FMO DATABASE

FMODB ID: QY8JY

Calculation Name: 1GME-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GME

Chain ID: B

ChEMBL ID:

UniProt ID: Q41560

Base Structure: X-ray

Registration Date: 2023-06-21

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-750866.765377
FMO2-HF: Nuclear repulsion	708259.225313
FMO2-HF: Total energy	-42607.540064
FMO2-MP2: Total energy	-42734.120727

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(B:43:ASN)

Summations of interaction energy for fragment #1(B:43:ASN)

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.
-2.815	0.92	0.129	-1.178	-2.689	0.005

Interaction energy analysis for fragmet #1(B:43:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.024

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	B	45	ARG	1	0.890	0.940	2.853	3.998	6.804	0.126	-0.986	-1.946	0.005
4	B	46	MET	0	0.025	0.001	4.644	-1.245	-1.152	-0.001	-0.024	-0.069	0.000
5	B	47	ASP	-1	-0.941	-0.939	7.679	0.739	0.739	0.000	0.000	0.000	0.000
6	B	48	TRP	0	-0.013	-0.021	10.985	0.172	0.172	0.000	0.000	0.000	0.000
7	B	49	LYS	1	0.912	0.958	13.738	-0.701	-0.701	0.000	0.000	0.000	0.000
8	B	50	GLU	-1	-0.846	-0.920	17.220	0.593	0.593	0.000	0.000	0.000	0.000
9	B	51	THR	0	-0.069	-0.032	20.619	-0.075	-0.075	0.000	0.000	0.000	0.000
10	B	52	PRO	0	-0.015	-0.039	23.699	0.019	0.019	0.000	0.000	0.000	0.000
11	B	53	GLU	-1	-0.791	-0.898	26.470	0.328	0.328	0.000	0.000	0.000	0.000
12	B	54	ALA	0	-0.028	-0.011	22.500	0.015	0.015	0.000	0.000	0.000	0.000
13	B	55	HIS	0	0.084	0.073	18.384	-0.034	-0.034	0.000	0.000	0.000	0.000
14	B	56	VAL	0	-0.034	-0.029	16.757	0.025	0.025	0.000	0.000	0.000	0.000
15	B	57	PHE	0	0.023	0.007	12.518	0.050	0.050	0.000	0.000	0.000	0.000
16	B	58	LYS	1	0.890	0.929	12.118	-0.770	-0.770	0.000	0.000	0.000	0.000
17	B	59	ALA	0	0.043	0.014	8.356	0.510	0.510	0.000	0.000	0.000	0.000
18	B	60	ASP	-1	-0.861	-0.907	7.376	-0.664	-0.664	0.000	0.000	0.000	0.000
19	B	61	LEU	0	-0.059	-0.050	6.969	0.189	0.189	0.000	0.000	0.000	0.000
20	B	62	PRO	0	0.014	-0.001	7.783	-0.046	-0.046	0.000	0.000	0.000	0.000
21	B	63	GLY	0	-0.065	-0.050	9.570	-0.092	-0.092	0.000	0.000	0.000	0.000
22	B	64	VAL	0	0.001	0.024	8.762	0.021	0.021	0.000	0.000	0.000	0.000
23	B	65	LYS	1	0.965	0.982	11.953	-0.083	-0.083	0.000	0.000	0.000	0.000
24	B	66	LYS	1	0.960	0.970	14.720	-0.228	-0.228	0.000	0.000	0.000	0.000
25	B	67	GLU	-1	-0.872	-0.939	16.706	0.429	0.429	0.000	0.000	0.000	0.000
26	B	68	GLU	-1	-0.891	-0.929	12.490	0.348	0.348	0.000	0.000	0.000	0.000
27	B	69	VAL	0	-0.058	-0.030	11.314	0.254	0.254	0.000	0.000	0.000	0.000
28	B	70	LYS	1	0.919	0.978	13.030	-1.238	-1.238	0.000	0.000	0.000	0.000
29	B	71	VAL	0	-0.028	-0.027	13.531	0.255	0.255	0.000	0.000	0.000	0.000
30	B	72	GLU	-1	-0.897	-0.962	15.491	0.894	0.894	0.000	0.000	0.000	0.000
31	B	73	VAL	0	0.027	0.008	16.755	0.148	0.148	0.000	0.000	0.000	0.000
32	B	74	GLU	-1	-0.825	-0.914	16.094	1.311	1.311	0.000	0.000	0.000	0.000
33	B	75	ASP	-1	-0.961	-1.001	19.507	0.921	0.921	0.000	0.000	0.000	0.000
34	B	76	GLY	0	0.023	0.030	22.143	-0.038	-0.038	0.000	0.000	0.000	0.000
35	B	77	ASN	0	0.049	0.022	21.484	0.014	0.014	0.000	0.000	0.000	0.000
36	B	78	VAL	0	-0.027	-0.015	15.400	0.083	0.083	0.000	0.000	0.000	0.000
37	B	79	LEU	0	-0.011	0.020	13.816	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	80	VAL	0	-0.038	-0.027	12.062	0.355	0.355	0.000	0.000	0.000	0.000
39	B	81	VAL	0	0.004	0.004	9.575	-0.211	-0.211	0.000	0.000	0.000	0.000
40	B	82	SER	0	-0.042	-0.035	9.025	0.638	0.638	0.000	0.000	0.000	0.000
41	B	83	GLY	0	0.078	0.031	9.114	-0.449	-0.449	0.000	0.000	0.000	0.000
42	B	84	GLU	-1	-0.981	-0.996	8.362	1.234	1.234	0.000	0.000	0.000	0.000
43	B	85	ARG	1	0.905	0.966	6.520	1.130	1.130	0.000	0.000	0.000	0.000
44	B	86	THR	0	0.016	-0.026	8.457	-0.242	-0.242	0.000	0.000	0.000	0.000
45	B	87	LYS	1	0.907	0.954	11.248	0.800	0.800	0.000	0.000	0.000	0.000
46	B	88	GLU	-1	-0.918	-0.954	12.383	-0.126	-0.126	0.000	0.000	0.000	0.000
47	B	89	LYS	1	0.858	0.914	15.699	0.160	0.160	0.000	0.000	0.000	0.000
48	B	90	GLU	-1	-0.847	-0.909	17.569	-0.466	-0.466	0.000	0.000	0.000	0.000
49	B	91	ASP	-1	-0.875	-0.937	20.890	-0.203	-0.203	0.000	0.000	0.000	0.000
50	B	92	LYS	1	0.878	0.917	23.518	0.184	0.184	0.000	0.000	0.000	0.000
51	B	93	ASN	0	-0.016	-0.002	25.498	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	94	ASP	-1	-0.871	-0.907	22.549	-0.347	-0.347	0.000	0.000	0.000	0.000
53	B	95	LYS	1	0.914	0.943	23.638	0.392	0.392	0.000	0.000	0.000	0.000
54	B	96	TRP	0	-0.026	-0.005	16.381	-0.108	-0.108	0.000	0.000	0.000	0.000
55	B	97	HIS	0	0.002	-0.002	20.592	-0.022	-0.022	0.000	0.000	0.000	0.000
56	B	98	ARG	1	0.856	0.904	15.295	1.255	1.255	0.000	0.000	0.000	0.000
57	B	99	VAL	0	-0.011	-0.007	12.225	0.032	0.032	0.000	0.000	0.000	0.000
58	B	100	GLU	-1	-0.823	-0.892	10.858	-1.867	-1.867	0.000	0.000	0.000	0.000
59	B	101	ARG	1	0.920	0.967	8.721	0.589	0.589	0.000	0.000	0.000	0.000
60	B	102	SER	0	0.019	0.015	3.450	0.945	1.087	0.000	-0.040	-0.103	0.000
61	B	103	SER	0	0.001	-0.018	6.350	0.291	0.291	0.000	0.000	0.000	0.000
62	B	104	GLY	0	-0.015	0.009	6.323	-0.238	-0.238	0.000	0.000	0.000	0.000
63	B	105	LYS	1	0.985	0.999	6.887	-0.960	-0.960	0.000	0.000	0.000	0.000
64	B	106	PHE	0	-0.001	0.017	4.057	1.198	1.623	0.005	-0.110	-0.321	0.000
65	B	107	VAL	0	0.008	-0.012	5.211	-1.686	-1.686	0.000	0.000	0.000	0.000
66	B	108	ARG	1	0.890	0.945	4.379	-8.306	-8.037	-0.001	-0.018	-0.250	0.000
67	B	109	ARG	1	0.903	0.958	7.938	-2.499	-2.499	0.000	0.000	0.000	0.000
68	B	110	PHE	0	-0.017	-0.004	9.268	0.195	0.195	0.000	0.000	0.000	0.000
69	B	111	ARG	1	0.943	0.981	13.716	-1.071	-1.071	0.000	0.000	0.000	0.000
70	B	112	LEU	0	-0.028	-0.016	17.342	-0.027	-0.027	0.000	0.000	0.000	0.000
71	B	113	LEU	0	0.005	-0.009	19.698	-0.015	-0.015	0.000	0.000	0.000	0.000
72	B	114	GLU	-1	-0.946	-0.981	23.214	0.587	0.587	0.000	0.000	0.000	0.000
73	B	115	ASP	-1	-0.925	-0.971	25.959	0.453	0.453	0.000	0.000	0.000	0.000
74	B	116	ALA	0	0.012	0.023	23.468	-0.006	-0.006	0.000	0.000	0.000	0.000
75	B	117	LYS	1	0.950	0.988	25.448	-0.396	-0.396	0.000	0.000	0.000	0.000
76	B	118	VAL	0	0.011	-0.002	22.961	0.030	0.030	0.000	0.000	0.000	0.000
77	B	119	GLU	-1	-0.920	-0.966	24.034	0.552	0.552	0.000	0.000	0.000	0.000
78	B	120	GLU	-1	-0.999	-1.006	25.917	0.384	0.384	0.000	0.000	0.000	0.000
79	B	121	VAL	0	-0.029	-0.012	19.251	0.008	0.008	0.000	0.000	0.000	0.000
80	B	122	LYS	1	0.913	0.968	21.751	-0.506	-0.506	0.000	0.000	0.000	0.000
81	B	123	ALA	0	0.035	-0.008	17.259	0.092	0.092	0.000	0.000	0.000	0.000
82	B	124	GLY	0	-0.011	0.012	18.275	-0.077	-0.077	0.000	0.000	0.000	0.000
83	B	125	LEU	0	-0.040	-0.027	13.535	0.111	0.111	0.000	0.000	0.000	0.000
84	B	126	GLU	-1	-0.909	-0.952	16.865	0.116	0.116	0.000	0.000	0.000	0.000
85	B	127	ASN	0	-0.013	-0.011	16.909	0.034	0.034	0.000	0.000	0.000	0.000
86	B	128	GLY	0	-0.012	-0.001	13.103	-0.088	-0.088	0.000	0.000	0.000	0.000
87	B	129	VAL	0	0.016	0.025	11.835	0.044	0.044	0.000	0.000	0.000	0.000
88	B	130	LEU	0	0.001	0.000	11.753	-0.031	-0.031	0.000	0.000	0.000	0.000
89	B	131	THR	0	-0.035	-0.023	13.325	0.071	0.071	0.000	0.000	0.000	0.000
90	B	132	VAL	0	0.027	0.025	14.589	-0.073	-0.073	0.000	0.000	0.000	0.000
91	B	133	THR	0	-0.088	-0.048	16.920	-0.027	-0.027	0.000	0.000	0.000	0.000
92	B	134	VAL	0	0.072	0.031	18.476	-0.023	-0.023	0.000	0.000	0.000	0.000
93	B	135	PRO	0	0.005	-0.008	21.182	-0.009	-0.009	0.000	0.000	0.000	0.000
94	B	136	LYS	1	0.840	0.939	23.913	-0.429	-0.429	0.000	0.000	0.000	0.000
95	B	137	ALA	0	0.018	0.031	26.185	-0.029	-0.029	0.000	0.000	0.000	0.000
96	B	138	GLU	-1	-0.966	-0.991	29.389	0.276	0.276	0.000	0.000	0.000	0.000
97	B	139	VAL	0	-0.036	-0.013	29.339	0.008	0.008	0.000	0.000	0.000	0.000
98	B	140	LYS	1	0.960	0.965	29.024	-0.314	-0.314	0.000	0.000	0.000	0.000
99	B	141	LYS	1	0.918	0.965	27.692	-0.204	-0.204	0.000	0.000	0.000	0.000
100	B	142	PRO	0	0.016	0.018	24.073	-0.023	-0.023	0.000	0.000	0.000	0.000
101	B	143	GLU	-1	-0.941	-0.973	27.220	0.217	0.217	0.000	0.000	0.000	0.000
102	B	144	VAL	0	-0.019	-0.010	25.455	0.009	0.009	0.000	0.000	0.000	0.000
103	B	145	LYS	1	0.931	0.965	28.494	-0.178	-0.178	0.000	0.000	0.000	0.000
104	B	146	ALA	0	0.008	0.012	29.076	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	147	ILE	0	0.024	0.004	29.703	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	148	GLN	0	-0.027	-0.014	30.677	-0.009	-0.009	0.000	0.000	0.000	0.000
107	B	149	ILE	0	0.011	0.006	27.429	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	150	SER	0	-0.014	-0.012	31.785	-0.002	-0.002	0.000	0.000	0.000	0.000
109	B	151	GLY	0	0.019	0.026	34.039	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:43:ASN)