FMO DATABASE

FMODB ID: G6NK1

Calculation Name: 3W1Z-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W1Z

Chain ID: B

ChEMBL ID:

UniProt ID: O14368

Base Structure: X-ray

Registration Date: 2023-06-21

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1132630.024107
FMO2-HF: Nuclear repulsion	1077435.889267
FMO2-HF: Total energy	-55194.134841
FMO2-MP2: Total energy	-55358.041665

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:1:MET)

Summations of interaction energy for fragment #1(B: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.
-6.467	-1.385	1.528	-2.257	-4.354	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / 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

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	B	3	LEU	0	0.012	-0.005	2.266	-4.970	-0.546	1.528	-2.137	-3.816	0.004
4	B	4	GLN	0	0.014	0.009	3.701	-1.192	-0.679	0.001	-0.106	-0.408	0.000
5	B	5	PRO	0	-0.049	-0.022	5.147	0.072	0.217	-0.001	-0.014	-0.130	0.000
6	B	6	PHE	0	-0.011	0.002	7.263	0.162	0.162	0.000	0.000	0.000	0.000
7	B	7	PHE	0	-0.011	-0.001	7.281	-0.057	-0.057	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.015	0.006	10.745	-0.101	-0.101	0.000	0.000	0.000	0.000
9	B	9	PHE	0	-0.002	0.002	10.986	-0.059	-0.059	0.000	0.000	0.000	0.000
10	B	10	PRO	0	0.014	0.010	11.188	0.042	0.042	0.000	0.000	0.000	0.000
11	B	11	PRO	0	0.014	-0.012	14.098	-0.040	-0.040	0.000	0.000	0.000	0.000
12	B	12	THR	0	0.066	0.035	13.884	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.007	0.015	10.038	-0.035	-0.035	0.000	0.000	0.000	0.000
14	B	14	ASN	0	-0.012	-0.022	13.034	-0.022	-0.022	0.000	0.000	0.000	0.000
15	B	15	ASP	-1	-0.863	-0.922	15.932	-0.312	-0.312	0.000	0.000	0.000	0.000
16	B	16	LEU	0	-0.036	-0.006	11.395	0.002	0.002	0.000	0.000	0.000	0.000
17	B	17	PHE	0	-0.012	-0.026	11.539	-0.016	-0.016	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.001	0.013	15.987	0.042	0.042	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.812	-0.908	18.067	-0.341	-0.341	0.000	0.000	0.000	0.000
20	B	20	PHE	0	-0.083	-0.037	15.331	0.014	0.014	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.032	-0.019	17.767	0.031	0.031	0.000	0.000	0.000	0.000
22	B	22	SER	0	-0.033	-0.009	20.157	0.044	0.044	0.000	0.000	0.000	0.000
23	B	23	TYR	0	0.065	0.008	21.519	0.035	0.035	0.000	0.000	0.000	0.000
24	B	24	SER	0	-0.083	-0.038	19.260	0.014	0.014	0.000	0.000	0.000	0.000
25	B	25	PRO	0	0.035	0.009	21.392	0.010	0.010	0.000	0.000	0.000	0.000
26	B	26	ARG	1	0.947	0.963	17.844	0.384	0.384	0.000	0.000	0.000	0.000
27	B	27	LEU	0	-0.043	-0.008	17.933	0.009	0.009	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.018	-0.010	21.627	0.029	0.029	0.000	0.000	0.000	0.000
29	B	29	ASN	0	-0.031	-0.008	25.385	0.008	0.008	0.000	0.000	0.000	0.000
30	B	30	GLN	0	0.038	0.032	24.975	0.002	0.002	0.000	0.000	0.000	0.000
31	B	31	ILE	0	-0.004	0.024	27.370	0.006	0.006	0.000	0.000	0.000	0.000
32	B	32	PRO	0	-0.039	-0.039	26.847	0.006	0.006	0.000	0.000	0.000	0.000
33	B	33	GLY	0	-0.038	-0.028	28.838	-0.003	-0.003	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.826	-0.879	31.555	-0.100	-0.100	0.000	0.000	0.000	0.000
35	B	35	LEU	0	-0.055	-0.021	31.046	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	36	SER	0	-0.001	-0.024	27.771	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.003	0.016	29.411	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	38	SER	0	-0.017	-0.046	27.756	-0.013	-0.013	0.000	0.000	0.000	0.000
39	B	39	ILE	0	-0.075	-0.046	26.344	0.010	0.010	0.000	0.000	0.000	0.000
40	B	40	ASP	-1	-0.851	-0.896	25.996	-0.246	-0.246	0.000	0.000	0.000	0.000
41	B	41	VAL	0	-0.054	-0.028	25.213	0.016	0.016	0.000	0.000	0.000	0.000
42	B	42	HIS	0	-0.028	-0.015	25.792	-0.019	-0.019	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.813	-0.897	26.128	-0.199	-0.199	0.000	0.000	0.000	0.000
44	B	44	GLY	0	0.018	0.034	28.127	-0.006	-0.006	0.000	0.000	0.000	0.000
45	B	45	LYS	1	0.897	0.930	28.924	0.160	0.160	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.902	-0.943	31.278	-0.123	-0.123	0.000	0.000	0.000	0.000
47	B	47	THR	0	0.011	-0.007	34.137	0.001	0.001	0.000	0.000	0.000	0.000
48	B	48	VAL	0	0.004	0.001	28.905	-0.009	-0.009	0.000	0.000	0.000	0.000
49	B	49	SER	0	0.031	0.023	31.140	0.009	0.009	0.000	0.000	0.000	0.000
50	B	50	VAL	0	-0.043	-0.020	29.657	-0.013	-0.013	0.000	0.000	0.000	0.000
51	B	51	ASP	-1	-0.834	-0.894	30.685	-0.139	-0.139	0.000	0.000	0.000	0.000
52	B	52	VAL	0	-0.006	-0.015	30.885	-0.011	-0.011	0.000	0.000	0.000	0.000
53	B	53	GLU	-1	-0.869	-0.906	31.095	-0.147	-0.147	0.000	0.000	0.000	0.000
54	B	54	LEU	0	-0.052	-0.038	34.033	0.000	0.000	0.000	0.000	0.000	0.000
55	B	55	PRO	0	0.037	0.011	36.206	0.008	0.008	0.000	0.000	0.000	0.000
56	B	56	GLY	0	-0.059	-0.041	39.186	0.001	0.001	0.000	0.000	0.000	0.000
57	B	57	VAL	0	-0.014	0.008	39.243	0.003	0.003	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.828	0.905	42.412	0.067	0.067	0.000	0.000	0.000	0.000
59	B	59	LYS	1	0.981	0.978	44.359	0.073	0.073	0.000	0.000	0.000	0.000
60	B	60	GLU	-1	-0.901	-0.945	45.250	-0.066	-0.066	0.000	0.000	0.000	0.000
61	B	61	ASP	-1	-0.842	-0.914	43.860	-0.072	-0.072	0.000	0.000	0.000	0.000
62	B	62	VAL	0	-0.052	-0.015	39.136	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	63	GLN	0	-0.009	0.000	40.005	0.002	0.002	0.000	0.000	0.000	0.000
64	B	64	VAL	0	0.019	-0.001	36.890	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	65	HIS	0	-0.033	-0.010	37.386	0.002	0.002	0.000	0.000	0.000	0.000
66	B	66	TYR	0	0.025	-0.003	33.450	-0.005	-0.005	0.000	0.000	0.000	0.000
67	B	67	ASP	-1	-0.862	-0.914	35.774	-0.090	-0.090	0.000	0.000	0.000	0.000
68	B	68	SER	0	-0.069	-0.052	34.711	-0.008	-0.008	0.000	0.000	0.000	0.000
69	B	69	GLY	0	-0.004	0.002	31.726	-0.005	-0.005	0.000	0.000	0.000	0.000
70	B	70	LYS	1	0.883	0.951	26.789	0.161	0.161	0.000	0.000	0.000	0.000
71	B	71	LEU	0	0.003	0.011	31.282	0.011	0.011	0.000	0.000	0.000	0.000
72	B	72	THR	0	0.017	0.005	31.900	-0.014	-0.014	0.000	0.000	0.000	0.000
73	B	73	ILE	0	-0.012	0.010	32.568	0.008	0.008	0.000	0.000	0.000	0.000
74	B	74	SER	0	-0.017	-0.014	34.797	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	75	GLY	0	0.067	0.023	37.198	0.003	0.003	0.000	0.000	0.000	0.000
76	B	76	GLU	-1	-0.938	-0.965	39.087	-0.075	-0.075	0.000	0.000	0.000	0.000
77	B	77	VAL	0	-0.034	-0.010	37.605	0.000	0.000	0.000	0.000	0.000	0.000
78	B	78	VAL	0	0.076	0.036	40.709	0.001	0.001	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.038	-0.028	42.972	0.000	0.000	0.000	0.000	0.000	0.000
80	B	80	GLU	-1	-0.907	-0.963	44.564	-0.064	-0.064	0.000	0.000	0.000	0.000
81	B	81	ARG	1	0.838	0.880	46.628	0.060	0.060	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.920	0.968	45.659	0.055	0.055	0.000	0.000	0.000	0.000
83	B	83	ASN	0	-0.009	-0.008	47.615	0.001	0.001	0.000	0.000	0.000	0.000
84	B	84	GLU	-1	-0.723	-0.818	50.035	-0.051	-0.051	0.000	0.000	0.000	0.000
85	B	85	SER	0	-0.066	-0.042	46.411	0.000	0.000	0.000	0.000	0.000	0.000
86	B	86	THR	0	-0.081	-0.048	48.445	0.001	0.001	0.000	0.000	0.000	0.000
87	B	87	GLU	-1	-0.870	-0.926	50.317	-0.039	-0.039	0.000	0.000	0.000	0.000
88	B	88	GLY	0	-0.001	0.020	50.417	0.002	0.002	0.000	0.000	0.000	0.000
89	B	89	ASN	0	0.002	-0.011	51.048	0.002	0.002	0.000	0.000	0.000	0.000
90	B	90	GLN	0	-0.056	-0.026	42.895	-0.002	-0.002	0.000	0.000	0.000	0.000
91	B	91	ARG	1	0.849	0.919	46.311	0.047	0.047	0.000	0.000	0.000	0.000
92	B	92	TRP	0	0.003	-0.012	37.548	0.003	0.003	0.000	0.000	0.000	0.000
93	B	93	SER	0	-0.014	-0.011	40.189	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	94	GLU	-1	-0.829	-0.905	35.853	-0.093	-0.093	0.000	0.000	0.000	0.000
95	B	95	ARG	1	0.947	0.983	35.739	0.079	0.079	0.000	0.000	0.000	0.000
96	B	96	ARG	1	0.857	0.933	33.127	0.100	0.100	0.000	0.000	0.000	0.000
97	B	97	PHE	0	-0.010	-0.012	36.423	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	98	GLY	0	0.043	0.020	37.875	0.000	0.000	0.000	0.000	0.000	0.000
99	B	99	SER	0	0.021	0.000	37.438	0.001	0.001	0.000	0.000	0.000	0.000
100	B	100	PHE	0	-0.027	-0.018	34.257	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	101	SER	0	0.049	0.016	33.065	0.004	0.004	0.000	0.000	0.000	0.000
102	B	102	ARG	1	0.880	0.951	24.858	0.209	0.209	0.000	0.000	0.000	0.000
103	B	103	THR	0	-0.011	-0.015	29.364	0.007	0.007	0.000	0.000	0.000	0.000
104	B	104	ILE	0	-0.027	-0.009	26.232	-0.016	-0.016	0.000	0.000	0.000	0.000
105	B	105	THR	0	-0.026	-0.012	25.702	0.021	0.021	0.000	0.000	0.000	0.000
106	B	106	ILE	0	0.002	-0.003	26.203	-0.016	-0.016	0.000	0.000	0.000	0.000
107	B	107	PRO	0	0.015	0.023	23.926	0.016	0.016	0.000	0.000	0.000	0.000
108	B	108	ALA	0	0.005	-0.008	26.483	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	109	LYS	1	0.860	0.936	29.406	0.145	0.145	0.000	0.000	0.000	0.000
110	B	110	ILE	0	0.037	0.019	32.913	0.000	0.000	0.000	0.000	0.000	0.000
111	B	111	ASP	-1	-0.856	-0.917	35.508	-0.082	-0.082	0.000	0.000	0.000	0.000
112	B	112	ALA	0	0.046	-0.001	38.974	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	113	ASP	-1	-0.929	-0.962	39.854	-0.078	-0.078	0.000	0.000	0.000	0.000
114	B	114	ARG	1	0.804	0.886	41.486	0.082	0.082	0.000	0.000	0.000	0.000
115	B	115	ILE	0	-0.041	0.006	37.077	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	116	GLU	-1	-0.956	-0.961	39.872	-0.086	-0.086	0.000	0.000	0.000	0.000
117	B	117	ALA	0	0.005	-0.011	39.534	-0.007	-0.007	0.000	0.000	0.000	0.000
118	B	118	ASN	0	-0.048	-0.017	40.005	0.004	0.004	0.000	0.000	0.000	0.000
119	B	119	PHE	0	-0.011	-0.001	39.422	-0.003	-0.003	0.000	0.000	0.000	0.000
120	B	120	SER	0	-0.024	-0.017	40.883	0.006	0.006	0.000	0.000	0.000	0.000
121	B	121	ASN	0	-0.014	-0.018	40.644	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	122	GLY	0	0.011	0.015	39.695	-0.003	-0.003	0.000	0.000	0.000	0.000
123	B	123	LEU	0	0.020	0.028	33.771	-0.005	-0.005	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.051	-0.021	36.162	0.007	0.007	0.000	0.000	0.000	0.000
125	B	125	THR	0	0.044	-0.001	35.202	-0.005	-0.005	0.000	0.000	0.000	0.000
126	B	126	VAL	0	-0.049	-0.022	34.612	0.008	0.008	0.000	0.000	0.000	0.000
127	B	127	THR	0	0.039	0.013	34.820	-0.009	-0.009	0.000	0.000	0.000	0.000
128	B	128	LEU	0	-0.014	-0.015	32.684	0.007	0.007	0.000	0.000	0.000	0.000
129	B	129	PRO	0	0.028	0.016	34.665	-0.008	-0.008	0.000	0.000	0.000	0.000
130	B	130	LYS	1	0.759	0.847	29.257	0.172	0.172	0.000	0.000	0.000	0.000
131	B	131	VAL	0	-0.023	0.005	34.862	0.005	0.005	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.848	-0.928	34.168	-0.101	-0.101	0.000	0.000	0.000	0.000
133	B	133	LYS	1	0.816	0.906	34.605	0.088	0.088	0.000	0.000	0.000	0.000
134	B	134	SER	0	0.004	-0.002	35.232	0.003	0.003	0.000	0.000	0.000	0.000
135	B	135	GLN	0	0.036	0.001	37.131	0.003	0.003	0.000	0.000	0.000	0.000
136	B	136	THR	0	0.035	0.013	37.257	0.003	0.003	0.000	0.000	0.000	0.000
137	B	137	LYS	1	0.899	0.961	35.584	0.081	0.081	0.000	0.000	0.000	0.000
138	B	138	LYS	1	0.971	0.984	38.286	0.070	0.070	0.000	0.000	0.000	0.000
139	B	139	GLN	0	0.025	0.015	39.855	-0.002	-0.002	0.000	0.000	0.000	0.000
140	B	140	ILE	0	0.011	-0.001	38.914	0.002	0.002	0.000	0.000	0.000	0.000
141	B	141	ALA	0	-0.028	-0.002	41.833	0.001	0.001	0.000	0.000	0.000	0.000
142	B	142	ILE	0	0.022	0.012	40.513	0.000	0.000	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.999	1.002	43.483	0.034	0.034	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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