FMO DATABASE

FMODB ID: KGLN3

Calculation Name: 3A57-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A57

Chain ID: A

ChEMBL ID:

UniProt ID: P19250

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1541484.949048
FMO2-HF: Nuclear repulsion	1479526.559003
FMO2-HF: Total energy	-61958.390045
FMO2-MP2: Total energy	-62137.643217

3D Structure Molmil

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.
-1.182	1.797	0.115	-1.448	-1.644	-0.003

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 : 0.034 / q_NPA : 0.009

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	14	ASP	-1	-0.750	-0.816	3.813	-1.690	-0.108	-0.017	-0.824	-0.740	0.000
4	A	15	GLU	-1	-0.899	-0.970	6.546	0.216	0.216	0.000	0.000	0.000	0.000
5	A	16	ILE	0	0.019	0.020	10.274	-0.044	-0.044	0.000	0.000	0.000	0.000
6	A	17	LEU	0	-0.029	-0.011	13.186	0.033	0.033	0.000	0.000	0.000	0.000
7	A	18	PHE	0	0.041	0.017	16.348	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	19	VAL	0	0.003	-0.012	19.833	0.020	0.020	0.000	0.000	0.000	0.000
9	A	20	VAL	0	0.003	0.018	23.047	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	21	ARG	1	0.911	0.922	26.542	0.047	0.047	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.782	-0.878	29.152	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	23	THR	0	0.011	-0.025	32.681	0.003	0.003	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.056	-0.032	34.895	0.004	0.004	0.000	0.000	0.000	0.000
14	A	25	PHE	0	-0.014	0.009	35.897	0.003	0.003	0.000	0.000	0.000	0.000
15	A	26	ASN	0	-0.037	-0.010	38.207	0.001	0.001	0.000	0.000	0.000	0.000
16	A	27	THR	0	-0.058	-0.021	40.019	0.001	0.001	0.000	0.000	0.000	0.000
17	A	28	ASN	0	-0.067	-0.067	42.641	0.002	0.002	0.000	0.000	0.000	0.000
18	A	29	ALA	0	-0.057	-0.021	44.102	0.000	0.000	0.000	0.000	0.000	0.000
19	A	30	PRO	0	-0.013	0.001	40.150	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.005	0.002	36.688	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	32	ASN	0	-0.049	-0.031	38.307	0.003	0.003	0.000	0.000	0.000	0.000
22	A	33	VAL	0	0.008	0.002	31.896	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	34	GLU	-1	-0.849	-0.905	32.804	-0.044	-0.044	0.000	0.000	0.000	0.000
24	A	35	VAL	0	-0.093	-0.054	26.173	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	36	SER	0	-0.024	-0.036	29.335	0.002	0.002	0.000	0.000	0.000	0.000
26	A	37	ASP	-1	-0.783	-0.843	25.684	-0.130	-0.130	0.000	0.000	0.000	0.000
27	A	38	PHE	0	-0.028	-0.017	21.776	0.001	0.001	0.000	0.000	0.000	0.000
28	A	39	TRP	0	-0.037	-0.011	17.249	0.003	0.003	0.000	0.000	0.000	0.000
29	A	40	THR	0	0.041	-0.003	14.216	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	41	ASN	0	0.003	0.017	11.417	0.027	0.027	0.000	0.000	0.000	0.000
31	A	42	ARG	1	0.791	0.904	9.032	0.828	0.828	0.000	0.000	0.000	0.000
32	A	43	ASN	0	-0.018	-0.006	11.101	0.090	0.090	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.016	0.005	14.256	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	45	LYS	1	0.828	0.908	11.981	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	46	ARG	1	0.958	0.974	17.691	0.022	0.022	0.000	0.000	0.000	0.000
36	A	47	LYS	1	0.962	0.984	20.726	0.025	0.025	0.000	0.000	0.000	0.000
37	A	48	PRO	0	0.015	0.033	22.897	0.012	0.012	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.106	-0.067	25.438	0.001	0.001	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.839	0.906	29.177	0.041	0.041	0.000	0.000	0.000	0.000
40	A	51	ASP	-1	-0.750	-0.842	30.850	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	52	VAL	0	-0.011	-0.014	29.917	0.005	0.005	0.000	0.000	0.000	0.000
42	A	53	TYR	0	0.053	0.037	32.384	0.002	0.002	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.054	0.038	33.081	0.004	0.004	0.000	0.000	0.000	0.000
44	A	55	GLN	0	-0.053	-0.045	26.705	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	56	SER	0	-0.044	-0.017	26.874	0.008	0.008	0.000	0.000	0.000	0.000
46	A	57	VAL	0	-0.043	-0.033	21.007	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	58	PHE	0	-0.021	0.000	18.796	0.012	0.012	0.000	0.000	0.000	0.000
48	A	59	THR	0	0.016	0.010	15.389	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	60	THR	0	-0.019	0.003	14.219	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	61	SER	0	0.008	-0.001	10.193	0.058	0.058	0.000	0.000	0.000	0.000
51	A	62	GLY	0	0.025	0.003	8.490	0.146	0.146	0.000	0.000	0.000	0.000
52	A	63	THR	0	0.026	0.020	4.569	-0.159	-0.116	-0.001	-0.029	-0.013	0.000
53	A	64	LYS	1	0.862	0.951	2.998	2.785	3.400	0.081	-0.228	-0.468	0.000
54	A	65	TRP	0	-0.016	-0.012	5.563	0.074	0.074	0.000	0.000	0.000	0.000
55	A	66	LEU	0	-0.033	-0.003	8.222	0.145	0.145	0.000	0.000	0.000	0.000
56	A	67	THR	0	0.008	-0.002	10.024	0.026	0.026	0.000	0.000	0.000	0.000
57	A	68	SER	0	0.005	-0.016	13.690	0.028	0.028	0.000	0.000	0.000	0.000
58	A	69	TYR	0	-0.014	-0.031	16.209	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	70	MET	0	-0.031	-0.015	19.752	0.017	0.017	0.000	0.000	0.000	0.000
60	A	71	THR	0	-0.024	-0.029	22.870	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	72	VAL	0	-0.005	-0.013	26.441	0.008	0.008	0.000	0.000	0.000	0.000
62	A	73	ASN	0	0.002	-0.007	29.094	0.001	0.001	0.000	0.000	0.000	0.000
63	A	74	ILE	0	0.015	-0.003	31.362	0.004	0.004	0.000	0.000	0.000	0.000
64	A	75	ASN	0	-0.012	-0.018	34.986	0.000	0.000	0.000	0.000	0.000	0.000
65	A	76	ASP	-1	-0.906	-0.941	37.483	-0.049	-0.049	0.000	0.000	0.000	0.000
66	A	77	LYS	1	0.829	0.927	35.135	0.065	0.065	0.000	0.000	0.000	0.000
67	A	78	ASP	-1	-0.783	-0.858	30.412	-0.085	-0.085	0.000	0.000	0.000	0.000
68	A	79	TYR	0	-0.066	-0.065	28.868	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	80	THR	0	-0.011	-0.003	23.168	0.000	0.000	0.000	0.000	0.000	0.000
70	A	81	MET	0	-0.049	0.000	21.417	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	82	ALA	0	-0.008	-0.026	19.172	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	83	ALA	0	0.029	0.016	14.479	0.005	0.005	0.000	0.000	0.000	0.000
73	A	84	VAL	0	-0.009	-0.013	11.745	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	85	SER	0	-0.021	-0.026	7.482	-0.183	-0.183	0.000	0.000	0.000	0.000
75	A	86	GLY	0	0.019	-0.025	7.465	-0.248	-0.248	0.000	0.000	0.000	0.000
76	A	87	TYR	0	-0.040	-0.011	3.247	-1.500	-0.761	0.052	-0.367	-0.423	-0.003
77	A	88	LYS	1	0.885	0.941	9.187	0.458	0.458	0.000	0.000	0.000	0.000
78	A	89	HIS	0	-0.012	-0.015	12.644	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	90	GLY	0	-0.011	-0.003	10.557	0.039	0.039	0.000	0.000	0.000	0.000
80	A	91	HIS	0	-0.022	-0.008	8.833	-0.080	-0.080	0.000	0.000	0.000	0.000
81	A	92	SER	0	-0.009	-0.006	5.460	-0.241	-0.241	0.000	0.000	0.000	0.000
82	A	93	ALA	0	0.029	0.020	7.432	0.194	0.194	0.000	0.000	0.000	0.000
83	A	94	VAL	0	-0.008	-0.011	9.276	-0.201	-0.201	0.000	0.000	0.000	0.000
84	A	95	PHE	0	0.014	0.021	11.543	0.066	0.066	0.000	0.000	0.000	0.000
85	A	96	VAL	0	0.010	-0.019	15.044	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	97	LYS	1	0.898	0.956	17.798	0.189	0.189	0.000	0.000	0.000	0.000
87	A	98	SER	0	0.011	-0.009	21.386	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	99	ASP	-1	-0.828	-0.913	24.204	-0.127	-0.127	0.000	0.000	0.000	0.000
89	A	100	GLN	0	0.017	0.031	27.695	0.003	0.003	0.000	0.000	0.000	0.000
90	A	101	VAL	0	-0.001	0.000	26.247	0.002	0.002	0.000	0.000	0.000	0.000
91	A	102	GLN	0	-0.038	-0.002	27.810	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	103	LEU	0	-0.022	-0.008	21.587	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	104	GLN	0	0.026	0.007	23.992	0.009	0.009	0.000	0.000	0.000	0.000
94	A	105	HIS	1	0.798	0.871	21.732	0.118	0.118	0.000	0.000	0.000	0.000
95	A	106	SER	0	0.019	-0.001	20.121	0.003	0.003	0.000	0.000	0.000	0.000
96	A	107	TYR	0	0.036	0.007	12.027	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	108	ASP	-1	-0.857	-0.925	17.329	-0.273	-0.273	0.000	0.000	0.000	0.000
98	A	109	SER	0	-0.033	0.020	19.696	0.007	0.007	0.000	0.000	0.000	0.000
99	A	110	VAL	0	0.043	0.017	16.888	0.003	0.003	0.000	0.000	0.000	0.000
100	A	111	ALA	0	-0.011	-0.019	15.786	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	112	SER	0	-0.063	-0.043	17.395	0.011	0.011	0.000	0.000	0.000	0.000
102	A	113	PHE	0	-0.031	-0.012	20.802	0.015	0.015	0.000	0.000	0.000	0.000
103	A	114	VAL	0	-0.050	-0.024	16.598	0.011	0.011	0.000	0.000	0.000	0.000
104	A	115	GLY	0	-0.004	0.013	19.063	0.013	0.013	0.000	0.000	0.000	0.000
105	A	116	GLU	-1	-0.922	-0.970	15.118	-0.453	-0.453	0.000	0.000	0.000	0.000
106	A	117	ASP	-1	-0.831	-0.919	16.992	-0.229	-0.229	0.000	0.000	0.000	0.000
107	A	118	GLU	-1	-0.927	-0.970	14.179	-0.400	-0.400	0.000	0.000	0.000	0.000
108	A	119	ASP	-1	-0.909	-0.939	16.549	-0.208	-0.208	0.000	0.000	0.000	0.000
109	A	120	SER	0	-0.073	-0.037	17.779	0.013	0.013	0.000	0.000	0.000	0.000
110	A	121	ILE	0	-0.085	0.000	14.084	0.022	0.022	0.000	0.000	0.000	0.000
111	A	122	PRO	0	0.028	0.004	16.664	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	123	SER	0	-0.066	-0.056	18.949	0.013	0.013	0.000	0.000	0.000	0.000
113	A	124	LYS	1	0.859	0.914	22.234	0.079	0.079	0.000	0.000	0.000	0.000
114	A	125	MET	0	0.011	0.025	25.051	0.006	0.006	0.000	0.000	0.000	0.000
115	A	126	TYR	0	-0.035	-0.038	26.797	0.008	0.008	0.000	0.000	0.000	0.000
116	A	127	LEU	0	-0.044	-0.020	26.851	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	128	ASP	-1	-0.755	-0.865	30.808	-0.072	-0.072	0.000	0.000	0.000	0.000
118	A	129	GLU	-1	-0.989	-0.991	34.431	-0.051	-0.051	0.000	0.000	0.000	0.000
119	A	130	THR	0	0.015	0.023	37.559	0.002	0.002	0.000	0.000	0.000	0.000
120	A	131	PRO	0	-0.057	-0.051	40.483	0.002	0.002	0.000	0.000	0.000	0.000
121	A	132	GLU	-1	-0.865	-0.933	41.317	-0.038	-0.038	0.000	0.000	0.000	0.000
122	A	133	TYR	0	-0.017	-0.020	35.200	0.003	0.003	0.000	0.000	0.000	0.000
123	A	134	PHE	0	-0.049	-0.013	35.300	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	135	VAL	0	0.030	0.014	29.837	0.001	0.001	0.000	0.000	0.000	0.000
125	A	136	ASN	0	-0.063	-0.033	28.296	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	137	VAL	0	0.044	0.013	22.572	0.002	0.002	0.000	0.000	0.000	0.000
127	A	138	GLU	-1	-0.834	-0.876	22.415	-0.080	-0.080	0.000	0.000	0.000	0.000
128	A	139	ALA	0	0.022	0.014	18.008	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	140	TYR	0	0.005	-0.012	17.543	0.011	0.011	0.000	0.000	0.000	0.000
130	A	141	GLU	-1	-0.857	-0.921	11.989	-0.302	-0.302	0.000	0.000	0.000	0.000
131	A	142	SER	0	-0.051	-0.036	13.857	0.044	0.044	0.000	0.000	0.000	0.000
132	A	143	GLY	0	-0.005	0.005	13.599	0.014	0.014	0.000	0.000	0.000	0.000
133	A	144	SER	0	-0.029	-0.030	8.018	0.030	0.030	0.000	0.000	0.000	0.000
134	A	145	GLY	0	-0.026	0.003	8.669	-0.059	-0.059	0.000	0.000	0.000	0.000
135	A	146	ASN	0	0.030	0.015	9.385	0.013	0.013	0.000	0.000	0.000	0.000
136	A	147	ILE	0	-0.036	-0.029	13.136	0.023	0.023	0.000	0.000	0.000	0.000
137	A	148	LEU	0	0.020	0.021	16.263	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	149	VAL	0	-0.011	-0.016	19.513	0.013	0.013	0.000	0.000	0.000	0.000
139	A	150	MET	0	0.023	0.018	23.021	0.000	0.000	0.000	0.000	0.000	0.000
140	A	151	CYS	0	-0.182	-0.055	26.080	0.011	0.011	0.000	0.000	0.000	0.000
141	A	152	ILE	0	0.052	0.022	29.247	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	153	SER	0	0.049	0.023	32.610	0.005	0.005	0.000	0.000	0.000	0.000
143	A	154	ASN	0	0.083	0.031	35.847	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	155	LYS	1	0.864	0.906	39.503	0.039	0.039	0.000	0.000	0.000	0.000
145	A	156	GLU	-1	-0.864	-0.911	42.222	-0.021	-0.021	0.000	0.000	0.000	0.000
146	A	157	SER	0	0.100	0.047	37.377	0.000	0.000	0.000	0.000	0.000	0.000
147	A	158	PHE	0	-0.033	0.008	37.042	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	159	PHE	0	0.018	-0.026	35.928	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	160	GLU	-1	-0.885	-0.945	34.392	-0.026	-0.026	0.000	0.000	0.000	0.000
150	A	162	LYS	1	0.877	0.942	30.744	0.048	0.048	0.000	0.000	0.000	0.000
151	A	163	HIS	0	-0.026	0.002	30.180	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	164	GLN	0	-0.040	-0.027	24.659	0.002	0.002	0.000	0.000	0.000	0.000
153	A	165	GLN	0	0.001	0.006	23.745	-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:12:GLY)