FMO DATABASE

FMODB ID: VRMK1

Calculation Name: 4LBI-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LBI

Chain ID: C

ChEMBL ID:

UniProt ID: Q45075

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-653589.118466
FMO2-HF: Nuclear repulsion	616977.44398
FMO2-HF: Total energy	-36611.674486
FMO2-MP2: Total energy	-36718.675007

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(C:1:MET)

Summations of interaction energy for fragment #1(C:1:MET)

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.
-38.98	-40.866	26.74	-11.946	-12.909	0.031

Interaction energy analysis for fragmet #1(C:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.047

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	C	3	PHE	0	0.025	0.001	2.469	0.391	4.510	1.338	-2.211	-3.246	-0.004
4	C	4	LEU	0	-0.031	0.003	6.241	-0.347	-0.347	0.000	0.000	0.000	0.000
5	C	5	ILE	0	0.015	-0.001	9.383	0.192	0.192	0.000	0.000	0.000	0.000
6	C	6	TYR	0	0.018	0.005	12.085	-0.055	-0.055	0.000	0.000	0.000	0.000
7	C	7	ARG	1	0.850	0.921	15.661	0.514	0.514	0.000	0.000	0.000	0.000
8	C	8	LYS	1	0.873	0.944	18.649	0.031	0.031	0.000	0.000	0.000	0.000
9	C	9	ASP	-1	-0.710	-0.843	22.396	-0.171	-0.171	0.000	0.000	0.000	0.000
10	C	10	ARG	1	0.893	0.935	25.328	0.109	0.109	0.000	0.000	0.000	0.000
11	C	11	PRO	0	0.023	0.001	27.997	-0.012	-0.012	0.000	0.000	0.000	0.000
12	C	12	GLY	0	0.005	-0.005	31.150	0.000	0.000	0.000	0.000	0.000	0.000
13	C	13	SER	0	-0.034	-0.013	29.224	-0.005	-0.005	0.000	0.000	0.000	0.000
14	C	14	LEU	0	0.022	0.017	29.901	-0.016	-0.016	0.000	0.000	0.000	0.000
15	C	15	GLN	0	-0.041	-0.032	30.982	-0.008	-0.008	0.000	0.000	0.000	0.000
16	C	16	VAL	0	0.046	0.031	28.237	-0.013	-0.013	0.000	0.000	0.000	0.000
17	C	17	ARG	1	0.757	0.831	22.566	0.213	0.213	0.000	0.000	0.000	0.000
18	C	18	ILE	0	0.000	-0.008	28.012	-0.028	-0.028	0.000	0.000	0.000	0.000
19	C	19	ASP	-1	-0.851	-0.917	30.605	-0.178	-0.178	0.000	0.000	0.000	0.000
20	C	20	ASN	0	-0.058	-0.037	26.270	-0.023	-0.023	0.000	0.000	0.000	0.000
21	C	21	TYR	0	-0.077	-0.033	24.612	-0.057	-0.057	0.000	0.000	0.000	0.000
22	C	22	ALA	0	0.040	0.012	25.338	-0.037	-0.037	0.000	0.000	0.000	0.000
23	C	23	ALA	0	0.031	0.018	25.577	-0.032	-0.032	0.000	0.000	0.000	0.000
24	C	24	HIS	1	0.845	0.903	18.656	0.474	0.474	0.000	0.000	0.000	0.000
25	C	25	LEU	0	-0.015	-0.012	20.766	-0.070	-0.070	0.000	0.000	0.000	0.000
26	C	26	ALA	0	-0.009	-0.009	21.219	-0.057	-0.057	0.000	0.000	0.000	0.000
27	C	27	TYR	0	-0.060	-0.047	15.726	-0.042	-0.042	0.000	0.000	0.000	0.000
28	C	28	LEU	0	0.006	-0.005	15.570	-0.085	-0.085	0.000	0.000	0.000	0.000
29	C	29	GLU	-1	-0.795	-0.860	16.529	-0.798	-0.798	0.000	0.000	0.000	0.000
30	C	30	PRO	0	-0.041	-0.029	17.109	-0.055	-0.055	0.000	0.000	0.000	0.000
31	C	31	LEU	0	0.015	0.011	12.116	-0.098	-0.098	0.000	0.000	0.000	0.000
32	C	32	LYS	1	0.807	0.890	12.702	0.477	0.477	0.000	0.000	0.000	0.000
33	C	33	ALA	0	-0.017	-0.016	12.780	-0.035	-0.035	0.000	0.000	0.000	0.000
34	C	34	LYS	1	0.826	0.912	5.264	5.549	5.549	0.000	0.000	0.000	0.000
35	C	35	ILE	0	-0.039	-0.018	8.781	-0.462	-0.462	0.000	0.000	0.000	0.000
36	C	36	GLN	0	0.013	0.019	7.268	0.681	0.681	0.000	0.000	0.000	0.000
37	C	37	VAL	0	-0.006	-0.008	11.540	0.272	0.272	0.000	0.000	0.000	0.000
38	C	38	GLY	0	0.007	-0.003	13.814	-0.122	-0.122	0.000	0.000	0.000	0.000
39	C	39	GLY	0	-0.003	0.016	16.500	0.043	0.043	0.000	0.000	0.000	0.000
40	C	40	PRO	0	0.013	0.009	19.744	-0.002	-0.002	0.000	0.000	0.000	0.000
41	C	41	THR	0	-0.030	-0.019	20.746	0.023	0.023	0.000	0.000	0.000	0.000
42	C	42	LEU	0	0.031	0.021	23.219	0.000	0.000	0.000	0.000	0.000	0.000
43	C	43	GLY	0	0.041	0.021	26.976	0.015	0.015	0.000	0.000	0.000	0.000
44	C	44	ALA	0	-0.040	-0.016	29.914	0.005	0.005	0.000	0.000	0.000	0.000
45	C	45	GLY	0	0.000	0.009	32.994	-0.008	-0.008	0.000	0.000	0.000	0.000
46	C	46	THR	0	-0.001	-0.019	32.811	0.007	0.007	0.000	0.000	0.000	0.000
47	C	47	GLY	0	-0.015	0.015	33.524	-0.005	-0.005	0.000	0.000	0.000	0.000
48	C	48	THR	0	-0.005	-0.020	29.507	0.004	0.004	0.000	0.000	0.000	0.000
49	C	49	ASP	-1	-0.882	-0.934	29.951	-0.153	-0.153	0.000	0.000	0.000	0.000
50	C	50	ASP	-1	-0.811	-0.921	29.047	-0.235	-0.235	0.000	0.000	0.000	0.000
51	C	51	LYS	1	0.781	0.878	30.362	0.112	0.112	0.000	0.000	0.000	0.000
52	C	52	ASP	-1	-0.798	-0.891	30.666	-0.098	-0.098	0.000	0.000	0.000	0.000
53	C	53	MET	0	-0.053	0.009	26.220	-0.006	-0.006	0.000	0.000	0.000	0.000
54	C	54	THR	0	-0.018	-0.017	26.126	0.017	0.017	0.000	0.000	0.000	0.000
55	C	55	GLY	0	0.046	0.005	22.563	0.028	0.028	0.000	0.000	0.000	0.000
56	C	56	SER	0	-0.071	-0.026	19.006	-0.011	-0.011	0.000	0.000	0.000	0.000
57	C	57	PHE	0	-0.003	0.006	13.600	0.022	0.022	0.000	0.000	0.000	0.000
58	C	58	LEU	0	0.013	-0.001	12.687	-0.039	-0.039	0.000	0.000	0.000	0.000
59	C	59	ILE	0	-0.017	0.000	8.865	0.161	0.161	0.000	0.000	0.000	0.000
60	C	60	MET	0	-0.024	-0.012	8.112	0.224	0.224	0.000	0.000	0.000	0.000
61	C	61	GLU	-1	-0.850	-0.923	3.515	-5.535	-5.098	0.005	-0.103	-0.340	0.000
62	C	62	ALA	0	-0.013	-0.007	3.162	1.829	2.549	0.007	-0.283	-0.444	0.000
63	C	63	GLU	-1	-0.842	-0.920	1.934	-18.907	-19.433	6.731	-3.436	-2.769	-0.041
64	C	64	SER	0	-0.061	-0.029	3.921	1.093	1.429	-0.001	-0.027	-0.309	0.000
65	C	65	TRP	0	0.038	0.000	5.614	0.092	0.092	0.000	0.000	0.000	0.000
66	C	66	ASP	-1	-0.900	-0.949	6.745	-0.460	-0.460	0.000	0.000	0.000	0.000
67	C	67	GLU	-1	-0.849	-0.920	6.649	-4.200	-4.200	0.000	0.000	0.000	0.000
68	C	68	VAL	0	0.015	0.009	5.945	0.110	0.110	0.000	0.000	0.000	0.000
69	C	69	HIS	0	0.015	-0.005	8.931	0.042	0.042	0.000	0.000	0.000	0.000
70	C	70	SER	0	0.002	0.008	11.841	0.089	0.089	0.000	0.000	0.000	0.000
71	C	71	PHE	0	0.021	0.017	11.429	0.082	0.082	0.000	0.000	0.000	0.000
72	C	72	VAL	0	0.001	0.011	12.329	0.090	0.090	0.000	0.000	0.000	0.000
73	C	73	GLU	-1	-0.897	-0.946	14.789	-0.174	-0.174	0.000	0.000	0.000	0.000
74	C	74	ASN	0	-0.087	-0.061	16.572	0.100	0.100	0.000	0.000	0.000	0.000
75	C	75	ASP	-1	-0.765	-0.834	17.354	-0.513	-0.513	0.000	0.000	0.000	0.000
76	C	76	PRO	0	-0.008	-0.013	19.192	0.069	0.069	0.000	0.000	0.000	0.000
77	C	77	PHE	0	-0.011	-0.013	21.234	0.037	0.037	0.000	0.000	0.000	0.000
78	C	78	THR	0	-0.016	-0.029	18.265	0.056	0.056	0.000	0.000	0.000	0.000
79	C	79	LYS	1	0.926	0.975	21.436	0.382	0.382	0.000	0.000	0.000	0.000
80	C	80	ALA	0	-0.024	0.009	23.944	0.025	0.025	0.000	0.000	0.000	0.000
81	C	81	GLY	0	0.000	0.004	24.945	0.024	0.024	0.000	0.000	0.000	0.000
82	C	82	LEU	0	-0.049	-0.004	23.603	0.029	0.029	0.000	0.000	0.000	0.000
83	C	83	PHE	0	-0.008	-0.018	20.165	0.010	0.010	0.000	0.000	0.000	0.000
84	C	84	ALA	0	-0.016	-0.005	23.574	0.009	0.009	0.000	0.000	0.000	0.000
85	C	85	ALA	0	-0.026	-0.003	21.290	0.035	0.035	0.000	0.000	0.000	0.000
86	C	86	THR	0	0.024	-0.002	15.552	-0.068	-0.068	0.000	0.000	0.000	0.000
87	C	87	ILE	0	-0.018	0.003	13.506	0.069	0.069	0.000	0.000	0.000	0.000
88	C	88	VAL	0	-0.001	0.004	8.668	-0.155	-0.155	0.000	0.000	0.000	0.000
89	C	89	GLU	-1	-0.873	-0.942	9.288	1.956	1.956	0.000	0.000	0.000	0.000
90	C	90	ARG	1	0.844	0.930	2.212	-21.000	-28.213	18.662	-5.867	-5.582	0.076
91	C	91	TRP	0	-0.011	-0.014	4.624	0.093	0.229	-0.001	-0.006	-0.128	0.000
92	C	92	LYS	1	0.895	0.934	4.571	-1.046	-0.941	-0.001	-0.013	-0.091	0.000
93	C	93	HIS	0	0.043	0.027	7.024	0.237	0.237	0.000	0.000	0.000	0.000
94	C	94	GLY	0	-0.006	0.004	9.988	0.319	0.319	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:MET)