FMO DATABASE

FMODB ID: V5261

Calculation Name: 1GME-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GME

Chain ID: A

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	OptAll
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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1205446.249829
FMO2-HF: Nuclear repulsion	1147844.263292
FMO2-HF: Total energy	-57601.986537
FMO2-MP2: Total energy	-57773.464965

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-2.288	-0.795	0.009	-0.621	-0.881	0.002

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.002

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	4	VAL	0	0.012	0.005	3.879	-0.220	0.997	-0.010	-0.511	-0.696	0.002
4	A	5	ARG	1	0.972	0.980	6.078	-2.000	-2.000	0.000	0.000	0.000	0.000
5	A	6	ARG	1	0.902	0.952	9.151	-0.499	-0.499	0.000	0.000	0.000	0.000
6	A	7	SER	0	0.006	0.009	10.404	-0.016	-0.016	0.000	0.000	0.000	0.000
7	A	8	ASN	0	0.000	-0.008	10.962	0.188	0.188	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.015	-0.015	12.209	-0.032	-0.032	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.013	0.014	14.858	0.043	0.043	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.752	-0.880	16.508	0.279	0.279	0.000	0.000	0.000	0.000
11	A	12	PRO	0	-0.014	0.007	17.821	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.020	-0.027	19.855	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.000	0.015	14.726	0.026	0.026	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.863	-0.944	14.620	0.463	0.463	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.051	-0.015	11.748	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	17	TRP	0	-0.067	-0.048	14.344	-0.093	-0.093	0.000	0.000	0.000	0.000
17	A	18	ALA	0	-0.031	-0.006	17.682	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.822	-0.907	16.891	0.076	0.076	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.027	0.012	16.058	0.003	0.003	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.038	-0.011	16.240	-0.055	-0.055	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.890	-0.961	14.078	0.144	0.144	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.019	0.011	11.475	0.014	0.014	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.045	-0.032	11.404	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.905	0.951	12.708	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.011	-0.007	8.800	-0.047	-0.047	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.034	-0.017	7.363	-0.188	-0.188	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.005	0.006	8.580	-0.312	-0.312	0.000	0.000	0.000	0.000
28	A	29	PRO	0	-0.062	-0.037	9.321	-0.126	-0.126	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.022	-0.008	4.474	-0.273	-0.229	-0.001	-0.010	-0.033	0.000
30	A	31	ILE	0	-0.016	0.007	5.854	-0.502	-0.502	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.051	-0.016	8.564	0.055	0.055	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.007	-0.007	5.401	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.023	-0.002	3.487	-0.447	-0.273	0.018	-0.069	-0.123	0.000
34	A	35	GLY	0	0.024	0.007	4.002	0.804	0.862	0.002	-0.031	-0.029	0.000
35	A	36	SER	0	-0.002	0.002	7.181	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.826	-0.905	9.915	-0.216	-0.216	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.001	-0.011	12.680	0.090	0.090	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.013	0.009	14.694	0.061	0.061	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.017	0.007	16.349	0.046	0.046	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.018	-0.035	13.717	0.037	0.037	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.025	0.003	18.269	0.034	0.034	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.006	-0.001	20.738	0.018	0.018	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.014	0.023	21.701	0.020	0.020	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.934	0.967	22.011	0.181	0.181	0.000	0.000	0.000	0.000
45	A	46	MET	0	-0.021	-0.020	22.226	0.010	0.010	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.890	-0.917	23.335	-0.061	-0.061	0.000	0.000	0.000	0.000
47	A	48	TRP	0	-0.045	-0.036	21.453	0.004	0.004	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.928	0.975	26.147	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.763	-0.855	28.969	0.081	0.081	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.079	-0.056	30.635	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.027	-0.041	34.023	0.007	0.007	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.831	-0.897	36.176	0.037	0.037	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.034	0.016	33.737	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	HIS	0	-0.012	-0.002	28.188	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.044	-0.030	30.078	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	57	PHE	0	0.047	0.014	23.732	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.850	0.905	27.402	0.020	0.020	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.014	-0.004	25.785	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.893	-0.917	27.014	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.051	-0.033	25.704	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.051	0.022	29.285	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.004	-0.006	31.960	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.064	-0.032	29.038	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.852	0.914	32.396	0.076	0.076	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.942	0.933	32.755	0.020	0.020	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.851	-0.907	33.341	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.815	-0.867	30.508	-0.077	-0.077	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.014	-0.016	27.315	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.778	0.890	24.684	0.023	0.023	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.016	-0.003	26.502	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.820	-0.897	24.957	0.006	0.006	0.000	0.000	0.000	0.000
72	A	73	VAL	0	0.009	-0.008	25.063	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.830	-0.897	19.740	0.114	0.114	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.940	-0.987	20.026	0.248	0.248	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.033	0.044	23.520	0.012	0.012	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.013	-0.026	22.205	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.025	-0.003	18.960	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.026	0.030	21.887	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.022	-0.019	20.421	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.015	0.007	21.899	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.036	-0.020	21.885	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.057	0.025	23.409	0.012	0.012	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.847	-0.913	24.243	-0.170	-0.170	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.792	0.910	26.671	0.132	0.132	0.000	0.000	0.000	0.000
85	A	86	THR	0	-0.061	-0.047	29.639	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.930	0.952	29.539	0.127	0.127	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.711	-0.819	32.887	-0.102	-0.102	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.891	0.951	35.909	0.062	0.062	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.908	-0.948	38.938	-0.079	-0.079	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.880	-0.939	40.922	-0.068	-0.068	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.935	0.966	37.178	0.092	0.092	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.089	-0.066	41.796	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.805	-0.892	41.045	-0.089	-0.089	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.825	0.925	40.768	0.090	0.090	0.000	0.000	0.000	0.000
95	A	96	TRP	0	0.008	-0.009	32.973	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	HIS	0	0.015	0.008	37.356	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.824	0.875	33.890	0.134	0.134	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.003	0.004	31.211	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.759	-0.845	29.955	-0.156	-0.156	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.843	0.909	29.049	0.099	0.099	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.002	0.007	25.405	0.009	0.009	0.000	0.000	0.000	0.000
102	A	103	SER	0	0.002	-0.010	24.928	0.005	0.005	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.000	0.003	23.745	0.005	0.005	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.806	0.878	20.797	0.153	0.153	0.000	0.000	0.000	0.000
105	A	106	PHE	0	-0.014	0.009	19.483	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.003	-0.018	16.724	0.026	0.026	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.834	0.929	17.477	0.091	0.091	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.856	0.911	16.388	-0.041	-0.041	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.010	-0.010	18.014	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.875	0.940	16.417	-0.313	-0.313	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.021	-0.010	20.860	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.034	-0.025	24.173	0.019	0.019	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.855	-0.926	26.164	0.100	0.100	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.856	-0.932	26.795	0.166	0.166	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.031	-0.013	28.423	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.891	0.939	30.236	-0.060	-0.060	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.005	-0.007	30.326	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.871	-0.937	32.818	0.057	0.057	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.803	-0.909	35.961	0.046	0.046	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.040	0.006	30.430	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.773	0.882	33.634	-0.034	-0.034	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.019	-0.004	31.759	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	GLY	0	-0.008	0.001	33.533	0.001	0.001	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.050	-0.021	32.018	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.875	-0.922	34.887	-0.026	-0.026	0.000	0.000	0.000	0.000
126	A	127	ASN	0	-0.049	-0.037	36.065	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	128	GLY	0	-0.014	0.005	34.143	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	129	VAL	0	0.020	0.006	31.280	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.008	-0.005	27.570	0.007	0.007	0.000	0.000	0.000	0.000
130	A	131	THR	0	0.005	-0.002	30.792	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.031	0.017	28.114	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.054	-0.037	30.771	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	134	VAL	0	0.059	0.029	28.584	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	135	PRO	0	-0.014	-0.007	31.934	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.789	0.906	30.939	-0.060	-0.060	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.006	-0.001	34.359	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.929	-0.960	36.498	0.058	0.058	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.015	0.008	35.556	0.003	0.003	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.914	0.947	38.938	-0.058	-0.058	0.000	0.000	0.000	0.000
140	A	141	LYS	1	0.932	0.952	37.550	-0.045	-0.045	0.000	0.000	0.000	0.000
141	A	142	PRO	0	0.004	-0.001	36.974	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.827	-0.879	39.793	0.059	0.059	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.012	0.008	38.358	0.005	0.005	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.795	0.886	39.396	-0.072	-0.072	0.000	0.000	0.000	0.000
145	A	146	ALA	0	0.027	0.013	40.103	0.001	0.001	0.000	0.000	0.000	0.000
146	A	147	ILE	0	-0.004	-0.007	39.372	0.000	0.000	0.000	0.000	0.000	0.000
147	A	148	GLN	0	-0.014	-0.006	43.107	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	149	ILE	0	0.019	0.004	40.996	0.003	0.003	0.000	0.000	0.000	0.000
149	A	150	SER	0	-0.012	0.004	44.177	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	151	GLY	0	0.004	0.009	45.100	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)