FMO DATABASE

FMODB ID: YVNV2

Calculation Name: 1WNC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WNC

Chain ID: B

ChEMBL ID:

UniProt ID: P59594

Base Structure: X-ray

Registration Date: 2023-09-22

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-415209.313972
FMO2-HF: Nuclear repulsion	384382.765461
FMO2-HF: Total energy	-30826.548512
FMO2-MP2: Total energy	-30918.195879

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:902:GLN)

Summations of interaction energy for fragment #1(B:902:GLN)

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.
-15.232	-8.784	1.44	-2.299	-5.587	0.011

Interaction energy analysis for fragmet #1(B:902:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.015

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	904	GLN	0	-0.005	0.005	3.882	-2.091	-0.460	-0.004	-0.709	-0.918	0.002
4	B	905	ILE	0	0.025	0.021	2.445	-1.624	-0.279	0.594	-0.480	-1.458	0.000
5	B	906	ALA	0	0.081	0.047	2.735	-2.410	-0.602	0.417	-0.783	-1.442	0.009
6	B	907	ASN	0	0.015	-0.001	4.468	-1.784	-1.644	0.001	-0.039	-0.102	0.000
7	B	908	GLN	0	-0.013	-0.036	7.328	-0.193	-0.193	0.000	0.000	0.000	0.000
8	B	909	PHE	0	0.019	0.025	7.222	-0.321	-0.321	0.000	0.000	0.000	0.000
9	B	910	ASN	0	0.070	0.029	8.798	-0.368	-0.368	0.000	0.000	0.000	0.000
10	B	911	LYS	1	0.876	0.947	10.778	-1.577	-1.577	0.000	0.000	0.000	0.000
11	B	912	ALA	0	-0.009	-0.004	12.535	-0.166	-0.166	0.000	0.000	0.000	0.000
12	B	913	ILE	0	0.027	0.020	12.512	-0.140	-0.140	0.000	0.000	0.000	0.000
13	B	914	SER	0	0.046	0.023	15.022	-0.116	-0.116	0.000	0.000	0.000	0.000
14	B	915	GLN	0	-0.034	-0.019	17.037	-0.083	-0.083	0.000	0.000	0.000	0.000
15	B	916	ILE	0	-0.008	0.007	16.460	-0.069	-0.069	0.000	0.000	0.000	0.000
16	B	917	GLN	0	-0.025	-0.030	19.208	-0.025	-0.025	0.000	0.000	0.000	0.000
17	B	918	GLU	-1	-0.856	-0.905	20.978	0.266	0.266	0.000	0.000	0.000	0.000
18	B	919	SER	0	-0.027	-0.026	22.422	-0.037	-0.037	0.000	0.000	0.000	0.000
19	B	920	LEU	0	-0.022	0.005	22.127	-0.032	-0.032	0.000	0.000	0.000	0.000
20	B	921	THR	0	0.024	0.026	24.842	-0.037	-0.037	0.000	0.000	0.000	0.000
21	B	922	THR	0	-0.018	-0.024	27.259	-0.029	-0.029	0.000	0.000	0.000	0.000
22	B	923	THR	0	-0.070	-0.052	27.738	-0.021	-0.021	0.000	0.000	0.000	0.000
23	B	924	SER	0	-0.016	-0.026	29.037	-0.021	-0.021	0.000	0.000	0.000	0.000
24	B	925	THR	0	-0.007	-0.003	31.437	-0.019	-0.019	0.000	0.000	0.000	0.000
25	B	926	ALA	0	-0.006	0.004	33.181	-0.012	-0.012	0.000	0.000	0.000	0.000
26	B	927	LEU	0	-0.021	-0.013	32.647	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	928	GLY	0	0.053	0.029	35.849	-0.011	-0.011	0.000	0.000	0.000	0.000
28	B	929	LYN	0	-0.027	-0.019	36.016	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	930	LEU	0	-0.036	-0.017	37.838	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	931	GLN	0	0.010	0.003	39.807	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	932	ASP	-1	-0.853	-0.920	41.787	0.098	0.098	0.000	0.000	0.000	0.000
32	B	933	VAL	0	-0.007	-0.008	43.833	-0.007	-0.007	0.000	0.000	0.000	0.000
33	B	934	VAL	0	-0.020	-0.004	44.143	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	935	ASN	0	-0.017	-0.027	44.775	-0.010	-0.010	0.000	0.000	0.000	0.000
35	B	936	GLN	0	-0.022	-0.007	47.916	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	937	ASN	0	0.011	-0.003	49.198	-0.006	-0.006	0.000	0.000	0.000	0.000
37	B	938	ALA	0	0.017	0.018	50.524	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	939	GLN	0	-0.012	-0.012	52.059	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	940	ALA	0	0.049	0.028	53.889	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	941	LEU	0	-0.009	0.002	55.017	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	942	ASN	0	-0.003	-0.018	55.592	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	943	THR	0	-0.038	-0.024	57.562	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	944	LEU	0	0.007	0.006	59.816	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	945	VAL	0	-0.025	-0.018	60.639	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	946	LYS	1	0.839	0.929	59.584	-0.051	-0.051	0.000	0.000	0.000	0.000
46	B	947	GLN	0	-0.064	-0.012	63.863	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	1150	ILE	0	-0.001	-0.014	64.729	0.000	0.000	0.000	0.000	0.000	0.000
48	B	1151	SER	0	0.005	0.003	63.715	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	1152	GLY	0	0.056	0.023	60.630	0.001	0.001	0.000	0.000	0.000	0.000
50	B	1153	ILE	0	-0.038	-0.001	59.346	0.002	0.002	0.000	0.000	0.000	0.000
51	B	1154	ASN	0	-0.057	-0.033	56.608	0.001	0.001	0.000	0.000	0.000	0.000
52	B	1155	ALA	0	0.013	0.002	53.954	0.002	0.002	0.000	0.000	0.000	0.000
53	B	1156	SER	0	-0.033	-0.014	49.049	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	1157	VAL	0	0.011	0.010	47.514	0.003	0.003	0.000	0.000	0.000	0.000
55	B	1158	VAL	0	-0.004	-0.004	42.726	0.000	0.000	0.000	0.000	0.000	0.000
56	B	1159	ASN	0	0.001	0.002	40.721	0.000	0.000	0.000	0.000	0.000	0.000
57	B	1160	ILE	0	0.006	0.001	36.242	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	1161	GLN	0	0.016	0.018	36.601	0.009	0.009	0.000	0.000	0.000	0.000
59	B	1162	GLU	-1	-0.800	-0.881	35.261	0.083	0.083	0.000	0.000	0.000	0.000
60	B	1163	GLU	-1	-0.867	-0.924	33.156	0.111	0.111	0.000	0.000	0.000	0.000
61	B	1164	ILE	0	-0.002	-0.003	31.740	0.015	0.015	0.000	0.000	0.000	0.000
62	B	1165	ASP	-1	-0.869	-0.927	31.290	0.129	0.129	0.000	0.000	0.000	0.000
63	B	1166	ARG	1	0.783	0.855	29.838	-0.093	-0.093	0.000	0.000	0.000	0.000
64	B	1167	LEU	0	-0.040	-0.020	27.325	0.014	0.014	0.000	0.000	0.000	0.000
65	B	1168	ASN	0	-0.037	-0.031	26.200	0.033	0.033	0.000	0.000	0.000	0.000
66	B	1169	GLU	-1	-0.857	-0.917	26.093	0.140	0.140	0.000	0.000	0.000	0.000
67	B	1170	VAL	0	-0.035	-0.007	22.122	0.013	0.013	0.000	0.000	0.000	0.000
68	B	1171	ALA	0	0.017	0.006	21.814	0.031	0.031	0.000	0.000	0.000	0.000
69	B	1172	LYS	1	0.853	0.922	21.667	-0.121	-0.121	0.000	0.000	0.000	0.000
70	B	1173	ASN	0	0.023	-0.005	20.971	0.017	0.017	0.000	0.000	0.000	0.000
71	B	1174	LEU	0	0.006	0.019	16.987	0.016	0.016	0.000	0.000	0.000	0.000
72	B	1175	ASN	0	-0.024	-0.015	15.994	0.112	0.112	0.000	0.000	0.000	0.000
73	B	1176	GLU	-1	-0.988	-0.984	16.526	0.068	0.068	0.000	0.000	0.000	0.000
74	B	1177	SER	0	-0.029	-0.011	13.590	-0.029	-0.029	0.000	0.000	0.000	0.000
75	B	1178	LEU	0	-0.063	-0.022	11.269	0.202	0.202	0.000	0.000	0.000	0.000
76	B	1179	ILE	0	0.002	0.013	4.988	-0.038	0.074	-0.001	0.000	-0.110	0.000
77	B	1180	ASP	-1	-0.793	-0.916	6.812	-0.788	-0.788	0.000	0.000	0.000	0.000
78	B	1181	LEU	0	-0.043	-0.042	7.913	-0.302	-0.302	0.000	0.000	0.000	0.000
79	B	1182	GLN	0	-0.091	-0.047	8.205	0.085	0.085	0.000	0.000	0.000	0.000
80	B	1183	GLU	-1	-0.928	-0.944	8.606	-0.751	-0.751	0.000	0.000	0.000	0.000
81	B	1184	LEU	0	-0.128	-0.048	2.871	-3.222	-1.810	0.433	-0.288	-1.557	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:902:GLN)