FMO DATABASE

FMODB ID: 175LZ

Calculation Name: 1F3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F3V

Chain ID: A

ChEMBL ID:

UniProt ID: Q15628

Base Structure: X-ray

Registration Date: 2023-06-22

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

DOI:

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1540325.947663
FMO2-HF: Nuclear repulsion	1478481.626903
FMO2-HF: Total energy	-61844.32076
FMO2-MP2: Total energy	-62023.792516

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:8:HIS)

Summations of interaction energy for fragment #1(A:8:HIS)

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.
-7.336	-2.074	0.225	-2.429	-3.059	0.008

Interaction energy analysis for fragmet #1(A:8:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.016

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	10	GLU	-1	-0.858	-0.930	3.473	-5.487	-2.235	0.031	-1.692	-1.591	0.010
4	A	11	TRP	0	-0.053	-0.024	3.007	-0.146	1.244	0.186	-0.606	-0.971	-0.003
5	A	12	VAL	0	0.029	0.007	3.835	-1.606	-1.306	0.002	-0.034	-0.268	0.000
6	A	13	GLY	0	0.041	0.017	6.102	1.530	1.530	0.000	0.000	0.000	0.000
7	A	14	SER	0	-0.067	-0.056	8.852	-0.647	-0.647	0.000	0.000	0.000	0.000
8	A	15	ALA	0	-0.003	-0.013	12.198	0.235	0.235	0.000	0.000	0.000	0.000
9	A	16	TYR	0	-0.006	0.006	15.869	-0.172	-0.172	0.000	0.000	0.000	0.000
10	A	17	LEU	0	0.002	0.002	19.341	0.059	0.059	0.000	0.000	0.000	0.000
11	A	18	PHE	0	0.002	0.000	22.173	-0.055	-0.055	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.005	-0.012	25.581	0.016	0.016	0.000	0.000	0.000	0.000
13	A	20	GLU	-1	-0.802	-0.889	28.699	0.162	0.162	0.000	0.000	0.000	0.000
14	A	21	SER	0	0.028	0.014	32.393	0.011	0.011	0.000	0.000	0.000	0.000
15	A	22	SER	0	-0.005	-0.019	35.911	0.004	0.004	0.000	0.000	0.000	0.000
16	A	23	LEU	0	-0.063	-0.029	38.289	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.855	-0.923	40.427	0.096	0.096	0.000	0.000	0.000	0.000
18	A	25	LYS	1	0.903	0.944	41.171	-0.048	-0.048	0.000	0.000	0.000	0.000
19	A	26	VAL	0	-0.073	-0.030	37.297	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	27	VAL	0	0.027	0.010	36.568	0.011	0.011	0.000	0.000	0.000	0.000
21	A	28	LEU	0	0.040	0.010	31.465	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	29	SER	0	0.040	0.012	31.642	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	30	ASP	-1	-0.921	-0.954	33.121	0.013	0.013	0.000	0.000	0.000	0.000
24	A	31	ALA	0	-0.026	-0.009	34.880	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	32	TYR	0	-0.015	-0.033	26.564	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	33	ALA	0	-0.011	-0.008	32.656	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	34	HIS	0	0.006	0.010	34.808	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	35	PRO	0	0.028	0.004	36.350	0.000	0.000	0.000	0.000	0.000	0.000
29	A	36	GLN	0	-0.052	-0.014	36.751	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	37	GLN	0	-0.006	-0.011	36.570	0.010	0.010	0.000	0.000	0.000	0.000
31	A	38	LYS	1	0.890	0.954	29.590	0.099	0.099	0.000	0.000	0.000	0.000
32	A	39	VAL	0	0.034	0.013	31.513	0.001	0.001	0.000	0.000	0.000	0.000
33	A	40	ALA	0	-0.024	-0.001	31.843	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	41	VAL	0	0.023	0.003	29.890	0.010	0.010	0.000	0.000	0.000	0.000
35	A	42	TYR	0	-0.027	-0.034	23.919	0.021	0.021	0.000	0.000	0.000	0.000
36	A	43	ARG	1	0.955	0.972	27.662	0.071	0.071	0.000	0.000	0.000	0.000
37	A	44	ALA	0	-0.008	-0.003	29.411	0.008	0.008	0.000	0.000	0.000	0.000
38	A	45	LEU	0	0.018	0.012	25.526	0.023	0.023	0.000	0.000	0.000	0.000
39	A	46	GLN	0	-0.036	-0.036	24.499	0.038	0.038	0.000	0.000	0.000	0.000
40	A	47	ALA	0	-0.012	-0.008	25.188	0.013	0.013	0.000	0.000	0.000	0.000
41	A	48	ALA	0	0.004	0.002	26.941	0.013	0.013	0.000	0.000	0.000	0.000
42	A	49	LEU	0	0.014	0.003	20.616	0.038	0.038	0.000	0.000	0.000	0.000
43	A	50	ALA	0	-0.008	-0.001	22.110	0.027	0.027	0.000	0.000	0.000	0.000
44	A	51	GLU	-1	-0.852	-0.874	23.630	0.152	0.152	0.000	0.000	0.000	0.000
45	A	52	SER	0	-0.026	-0.025	24.607	0.020	0.020	0.000	0.000	0.000	0.000
46	A	53	GLY	0	0.041	0.012	20.644	0.047	0.047	0.000	0.000	0.000	0.000
47	A	54	GLY	0	-0.058	-0.050	18.270	0.078	0.078	0.000	0.000	0.000	0.000
48	A	55	SER	0	0.004	0.003	18.678	0.000	0.000	0.000	0.000	0.000	0.000
49	A	56	PRO	0	0.070	0.029	18.164	0.026	0.026	0.000	0.000	0.000	0.000
50	A	57	ASP	-1	-0.844	-0.911	16.790	-0.295	-0.295	0.000	0.000	0.000	0.000
51	A	58	VAL	0	-0.057	-0.036	13.241	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.042	-0.007	13.787	0.166	0.166	0.000	0.000	0.000	0.000
53	A	60	GLN	0	0.008	0.010	13.173	-0.141	-0.141	0.000	0.000	0.000	0.000
54	A	61	MET	0	0.004	0.015	16.183	0.046	0.046	0.000	0.000	0.000	0.000
55	A	62	LEU	0	-0.009	0.007	12.763	-0.067	-0.067	0.000	0.000	0.000	0.000
56	A	63	LYS	1	0.862	0.907	17.223	0.093	0.093	0.000	0.000	0.000	0.000
57	A	64	ILE	0	-0.012	0.005	20.536	0.059	0.059	0.000	0.000	0.000	0.000
58	A	65	HIS	0	-0.014	-0.002	19.836	-0.043	-0.043	0.000	0.000	0.000	0.000
59	A	66	ARG	1	0.895	0.929	25.264	0.016	0.016	0.000	0.000	0.000	0.000
60	A	67	SER	0	-0.032	-0.035	27.298	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	68	ASP	-1	-0.909	-0.928	29.589	0.094	0.094	0.000	0.000	0.000	0.000
62	A	69	PRO	0	0.020	0.013	33.084	0.012	0.012	0.000	0.000	0.000	0.000
63	A	70	GLN	0	-0.036	-0.037	29.166	0.003	0.003	0.000	0.000	0.000	0.000
64	A	71	LEU	0	-0.032	-0.001	27.425	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	72	ILE	0	0.013	0.008	22.099	0.034	0.034	0.000	0.000	0.000	0.000
66	A	73	VAL	0	-0.002	-0.004	20.343	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	74	GLN	0	0.002	0.009	14.371	0.036	0.036	0.000	0.000	0.000	0.000
68	A	75	LEU	0	-0.030	-0.022	16.188	-0.097	-0.097	0.000	0.000	0.000	0.000
69	A	76	ARG	1	0.900	0.939	7.392	1.213	1.213	0.000	0.000	0.000	0.000
70	A	77	PHE	0	-0.009	-0.013	10.725	-0.044	-0.044	0.000	0.000	0.000	0.000
71	A	78	CYS	0	-0.043	-0.010	9.136	0.050	0.050	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.060	0.024	7.614	-0.085	-0.085	0.000	0.000	0.000	0.000
73	A	80	ARG	1	0.795	0.850	7.338	-2.578	-2.578	0.000	0.000	0.000	0.000
74	A	81	GLN	0	0.062	0.029	9.046	-0.138	-0.138	0.000	0.000	0.000	0.000
75	A	82	PRO	0	-0.024	-0.013	11.347	-0.064	-0.064	0.000	0.000	0.000	0.000
76	A	83	CYS	0	-0.001	0.028	11.253	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	84	GLY	0	0.070	0.034	13.121	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.839	0.928	14.974	-0.457	-0.457	0.000	0.000	0.000	0.000
79	A	86	PHE	0	0.032	0.015	16.114	-0.075	-0.075	0.000	0.000	0.000	0.000
80	A	87	LEU	0	0.014	0.000	14.614	-0.052	-0.052	0.000	0.000	0.000	0.000
81	A	88	ARG	1	0.784	0.882	15.797	-0.919	-0.919	0.000	0.000	0.000	0.000
82	A	89	ALA	0	0.044	0.018	20.937	-0.042	-0.042	0.000	0.000	0.000	0.000
83	A	90	TYR	0	-0.061	-0.046	21.212	-0.063	-0.063	0.000	0.000	0.000	0.000
84	A	91	ARG	1	0.776	0.869	20.674	-0.711	-0.711	0.000	0.000	0.000	0.000
85	A	92	GLU	-1	-0.904	-0.931	24.219	0.466	0.466	0.000	0.000	0.000	0.000
86	A	93	GLY	0	-0.024	-0.004	26.216	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	94	ALA	0	-0.001	0.002	25.710	-0.031	-0.031	0.000	0.000	0.000	0.000
88	A	95	LEU	0	0.048	0.012	21.795	-0.033	-0.033	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.890	0.946	25.789	-0.271	-0.271	0.000	0.000	0.000	0.000
90	A	97	ALA	0	-0.013	-0.012	28.669	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	98	ALA	0	-0.004	-0.002	27.688	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	99	LEU	0	0.010	0.004	25.996	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	100	GLN	0	-0.008	-0.004	29.999	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	101	ARG	1	0.780	0.867	30.527	-0.153	-0.153	0.000	0.000	0.000	0.000
95	A	102	SER	0	-0.034	-0.024	30.080	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	103	LEU	0	0.049	0.005	30.638	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.025	0.006	34.343	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	105	ALA	0	0.004	0.000	36.637	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	106	ALA	0	-0.043	-0.021	34.617	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	107	LEU	0	-0.041	-0.013	35.310	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	108	ALA	0	-0.045	-0.014	38.809	0.002	0.002	0.000	0.000	0.000	0.000
102	A	109	GLN	0	0.010	0.010	40.949	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	110	HIS	0	0.024	0.018	41.592	0.002	0.002	0.000	0.000	0.000	0.000
104	A	111	SER	0	-0.022	-0.029	39.617	0.007	0.007	0.000	0.000	0.000	0.000
105	A	112	VAL	0	0.022	0.012	35.349	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	113	PRO	0	-0.008	0.009	35.896	0.008	0.008	0.000	0.000	0.000	0.000
107	A	114	LEU	0	0.016	0.008	30.856	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	115	GLN	0	-0.022	-0.003	31.663	0.014	0.014	0.000	0.000	0.000	0.000
109	A	116	LEU	0	-0.017	-0.024	25.910	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	117	GLU	-1	-0.789	-0.866	25.332	0.362	0.362	0.000	0.000	0.000	0.000
111	A	118	LEU	0	0.000	0.014	17.900	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	119	ARG	1	0.805	0.889	19.994	-0.370	-0.370	0.000	0.000	0.000	0.000
113	A	120	ALA	0	0.048	0.020	14.603	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	121	GLY	0	0.046	0.025	16.509	0.091	0.091	0.000	0.000	0.000	0.000
115	A	122	ALA	0	-0.036	-0.027	17.642	-0.075	-0.075	0.000	0.000	0.000	0.000
116	A	123	GLU	-1	-0.815	-0.889	17.113	1.019	1.019	0.000	0.000	0.000	0.000
117	A	124	ARG	1	0.803	0.870	19.351	-0.418	-0.418	0.000	0.000	0.000	0.000
118	A	125	LEU	0	0.056	0.014	15.968	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	126	ASP	-1	-0.717	-0.830	20.389	0.496	0.496	0.000	0.000	0.000	0.000
120	A	127	ALA	0	-0.049	-0.018	23.892	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	128	LEU	0	-0.017	-0.013	19.219	0.017	0.017	0.000	0.000	0.000	0.000
122	A	129	LEU	0	-0.006	0.002	20.778	0.063	0.063	0.000	0.000	0.000	0.000
123	A	130	ALA	0	-0.029	-0.009	21.899	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	131	ASP	-1	-0.873	-0.931	18.127	1.268	1.268	0.000	0.000	0.000	0.000
125	A	132	GLU	-1	-0.723	-0.855	16.006	1.008	1.008	0.000	0.000	0.000	0.000
126	A	133	GLU	-1	-0.774	-0.840	13.019	2.178	2.178	0.000	0.000	0.000	0.000
127	A	134	ARG	1	0.877	0.929	13.313	-0.831	-0.831	0.000	0.000	0.000	0.000
128	A	135	CYS	0	-0.036	-0.008	14.389	0.127	0.127	0.000	0.000	0.000	0.000
129	A	136	LEU	0	-0.001	-0.013	10.534	0.130	0.130	0.000	0.000	0.000	0.000
130	A	137	SER	0	-0.005	-0.005	9.822	0.580	0.580	0.000	0.000	0.000	0.000
131	A	138	CYS	0	-0.079	-0.037	10.571	0.283	0.283	0.000	0.000	0.000	0.000
132	A	139	ILE	0	0.004	-0.008	10.215	-0.043	-0.043	0.000	0.000	0.000	0.000
133	A	140	LEU	0	-0.050	-0.013	3.883	-0.490	-0.170	0.006	-0.097	-0.229	0.001
134	A	141	ALA	0	-0.009	-0.006	7.436	0.353	0.353	0.000	0.000	0.000	0.000
135	A	142	GLN	0	-0.071	-0.011	9.679	-0.629	-0.629	0.000	0.000	0.000	0.000
136	A	143	GLN	0	0.048	0.030	5.433	-0.966	-0.966	0.000	0.000	0.000	0.000
137	A	144	PRO	0	-0.038	-0.022	6.615	-0.308	-0.308	0.000	0.000	0.000	0.000
138	A	145	ASP	-1	-0.784	-0.868	8.659	-0.740	-0.740	0.000	0.000	0.000	0.000
139	A	146	ARG	1	0.795	0.897	11.244	0.149	0.149	0.000	0.000	0.000	0.000
140	A	147	LEU	0	0.030	0.012	12.133	-0.017	-0.017	0.000	0.000	0.000	0.000
141	A	148	ARG	1	0.788	0.884	14.369	0.395	0.395	0.000	0.000	0.000	0.000
142	A	149	ASP	-1	-0.814	-0.903	17.665	-0.303	-0.303	0.000	0.000	0.000	0.000
143	A	150	GLU	-1	-0.860	-0.940	20.459	-0.438	-0.438	0.000	0.000	0.000	0.000
144	A	151	GLU	-1	-0.790	-0.854	23.483	-0.086	-0.086	0.000	0.000	0.000	0.000
145	A	152	LEU	0	-0.032	-0.034	20.782	0.032	0.032	0.000	0.000	0.000	0.000
146	A	153	ALA	0	-0.021	-0.001	23.121	0.002	0.002	0.000	0.000	0.000	0.000
147	A	154	GLU	-1	-0.896	-0.952	24.752	-0.200	-0.200	0.000	0.000	0.000	0.000
148	A	155	LEU	0	-0.020	-0.016	26.972	0.023	0.023	0.000	0.000	0.000	0.000
149	A	156	GLU	-1	-0.775	-0.851	24.421	-0.166	-0.166	0.000	0.000	0.000	0.000
150	A	157	ASP	-1	-0.824	-0.894	27.429	-0.276	-0.276	0.000	0.000	0.000	0.000
151	A	158	ALA	0	-0.006	0.003	30.080	0.017	0.017	0.000	0.000	0.000	0.000
152	A	159	LEU	0	-0.050	-0.021	28.681	0.020	0.020	0.000	0.000	0.000	0.000
153	A	160	ARG	1	0.840	0.902	27.431	0.263	0.263	0.000	0.000	0.000	0.000
154	A	161	ASN	0	0.017	-0.011	32.521	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	162	LEU	0	0.004	0.012	35.458	0.009	0.009	0.000	0.000	0.000	0.000
156	A	163	LYS	1	0.901	0.955	34.637	0.111	0.111	0.000	0.000	0.000	0.000
157	A	164	CYS	0	-0.096	-0.055	35.993	0.000	0.000	0.000	0.000	0.000	0.000
158	A	165	GLY	0	-0.010	0.016	38.628	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:HIS)