FMO DATABASE

FMODB ID: Z2MYN

Calculation Name: 3GIO-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GIO

Chain ID: A

ChEMBL ID:

UniProt ID: O25318

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	150
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1378760.252857
FMO2-HF: Nuclear repulsion	1318887.032043
FMO2-HF: Total energy	-59873.220814
FMO2-MP2: Total energy	-60047.941745

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:33:ACE )

Summations of interaction energy for fragment #1(A:33:ACE )

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.
6.878	2.226	9.835	-1.043	-4.139	-0.032

Interaction energy analysis for fragmet #1(A:33:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.011

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	35	SER	0	0.009	0.018	3.782	0.838	1.658	-0.007	-0.373	-0.440	0.000
4	A	36	PHE	0	-0.008	-0.013	7.169	-0.101	-0.101	0.000	0.000	0.000	0.000
5	A	37	LEU	0	-0.010	-0.001	6.728	-0.028	-0.028	0.000	0.000	0.000	0.000
6	A	38	GLN	0	0.001	-0.004	8.667	0.029	0.029	0.000	0.000	0.000	0.000
7	A	39	ASP	-1	-0.934	-0.959	11.312	0.100	0.100	0.000	0.000	0.000	0.000
8	A	40	VAL	0	-0.013	0.007	12.696	0.020	0.020	0.000	0.000	0.000	0.000
9	A	41	PRO	0	0.003	-0.005	14.273	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	42	TYR	0	0.058	0.008	17.538	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	43	TRP	0	0.029	0.003	17.773	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	44	MET	0	-0.062	-0.001	13.404	0.005	0.005	0.000	0.000	0.000	0.000
13	A	45	LEU	0	-0.011	0.000	16.264	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	46	GLN	0	-0.004	-0.003	16.677	0.019	0.019	0.000	0.000	0.000	0.000
15	A	47	ASN	0	-0.012	0.001	19.426	0.001	0.001	0.000	0.000	0.000	0.000
16	A	48	ARG	1	0.933	0.939	21.392	0.115	0.115	0.000	0.000	0.000	0.000
17	A	49	SER	0	0.008	0.005	24.052	0.005	0.005	0.000	0.000	0.000	0.000
18	A	50	GLU	-1	-0.984	-0.975	26.256	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	51	TYR	0	0.019	0.026	28.250	0.004	0.004	0.000	0.000	0.000	0.000
20	A	52	ILE	0	0.045	0.024	29.264	0.002	0.002	0.000	0.000	0.000	0.000
21	A	53	THR	0	0.006	0.000	30.428	0.000	0.000	0.000	0.000	0.000	0.000
22	A	54	GLN	0	-0.032	-0.032	26.460	0.002	0.002	0.000	0.000	0.000	0.000
23	A	55	GLY	0	-0.008	0.003	24.814	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	56	VAL	0	0.002	-0.006	18.447	0.008	0.008	0.000	0.000	0.000	0.000
25	A	57	ASP	-1	-0.872	-0.934	18.618	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	58	SER	0	-0.049	-0.052	13.845	0.017	0.017	0.000	0.000	0.000	0.000
27	A	59	SER	0	-0.006	-0.022	14.998	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	60	HIS	0	0.015	0.029	9.157	0.026	0.026	0.000	0.000	0.000	0.000
29	A	61	ILE	0	-0.005	0.004	11.274	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	62	VAL	0	-0.026	-0.009	12.474	0.005	0.005	0.000	0.000	0.000	0.000
31	A	63	ASP	-1	-0.876	-0.932	15.015	0.250	0.250	0.000	0.000	0.000	0.000
32	A	64	GLY	0	-0.046	-0.036	16.974	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	65	LYS	1	0.910	0.970	18.197	-0.119	-0.119	0.000	0.000	0.000	0.000
34	A	66	LYS	1	0.974	1.010	17.633	-0.117	-0.117	0.000	0.000	0.000	0.000
35	A	67	THR	0	0.126	0.036	14.788	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	68	GLU	-1	-0.854	-0.924	17.079	0.093	0.093	0.000	0.000	0.000	0.000
37	A	69	GLU	-1	-0.901	-0.955	20.470	0.090	0.090	0.000	0.000	0.000	0.000
38	A	70	ILE	0	-0.028	-0.023	14.974	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	71	GLU	-1	-0.849	-0.934	17.729	0.112	0.112	0.000	0.000	0.000	0.000
40	A	72	LYS	1	0.847	0.930	19.236	-0.103	-0.103	0.000	0.000	0.000	0.000
41	A	73	ILE	0	-0.022	0.002	19.454	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	74	ALA	0	0.034	0.017	17.488	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	75	THR	0	0.002	-0.010	19.523	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	76	LYS	1	0.947	0.978	22.716	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	77	ARG	1	0.874	0.932	17.350	-0.042	-0.042	0.000	0.000	0.000	0.000
46	A	78	ALA	0	0.044	0.029	21.677	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	79	THR	0	-0.010	-0.013	23.195	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	80	ILE	0	-0.003	0.002	25.616	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	81	ARG	1	0.911	0.976	21.714	0.028	0.028	0.000	0.000	0.000	0.000
50	A	82	VAL	0	0.002	0.025	25.852	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	83	ALA	0	0.033	0.013	28.634	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	84	GLN	0	0.006	-0.017	25.778	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	85	ASN	0	-0.020	0.010	26.615	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	86	ILE	0	0.008	0.011	30.135	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	87	VAL	0	-0.003	-0.003	32.543	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	88	HIS	0	-0.076	-0.071	29.218	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	89	LYS	1	1.020	1.029	33.378	0.023	0.023	0.000	0.000	0.000	0.000
58	A	90	LEU	0	-0.006	-0.009	35.806	0.000	0.000	0.000	0.000	0.000	0.000
59	A	91	LYS	1	0.871	0.958	32.622	0.031	0.031	0.000	0.000	0.000	0.000
60	A	92	GLU	-1	-0.913	-0.949	35.056	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	93	ALA	0	-0.047	-0.024	38.782	0.001	0.001	0.000	0.000	0.000	0.000
62	A	94	TYR	0	-0.040	-0.022	41.302	0.001	0.001	0.000	0.000	0.000	0.000
63	A	95	LEU	0	-0.011	-0.021	39.053	0.000	0.000	0.000	0.000	0.000	0.000
64	A	96	SER	0	-0.010	0.018	42.696	0.000	0.000	0.000	0.000	0.000	0.000
65	A	97	LYS	1	1.003	0.991	44.441	0.023	0.023	0.000	0.000	0.000	0.000
66	A	98	THR	0	-0.090	-0.040	47.062	0.001	0.001	0.000	0.000	0.000	0.000
67	A	99	ASN	0	0.038	0.028	46.044	0.002	0.002	0.000	0.000	0.000	0.000
68	A	100	ARG	1	0.922	0.953	47.990	0.012	0.012	0.000	0.000	0.000	0.000
69	A	101	ILE	0	-0.035	-0.005	45.009	0.001	0.001	0.000	0.000	0.000	0.000
70	A	102	LYS	1	0.969	0.982	49.030	0.012	0.012	0.000	0.000	0.000	0.000
71	A	103	GLN	0	0.054	0.054	47.154	0.000	0.000	0.000	0.000	0.000	0.000
72	A	104	LYS	1	0.953	0.972	44.972	0.016	0.016	0.000	0.000	0.000	0.000
73	A	105	ILE	0	0.020	0.007	41.003	0.001	0.001	0.000	0.000	0.000	0.000
74	A	106	THR	0	0.013	-0.011	40.344	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	107	ASN	0	0.064	0.021	33.087	0.000	0.000	0.000	0.000	0.000	0.000
76	A	108	GLU	-1	-0.867	-0.944	35.836	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	109	MET	0	0.004	0.021	36.777	0.001	0.001	0.000	0.000	0.000	0.000
78	A	110	PHE	0	0.024	-0.002	35.953	0.001	0.001	0.000	0.000	0.000	0.000
79	A	111	ILE	0	-0.029	-0.017	31.552	0.001	0.001	0.000	0.000	0.000	0.000
80	A	112	GLN	0	0.003	0.008	33.576	0.003	0.003	0.000	0.000	0.000	0.000
81	A	113	MET	0	0.026	0.015	36.075	0.002	0.002	0.000	0.000	0.000	0.000
82	A	114	THR	0	-0.033	-0.038	30.111	0.000	0.000	0.000	0.000	0.000	0.000
83	A	115	GLN	0	-0.003	0.005	33.258	0.001	0.001	0.000	0.000	0.000	0.000
84	A	116	PRO	0	0.020	0.024	34.355	0.002	0.002	0.000	0.000	0.000	0.000
85	A	117	ILE	0	-0.008	0.003	34.444	0.001	0.001	0.000	0.000	0.000	0.000
86	A	118	TYR	0	-0.017	-0.020	28.553	0.003	0.003	0.000	0.000	0.000	0.000
87	A	119	ASP	-1	-0.906	-0.961	33.219	0.012	0.012	0.000	0.000	0.000	0.000
88	A	120	SER	0	-0.083	-0.023	35.770	0.001	0.001	0.000	0.000	0.000	0.000
89	A	121	LEU	0	-0.043	-0.012	31.449	0.000	0.000	0.000	0.000	0.000	0.000
90	A	122	MET	0	0.016	0.002	35.289	0.003	0.003	0.000	0.000	0.000	0.000
91	A	123	ASN	0	-0.088	-0.037	34.877	0.000	0.000	0.000	0.000	0.000	0.000
92	A	124	VAL	0	0.037	0.014	28.590	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	125	ASP	-1	-0.862	-0.933	29.778	0.023	0.023	0.000	0.000	0.000	0.000
94	A	126	ARG	1	0.858	0.913	21.849	-0.078	-0.078	0.000	0.000	0.000	0.000
95	A	127	LEU	0	-0.023	-0.018	24.548	0.002	0.002	0.000	0.000	0.000	0.000
96	A	128	GLY	0	-0.009	0.001	21.236	0.001	0.001	0.000	0.000	0.000	0.000
97	A	129	ILE	0	-0.026	-0.008	16.413	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	130	TYR	0	0.039	0.006	9.758	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	131	ILE	0	0.008	0.005	9.890	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	132	ASN	0	0.017	0.038	5.692	0.260	0.260	0.000	0.000	0.000	0.000
101	A	133	PRO	0	0.027	-0.012	5.340	0.077	0.077	0.000	0.000	0.000	0.000
102	A	134	ASN	0	-0.033	0.005	2.160	3.534	0.081	9.362	-3.353	-2.555	-0.014
103	A	135	ASN	0	-0.019	-0.023	2.752	1.749	-0.264	0.480	2.688	-1.156	-0.018
104	A	136	GLU	-1	-0.907	-0.941	5.083	0.636	0.630	0.000	-0.005	0.012	0.000
105	A	137	GLU	-1	-0.857	-0.899	8.085	-0.207	-0.207	0.000	0.000	0.000	0.000
106	A	138	VAL	0	-0.013	-0.031	10.291	0.000	0.000	0.000	0.000	0.000	0.000
107	A	139	PHE	0	0.031	-0.006	11.000	-0.032	-0.032	0.000	0.000	0.000	0.000
108	A	140	ALA	0	-0.018	-0.009	15.571	0.016	0.016	0.000	0.000	0.000	0.000
109	A	141	LEU	0	-0.019	0.002	19.299	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	142	VAL	0	-0.044	-0.031	22.049	0.009	0.009	0.000	0.000	0.000	0.000
111	A	143	ARG	1	0.974	0.967	25.502	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	144	ALA	0	0.009	0.025	29.086	0.004	0.004	0.000	0.000	0.000	0.000
113	A	145	ARG	1	0.905	0.950	32.179	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	146	GLY	0	0.005	-0.004	35.302	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	147	PHE	0	-0.041	-0.009	36.720	0.001	0.001	0.000	0.000	0.000	0.000
116	A	148	ASP	-1	-0.815	-0.915	38.838	0.006	0.006	0.000	0.000	0.000	0.000
117	A	149	LYS	1	0.953	0.961	41.690	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	150	ASP	-1	-0.859	-0.935	43.737	0.002	0.002	0.000	0.000	0.000	0.000
119	A	151	ALA	0	0.041	0.039	41.155	0.000	0.000	0.000	0.000	0.000	0.000
120	A	152	LEU	0	-0.045	-0.025	39.310	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	153	SER	0	-0.023	-0.038	41.812	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	154	GLU	-1	-0.950	-0.956	44.641	0.005	0.005	0.000	0.000	0.000	0.000
123	A	155	GLY	0	-0.011	-0.012	41.367	0.000	0.000	0.000	0.000	0.000	0.000
124	A	156	LEU	0	-0.029	-0.033	40.287	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	157	HIS	0	-0.004	-0.005	43.302	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	158	LYS	1	0.923	0.980	41.365	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	159	MET	0	-0.059	-0.005	39.547	0.000	0.000	0.000	0.000	0.000	0.000
128	A	160	SER	0	-0.098	-0.041	43.838	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	161	LEU	0	0.006	0.008	42.504	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	162	ASP	-1	-0.851	-0.948	46.983	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	163	ASN	0	0.020	-0.008	49.246	0.000	0.000	0.000	0.000	0.000	0.000
132	A	164	GLN	0	-0.001	0.005	50.690	0.000	0.000	0.000	0.000	0.000	0.000
133	A	165	ALA	0	0.027	0.004	46.235	0.000	0.000	0.000	0.000	0.000	0.000
134	A	166	VAL	0	0.036	0.027	45.723	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	167	SER	0	-0.004	0.002	46.167	0.000	0.000	0.000	0.000	0.000	0.000
136	A	168	ILE	0	-0.017	-0.022	46.185	0.000	0.000	0.000	0.000	0.000	0.000
137	A	169	LEU	0	-0.023	-0.022	41.301	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	170	VAL	0	0.029	0.015	42.598	0.000	0.000	0.000	0.000	0.000	0.000
139	A	171	ALA	0	0.014	0.013	43.709	0.000	0.000	0.000	0.000	0.000	0.000
140	A	172	LYS	1	0.933	0.950	41.811	0.014	0.014	0.000	0.000	0.000	0.000
141	A	173	VAL	0	0.006	0.016	38.092	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	174	GLU	-1	-0.926	-0.975	39.874	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	175	GLU	-1	-0.985	-0.995	42.015	-0.013	-0.013	0.000	0.000	0.000	0.000
144	A	176	ILE	0	-0.007	0.014	35.831	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	177	PHE	0	0.000	-0.016	35.085	0.000	0.000	0.000	0.000	0.000	0.000
146	A	178	LYS	1	0.903	0.979	38.663	0.006	0.006	0.000	0.000	0.000	0.000
147	A	179	ASP	-1	-0.889	-0.939	38.904	-0.014	-0.014	0.000	0.000	0.000	0.000
148	A	180	SER	0	-0.163	-0.090	35.419	0.000	0.000	0.000	0.000	0.000	0.000
149	A	181	VAL	0	-0.060	-0.032	37.184	0.001	0.001	0.000	0.000	0.000	0.000
150	A	182	NME	0	0.007	0.012	39.132	-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:33:ACE )