FMO DATABASE

FMODB ID: JQR99

Calculation Name: 2C0L-B-Xray372

Preferred Name: Non-specific lipid-transfer protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2C0L

Chain ID: B

ChEMBL ID: CHEMBL5950

UniProt ID: P22307

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-973863.432526
FMO2-HF: Nuclear repulsion	927208.144071
FMO2-HF: Total energy	-46655.288456
FMO2-MP2: Total energy	-46789.216048

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(B:22:SER)

Summations of interaction energy for fragment #1(B:22: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.
-23.801	-16.411	5.58	-6.627	-6.344	-0.053

Interaction energy analysis for fragmet #1(B:22:SER)

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 : 0.005

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	B	24	SER	0	0.036	0.020	3.593	-2.217	0.108	0.008	-1.094	-1.238	0.006
4	B	25	ASP	-1	-0.822	-0.913	2.099	-26.906	-22.148	5.568	-5.388	-4.938	-0.059
5	B	26	GLY	0	0.006	0.006	4.354	0.520	0.548	-0.001	-0.023	-0.005	0.000
6	B	27	PHE	0	-0.080	-0.041	7.121	0.878	0.878	0.000	0.000	0.000	0.000
7	B	28	LYS	1	0.875	0.924	9.515	1.060	1.060	0.000	0.000	0.000	0.000
8	B	29	ALA	0	0.026	0.007	11.211	0.050	0.050	0.000	0.000	0.000	0.000
9	B	30	ASN	0	0.012	0.019	5.640	0.875	0.875	0.000	0.000	0.000	0.000
10	B	31	LEU	0	-0.017	-0.002	9.292	0.078	0.078	0.000	0.000	0.000	0.000
11	B	32	VAL	0	0.002	0.005	12.102	0.116	0.116	0.000	0.000	0.000	0.000
12	B	33	PHE	0	0.008	-0.013	10.506	0.110	0.110	0.000	0.000	0.000	0.000
13	B	34	LYS	1	0.961	0.980	6.123	1.893	1.893	0.000	0.000	0.000	0.000
14	B	35	GLU	-1	-0.841	-0.903	12.031	-0.292	-0.292	0.000	0.000	0.000	0.000
15	B	36	ILE	0	-0.060	-0.023	15.148	0.057	0.057	0.000	0.000	0.000	0.000
16	B	37	GLU	-1	-0.902	-0.978	10.794	-0.287	-0.287	0.000	0.000	0.000	0.000
17	B	38	LYS	1	0.847	0.922	14.454	0.470	0.470	0.000	0.000	0.000	0.000
18	B	39	LYS	1	0.904	0.953	17.206	0.263	0.263	0.000	0.000	0.000	0.000
19	B	40	LEU	0	-0.099	-0.045	17.288	0.022	0.022	0.000	0.000	0.000	0.000
20	B	41	GLU	-1	-0.882	-0.948	17.040	0.024	0.024	0.000	0.000	0.000	0.000
21	B	42	GLU	-1	-0.993	-0.971	19.833	-0.155	-0.155	0.000	0.000	0.000	0.000
22	B	43	GLU	-1	-1.004	-1.018	23.016	-0.073	-0.073	0.000	0.000	0.000	0.000
23	B	44	GLY	0	0.067	0.029	22.387	0.001	0.001	0.000	0.000	0.000	0.000
24	B	45	GLU	-1	-0.930	-0.965	23.019	0.018	0.018	0.000	0.000	0.000	0.000
25	B	46	GLN	0	-0.001	-0.002	26.323	0.009	0.009	0.000	0.000	0.000	0.000
26	B	47	PHE	0	-0.007	-0.013	23.576	0.002	0.002	0.000	0.000	0.000	0.000
27	B	48	VAL	0	-0.008	0.019	23.517	0.001	0.001	0.000	0.000	0.000	0.000
28	B	49	LYS	1	0.913	0.964	25.816	0.007	0.007	0.000	0.000	0.000	0.000
29	B	50	LYS	1	0.920	0.983	27.708	0.066	0.066	0.000	0.000	0.000	0.000
30	B	51	ILE	0	-0.026	-0.003	23.496	0.000	0.000	0.000	0.000	0.000	0.000
31	B	52	GLY	0	0.078	0.053	26.280	0.003	0.003	0.000	0.000	0.000	0.000
32	B	53	GLY	0	-0.017	-0.025	24.834	0.006	0.006	0.000	0.000	0.000	0.000
33	B	54	ILE	0	-0.090	-0.021	19.152	0.001	0.001	0.000	0.000	0.000	0.000
34	B	55	PHE	0	0.014	-0.001	18.319	-0.012	-0.012	0.000	0.000	0.000	0.000
35	B	56	ALA	0	0.054	0.031	16.140	0.033	0.033	0.000	0.000	0.000	0.000
36	B	57	PHE	0	-0.008	-0.020	13.756	-0.050	-0.050	0.000	0.000	0.000	0.000
37	B	58	LYS	1	0.963	0.978	13.631	-0.035	-0.035	0.000	0.000	0.000	0.000
38	B	59	VAL	0	0.001	0.005	12.129	-0.017	-0.017	0.000	0.000	0.000	0.000
39	B	60	LYS	1	0.852	0.906	12.996	0.069	0.069	0.000	0.000	0.000	0.000
40	B	61	ASP	-1	-0.866	-0.949	15.269	-0.342	-0.342	0.000	0.000	0.000	0.000
41	B	62	GLY	0	0.032	0.021	11.354	-0.037	-0.037	0.000	0.000	0.000	0.000
42	B	63	PRO	0	-0.046	-0.028	8.350	0.115	0.115	0.000	0.000	0.000	0.000
43	B	64	GLY	0	0.006	0.000	10.088	-0.068	-0.068	0.000	0.000	0.000	0.000
44	B	65	GLY	0	0.023	0.021	12.281	0.087	0.087	0.000	0.000	0.000	0.000
45	B	66	LYS	1	0.861	0.941	6.077	1.701	1.701	0.000	0.000	0.000	0.000
46	B	67	GLU	-1	-0.794	-0.895	10.626	-0.100	-0.100	0.000	0.000	0.000	0.000
47	B	68	ALA	0	-0.022	0.002	7.818	0.012	0.012	0.000	0.000	0.000	0.000
48	B	69	THR	0	-0.021	-0.023	8.775	-0.037	-0.037	0.000	0.000	0.000	0.000
49	B	70	TRP	0	0.028	0.020	7.431	0.215	0.215	0.000	0.000	0.000	0.000
50	B	71	VAL	0	0.007	0.004	11.281	-0.064	-0.064	0.000	0.000	0.000	0.000
51	B	72	VAL	0	0.009	0.016	14.031	0.018	0.018	0.000	0.000	0.000	0.000
52	B	73	ASP	-1	-0.811	-0.906	16.285	0.116	0.116	0.000	0.000	0.000	0.000
53	B	74	VAL	0	0.070	0.035	18.668	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	75	LYS	1	0.831	0.908	21.635	-0.080	-0.080	0.000	0.000	0.000	0.000
55	B	76	ASN	0	-0.042	-0.038	21.618	-0.011	-0.011	0.000	0.000	0.000	0.000
56	B	77	GLY	0	0.044	0.016	22.478	0.001	0.001	0.000	0.000	0.000	0.000
57	B	78	LYS	1	0.897	0.932	21.957	-0.017	-0.017	0.000	0.000	0.000	0.000
58	B	79	GLY	0	0.049	0.038	20.017	-0.020	-0.020	0.000	0.000	0.000	0.000
59	B	80	SER	0	-0.062	-0.041	15.140	0.021	0.021	0.000	0.000	0.000	0.000
60	B	81	VAL	0	0.024	0.010	10.828	-0.023	-0.023	0.000	0.000	0.000	0.000
61	B	82	LEU	0	-0.026	-0.014	10.839	0.053	0.053	0.000	0.000	0.000	0.000
62	B	83	PRO	0	0.009	-0.013	5.815	-0.123	-0.123	0.000	0.000	0.000	0.000
63	B	84	ASN	0	-0.037	-0.034	3.742	-1.362	-1.083	0.005	-0.122	-0.163	0.000
64	B	85	SER	0	-0.016	0.014	7.571	-0.039	-0.039	0.000	0.000	0.000	0.000
65	B	86	ASP	-1	-0.914	-0.953	10.923	0.415	0.415	0.000	0.000	0.000	0.000
66	B	87	LYS	1	0.895	0.944	13.770	-0.253	-0.253	0.000	0.000	0.000	0.000
67	B	88	LYS	1	0.933	0.960	16.595	-0.176	-0.176	0.000	0.000	0.000	0.000
68	B	89	ALA	0	0.038	0.005	19.079	0.005	0.005	0.000	0.000	0.000	0.000
69	B	90	ASP	-1	-0.812	-0.880	21.157	0.056	0.056	0.000	0.000	0.000	0.000
70	B	91	CYS	0	-0.074	-0.019	22.463	-0.016	-0.016	0.000	0.000	0.000	0.000
71	B	92	THR	0	-0.007	-0.002	18.848	0.020	0.020	0.000	0.000	0.000	0.000
72	B	93	ILE	0	0.020	0.011	18.544	-0.015	-0.015	0.000	0.000	0.000	0.000
73	B	94	THR	0	-0.033	-0.007	17.913	0.006	0.006	0.000	0.000	0.000	0.000
74	B	95	MET	0	-0.026	-0.002	17.773	0.009	0.009	0.000	0.000	0.000	0.000
75	B	96	ALA	0	0.095	0.067	17.167	-0.023	-0.023	0.000	0.000	0.000	0.000
76	B	97	ASP	-1	-0.706	-0.875	12.769	-0.960	-0.960	0.000	0.000	0.000	0.000
77	B	98	SER	0	0.009	0.000	15.471	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	99	ASP	-1	-0.824	-0.920	18.021	-0.232	-0.232	0.000	0.000	0.000	0.000
79	B	100	PHE	0	-0.003	-0.004	14.485	0.032	0.032	0.000	0.000	0.000	0.000
80	B	101	LEU	0	0.023	0.013	16.012	0.014	0.014	0.000	0.000	0.000	0.000
81	B	102	ALA	0	0.006	0.017	18.055	0.029	0.029	0.000	0.000	0.000	0.000
82	B	103	LEU	0	-0.030	-0.021	21.100	0.024	0.024	0.000	0.000	0.000	0.000
83	B	104	MET	0	0.018	0.011	17.916	0.031	0.031	0.000	0.000	0.000	0.000
84	B	105	THR	0	-0.042	-0.032	19.407	0.004	0.004	0.000	0.000	0.000	0.000
85	B	106	GLY	0	0.023	0.008	22.013	0.010	0.010	0.000	0.000	0.000	0.000
86	B	107	LYS	1	0.823	0.924	24.143	0.270	0.270	0.000	0.000	0.000	0.000
87	B	108	MET	0	-0.035	-0.008	23.732	0.019	0.019	0.000	0.000	0.000	0.000
88	B	109	ASN	0	0.030	0.031	26.323	-0.011	-0.011	0.000	0.000	0.000	0.000
89	B	110	PRO	0	0.063	0.021	25.277	-0.005	-0.005	0.000	0.000	0.000	0.000
90	B	111	GLN	0	0.084	0.026	26.692	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	112	SER	0	0.014	0.006	29.574	0.004	0.004	0.000	0.000	0.000	0.000
92	B	113	ALA	0	0.007	0.008	25.036	0.001	0.001	0.000	0.000	0.000	0.000
93	B	114	PHE	0	-0.023	-0.009	27.194	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	115	PHE	0	0.005	-0.002	28.341	0.004	0.004	0.000	0.000	0.000	0.000
95	B	116	GLN	0	-0.037	-0.026	28.460	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	117	GLY	0	-0.002	0.016	28.566	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	118	LYS	1	0.861	0.922	24.138	0.201	0.201	0.000	0.000	0.000	0.000
98	B	119	LEU	0	-0.019	0.004	22.038	-0.017	-0.017	0.000	0.000	0.000	0.000
99	B	120	LYS	1	0.880	0.931	22.790	0.116	0.116	0.000	0.000	0.000	0.000
100	B	121	ILE	0	0.024	-0.001	22.694	0.000	0.000	0.000	0.000	0.000	0.000
101	B	122	THR	0	-0.020	0.001	23.369	0.010	0.010	0.000	0.000	0.000	0.000
102	B	123	GLY	0	0.045	0.020	24.932	0.003	0.003	0.000	0.000	0.000	0.000
103	B	124	ASN	0	0.017	0.001	27.026	-0.016	-0.016	0.000	0.000	0.000	0.000
104	B	125	MET	0	0.079	0.034	27.089	-0.006	-0.006	0.000	0.000	0.000	0.000
105	B	126	GLY	0	0.021	0.011	28.859	-0.009	-0.009	0.000	0.000	0.000	0.000
106	B	127	LEU	0	-0.030	-0.019	23.459	-0.008	-0.008	0.000	0.000	0.000	0.000
107	B	128	ALA	0	0.070	0.019	24.250	-0.008	-0.008	0.000	0.000	0.000	0.000
108	B	129	MET	0	-0.046	-0.013	25.119	-0.018	-0.018	0.000	0.000	0.000	0.000
109	B	130	LYS	1	0.822	0.904	26.462	0.013	0.013	0.000	0.000	0.000	0.000
110	B	131	LEU	0	0.015	0.013	19.822	-0.002	-0.002	0.000	0.000	0.000	0.000
111	B	132	GLN	0	0.018	0.002	23.011	-0.016	-0.016	0.000	0.000	0.000	0.000
112	B	133	ASN	0	-0.074	-0.042	25.230	0.003	0.003	0.000	0.000	0.000	0.000
113	B	134	LEU	0	-0.005	-0.002	19.089	0.000	0.000	0.000	0.000	0.000	0.000
114	B	135	GLN	0	-0.017	-0.002	20.647	-0.018	-0.018	0.000	0.000	0.000	0.000
115	B	136	LEU	0	-0.010	0.011	17.080	0.005	0.005	0.000	0.000	0.000	0.000
116	B	137	GLN	0	-0.033	-0.031	21.757	0.007	0.007	0.000	0.000	0.000	0.000
117	B	138	PRO	0	-0.012	0.012	24.904	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	139	GLY	0	0.041	0.023	26.836	0.012	0.012	0.000	0.000	0.000	0.000
119	B	140	ASN	0	0.000	-0.008	29.226	-0.006	-0.006	0.000	0.000	0.000	0.000
120	B	141	ALA	0	0.018	0.003	32.914	-0.004	-0.004	0.000	0.000	0.000	0.000
121	B	142	LYS	1	0.891	0.943	32.075	0.123	0.123	0.000	0.000	0.000	0.000
122	B	143	LEU	0	0.063	0.044	36.899	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:22:SER)