FMO DATABASE

FMODB ID: 3JM4L

Calculation Name: 3CAE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3CAE

Chain ID: A

ChEMBL ID:

UniProt ID: P00641

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1027937.038748
FMO2-HF: Nuclear repulsion	974008.967684
FMO2-HF: Total energy	-53928.071064
FMO2-MP2: Total energy	-54088.33164

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:17:MET)

Summations of interaction energy for fragment #1(A:17:MET)

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.
-9.966	-8.657	11.39	-3.512	-9.187	-0.018

Interaction energy analysis for fragmet #1(A:17:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.025

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	19	LEU	0	-0.011	0.004	2.025	-3.067	-3.409	5.081	-1.142	-3.597	0.002
4	A	20	GLH	0	-0.023	-0.058	2.096	-3.442	-3.335	6.280	-2.193	-4.194	-0.018
5	A	21	ASP	-1	-0.829	-0.915	3.056	-1.764	-0.446	0.030	-0.156	-1.192	-0.002
6	A	22	LYS	1	0.944	0.957	4.600	0.230	0.456	-0.001	-0.021	-0.204	0.000
7	A	23	VAL	0	-0.040	-0.015	6.552	0.414	0.414	0.000	0.000	0.000	0.000
8	A	24	SER	0	0.022	0.016	7.047	0.287	0.287	0.000	0.000	0.000	0.000
9	A	25	LYS	1	0.991	1.001	7.970	0.725	0.725	0.000	0.000	0.000	0.000
10	A	26	GLN	0	-0.040	-0.014	10.569	0.336	0.336	0.000	0.000	0.000	0.000
11	A	27	LEU	0	-0.036	-0.014	11.123	0.150	0.150	0.000	0.000	0.000	0.000
12	A	28	GLU	-1	-0.876	-0.950	11.088	-0.852	-0.852	0.000	0.000	0.000	0.000
13	A	29	SER	0	-0.120	-0.054	14.434	0.126	0.126	0.000	0.000	0.000	0.000
14	A	30	LYS	1	0.897	0.949	16.430	0.551	0.551	0.000	0.000	0.000	0.000
15	A	31	GLY	0	0.002	0.001	17.850	0.024	0.024	0.000	0.000	0.000	0.000
16	A	32	ILE	0	-0.048	-0.019	16.420	0.028	0.028	0.000	0.000	0.000	0.000
17	A	33	LYS	1	0.936	0.962	16.529	0.410	0.410	0.000	0.000	0.000	0.000
18	A	34	PHE	0	-0.020	-0.008	10.798	0.025	0.025	0.000	0.000	0.000	0.000
19	A	35	GLU	-1	-0.837	-0.927	14.950	-0.650	-0.650	0.000	0.000	0.000	0.000
20	A	36	TYR	0	-0.068	-0.038	4.949	-0.365	-0.365	0.000	0.000	0.000	0.000
21	A	37	GLU	-1	-0.887	-0.919	6.087	-3.522	-3.522	0.000	0.000	0.000	0.000
22	A	38	GLU	-1	-0.926	-0.941	10.735	-0.578	-0.578	0.000	0.000	0.000	0.000
23	A	39	TRP	0	-0.051	-0.022	14.457	0.127	0.127	0.000	0.000	0.000	0.000
24	A	40	LYS	1	0.938	0.957	14.635	0.492	0.492	0.000	0.000	0.000	0.000
25	A	41	VAL	0	0.021	0.008	16.468	0.073	0.073	0.000	0.000	0.000	0.000
26	A	42	PRO	0	-0.044	-0.028	18.592	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	43	TYR	0	-0.004	0.014	16.658	0.043	0.043	0.000	0.000	0.000	0.000
28	A	44	SER	0	0.009	0.002	22.006	0.007	0.007	0.000	0.000	0.000	0.000
29	A	45	ASN	0	-0.020	-0.017	19.616	0.027	0.027	0.000	0.000	0.000	0.000
30	A	46	ASN	0	-0.002	0.002	22.955	0.004	0.004	0.000	0.000	0.000	0.000
31	A	47	GLN	0	0.025	0.020	24.332	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	48	GLN	0	-0.005	-0.014	26.359	0.005	0.005	0.000	0.000	0.000	0.000
33	A	49	ASN	0	0.010	0.008	29.035	0.003	0.003	0.000	0.000	0.000	0.000
34	A	50	TYR	0	0.011	0.005	31.217	0.002	0.002	0.000	0.000	0.000	0.000
35	A	51	SER	0	-0.011	0.006	34.229	0.006	0.006	0.000	0.000	0.000	0.000
36	A	52	SER	0	-0.029	-0.010	36.871	0.000	0.000	0.000	0.000	0.000	0.000
37	A	53	HIS	0	0.013	-0.009	39.702	0.001	0.001	0.000	0.000	0.000	0.000
38	A	54	THR	0	-0.029	-0.023	43.199	0.001	0.001	0.000	0.000	0.000	0.000
39	A	55	TYR	0	0.032	0.003	46.834	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	56	THR	0	-0.057	-0.031	49.596	0.003	0.003	0.000	0.000	0.000	0.000
41	A	57	PRO	0	0.005	0.023	53.228	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	58	ASP	-1	-0.747	-0.847	55.775	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	59	PHE	0	-0.057	-0.044	59.161	0.002	0.002	0.000	0.000	0.000	0.000
44	A	60	LEU	0	-0.023	-0.001	58.248	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	61	LEU	0	-0.030	-0.004	61.090	0.001	0.001	0.000	0.000	0.000	0.000
46	A	62	PRO	0	0.048	0.005	62.935	0.000	0.000	0.000	0.000	0.000	0.000
47	A	63	ASN	0	-0.035	-0.021	63.943	0.001	0.001	0.000	0.000	0.000	0.000
48	A	64	GLY	0	0.039	0.005	60.191	0.000	0.000	0.000	0.000	0.000	0.000
49	A	65	ILE	0	-0.094	-0.038	58.707	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	66	PHE	0	0.027	0.013	55.623	0.001	0.001	0.000	0.000	0.000	0.000
51	A	67	VAL	0	-0.021	-0.019	58.396	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	68	GLU	-1	-0.898	-0.950	55.007	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	69	THR	0	-0.099	-0.049	58.053	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	70	LYS	1	0.871	0.927	53.783	0.038	0.038	0.000	0.000	0.000	0.000
55	A	71	GLY	0	-0.005	-0.002	58.724	0.000	0.000	0.000	0.000	0.000	0.000
56	A	72	LEU	0	-0.006	-0.004	55.459	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	73	TRP	0	-0.011	-0.028	52.197	0.000	0.000	0.000	0.000	0.000	0.000
58	A	74	GLU	-1	-0.847	-0.931	49.965	-0.058	-0.058	0.000	0.000	0.000	0.000
59	A	75	SER	0	-0.032	-0.024	45.514	0.001	0.001	0.000	0.000	0.000	0.000
60	A	76	ASP	-1	-0.877	-0.937	45.240	-0.068	-0.068	0.000	0.000	0.000	0.000
61	A	77	ASP	-1	-0.800	-0.915	46.291	-0.044	-0.044	0.000	0.000	0.000	0.000
62	A	78	ARG	1	0.877	0.962	48.238	0.063	0.063	0.000	0.000	0.000	0.000
63	A	79	LYS	1	0.973	0.988	40.786	0.089	0.089	0.000	0.000	0.000	0.000
64	A	80	LYS	1	0.916	0.961	44.522	0.046	0.046	0.000	0.000	0.000	0.000
65	A	81	HIS	0	-0.009	0.002	45.496	0.001	0.001	0.000	0.000	0.000	0.000
66	A	82	LEU	0	0.034	-0.013	45.246	0.002	0.002	0.000	0.000	0.000	0.000
67	A	83	LEU	0	0.017	0.033	39.788	0.001	0.001	0.000	0.000	0.000	0.000
68	A	84	ILE	0	-0.065	-0.034	43.642	0.003	0.003	0.000	0.000	0.000	0.000
69	A	85	ARG	1	0.881	0.954	46.274	0.046	0.046	0.000	0.000	0.000	0.000
70	A	86	GLU	-1	-0.929	-0.963	41.257	-0.064	-0.064	0.000	0.000	0.000	0.000
71	A	87	GLN	0	-0.029	-0.032	40.539	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	88	HIS	1	0.768	0.866	43.211	0.031	0.031	0.000	0.000	0.000	0.000
73	A	89	PRO	0	0.042	0.033	45.656	0.001	0.001	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.817	-0.879	48.317	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	91	LEU	0	-0.069	-0.029	50.245	0.002	0.002	0.000	0.000	0.000	0.000
76	A	92	ASP	-1	-0.826	-0.913	52.588	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	93	ILE	0	0.015	0.005	51.329	0.001	0.001	0.000	0.000	0.000	0.000
78	A	94	ARG	1	0.676	0.816	55.027	0.024	0.024	0.000	0.000	0.000	0.000
79	A	95	ILE	0	-0.008	0.000	53.832	0.001	0.001	0.000	0.000	0.000	0.000
80	A	96	VAL	0	-0.004	0.014	58.325	0.000	0.000	0.000	0.000	0.000	0.000
81	A	97	PHE	0	0.050	0.006	55.993	0.000	0.000	0.000	0.000	0.000	0.000
82	A	98	SER	0	-0.014	-0.010	61.667	0.002	0.002	0.000	0.000	0.000	0.000
83	A	99	SER	0	0.024	-0.012	62.588	0.001	0.001	0.000	0.000	0.000	0.000
84	A	100	SER	0	0.012	0.042	60.562	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	101	ARG	1	1.024	0.993	60.478	0.039	0.039	0.000	0.000	0.000	0.000
86	A	102	THR	0	-0.055	-0.040	58.454	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	103	LYS	1	0.856	0.933	57.269	0.049	0.049	0.000	0.000	0.000	0.000
88	A	104	LEU	0	-0.060	-0.032	51.152	0.000	0.000	0.000	0.000	0.000	0.000
89	A	105	TYR	0	0.047	0.023	48.272	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	106	LYS	1	1.037	1.003	53.867	0.061	0.061	0.000	0.000	0.000	0.000
91	A	107	GLY	0	-0.021	-0.013	55.887	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	108	SER	0	-0.026	-0.001	53.597	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	109	PRO	0	0.043	0.013	54.451	0.003	0.003	0.000	0.000	0.000	0.000
94	A	110	THR	0	0.019	0.011	53.262	0.001	0.001	0.000	0.000	0.000	0.000
95	A	111	SER	0	-0.103	-0.053	55.784	0.000	0.000	0.000	0.000	0.000	0.000
96	A	112	TYR	0	0.008	0.004	55.452	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	113	GLY	0	0.089	0.035	56.052	0.000	0.000	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.748	-0.846	56.339	-0.052	-0.052	0.000	0.000	0.000	0.000
99	A	115	PHE	0	-0.069	-0.028	48.209	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	116	CYS	0	-0.047	-0.024	52.528	0.000	0.000	0.000	0.000	0.000	0.000
101	A	117	GLU	-1	-0.868	-0.927	54.300	-0.045	-0.045	0.000	0.000	0.000	0.000
102	A	118	LYS	1	0.915	0.962	48.062	0.071	0.071	0.000	0.000	0.000	0.000
103	A	119	HIS	0	-0.056	-0.028	47.015	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	120	GLY	0	0.006	0.011	50.568	0.002	0.002	0.000	0.000	0.000	0.000
105	A	121	ILE	0	-0.062	-0.038	50.798	0.002	0.002	0.000	0.000	0.000	0.000
106	A	122	LYS	1	0.939	0.969	54.671	0.029	0.029	0.000	0.000	0.000	0.000
107	A	123	PHE	0	0.028	-0.005	58.241	0.000	0.000	0.000	0.000	0.000	0.000
108	A	124	ALA	0	0.022	0.009	60.066	0.001	0.001	0.000	0.000	0.000	0.000
109	A	125	ASP	-1	-0.799	-0.886	62.938	-0.036	-0.036	0.000	0.000	0.000	0.000
110	A	126	LYS	1	0.882	0.937	65.410	0.031	0.031	0.000	0.000	0.000	0.000
111	A	127	LEU	0	-0.008	-0.021	67.224	0.001	0.001	0.000	0.000	0.000	0.000
112	A	128	ILE	0	0.009	0.016	64.420	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	129	PRO	0	0.017	0.011	65.245	0.001	0.001	0.000	0.000	0.000	0.000
114	A	130	ALA	0	0.048	0.011	68.026	0.001	0.001	0.000	0.000	0.000	0.000
115	A	131	GLU	-1	-0.910	-0.959	67.667	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	132	TRP	0	0.027	0.007	61.274	0.001	0.001	0.000	0.000	0.000	0.000
117	A	133	ILE	0	-0.032	-0.011	65.837	0.001	0.001	0.000	0.000	0.000	0.000
118	A	134	LYS	1	0.915	0.958	67.909	0.018	0.018	0.000	0.000	0.000	0.000
119	A	135	GLU	-1	-0.816	-0.871	62.860	-0.023	-0.023	0.000	0.000	0.000	0.000
120	A	136	PRO	0	-0.010	-0.007	64.382	0.001	0.001	0.000	0.000	0.000	0.000
121	A	137	LYS	1	0.945	0.970	63.077	0.007	0.007	0.000	0.000	0.000	0.000
122	A	138	LYS	1	0.911	0.974	57.343	0.021	0.021	0.000	0.000	0.000	0.000
123	A	139	GLU	-1	-0.922	-0.969	57.593	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	140	VAL	0	0.007	0.023	55.414	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	141	PRO	0	0.032	0.019	51.466	0.002	0.002	0.000	0.000	0.000	0.000
126	A	142	PHE	0	0.041	-0.015	52.413	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	143	ASP	-1	-0.891	-0.927	51.530	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	144	ARG	1	0.884	0.947	45.158	0.015	0.015	0.000	0.000	0.000	0.000
129	A	145	LEU	0	-0.074	-0.025	48.480	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	146	LYS	1	0.982	0.986	44.147	0.014	0.014	0.000	0.000	0.000	0.000
131	A	147	ARG	1	0.951	0.986	51.170	0.002	0.002	0.000	0.000	0.000	0.000
132	A	148	LYS	1	1.026	1.010	53.551	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:MET)