FMO DATABASE

FMODB ID: 5J52Z

Calculation Name: 2GEC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GEC

Chain ID: A

ChEMBL ID:

UniProt ID: P32923

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	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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1205509.275136
FMO2-HF: Nuclear repulsion	1152367.21782
FMO2-HF: Total energy	-53142.057316
FMO2-MP2: Total energy	-53301.729024

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:23:ARG)

Summations of interaction energy for fragment #1(A:23:ARG)

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.
87.869	91.568	0.47	-1.919	-2.25	-0.011

Interaction energy analysis for fragmet #1(A:23:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.989 / q_NPA : 0.995

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	25	PRO	0	0.018	0.005	2.706	-9.883	-6.342	0.471	-1.913	-2.099	-0.011
4	A	26	LYS	1	0.969	0.972	4.768	40.363	40.521	-0.001	-0.006	-0.151	0.000
5	A	27	VAL	0	-0.018	-0.018	6.739	1.857	1.857	0.000	0.000	0.000	0.000
6	A	28	GLY	0	0.036	0.026	10.072	0.384	0.384	0.000	0.000	0.000	0.000
7	A	29	SER	0	-0.017	-0.016	12.634	1.276	1.276	0.000	0.000	0.000	0.000
8	A	30	SER	0	0.027	0.004	15.922	-0.186	-0.186	0.000	0.000	0.000	0.000
9	A	31	GLY	0	0.062	0.040	18.431	0.479	0.479	0.000	0.000	0.000	0.000
10	A	32	ASN	0	-0.005	0.006	16.017	0.449	0.449	0.000	0.000	0.000	0.000
11	A	33	ALA	0	0.022	0.036	20.331	0.263	0.263	0.000	0.000	0.000	0.000
12	A	34	SER	0	0.019	-0.016	23.663	0.210	0.210	0.000	0.000	0.000	0.000
13	A	35	TRP	0	0.017	0.008	26.728	0.127	0.127	0.000	0.000	0.000	0.000
14	A	36	PHE	0	0.020	0.023	29.686	0.175	0.175	0.000	0.000	0.000	0.000
15	A	37	GLN	0	0.012	0.006	30.256	-0.184	-0.184	0.000	0.000	0.000	0.000
16	A	38	ALA	0	-0.041	-0.017	29.435	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	39	ILE	0	0.006	0.023	31.330	0.319	0.319	0.000	0.000	0.000	0.000
18	A	40	LYS	1	0.807	0.872	32.175	8.749	8.749	0.000	0.000	0.000	0.000
19	A	41	ALA	0	0.048	0.038	33.674	0.275	0.275	0.000	0.000	0.000	0.000
20	A	42	LYS	1	0.827	0.898	35.492	7.564	7.564	0.000	0.000	0.000	0.000
21	A	43	LYS	1	0.919	0.944	37.240	7.649	7.649	0.000	0.000	0.000	0.000
22	A	44	LEU	0	-0.035	-0.025	32.845	-0.164	-0.164	0.000	0.000	0.000	0.000
23	A	45	ASN	0	0.029	0.024	33.406	-0.439	-0.439	0.000	0.000	0.000	0.000
24	A	46	SER	0	-0.019	-0.007	35.620	0.202	0.202	0.000	0.000	0.000	0.000
25	A	47	PRO	0	0.008	0.007	34.746	-0.255	-0.255	0.000	0.000	0.000	0.000
26	A	48	GLN	0	0.022	0.019	32.603	-0.183	-0.183	0.000	0.000	0.000	0.000
27	A	49	PRO	0	-0.037	-0.009	32.534	0.277	0.277	0.000	0.000	0.000	0.000
28	A	50	LYS	1	0.949	0.975	35.589	7.636	7.636	0.000	0.000	0.000	0.000
29	A	51	PHE	0	-0.012	-0.009	34.985	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	52	GLU	-1	-0.914	-0.941	40.498	-6.720	-6.720	0.000	0.000	0.000	0.000
31	A	53	GLY	0	0.056	0.044	42.694	0.132	0.132	0.000	0.000	0.000	0.000
32	A	54	SER	0	-0.112	-0.096	39.155	-0.208	-0.208	0.000	0.000	0.000	0.000
33	A	55	GLY	0	0.035	-0.004	37.237	-0.228	-0.228	0.000	0.000	0.000	0.000
34	A	56	VAL	0	-0.049	-0.016	34.676	-0.337	-0.337	0.000	0.000	0.000	0.000
35	A	57	PRO	0	-0.043	-0.023	33.537	0.217	0.217	0.000	0.000	0.000	0.000
36	A	58	ASP	-1	-0.810	-0.876	36.748	-7.444	-7.444	0.000	0.000	0.000	0.000
37	A	59	ASN	0	-0.028	-0.047	34.475	0.046	0.046	0.000	0.000	0.000	0.000
38	A	60	GLU	-1	-0.905	-0.951	38.167	-7.137	-7.137	0.000	0.000	0.000	0.000
39	A	61	ASN	0	-0.071	-0.022	34.393	0.219	0.219	0.000	0.000	0.000	0.000
40	A	62	LEU	0	-0.042	-0.018	33.048	-0.196	-0.196	0.000	0.000	0.000	0.000
41	A	63	LYS	1	0.996	1.000	37.552	8.229	8.229	0.000	0.000	0.000	0.000
42	A	64	THR	0	0.063	0.017	38.455	-0.220	-0.220	0.000	0.000	0.000	0.000
43	A	65	SER	0	0.021	0.014	38.519	-0.097	-0.097	0.000	0.000	0.000	0.000
44	A	66	GLN	0	-0.031	-0.041	33.610	0.052	0.052	0.000	0.000	0.000	0.000
45	A	67	GLN	0	-0.013	0.005	33.977	-0.488	-0.488	0.000	0.000	0.000	0.000
46	A	68	HIS	0	0.012	0.021	30.914	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	69	GLY	0	0.040	0.012	29.614	-0.250	-0.250	0.000	0.000	0.000	0.000
48	A	70	TYR	0	-0.045	-0.035	22.958	0.031	0.031	0.000	0.000	0.000	0.000
49	A	71	TRP	0	-0.020	-0.011	28.554	-0.241	-0.241	0.000	0.000	0.000	0.000
50	A	72	ARG	1	0.952	0.969	19.069	14.236	14.236	0.000	0.000	0.000	0.000
51	A	73	ARG	1	0.773	0.869	24.545	11.906	11.906	0.000	0.000	0.000	0.000
52	A	74	GLN	0	-0.018	-0.023	23.181	-0.528	-0.528	0.000	0.000	0.000	0.000
53	A	75	ALA	0	0.079	0.049	24.348	0.462	0.462	0.000	0.000	0.000	0.000
54	A	76	ARG	1	0.846	0.923	25.300	9.546	9.546	0.000	0.000	0.000	0.000
55	A	77	PHE	0	0.028	-0.007	24.081	0.090	0.090	0.000	0.000	0.000	0.000
56	A	78	LYS	1	0.937	0.992	28.524	8.871	8.871	0.000	0.000	0.000	0.000
57	A	79	PRO	0	0.065	0.049	30.256	-0.138	-0.138	0.000	0.000	0.000	0.000
58	A	80	GLY	0	0.002	0.005	31.462	0.270	0.270	0.000	0.000	0.000	0.000
59	A	81	LYS	1	0.931	0.953	30.888	7.735	7.735	0.000	0.000	0.000	0.000
60	A	82	GLY	0	0.050	0.027	32.393	0.250	0.250	0.000	0.000	0.000	0.000
61	A	83	ARG	1	0.953	0.970	24.695	11.222	11.222	0.000	0.000	0.000	0.000
62	A	84	ARG	1	0.969	0.990	21.384	13.196	13.196	0.000	0.000	0.000	0.000
63	A	85	LYS	1	0.964	0.986	28.794	9.233	9.233	0.000	0.000	0.000	0.000
64	A	86	PRO	0	0.058	0.021	29.297	-0.054	-0.054	0.000	0.000	0.000	0.000
65	A	87	VAL	0	-0.054	-0.046	30.552	0.452	0.452	0.000	0.000	0.000	0.000
66	A	88	PRO	0	0.033	0.027	31.178	-0.283	-0.283	0.000	0.000	0.000	0.000
67	A	89	ASP	-1	-0.765	-0.880	28.734	-10.749	-10.749	0.000	0.000	0.000	0.000
68	A	90	ALA	0	-0.072	-0.031	28.190	0.418	0.418	0.000	0.000	0.000	0.000
69	A	91	TRP	0	0.012	-0.019	28.363	-0.384	-0.384	0.000	0.000	0.000	0.000
70	A	92	TYR	0	-0.014	-0.020	26.117	0.458	0.458	0.000	0.000	0.000	0.000
71	A	93	PHE	0	0.074	0.049	27.700	-0.257	-0.257	0.000	0.000	0.000	0.000
72	A	94	TYR	0	-0.037	-0.013	23.024	-0.219	-0.219	0.000	0.000	0.000	0.000
73	A	95	TYR	0	0.082	0.058	27.269	0.134	0.134	0.000	0.000	0.000	0.000
74	A	96	THR	0	0.002	-0.023	26.511	-0.552	-0.552	0.000	0.000	0.000	0.000
75	A	97	GLY	0	-0.016	0.008	23.981	0.252	0.252	0.000	0.000	0.000	0.000
76	A	98	THR	0	-0.056	-0.025	22.841	-0.272	-0.272	0.000	0.000	0.000	0.000
77	A	99	GLY	0	0.072	0.041	21.391	0.124	0.124	0.000	0.000	0.000	0.000
78	A	100	PRO	0	-0.093	-0.059	18.167	-0.472	-0.472	0.000	0.000	0.000	0.000
79	A	101	ALA	0	-0.006	0.000	18.305	-0.752	-0.752	0.000	0.000	0.000	0.000
80	A	102	ALA	0	-0.028	0.005	19.620	0.482	0.482	0.000	0.000	0.000	0.000
81	A	103	ASP	-1	-0.920	-0.965	17.580	-16.567	-16.567	0.000	0.000	0.000	0.000
82	A	104	LEU	0	-0.065	-0.009	20.520	0.325	0.325	0.000	0.000	0.000	0.000
83	A	105	ASN	0	-0.059	-0.047	23.270	0.703	0.703	0.000	0.000	0.000	0.000
84	A	106	TRP	0	-0.019	-0.036	26.771	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	107	GLY	0	0.018	0.001	29.583	0.272	0.272	0.000	0.000	0.000	0.000
86	A	108	ASP	-1	-0.827	-0.888	24.872	-12.048	-12.048	0.000	0.000	0.000	0.000
87	A	109	SER	0	-0.029	-0.009	26.793	-0.071	-0.071	0.000	0.000	0.000	0.000
88	A	110	GLN	0	0.001	-0.019	21.210	-0.875	-0.875	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.746	-0.839	24.277	-11.506	-11.506	0.000	0.000	0.000	0.000
90	A	112	GLY	0	-0.049	-0.018	24.375	-0.480	-0.480	0.000	0.000	0.000	0.000
91	A	113	ILE	0	-0.009	0.000	23.652	-0.165	-0.165	0.000	0.000	0.000	0.000
92	A	114	VAL	0	-0.024	-0.010	27.388	0.245	0.245	0.000	0.000	0.000	0.000
93	A	115	TRP	0	-0.019	-0.004	25.909	0.105	0.105	0.000	0.000	0.000	0.000
94	A	116	VAL	0	-0.013	0.008	31.726	0.245	0.245	0.000	0.000	0.000	0.000
95	A	117	ALA	0	0.007	-0.003	33.933	-0.233	-0.233	0.000	0.000	0.000	0.000
96	A	118	ALA	0	0.066	0.046	36.557	0.205	0.205	0.000	0.000	0.000	0.000
97	A	119	LYS	1	0.973	0.973	39.759	6.723	6.723	0.000	0.000	0.000	0.000
98	A	120	GLY	0	0.001	-0.009	41.820	0.167	0.167	0.000	0.000	0.000	0.000
99	A	121	ALA	0	-0.062	-0.013	36.665	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	122	ASP	-1	-0.825	-0.916	35.726	-8.784	-8.784	0.000	0.000	0.000	0.000
101	A	123	VAL	0	0.019	0.012	32.717	-0.178	-0.178	0.000	0.000	0.000	0.000
102	A	124	LYS	1	0.873	0.933	28.811	10.127	10.127	0.000	0.000	0.000	0.000
103	A	125	SER	0	-0.008	0.003	30.927	-0.311	-0.311	0.000	0.000	0.000	0.000
104	A	126	ARG	1	0.882	0.928	26.172	10.831	10.831	0.000	0.000	0.000	0.000
105	A	127	SER	0	0.021	0.020	29.598	0.258	0.258	0.000	0.000	0.000	0.000
106	A	128	ASN	0	0.010	0.003	28.920	-0.492	-0.492	0.000	0.000	0.000	0.000
107	A	129	GLN	0	0.050	0.049	29.711	0.262	0.262	0.000	0.000	0.000	0.000
108	A	130	GLY	0	0.048	0.025	25.678	-0.081	-0.081	0.000	0.000	0.000	0.000
109	A	131	THR	0	-0.083	-0.062	21.923	0.207	0.207	0.000	0.000	0.000	0.000
110	A	132	ARG	1	0.801	0.905	25.110	10.527	10.527	0.000	0.000	0.000	0.000
111	A	133	ASP	-1	-0.760	-0.876	24.369	-12.258	-12.258	0.000	0.000	0.000	0.000
112	A	134	PRO	0	-0.063	-0.049	23.538	0.406	0.406	0.000	0.000	0.000	0.000
113	A	135	ASP	-1	-0.876	-0.909	25.210	-10.753	-10.753	0.000	0.000	0.000	0.000
114	A	136	LYS	1	0.757	0.851	25.672	11.542	11.542	0.000	0.000	0.000	0.000
115	A	137	PHE	0	0.004	0.003	29.294	0.347	0.347	0.000	0.000	0.000	0.000
116	A	138	ASP	-1	-0.804	-0.890	29.986	-9.308	-9.308	0.000	0.000	0.000	0.000
117	A	139	GLN	0	-0.116	-0.066	30.941	-0.330	-0.330	0.000	0.000	0.000	0.000
118	A	140	TYR	0	0.037	0.007	32.173	0.348	0.348	0.000	0.000	0.000	0.000
119	A	141	PRO	0	-0.027	-0.012	34.737	-0.152	-0.152	0.000	0.000	0.000	0.000
120	A	142	LEU	0	-0.017	-0.009	34.074	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	143	ARG	1	0.791	0.885	37.565	7.609	7.609	0.000	0.000	0.000	0.000
122	A	144	PHE	0	0.058	0.015	36.156	-0.245	-0.245	0.000	0.000	0.000	0.000
123	A	145	SER	0	-0.027	-0.036	41.617	0.177	0.177	0.000	0.000	0.000	0.000
124	A	146	ASP	-1	-0.850	-0.891	42.239	-7.366	-7.366	0.000	0.000	0.000	0.000
125	A	147	GLY	0	0.056	0.030	44.063	0.085	0.085	0.000	0.000	0.000	0.000
126	A	148	GLY	0	-0.028	-0.004	41.582	-0.208	-0.208	0.000	0.000	0.000	0.000
127	A	149	PRO	0	-0.024	-0.016	37.873	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	150	ASP	-1	-0.790	-0.894	40.001	-7.646	-7.646	0.000	0.000	0.000	0.000
129	A	151	GLY	0	0.061	0.024	41.090	-0.098	-0.098	0.000	0.000	0.000	0.000
130	A	152	ASN	0	-0.078	-0.050	38.520	-0.022	-0.022	0.000	0.000	0.000	0.000
131	A	153	PHE	0	-0.016	-0.004	33.363	-0.184	-0.184	0.000	0.000	0.000	0.000
132	A	154	ARG	1	0.802	0.883	37.676	8.275	8.275	0.000	0.000	0.000	0.000
133	A	155	TRP	0	0.062	0.029	36.661	-0.340	-0.340	0.000	0.000	0.000	0.000
134	A	156	ASP	-1	-0.803	-0.873	36.264	-8.193	-8.193	0.000	0.000	0.000	0.000
135	A	157	PHE	0	0.047	0.020	39.044	-0.111	-0.111	0.000	0.000	0.000	0.000
136	A	158	ILE	0	0.038	0.046	35.592	0.038	0.038	0.000	0.000	0.000	0.000
137	A	159	PRO	0	0.015	0.015	40.137	0.066	0.066	0.000	0.000	0.000	0.000
138	A	160	LEU	0	0.044	0.021	41.484	-0.111	-0.111	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:ARG)