FMO DATABASE

FMODB ID: ZV1KN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-917493.150219
FMO2-HF: Nuclear repulsion	871171.219107
FMO2-HF: Total energy	-46321.931112
FMO2-MP2: Total energy	-46458.022515

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.
-6.394	-1.182	0.28	-2.294	-3.196	0.004

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 : 0.009

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

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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	0.040	0.040	3.683	-1.574	0.746	-0.009	-1.228	-1.083	0.003
4	A	7	ILE	0	-0.035	-0.018	6.166	-0.140	-0.140	0.000	0.000	0.000	0.000
5	A	8	ILE	0	0.022	0.004	9.637	0.002	0.002	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.009	0.001	12.600	-0.024	-0.024	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.005	-0.005	16.096	0.000	0.000	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.046	0.027	18.670	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	12	HIS	0	0.043	0.004	22.083	0.004	0.004	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.047	0.031	25.353	0.001	0.001	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.002	-0.003	25.848	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.050	0.018	28.662	0.001	0.001	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.885	-0.927	31.308	0.032	0.032	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.057	0.010	29.889	0.003	0.003	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.906	0.934	29.637	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	19	TRP	0	-0.040	-0.007	26.906	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	20	CYS	0	0.001	-0.011	25.453	0.004	0.004	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.903	-0.934	25.172	0.048	0.048	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.015	-0.019	26.129	0.000	0.000	0.000	0.000	0.000	0.000
20	A	23	PHE	0	-0.049	-0.037	22.926	0.002	0.002	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.849	-0.916	20.531	0.089	0.089	0.000	0.000	0.000	0.000
22	A	25	LYS	1	0.852	0.911	21.505	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	26	LEU	0	-0.071	-0.040	22.960	0.000	0.000	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.031	-0.013	17.690	0.003	0.003	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.818	-0.875	17.805	0.054	0.054	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.029	0.025	18.202	0.002	0.002	0.000	0.000	0.000	0.000
27	A	30	THR	0	-0.038	-0.016	13.846	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	VAL	0	-0.047	-0.032	13.667	0.011	0.011	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.945	-0.966	13.703	0.046	0.046	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.101	-0.049	14.881	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.086	-0.054	9.295	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.856	-0.924	5.701	-0.070	-0.070	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.063	-0.039	4.741	0.020	0.081	-0.001	0.000	-0.060	0.000
34	A	37	ALA	0	-0.046	-0.005	8.100	0.072	0.072	0.000	0.000	0.000	0.000
35	A	38	ALA	0	-0.002	-0.003	10.321	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	39	ILE	0	-0.009	0.013	13.032	0.010	0.010	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.014	-0.007	15.908	0.006	0.006	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.064	-0.051	17.706	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	42	MET	0	-0.069	-0.043	21.289	0.002	0.002	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.936	-0.974	23.023	0.049	0.049	0.000	0.000	0.000	0.000
41	A	44	LEU	0	-0.038	-0.021	25.754	0.001	0.001	0.000	0.000	0.000	0.000
42	A	45	ALA	0	-0.005	0.024	24.475	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.840	-0.904	20.822	0.103	0.103	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.016	-0.006	17.015	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	48	SER	0	0.077	0.033	19.357	0.007	0.007	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.076	0.005	15.082	0.016	0.016	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.766	-0.838	15.534	0.141	0.141	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.079	-0.041	15.712	0.020	0.020	0.000	0.000	0.000	0.000
49	A	52	ILE	0	0.004	-0.003	11.483	0.014	0.014	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.018	0.017	11.259	0.073	0.073	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.021	-0.023	10.952	0.052	0.052	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.897	0.949	11.660	-0.155	-0.155	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.042	0.031	7.332	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.903	0.949	6.847	0.113	0.113	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.057	-0.024	8.002	-0.099	-0.099	0.000	0.000	0.000	0.000
56	A	59	GLN	0	-0.062	-0.033	5.907	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.002	0.004	4.560	-0.301	-0.187	-0.001	-0.009	-0.104	0.000
58	A	61	VAL	0	-0.063	-0.011	3.159	-3.100	-0.899	0.289	-0.990	-1.499	0.001
59	A	62	GLU	-1	-0.909	-0.972	4.131	-1.250	-0.965	0.003	-0.036	-0.251	0.000
60	A	63	GLN	0	-0.033	-0.008	4.907	-0.398	-0.167	-0.001	-0.031	-0.199	0.000
61	A	64	PHE	0	0.050	0.012	6.129	0.254	0.254	0.000	0.000	0.000	0.000
62	A	65	THR	0	-0.043	-0.054	8.831	-0.104	-0.104	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.020	0.012	11.290	0.025	0.025	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.002	-0.017	14.177	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	68	PRO	0	-0.006	0.011	16.712	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.040	0.018	19.312	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.004	-0.010	21.900	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	71	LEU	0	0.038	0.001	25.259	0.001	0.001	0.000	0.000	0.000	0.000
69	A	72	ALA	0	0.007	-0.001	27.969	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	73	ALA	0	0.060	0.042	26.721	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	GLY	0	0.029	0.008	28.812	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.876	0.905	30.383	-0.035	-0.035	0.000	0.000	0.000	0.000
73	A	76	HIS	0	0.091	0.053	31.387	0.002	0.002	0.000	0.000	0.000	0.000
74	A	77	LEU	0	0.085	0.055	25.840	0.001	0.001	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.884	0.934	26.504	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	79	LYS	1	0.906	0.973	26.845	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.848	-0.944	26.492	0.048	0.048	0.000	0.000	0.000	0.000
78	A	81	VAL	0	-0.008	-0.003	21.154	0.003	0.003	0.000	0.000	0.000	0.000
79	A	82	PRO	0	0.008	-0.004	21.250	0.006	0.006	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.027	0.033	21.608	0.001	0.001	0.000	0.000	0.000	0.000
81	A	84	MET	0	-0.020	-0.009	20.399	0.003	0.003	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.020	-0.014	16.251	0.009	0.009	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.870	-0.938	17.727	0.064	0.064	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.730	0.843	19.503	-0.090	-0.090	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.040	-0.025	15.816	0.000	0.000	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.812	-0.905	14.230	0.102	0.102	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.019	-0.011	15.541	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.955	-0.968	18.066	0.073	0.073	0.000	0.000	0.000	0.000
89	A	92	HIS	1	0.813	0.891	13.067	-0.136	-0.136	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.026	0.038	12.834	0.007	0.007	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.050	-0.016	9.484	0.006	0.006	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.001	0.006	9.590	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.040	-0.039	10.065	0.046	0.046	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.987	1.010	12.072	-0.140	-0.140	0.000	0.000	0.000	0.000
95	A	98	LEU	0	0.001	-0.004	14.002	0.019	0.019	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.066	-0.031	15.615	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.889	-0.968	17.435	0.057	0.057	0.000	0.000	0.000	0.000
98	A	101	PRO	0	-0.050	-0.020	20.265	0.005	0.005	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.069	0.026	20.339	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	103	GLY	0	-0.030	-0.011	22.691	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.864	0.945	24.542	-0.052	-0.052	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.013	-0.001	21.171	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	106	PRO	0	0.067	0.023	24.622	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.953	0.967	21.905	-0.055	-0.055	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.043	0.026	23.712	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.023	0.021	27.253	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.082	-0.050	28.220	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.077	0.046	27.689	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	112	ILE	0	0.019	0.012	29.842	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	113	ARG	1	0.918	0.959	32.628	-0.028	-0.028	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.918	-0.959	31.221	0.028	0.028	0.000	0.000	0.000	0.000
112	A	115	VAL	0	0.045	0.019	31.736	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	116	VAL	0	-0.020	-0.013	34.612	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	117	LYS	1	0.904	0.939	37.339	-0.023	-0.023	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.857	-0.903	33.964	0.025	0.025	0.000	0.000	0.000	0.000
116	A	119	GLU	-1	-0.884	-0.955	37.897	0.022	0.022	0.000	0.000	0.000	0.000
117	A	120	LEU	0	-0.103	-0.052	40.305	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	121	GLU	-1	-0.975	-0.964	41.644	0.015	0.015	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.767	0.874	35.974	-0.024	-0.024	0.000	0.000	0.000	0.000
120	A	123	SER	0	-0.068	-0.021	43.705	-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)