FMO DATABASE

FMODB ID: 4JY9N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1205641.305412
FMO2-HF: Nuclear repulsion	1152500.138268
FMO2-HF: Total energy	-53141.167145
FMO2-MP2: Total energy	-53300.817889

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.
85.918	90.001	0.816	-2.1	-2.799	-0.013

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 : 0.978 / q_NPA : 0.993

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	0.031	0.002	2.555	-11.153	-7.259	0.817	-2.093	-2.618	-0.013
4	A	26	LYS	1	0.968	0.974	4.576	41.023	41.212	-0.001	-0.007	-0.181	0.000
5	A	27	VAL	0	-0.013	-0.017	6.602	1.434	1.434	0.000	0.000	0.000	0.000
6	A	28	GLY	0	0.046	0.021	10.064	0.336	0.336	0.000	0.000	0.000	0.000
7	A	29	SER	0	-0.008	-0.005	12.698	1.192	1.192	0.000	0.000	0.000	0.000
8	A	30	SER	0	0.036	0.014	15.887	-0.244	-0.244	0.000	0.000	0.000	0.000
9	A	31	GLY	0	0.044	0.019	18.477	0.560	0.560	0.000	0.000	0.000	0.000
10	A	32	ASN	0	-0.030	-0.006	16.462	0.387	0.387	0.000	0.000	0.000	0.000
11	A	33	ALA	0	0.018	0.042	20.682	0.208	0.208	0.000	0.000	0.000	0.000
12	A	34	SER	0	0.029	-0.020	23.873	0.270	0.270	0.000	0.000	0.000	0.000
13	A	35	TRP	0	0.029	0.008	26.833	0.156	0.156	0.000	0.000	0.000	0.000
14	A	36	PHE	0	0.012	0.021	29.756	0.222	0.222	0.000	0.000	0.000	0.000
15	A	37	GLN	0	-0.012	-0.004	30.673	-0.168	-0.168	0.000	0.000	0.000	0.000
16	A	38	ALA	0	-0.040	-0.018	30.207	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	39	ILE	0	0.002	0.017	31.956	0.340	0.340	0.000	0.000	0.000	0.000
18	A	40	LYS	1	0.805	0.872	32.851	8.695	8.695	0.000	0.000	0.000	0.000
19	A	41	ALA	0	0.055	0.039	33.894	0.282	0.282	0.000	0.000	0.000	0.000
20	A	42	LYS	1	0.824	0.897	35.743	7.506	7.506	0.000	0.000	0.000	0.000
21	A	43	LYS	1	0.904	0.950	37.361	7.632	7.632	0.000	0.000	0.000	0.000
22	A	44	LEU	0	-0.022	-0.025	33.193	-0.168	-0.168	0.000	0.000	0.000	0.000
23	A	45	ASN	0	0.023	0.017	33.587	-0.433	-0.433	0.000	0.000	0.000	0.000
24	A	46	SER	0	-0.018	-0.002	35.617	0.180	0.180	0.000	0.000	0.000	0.000
25	A	47	PRO	0	0.040	0.022	34.912	-0.244	-0.244	0.000	0.000	0.000	0.000
26	A	48	GLN	0	0.002	0.015	32.586	-0.263	-0.263	0.000	0.000	0.000	0.000
27	A	49	PRO	0	-0.038	-0.016	32.806	0.257	0.257	0.000	0.000	0.000	0.000
28	A	50	LYS	1	0.956	0.982	35.943	7.580	7.580	0.000	0.000	0.000	0.000
29	A	51	PHE	0	-0.003	-0.018	34.958	-0.030	-0.030	0.000	0.000	0.000	0.000
30	A	52	GLU	-1	-0.957	-0.945	40.662	-6.696	-6.696	0.000	0.000	0.000	0.000
31	A	53	GLY	0	0.037	0.025	43.247	0.113	0.113	0.000	0.000	0.000	0.000
32	A	54	SER	0	-0.113	-0.087	39.442	-0.209	-0.209	0.000	0.000	0.000	0.000
33	A	55	GLY	0	0.044	-0.004	37.480	-0.210	-0.210	0.000	0.000	0.000	0.000
34	A	56	VAL	0	-0.050	-0.021	35.111	-0.340	-0.340	0.000	0.000	0.000	0.000
35	A	57	PRO	0	-0.073	-0.035	33.914	0.227	0.227	0.000	0.000	0.000	0.000
36	A	58	ASP	-1	-0.769	-0.862	37.155	-7.422	-7.422	0.000	0.000	0.000	0.000
37	A	59	ASN	0	-0.048	-0.066	34.608	0.009	0.009	0.000	0.000	0.000	0.000
38	A	60	GLU	-1	-0.904	-0.946	38.430	-7.127	-7.127	0.000	0.000	0.000	0.000
39	A	61	ASN	0	-0.063	-0.023	34.743	0.212	0.212	0.000	0.000	0.000	0.000
40	A	62	LEU	0	-0.047	-0.009	33.265	-0.169	-0.169	0.000	0.000	0.000	0.000
41	A	63	LYS	1	1.011	1.001	37.529	8.263	8.263	0.000	0.000	0.000	0.000
42	A	64	THR	0	0.065	0.017	38.476	-0.200	-0.200	0.000	0.000	0.000	0.000
43	A	65	SER	0	0.017	0.011	38.364	-0.090	-0.090	0.000	0.000	0.000	0.000
44	A	66	GLN	0	-0.044	-0.039	33.654	0.017	0.017	0.000	0.000	0.000	0.000
45	A	67	GLN	0	-0.006	0.012	34.142	-0.474	-0.474	0.000	0.000	0.000	0.000
46	A	68	HIS	0	0.025	0.030	31.162	-0.044	-0.044	0.000	0.000	0.000	0.000
47	A	69	GLY	0	0.026	0.007	29.942	-0.231	-0.231	0.000	0.000	0.000	0.000
48	A	70	TYR	0	-0.058	-0.040	23.275	0.018	0.018	0.000	0.000	0.000	0.000
49	A	71	TRP	0	-0.017	-0.007	28.943	-0.214	-0.214	0.000	0.000	0.000	0.000
50	A	72	ARG	1	0.976	0.973	19.501	14.245	14.245	0.000	0.000	0.000	0.000
51	A	73	ARG	1	0.748	0.860	24.915	11.801	11.801	0.000	0.000	0.000	0.000
52	A	74	GLN	0	-0.037	-0.031	23.304	-0.558	-0.558	0.000	0.000	0.000	0.000
53	A	75	ALA	0	0.088	0.051	24.102	0.474	0.474	0.000	0.000	0.000	0.000
54	A	76	ARG	1	0.866	0.925	25.202	9.617	9.617	0.000	0.000	0.000	0.000
55	A	77	PHE	0	0.003	-0.021	23.845	0.163	0.163	0.000	0.000	0.000	0.000
56	A	78	LYS	1	0.957	0.998	28.298	8.855	8.855	0.000	0.000	0.000	0.000
57	A	79	PRO	0	0.194	0.101	29.880	-0.193	-0.193	0.000	0.000	0.000	0.000
58	A	80	GLY	0	-0.119	-0.055	31.092	0.325	0.325	0.000	0.000	0.000	0.000
59	A	81	LYS	1	0.909	1.115	31.410	7.846	7.846	0.000	0.000	0.000	0.000
60	A	82	GLY	0	0.063	-0.128	32.207	0.213	0.213	0.000	0.000	0.000	0.000
61	A	83	ARG	1	0.972	0.960	25.153	11.003	11.003	0.000	0.000	0.000	0.000
62	A	84	ARG	1	0.957	1.009	21.116	13.343	13.343	0.000	0.000	0.000	0.000
63	A	85	LYS	1	0.949	0.969	28.545	9.193	9.193	0.000	0.000	0.000	0.000
64	A	86	PRO	0	0.067	0.031	29.340	-0.062	-0.062	0.000	0.000	0.000	0.000
65	A	87	VAL	0	-0.069	-0.053	30.418	0.448	0.448	0.000	0.000	0.000	0.000
66	A	88	PRO	0	0.038	0.029	31.260	-0.262	-0.262	0.000	0.000	0.000	0.000
67	A	89	ASP	-1	-0.790	-0.888	28.689	-10.853	-10.853	0.000	0.000	0.000	0.000
68	A	90	ALA	0	-0.080	-0.036	28.765	0.417	0.417	0.000	0.000	0.000	0.000
69	A	91	TRP	0	0.039	0.002	28.663	-0.404	-0.404	0.000	0.000	0.000	0.000
70	A	92	TYR	0	-0.003	-0.005	26.577	0.460	0.460	0.000	0.000	0.000	0.000
71	A	93	PHE	0	0.086	0.049	28.143	-0.251	-0.251	0.000	0.000	0.000	0.000
72	A	94	TYR	0	-0.047	-0.016	23.197	-0.186	-0.186	0.000	0.000	0.000	0.000
73	A	95	TYR	0	0.105	0.068	27.489	0.131	0.131	0.000	0.000	0.000	0.000
74	A	96	THR	0	-0.008	-0.041	26.686	-0.564	-0.564	0.000	0.000	0.000	0.000
75	A	97	GLY	0	0.001	0.023	23.960	0.176	0.176	0.000	0.000	0.000	0.000
76	A	98	THR	0	-0.058	-0.024	22.609	-0.360	-0.360	0.000	0.000	0.000	0.000
77	A	99	GLY	0	0.049	0.034	21.398	0.197	0.197	0.000	0.000	0.000	0.000
78	A	100	PRO	0	-0.053	-0.035	18.390	-0.473	-0.473	0.000	0.000	0.000	0.000
79	A	101	ALA	0	-0.020	-0.016	18.570	-0.807	-0.807	0.000	0.000	0.000	0.000
80	A	102	ALA	0	-0.032	0.007	19.505	0.504	0.504	0.000	0.000	0.000	0.000
81	A	103	ASP	-1	-0.891	-0.955	16.690	-17.044	-17.044	0.000	0.000	0.000	0.000
82	A	104	LEU	0	-0.088	-0.021	20.170	0.284	0.284	0.000	0.000	0.000	0.000
83	A	105	ASN	0	-0.034	-0.026	22.880	0.695	0.695	0.000	0.000	0.000	0.000
84	A	106	TRP	0	-0.007	-0.026	26.202	0.055	0.055	0.000	0.000	0.000	0.000
85	A	107	GLY	0	0.002	-0.008	29.288	0.201	0.201	0.000	0.000	0.000	0.000
86	A	108	ASP	-1	-0.859	-0.907	24.745	-12.074	-12.074	0.000	0.000	0.000	0.000
87	A	109	SER	0	-0.019	-0.003	27.024	-0.067	-0.067	0.000	0.000	0.000	0.000
88	A	110	GLN	0	0.022	-0.012	21.191	-0.903	-0.903	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.768	-0.845	24.405	-11.495	-11.495	0.000	0.000	0.000	0.000
90	A	112	GLY	0	-0.031	-0.011	24.551	-0.472	-0.472	0.000	0.000	0.000	0.000
91	A	113	ILE	0	-0.010	-0.001	23.556	-0.101	-0.101	0.000	0.000	0.000	0.000
92	A	114	VAL	0	-0.030	-0.012	27.276	0.227	0.227	0.000	0.000	0.000	0.000
93	A	115	TRP	0	-0.027	-0.008	25.776	0.062	0.062	0.000	0.000	0.000	0.000
94	A	116	VAL	0	-0.019	0.001	31.661	0.241	0.241	0.000	0.000	0.000	0.000
95	A	117	ALA	0	0.006	-0.007	34.091	-0.215	-0.215	0.000	0.000	0.000	0.000
96	A	118	ALA	0	0.039	0.035	36.627	0.194	0.194	0.000	0.000	0.000	0.000
97	A	119	LYS	1	0.997	0.986	39.963	6.747	6.747	0.000	0.000	0.000	0.000
98	A	120	GLY	0	-0.012	-0.015	42.464	0.070	0.070	0.000	0.000	0.000	0.000
99	A	121	ALA	0	-0.050	-0.008	36.834	-0.042	-0.042	0.000	0.000	0.000	0.000
100	A	122	ASP	-1	-0.852	-0.937	35.983	-8.735	-8.735	0.000	0.000	0.000	0.000
101	A	123	VAL	0	0.019	0.011	32.542	-0.174	-0.174	0.000	0.000	0.000	0.000
102	A	124	LYS	1	0.917	0.962	28.588	10.209	10.209	0.000	0.000	0.000	0.000
103	A	125	SER	0	-0.035	0.000	31.309	-0.279	-0.279	0.000	0.000	0.000	0.000
104	A	126	ARG	1	0.913	0.933	26.391	10.858	10.858	0.000	0.000	0.000	0.000
105	A	127	SER	0	0.006	0.014	30.173	0.169	0.169	0.000	0.000	0.000	0.000
106	A	128	ASN	0	0.018	0.007	28.791	-0.515	-0.515	0.000	0.000	0.000	0.000
107	A	129	GLN	0	0.036	0.032	29.363	0.227	0.227	0.000	0.000	0.000	0.000
108	A	130	GLY	0	0.046	0.028	25.580	-0.062	-0.062	0.000	0.000	0.000	0.000
109	A	131	THR	0	-0.090	-0.059	22.311	0.173	0.173	0.000	0.000	0.000	0.000
110	A	132	ARG	1	0.840	0.928	25.494	10.674	10.674	0.000	0.000	0.000	0.000
111	A	133	ASP	-1	-0.772	-0.884	24.502	-12.302	-12.302	0.000	0.000	0.000	0.000
112	A	134	PRO	0	-0.066	-0.049	23.733	0.403	0.403	0.000	0.000	0.000	0.000
113	A	135	ASP	-1	-0.896	-0.932	25.567	-10.670	-10.670	0.000	0.000	0.000	0.000
114	A	136	LYS	1	0.788	0.888	25.947	11.474	11.474	0.000	0.000	0.000	0.000
115	A	137	PHE	0	0.010	0.001	29.339	0.338	0.338	0.000	0.000	0.000	0.000
116	A	138	ASP	-1	-0.847	-0.909	30.196	-9.305	-9.305	0.000	0.000	0.000	0.000
117	A	139	GLN	0	-0.101	-0.063	31.078	-0.274	-0.274	0.000	0.000	0.000	0.000
118	A	140	TYR	0	0.048	0.018	32.262	0.340	0.340	0.000	0.000	0.000	0.000
119	A	141	PRO	0	-0.038	-0.029	35.016	-0.158	-0.158	0.000	0.000	0.000	0.000
120	A	142	LEU	0	-0.013	0.001	34.281	-0.045	-0.045	0.000	0.000	0.000	0.000
121	A	143	ARG	1	0.815	0.902	37.827	7.611	7.611	0.000	0.000	0.000	0.000
122	A	144	PHE	0	0.056	0.016	36.553	-0.204	-0.204	0.000	0.000	0.000	0.000
123	A	145	SER	0	-0.032	-0.041	42.041	0.183	0.183	0.000	0.000	0.000	0.000
124	A	146	ASP	-1	-0.846	-0.888	42.524	-7.380	-7.380	0.000	0.000	0.000	0.000
125	A	147	GLY	0	0.096	0.055	44.846	0.050	0.050	0.000	0.000	0.000	0.000
126	A	148	GLY	0	-0.030	-0.024	41.255	-0.188	-0.188	0.000	0.000	0.000	0.000
127	A	149	PRO	0	-0.041	-0.020	38.071	0.053	0.053	0.000	0.000	0.000	0.000
128	A	150	ASP	-1	-0.756	-0.862	40.335	-7.632	-7.632	0.000	0.000	0.000	0.000
129	A	151	GLY	0	0.070	0.028	41.453	-0.087	-0.087	0.000	0.000	0.000	0.000
130	A	152	ASN	0	-0.106	-0.065	38.928	0.015	0.015	0.000	0.000	0.000	0.000
131	A	153	PHE	0	-0.023	-0.011	33.785	-0.211	-0.211	0.000	0.000	0.000	0.000
132	A	154	ARG	1	0.812	0.889	38.157	8.298	8.298	0.000	0.000	0.000	0.000
133	A	155	TRP	0	0.036	0.004	37.164	-0.338	-0.338	0.000	0.000	0.000	0.000
134	A	156	ASP	-1	-0.789	-0.862	36.851	-8.166	-8.166	0.000	0.000	0.000	0.000
135	A	157	PHE	0	0.075	0.044	39.470	-0.100	-0.100	0.000	0.000	0.000	0.000
136	A	158	ILE	0	0.010	0.013	36.157	-0.048	-0.048	0.000	0.000	0.000	0.000
137	A	159	PRO	0	0.032	0.029	40.666	0.042	0.042	0.000	0.000	0.000	0.000
138	A	160	LEU	0	0.035	0.023	41.906	-0.102	-0.102	0.000	0.000	0.000	0.000

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