FMO DATABASE

FMODB ID: 3J4VL

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	-974437.43726
FMO2-HF: Nuclear repulsion	927781.715716
FMO2-HF: Total energy	-46655.721544
FMO2-MP2: Total energy	-46789.705583

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.
-34.013	-35.127	23.782	-12.806	-9.862	-0.057

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 : 0.013 / q_NPA : -0.011

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	0.018	0.000	2.527	-6.447	-2.008	1.229	-2.667	-3.001	0.022
4	B	25	ASP	-1	-0.811	-0.878	1.722	-31.336	-38.225	22.380	-9.441	-6.051	-0.086
5	B	26	GLY	0	0.013	0.003	4.283	1.061	1.157	0.000	-0.036	-0.059	0.000
6	B	27	PHE	0	-0.045	-0.021	7.043	0.740	0.740	0.000	0.000	0.000	0.000
7	B	28	LYS	1	0.825	0.879	9.364	0.963	0.963	0.000	0.000	0.000	0.000
8	B	29	ALA	0	0.040	0.015	10.649	0.037	0.037	0.000	0.000	0.000	0.000
9	B	30	ASN	0	0.011	0.012	5.152	0.884	0.884	0.000	0.000	0.000	0.000
10	B	31	LEU	0	-0.017	-0.002	8.452	0.053	0.053	0.000	0.000	0.000	0.000
11	B	32	VAL	0	0.007	0.010	11.301	0.116	0.116	0.000	0.000	0.000	0.000
12	B	33	PHE	0	0.000	-0.010	9.657	0.106	0.106	0.000	0.000	0.000	0.000
13	B	34	LYS	1	0.955	0.965	5.091	2.225	2.225	0.000	0.000	0.000	0.000
14	B	35	GLU	-1	-0.836	-0.889	11.207	-0.236	-0.236	0.000	0.000	0.000	0.000
15	B	36	ILE	0	-0.039	-0.018	14.364	0.056	0.056	0.000	0.000	0.000	0.000
16	B	37	GLU	-1	-0.931	-0.980	9.914	-0.206	-0.206	0.000	0.000	0.000	0.000
17	B	38	LYS	1	0.852	0.923	14.021	0.384	0.384	0.000	0.000	0.000	0.000
18	B	39	LYS	1	0.815	0.888	16.583	0.185	0.185	0.000	0.000	0.000	0.000
19	B	40	LEU	0	-0.053	-0.018	16.412	0.018	0.018	0.000	0.000	0.000	0.000
20	B	41	GLU	-1	-0.895	-0.946	16.913	0.089	0.089	0.000	0.000	0.000	0.000
21	B	42	GLU	-1	-0.926	-0.949	19.675	-0.122	-0.122	0.000	0.000	0.000	0.000
22	B	43	GLU	-1	-0.878	-0.944	22.181	-0.029	-0.029	0.000	0.000	0.000	0.000
23	B	44	GLY	0	0.034	0.020	21.644	0.002	0.002	0.000	0.000	0.000	0.000
24	B	45	GLU	-1	-0.892	-0.926	22.457	0.063	0.063	0.000	0.000	0.000	0.000
25	B	46	GLN	0	0.017	0.007	25.688	0.010	0.010	0.000	0.000	0.000	0.000
26	B	47	PHE	0	0.003	-0.008	22.947	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	48	VAL	0	-0.024	0.003	23.025	0.002	0.002	0.000	0.000	0.000	0.000
28	B	49	LYS	1	0.903	0.945	25.279	-0.032	-0.032	0.000	0.000	0.000	0.000
29	B	50	LYS	1	0.814	0.927	26.202	0.021	0.021	0.000	0.000	0.000	0.000
30	B	51	ILE	0	-0.023	0.000	22.748	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	52	GLY	0	0.042	0.031	26.098	0.000	0.000	0.000	0.000	0.000	0.000
32	B	53	GLY	0	-0.015	-0.030	24.236	0.001	0.001	0.000	0.000	0.000	0.000
33	B	54	ILE	0	-0.090	-0.021	18.638	0.007	0.007	0.000	0.000	0.000	0.000
34	B	55	PHE	0	0.035	0.011	17.752	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	56	ALA	0	0.039	0.026	15.547	0.044	0.044	0.000	0.000	0.000	0.000
36	B	57	PHE	0	-0.001	-0.019	13.274	-0.079	-0.079	0.000	0.000	0.000	0.000
37	B	58	LYS	1	0.943	0.980	12.794	-0.124	-0.124	0.000	0.000	0.000	0.000
38	B	59	VAL	0	-0.014	-0.006	11.237	-0.057	-0.057	0.000	0.000	0.000	0.000
39	B	60	LYS	1	0.854	0.901	12.358	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	61	ASP	-1	-0.855	-0.951	14.666	-0.312	-0.312	0.000	0.000	0.000	0.000
41	B	62	GLY	0	0.033	0.027	11.639	-0.033	-0.033	0.000	0.000	0.000	0.000
42	B	63	PRO	0	-0.062	-0.036	8.559	0.094	0.094	0.000	0.000	0.000	0.000
43	B	64	GLY	0	0.013	0.004	10.212	-0.118	-0.118	0.000	0.000	0.000	0.000
44	B	65	GLY	0	0.021	0.019	12.525	0.079	0.079	0.000	0.000	0.000	0.000
45	B	66	LYS	1	0.856	0.938	6.464	2.007	2.007	0.000	0.000	0.000	0.000
46	B	67	GLU	-1	-0.778	-0.875	11.700	0.016	0.016	0.000	0.000	0.000	0.000
47	B	68	ALA	0	-0.005	0.005	7.252	0.011	0.011	0.000	0.000	0.000	0.000
48	B	69	THR	0	-0.038	-0.037	8.236	-0.173	-0.173	0.000	0.000	0.000	0.000
49	B	70	TRP	0	0.028	0.025	6.425	0.525	0.525	0.000	0.000	0.000	0.000
50	B	71	VAL	0	-0.023	-0.001	10.453	-0.146	-0.146	0.000	0.000	0.000	0.000
51	B	72	VAL	0	0.014	0.003	13.085	0.027	0.027	0.000	0.000	0.000	0.000
52	B	73	ASP	-1	-0.799	-0.890	15.647	0.178	0.178	0.000	0.000	0.000	0.000
53	B	74	VAL	0	0.048	0.015	18.275	-0.014	-0.014	0.000	0.000	0.000	0.000
54	B	75	LYS	1	0.818	0.904	21.223	-0.140	-0.140	0.000	0.000	0.000	0.000
55	B	76	ASN	0	-0.037	-0.028	21.467	-0.019	-0.019	0.000	0.000	0.000	0.000
56	B	77	GLY	0	0.045	0.023	22.086	0.009	0.009	0.000	0.000	0.000	0.000
57	B	78	LYS	1	0.923	0.936	21.408	-0.066	-0.066	0.000	0.000	0.000	0.000
58	B	79	GLY	0	0.047	0.025	19.686	-0.017	-0.017	0.000	0.000	0.000	0.000
59	B	80	SER	0	-0.065	-0.047	14.775	0.025	0.025	0.000	0.000	0.000	0.000
60	B	81	VAL	0	0.006	0.016	10.082	0.010	0.010	0.000	0.000	0.000	0.000
61	B	82	LEU	0	-0.014	-0.009	10.408	0.041	0.041	0.000	0.000	0.000	0.000
62	B	83	PRO	0	0.023	-0.008	5.354	-0.110	-0.110	0.000	0.000	0.000	0.000
63	B	84	ASN	0	-0.035	-0.017	2.813	-3.489	-2.249	0.173	-0.662	-0.751	0.007
64	B	85	SER	0	-0.018	0.015	7.159	-0.266	-0.266	0.000	0.000	0.000	0.000
65	B	86	ASP	-1	-0.889	-0.950	10.636	0.545	0.545	0.000	0.000	0.000	0.000
66	B	87	LYS	1	0.857	0.935	13.768	-0.409	-0.409	0.000	0.000	0.000	0.000
67	B	88	LYS	1	0.965	0.975	16.197	-0.224	-0.224	0.000	0.000	0.000	0.000
68	B	89	ALA	0	0.016	-0.006	18.383	0.007	0.007	0.000	0.000	0.000	0.000
69	B	90	ASP	-1	-0.788	-0.872	20.466	0.110	0.110	0.000	0.000	0.000	0.000
70	B	91	CYS	0	-0.079	-0.017	21.847	-0.022	-0.022	0.000	0.000	0.000	0.000
71	B	92	THR	0	0.003	0.003	17.925	0.039	0.039	0.000	0.000	0.000	0.000
72	B	93	ILE	0	0.030	0.019	17.835	-0.027	-0.027	0.000	0.000	0.000	0.000
73	B	94	THR	0	-0.065	-0.037	17.425	0.030	0.030	0.000	0.000	0.000	0.000
74	B	95	MET	0	-0.008	0.012	17.123	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	96	ALA	0	0.099	0.071	16.516	0.000	0.000	0.000	0.000	0.000	0.000
76	B	97	ASP	-1	-0.724	-0.869	12.295	-0.884	-0.884	0.000	0.000	0.000	0.000
77	B	98	SER	0	-0.021	-0.014	14.763	-0.023	-0.023	0.000	0.000	0.000	0.000
78	B	99	ASP	-1	-0.812	-0.909	17.919	-0.215	-0.215	0.000	0.000	0.000	0.000
79	B	100	PHE	0	0.043	0.014	13.688	0.033	0.033	0.000	0.000	0.000	0.000
80	B	101	LEU	0	0.012	0.011	15.426	0.011	0.011	0.000	0.000	0.000	0.000
81	B	102	ALA	0	0.001	0.014	17.345	0.025	0.025	0.000	0.000	0.000	0.000
82	B	103	LEU	0	-0.020	-0.012	20.581	0.018	0.018	0.000	0.000	0.000	0.000
83	B	104	MET	0	0.002	0.006	17.067	0.025	0.025	0.000	0.000	0.000	0.000
84	B	105	THR	0	-0.020	-0.010	18.639	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	106	GLY	0	0.003	-0.002	21.280	0.004	0.004	0.000	0.000	0.000	0.000
86	B	107	LYS	1	0.830	0.920	22.697	0.251	0.251	0.000	0.000	0.000	0.000
87	B	108	MET	0	-0.066	-0.012	22.888	0.015	0.015	0.000	0.000	0.000	0.000
88	B	109	ASN	0	0.053	0.036	25.245	-0.008	-0.008	0.000	0.000	0.000	0.000
89	B	110	PRO	0	0.043	0.017	24.316	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	111	GLN	0	0.086	0.027	25.885	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	112	SER	0	0.016	0.008	28.597	0.002	0.002	0.000	0.000	0.000	0.000
92	B	113	ALA	0	0.018	0.014	24.075	-0.004	-0.004	0.000	0.000	0.000	0.000
93	B	114	PHE	0	-0.018	-0.007	26.227	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	115	PHE	0	0.004	-0.005	27.475	0.002	0.002	0.000	0.000	0.000	0.000
95	B	116	GLN	0	-0.028	-0.028	27.600	-0.011	-0.011	0.000	0.000	0.000	0.000
96	B	117	GLY	0	0.006	0.016	27.868	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	118	LYS	1	0.861	0.928	23.324	0.171	0.171	0.000	0.000	0.000	0.000
98	B	119	LEU	0	-0.034	-0.005	21.206	-0.013	-0.013	0.000	0.000	0.000	0.000
99	B	120	LYS	1	0.870	0.927	22.006	0.070	0.070	0.000	0.000	0.000	0.000
100	B	121	ILE	0	0.033	-0.003	21.997	0.006	0.006	0.000	0.000	0.000	0.000
101	B	122	THR	0	-0.014	0.002	22.730	0.005	0.005	0.000	0.000	0.000	0.000
102	B	123	GLY	0	0.048	0.027	24.020	0.010	0.010	0.000	0.000	0.000	0.000
103	B	124	ASN	0	0.025	-0.006	26.062	-0.021	-0.021	0.000	0.000	0.000	0.000
104	B	125	MET	0	0.064	0.032	26.369	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	126	GLY	0	0.025	0.016	27.974	-0.008	-0.008	0.000	0.000	0.000	0.000
106	B	127	LEU	0	-0.038	-0.016	22.518	-0.007	-0.007	0.000	0.000	0.000	0.000
107	B	128	ALA	0	0.066	0.007	23.424	-0.005	-0.005	0.000	0.000	0.000	0.000
108	B	129	MET	0	-0.070	-0.028	24.443	-0.019	-0.019	0.000	0.000	0.000	0.000
109	B	130	LYS	1	0.828	0.904	25.905	-0.032	-0.032	0.000	0.000	0.000	0.000
110	B	131	LEU	0	0.010	0.015	19.257	-0.002	-0.002	0.000	0.000	0.000	0.000
111	B	132	GLN	0	0.044	0.017	22.465	-0.008	-0.008	0.000	0.000	0.000	0.000
112	B	133	ASN	0	-0.084	-0.046	24.612	0.001	0.001	0.000	0.000	0.000	0.000
113	B	134	LEU	0	-0.008	-0.005	18.607	0.005	0.005	0.000	0.000	0.000	0.000
114	B	135	GLN	0	-0.018	-0.010	19.894	-0.012	-0.012	0.000	0.000	0.000	0.000
115	B	136	LEU	0	-0.007	0.011	16.292	0.003	0.003	0.000	0.000	0.000	0.000
116	B	137	GLN	0	-0.044	-0.031	20.967	0.000	0.000	0.000	0.000	0.000	0.000
117	B	138	PRO	0	0.011	0.013	24.036	-0.003	-0.003	0.000	0.000	0.000	0.000
118	B	139	GLY	0	0.044	0.025	26.139	0.013	0.013	0.000	0.000	0.000	0.000
119	B	140	ASN	0	-0.002	-0.012	28.483	-0.008	-0.008	0.000	0.000	0.000	0.000
120	B	141	ALA	0	0.034	0.015	32.228	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	142	LYS	1	0.873	0.930	32.295	0.093	0.093	0.000	0.000	0.000	0.000
122	B	143	LEU	0	0.062	0.049	36.562	-0.002	-0.002	0.000	0.000	0.000	0.000

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