FMO DATABASE

FMODB ID: R8V68

Calculation Name: 3LYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYH

Chain ID: A

ChEMBL ID:

UniProt ID: A1TZQ9

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	OptHSide
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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-918056.991218
FMO2-HF: Nuclear repulsion	871734.361078
FMO2-HF: Total energy	-46322.63014
FMO2-MP2: Total energy	-46458.741644

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:PRO)

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

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.
-5.633	-0.759	0.434	-2.298	-3.009	0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

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

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	6	GLN	0	0.001	0.012	3.826	-1.137	1.023	-0.017	-1.142	-1.001	0.004
4	A	7	ILE	0	-0.024	-0.008	6.652	-0.222	-0.222	0.000	0.000	0.000	0.000
5	A	8	ILE	0	0.027	0.005	10.082	0.016	0.016	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.015	0.000	13.080	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.004	-0.002	16.557	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.048	0.027	19.156	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	12	HIS	0	0.033	0.003	22.562	0.004	0.004	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.047	0.038	25.839	0.003	0.003	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.015	-0.013	26.323	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.053	0.019	29.114	0.002	0.002	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.837	-0.881	31.758	0.045	0.045	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.063	0.013	30.300	0.004	0.004	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.876	0.903	30.038	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	19	TRP	0	-0.055	-0.020	27.224	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	20	CYS	0	-0.003	-0.011	25.964	0.004	0.004	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.894	-0.929	25.578	0.077	0.077	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.030	-0.032	26.502	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	PHE	0	-0.040	-0.034	23.241	0.002	0.002	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.834	-0.889	20.723	0.137	0.137	0.000	0.000	0.000	0.000
22	A	25	LYS	1	0.801	0.884	21.857	-0.070	-0.070	0.000	0.000	0.000	0.000
23	A	26	LEU	0	-0.073	-0.043	23.353	0.001	0.001	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.024	-0.013	18.199	0.004	0.004	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.777	-0.851	18.141	0.100	0.100	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.035	0.022	18.467	0.008	0.008	0.000	0.000	0.000	0.000
27	A	30	THR	0	-0.038	-0.020	14.136	0.005	0.005	0.000	0.000	0.000	0.000
28	A	31	VAL	0	-0.043	-0.028	13.969	0.022	0.022	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.956	-0.964	13.932	0.112	0.112	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.089	-0.043	15.032	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.090	-0.056	9.517	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.854	-0.931	5.878	0.271	0.271	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.055	-0.027	5.119	0.070	0.070	0.000	0.000	0.000	0.000
34	A	37	ALA	0	-0.038	-0.002	8.389	0.065	0.065	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.001	0.001	10.698	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	39	ILE	0	-0.014	0.009	13.448	0.003	0.003	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.015	-0.005	16.320	0.008	0.008	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.067	-0.071	18.178	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	42	MET	0	-0.069	-0.042	21.770	0.000	0.000	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.930	-0.972	23.506	0.054	0.054	0.000	0.000	0.000	0.000
41	A	44	LEU	0	-0.026	-0.017	26.179	0.003	0.003	0.000	0.000	0.000	0.000
42	A	45	ALA	0	-0.011	0.019	24.992	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.823	-0.879	20.901	0.131	0.131	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.020	-0.010	17.454	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	48	SER	0	0.058	0.012	19.816	0.004	0.004	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.074	0.005	15.167	0.021	0.021	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.760	-0.823	15.529	0.133	0.133	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.084	-0.051	15.572	0.015	0.015	0.000	0.000	0.000	0.000
49	A	52	ILE	0	0.009	0.003	12.004	0.016	0.016	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.015	0.016	11.203	0.084	0.084	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.037	-0.030	10.815	0.030	0.030	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.904	0.953	11.817	-0.220	-0.220	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.054	0.038	7.468	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.832	0.920	6.757	0.244	0.244	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.050	-0.021	7.916	-0.128	-0.128	0.000	0.000	0.000	0.000
56	A	59	GLN	0	-0.066	-0.035	6.093	-0.027	-0.027	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.001	0.006	4.550	-0.149	-0.028	-0.001	-0.010	-0.109	0.000
58	A	61	VAL	0	-0.066	-0.015	3.013	-3.856	-1.549	0.449	-1.112	-1.644	0.001
59	A	62	GLU	-1	-0.836	-0.925	3.989	-1.109	-0.823	0.003	-0.034	-0.255	0.000
60	A	63	GLN	0	-0.049	-0.016	4.932	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	64	PHE	0	0.064	0.021	6.129	0.295	0.295	0.000	0.000	0.000	0.000
62	A	65	THR	0	-0.045	-0.028	8.831	-0.121	-0.121	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.028	0.017	11.402	0.042	0.042	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.000	-0.018	14.290	-0.030	-0.030	0.000	0.000	0.000	0.000
65	A	68	PRO	0	-0.010	0.009	16.823	0.003	0.003	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.038	0.018	19.588	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.006	-0.018	22.333	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	71	LEU	0	0.041	0.009	25.468	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	ALA	0	0.014	0.003	28.077	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	73	ALA	0	0.058	0.041	26.775	0.002	0.002	0.000	0.000	0.000	0.000
71	A	74	GLY	0	0.042	0.021	28.925	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.895	0.919	30.458	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	76	HIS	0	0.077	0.048	31.387	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	LEU	0	0.082	0.051	26.337	0.000	0.000	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.881	0.920	26.504	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	79	LYS	1	0.852	0.937	26.845	-0.036	-0.036	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.818	-0.924	26.492	0.042	0.042	0.000	0.000	0.000	0.000
78	A	81	VAL	0	0.011	0.009	21.182	0.002	0.002	0.000	0.000	0.000	0.000
79	A	82	PRO	0	0.005	-0.003	21.247	0.005	0.005	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.024	0.032	21.608	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	84	MET	0	-0.015	-0.007	20.376	0.002	0.002	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.030	-0.020	16.214	0.008	0.008	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.868	-0.935	17.727	0.025	0.025	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.721	0.811	19.352	-0.082	-0.082	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.040	-0.022	15.677	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.817	-0.905	14.101	0.039	0.039	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.022	-0.011	15.399	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.927	-0.948	17.931	0.055	0.055	0.000	0.000	0.000	0.000
89	A	92	HIS	1	0.822	0.897	13.044	-0.100	-0.100	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.030	0.030	12.703	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.073	-0.034	9.335	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.011	0.012	9.666	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.041	-0.037	10.065	0.036	0.036	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.956	0.997	12.070	-0.132	-0.132	0.000	0.000	0.000	0.000
95	A	98	LEU	0	0.011	0.002	14.002	0.028	0.028	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.065	-0.032	15.715	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.754	-0.884	17.547	0.052	0.052	0.000	0.000	0.000	0.000
98	A	101	PRO	0	-0.054	-0.019	20.375	0.008	0.008	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.075	0.029	20.430	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	103	GLY	0	-0.029	-0.014	22.797	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.743	0.868	24.658	-0.056	-0.056	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.032	-0.001	21.001	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	106	PRO	0	0.075	0.027	24.723	0.000	0.000	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.948	0.959	22.003	-0.073	-0.073	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.042	0.026	23.743	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.029	0.022	27.348	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.064	-0.037	28.166	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.049	0.026	27.780	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	112	ILE	0	0.022	0.015	29.927	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	113	ARG	1	0.819	0.892	32.454	-0.041	-0.041	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.772	-0.868	32.204	0.038	0.038	0.000	0.000	0.000	0.000
112	A	115	VAL	0	0.082	0.043	32.130	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	116	VAL	0	-0.010	-0.009	34.871	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	117	LYS	1	0.814	0.895	35.859	-0.035	-0.035	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.841	-0.899	34.517	0.040	0.040	0.000	0.000	0.000	0.000
116	A	119	GLU	-1	-0.864	-0.929	38.184	0.033	0.033	0.000	0.000	0.000	0.000
117	A	120	LEU	0	-0.095	-0.039	40.616	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	121	GLU	-1	-0.970	-0.966	41.924	0.024	0.024	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.721	0.839	36.347	-0.037	-0.037	0.000	0.000	0.000	0.000
120	A	123	SER	0	-0.074	-0.031	43.994	-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:4:PRO)