FMO DATABASE

FMODB ID: GNLM1

Calculation Name: 4A0E-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A0E

Chain ID: A

ChEMBL ID:

UniProt ID: Q56975

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-824641.625149
FMO2-HF: Nuclear repulsion	783264.209733
FMO2-HF: Total energy	-41377.415416
FMO2-MP2: Total energy	-41497.817274

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:0:ACE )

Summations of interaction energy for fragment #1(A:0:ACE )

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.
2.19	-6.525	22.549	-8.596	-5.238	-0.025

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.072 / q_NPA : -0.087

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	2	SER	0	-0.032	-0.017	3.808	0.652	2.064	-0.009	-0.704	-0.700	-0.003
4	A	3	TRP	0	-0.045	-0.018	5.891	0.349	0.349	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.036	0.033	7.070	-0.218	-0.218	0.000	0.000	0.000	0.000
6	A	5	CYS	0	-0.012	-0.007	9.805	0.125	0.125	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.875	0.949	12.303	0.138	0.138	0.000	0.000	0.000	0.000
8	A	7	PHE	0	0.022	0.016	13.791	0.029	0.029	0.000	0.000	0.000	0.000
9	A	8	TYR	0	-0.025	-0.058	18.293	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	9	GLN	0	-0.035	-0.020	21.989	0.000	0.000	0.000	0.000	0.000	0.000
11	A	10	GLY	0	0.009	0.009	22.733	0.001	0.001	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.833	0.893	23.016	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	12	HIS	0	0.048	0.049	18.332	0.007	0.007	0.000	0.000	0.000	0.000
14	A	13	ARG	1	0.951	1.003	19.425	0.055	0.055	0.000	0.000	0.000	0.000
15	A	14	GLY	0	-0.063	-0.033	20.476	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	15	VAL	0	-0.040	-0.015	15.159	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.861	-0.937	13.457	-0.294	-0.294	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.029	-0.028	9.063	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.924	-0.947	4.728	-3.414	-3.456	0.000	-0.046	0.088	0.000
20	A	19	LEU	0	-0.033	-0.033	5.679	0.246	0.246	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.038	0.027	2.293	-0.741	-0.690	1.357	-1.057	-0.350	-0.005
22	A	21	HIS	0	0.065	0.054	2.056	5.125	-4.971	21.180	-6.851	-4.233	-0.017
23	A	22	GLY	0	-0.011	-0.003	3.685	-0.520	-0.560	0.021	0.062	-0.043	0.000
24	A	23	ARG	1	0.927	0.954	7.343	-0.598	-0.598	0.000	0.000	0.000	0.000
25	A	24	CYS	0	0.019	0.023	7.521	0.053	0.053	0.000	0.000	0.000	0.000
26	A	25	VAL	0	-0.039	-0.014	9.332	-0.124	-0.124	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.026	0.008	11.256	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.051	0.001	14.453	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	SER	0	-0.026	0.007	17.718	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.859	-0.915	19.699	0.123	0.123	0.000	0.000	0.000	0.000
31	A	30	PRO	0	0.006	-0.009	17.235	0.022	0.022	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.065	-0.032	16.931	0.022	0.022	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.107	-0.070	17.214	0.032	0.032	0.000	0.000	0.000	0.000
34	A	33	SER	0	-0.042	-0.008	14.424	0.033	0.033	0.000	0.000	0.000	0.000
35	A	34	ASP	-1	-0.845	-0.911	9.117	0.610	0.610	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.045	-0.023	8.758	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	36	VAL	0	-0.004	-0.010	12.349	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.028	-0.013	15.941	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	38	SER	0	0.011	-0.024	18.593	0.010	0.010	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.867	-0.927	22.139	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.057	-0.029	24.282	0.008	0.008	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.894	-0.959	25.782	0.019	0.019	0.000	0.000	0.000	0.000
43	A	42	ILE	0	-0.053	-0.006	19.668	0.004	0.004	0.000	0.000	0.000	0.000
44	A	43	ALA	0	0.027	0.005	22.477	0.001	0.001	0.000	0.000	0.000	0.000
45	A	44	PRO	0	-0.009	-0.017	21.078	0.007	0.007	0.000	0.000	0.000	0.000
46	A	45	VAL	0	0.031	0.014	17.474	0.015	0.015	0.000	0.000	0.000	0.000
47	A	46	HIS	0	-0.016	-0.017	18.200	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	47	LEU	0	0.002	0.000	14.751	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	48	VAL	0	-0.032	-0.002	13.911	0.033	0.033	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.010	-0.004	10.602	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	50	MET	0	-0.032	-0.003	10.258	0.156	0.156	0.000	0.000	0.000	0.000
52	A	51	VAL	0	0.011	0.004	5.419	-0.215	-0.215	0.000	0.000	0.000	0.000
53	A	52	ASP	-1	-0.877	-0.942	5.985	0.933	0.933	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.932	-0.976	6.638	-0.433	-0.433	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.953	-0.967	7.627	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	55	GLY	0	-0.069	-0.036	9.954	-0.078	-0.078	0.000	0.000	0.000	0.000
57	A	56	ILE	0	0.011	0.015	9.108	0.130	0.130	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.897	0.940	11.438	-0.271	-0.271	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.018	0.023	13.716	0.051	0.051	0.000	0.000	0.000	0.000
60	A	59	THR	0	-0.083	-0.042	14.519	0.021	0.021	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.896	-0.966	16.724	0.150	0.150	0.000	0.000	0.000	0.000
62	A	61	SER	0	-0.072	-0.063	17.876	0.013	0.013	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.001	0.014	20.253	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.950	-0.980	23.012	0.037	0.037	0.000	0.000	0.000	0.000
65	A	64	PRO	0	-0.021	0.011	23.140	0.008	0.008	0.000	0.000	0.000	0.000
66	A	65	LEU	0	0.066	0.044	18.071	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.040	-0.014	22.001	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	67	GLN	0	0.057	0.018	19.672	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.905	-0.959	22.768	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	69	GLY	0	0.038	0.028	25.449	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.081	-0.040	26.321	0.004	0.004	0.000	0.000	0.000	0.000
72	A	71	PRO	0	0.018	0.013	25.125	0.003	0.003	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.016	-0.008	19.922	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.019	-0.001	22.948	0.009	0.009	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.062	0.048	20.427	0.006	0.006	0.000	0.000	0.000	0.000
76	A	75	GLY	0	-0.006	0.004	18.144	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	76	THR	0	-0.085	-0.074	18.280	0.003	0.003	0.000	0.000	0.000	0.000
78	A	77	LEU	0	-0.005	-0.010	14.391	0.020	0.020	0.000	0.000	0.000	0.000
79	A	78	LEU	0	-0.014	0.003	14.479	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	79	ARG	1	0.923	0.960	16.136	0.002	0.002	0.000	0.000	0.000	0.000
81	A	80	ALA	0	0.047	0.028	14.964	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	81	GLY	0	-0.038	-0.026	16.307	0.008	0.008	0.000	0.000	0.000	0.000
83	A	82	SER	0	-0.089	-0.041	18.530	0.012	0.012	0.000	0.000	0.000	0.000
84	A	83	CYS	0	0.021	0.019	19.592	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	84	LEU	0	-0.044	-0.002	16.274	0.015	0.015	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.882	-0.964	20.244	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	86	VAL	0	0.017	0.011	19.119	0.011	0.011	0.000	0.000	0.000	0.000
88	A	87	GLY	0	0.088	0.068	22.107	0.001	0.001	0.000	0.000	0.000	0.000
89	A	88	PHE	0	-0.023	-0.022	23.607	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.026	0.005	16.570	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	90	LEU	0	0.015	0.021	21.024	0.003	0.003	0.000	0.000	0.000	0.000
92	A	91	TRP	0	-0.005	-0.035	12.733	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	92	THR	0	0.023	-0.005	16.669	0.002	0.002	0.000	0.000	0.000	0.000
94	A	93	PHE	0	0.005	0.000	11.557	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.006	0.004	12.659	0.046	0.046	0.000	0.000	0.000	0.000
96	A	95	ALA	0	0.044	0.014	11.052	-0.065	-0.065	0.000	0.000	0.000	0.000
97	A	96	VAL	0	0.022	0.005	8.722	0.098	0.098	0.000	0.000	0.000	0.000
98	A	97	GLY	0	-0.022	-0.012	10.839	0.071	0.071	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.061	-0.028	14.263	0.110	0.110	0.000	0.000	0.000	0.000
100	A	99	PRO	0	-0.007	-0.005	16.120	-0.019	-0.019	0.000	0.000	0.000	0.000
101	A	100	LEU	0	0.026	0.023	14.080	0.019	0.019	0.000	0.000	0.000	0.000
102	A	101	PRO	0	-0.009	0.007	18.337	0.010	0.010	0.000	0.000	0.000	0.000
103	A	102	GLU	-1	-0.929	-0.960	21.271	-0.091	-0.091	0.000	0.000	0.000	0.000
104	A	103	THR	0	-0.061	-0.028	23.790	0.008	0.008	0.000	0.000	0.000	0.000
105	A	104	LEU	0	0.035	0.016	20.315	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	105	GLN	0	-0.051	-0.028	24.592	0.008	0.008	0.000	0.000	0.000	0.000
107	A	106	VAL	0	0.035	0.018	26.017	0.000	0.000	0.000	0.000	0.000	0.000
108	A	107	PRO	0	-0.015	0.003	26.916	0.001	0.001	0.000	0.000	0.000	0.000
109	A	108	THR	0	0.015	-0.001	30.128	0.005	0.005	0.000	0.000	0.000	0.000
110	A	109	NME	0	-0.037	-0.007	33.114	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )