	0.000	0.000	0.000
72	F	85	HIS	0	-0.016	-0.022	35.813	-0.001	-0.001	0.000	0.000	0.000	0.000
73	F	86	ASP	-1	-0.891	-0.929	38.456	-0.008	-0.008	0.000	0.000	0.000	0.000
74	F	87	THR	0	-0.062	-0.028	37.620	0.003	0.003	0.000	0.000	0.000	0.000
75	F	88	ASP	-1	-0.900	-0.943	36.123	0.005	0.005	0.000	0.000	0.000	0.000
76	F	89	PHE	0	-0.097	-0.050	29.457	-0.002	-0.002	0.000	0.000	0.000	0.000
77	F	90	ALA	0	0.024	0.032	29.418	0.006	0.006	0.000	0.000	0.000	0.000
78	F	91	SER	0	-0.004	-0.016	25.661	-0.011	-0.011	0.000	0.000	0.000	0.000
79	F	92	VAL	0	-0.003	0.002	22.303	0.018	0.018	0.000	0.000	0.000	0.000
80	F	93	ILE	0	-0.005	-0.002	18.252	-0.022	-0.022	0.000	0.000	0.000	0.000
81	F	94	GLN	0	-0.006	-0.015	17.520	0.053	0.053	0.000	0.000	0.000	0.000
82	F	95	SER	0	-0.001	-0.011	12.398	-0.070	-0.070	0.000	0.000	0.000	0.000
83	F	96	ASN	0	-0.007	-0.009	12.293	0.129	0.129	0.000	0.000	0.000	0.000
84	F	97	VAL	0	0.008	0.013	8.110	0.068	0.068	0.000	0.000	0.000	0.000
85	F	98	PRO	0	-0.049	-0.032	6.941	-0.033	-0.033	0.000	0.000	0.000	0.000
86	F	99	ILE	0	0.014	0.025	8.682	-0.310	-0.310	0.000	0.000	0.000	0.000
87	F	100	VAL	0	0.012	-0.006	10.349	0.202	0.202	0.000	0.000	0.000	0.000
88	F	101	VAL	0	-0.008	-0.006	12.938	-0.093	-0.093	0.000	0.000	0.000	0.000
89	F	102	GLN	0	-0.037	-0.017	16.748	0.057	0.057	0.000	0.000	0.000	0.000
90	F	103	HIS	0	0.000	0.005	19.664	-0.019	-0.019	0.000	0.000	0.000	0.000
91	F	104	THR	0	0.021	0.012	23.153	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:2:LEU)