FMO DATABASE

FMODB ID: GNR21

Calculation Name: 2E4M-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2E4M

Chain ID: C

ChEMBL ID:

UniProt ID: Q9LBR4

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptH
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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1404619.571586
FMO2-HF: Nuclear repulsion	1348023.920965
FMO2-HF: Total energy	-56595.650622
FMO2-MP2: Total energy	-56764.52459

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(C:4:GLU)

Summations of interaction energy for fragment #1(C:4: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.
5.178	11.444	5.619	-6.139	-5.746	0.036

Interaction energy analysis for fragmet #1(C:4:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.878 / q_NPA : -0.952

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	C	6	THR	0	0.073	0.073	3.824	0.988	2.913	-0.020	-0.938	-0.967	0.005
4	C	7	PHE	0	-0.062	-0.048	5.922	-2.552	-2.552	0.000	0.000	0.000	0.000
5	C	8	LEU	0	0.040	0.022	9.504	-1.424	-1.424	0.000	0.000	0.000	0.000
6	C	9	PRO	0	-0.019	0.012	11.465	-0.124	-0.124	0.000	0.000	0.000	0.000
7	C	10	ASN	0	0.130	0.068	14.834	1.195	1.195	0.000	0.000	0.000	0.000
8	C	11	GLY	0	-0.057	-0.032	17.168	-0.670	-0.670	0.000	0.000	0.000	0.000
9	C	12	ASN	0	0.027	0.016	19.287	0.759	0.759	0.000	0.000	0.000	0.000
10	C	13	TYR	0	-0.024	-0.044	15.157	0.076	0.076	0.000	0.000	0.000	0.000
11	C	14	LYS	1	0.889	0.968	19.703	-12.618	-12.618	0.000	0.000	0.000	0.000
12	C	15	ILE	0	0.020	0.007	16.482	0.797	0.797	0.000	0.000	0.000	0.000
13	C	16	LYS	1	0.893	0.970	17.861	-15.124	-15.124	0.000	0.000	0.000	0.000
14	C	17	SER	0	0.049	0.032	17.098	1.163	1.163	0.000	0.000	0.000	0.000
15	C	18	LEU	0	0.000	-0.022	14.588	-0.354	-0.354	0.000	0.000	0.000	0.000
16	C	19	PHE	0	0.004	0.018	18.398	-0.433	-0.433	0.000	0.000	0.000	0.000
17	C	20	SER	0	-0.003	-0.002	21.889	-0.776	-0.776	0.000	0.000	0.000	0.000
18	C	21	ASP	-1	-0.870	-0.934	22.452	13.568	13.568	0.000	0.000	0.000	0.000
19	C	22	SER	0	-0.038	-0.027	24.037	-0.063	-0.063	0.000	0.000	0.000	0.000
20	C	23	LEU	0	-0.008	0.004	24.481	-0.293	-0.293	0.000	0.000	0.000	0.000
21	C	24	TYR	0	-0.074	-0.065	21.521	0.492	0.492	0.000	0.000	0.000	0.000
22	C	25	LEU	0	-0.017	-0.006	19.275	-0.452	-0.452	0.000	0.000	0.000	0.000
23	C	26	THR	0	-0.066	-0.037	22.533	-0.136	-0.136	0.000	0.000	0.000	0.000
24	C	27	TYR	0	0.039	0.024	25.814	0.204	0.204	0.000	0.000	0.000	0.000
25	C	28	SER	0	0.022	-0.001	27.585	-0.402	-0.402	0.000	0.000	0.000	0.000
26	C	29	SER	0	-0.006	-0.001	31.196	-0.131	-0.131	0.000	0.000	0.000	0.000
27	C	30	GLY	0	-0.008	-0.002	31.018	-0.121	-0.121	0.000	0.000	0.000	0.000
28	C	31	SER	0	-0.031	-0.008	28.542	0.277	0.277	0.000	0.000	0.000	0.000
29	C	32	LEU	0	-0.007	-0.006	21.409	-0.032	-0.032	0.000	0.000	0.000	0.000
30	C	33	SER	0	0.032	0.020	24.589	0.016	0.016	0.000	0.000	0.000	0.000
31	C	34	PHE	0	0.017	0.007	18.824	0.223	0.223	0.000	0.000	0.000	0.000
32	C	35	LEU	0	0.023	0.020	24.883	-0.490	-0.490	0.000	0.000	0.000	0.000
33	C	36	ASN	0	0.042	0.011	27.212	0.406	0.406	0.000	0.000	0.000	0.000
34	C	37	THR	0	-0.054	-0.012	27.179	0.016	0.016	0.000	0.000	0.000	0.000
35	C	38	SER	0	0.022	0.011	28.589	-0.382	-0.382	0.000	0.000	0.000	0.000
36	C	39	SER	0	-0.018	-0.023	29.073	0.335	0.335	0.000	0.000	0.000	0.000
37	C	40	LEU	0	0.005	-0.008	30.914	0.028	0.028	0.000	0.000	0.000	0.000
38	C	41	ASP	-1	-0.860	-0.943	28.756	10.896	10.896	0.000	0.000	0.000	0.000
39	C	42	ASN	0	0.022	0.012	27.590	0.489	0.489	0.000	0.000	0.000	0.000
40	C	43	GLN	0	0.030	0.042	25.277	0.512	0.512	0.000	0.000	0.000	0.000
41	C	44	LYS	1	0.910	0.967	23.580	-10.765	-10.765	0.000	0.000	0.000	0.000
42	C	45	TRP	0	-0.004	-0.011	19.500	0.038	0.038	0.000	0.000	0.000	0.000
43	C	46	LYS	1	0.954	0.991	20.393	-13.831	-13.831	0.000	0.000	0.000	0.000
44	C	47	LEU	0	-0.020	-0.015	13.187	0.330	0.330	0.000	0.000	0.000	0.000
45	C	48	GLU	-1	-0.973	-1.000	16.423	14.541	14.541	0.000	0.000	0.000	0.000
46	C	49	TYR	0	-0.018	-0.002	9.982	-0.382	-0.382	0.000	0.000	0.000	0.000
47	C	50	ILE	0	-0.030	-0.014	13.977	-1.820	-1.820	0.000	0.000	0.000	0.000
48	C	51	SER	0	0.033	0.001	14.008	0.878	0.878	0.000	0.000	0.000	0.000
49	C	52	SER	0	-0.041	-0.027	15.375	0.532	0.532	0.000	0.000	0.000	0.000
50	C	53	SER	0	-0.002	-0.006	14.299	-0.942	-0.942	0.000	0.000	0.000	0.000
51	C	54	ASN	0	0.000	0.008	9.729	3.494	3.494	0.000	0.000	0.000	0.000
52	C	55	GLY	0	0.058	0.039	9.431	-0.580	-0.580	0.000	0.000	0.000	0.000
53	C	56	PHE	0	-0.025	-0.020	8.481	-2.245	-2.245	0.000	0.000	0.000	0.000
54	C	57	ARG	1	0.921	0.966	12.767	-17.351	-17.351	0.000	0.000	0.000	0.000
55	C	58	PHE	0	0.029	0.016	12.680	-0.328	-0.328	0.000	0.000	0.000	0.000
56	C	59	SER	0	0.000	-0.001	17.937	-0.653	-0.653	0.000	0.000	0.000	0.000
57	C	60	ASN	0	0.030	-0.007	21.714	-0.236	-0.236	0.000	0.000	0.000	0.000
58	C	61	VAL	0	-0.022	-0.020	24.206	-0.198	-0.198	0.000	0.000	0.000	0.000
59	C	62	ALA	0	-0.030	-0.001	26.326	-0.369	-0.369	0.000	0.000	0.000	0.000
60	C	63	GLU	-1	-0.904	-0.958	27.674	10.096	10.096	0.000	0.000	0.000	0.000
61	C	64	PRO	0	0.021	0.026	26.437	0.527	0.527	0.000	0.000	0.000	0.000
62	C	65	ASN	0	-0.039	-0.040	26.527	-0.280	-0.280	0.000	0.000	0.000	0.000
63	C	66	LYS	1	0.888	0.957	25.122	-10.961	-10.961	0.000	0.000	0.000	0.000
64	C	67	TYR	0	-0.015	-0.022	19.725	0.180	0.180	0.000	0.000	0.000	0.000
65	C	68	LEU	0	-0.012	0.005	18.138	-0.445	-0.445	0.000	0.000	0.000	0.000
66	C	69	ALA	0	-0.018	-0.001	18.061	0.953	0.953	0.000	0.000	0.000	0.000
67	C	70	TYR	0	0.038	0.025	15.498	-0.422	-0.422	0.000	0.000	0.000	0.000
68	C	71	ASN	0	0.023	-0.006	19.539	0.122	0.122	0.000	0.000	0.000	0.000
69	C	72	ASP	-1	-0.850	-0.933	21.987	13.358	13.358	0.000	0.000	0.000	0.000
70	C	73	TYR	0	-0.094	-0.035	24.334	-0.215	-0.215	0.000	0.000	0.000	0.000
71	C	74	GLY	0	0.014	0.015	20.718	0.050	0.050	0.000	0.000	0.000	0.000
72	C	75	PHE	0	-0.001	0.002	20.869	0.500	0.500	0.000	0.000	0.000	0.000
73	C	76	ILE	0	-0.025	-0.014	17.046	0.212	0.212	0.000	0.000	0.000	0.000
74	C	77	TYR	0	-0.037	-0.030	20.468	-0.998	-0.998	0.000	0.000	0.000	0.000
75	C	78	LEU	0	0.007	0.001	22.113	0.616	0.616	0.000	0.000	0.000	0.000
76	C	79	SER	0	0.000	0.001	23.148	-0.596	-0.596	0.000	0.000	0.000	0.000
77	C	80	SER	0	-0.003	0.001	24.440	0.221	0.221	0.000	0.000	0.000	0.000
78	C	81	SER	0	-0.052	-0.004	21.855	-0.424	-0.424	0.000	0.000	0.000	0.000
79	C	82	SER	0	0.079	0.106	22.640	-0.463	-0.463	0.000	0.000	0.000	0.000
80	C	83	ASN	0	-0.090	-0.083	18.129	0.811	0.811	0.000	0.000	0.000	0.000
81	C	84	ASN	0	0.116	0.007	17.182	0.394	0.394	0.000	0.000	0.000	0.000
82	C	85	SER	0	0.013	-0.010	17.060	-0.095	-0.095	0.000	0.000	0.000	0.000
83	C	86	LEU	0	-0.063	-0.007	12.438	-0.272	-0.272	0.000	0.000	0.000	0.000
84	C	87	TRP	0	0.017	0.005	10.569	0.796	0.796	0.000	0.000	0.000	0.000
85	C	88	ASN	0	0.028	0.000	2.859	-13.940	-11.759	0.109	-1.333	-0.957	0.015
86	C	89	PRO	0	-0.047	-0.019	6.684	2.628	2.628	0.000	0.000	0.000	0.000
87	C	90	ILE	0	0.048	0.041	1.888	-3.628	-1.913	5.532	-3.797	-3.449	0.016
88	C	91	LYS	1	0.850	0.917	4.324	-31.852	-31.619	-0.001	-0.027	-0.205	0.000
89	C	92	ILE	0	0.028	0.013	4.309	4.437	4.523	0.000	-0.038	-0.049	0.000
90	C	93	ALA	0	-0.022	-0.019	6.650	-3.182	-3.182	0.000	0.000	0.000	0.000
91	C	94	ILE	0	-0.037	-0.017	9.856	1.088	1.088	0.000	0.000	0.000	0.000
92	C	95	ASN	0	-0.004	-0.017	12.221	0.419	0.419	0.000	0.000	0.000	0.000
93	C	96	SER	0	-0.010	0.003	10.544	-1.507	-1.507	0.000	0.000	0.000	0.000
94	C	97	TYR	0	-0.004	-0.017	7.413	1.030	1.030	0.000	0.000	0.000	0.000
95	C	98	ILE	0	0.094	0.082	6.858	-3.416	-3.416	0.000	0.000	0.000	0.000
96	C	99	ILE	0	-0.054	-0.024	7.705	4.077	4.077	0.000	0.000	0.000	0.000
97	C	100	CYS	0	0.039	0.022	6.124	-3.917	-3.917	0.000	0.000	0.000	0.000
98	C	101	THR	0	0.031	0.012	8.556	-1.771	-1.771	0.000	0.000	0.000	0.000
99	C	102	LEU	0	-0.044	-0.011	8.132	3.678	3.678	0.000	0.000	0.000	0.000
100	C	103	SER	0	-0.030	-0.034	9.626	-3.111	-3.111	0.000	0.000	0.000	0.000
101	C	104	ILE	0	-0.002	0.005	11.817	-0.739	-0.739	0.000	0.000	0.000	0.000
102	C	105	VAL	0	0.060	0.026	10.844	1.599	1.599	0.000	0.000	0.000	0.000
103	C	106	ASN	0	-0.056	-0.039	11.627	-1.636	-1.636	0.000	0.000	0.000	0.000
104	C	107	VAL	0	-0.015	0.020	12.975	-1.263	-1.263	0.000	0.000	0.000	0.000
105	C	108	THR	0	-0.014	-0.017	12.254	1.540	1.540	0.000	0.000	0.000	0.000
106	C	109	ASP	-1	-0.849	-0.901	7.471	40.538	40.538	0.000	0.000	0.000	0.000
107	C	110	TYR	0	-0.040	-0.023	10.376	-2.927	-2.927	0.000	0.000	0.000	0.000
108	C	111	ALA	0	0.016	0.007	10.312	3.071	3.071	0.000	0.000	0.000	0.000
109	C	112	TRP	0	-0.037	-0.023	12.003	-2.537	-2.537	0.000	0.000	0.000	0.000
110	C	113	THR	0	-0.008	0.003	14.416	1.057	1.057	0.000	0.000	0.000	0.000
111	C	114	ILE	0	-0.048	-0.029	17.008	-0.989	-0.989	0.000	0.000	0.000	0.000
112	C	115	TYR	0	0.031	0.024	19.547	0.026	0.026	0.000	0.000	0.000	0.000
113	C	116	ASP	-1	-0.795	-0.879	22.185	13.511	13.511	0.000	0.000	0.000	0.000
114	C	117	ASN	0	-0.021	-0.012	24.177	-0.066	-0.066	0.000	0.000	0.000	0.000
115	C	118	ASN	0	-0.016	-0.015	27.078	-0.017	-0.017	0.000	0.000	0.000	0.000
116	C	119	ASN	0	0.010	-0.016	23.718	0.212	0.212	0.000	0.000	0.000	0.000
117	C	120	ASN	0	-0.019	0.008	25.453	0.244	0.244	0.000	0.000	0.000	0.000
118	C	121	ILE	0	0.032	-0.003	22.201	0.155	0.155	0.000	0.000	0.000	0.000
119	C	122	THR	0	-0.036	-0.027	25.663	0.136	0.136	0.000	0.000	0.000	0.000
120	C	123	ASP	-1	-0.938	-0.969	28.783	10.122	10.122	0.000	0.000	0.000	0.000
121	C	124	GLN	0	-0.040	-0.003	24.439	0.243	0.243	0.000	0.000	0.000	0.000
122	C	125	PRO	0	-0.015	0.006	24.094	0.188	0.188	0.000	0.000	0.000	0.000
123	C	126	ILE	0	-0.028	-0.017	17.917	0.390	0.390	0.000	0.000	0.000	0.000
124	C	127	LEU	0	-0.008	-0.007	19.799	-0.352	-0.352	0.000	0.000	0.000	0.000
125	C	128	ASN	0	0.036	0.000	14.825	2.505	2.505	0.000	0.000	0.000	0.000
126	C	129	LEU	0	-0.033	-0.023	15.732	-1.041	-1.041	0.000	0.000	0.000	0.000
127	C	130	PRO	0	0.013	0.008	14.053	1.675	1.675	0.000	0.000	0.000	0.000
128	C	131	ASN	0	-0.078	-0.055	8.428	2.495	2.495	0.000	0.000	0.000	0.000
129	C	132	PHE	0	0.021	0.008	10.688	0.492	0.492	0.000	0.000	0.000	0.000
130	C	133	ASP	-1	-0.843	-0.923	8.740	25.091	25.091	0.000	0.000	0.000	0.000
131	C	134	ILE	0	-0.015	-0.020	4.649	1.058	1.184	-0.001	-0.006	-0.119	0.000
132	C	135	ASN	0	-0.032	-0.021	8.102	-1.256	-1.256	0.000	0.000	0.000	0.000
133	C	136	ASN	0	0.032	0.031	11.578	-2.727	-2.727	0.000	0.000	0.000	0.000
134	C	137	SER	0	0.060	0.013	13.614	0.617	0.617	0.000	0.000	0.000	0.000
135	C	138	ASN	0	-0.075	-0.042	15.881	0.209	0.209	0.000	0.000	0.000	0.000
136	C	139	GLN	0	-0.035	-0.010	12.221	1.204	1.204	0.000	0.000	0.000	0.000
137	C	140	ILE	0	-0.021	0.008	10.554	2.371	2.371	0.000	0.000	0.000	0.000
138	C	141	LEU	0	-0.015	-0.012	11.820	-2.103	-2.103	0.000	0.000	0.000	0.000
139	C	142	LYS	1	0.927	0.965	12.357	-15.785	-15.785	0.000	0.000	0.000	0.000
140	C	143	LEU	0	-0.004	0.002	11.928	-0.960	-0.960	0.000	0.000	0.000	0.000
141	C	144	GLU	-1	-0.855	-0.922	15.174	14.632	14.632	0.000	0.000	0.000	0.000
142	C	145	LYS	1	0.907	0.956	17.392	-15.947	-15.947	0.000	0.000	0.000	0.000
143	C	146	LEU	0	-0.016	0.001	19.364	-0.532	-0.532	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:4:GLU)