FMO DATABASE

FMODB ID: 989J2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-717799.940675
FMO2-HF: Nuclear repulsion	675357.191631
FMO2-HF: Total energy	-42442.749044
FMO2-MP2: Total energy	-42564.996519

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.
-12.054	-14.457	18.66	-8.902	-7.355	-0.068

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 : 0.046 / q_NPA : 0.005

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	-0.006	-0.009	3.817	-0.737	0.859	-0.003	-0.859	-0.734	0.005
4	A	2	SER	0	0.028	-0.003	2.128	-4.937	-4.829	3.828	-1.966	-1.969	-0.020
5	A	3	GLU	-1	-0.917	-0.960	3.204	1.462	2.602	0.024	-0.361	-0.804	-0.001
6	A	4	HIS	0	-0.071	-0.048	5.001	1.086	1.176	-0.001	-0.008	-0.081	0.000
7	A	5	VAL	0	0.015	0.015	7.088	0.458	0.458	0.000	0.000	0.000	0.000
8	A	6	HIS	0	-0.021	-0.029	5.579	0.726	0.726	0.000	0.000	0.000	0.000
9	A	7	LYS	1	0.925	0.970	8.955	0.846	0.846	0.000	0.000	0.000	0.000
10	A	8	GLU	-1	-0.954	-0.983	10.979	-0.631	-0.631	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.029	-0.011	11.022	0.152	0.152	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.021	-0.008	12.290	0.108	0.108	0.000	0.000	0.000	0.000
13	A	11	HIS	0	-0.008	0.004	15.110	0.067	0.067	0.000	0.000	0.000	0.000
14	A	12	LEU	0	-0.011	-0.012	16.602	0.053	0.053	0.000	0.000	0.000	0.000
15	A	13	GLY	0	0.017	0.009	17.664	0.041	0.041	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.824	-0.910	19.350	-0.164	-0.164	0.000	0.000	0.000	0.000
17	A	15	VAL	0	-0.038	0.006	21.096	0.031	0.031	0.000	0.000	0.000	0.000
18	A	16	PHE	0	-0.042	-0.030	21.154	0.027	0.027	0.000	0.000	0.000	0.000
19	A	17	ARG	1	0.820	0.914	20.964	0.213	0.213	0.000	0.000	0.000	0.000
20	A	18	SER	0	-0.011	-0.021	24.866	0.022	0.022	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.060	-0.030	27.112	0.015	0.015	0.000	0.000	0.000	0.000
22	A	20	ARG	1	0.679	0.801	26.701	0.153	0.153	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.867	-0.941	28.332	-0.115	-0.115	0.000	0.000	0.000	0.000
24	A	22	GLU	-1	-0.944	-0.953	31.223	-0.111	-0.111	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.888	0.939	33.195	0.120	0.120	0.000	0.000	0.000	0.000
26	A	24	ALA	0	-0.025	-0.004	34.452	0.005	0.005	0.000	0.000	0.000	0.000
27	A	25	LEU	0	-0.040	-0.001	33.161	0.004	0.004	0.000	0.000	0.000	0.000
28	A	26	SER	0	-0.020	-0.046	32.339	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.049	0.002	26.263	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	28	LYS	1	0.986	0.985	30.261	0.080	0.080	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.804	-0.855	33.210	-0.087	-0.087	0.000	0.000	0.000	0.000
32	A	30	VAL	0	0.013	0.006	29.233	0.000	0.000	0.000	0.000	0.000	0.000
33	A	31	GLU	-1	-0.858	-0.918	30.955	-0.115	-0.115	0.000	0.000	0.000	0.000
34	A	32	ALA	0	-0.039	-0.016	32.257	0.001	0.001	0.000	0.000	0.000	0.000
35	A	33	ALA	0	-0.036	-0.008	34.832	0.003	0.003	0.000	0.000	0.000	0.000
36	A	34	THR	0	-0.049	-0.049	30.957	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	35	SER	0	-0.035	-0.011	32.863	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	36	ILE	0	-0.034	-0.005	26.529	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.931	0.956	27.453	0.119	0.119	0.000	0.000	0.000	0.000
40	A	38	LEU	0	0.048	0.021	27.122	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	39	SER	0	0.000	-0.011	24.422	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	40	ALA	0	-0.011	-0.002	22.677	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	41	LEU	0	0.021	0.011	22.415	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	42	GLU	-1	-0.928	-0.970	23.023	-0.151	-0.151	0.000	0.000	0.000	0.000
45	A	43	ALA	0	-0.058	-0.031	18.686	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	44	ILE	0	0.005	0.005	18.174	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.784	-0.871	19.001	-0.195	-0.195	0.000	0.000	0.000	0.000
48	A	46	ALA	0	-0.074	-0.033	18.071	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	47	GLY	0	0.053	0.038	15.158	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	48	HIS	0	-0.021	-0.008	13.436	-0.102	-0.102	0.000	0.000	0.000	0.000
51	A	49	LEU	0	0.108	0.044	9.481	0.067	0.067	0.000	0.000	0.000	0.000
52	A	50	GLY	0	0.065	0.034	12.838	0.044	0.044	0.000	0.000	0.000	0.000
53	A	51	LYS	1	0.920	0.958	14.138	0.243	0.243	0.000	0.000	0.000	0.000
54	A	52	LEU	0	-0.017	0.003	15.684	0.039	0.039	0.000	0.000	0.000	0.000
55	A	53	ILE	0	0.003	0.008	14.034	0.037	0.037	0.000	0.000	0.000	0.000
56	A	54	SER	0	0.023	-0.001	16.179	0.020	0.020	0.000	0.000	0.000	0.000
57	A	55	PRO	0	-0.072	-0.018	17.831	0.034	0.034	0.000	0.000	0.000	0.000
58	A	56	VAL	0	0.045	0.043	21.613	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	57	TYR	0	-0.026	-0.053	20.455	0.039	0.039	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.022	0.014	25.826	0.013	0.013	0.000	0.000	0.000	0.000
61	A	59	GLN	0	0.076	0.054	26.444	0.020	0.020	0.000	0.000	0.000	0.000
62	A	60	GLY	0	-0.001	0.001	28.189	0.010	0.010	0.000	0.000	0.000	0.000
63	A	61	PHE	0	-0.022	-0.033	28.045	0.009	0.009	0.000	0.000	0.000	0.000
64	A	62	MET	0	0.017	0.015	31.909	0.008	0.008	0.000	0.000	0.000	0.000
65	A	63	LYS	1	0.913	0.957	29.577	0.091	0.091	0.000	0.000	0.000	0.000
66	A	64	LYS	1	0.929	0.964	30.338	0.108	0.108	0.000	0.000	0.000	0.000
67	A	65	TYR	0	0.000	0.011	35.095	0.004	0.004	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.021	0.004	37.366	0.004	0.004	0.000	0.000	0.000	0.000
69	A	67	ALA	0	0.002	-0.004	37.812	0.004	0.004	0.000	0.000	0.000	0.000
70	A	68	PHE	0	-0.054	-0.016	39.426	0.003	0.003	0.000	0.000	0.000	0.000
71	A	69	LEU	0	-0.039	-0.020	41.267	0.002	0.002	0.000	0.000	0.000	0.000
72	A	70	ASP	-1	-0.921	-0.941	43.160	-0.043	-0.043	0.000	0.000	0.000	0.000
73	A	71	MET	0	-0.068	-0.034	41.580	0.003	0.003	0.000	0.000	0.000	0.000
74	A	72	ASP	-1	-0.847	-0.925	39.254	-0.047	-0.047	0.000	0.000	0.000	0.000
75	A	73	GLY	0	0.027	-0.010	36.837	0.000	0.000	0.000	0.000	0.000	0.000
76	A	74	ASP	-1	-0.877	-0.915	34.455	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	75	ARG	1	0.838	0.875	36.169	0.042	0.042	0.000	0.000	0.000	0.000
78	A	76	LEU	0	0.021	0.015	38.587	0.000	0.000	0.000	0.000	0.000	0.000
79	A	77	LEU	0	-0.019	-0.021	32.242	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	78	LYS	1	0.832	0.895	34.548	0.043	0.043	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.835	-0.864	36.864	-0.039	-0.039	0.000	0.000	0.000	0.000
82	A	80	HIS	0	-0.090	-0.042	36.619	0.000	0.000	0.000	0.000	0.000	0.000
83	A	81	PRO	0	0.043	0.014	34.993	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	82	TYR	0	0.019	-0.001	33.396	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	83	VAL	0	0.030	0.021	31.983	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	84	LEU	0	-0.023	-0.010	30.465	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	85	LYS	1	0.899	0.957	27.540	0.054	0.054	0.000	0.000	0.000	0.000
88	A	86	ILE	0	0.067	0.034	27.433	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	87	PHE	0	-0.043	-0.033	25.995	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	88	GLN	0	-0.001	-0.007	24.755	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	89	GLU	-1	-0.841	-0.918	23.138	-0.091	-0.091	0.000	0.000	0.000	0.000
92	A	90	PHE	0	-0.031	-0.022	21.544	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	91	SER	0	-0.027	-0.023	20.189	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	92	ASP	-1	-0.930	-0.967	18.834	-0.123	-0.123	0.000	0.000	0.000	0.000
95	A	93	GLN	0	-0.005	0.003	15.661	0.007	0.007	0.000	0.000	0.000	0.000
96	A	94	ASN	0	-0.060	-0.036	15.639	-0.057	-0.057	0.000	0.000	0.000	0.000
97	A	95	MET	0	-0.040	-0.026	14.180	-0.077	-0.077	0.000	0.000	0.000	0.000
98	A	96	ASP	-1	-0.872	-0.925	12.662	-0.201	-0.201	0.000	0.000	0.000	0.000
99	A	97	MET	0	-0.053	-0.017	11.268	-0.042	-0.042	0.000	0.000	0.000	0.000
100	A	98	LEU	0	-0.061	-0.045	9.695	-0.201	-0.201	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.003	0.008	8.108	-0.209	-0.209	0.000	0.000	0.000	0.000
102	A	100	ASP	-1	-0.908	-0.972	6.896	-0.477	-0.477	0.000	0.000	0.000	0.000
103	A	101	LEU	0	-0.099	-0.042	5.500	-0.190	-0.190	0.000	0.000	0.000	0.000
104	A	102	GLU	-1	-0.821	-0.884	3.045	-4.861	-3.990	0.053	-0.454	-0.470	-0.002
105	A	103	SER	0	-0.075	-0.009	1.746	-4.509	-10.717	14.759	-5.254	-3.297	-0.050

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