FMO DATABASE

FMODB ID: PGM1P

Calculation Name: 2AXW-A-Xray13

Preferred Name:

Target Type:

Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 2AXW

Chain ID: A

ChEMBL ID:

UniProt ID: Q47038

Base Structure: X-ray

Registration Date: 2017-11-22

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	No
Procedure	Auto-FMO protocol ver. 1.20171117

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandCharge	CL-=-1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1022078.890627
FMO2-HF: Nuclear repulsion	969822.118985
FMO2-HF: Total energy	-52256.771642
FMO2-MP2: Total energy	-52407.530136

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:1:ALA)

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

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.
-11.878	-8.771	9.654	-5.879	-6.879	-0.044

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.899

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	3	LEU	0	0.031	0.016	3.805	2.701	4.141	-0.024	-0.625	-0.791	-0.001
4	A	4	HIS	0	-0.067	-0.046	6.887	4.027	4.027	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.014	-0.007	10.306	0.382	0.382	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.912	-0.950	13.557	-15.908	-15.908	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.022	0.006	17.103	0.088	0.088	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.845	0.925	18.894	15.590	15.590	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.014	0.004	22.582	0.120	0.120	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.064	0.040	25.933	-0.110	-0.110	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.049	-0.014	27.271	0.190	0.190	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.043	0.028	30.982	-0.086	-0.086	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.082	-0.057	32.308	0.319	0.319	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.061	0.049	32.363	-0.297	-0.297	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.029	-0.007	26.546	-0.165	-0.165	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.964	0.966	29.615	10.038	10.038	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.785	-0.884	27.084	-11.387	-11.387	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.021	0.009	24.240	0.121	0.121	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.091	-0.039	24.015	-0.388	-0.388	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.897	0.953	20.290	13.569	13.569	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.038	0.013	19.971	0.350	0.350	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.030	-0.012	16.726	-0.142	-0.142	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.068	-0.032	15.622	0.478	0.478	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.013	0.001	12.122	-0.212	-0.212	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.900	0.970	9.131	27.822	27.822	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.020	-0.003	3.210	-1.935	-1.679	0.015	-0.066	-0.204	0.000
27	A	27	ILE	0	0.010	0.012	4.406	3.804	4.008	-0.001	-0.082	-0.121	0.000
28		116	CYS	0	-0.085	-0.054	2.281	-29.697	-29.159	9.600	-4.908	-5.230	-0.042
29	A	29	ARG	1	0.966	0.976	3.435	54.622	55.009	0.011	-0.092	-0.305	-0.001
30	A	30	GLU	-1	-0.866	-0.915	4.630	-34.590	-34.581	-0.001	-0.003	-0.005	0.000
31	A	31	ALA	0	0.002	0.016	6.563	-1.095	-1.095	0.000	0.000	0.000	0.000
32	A	32	HIS	1	0.823	0.894	6.618	33.666	33.666	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.018	-0.011	8.735	1.410	1.410	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.045	0.032	9.021	2.417	2.417	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.048	-0.010	6.094	-4.417	-4.417	0.000	0.000	0.000	0.000
36	A	36	HIS	0	-0.075	-0.047	6.615	2.130	2.130	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.021	0.013	6.838	-3.933	-3.933	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.048	-0.016	7.244	1.893	1.893	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.015	0.013	11.504	-0.936	-0.936	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.087	-0.046	11.327	0.420	0.420	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.781	-0.895	15.155	-15.167	-15.167	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.977	0.992	18.633	11.020	11.020	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.031	-0.013	18.168	0.304	0.304	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.024	-0.009	21.778	0.562	0.562	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.896	-0.957	24.868	-10.634	-10.634	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.005	-0.004	25.114	0.151	0.151	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.858	0.934	22.365	10.890	10.890	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.052	0.037	17.517	-0.197	-0.197	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.839	-0.934	16.910	-14.746	-14.746	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.759	0.857	18.140	12.384	12.384	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.052	0.009	15.494	-0.282	-0.282	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.044	-0.005	21.271	0.344	0.344	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.004	-0.005	19.751	-0.334	-0.334	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.048	0.011	22.755	0.848	0.848	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.009	-0.016	24.266	-0.459	-0.459	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.902	0.947	25.787	11.068	11.068	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.898	-0.951	26.737	-9.877	-9.877	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.012	-0.006	28.137	0.284	0.284	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.891	0.950	29.137	8.963	8.963	0.000	0.000	0.000	0.000
60	A	60	HIS	0	-0.013	0.003	29.991	0.506	0.506	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.935	-0.973	27.371	-10.784	-10.784	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.011	0.004	23.607	0.252	0.252	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.917	0.973	24.518	10.149	10.149	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.015	0.006	19.588	0.072	0.072	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.889	0.935	19.468	12.520	12.520	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.005	0.008	13.844	-0.375	-0.375	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.004	-0.014	16.237	0.445	0.445	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.059	0.027	16.000	-0.731	-0.731	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.917	-0.957	17.347	-15.124	-15.124	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.017	-0.023	16.062	-1.024	-1.024	0.000	0.000	0.000	0.000
71	A	71	TRP	0	-0.070	-0.037	8.916	-0.986	-0.986	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.010	-0.008	15.645	1.370	1.370	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.004	-0.002	16.062	-1.011	-1.011	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.046	-0.012	13.467	0.370	0.370	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.950	0.968	16.780	14.038	14.038	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.027	0.008	19.176	-0.427	-0.427	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.948	-0.983	20.792	-13.844	-13.844	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.079	0.050	19.111	-0.411	-0.411	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.066	-0.010	16.598	-0.999	-0.999	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.952	0.957	11.903	21.690	21.690	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.036	0.025	13.315	-1.331	-1.331	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.012	-0.003	12.371	1.201	1.201	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.011	-0.016	11.385	-1.825	-1.825	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.959	0.993	11.405	21.597	21.597	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.013	0.000	11.441	-2.051	-2.051	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.025	-0.005	12.618	0.588	0.588	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.018	-0.014	10.890	-1.966	-1.966	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.911	-0.942	10.873	-23.066	-23.066	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.930	-0.970	7.781	-32.622	-32.622	0.000	0.000	0.000	0.000
90	A	90	GLN	0	0.027	-0.003	6.726	-6.601	-6.601	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.030	0.007	8.572	3.255	3.255	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.026	-0.002	9.881	-2.182	-2.182	0.000	0.000	0.000	0.000
93	A	93	PHE	0	-0.032	0.007	8.963	0.489	0.489	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.795	-0.908	13.623	-16.684	-16.684	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.010	0.000	15.129	-0.261	-0.261	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.048	-0.023	17.521	0.635	0.635	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.030	0.016	21.158	-0.069	-0.069	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.869	-0.934	23.474	-11.831	-11.831	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.051	0.016	25.324	0.297	0.297	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.048	-0.044	28.899	-0.361	-0.361	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.040	-0.017	26.560	0.156	0.156	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.877	-0.930	31.706	-8.684	-8.684	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.019	-0.007	27.740	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.010	0.014	31.784	0.215	0.215	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.017	0.010	31.174	-0.363	-0.363	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.025	0.006	30.308	0.138	0.138	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.890	-0.926	24.632	-12.664	-12.664	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.003	-0.023	23.583	0.100	0.100	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.837	0.914	20.795	12.797	12.797	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.022	0.008	15.943	0.243	0.243	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.039	-0.002	13.828	-1.191	-1.191	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.013	0.002	9.585	0.628	0.628	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.006	0.001	8.334	-1.281	-1.281	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.023	-0.008	5.546	1.802	1.802	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.037	-0.012	3.102	-4.555	-4.324	0.054	-0.098	-0.187	0.000
116	A	117	VAL	0	0.005	-0.002	4.187	0.443	0.485	0.000	-0.005	-0.036	0.000
117	A	118	VAL	0	0.024	0.005	5.313	0.348	0.348	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.033	-0.005	8.077	1.496	1.496	0.000	0.000	0.000	0.000
119	A	120	GLN	0	0.025	0.014	8.837	0.574	0.574	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.918	-0.957	13.120	-15.897	-15.897	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.927	0.963	16.806	13.724	13.724	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.014	0.001	19.522	0.480	0.480	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.017	0.003	22.454	0.253	0.253	0.000	0.000	0.000	0.000
124	A	125	ALA	0	-0.003	-0.007	26.107	-0.138	-0.138	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.001	0.002	28.612	0.126	0.126	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.000	-0.005	29.841	0.246	0.246	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.956	-0.972	33.263	-8.469	-8.469	0.000	0.000	0.000	0.000
128	A	129	HIS	0	-0.038	-0.018	35.895	0.120	0.120	0.000	0.000	0.000	0.000
129	A	130	HIS	0	0.028	0.015	38.180	0.110	0.110	0.000	0.000	0.000	0.000
130	A	131	HIS	0	-0.013	-0.011	41.231	0.017	0.017	0.000	0.000	0.000	0.000
131	A	132	HIS	0	-0.003	-0.002	43.004	0.002	0.002	0.000	0.000	0.000	0.000
132	A	133	HIS	0	-0.018	-0.006	46.076	-0.056	-0.056	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.008	0.009	47.752	0.203	0.203	0.000	0.000	0.000	0.000
134	A	501	CL-	-1	-0.862	-0.909	25.708	-11.685	-11.685	0.000	0.000	0.000	0.000

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