FMO DATABASE

FMODB ID: 2NLGR

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	OptHSide
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	-1737828.289236
FMO2-HF: Nuclear repulsion	1672480.229995
FMO2-HF: Total energy	-65348.05924
FMO2-MP2: Total energy	-65541.619559

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.
-5.419	-12.573	22.339	-6.973	-8.213	0.061

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 : -0.937 / q_NPA : -0.953

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	0.026	-0.007	3.816	-1.347	0.101	-0.014	-0.661	-0.774	0.003
4	A	19	ASP	-1	-0.848	-0.930	6.123	35.809	35.809	0.000	0.000	0.000	0.000
5	A	20	PHE	0	0.001	0.001	7.721	-1.733	-1.733	0.000	0.000	0.000	0.000
6	A	21	LEU	0	0.030	0.013	8.567	-1.308	-1.308	0.000	0.000	0.000	0.000
7	A	22	VAL	0	-0.040	-0.027	6.162	-1.136	-1.136	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.122	-0.059	9.270	-1.679	-1.679	0.000	0.000	0.000	0.000
9	A	24	VAL	0	0.022	0.001	12.261	-1.456	-1.456	0.000	0.000	0.000	0.000
10	A	25	ALA	0	0.027	0.016	11.885	-1.033	-1.033	0.000	0.000	0.000	0.000
11	A	26	ASN	0	-0.046	-0.024	13.981	-0.619	-0.619	0.000	0.000	0.000	0.000
12	A	27	GLN	0	-0.050	-0.025	16.938	-0.515	-0.515	0.000	0.000	0.000	0.000
13	A	28	ILE	0	-0.034	0.000	14.769	-0.646	-0.646	0.000	0.000	0.000	0.000
14	A	29	PRO	0	0.061	0.055	18.859	0.440	0.440	0.000	0.000	0.000	0.000
15	A	30	GLN	0	-0.063	-0.050	19.479	-0.159	-0.159	0.000	0.000	0.000	0.000
16	A	31	GLY	0	0.090	0.041	19.730	-0.640	-0.640	0.000	0.000	0.000	0.000
17	A	32	LYS	1	0.829	0.927	19.230	-12.067	-12.067	0.000	0.000	0.000	0.000
18	A	33	ILE	0	0.026	0.014	14.768	-0.125	-0.125	0.000	0.000	0.000	0.000
19	A	34	LEU	0	-0.019	-0.003	17.076	0.328	0.328	0.000	0.000	0.000	0.000
20	A	35	CYS	0	-0.058	-0.023	13.225	0.527	0.527	0.000	0.000	0.000	0.000
21	A	36	LEU	0	0.029	0.005	15.284	-0.356	-0.356	0.000	0.000	0.000	0.000
22	A	37	ALA	0	0.032	0.000	15.634	0.585	0.585	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.823	-0.928	10.052	24.814	24.814	0.000	0.000	0.000	0.000
24	A	39	GLY	0	-0.023	-0.024	11.079	1.661	1.661	0.000	0.000	0.000	0.000
25	A	40	GLU	-1	-0.881	-0.930	5.583	40.992	40.992	0.000	0.000	0.000	0.000
26	A	41	GLY	0	0.101	0.055	8.864	-0.821	-0.821	0.000	0.000	0.000	0.000
27	A	42	ARG	1	0.807	0.867	1.859	-86.219	-94.816	22.354	-6.304	-7.453	0.058
28	A	43	ASN	0	0.022	0.013	5.124	2.288	2.283	-0.001	-0.008	0.014	0.000
29	A	44	ALA	0	0.059	0.035	7.250	-1.048	-1.048	0.000	0.000	0.000	0.000
30	A	45	CYS	0	-0.036	-0.018	7.011	-1.870	-1.870	0.000	0.000	0.000	0.000
31	A	46	PHE	0	-0.026	-0.015	5.156	0.111	0.111	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.055	0.039	7.064	-1.308	-1.308	0.000	0.000	0.000	0.000
33	A	48	ALA	0	0.024	0.017	10.638	-1.240	-1.240	0.000	0.000	0.000	0.000
34	A	49	SER	0	-0.089	-0.050	8.994	0.230	0.230	0.000	0.000	0.000	0.000
35	A	50	LEU	0	-0.029	-0.021	10.276	-0.242	-0.242	0.000	0.000	0.000	0.000
36	A	51	GLY	0	-0.010	0.015	13.310	-1.111	-1.111	0.000	0.000	0.000	0.000
37	A	52	TYR	0	-0.061	-0.026	13.594	-0.672	-0.672	0.000	0.000	0.000	0.000
38	A	53	GLU	-1	-0.881	-0.946	16.005	13.299	13.299	0.000	0.000	0.000	0.000
39	A	54	VAL	0	-0.027	-0.030	12.695	-0.378	-0.378	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.062	-0.032	15.810	-0.489	-0.489	0.000	0.000	0.000	0.000
41	A	56	ALA	0	0.009	0.015	13.404	0.060	0.060	0.000	0.000	0.000	0.000
42	A	57	VAL	0	-0.002	-0.010	15.263	-0.644	-0.644	0.000	0.000	0.000	0.000
43	A	58	ASP	-1	-0.798	-0.893	15.805	17.370	17.370	0.000	0.000	0.000	0.000
44	A	59	GLN	0	0.029	-0.006	17.934	-1.250	-1.250	0.000	0.000	0.000	0.000
45	A	60	SER	0	-0.070	-0.027	16.648	-0.425	-0.425	0.000	0.000	0.000	0.000
46	A	61	SER	0	0.043	0.003	18.074	0.526	0.526	0.000	0.000	0.000	0.000
47	A	62	VAL	0	-0.014	-0.012	16.597	0.163	0.163	0.000	0.000	0.000	0.000
48	A	63	GLY	0	0.039	0.027	14.196	0.848	0.848	0.000	0.000	0.000	0.000
49	A	64	LEU	0	0.045	0.023	13.991	1.039	1.039	0.000	0.000	0.000	0.000
50	A	65	ALA	0	-0.031	-0.012	15.671	0.230	0.230	0.000	0.000	0.000	0.000
51	A	66	LYS	1	0.835	0.913	10.567	-25.170	-25.170	0.000	0.000	0.000	0.000
52	A	67	ALA	0	0.074	0.043	10.968	1.640	1.640	0.000	0.000	0.000	0.000
53	A	68	LYS	1	0.844	0.917	11.769	-15.920	-15.920	0.000	0.000	0.000	0.000
54	A	69	GLN	0	-0.039	-0.030	13.807	0.355	0.355	0.000	0.000	0.000	0.000
55	A	70	LEU	0	0.047	0.047	5.697	0.512	0.512	0.000	0.000	0.000	0.000
56	A	71	ALA	0	0.024	-0.001	9.978	0.838	0.838	0.000	0.000	0.000	0.000
57	A	72	GLN	0	-0.082	-0.045	11.639	-0.324	-0.324	0.000	0.000	0.000	0.000
58	A	73	GLU	-1	-0.880	-0.924	10.354	26.053	26.053	0.000	0.000	0.000	0.000
59	A	74	LYS	1	0.866	0.934	5.806	-34.281	-34.281	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.005	0.017	10.212	-0.487	-0.487	0.000	0.000	0.000	0.000
61	A	76	VAL	0	-0.018	0.007	10.641	-0.908	-0.908	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.892	0.935	13.654	-14.306	-14.306	0.000	0.000	0.000	0.000
63	A	78	ILE	0	-0.004	0.006	14.070	-0.931	-0.931	0.000	0.000	0.000	0.000
64	A	79	THR	0	0.081	0.026	12.321	0.729	0.729	0.000	0.000	0.000	0.000
65	A	80	THR	0	-0.053	-0.012	15.214	-0.243	-0.243	0.000	0.000	0.000	0.000
66	A	81	VAL	0	0.038	0.033	16.579	0.156	0.156	0.000	0.000	0.000	0.000
67	A	82	GLN	0	-0.032	-0.023	18.518	-1.086	-1.086	0.000	0.000	0.000	0.000
68	A	83	SER	0	0.010	0.005	21.061	-0.200	-0.200	0.000	0.000	0.000	0.000
69	A	84	ASN	0	0.010	0.005	21.357	0.367	0.367	0.000	0.000	0.000	0.000
70	A	85	LEU	0	0.033	-0.002	19.729	-0.086	-0.086	0.000	0.000	0.000	0.000
71	A	86	ALA	0	-0.045	-0.013	23.817	-0.268	-0.268	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.956	-0.968	27.067	9.159	9.159	0.000	0.000	0.000	0.000
73	A	88	PHE	0	-0.010	0.008	22.193	0.115	0.115	0.000	0.000	0.000	0.000
74	A	89	ASP	-1	-0.956	-0.989	27.003	9.722	9.722	0.000	0.000	0.000	0.000
75	A	90	ILE	0	-0.020	0.000	23.509	0.210	0.210	0.000	0.000	0.000	0.000
76	A	91	VAL	0	0.011	0.002	26.778	-0.278	-0.278	0.000	0.000	0.000	0.000
77	A	92	ALA	0	0.018	-0.006	27.874	0.276	0.276	0.000	0.000	0.000	0.000
78	A	93	ASP	-1	-0.850	-0.928	28.723	9.651	9.651	0.000	0.000	0.000	0.000
79	A	94	ALA	0	-0.007	0.001	26.545	-0.125	-0.125	0.000	0.000	0.000	0.000
80	A	95	TRP	0	-0.059	-0.037	19.884	0.567	0.567	0.000	0.000	0.000	0.000
81	A	96	GLU	-1	-0.804	-0.904	20.993	11.417	11.417	0.000	0.000	0.000	0.000
82	A	97	GLY	0	0.017	0.002	18.615	0.199	0.199	0.000	0.000	0.000	0.000
83	A	98	ILE	0	-0.053	-0.012	18.516	0.107	0.107	0.000	0.000	0.000	0.000
84	A	99	VAL	0	0.008	-0.004	12.597	-0.057	-0.057	0.000	0.000	0.000	0.000
85	A	100	SER	0	0.011	0.000	16.030	-0.193	-0.193	0.000	0.000	0.000	0.000
86	A	101	ILE	0	-0.006	-0.009	9.785	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	102	PHE	0	-0.026	-0.027	10.473	0.222	0.222	0.000	0.000	0.000	0.000
88	A	103	CYS	0	-0.015	0.015	14.241	-0.294	-0.294	0.000	0.000	0.000	0.000
89	A	104	HIS	0	-0.064	-0.031	16.747	0.029	0.029	0.000	0.000	0.000	0.000
90	A	105	LEU	0	0.014	-0.005	19.689	-0.163	-0.163	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.023	0.012	23.147	-0.080	-0.080	0.000	0.000	0.000	0.000
92	A	107	SER	0	0.050	-0.023	26.709	0.145	0.145	0.000	0.000	0.000	0.000
93	A	108	SER	0	-0.061	-0.019	28.914	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	109	LEU	0	0.015	-0.004	25.113	-0.132	-0.132	0.000	0.000	0.000	0.000
95	A	110	ARG	1	0.797	0.886	24.083	-10.956	-10.956	0.000	0.000	0.000	0.000
96	A	111	GLN	0	0.000	-0.014	26.941	-0.031	-0.031	0.000	0.000	0.000	0.000
97	A	112	GLN	0	-0.032	-0.001	29.601	-0.328	-0.328	0.000	0.000	0.000	0.000
98	A	113	LEU	0	0.016	0.000	22.694	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	114	TYR	0	0.060	0.022	21.320	0.021	0.021	0.000	0.000	0.000	0.000
100	A	115	PRO	0	0.059	0.038	26.833	0.058	0.058	0.000	0.000	0.000	0.000
101	A	116	LYS	1	0.880	0.945	27.616	-10.192	-10.192	0.000	0.000	0.000	0.000
102	A	117	VAL	0	-0.004	0.009	22.892	0.123	0.123	0.000	0.000	0.000	0.000
103	A	118	TYR	0	0.025	0.004	25.587	0.095	0.095	0.000	0.000	0.000	0.000
104	A	119	GLN	0	-0.057	-0.041	27.802	-0.239	-0.239	0.000	0.000	0.000	0.000
105	A	120	GLY	0	0.022	0.032	26.250	-0.174	-0.174	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.059	-0.010	22.338	0.138	0.138	0.000	0.000	0.000	0.000
107	A	122	LYS	1	0.828	0.920	25.651	-10.741	-10.741	0.000	0.000	0.000	0.000
108	A	123	PRO	0	-0.055	-0.022	26.953	0.260	0.260	0.000	0.000	0.000	0.000
109	A	124	GLY	0	0.068	0.047	26.975	0.064	0.064	0.000	0.000	0.000	0.000
110	A	125	GLY	0	-0.022	-0.008	23.346	0.495	0.495	0.000	0.000	0.000	0.000
111	A	126	VAL	0	-0.060	-0.054	18.953	-0.219	-0.219	0.000	0.000	0.000	0.000
112	A	127	PHE	0	-0.001	-0.005	20.079	0.334	0.334	0.000	0.000	0.000	0.000
113	A	128	ILE	0	0.001	0.010	13.340	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	129	LEU	0	-0.020	-0.011	16.462	0.187	0.187	0.000	0.000	0.000	0.000
115	A	130	GLU	-1	-0.812	-0.922	11.215	21.540	21.540	0.000	0.000	0.000	0.000
116	A	131	GLY	0	0.038	0.039	14.668	0.333	0.333	0.000	0.000	0.000	0.000
117	A	132	PHE	0	-0.011	-0.009	13.854	-0.108	-0.108	0.000	0.000	0.000	0.000
118	A	133	ALA	0	0.024	0.012	17.700	-0.487	-0.487	0.000	0.000	0.000	0.000
119	A	134	PRO	0	0.054	0.012	20.968	0.104	0.104	0.000	0.000	0.000	0.000
120	A	135	GLU	-1	-0.817	-0.926	23.022	11.388	11.388	0.000	0.000	0.000	0.000
121	A	136	GLN	0	-0.010	-0.009	17.181	0.075	0.075	0.000	0.000	0.000	0.000
122	A	137	LEU	0	-0.031	-0.006	21.082	0.145	0.145	0.000	0.000	0.000	0.000
123	A	138	GLN	0	-0.083	-0.028	23.860	-0.628	-0.628	0.000	0.000	0.000	0.000
124	A	139	TYR	0	-0.138	-0.075	19.513	0.062	0.062	0.000	0.000	0.000	0.000
125	A	140	ASN	0	0.013	-0.008	20.468	0.068	0.068	0.000	0.000	0.000	0.000
126	A	141	THR	0	-0.038	-0.040	14.978	-0.089	-0.089	0.000	0.000	0.000	0.000
127	A	142	GLY	0	0.018	0.025	14.954	1.115	1.115	0.000	0.000	0.000	0.000
128	A	143	GLY	0	0.062	0.037	16.674	-0.328	-0.328	0.000	0.000	0.000	0.000
129	A	144	PRO	0	-0.048	-0.020	17.905	-0.347	-0.347	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.931	0.942	21.266	-10.539	-10.539	0.000	0.000	0.000	0.000
131	A	146	ASP	-1	-0.881	-0.942	24.523	9.780	9.780	0.000	0.000	0.000	0.000
132	A	147	LEU	0	0.080	0.034	25.428	0.317	0.317	0.000	0.000	0.000	0.000
133	A	148	ASP	-1	-0.809	-0.865	27.040	10.175	10.175	0.000	0.000	0.000	0.000
134	A	149	LEU	0	-0.043	-0.021	22.146	0.059	0.059	0.000	0.000	0.000	0.000
135	A	150	LEU	0	-0.095	-0.031	20.524	0.652	0.652	0.000	0.000	0.000	0.000
136	A	151	PRO	0	0.040	0.027	23.194	-0.308	-0.308	0.000	0.000	0.000	0.000
137	A	152	LYS	1	0.928	0.957	24.006	-10.473	-10.473	0.000	0.000	0.000	0.000
138	A	153	LEU	0	0.052	0.025	21.910	0.022	0.022	0.000	0.000	0.000	0.000
139	A	154	GLU	-1	-0.858	-0.944	24.612	10.360	10.360	0.000	0.000	0.000	0.000
140	A	155	THR	0	-0.062	-0.025	27.623	-0.195	-0.195	0.000	0.000	0.000	0.000
141	A	156	LEU	0	0.022	0.025	21.699	-0.115	-0.115	0.000	0.000	0.000	0.000
142	A	157	GLN	0	0.024	0.010	25.508	-0.276	-0.276	0.000	0.000	0.000	0.000
143	A	158	SER	0	-0.082	-0.040	27.289	-0.274	-0.274	0.000	0.000	0.000	0.000
144	A	159	GLU	-1	-0.817	-0.896	26.883	10.527	10.527	0.000	0.000	0.000	0.000
145	A	160	LEU	0	-0.055	-0.030	24.330	0.034	0.034	0.000	0.000	0.000	0.000
146	A	161	PRO	0	0.003	-0.001	28.688	0.116	0.116	0.000	0.000	0.000	0.000
147	A	162	SER	0	-0.053	-0.023	31.514	-0.113	-0.113	0.000	0.000	0.000	0.000
148	A	163	LEU	0	-0.064	-0.001	24.276	-0.042	-0.042	0.000	0.000	0.000	0.000
149	A	164	ASN	0	-0.015	0.001	27.775	-0.302	-0.302	0.000	0.000	0.000	0.000
150	A	165	TRP	0	0.015	-0.005	22.763	0.696	0.696	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.002	0.016	22.278	-0.150	-0.150	0.000	0.000	0.000	0.000
152	A	167	ILE	0	-0.024	-0.012	18.162	0.185	0.185	0.000	0.000	0.000	0.000
153	A	168	ALA	0	0.029	0.010	21.841	0.044	0.044	0.000	0.000	0.000	0.000
154	A	169	ASN	0	-0.054	-0.020	17.626	-0.969	-0.969	0.000	0.000	0.000	0.000
155	A	170	ASN	0	0.039	0.007	20.176	0.090	0.090	0.000	0.000	0.000	0.000
156	A	171	LEU	0	-0.054	-0.023	15.700	-0.127	-0.127	0.000	0.000	0.000	0.000
157	A	172	GLU	-1	-0.820	-0.903	19.163	12.638	12.638	0.000	0.000	0.000	0.000
158	A	173	ARG	1	0.910	0.978	11.453	-20.760	-20.760	0.000	0.000	0.000	0.000
159	A	174	ASN	0	0.047	0.014	18.500	0.785	0.785	0.000	0.000	0.000	0.000
160	A	184	LYS	1	0.872	0.935	15.490	-13.458	-13.458	0.000	0.000	0.000	0.000
161	A	185	ALA	0	0.002	0.002	14.853	0.402	0.402	0.000	0.000	0.000	0.000
162	A	186	ALA	0	0.038	0.032	16.867	-0.127	-0.127	0.000	0.000	0.000	0.000
163	A	187	LEU	0	-0.055	-0.022	12.934	0.271	0.271	0.000	0.000	0.000	0.000
164	A	188	ILE	0	0.006	0.010	17.209	-0.681	-0.681	0.000	0.000	0.000	0.000
165	A	189	GLN	0	0.017	0.007	13.420	0.186	0.186	0.000	0.000	0.000	0.000
166	A	190	LEU	0	-0.026	-0.005	17.518	-0.815	-0.815	0.000	0.000	0.000	0.000
167	A	191	LEU	0	0.030	0.013	17.654	0.740	0.740	0.000	0.000	0.000	0.000
168	A	192	GLY	0	-0.001	-0.008	20.030	-0.554	-0.554	0.000	0.000	0.000	0.000
169	A	193	GLN	0	0.037	0.002	22.944	0.121	0.121	0.000	0.000	0.000	0.000
170	A	194	LYS	1	0.830	0.902	24.955	-10.524	-10.524	0.000	0.000	0.000	0.000
171	A	195	LEU	0	-0.002	0.002	27.928	0.044	0.044	0.000	0.000	0.000	0.000
172	A	196	GLU	-1	-0.858	-0.928	29.382	10.106	10.106	0.000	0.000	0.000	0.000
173	A	197	HIS	0	-0.050	-0.026	32.664	-0.304	-0.304	0.000	0.000	0.000	0.000

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