FMO DATABASE

FMODB ID: 89QLY

Calculation Name: 3GAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GAX

Chain ID: A

ChEMBL ID:

UniProt ID: P01034

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	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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-833429.54495
FMO2-HF: Nuclear repulsion	788543.001259
FMO2-HF: Total energy	-44886.543691
FMO2-MP2: Total energy	-45011.695762

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
-4.623	-1.609	1.78	-2.331	-2.464	-0.015

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / 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

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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	14	MET	0	-0.006	0.005	3.844	-0.190	1.326	-0.007	-0.823	-0.686	0.004
4	A	15	ASP	-1	-0.887	-0.956	6.552	-0.642	-0.642	0.000	0.000	0.000	0.000
5	A	16	ALA	0	-0.024	-0.011	9.873	-0.114	-0.114	0.000	0.000	0.000	0.000
6	A	17	SER	0	0.027	0.005	12.485	0.128	0.128	0.000	0.000	0.000	0.000
7	A	18	VAL	0	0.057	0.016	16.126	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	19	GLU	-1	-0.899	-0.958	18.971	-0.355	-0.355	0.000	0.000	0.000	0.000
9	A	20	GLU	-1	-0.896	-0.942	14.183	-1.034	-1.034	0.000	0.000	0.000	0.000
10	A	21	GLU	-1	-0.872	-0.935	18.454	-0.444	-0.444	0.000	0.000	0.000	0.000
11	A	22	GLY	0	0.043	0.022	16.920	0.023	0.023	0.000	0.000	0.000	0.000
12	A	23	VAL	0	0.010	0.003	14.082	0.002	0.002	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.900	0.966	16.764	0.446	0.446	0.000	0.000	0.000	0.000
14	A	25	ARG	1	0.897	0.936	20.083	0.391	0.391	0.000	0.000	0.000	0.000
15	A	26	ALA	0	-0.001	-0.002	16.187	0.039	0.039	0.000	0.000	0.000	0.000
16	A	27	LEU	0	-0.009	-0.013	18.142	0.036	0.036	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.897	-0.942	19.695	-0.271	-0.271	0.000	0.000	0.000	0.000
18	A	29	PHE	0	-0.025	-0.020	19.258	0.027	0.027	0.000	0.000	0.000	0.000
19	A	30	ALA	0	0.010	0.008	18.667	0.030	0.030	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.007	-0.010	20.782	0.036	0.036	0.000	0.000	0.000	0.000
21	A	32	GLY	0	0.011	0.009	23.729	0.027	0.027	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.965	-0.993	22.446	-0.184	-0.184	0.000	0.000	0.000	0.000
23	A	34	TYR	0	-0.021	-0.016	23.560	0.025	0.025	0.000	0.000	0.000	0.000
24	A	35	ASN	0	-0.016	-0.021	25.252	0.032	0.032	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.927	0.969	28.030	0.167	0.167	0.000	0.000	0.000	0.000
26	A	37	ALA	0	-0.017	-0.012	26.815	0.012	0.012	0.000	0.000	0.000	0.000
27	A	38	SER	0	0.001	0.033	28.766	0.014	0.014	0.000	0.000	0.000	0.000
28	A	39	ASN	0	0.016	-0.014	30.610	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	40	ASP	-1	-0.788	-0.857	32.967	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	41	MET	0	0.019	0.002	34.824	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	42	TYR	0	-0.064	-0.037	35.848	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	43	HIS	0	0.088	0.053	31.711	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	44	SER	0	-0.036	-0.010	28.549	0.009	0.009	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.893	0.967	27.404	0.150	0.150	0.000	0.000	0.000	0.000
35	A	46	ALA	0	0.045	0.018	23.284	0.011	0.011	0.000	0.000	0.000	0.000
36	A	47	CYS	0	-0.101	-0.042	25.182	0.000	0.000	0.000	0.000	0.000	0.000
37	A	48	GLN	0	0.002	-0.005	22.189	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	49	VAL	0	-0.002	0.008	17.976	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	50	VAL	0	-0.041	-0.009	17.603	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	51	ARG	1	0.880	0.901	10.508	0.317	0.317	0.000	0.000	0.000	0.000
41	A	52	ALA	0	0.006	0.006	13.229	0.007	0.007	0.000	0.000	0.000	0.000
42	A	53	ARG	1	0.968	0.994	6.969	0.784	0.784	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.884	0.935	8.080	1.625	1.625	0.000	0.000	0.000	0.000
44	A	55	GLN	0	0.029	0.024	2.332	-6.258	-4.760	1.787	-1.508	-1.778	-0.019
45	A	56	ILE	0	-0.005	0.013	5.969	0.935	0.935	0.000	0.000	0.000	0.000
46	A	57	VAL	0	0.008	-0.003	6.146	-0.431	-0.431	0.000	0.000	0.000	0.000
47	A	58	ALA	0	0.040	0.029	8.455	0.107	0.107	0.000	0.000	0.000	0.000
48	A	59	GLY	0	0.015	0.031	11.861	0.132	0.132	0.000	0.000	0.000	0.000
49	A	60	VAL	0	-0.046	-0.037	10.131	-0.231	-0.231	0.000	0.000	0.000	0.000
50	A	61	ASN	0	0.011	0.017	7.782	0.504	0.504	0.000	0.000	0.000	0.000
51	A	62	TYR	0	0.024	0.001	9.166	-0.420	-0.420	0.000	0.000	0.000	0.000
52	A	63	PHE	0	-0.031	-0.020	6.455	0.174	0.174	0.000	0.000	0.000	0.000
53	A	64	LEU	0	-0.024	-0.009	10.896	-0.059	-0.059	0.000	0.000	0.000	0.000
54	A	65	ASP	-1	-0.787	-0.848	14.005	-0.275	-0.275	0.000	0.000	0.000	0.000
55	A	66	VAL	0	0.006	-0.003	16.322	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	67	GLU	-1	-0.888	-0.954	19.883	-0.110	-0.110	0.000	0.000	0.000	0.000
57	A	68	LEU	0	0.001	-0.005	23.335	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	69	CYS	0	-0.064	-0.028	25.768	0.022	0.022	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.810	0.874	29.515	0.077	0.077	0.000	0.000	0.000	0.000
60	A	71	THR	0	-0.020	-0.029	32.282	0.003	0.003	0.000	0.000	0.000	0.000
61	A	72	THR	0	0.002	-0.008	34.812	0.004	0.004	0.000	0.000	0.000	0.000
62	A	73	CYS	0	-0.039	0.021	35.118	0.012	0.012	0.000	0.000	0.000	0.000
63	A	74	THR	0	0.002	-0.002	36.816	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	75	LYS	1	0.866	0.938	32.173	0.104	0.104	0.000	0.000	0.000	0.000
65	A	76	THR	0	-0.041	-0.004	36.260	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	77	GLN	0	0.038	-0.011	38.796	0.001	0.001	0.000	0.000	0.000	0.000
67	A	78	PRO	0	-0.060	0.028	36.517	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	79	ASN	0	0.048	-0.021	38.228	0.001	0.001	0.000	0.000	0.000	0.000
69	A	80	LEU	0	-0.054	-0.032	35.166	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	81	ASP	-1	-0.804	-0.910	30.003	-0.169	-0.169	0.000	0.000	0.000	0.000
71	A	82	ASN	0	-0.042	-0.032	32.553	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.035	0.022	34.707	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	85	PHE	0	-0.017	-0.030	29.007	0.003	0.003	0.000	0.000	0.000	0.000
74	A	86	HIS	0	0.027	0.003	34.477	0.002	0.002	0.000	0.000	0.000	0.000
75	A	87	ASP	-1	-0.899	-0.941	35.797	-0.072	-0.072	0.000	0.000	0.000	0.000
76	A	88	GLN	0	0.047	0.014	38.152	0.003	0.003	0.000	0.000	0.000	0.000
77	A	89	PRO	0	0.021	0.018	35.481	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	90	HIS	0	0.007	-0.007	35.252	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	91	LEU	0	-0.017	-0.002	37.292	0.001	0.001	0.000	0.000	0.000	0.000
80	A	92	LYS	1	0.942	0.983	31.513	0.087	0.087	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.937	0.963	32.048	0.050	0.050	0.000	0.000	0.000	0.000
82	A	94	LYS	1	0.944	0.981	26.535	0.101	0.101	0.000	0.000	0.000	0.000
83	A	95	ALA	0	0.041	0.039	25.346	0.012	0.012	0.000	0.000	0.000	0.000
84	A	96	PHE	0	-0.002	-0.006	17.110	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	97	CYS	0	-0.016	-0.003	19.554	0.001	0.001	0.000	0.000	0.000	0.000
86	A	98	SER	0	0.007	-0.003	14.516	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	99	PHE	0	-0.019	-0.017	15.538	0.038	0.038	0.000	0.000	0.000	0.000
88	A	100	GLN	0	-0.014	-0.012	10.312	0.047	0.047	0.000	0.000	0.000	0.000
89	A	101	ILE	0	-0.017	-0.009	12.999	0.087	0.087	0.000	0.000	0.000	0.000
90	A	102	TYR	0	-0.039	-0.034	12.158	-0.125	-0.125	0.000	0.000	0.000	0.000
91	A	103	ALA	0	0.023	-0.001	13.820	0.110	0.110	0.000	0.000	0.000	0.000
92	A	104	VAL	0	0.034	0.015	14.377	-0.123	-0.123	0.000	0.000	0.000	0.000
93	A	105	PRO	0	0.005	-0.002	15.896	0.070	0.070	0.000	0.000	0.000	0.000
94	A	106	TRP	0	0.032	0.015	13.538	0.031	0.031	0.000	0.000	0.000	0.000
95	A	107	GLN	0	-0.032	-0.023	20.068	0.055	0.055	0.000	0.000	0.000	0.000
96	A	108	GLY	0	-0.001	0.021	21.565	0.029	0.029	0.000	0.000	0.000	0.000
97	A	109	THR	0	-0.037	-0.015	19.626	0.006	0.006	0.000	0.000	0.000	0.000
98	A	110	MET	0	0.021	-0.009	17.798	-0.075	-0.075	0.000	0.000	0.000	0.000
99	A	111	THR	0	-0.045	-0.003	17.358	0.058	0.058	0.000	0.000	0.000	0.000
100	A	112	LEU	0	0.034	0.018	16.975	-0.062	-0.062	0.000	0.000	0.000	0.000
101	A	113	SER	0	-0.033	-0.006	13.892	0.012	0.012	0.000	0.000	0.000	0.000
102	A	114	LYS	1	0.975	0.980	13.878	0.089	0.089	0.000	0.000	0.000	0.000
103	A	115	SER	0	0.014	0.003	16.435	-0.052	-0.052	0.000	0.000	0.000	0.000
104	A	116	THR	0	-0.025	-0.003	17.620	0.034	0.034	0.000	0.000	0.000	0.000
105	A	118	GLN	0	0.017	0.016	22.378	0.022	0.022	0.000	0.000	0.000	0.000
106	A	119	ASP	-1	-0.912	-0.951	24.883	-0.067	-0.067	0.000	0.000	0.000	0.000
107	A	120	ALA	0	-0.057	-0.027	25.477	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)