FMO DATABASE

FMODB ID: LN489

Calculation Name: 4GQM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GQM

Chain ID: A

ChEMBL ID:

UniProt ID: A0A654

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:

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-718086.989033
FMO2-HF: Nuclear repulsion	675644.632071
FMO2-HF: Total energy	-42442.356962
FMO2-MP2: Total energy	-42564.593099

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:-1:GLY)

Summations of interaction energy for fragment #1(A:-1:GLY)

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.
-6.137	-7.563	14.346	-6.291	-6.629	-0.039

Interaction energy analysis for fragmet #1(A:-1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.021

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	1	MET	0	-0.004	-0.007	3.817	-0.604	0.687	-0.003	-0.643	-0.646	0.003
4	A	2	SER	0	0.051	0.027	2.413	0.958	0.372	3.268	-1.148	-1.534	-0.003
5	A	3	GLU	-1	-0.933	-0.968	3.125	-4.260	-2.786	0.051	-0.613	-0.911	-0.003
6	A	4	HIS	0	-0.077	-0.048	5.143	0.475	0.570	-0.001	-0.008	-0.086	0.000
7	A	5	VAL	0	0.007	0.014	7.582	0.117	0.117	0.000	0.000	0.000	0.000
8	A	6	HIS	0	-0.016	-0.020	5.632	0.178	0.178	0.000	0.000	0.000	0.000
9	A	7	LYS	1	0.921	0.968	9.154	0.528	0.528	0.000	0.000	0.000	0.000
10	A	8	GLU	-1	-0.948	-0.981	11.124	-0.075	-0.075	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.032	-0.010	11.388	0.052	0.052	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.023	-0.010	12.587	0.032	0.032	0.000	0.000	0.000	0.000
13	A	11	HIS	0	-0.003	0.005	15.264	0.022	0.022	0.000	0.000	0.000	0.000
14	A	12	LEU	0	-0.004	-0.007	16.887	0.027	0.027	0.000	0.000	0.000	0.000
15	A	13	GLY	0	0.019	0.008	17.917	0.020	0.020	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.851	-0.924	19.530	-0.138	-0.138	0.000	0.000	0.000	0.000
17	A	15	VAL	0	-0.031	0.006	21.328	0.015	0.015	0.000	0.000	0.000	0.000
18	A	16	PHE	0	-0.047	-0.033	21.495	0.014	0.014	0.000	0.000	0.000	0.000
19	A	17	ARG	1	0.874	0.935	20.883	0.148	0.148	0.000	0.000	0.000	0.000
20	A	18	SER	0	0.006	-0.004	25.112	0.008	0.008	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.034	-0.014	27.339	0.011	0.011	0.000	0.000	0.000	0.000
22	A	20	ARG	1	0.726	0.829	26.811	0.087	0.087	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.957	-0.994	28.425	-0.087	-0.087	0.000	0.000	0.000	0.000
24	A	22	GLU	-1	-0.972	-0.967	31.390	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.877	0.935	33.399	0.047	0.047	0.000	0.000	0.000	0.000
26	A	24	ALA	0	-0.026	-0.006	34.623	0.003	0.003	0.000	0.000	0.000	0.000
27	A	25	LEU	0	-0.031	0.003	33.353	0.003	0.003	0.000	0.000	0.000	0.000
28	A	26	SER	0	-0.018	-0.007	32.493	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.050	0.004	26.456	0.003	0.003	0.000	0.000	0.000	0.000
30	A	28	LYS	1	0.987	0.983	30.449	0.052	0.052	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.813	-0.892	33.409	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	30	VAL	0	-0.009	-0.006	29.600	0.003	0.003	0.000	0.000	0.000	0.000
33	A	31	GLU	-1	-0.877	-0.937	31.321	-0.039	-0.039	0.000	0.000	0.000	0.000
34	A	32	ALA	0	-0.036	-0.014	32.558	0.004	0.004	0.000	0.000	0.000	0.000
35	A	33	ALA	0	-0.036	-0.008	35.202	0.003	0.003	0.000	0.000	0.000	0.000
36	A	34	THR	0	-0.049	-0.040	31.381	0.002	0.002	0.000	0.000	0.000	0.000
37	A	35	SER	0	-0.029	-0.011	33.287	0.003	0.003	0.000	0.000	0.000	0.000
38	A	36	ILE	0	-0.027	-0.001	26.923	0.002	0.002	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.925	0.949	27.709	0.026	0.026	0.000	0.000	0.000	0.000
40	A	38	LEU	0	0.058	0.031	27.421	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	39	SER	0	-0.004	-0.010	24.602	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	40	ALA	0	0.005	0.004	22.985	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	41	LEU	0	0.012	0.008	22.719	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	42	GLU	-1	-0.916	-0.967	23.302	-0.090	-0.090	0.000	0.000	0.000	0.000
45	A	43	ALA	0	-0.050	-0.024	18.897	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	44	ILE	0	0.000	0.002	18.412	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.767	-0.859	19.259	-0.107	-0.107	0.000	0.000	0.000	0.000
48	A	46	ALA	0	-0.083	-0.039	18.049	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	47	GLY	0	0.050	0.036	15.348	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	48	HIS	0	-0.020	-0.008	13.630	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	49	LEU	0	0.114	0.049	9.988	0.028	0.028	0.000	0.000	0.000	0.000
52	A	50	GLY	0	0.045	0.026	13.070	0.037	0.037	0.000	0.000	0.000	0.000
53	A	51	LYS	1	0.911	0.936	14.397	0.167	0.167	0.000	0.000	0.000	0.000
54	A	52	LEU	0	-0.009	0.006	16.039	0.015	0.015	0.000	0.000	0.000	0.000
55	A	53	ILE	0	0.016	0.015	14.493	0.012	0.012	0.000	0.000	0.000	0.000
56	A	54	SER	0	0.017	0.013	16.266	0.015	0.015	0.000	0.000	0.000	0.000
57	A	55	PRO	0	-0.070	-0.018	18.182	0.009	0.009	0.000	0.000	0.000	0.000
58	A	56	VAL	0	0.053	0.048	21.971	0.007	0.007	0.000	0.000	0.000	0.000
59	A	57	TYR	0	-0.026	-0.054	20.904	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.027	0.014	26.260	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	59	GLN	0	0.037	0.027	26.309	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	60	GLY	0	-0.017	-0.007	28.580	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	61	PHE	0	-0.014	-0.028	28.650	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	62	MET	0	0.022	0.015	32.313	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	63	LYS	1	0.957	0.988	29.438	0.013	0.013	0.000	0.000	0.000	0.000
66	A	64	LYS	1	0.918	0.960	30.687	0.026	0.026	0.000	0.000	0.000	0.000
67	A	65	TYR	0	-0.014	0.005	35.420	0.000	0.000	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.029	0.004	37.727	0.000	0.000	0.000	0.000	0.000	0.000
69	A	67	ALA	0	0.000	-0.005	38.137	0.000	0.000	0.000	0.000	0.000	0.000
70	A	68	PHE	0	-0.057	-0.014	39.742	0.000	0.000	0.000	0.000	0.000	0.000
71	A	69	LEU	0	-0.036	-0.021	41.585	0.000	0.000	0.000	0.000	0.000	0.000
72	A	70	ASP	-1	-0.916	-0.937	43.501	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	71	MET	0	-0.068	-0.036	41.889	0.002	0.002	0.000	0.000	0.000	0.000
74	A	72	ASP	-1	-0.846	-0.927	39.388	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	73	GLY	0	0.020	-0.014	37.068	0.002	0.002	0.000	0.000	0.000	0.000
76	A	74	ASP	-1	-0.889	-0.916	34.512	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	75	ARG	1	0.844	0.899	36.359	0.004	0.004	0.000	0.000	0.000	0.000
78	A	76	LEU	0	0.017	0.008	38.901	0.002	0.002	0.000	0.000	0.000	0.000
79	A	77	LEU	0	-0.009	-0.015	32.638	0.002	0.002	0.000	0.000	0.000	0.000
80	A	78	LYS	1	0.861	0.902	34.898	0.007	0.007	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.858	-0.892	37.091	0.003	0.003	0.000	0.000	0.000	0.000
82	A	80	HIS	0	-0.086	-0.041	36.957	0.002	0.002	0.000	0.000	0.000	0.000
83	A	81	PRO	0	0.043	0.015	35.273	0.001	0.001	0.000	0.000	0.000	0.000
84	A	82	TYR	0	0.018	-0.003	33.687	0.002	0.002	0.000	0.000	0.000	0.000
85	A	83	VAL	0	0.026	0.019	32.329	0.003	0.003	0.000	0.000	0.000	0.000
86	A	84	LEU	0	-0.019	-0.001	30.608	0.001	0.001	0.000	0.000	0.000	0.000
87	A	85	LYS	1	0.916	0.958	28.376	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	86	ILE	0	0.062	0.028	27.777	0.002	0.002	0.000	0.000	0.000	0.000
89	A	87	PHE	0	-0.038	-0.027	26.348	0.002	0.002	0.000	0.000	0.000	0.000
90	A	88	GLN	0	0.000	-0.005	25.058	0.002	0.002	0.000	0.000	0.000	0.000
91	A	89	GLU	-1	-0.867	-0.926	23.400	0.047	0.047	0.000	0.000	0.000	0.000
92	A	90	PHE	0	-0.035	-0.023	21.878	0.007	0.007	0.000	0.000	0.000	0.000
93	A	91	SER	0	-0.036	-0.024	20.545	0.001	0.001	0.000	0.000	0.000	0.000
94	A	92	ASP	-1	-0.927	-0.968	19.102	0.019	0.019	0.000	0.000	0.000	0.000
95	A	93	GLN	0	0.031	0.031	16.027	0.001	0.001	0.000	0.000	0.000	0.000
96	A	94	ASN	0	-0.076	-0.054	16.012	0.032	0.032	0.000	0.000	0.000	0.000
97	A	95	MET	0	-0.050	-0.030	14.515	0.003	0.003	0.000	0.000	0.000	0.000
98	A	96	ASP	-1	-0.866	-0.919	12.884	0.083	0.083	0.000	0.000	0.000	0.000
99	A	97	MET	0	-0.053	-0.018	11.584	0.031	0.031	0.000	0.000	0.000	0.000
100	A	98	LEU	0	-0.061	-0.046	10.128	0.089	0.089	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.019	0.006	8.367	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	100	ASP	-1	-0.887	-0.966	7.085	0.292	0.292	0.000	0.000	0.000	0.000
103	A	101	LEU	0	-0.111	-0.044	6.031	0.259	0.259	0.000	0.000	0.000	0.000
104	A	102	GLU	-1	-0.858	-0.929	3.328	-0.129	0.493	0.037	-0.325	-0.334	0.000
105	A	103	SER	0	-0.086	-0.028	1.853	-4.384	-8.706	10.994	-3.554	-3.118	-0.036

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:GLY)