FMO DATABASE

FMODB ID: 4JY2N

Calculation Name: 3FFM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FFM

Chain ID: A

ChEMBL ID:

UniProt ID: O95257

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1255051.10973
FMO2-HF: Nuclear repulsion	1199524.787464
FMO2-HF: Total energy	-55526.322266
FMO2-MP2: Total energy	-55685.022829

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:15:SER)

Summations of interaction energy for fragment #1(A:15: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.
-4.016	1.154	1.756	-2.786	-4.141	0.01

Interaction energy analysis for fragmet #1(A:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.040

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	17	ALA	0	0.029	0.007	3.682	-0.658	1.340	-0.003	-1.129	-0.867	0.005
4	A	18	ARG	1	0.829	0.905	6.337	0.810	0.810	0.000	0.000	0.000	0.000
5	A	19	MET	0	0.008	0.018	2.545	-0.676	0.107	0.363	-0.309	-0.837	-0.002
6	A	20	GLN	0	-0.059	-0.043	2.756	-1.551	0.740	1.397	-1.337	-2.351	0.007
7	A	21	GLY	0	-0.002	0.001	4.629	-0.284	-0.186	-0.001	-0.011	-0.086	0.000
8	A	22	ALA	0	0.074	0.037	7.530	0.011	0.011	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.066	0.031	6.841	-0.050	-0.050	0.000	0.000	0.000	0.000
10	A	24	LYS	1	0.834	0.907	5.566	-2.776	-2.776	0.000	0.000	0.000	0.000
11	A	25	ALA	0	0.041	0.026	10.243	-0.117	-0.117	0.000	0.000	0.000	0.000
12	A	26	LEU	0	0.056	0.033	11.475	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	27	HIS	0	-0.029	-0.019	12.451	-0.040	-0.040	0.000	0.000	0.000	0.000
14	A	28	GLU	-1	-0.848	-0.921	13.480	0.343	0.343	0.000	0.000	0.000	0.000
15	A	29	LEU	0	0.019	0.021	16.011	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	30	LEU	0	0.018	0.016	15.751	-0.035	-0.035	0.000	0.000	0.000	0.000
17	A	31	LEU	0	0.019	0.020	18.069	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	32	SER	0	-0.104	-0.048	20.311	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	33	ALA	0	0.091	0.033	21.688	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	34	GLN	0	-0.036	-0.034	22.946	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	35	ARG	1	0.820	0.883	21.259	-0.229	-0.229	0.000	0.000	0.000	0.000
22	A	36	GLN	0	-0.052	-0.034	25.354	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	37	GLY	0	-0.018	0.005	28.038	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	38	CYS	0	-0.071	-0.005	26.020	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	39	LEU	0	0.010	0.006	21.612	0.007	0.007	0.000	0.000	0.000	0.000
26	A	40	THR	0	-0.004	0.003	25.265	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	41	ALA	0	0.011	-0.012	24.751	0.013	0.013	0.000	0.000	0.000	0.000
28	A	42	GLY	0	0.060	0.039	25.203	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	43	VAL	0	-0.018	-0.014	25.915	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	44	TYR	0	-0.030	-0.014	27.828	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.763	-0.876	29.402	0.091	0.091	0.000	0.000	0.000	0.000
32	A	46	SER	0	0.014	-0.001	26.110	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	47	ALA	0	0.024	0.003	28.308	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	48	LYS	1	0.746	0.860	30.964	-0.096	-0.096	0.000	0.000	0.000	0.000
35	A	49	VAL	0	0.021	0.011	29.396	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	50	LEU	0	0.024	0.008	27.023	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	51	ASN	0	-0.067	-0.025	31.279	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	52	VAL	0	-0.113	-0.060	34.491	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	53	ASP	-1	-0.871	-0.924	33.489	0.061	0.061	0.000	0.000	0.000	0.000
40	A	54	PRO	0	-0.005	0.001	30.565	0.007	0.007	0.000	0.000	0.000	0.000
41	A	55	ASP	-1	-0.911	-0.952	29.814	0.048	0.048	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.031	-0.018	30.017	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	57	VAL	0	-0.038	-0.006	25.025	0.012	0.012	0.000	0.000	0.000	0.000
44	A	58	THR	0	-0.033	-0.030	23.568	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	59	PHE	0	-0.004	-0.016	14.849	0.011	0.011	0.000	0.000	0.000	0.000
46	A	60	CYS	0	-0.018	0.002	19.564	0.000	0.000	0.000	0.000	0.000	0.000
47	A	61	VAL	0	-0.008	-0.007	15.580	0.018	0.018	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.016	0.011	17.877	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.019	-0.023	16.996	0.039	0.039	0.000	0.000	0.000	0.000
50	A	64	ALA	0	0.008	-0.013	17.341	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	65	GLY	0	-0.007	-0.004	17.096	0.044	0.044	0.000	0.000	0.000	0.000
52	A	66	GLU	-1	-0.919	-0.963	18.339	0.237	0.237	0.000	0.000	0.000	0.000
53	A	67	GLU	-1	-0.961	-0.973	20.708	0.152	0.152	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.810	-0.881	21.749	0.189	0.189	0.000	0.000	0.000	0.000
55	A	69	GLU	-1	-1.004	-1.000	22.005	0.139	0.139	0.000	0.000	0.000	0.000
56	A	70	GLY	0	0.001	-0.009	24.358	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	71	ASP	-1	-0.880	-0.929	26.808	0.101	0.101	0.000	0.000	0.000	0.000
58	A	72	ILE	0	0.006	-0.021	27.373	0.002	0.002	0.000	0.000	0.000	0.000
59	A	73	ALA	0	-0.020	-0.005	29.532	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	74	LEU	0	0.006	0.012	23.436	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	75	GLN	0	0.006	0.007	23.349	0.004	0.004	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.035	0.000	26.154	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	77	HIS	0	0.016	-0.001	27.466	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	78	PHE	0	-0.001	-0.006	21.399	0.000	0.000	0.000	0.000	0.000	0.000
65	A	79	THR	0	-0.025	-0.019	24.439	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	80	LEU	0	-0.046	-0.025	26.365	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	81	ILE	0	0.024	0.014	23.524	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	82	GLN	0	0.030	0.015	21.450	0.006	0.006	0.000	0.000	0.000	0.000
69	A	83	ALA	0	-0.024	-0.012	23.954	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	84	PHE	0	0.017	0.004	27.229	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	85	CYS	0	-0.036	-0.022	23.006	0.001	0.001	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.090	-0.047	23.367	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.958	-0.977	25.090	0.014	0.014	0.000	0.000	0.000	0.000
74	A	88	ASN	0	-0.080	-0.045	27.379	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.937	-0.953	24.683	0.018	0.018	0.000	0.000	0.000	0.000
76	A	90	ILE	0	-0.033	0.002	22.482	0.005	0.005	0.000	0.000	0.000	0.000
77	A	91	ASP	-1	-0.774	-0.863	18.104	0.053	0.053	0.000	0.000	0.000	0.000
78	A	92	ILE	0	-0.007	-0.016	18.353	0.020	0.020	0.000	0.000	0.000	0.000
79	A	93	VAL	0	-0.024	-0.010	13.278	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	94	ARG	1	0.828	0.908	12.452	-0.143	-0.143	0.000	0.000	0.000	0.000
81	A	95	VAL	0	-0.018	-0.020	12.154	0.055	0.055	0.000	0.000	0.000	0.000
82	A	96	GLY	0	0.008	0.000	12.045	-0.046	-0.046	0.000	0.000	0.000	0.000
83	A	97	ASP	-1	-0.839	-0.894	12.335	0.532	0.532	0.000	0.000	0.000	0.000
84	A	98	VAL	0	0.077	0.025	14.138	0.021	0.021	0.000	0.000	0.000	0.000
85	A	99	GLN	0	-0.015	-0.006	15.609	-0.057	-0.057	0.000	0.000	0.000	0.000
86	A	100	ARG	1	0.818	0.899	11.839	-0.689	-0.689	0.000	0.000	0.000	0.000
87	A	101	LEU	0	0.047	0.015	15.337	0.007	0.007	0.000	0.000	0.000	0.000
88	A	102	ALA	0	0.048	0.020	16.704	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	103	ALA	0	-0.052	-0.020	17.312	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	104	ILE	0	-0.103	-0.047	14.989	0.024	0.024	0.000	0.000	0.000	0.000
91	A	105	VAL	0	-0.004	-0.012	18.505	-0.030	-0.030	0.000	0.000	0.000	0.000
92	A	106	GLY	0	0.060	0.049	21.550	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	107	ALA	0	-0.069	-0.027	22.006	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	108	GLY	0	-0.041	-0.017	23.902	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	109	GLU	-1	-0.977	-0.998	27.628	0.138	0.138	0.000	0.000	0.000	0.000
96	A	110	GLU	-1	-0.875	-0.936	25.225	0.207	0.207	0.000	0.000	0.000	0.000
97	A	111	ALA	0	-0.021	-0.003	29.699	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	112	GLY	0	-0.085	-0.050	31.811	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	113	ALA	0	0.053	0.012	26.861	0.008	0.008	0.000	0.000	0.000	0.000
100	A	114	PRO	0	-0.020	-0.010	24.821	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	115	GLY	0	-0.025	0.000	26.428	0.007	0.007	0.000	0.000	0.000	0.000
102	A	116	ASP	-1	-0.825	-0.904	25.769	0.158	0.158	0.000	0.000	0.000	0.000
103	A	117	LEU	0	0.016	0.011	21.171	0.002	0.002	0.000	0.000	0.000	0.000
104	A	118	HIS	1	0.775	0.861	21.302	-0.168	-0.168	0.000	0.000	0.000	0.000
105	A	119	CYS	0	-0.023	-0.016	21.680	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.032	0.007	19.889	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	121	LEU	0	0.024	0.013	21.765	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	122	ILE	0	-0.023	-0.014	20.007	0.012	0.012	0.000	0.000	0.000	0.000
109	A	123	SER	0	0.030	0.009	23.755	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	124	ASN	0	-0.017	-0.007	26.464	0.015	0.015	0.000	0.000	0.000	0.000
111	A	125	PRO	0	-0.038	-0.030	27.222	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	126	ASN	0	-0.113	-0.046	30.422	0.000	0.000	0.000	0.000	0.000	0.000
113	A	127	GLU	-1	-0.894	-0.953	31.710	0.048	0.048	0.000	0.000	0.000	0.000
114	A	128	ASP	-1	-0.922	-0.951	31.951	0.049	0.049	0.000	0.000	0.000	0.000
115	A	129	ALA	0	0.021	0.006	27.962	0.006	0.006	0.000	0.000	0.000	0.000
116	A	130	TRP	0	0.045	0.019	22.450	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	131	LYS	1	0.957	0.987	24.171	-0.023	-0.023	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.777	-0.879	19.684	0.186	0.186	0.000	0.000	0.000	0.000
119	A	133	PRO	0	-0.023	-0.027	18.812	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	134	ALA	0	-0.025	-0.031	15.627	0.002	0.002	0.000	0.000	0.000	0.000
121	A	135	LEU	0	0.031	0.023	15.733	0.016	0.016	0.000	0.000	0.000	0.000
122	A	136	GLU	-1	-0.950	-0.968	17.682	0.016	0.016	0.000	0.000	0.000	0.000
123	A	137	LYS	1	0.724	0.851	11.906	-0.344	-0.344	0.000	0.000	0.000	0.000
124	A	138	LEU	0	-0.027	-0.017	11.640	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	139	SER	0	0.010	0.010	14.217	-0.026	-0.026	0.000	0.000	0.000	0.000
126	A	140	LEU	0	0.024	0.014	14.682	-0.024	-0.024	0.000	0.000	0.000	0.000
127	A	141	PHE	0	-0.014	-0.008	7.382	-0.037	-0.037	0.000	0.000	0.000	0.000
128	A	142	CYS	0	-0.011	-0.016	12.721	-0.027	-0.027	0.000	0.000	0.000	0.000
129	A	143	GLU	-1	-0.920	-0.948	15.165	-0.085	-0.085	0.000	0.000	0.000	0.000
130	A	144	GLU	-1	-0.869	-0.921	12.183	-0.310	-0.310	0.000	0.000	0.000	0.000
131	A	145	SER	0	-0.016	-0.019	11.844	-0.045	-0.045	0.000	0.000	0.000	0.000
132	A	146	ARG	1	0.878	0.932	14.198	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.054	-0.033	17.500	0.005	0.005	0.000	0.000	0.000	0.000
134	A	148	VAL	0	-0.115	-0.057	14.233	-0.017	-0.017	0.000	0.000	0.000	0.000
135	A	149	ASN	0	-0.044	-0.024	17.675	0.008	0.008	0.000	0.000	0.000	0.000
136	A	150	ASP	-1	-0.827	-0.897	12.981	0.041	0.041	0.000	0.000	0.000	0.000
137	A	151	TRP	0	-0.001	-0.029	15.878	0.007	0.007	0.000	0.000	0.000	0.000
138	A	152	VAL	0	0.027	0.036	16.575	0.010	0.010	0.000	0.000	0.000	0.000
139	A	153	PRO	0	-0.013	0.019	11.283	0.013	0.013	0.000	0.000	0.000	0.000
140	A	154	SER	0	-0.017	-0.013	9.556	0.033	0.033	0.000	0.000	0.000	0.000
141	A	155	ILE	0	-0.002	-0.002	7.993	-0.028	-0.028	0.000	0.000	0.000	0.000
142	A	156	THR	0	-0.045	-0.022	5.216	-0.176	-0.176	0.000	0.000	0.000	0.000
143	A	157	LEU	0	0.032	0.020	6.915	0.450	0.450	0.000	0.000	0.000	0.000
144	A	158	PRO	0	-0.071	-0.026	7.516	0.359	0.359	0.000	0.000	0.000	0.000
145	A	159	GLU	-1	-0.880	-0.941	8.500	0.466	0.466	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:SER)