FMO DATABASE

FMODB ID: 4JY7N

Calculation Name: 3GL3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GL3

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KDH8

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1286631.737145
FMO2-HF: Nuclear repulsion	1232444.266855
FMO2-HF: Total energy	-54187.470289
FMO2-MP2: Total energy	-54344.798546

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:28:SER)

Summations of interaction energy for fragment #1(A:28:SER)

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.
-18.324	-15.815	2.356	-1.406	-3.458	0.016

Interaction energy analysis for fragmet #1(A:28:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.028

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	30	ASP	-1	-0.855	-0.904	3.797	-5.850	-3.925	-0.023	-0.864	-1.038	0.004
4	A	31	LYS	1	0.889	0.928	6.512	1.650	1.650	0.000	0.000	0.000	0.000
5	A	32	GLY	0	0.001	0.004	9.865	-0.032	-0.032	0.000	0.000	0.000	0.000
6	A	33	ASP	-1	-0.856	-0.935	6.545	-5.032	-5.032	0.000	0.000	0.000	0.000
7	A	34	LYS	1	0.868	0.934	9.627	1.502	1.502	0.000	0.000	0.000	0.000
8	A	35	ALA	0	0.022	0.011	8.424	-0.451	-0.451	0.000	0.000	0.000	0.000
9	A	36	PRO	0	-0.015	-0.008	6.096	0.341	0.341	0.000	0.000	0.000	0.000
10	A	37	ASP	-1	-0.811	-0.891	9.318	-0.194	-0.194	0.000	0.000	0.000	0.000
11	A	38	PHE	0	-0.037	-0.034	11.719	0.082	0.082	0.000	0.000	0.000	0.000
12	A	39	ALA	0	0.018	0.008	14.382	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	40	LEU	0	-0.043	-0.013	14.634	0.043	0.043	0.000	0.000	0.000	0.000
14	A	41	PRO	0	0.030	0.023	18.787	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	42	GLY	0	0.049	0.010	21.411	0.018	0.018	0.000	0.000	0.000	0.000
16	A	43	LYS	1	0.865	0.963	23.684	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	44	THR	0	-0.008	-0.008	26.984	0.003	0.003	0.000	0.000	0.000	0.000
18	A	45	GLY	0	0.075	0.027	26.459	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	46	VAL	0	-0.051	-0.007	21.581	0.018	0.018	0.000	0.000	0.000	0.000
20	A	47	VAL	0	-0.023	-0.014	18.598	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	48	LYS	1	1.001	0.990	17.925	0.172	0.172	0.000	0.000	0.000	0.000
22	A	49	LEU	0	-0.019	0.018	12.367	0.004	0.004	0.000	0.000	0.000	0.000
23	A	50	SER	0	-0.015	-0.014	16.322	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	51	ASP	-1	-0.884	-0.940	18.137	-0.192	-0.192	0.000	0.000	0.000	0.000
25	A	52	LYS	1	0.768	0.877	18.381	0.171	0.171	0.000	0.000	0.000	0.000
26	A	53	THR	0	0.013	0.024	18.958	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	54	GLY	0	0.024	0.016	20.035	0.046	0.046	0.000	0.000	0.000	0.000
28	A	55	SER	0	-0.077	-0.035	21.258	0.035	0.035	0.000	0.000	0.000	0.000
29	A	56	VAL	0	-0.003	0.015	18.607	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	57	VAL	0	-0.013	-0.024	15.518	0.068	0.068	0.000	0.000	0.000	0.000
31	A	58	TYR	0	0.014	0.012	15.965	-0.050	-0.050	0.000	0.000	0.000	0.000
32	A	59	LEU	0	-0.021	-0.015	10.459	0.044	0.044	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.832	-0.942	13.305	0.347	0.347	0.000	0.000	0.000	0.000
34	A	61	PHE	0	-0.013	0.003	9.659	0.076	0.076	0.000	0.000	0.000	0.000
35	A	62	TRP	0	-0.021	-0.019	13.916	0.058	0.058	0.000	0.000	0.000	0.000
36	A	63	ALA	0	0.015	-0.012	17.220	0.019	0.019	0.000	0.000	0.000	0.000
37	A	64	SER	0	-0.042	-0.059	19.801	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	65	TRP	0	0.017	0.013	17.865	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	66	CYS	0	-0.052	-0.007	17.782	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	67	GLY	0	0.078	0.034	21.399	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	68	PRO	0	0.039	0.009	19.613	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	69	CYS	0	0.031	0.032	19.504	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	70	ARG	1	0.903	0.957	21.529	-0.188	-0.188	0.000	0.000	0.000	0.000
44	A	71	GLN	0	-0.033	-0.025	23.666	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	72	SER	0	0.045	0.018	19.856	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	73	PHE	0	0.064	0.021	20.858	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	74	PRO	0	-0.042	-0.017	24.190	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	75	TRP	0	0.062	0.022	19.349	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	76	MET	0	0.002	0.008	19.802	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	77	ASN	0	0.027	0.017	23.263	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.003	0.008	26.776	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	79	MET	0	-0.030	-0.011	22.477	-0.026	-0.026	0.000	0.000	0.000	0.000
53	A	80	GLN	0	-0.021	-0.015	24.036	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	81	ALA	0	0.010	-0.008	25.961	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	82	LYS	1	0.821	0.906	27.979	0.073	0.073	0.000	0.000	0.000	0.000
56	A	83	TYR	0	-0.003	-0.043	25.241	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	84	LYS	1	0.967	1.001	26.646	0.057	0.057	0.000	0.000	0.000	0.000
58	A	85	ALA	0	-0.029	-0.009	27.689	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	86	LYS	1	0.957	0.987	27.291	0.164	0.164	0.000	0.000	0.000	0.000
60	A	87	GLY	0	0.030	0.035	25.843	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	88	PHE	0	0.028	0.015	19.837	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	89	GLN	0	0.024	0.004	21.298	0.061	0.061	0.000	0.000	0.000	0.000
63	A	90	VAL	0	0.039	0.039	19.359	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	91	VAL	0	-0.044	-0.030	16.556	0.008	0.008	0.000	0.000	0.000	0.000
65	A	92	ALA	0	0.036	0.018	16.599	0.015	0.015	0.000	0.000	0.000	0.000
66	A	93	VAL	0	0.001	-0.001	13.738	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	94	ASN	0	-0.049	-0.049	16.043	0.091	0.091	0.000	0.000	0.000	0.000
68	A	95	LEU	0	-0.002	-0.019	12.800	0.036	0.036	0.000	0.000	0.000	0.000
69	A	96	ASP	-1	-0.767	-0.831	17.214	0.421	0.421	0.000	0.000	0.000	0.000
70	A	97	ALA	0	0.008	0.003	20.779	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	98	LYS	1	0.935	0.971	21.915	-0.282	-0.282	0.000	0.000	0.000	0.000
72	A	99	THR	0	0.067	0.022	22.463	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	100	GLY	0	0.026	0.018	24.557	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	101	ASP	-1	-0.860	-0.952	25.730	0.253	0.253	0.000	0.000	0.000	0.000
75	A	102	ALA	0	0.012	0.022	23.179	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	103	MET	0	-0.018	-0.028	25.016	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	104	LYS	1	0.924	0.977	28.039	-0.214	-0.214	0.000	0.000	0.000	0.000
78	A	105	PHE	0	0.027	0.011	24.702	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	106	LEU	0	-0.003	-0.027	24.440	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	107	ALA	0	-0.044	0.005	28.172	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	108	GLN	0	-0.067	-0.034	30.994	0.003	0.003	0.000	0.000	0.000	0.000
82	A	109	VAL	0	-0.095	-0.038	26.924	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	110	PRO	0	0.041	0.025	28.494	0.003	0.003	0.000	0.000	0.000	0.000
84	A	111	ALA	0	0.031	0.016	24.975	0.009	0.009	0.000	0.000	0.000	0.000
85	A	112	GLU	-1	-0.984	-0.986	26.848	0.015	0.015	0.000	0.000	0.000	0.000
86	A	113	PHE	0	0.004	-0.017	21.999	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	114	THR	0	-0.055	-0.019	20.742	0.013	0.013	0.000	0.000	0.000	0.000
88	A	115	VAL	0	0.019	0.004	20.817	0.005	0.005	0.000	0.000	0.000	0.000
89	A	116	ALA	0	0.001	-0.003	17.653	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	117	PHE	0	-0.006	-0.007	19.230	0.039	0.039	0.000	0.000	0.000	0.000
91	A	118	ASP	-1	-0.727	-0.857	13.614	0.528	0.528	0.000	0.000	0.000	0.000
92	A	119	PRO	0	0.023	0.017	16.686	0.083	0.083	0.000	0.000	0.000	0.000
93	A	120	LYS	1	0.902	0.957	16.999	-0.287	-0.287	0.000	0.000	0.000	0.000
94	A	121	GLY	0	0.013	0.019	14.099	0.080	0.080	0.000	0.000	0.000	0.000
95	A	122	GLN	0	-0.064	-0.057	12.085	0.155	0.155	0.000	0.000	0.000	0.000
96	A	123	THR	0	-0.005	-0.031	9.908	0.156	0.156	0.000	0.000	0.000	0.000
97	A	124	PRO	0	0.036	0.022	8.011	0.077	0.077	0.000	0.000	0.000	0.000
98	A	125	ARG	1	0.947	0.971	6.568	-0.486	-0.486	0.000	0.000	0.000	0.000
99	A	126	LEU	0	-0.009	0.005	4.936	1.244	1.321	-0.001	-0.001	-0.074	0.000
100	A	127	TYR	0	-0.014	-0.047	4.116	-1.744	-1.633	0.000	-0.056	-0.055	0.000
101	A	128	GLY	0	0.028	0.037	2.605	0.790	1.322	2.228	-1.473	-1.288	0.007
102	A	129	VAL	0	-0.037	-0.025	3.476	-1.545	-2.501	0.061	1.317	-0.422	0.003
103	A	130	LYS	1	0.879	0.933	2.801	-8.978	-8.235	0.092	-0.322	-0.513	0.002
104	A	131	GLY	0	0.018	0.012	8.318	-0.383	-0.383	0.000	0.000	0.000	0.000
105	A	132	MET	0	-0.035	0.043	11.596	0.051	0.051	0.000	0.000	0.000	0.000
106	A	133	PRO	0	0.007	-0.014	14.549	-0.064	-0.064	0.000	0.000	0.000	0.000
107	A	134	THR	0	0.001	-0.031	8.243	0.166	0.166	0.000	0.000	0.000	0.000
108	A	135	SER	0	-0.008	0.007	11.701	-0.063	-0.063	0.000	0.000	0.000	0.000
109	A	136	PHE	0	-0.007	-0.013	5.912	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	137	LEU	0	-0.022	0.014	11.358	0.072	0.072	0.000	0.000	0.000	0.000
111	A	138	ILE	0	-0.013	-0.010	11.237	-0.184	-0.184	0.000	0.000	0.000	0.000
112	A	139	ASP	-1	-0.756	-0.868	14.246	-0.756	-0.756	0.000	0.000	0.000	0.000
113	A	140	ARG	1	0.867	0.893	16.997	0.320	0.320	0.000	0.000	0.000	0.000
114	A	141	ASN	0	-0.034	-0.022	17.643	0.082	0.082	0.000	0.000	0.000	0.000
115	A	142	GLY	0	-0.029	-0.014	14.976	-0.051	-0.051	0.000	0.000	0.000	0.000
116	A	143	LYS	1	0.889	0.953	12.064	1.125	1.125	0.000	0.000	0.000	0.000
117	A	144	VAL	0	0.010	0.012	7.599	0.372	0.372	0.000	0.000	0.000	0.000
118	A	145	LEU	0	0.030	0.018	10.839	-0.076	-0.076	0.000	0.000	0.000	0.000
119	A	146	LEU	0	-0.100	-0.066	10.544	0.005	0.005	0.000	0.000	0.000	0.000
120	A	147	GLN	0	0.040	0.029	4.599	-1.014	-0.937	-0.001	-0.007	-0.068	0.000
121	A	148	HIS	0	-0.069	-0.038	8.970	0.003	0.003	0.000	0.000	0.000	0.000
122	A	149	VAL	0	0.022	0.005	9.333	0.143	0.143	0.000	0.000	0.000	0.000
123	A	150	GLY	0	-0.010	0.000	11.935	-0.091	-0.091	0.000	0.000	0.000	0.000
124	A	151	PHE	0	-0.017	-0.016	15.411	-0.068	-0.068	0.000	0.000	0.000	0.000
125	A	152	ARG	1	0.992	0.998	17.885	-0.195	-0.195	0.000	0.000	0.000	0.000
126	A	153	PRO	0	-0.011	-0.021	21.754	-0.025	-0.025	0.000	0.000	0.000	0.000
127	A	154	ALA	0	0.018	0.008	22.809	-0.018	-0.018	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.798	-0.900	18.309	0.161	0.161	0.000	0.000	0.000	0.000
129	A	156	LYS	1	0.895	0.947	20.595	-0.106	-0.106	0.000	0.000	0.000	0.000
130	A	157	GLU	-1	-0.890	-0.931	22.733	-0.068	-0.068	0.000	0.000	0.000	0.000
131	A	158	ALA	0	0.051	0.022	19.654	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	159	LEU	0	-0.023	-0.014	15.853	-0.049	-0.049	0.000	0.000	0.000	0.000
133	A	160	GLU	-1	-0.764	-0.860	19.351	-0.119	-0.119	0.000	0.000	0.000	0.000
134	A	161	GLN	0	0.006	0.015	22.070	-0.026	-0.026	0.000	0.000	0.000	0.000
135	A	162	GLN	0	-0.022	-0.011	15.595	-0.038	-0.038	0.000	0.000	0.000	0.000
136	A	163	ILE	0	-0.039	-0.016	19.389	-0.044	-0.044	0.000	0.000	0.000	0.000
137	A	164	LEU	0	-0.027	-0.019	20.674	-0.020	-0.020	0.000	0.000	0.000	0.000
138	A	165	ALA	0	0.023	0.014	21.081	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	166	ALA	0	-0.017	-0.001	18.895	-0.019	-0.019	0.000	0.000	0.000	0.000
140	A	167	LEU	0	-0.114	-0.053	20.906	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	168	GLY	0	-0.049	-0.014	24.160	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:SER)