FMO DATABASE

FMODB ID: ZN28N

Calculation Name: 1VR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VR9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZZ4

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1075582.105268
FMO2-HF: Nuclear repulsion	1025451.190887
FMO2-HF: Total energy	-50130.914381
FMO2-MP2: Total energy	-50275.435023

3D Structure Molmil

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:MET)

Summations of interaction energy for fragment #1(A: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.
-17.166	-8.071	10.407	-6.894	-12.61	-0.038

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : 0.004

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	VAL	0	0.048	0.021	2.899	-4.731	-1.591	0.246	-1.633	-1.753	-0.007
4	A	4	LYS	1	0.837	0.890	5.475	-1.105	-1.105	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.704	0.860	2.700	3.687	3.174	6.544	-1.740	-4.293	-0.001
6	A	6	TRP	0	0.017	0.001	2.107	-1.242	-0.085	1.747	-0.778	-2.126	-0.001
7	A	7	VAL	0	-0.017	0.015	6.457	-0.183	-0.183	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.032	0.026	9.698	0.115	0.115	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.016	-0.058	12.714	0.007	0.007	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.919	-0.919	16.056	-0.186	-0.186	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.011	0.008	16.601	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.020	0.012	18.926	0.036	0.036	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.004	0.003	21.391	0.007	0.007	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.024	-0.035	23.259	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.771	-0.846	25.868	0.021	0.021	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.773	-0.879	28.354	0.018	0.018	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.080	-0.064	29.898	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.014	0.036	30.924	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.003	-0.040	32.902	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.033	0.016	33.406	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.753	0.833	33.669	0.035	0.035	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.870	-0.903	31.611	-0.037	-0.037	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.007	0.017	28.042	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.059	0.018	28.828	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.014	0.002	30.268	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.945	0.972	25.759	0.059	0.059	0.000	0.000	0.000	0.000
27	A	27	MET	0	0.061	0.038	25.409	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.839	0.924	26.466	0.083	0.083	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.077	-0.040	26.477	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.025	-0.029	20.492	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.098	-0.044	23.175	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.044	0.034	21.737	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.022	-0.027	24.133	0.010	0.010	0.000	0.000	0.000	0.000
34	A	34	GLH	0	0.079	0.041	18.575	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	CYS	0	-0.089	-0.043	23.142	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.039	0.026	17.496	0.008	0.008	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.006	0.000	21.851	0.013	0.013	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.970	0.991	22.862	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.765	-0.879	24.710	0.076	0.076	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.764	0.831	27.167	-0.037	-0.037	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.949	-0.960	27.736	0.105	0.105	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.042	-0.019	24.153	0.017	0.017	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.057	-0.025	22.507	0.028	0.028	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.017	0.000	19.770	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.818	0.893	21.908	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.042	0.027	22.750	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.044	-0.015	20.454	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.026	0.009	23.553	0.013	0.013	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.025	-0.024	24.109	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.880	0.920	27.358	0.175	0.175	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.903	-0.955	28.749	-0.155	-0.155	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.812	-0.896	31.112	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.038	-0.034	30.381	0.012	0.012	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.046	-0.004	33.836	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.941	-0.969	36.330	-0.076	-0.076	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.055	-0.022	35.472	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.856	-0.925	39.406	-0.042	-0.042	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.000	-0.004	37.756	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.797	-0.864	38.287	-0.036	-0.036	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.064	-0.031	38.785	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.032	-0.047	35.315	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.016	-0.009	29.948	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.013	0.015	31.843	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.081	-0.050	32.608	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.801	0.883	31.813	0.066	0.066	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.043	0.003	26.365	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.006	0.003	26.577	0.008	0.008	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.005	-0.004	21.736	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.022	0.008	22.164	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.893	-0.957	21.450	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.034	-0.015	16.335	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.031	-0.017	15.450	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.004	0.003	9.865	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	74	HIS	0	0.007	-0.012	12.327	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.838	-0.932	10.059	0.697	0.697	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.853	-0.927	8.426	2.233	2.233	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.765	-0.845	8.855	0.721	0.721	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.029	-0.024	3.787	1.057	1.358	0.000	-0.061	-0.240	0.000
79	A	79	ILE	0	0.054	0.018	2.496	-1.240	0.118	1.095	-0.736	-1.717	-0.003
80	A	80	THR	0	-0.011	-0.025	4.193	0.267	0.529	-0.001	-0.022	-0.239	0.000
81	A	81	HIS	0	-0.012	0.000	6.257	0.256	0.256	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.060	0.025	8.461	0.092	0.092	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.017	-0.002	9.338	0.072	0.072	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.032	-0.006	11.065	0.095	0.095	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.048	0.028	13.002	0.031	0.031	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.010	-0.002	10.562	0.027	0.027	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.075	-0.026	15.111	0.033	0.033	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.951	-0.967	16.943	-0.128	-0.128	0.000	0.000	0.000	0.000
89	A	89	HIS	0	-0.011	-0.019	18.370	0.019	0.019	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.095	-0.042	17.980	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.834	-0.915	18.058	-0.237	-0.237	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.051	-0.027	16.969	-0.067	-0.067	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.034	-0.033	15.041	-0.069	-0.069	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.035	0.050	10.836	0.052	0.052	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.007	-0.006	13.334	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.006	0.010	10.570	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.021	0.013	13.395	0.026	0.026	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.767	-0.891	14.277	0.418	0.418	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.929	-0.978	16.585	0.558	0.558	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.917	-0.933	18.916	0.234	0.234	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.024	-0.015	18.787	-0.048	-0.048	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.782	0.885	19.883	-0.255	-0.255	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.002	-0.014	17.267	0.023	0.023	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.763	0.881	14.220	-0.381	-0.381	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.025	0.018	14.156	0.037	0.037	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.029	-0.002	13.488	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.020	0.013	8.028	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.017	-0.032	10.839	0.016	0.016	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.008	-0.008	11.502	-0.178	-0.178	0.000	0.000	0.000	0.000
110	A	110	HIS	0	-0.049	-0.033	12.600	-0.107	-0.107	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.779	-0.865	9.132	-0.929	-0.929	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.004	0.006	7.707	-0.502	-0.502	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.017	-0.013	8.309	-0.342	-0.342	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.927	-0.963	8.262	-1.543	-1.543	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.017	-0.013	4.125	-0.581	-0.460	-0.001	-0.015	-0.106	0.000
116	A	116	LEU	0	-0.046	-0.034	5.562	-0.520	-0.520	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.048	-0.011	7.915	0.308	0.308	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.837	-0.910	2.659	-14.431	-11.244	0.778	-1.905	-2.060	-0.026
119	A	119	ALA	0	-0.083	-0.036	4.737	0.061	0.143	-0.001	-0.004	-0.076	0.000
120	A	120	LEU	0	-0.029	-0.021	6.524	0.626	0.626	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.029	0.004	10.372	0.058	0.058	0.000	0.000	0.000	0.000

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