FMO DATABASE

FMODB ID: 6YG5Z

Calculation Name: 3MER-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MER

Chain ID: A

ChEMBL ID:

UniProt ID: P74712

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	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	173
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1737522.679866
FMO2-HF: Nuclear repulsion	1672174.087966
FMO2-HF: Total energy	-65348.591899
FMO2-MP2: Total energy	-65542.051688

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:16:GLU)

Summations of interaction energy for fragment #1(A:16:GLU)

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.
-11.095	-19.283	23.561	-7.298	-8.075	0.057

Interaction energy analysis for fragmet #1(A:16:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.932 / q_NPA : -0.947

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	18	ASN	0	0.007	-0.017	3.898	-1.180	0.112	-0.008	-0.607	-0.677	0.002
4	A	19	ASP	-1	-0.860	-0.934	6.220	34.119	34.119	0.000	0.000	0.000	0.000
5	A	20	PHE	0	-0.002	0.003	7.708	-1.472	-1.472	0.000	0.000	0.000	0.000
6	A	21	LEU	0	0.044	0.022	8.848	-1.109	-1.109	0.000	0.000	0.000	0.000
7	A	22	VAL	0	-0.027	-0.025	5.957	-1.130	-1.130	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.100	-0.046	9.204	-1.685	-1.685	0.000	0.000	0.000	0.000
9	A	24	VAL	0	0.015	-0.006	12.286	-1.418	-1.418	0.000	0.000	0.000	0.000
10	A	25	ALA	0	0.020	0.005	12.047	-1.009	-1.009	0.000	0.000	0.000	0.000
11	A	26	ASN	0	-0.050	-0.025	14.080	-0.782	-0.782	0.000	0.000	0.000	0.000
12	A	27	GLN	0	-0.042	-0.014	16.903	-0.539	-0.539	0.000	0.000	0.000	0.000
13	A	28	ILE	0	-0.020	0.006	14.970	-0.549	-0.549	0.000	0.000	0.000	0.000
14	A	29	PRO	0	0.051	0.038	19.117	0.306	0.306	0.000	0.000	0.000	0.000
15	A	30	GLN	0	-0.063	-0.048	19.625	-0.090	-0.090	0.000	0.000	0.000	0.000
16	A	31	GLY	0	0.076	0.034	20.140	-0.679	-0.679	0.000	0.000	0.000	0.000
17	A	32	LYS	1	0.808	0.923	19.742	-12.278	-12.278	0.000	0.000	0.000	0.000
18	A	33	ILE	0	0.016	0.009	15.003	-0.109	-0.109	0.000	0.000	0.000	0.000
19	A	34	LEU	0	0.000	0.008	17.939	0.165	0.165	0.000	0.000	0.000	0.000
20	A	35	CYS	0	-0.061	-0.028	13.511	0.771	0.771	0.000	0.000	0.000	0.000
21	A	36	LEU	0	0.021	0.006	15.580	-0.210	-0.210	0.000	0.000	0.000	0.000
22	A	37	ALA	0	0.023	-0.007	15.567	0.595	0.595	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.838	-0.918	10.135	25.142	25.142	0.000	0.000	0.000	0.000
24	A	39	GLY	0	0.024	0.012	10.748	1.896	1.896	0.000	0.000	0.000	0.000
25	A	40	GLU	-1	-0.881	-0.939	5.918	40.323	40.323	0.000	0.000	0.000	0.000
26	A	41	GLY	0	0.029	0.012	9.562	0.338	0.338	0.000	0.000	0.000	0.000
27	A	42	ARG	1	0.825	0.878	1.843	-93.241	-102.721	23.569	-6.691	-7.398	0.055
28	A	43	ASN	0	0.022	0.012	5.484	2.865	2.865	0.000	0.000	0.000	0.000
29	A	44	ALA	0	0.036	0.013	7.843	-0.957	-0.957	0.000	0.000	0.000	0.000
30	A	45	CYS	0	-0.014	-0.011	7.249	-1.696	-1.696	0.000	0.000	0.000	0.000
31	A	46	PHE	0	-0.009	0.018	5.774	1.020	1.020	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.059	0.033	7.562	-1.447	-1.447	0.000	0.000	0.000	0.000
33	A	48	ALA	0	0.035	0.018	11.230	-1.284	-1.284	0.000	0.000	0.000	0.000
34	A	49	SER	0	-0.104	-0.062	9.352	0.064	0.064	0.000	0.000	0.000	0.000
35	A	50	LEU	0	-0.018	-0.006	10.627	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	51	GLY	0	-0.001	0.013	13.723	-1.131	-1.131	0.000	0.000	0.000	0.000
37	A	52	TYR	0	-0.042	-0.019	13.971	-0.689	-0.689	0.000	0.000	0.000	0.000
38	A	53	GLU	-1	-0.862	-0.938	15.936	13.658	13.658	0.000	0.000	0.000	0.000
39	A	54	VAL	0	-0.016	-0.012	12.865	-0.410	-0.410	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.051	-0.032	16.070	-0.471	-0.471	0.000	0.000	0.000	0.000
41	A	56	ALA	0	-0.003	0.002	14.153	0.240	0.240	0.000	0.000	0.000	0.000
42	A	57	VAL	0	-0.002	-0.013	15.969	-0.571	-0.571	0.000	0.000	0.000	0.000
43	A	58	ASP	-1	-0.759	-0.865	16.076	17.267	17.267	0.000	0.000	0.000	0.000
44	A	59	GLN	0	0.022	-0.013	18.236	-1.209	-1.209	0.000	0.000	0.000	0.000
45	A	60	SER	0	-0.062	-0.038	16.418	-0.316	-0.316	0.000	0.000	0.000	0.000
46	A	61	SER	0	0.031	0.001	17.978	0.570	0.570	0.000	0.000	0.000	0.000
47	A	62	VAL	0	-0.008	-0.003	16.588	0.169	0.169	0.000	0.000	0.000	0.000
48	A	63	GLY	0	0.045	0.039	14.069	0.858	0.858	0.000	0.000	0.000	0.000
49	A	64	LEU	0	0.035	0.011	13.942	1.029	1.029	0.000	0.000	0.000	0.000
50	A	65	ALA	0	-0.016	-0.006	15.687	0.253	0.253	0.000	0.000	0.000	0.000
51	A	66	LYS	1	0.814	0.889	10.494	-25.802	-25.802	0.000	0.000	0.000	0.000
52	A	67	ALA	0	0.061	0.040	11.020	1.607	1.607	0.000	0.000	0.000	0.000
53	A	68	LYS	1	0.813	0.895	12.105	-16.402	-16.402	0.000	0.000	0.000	0.000
54	A	69	GLN	0	-0.031	-0.020	13.904	-0.055	-0.055	0.000	0.000	0.000	0.000
55	A	70	LEU	0	0.022	0.015	5.967	0.411	0.411	0.000	0.000	0.000	0.000
56	A	71	ALA	0	0.009	-0.005	10.016	1.042	1.042	0.000	0.000	0.000	0.000
57	A	72	GLN	0	-0.065	-0.022	11.965	-0.361	-0.361	0.000	0.000	0.000	0.000
58	A	73	GLU	-1	-0.831	-0.904	10.269	26.225	26.225	0.000	0.000	0.000	0.000
59	A	74	LYS	1	0.837	0.920	6.071	-32.866	-32.866	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.005	0.011	10.557	-0.535	-0.535	0.000	0.000	0.000	0.000
61	A	76	VAL	0	-0.021	0.004	10.869	-1.162	-1.162	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.907	0.945	13.923	-14.292	-14.292	0.000	0.000	0.000	0.000
63	A	78	ILE	0	-0.002	0.002	14.495	-0.944	-0.944	0.000	0.000	0.000	0.000
64	A	79	THR	0	0.084	0.032	12.357	0.890	0.890	0.000	0.000	0.000	0.000
65	A	80	THR	0	-0.044	-0.008	15.246	-0.344	-0.344	0.000	0.000	0.000	0.000
66	A	81	VAL	0	0.030	0.026	16.511	0.117	0.117	0.000	0.000	0.000	0.000
67	A	82	GLN	0	-0.012	-0.008	18.679	-1.075	-1.075	0.000	0.000	0.000	0.000
68	A	83	SER	0	-0.035	-0.017	21.307	-0.402	-0.402	0.000	0.000	0.000	0.000
69	A	84	ASN	0	0.023	-0.002	21.723	0.290	0.290	0.000	0.000	0.000	0.000
70	A	85	LEU	0	0.012	0.006	19.461	-0.118	-0.118	0.000	0.000	0.000	0.000
71	A	86	ALA	0	-0.050	-0.013	23.655	-0.222	-0.222	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.961	-0.974	26.878	9.157	9.157	0.000	0.000	0.000	0.000
73	A	88	PHE	0	0.007	0.013	22.719	0.162	0.162	0.000	0.000	0.000	0.000
74	A	89	ASP	-1	-0.968	-0.998	27.343	9.728	9.728	0.000	0.000	0.000	0.000
75	A	90	ILE	0	-0.018	-0.003	23.791	0.318	0.318	0.000	0.000	0.000	0.000
76	A	91	VAL	0	0.010	0.008	27.233	-0.249	-0.249	0.000	0.000	0.000	0.000
77	A	92	ALA	0	0.029	-0.004	28.372	0.302	0.302	0.000	0.000	0.000	0.000
78	A	93	ASP	-1	-0.852	-0.933	29.262	9.674	9.674	0.000	0.000	0.000	0.000
79	A	94	ALA	0	-0.015	0.003	27.109	-0.078	-0.078	0.000	0.000	0.000	0.000
80	A	95	TRP	0	-0.031	-0.026	20.393	0.595	0.595	0.000	0.000	0.000	0.000
81	A	96	GLU	-1	-0.818	-0.914	21.424	11.390	11.390	0.000	0.000	0.000	0.000
82	A	97	GLY	0	0.021	0.006	19.024	0.154	0.154	0.000	0.000	0.000	0.000
83	A	98	ILE	0	-0.060	-0.023	18.726	0.106	0.106	0.000	0.000	0.000	0.000
84	A	99	VAL	0	0.019	0.007	12.701	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	100	SER	0	0.013	-0.005	16.027	-0.384	-0.384	0.000	0.000	0.000	0.000
86	A	101	ILE	0	-0.005	-0.005	9.964	-0.208	-0.208	0.000	0.000	0.000	0.000
87	A	102	PHE	0	-0.003	-0.013	10.387	0.315	0.315	0.000	0.000	0.000	0.000
88	A	103	CYS	0	-0.030	0.009	14.079	-0.595	-0.595	0.000	0.000	0.000	0.000
89	A	104	HIS	0	-0.057	-0.025	16.331	-0.076	-0.076	0.000	0.000	0.000	0.000
90	A	105	LEU	0	0.018	0.002	19.327	-0.181	-0.181	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.025	0.019	22.801	-0.067	-0.067	0.000	0.000	0.000	0.000
92	A	107	SER	0	0.048	-0.013	26.415	0.136	0.136	0.000	0.000	0.000	0.000
93	A	108	SER	0	-0.038	-0.018	28.812	-0.124	-0.124	0.000	0.000	0.000	0.000
94	A	109	LEU	0	-0.047	-0.019	25.178	-0.161	-0.161	0.000	0.000	0.000	0.000
95	A	110	ARG	1	0.785	0.851	23.698	-11.069	-11.069	0.000	0.000	0.000	0.000
96	A	111	GLN	0	0.016	-0.011	26.680	0.004	0.004	0.000	0.000	0.000	0.000
97	A	112	GLN	0	-0.034	0.002	29.378	-0.309	-0.309	0.000	0.000	0.000	0.000
98	A	113	LEU	0	0.018	0.004	22.741	-0.040	-0.040	0.000	0.000	0.000	0.000
99	A	114	TYR	0	0.025	0.002	20.905	0.084	0.084	0.000	0.000	0.000	0.000
100	A	115	PRO	0	0.063	0.024	26.687	0.029	0.029	0.000	0.000	0.000	0.000
101	A	116	LYS	1	0.879	0.964	27.792	-10.134	-10.134	0.000	0.000	0.000	0.000
102	A	117	VAL	0	0.008	0.003	22.948	0.036	0.036	0.000	0.000	0.000	0.000
103	A	118	TYR	0	0.025	0.014	25.697	0.082	0.082	0.000	0.000	0.000	0.000
104	A	119	GLN	0	-0.056	-0.033	27.884	-0.331	-0.331	0.000	0.000	0.000	0.000
105	A	120	GLY	0	0.014	0.016	26.689	-0.151	-0.151	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.035	-0.012	22.732	0.114	0.114	0.000	0.000	0.000	0.000
107	A	122	LYS	1	0.805	0.920	25.643	-10.800	-10.800	0.000	0.000	0.000	0.000
108	A	123	PRO	0	-0.025	-0.020	27.112	0.230	0.230	0.000	0.000	0.000	0.000
109	A	124	GLY	0	0.074	0.065	27.220	0.146	0.146	0.000	0.000	0.000	0.000
110	A	125	GLY	0	-0.002	-0.012	23.479	0.471	0.471	0.000	0.000	0.000	0.000
111	A	126	VAL	0	-0.044	-0.026	19.282	-0.323	-0.323	0.000	0.000	0.000	0.000
112	A	127	PHE	0	0.005	0.001	20.288	0.542	0.542	0.000	0.000	0.000	0.000
113	A	128	ILE	0	0.003	0.002	13.580	0.030	0.030	0.000	0.000	0.000	0.000
114	A	129	LEU	0	-0.014	-0.004	16.475	0.245	0.245	0.000	0.000	0.000	0.000
115	A	130	GLU	-1	-0.774	-0.888	11.028	21.403	21.403	0.000	0.000	0.000	0.000
116	A	131	GLY	0	0.028	0.027	14.304	0.467	0.467	0.000	0.000	0.000	0.000
117	A	132	PHE	0	-0.026	-0.015	13.644	-0.205	-0.205	0.000	0.000	0.000	0.000
118	A	133	ALA	0	0.032	0.025	17.543	-0.446	-0.446	0.000	0.000	0.000	0.000
119	A	134	PRO	0	0.024	0.007	20.857	0.126	0.126	0.000	0.000	0.000	0.000
120	A	135	GLU	-1	-0.772	-0.897	22.698	11.400	11.400	0.000	0.000	0.000	0.000
121	A	136	GLN	0	-0.013	-0.016	17.123	0.032	0.032	0.000	0.000	0.000	0.000
122	A	137	LEU	0	-0.034	-0.018	21.063	0.141	0.141	0.000	0.000	0.000	0.000
123	A	138	GLN	0	-0.065	-0.014	23.859	-0.693	-0.693	0.000	0.000	0.000	0.000
124	A	139	TYR	0	-0.142	-0.097	19.520	0.058	0.058	0.000	0.000	0.000	0.000
125	A	140	ASN	0	-0.004	-0.014	19.726	-0.164	-0.164	0.000	0.000	0.000	0.000
126	A	141	THR	0	-0.023	-0.031	14.873	-0.151	-0.151	0.000	0.000	0.000	0.000
127	A	142	GLY	0	0.025	0.025	14.369	1.236	1.236	0.000	0.000	0.000	0.000
128	A	143	GLY	0	0.061	0.037	16.001	-0.417	-0.417	0.000	0.000	0.000	0.000
129	A	144	PRO	0	-0.038	-0.006	17.726	-0.273	-0.273	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.877	0.906	21.033	-10.570	-10.570	0.000	0.000	0.000	0.000
131	A	146	ASP	-1	-0.858	-0.924	24.127	9.778	9.778	0.000	0.000	0.000	0.000
132	A	147	LEU	0	0.080	0.043	25.117	0.315	0.315	0.000	0.000	0.000	0.000
133	A	148	ASP	-1	-0.799	-0.856	26.848	10.203	10.203	0.000	0.000	0.000	0.000
134	A	149	LEU	0	-0.040	-0.019	22.184	0.091	0.091	0.000	0.000	0.000	0.000
135	A	150	LEU	0	-0.072	-0.018	20.449	0.712	0.712	0.000	0.000	0.000	0.000
136	A	151	PRO	0	0.050	0.029	22.983	-0.368	-0.368	0.000	0.000	0.000	0.000
137	A	152	LYS	1	0.858	0.913	23.656	-10.762	-10.762	0.000	0.000	0.000	0.000
138	A	153	LEU	0	0.035	0.024	21.517	0.007	0.007	0.000	0.000	0.000	0.000
139	A	154	GLU	-1	-0.810	-0.925	24.198	10.602	10.602	0.000	0.000	0.000	0.000
140	A	155	THR	0	-0.056	-0.015	27.112	-0.190	-0.190	0.000	0.000	0.000	0.000
141	A	156	LEU	0	0.028	0.024	21.306	-0.137	-0.137	0.000	0.000	0.000	0.000
142	A	157	GLN	0	-0.008	-0.009	25.410	-0.216	-0.216	0.000	0.000	0.000	0.000
143	A	158	SER	0	-0.096	-0.061	27.172	-0.305	-0.305	0.000	0.000	0.000	0.000
144	A	159	GLU	-1	-0.811	-0.881	26.622	10.607	10.607	0.000	0.000	0.000	0.000
145	A	160	LEU	0	-0.060	-0.024	24.191	0.028	0.028	0.000	0.000	0.000	0.000
146	A	161	PRO	0	0.022	0.017	28.419	0.108	0.108	0.000	0.000	0.000	0.000
147	A	162	SER	0	-0.068	-0.033	31.139	-0.100	-0.100	0.000	0.000	0.000	0.000
148	A	163	LEU	0	-0.026	0.000	24.559	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	164	ASN	0	-0.014	-0.006	27.639	-0.200	-0.200	0.000	0.000	0.000	0.000
150	A	165	TRP	0	0.012	0.001	22.548	0.699	0.699	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.011	0.007	22.439	-0.074	-0.074	0.000	0.000	0.000	0.000
152	A	167	ILE	0	-0.020	-0.006	18.208	0.216	0.216	0.000	0.000	0.000	0.000
153	A	168	ALA	0	0.008	0.000	21.717	0.023	0.023	0.000	0.000	0.000	0.000
154	A	169	ASN	0	-0.025	-0.007	17.066	-0.909	-0.909	0.000	0.000	0.000	0.000
155	A	170	ASN	0	0.063	0.018	20.013	0.000	0.000	0.000	0.000	0.000	0.000
156	A	171	LEU	0	-0.052	-0.023	15.885	-0.244	-0.244	0.000	0.000	0.000	0.000
157	A	172	GLU	-1	-0.827	-0.898	18.949	12.625	12.625	0.000	0.000	0.000	0.000
158	A	173	ARG	1	0.924	0.978	11.083	-20.694	-20.694	0.000	0.000	0.000	0.000
159	A	174	ASN	0	0.051	0.020	18.207	0.697	0.697	0.000	0.000	0.000	0.000
160	A	184	LYS	1	0.868	0.937	15.616	-13.152	-13.152	0.000	0.000	0.000	0.000
161	A	185	ALA	0	-0.020	-0.004	14.579	0.605	0.605	0.000	0.000	0.000	0.000
162	A	186	ALA	0	0.035	0.032	16.591	-0.247	-0.247	0.000	0.000	0.000	0.000
163	A	187	LEU	0	-0.043	-0.026	12.839	0.345	0.345	0.000	0.000	0.000	0.000
164	A	188	ILE	0	-0.007	-0.003	17.100	-0.753	-0.753	0.000	0.000	0.000	0.000
165	A	189	GLN	0	-0.034	-0.024	13.155	0.136	0.136	0.000	0.000	0.000	0.000
166	A	190	LEU	0	-0.043	-0.010	17.426	-0.785	-0.785	0.000	0.000	0.000	0.000
167	A	191	LEU	0	0.015	0.003	17.532	0.775	0.775	0.000	0.000	0.000	0.000
168	A	192	GLY	0	0.025	-0.003	20.134	-0.522	-0.522	0.000	0.000	0.000	0.000
169	A	193	GLN	0	-0.005	0.005	23.366	0.069	0.069	0.000	0.000	0.000	0.000
170	A	194	LYS	1	0.827	0.899	25.028	-10.505	-10.505	0.000	0.000	0.000	0.000
171	A	195	LEU	0	-0.010	-0.010	28.021	0.022	0.022	0.000	0.000	0.000	0.000
172	A	196	GLU	-1	-0.867	-0.936	29.623	10.078	10.078	0.000	0.000	0.000	0.000
173	A	197	HIS	0	-0.052	-0.022	32.952	-0.354	-0.354	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLU)