FMO DATABASE

FMODB ID: 85KMY

Calculation Name: 3LLY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LLY

Chain ID: A

ChEMBL ID:

UniProt ID: P18674

Base Structure: X-ray

Registration Date: 2023-06-26

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1171439.88423
FMO2-HF: Nuclear repulsion	1120725.70654
FMO2-HF: Total energy	-50714.177689
FMO2-MP2: Total energy	-50865.927146

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-10.048	-10.008	14.779	-6.913	-7.906	-0.052

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.013

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	3	THR	0	-0.002	-0.008	3.794	-0.299	1.236	-0.011	-0.778	-0.745	0.004
4	A	4	PHE	0	-0.011	-0.011	6.442	0.655	0.655	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.784	-0.912	9.360	-0.924	-0.924	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.792	-0.852	12.897	-0.687	-0.687	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.014	0.038	15.521	0.089	0.089	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.057	-0.031	18.184	0.007	0.007	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.077	-0.056	18.588	0.043	0.043	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.001	-0.005	23.686	0.006	0.006	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.002	0.005	24.939	0.021	0.021	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.033	-0.019	20.799	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.830	0.906	23.592	0.194	0.194	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.777	-0.884	21.195	-0.131	-0.131	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.034	0.010	16.922	-0.038	-0.038	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.021	-0.022	17.327	0.057	0.057	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.016	0.000	13.569	-0.061	-0.061	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.844	-0.905	11.769	0.189	0.189	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.039	0.025	13.475	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.061	0.028	14.737	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.041	-0.030	16.498	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.919	-0.937	18.218	0.290	0.290	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.018	-0.019	13.172	0.027	0.027	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.018	-0.007	11.179	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.034	-0.017	10.888	0.031	0.031	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.028	0.009	9.268	0.112	0.112	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.011	-0.007	9.074	-0.180	-0.180	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.046	-0.029	10.072	0.040	0.040	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.861	0.928	11.976	0.185	0.185	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.002	0.011	14.746	0.058	0.058	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.012	-0.006	17.387	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.026	-0.015	15.967	0.031	0.031	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.771	-0.868	22.504	-0.169	-0.169	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.022	-0.002	24.974	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.038	-0.040	27.054	0.017	0.017	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.021	0.015	30.230	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.053	-0.020	29.323	0.016	0.016	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.005	-0.009	26.478	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.001	0.004	20.287	0.011	0.011	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.043	-0.018	19.232	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.027	0.030	16.221	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.906	-0.963	11.483	-0.906	-0.906	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.899	-0.965	13.186	-0.304	-0.304	0.000	0.000	0.000	0.000
44	A	44	HIS	1	0.827	0.926	8.233	0.932	0.932	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.983	0.985	9.081	0.166	0.166	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.029	0.013	6.624	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.049	-0.032	2.328	0.393	0.559	2.403	-1.247	-1.322	-0.004
48	A	48	ILE	0	-0.032	-0.008	7.510	-0.113	-0.113	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.028	0.004	10.705	-0.155	-0.155	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.009	0.008	13.823	0.058	0.058	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.062	-0.023	10.363	-0.049	-0.049	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.911	0.958	15.937	-0.102	-0.102	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.018	-0.002	17.362	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.041	-0.006	18.115	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.836	0.903	19.174	0.094	0.094	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.001	0.009	20.386	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.019	-0.010	22.840	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.021	-0.002	23.971	0.012	0.012	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.829	-0.892	27.102	-0.104	-0.104	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.029	0.012	28.032	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.018	-0.025	30.327	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.050	-0.064	31.972	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.748	-0.832	28.657	-0.116	-0.116	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.023	-0.017	27.443	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.005	-0.014	21.531	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.013	-0.014	25.731	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.850	-0.920	24.231	-0.125	-0.125	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.022	0.015	18.004	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.007	0.007	19.973	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.030	0.008	17.545	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.005	0.003	16.871	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.002	0.009	12.177	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.016	-0.016	12.850	0.018	0.018	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.904	0.948	12.010	-0.424	-0.424	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.016	-0.004	10.915	-0.096	-0.096	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.894	-0.952	10.882	1.665	1.665	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.021	-0.012	11.802	0.138	0.138	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.001	0.012	5.987	0.235	0.235	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.055	-0.027	8.596	-0.129	-0.129	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.040	0.030	6.536	-0.114	-0.114	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.029	0.013	9.014	0.034	0.034	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.864	0.928	11.490	-0.225	-0.225	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.044	-0.016	13.988	0.018	0.018	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.031	0.014	13.646	-0.047	-0.047	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.012	0.001	17.761	0.043	0.043	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.002	-0.001	16.573	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.911	0.958	22.460	0.132	0.132	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.015	-0.022	26.070	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.024	-0.010	28.140	0.005	0.005	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.841	0.924	30.905	0.108	0.108	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.033	-0.013	28.477	0.014	0.014	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.004	0.003	26.242	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.039	-0.026	23.591	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.026	0.024	22.578	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.030	-0.023	21.754	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.005	-0.004	18.775	0.017	0.017	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.016	-0.004	17.415	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.047	-0.014	16.829	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.017	-0.009	18.057	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.019	-0.009	19.088	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	101	GLY	0	-0.003	0.002	18.031	0.015	0.015	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.013	-0.015	17.251	0.002	0.002	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.014	0.026	17.882	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.020	-0.006	15.406	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.020	-0.020	19.613	0.016	0.016	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.026	-0.002	19.854	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.013	0.003	22.380	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.043	-0.026	23.357	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.967	-0.967	27.340	-0.115	-0.115	0.000	0.000	0.000	0.000
110	A	110	ASN	0	-0.007	-0.029	30.257	0.007	0.007	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.009	0.011	28.513	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.027	-0.013	26.657	0.007	0.007	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.025	0.014	20.040	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.039	-0.028	22.024	0.014	0.014	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.075	0.021	18.667	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.012	-0.004	13.725	0.032	0.032	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.917	0.980	11.944	1.152	1.152	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.016	-0.023	8.868	0.239	0.239	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.051	-0.025	2.525	-0.888	-0.091	0.144	-0.578	-0.364	0.003
120	A	120	ILE	0	-0.025	-0.001	3.653	0.459	0.994	0.006	-0.216	-0.326	0.000
121	A	121	GLY	0	0.114	0.060	2.393	-0.607	-1.183	6.464	-3.749	-2.139	-0.012
122	A	122	TYR	0	-0.043	-0.007	2.658	1.345	-1.836	0.560	2.652	-0.031	-0.002
123	A	123	TRP	0	0.048	0.021	5.636	-0.594	-0.594	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.006	0.011	5.191	-0.337	-0.227	-0.001	-0.004	-0.104	0.000
125	A	125	ASP	-1	-0.805	-0.895	2.028	-11.676	-11.022	5.214	-2.993	-2.875	-0.041
126	A	126	TYR	0	-0.021	-0.031	5.093	0.740	0.740	0.000	0.000	0.000	0.000
127	A	127	PHE	0	-0.023	-0.021	8.133	-0.307	-0.307	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.052	-0.023	10.773	0.102	0.102	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.018	0.003	14.016	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	130	TYR	0	-0.068	-0.036	16.196	0.060	0.060	0.000	0.000	0.000	0.000
131	A	131	LEU	0	0.000	-0.003	20.012	0.027	0.027	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.006	-0.014	23.451	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.030	0.034	26.829	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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