FMO DATABASE

FMODB ID: ZV8YN

Calculation Name: 3F7E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3F7E

Chain ID: A

ChEMBL ID:

UniProt ID: A0QXP8

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	OptH
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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1114253.273638
FMO2-HF: Nuclear repulsion	1064144.188633
FMO2-HF: Total energy	-50109.085005
FMO2-MP2: Total energy	-50258.0307

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(A:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-4.517	-2.29	13.061	-4.435	-10.851	-0.03

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.026

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	4	VAL	0	0.036	0.020	3.071	-2.569	0.038	0.119	-1.314	-1.412	-0.005
4	A	5	PRO	0	-0.029	-0.021	4.823	0.515	0.515	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.891	-0.905	7.450	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	7	GLY	0	0.045	-0.013	10.424	0.025	0.025	0.000	0.000	0.000	0.000
7	A	8	TYR	0	-0.052	-0.049	9.717	0.069	0.069	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.808	-0.892	9.136	-0.899	-0.899	0.000	0.000	0.000	0.000
9	A	10	SER	0	0.060	0.022	10.530	0.011	0.011	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.078	-0.040	12.703	0.041	0.041	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.046	-0.022	7.590	0.023	0.023	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.880	-0.939	12.083	-0.393	-0.393	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.878	0.945	14.718	0.334	0.334	0.000	0.000	0.000	0.000
14	A	15	PRO	0	-0.001	0.028	16.930	-0.044	-0.044	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.009	0.000	16.732	0.031	0.031	0.000	0.000	0.000	0.000
16	A	17	TYR	0	-0.008	-0.001	17.790	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.021	0.012	15.255	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	19	HIS	0	-0.042	-0.030	15.993	0.034	0.034	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.012	-0.008	12.764	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.001	-0.013	14.430	0.054	0.054	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.023	-0.014	14.522	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.045	0.013	16.521	0.018	0.018	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.905	0.966	19.053	0.158	0.158	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.013	-0.011	22.428	0.002	0.002	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.873	-0.918	24.137	-0.127	-0.127	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.004	0.007	22.280	0.007	0.007	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.046	-0.024	22.647	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.019	0.005	19.529	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.082	-0.038	19.849	0.033	0.033	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.045	0.017	17.685	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.022	-0.027	19.080	0.022	0.022	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.063	0.051	19.032	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	34	MET	0	-0.074	-0.040	17.363	0.040	0.040	0.000	0.000	0.000	0.000
34	A	35	TRP	0	0.043	0.044	18.680	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.011	-0.009	12.786	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.015	0.008	14.775	0.041	0.041	0.000	0.000	0.000	0.000
37	A	38	TRP	0	-0.042	-0.037	5.036	-0.093	-0.093	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.807	-0.891	10.591	-0.595	-0.595	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.049	0.036	9.293	0.131	0.131	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-1.014	-0.998	6.198	-0.455	-0.455	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.079	-0.053	6.015	-0.614	-0.614	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.012	-0.004	8.272	0.156	0.156	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.861	0.930	10.480	0.502	0.502	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.035	0.006	11.845	0.036	0.036	0.000	0.000	0.000	0.000
45	A	46	THR	0	0.042	0.041	16.876	0.027	0.027	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.029	-0.017	17.215	0.026	0.026	0.000	0.000	0.000	0.000
47	A	48	THR	0	0.016	0.010	21.978	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	THR	0	0.002	-0.007	24.327	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.931	0.969	25.801	0.114	0.114	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.915	0.957	25.034	0.165	0.165	0.000	0.000	0.000	0.000
51	A	52	GLN	0	0.019	-0.009	24.302	0.007	0.007	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.922	0.970	20.156	0.237	0.237	0.000	0.000	0.000	0.000
53	A	54	TYR	0	0.105	0.069	20.121	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.886	0.928	21.219	0.136	0.136	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.010	0.007	19.618	0.025	0.025	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.030	0.020	16.001	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.849	0.932	17.779	0.170	0.170	0.000	0.000	0.000	0.000
58	A	59	ALA	0	-0.024	0.000	20.435	0.013	0.013	0.000	0.000	0.000	0.000
59	A	60	ASN	0	0.010	0.002	15.747	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	61	PRO	0	0.051	0.035	13.324	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.003	0.010	11.304	-0.089	-0.089	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.027	-0.017	10.151	0.069	0.069	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.019	-0.013	9.903	-0.090	-0.090	0.000	0.000	0.000	0.000
64	A	65	MET	0	-0.018	0.011	10.161	0.103	0.103	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.005	0.023	11.148	-0.052	-0.052	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.019	0.008	12.346	0.034	0.034	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.017	-0.004	15.021	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.814	-0.911	17.696	-0.233	-0.233	0.000	0.000	0.000	0.000
69	A	70	PRO	0	-0.065	-0.028	19.524	0.010	0.010	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.873	-0.934	22.870	-0.155	-0.155	0.000	0.000	0.000	0.000
71	A	72	ASN	0	-0.031	-0.018	21.760	0.019	0.019	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.035	0.012	20.798	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.010	-0.024	19.866	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.840	0.947	14.992	0.297	0.297	0.000	0.000	0.000	0.000
75	A	76	TYR	0	0.019	0.000	13.450	0.005	0.005	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.026	-0.022	7.713	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.964	-0.971	10.164	-0.378	-0.378	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.008	0.000	5.280	-0.090	-0.090	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.958	0.970	6.073	0.666	0.666	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.086	0.036	5.041	-0.523	-0.457	-0.001	-0.006	-0.058	0.000
81	A	82	LEU	0	-0.030	-0.004	6.606	0.258	0.258	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.052	-0.035	9.301	-0.088	-0.088	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.844	-0.904	9.273	-0.618	-0.618	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.843	-0.920	12.198	-0.173	-0.173	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.107	-0.065	15.191	-0.034	-0.034	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.032	0.028	17.835	0.030	0.030	0.000	0.000	0.000	0.000
87	A	88	PRO	0	-0.031	-0.018	20.402	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.799	-0.917	23.033	-0.184	-0.184	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.030	0.019	24.979	0.003	0.003	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.046	-0.034	28.317	0.004	0.004	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.006	-0.001	26.902	0.005	0.005	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.043	0.029	26.069	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.015	-0.020	17.341	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	95	TYR	0	-0.023	-0.030	22.469	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	96	LEU	0	0.006	-0.001	24.152	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.954	0.985	21.821	0.178	0.178	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.047	-0.012	17.739	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	99	ASN	0	0.048	0.000	21.586	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.942	-0.962	24.657	-0.157	-0.157	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.831	0.914	16.263	0.386	0.386	0.000	0.000	0.000	0.000
101	A	102	TYR	0	-0.096	-0.079	17.824	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.925	-0.940	23.488	-0.153	-0.153	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.030	-0.013	26.690	0.008	0.008	0.000	0.000	0.000	0.000
104	A	105	PRO	0	0.002	-0.021	28.015	0.007	0.007	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.113	-0.035	27.096	0.008	0.008	0.000	0.000	0.000	0.000
106	A	107	THR	0	0.032	-0.016	29.189	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.896	-0.920	31.332	-0.102	-0.102	0.000	0.000	0.000	0.000
108	A	109	PRO	0	-0.062	-0.028	30.543	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	110	PRO	0	0.021	0.019	28.253	0.007	0.007	0.000	0.000	0.000	0.000
110	A	111	ALA	0	0.044	0.004	31.525	0.004	0.004	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.868	-0.910	29.247	-0.147	-0.147	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.994	0.987	29.208	0.095	0.095	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.012	0.011	29.087	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.888	-0.939	28.722	-0.117	-0.117	0.000	0.000	0.000	0.000
115	A	116	ARG	1	0.770	0.863	24.151	0.172	0.172	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.018	-0.009	20.850	0.009	0.009	0.000	0.000	0.000	0.000
117	A	118	ILE	0	0.008	0.002	16.719	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	119	ILE	0	-0.042	-0.019	14.327	0.014	0.014	0.000	0.000	0.000	0.000
119	A	120	VAL	0	0.054	0.020	11.085	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.016	-0.010	7.781	0.047	0.047	0.000	0.000	0.000	0.000
121	A	122	ARG	1	0.927	0.943	4.382	0.812	0.927	-0.001	-0.006	-0.109	0.000
122	A	123	PRO	0	-0.018	-0.007	2.378	-0.226	-0.192	1.836	-0.502	-1.367	0.000
123	A	124	THR	0	-0.035	-0.035	2.530	-1.690	-1.646	3.862	-1.157	-2.748	-0.014
124	A	125	ALA	0	-0.045	-0.026	2.391	-0.968	0.253	1.210	-0.689	-1.743	-0.005
125	A	126	PHE	0	0.042	0.022	1.905	1.164	-0.741	6.037	-0.761	-3.371	-0.006
126	A	127	SER	0	-0.027	-0.009	5.239	0.221	0.266	-0.001	0.000	-0.043	0.000
127	A	128	LYS	1	0.967	0.996	8.673	0.179	0.179	0.000	0.000	0.000	0.000
128	A	129	GLN	0	0.001	0.014	11.469	0.031	0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)