FMO DATABASE

FMODB ID: G5ZZ1

Calculation Name: 3LDZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LDZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q92783

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1277522.086014
FMO2-HF: Nuclear repulsion	1220769.04266
FMO2-HF: Total energy	-56753.043353
FMO2-MP2: Total energy	-56911.798

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:4:PHE)

Summations of interaction energy for fragment #1(A:4:PHE)

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.
-2.221	-0.786	-0.003	-0.654	-0.777	0.002

Interaction energy analysis for fragmet #1(A:4:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.022

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	6	THR	0	0.014	0.007	3.909	-2.155	-0.720	-0.003	-0.654	-0.777	0.002
4	A	7	ASN	0	0.007	-0.012	6.681	0.511	0.511	0.000	0.000	0.000	0.000
5	A	8	PRO	0	0.007	-0.004	9.574	-0.117	-0.117	0.000	0.000	0.000	0.000
6	A	9	PHE	0	-0.013	-0.019	12.653	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.857	-0.925	10.419	-0.482	-0.482	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.017	-0.011	13.841	0.057	0.057	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.868	-0.941	16.095	-0.164	-0.164	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.026	0.010	16.899	0.020	0.020	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.993	-0.958	16.434	-0.341	-0.341	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.919	0.954	19.078	0.250	0.250	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.041	0.027	21.964	0.014	0.014	0.000	0.000	0.000	0.000
14	A	17	THR	0	-0.031	-0.051	21.069	0.009	0.009	0.000	0.000	0.000	0.000
15	A	18	SER	0	0.026	0.025	23.111	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.923	-0.971	23.584	-0.172	-0.172	0.000	0.000	0.000	0.000
17	A	20	MET	0	-0.046	-0.028	26.282	0.014	0.014	0.000	0.000	0.000	0.000
18	A	21	ASN	0	-0.048	0.003	26.042	0.003	0.003	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.023	-0.028	29.415	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.015	-0.005	31.400	0.005	0.005	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.869	-0.932	27.393	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.911	-0.950	26.796	-0.091	-0.091	0.000	0.000	0.000	0.000
23	A	26	TRP	0	0.015	-0.030	27.457	0.002	0.002	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.029	0.003	29.133	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.038	0.009	23.356	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	29	ILE	0	-0.020	-0.004	24.252	0.001	0.001	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.001	-0.014	25.341	0.008	0.008	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.865	-0.912	24.185	-0.069	-0.069	0.000	0.000	0.000	0.000
29	A	32	ILE	0	-0.072	-0.037	20.313	0.006	0.006	0.000	0.000	0.000	0.000
30	A	33	CYS	0	-0.073	-0.054	22.038	0.017	0.017	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.882	-0.937	24.573	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.881	0.950	15.757	0.138	0.138	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.045	-0.035	19.800	0.022	0.022	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.013	0.003	20.471	0.024	0.024	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.023	0.004	19.994	0.009	0.009	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.021	-0.012	15.567	0.013	0.013	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.938	0.966	15.488	-0.222	-0.222	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.029	-0.031	11.823	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.056	0.061	14.975	0.005	0.005	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.023	0.009	17.339	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.949	0.978	14.177	-0.293	-0.293	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.915	-0.959	11.902	0.361	0.361	0.000	0.000	0.000	0.000
43	A	46	CYS	0	0.008	0.031	13.842	-0.073	-0.073	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.037	0.029	16.673	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.878	0.933	11.360	-0.352	-0.352	0.000	0.000	0.000	0.000
46	A	49	SER	0	-0.028	-0.004	13.645	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.031	-0.002	14.546	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	51	MET	0	0.016	0.006	17.159	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.953	0.991	9.580	0.246	0.246	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.892	0.956	16.185	0.204	0.204	0.000	0.000	0.000	0.000
51	A	54	VAL	0	-0.015	-0.016	19.043	0.005	0.005	0.000	0.000	0.000	0.000
52	A	55	ASN	0	-0.064	-0.048	18.500	0.012	0.012	0.000	0.000	0.000	0.000
53	A	56	HIS	0	0.011	0.025	19.509	0.002	0.002	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.944	0.963	21.148	0.198	0.198	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.844	-0.924	23.920	-0.107	-0.107	0.000	0.000	0.000	0.000
56	A	59	PRO	0	-0.008	-0.027	25.581	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	HIS	0	-0.037	-0.004	28.037	0.011	0.011	0.000	0.000	0.000	0.000
58	A	61	VAL	0	-0.008	0.024	21.714	0.002	0.002	0.000	0.000	0.000	0.000
59	A	62	ALA	0	-0.002	-0.003	23.831	0.004	0.004	0.000	0.000	0.000	0.000
60	A	63	MET	0	-0.055	-0.033	24.840	0.011	0.011	0.000	0.000	0.000	0.000
61	A	64	GLN	0	0.021	0.003	25.608	0.007	0.007	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.019	0.013	21.844	0.005	0.005	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.024	-0.018	23.614	0.013	0.013	0.000	0.000	0.000	0.000
64	A	67	THR	0	-0.036	-0.011	26.143	0.010	0.010	0.000	0.000	0.000	0.000
65	A	68	LEU	0	0.060	0.043	21.033	0.006	0.006	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.020	-0.018	22.370	0.011	0.011	0.000	0.000	0.000	0.000
67	A	70	GLY	0	0.000	-0.008	24.584	0.011	0.011	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.030	0.021	27.015	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	CYS	0	-0.011	-0.011	23.234	0.004	0.004	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.053	-0.022	25.623	0.011	0.011	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.019	0.019	27.719	0.004	0.004	0.000	0.000	0.000	0.000
72	A	75	ASN	0	-0.030	-0.021	28.450	0.004	0.004	0.000	0.000	0.000	0.000
73	A	76	CYS	0	-0.035	0.001	23.760	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	77	GLY	0	0.029	0.030	26.940	0.009	0.009	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.868	0.890	27.437	-0.063	-0.063	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.016	-0.005	22.962	0.008	0.008	0.000	0.000	0.000	0.000
77	A	80	PHE	0	0.049	0.024	20.385	0.015	0.015	0.000	0.000	0.000	0.000
78	A	81	HIS	0	0.009	-0.013	23.849	0.008	0.008	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.023	-0.020	24.102	0.001	0.001	0.000	0.000	0.000	0.000
80	A	83	GLU	-1	-0.941	-0.957	18.950	0.201	0.201	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.021	0.013	21.471	0.002	0.002	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.091	-0.021	23.616	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	86	SER	0	-0.010	-0.011	20.970	0.014	0.014	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.962	0.956	21.808	-0.124	-0.124	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.855	-0.933	16.424	0.197	0.197	0.000	0.000	0.000	0.000
86	A	89	PHE	0	0.038	0.025	19.268	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.046	0.007	21.389	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.064	-0.028	19.450	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.904	-0.959	17.546	-0.040	-0.040	0.000	0.000	0.000	0.000
90	A	93	VAL	0	-0.018	-0.005	20.930	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	94	SER	0	-0.012	-0.013	24.652	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	95	ASN	0	-0.023	-0.001	20.387	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	96	VAL	0	0.003	0.006	22.194	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.038	-0.034	24.653	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.022	-0.007	26.921	0.001	0.001	0.000	0.000	0.000	0.000
96	A	99	LYS	1	0.916	0.960	22.062	0.072	0.072	0.000	0.000	0.000	0.000
97	A	100	GLY	0	0.019	0.028	26.975	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	101	HIS	0	0.054	0.021	27.658	0.006	0.006	0.000	0.000	0.000	0.000
99	A	102	PRO	0	0.040	0.001	30.492	0.003	0.003	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.998	1.005	32.203	0.067	0.067	0.000	0.000	0.000	0.000
101	A	104	VAL	0	0.035	0.010	26.410	0.002	0.002	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.049	-0.018	29.669	0.005	0.005	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.976	-0.979	30.892	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.989	0.998	29.905	0.035	0.035	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.033	0.012	25.876	0.004	0.004	0.000	0.000	0.000	0.000
106	A	109	LYS	1	0.905	0.946	29.395	0.022	0.022	0.000	0.000	0.000	0.000
107	A	110	ALA	0	0.004	0.014	32.365	0.004	0.004	0.000	0.000	0.000	0.000
108	A	111	LEU	0	0.010	0.003	27.968	0.003	0.003	0.000	0.000	0.000	0.000
109	A	112	MET	0	-0.023	-0.005	29.336	0.004	0.004	0.000	0.000	0.000	0.000
110	A	113	VAL	0	-0.013	-0.012	31.720	0.005	0.005	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.950	-0.969	33.753	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	115	TRP	0	0.044	0.010	26.187	0.005	0.005	0.000	0.000	0.000	0.000
113	A	116	THR	0	-0.071	-0.027	32.908	0.004	0.004	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.892	-0.945	34.991	0.013	0.013	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.926	-0.968	33.104	0.019	0.019	0.000	0.000	0.000	0.000
116	A	119	PHE	0	-0.022	-0.038	29.079	0.004	0.004	0.000	0.000	0.000	0.000
117	A	120	LYS	1	0.856	0.947	34.764	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	121	ASN	0	-0.045	-0.024	38.115	0.001	0.001	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.785	-0.887	33.288	0.059	0.059	0.000	0.000	0.000	0.000
120	A	123	PRO	0	0.002	-0.004	34.909	0.001	0.001	0.000	0.000	0.000	0.000
121	A	124	GLN	0	-0.052	-0.017	29.955	0.002	0.002	0.000	0.000	0.000	0.000
122	A	125	LEU	0	-0.003	0.001	28.902	0.007	0.007	0.000	0.000	0.000	0.000
123	A	126	SER	0	0.043	0.028	31.296	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	127	LEU	0	0.007	0.009	26.568	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	128	ILE	0	0.073	0.037	27.067	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	129	SER	0	-0.010	-0.020	30.485	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	130	ALA	0	-0.023	-0.009	31.534	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	131	MET	0	-0.028	-0.006	26.129	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	132	ILE	0	0.018	0.018	30.946	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.927	0.964	33.895	-0.030	-0.030	0.000	0.000	0.000	0.000
131	A	134	ASN	0	-0.001	-0.002	31.361	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	135	LEU	0	0.023	0.005	29.610	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.918	0.961	33.660	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	137	GLU	-1	-0.979	-0.976	36.655	0.023	0.023	0.000	0.000	0.000	0.000
135	A	138	GLN	0	-0.076	-0.031	31.011	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.012	0.015	36.332	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	140	VAL	0	-0.029	-0.004	33.082	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	141	THR	0	0.000	-0.011	36.467	0.002	0.002	0.000	0.000	0.000	0.000
139	A	142	PHE	0	0.000	-0.027	32.490	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	143	PRO	0	0.016	0.024	37.890	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PHE)