FMO DATABASE

FMODB ID: LJVN9

Calculation Name: 3CW2-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CW2

Chain ID: M

ChEMBL ID:

UniProt ID: Q97Z79

Base Structure: X-ray

Registration Date: 2023-03-14

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	138
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1093182.077143
FMO2-HF: Nuclear repulsion	1036444.299375
FMO2-HF: Total energy	-56737.777768
FMO2-MP2: Total energy	-56897.426573

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(M:2:SER)

Summations of interaction energy for fragment #1(M:2: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.
-10.848	-5.398	8.447	-6.523	-7.372	-0.035

Interaction energy analysis for fragmet #1(M:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.021

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	M	4	GLU	-1	-0.913	-0.941	3.811	-1.815	-0.003	-0.027	-0.893	-0.891	0.000
4	M	5	LYS	1	0.853	0.906	5.708	1.394	1.394	0.000	0.000	0.000	0.000
5	M	6	GLU	-1	-0.773	-0.868	2.115	-3.504	-2.256	6.862	-4.012	-4.097	-0.025
6	M	7	TYR	0	-0.019	-0.013	3.397	-1.874	-1.130	0.041	-0.395	-0.390	-0.003
7	M	8	VAL	0	0.018	0.018	5.470	0.503	0.503	0.000	0.000	0.000	0.000
8	M	9	GLU	-1	-0.771	-0.897	3.080	-8.288	-7.002	0.030	-0.691	-0.625	-0.006
9	M	10	MET	0	-0.112	-0.061	2.300	0.883	1.243	1.541	-0.532	-1.369	-0.001
10	M	11	LEU	0	-0.022	0.003	6.585	0.378	0.378	0.000	0.000	0.000	0.000
11	M	12	ASP	-1	-0.851	-0.936	9.681	-0.752	-0.752	0.000	0.000	0.000	0.000
12	M	13	ARG	1	0.914	0.979	8.537	0.823	0.823	0.000	0.000	0.000	0.000
13	M	14	LEU	0	-0.030	-0.014	11.387	0.157	0.157	0.000	0.000	0.000	0.000
14	M	15	TYR	0	-0.005	-0.032	13.097	0.155	0.155	0.000	0.000	0.000	0.000
15	M	16	SER	0	0.032	-0.016	13.932	0.061	0.061	0.000	0.000	0.000	0.000
16	M	17	LYS	1	0.924	0.978	14.188	0.424	0.424	0.000	0.000	0.000	0.000
17	M	18	LEU	0	0.015	0.022	17.090	0.050	0.050	0.000	0.000	0.000	0.000
18	M	19	PRO	0	-0.041	-0.018	17.883	0.052	0.052	0.000	0.000	0.000	0.000
19	M	20	GLU	-1	-0.956	-0.974	20.992	-0.250	-0.250	0.000	0.000	0.000	0.000
20	M	21	LYS	1	0.880	0.907	23.327	0.211	0.211	0.000	0.000	0.000	0.000
21	M	22	GLY	0	-0.016	0.008	22.347	0.012	0.012	0.000	0.000	0.000	0.000
22	M	23	ARG	1	0.979	0.998	21.150	0.329	0.329	0.000	0.000	0.000	0.000
23	M	24	LYS	1	0.859	0.949	23.520	0.250	0.250	0.000	0.000	0.000	0.000
24	M	25	GLU	-1	-0.885	-0.923	26.458	-0.231	-0.231	0.000	0.000	0.000	0.000
25	M	26	GLY	0	0.006	-0.013	29.261	0.000	0.000	0.000	0.000	0.000	0.000
26	M	27	THR	0	-0.026	-0.010	32.859	0.000	0.000	0.000	0.000	0.000	0.000
27	M	28	GLN	0	0.025	0.011	33.481	0.009	0.009	0.000	0.000	0.000	0.000
28	M	29	SER	0	-0.066	-0.032	36.383	0.005	0.005	0.000	0.000	0.000	0.000
29	M	30	LEU	0	0.022	0.016	39.043	0.001	0.001	0.000	0.000	0.000	0.000
30	M	31	PRO	0	-0.023	0.004	40.947	0.005	0.005	0.000	0.000	0.000	0.000
31	M	32	ASN	0	-0.049	-0.040	43.122	0.003	0.003	0.000	0.000	0.000	0.000
32	M	33	MET	0	0.036	0.000	45.919	-0.003	-0.003	0.000	0.000	0.000	0.000
33	M	34	ILE	0	-0.078	-0.033	48.697	0.003	0.003	0.000	0.000	0.000	0.000
34	M	35	ILE	0	0.032	0.017	52.178	-0.001	-0.001	0.000	0.000	0.000	0.000
35	M	36	LEU	0	-0.004	0.005	55.115	0.000	0.000	0.000	0.000	0.000	0.000
36	M	37	ASN	0	-0.023	-0.023	57.323	0.003	0.003	0.000	0.000	0.000	0.000
37	M	38	ILE	0	-0.033	-0.005	56.618	0.000	0.000	0.000	0.000	0.000	0.000
38	M	39	GLY	0	0.000	-0.001	60.806	0.001	0.001	0.000	0.000	0.000	0.000
39	M	40	ASN	0	-0.030	-0.008	64.072	0.002	0.002	0.000	0.000	0.000	0.000
40	M	41	THR	0	0.044	0.015	63.330	0.001	0.001	0.000	0.000	0.000	0.000
41	M	42	THR	0	-0.019	-0.005	60.757	-0.001	-0.001	0.000	0.000	0.000	0.000
42	M	43	ILE	0	0.003	0.010	58.696	0.000	0.000	0.000	0.000	0.000	0.000
43	M	44	ILE	0	-0.039	-0.008	52.143	-0.002	-0.002	0.000	0.000	0.000	0.000
44	M	45	ARG	1	0.951	0.971	51.695	0.062	0.062	0.000	0.000	0.000	0.000
45	M	46	ASN	0	0.052	0.003	53.025	0.002	0.002	0.000	0.000	0.000	0.000
46	M	47	PHE	0	-0.034	-0.013	50.035	-0.003	-0.003	0.000	0.000	0.000	0.000
47	M	48	ALA	0	0.058	0.036	50.776	-0.002	-0.002	0.000	0.000	0.000	0.000
48	M	49	GLU	-1	-0.893	-0.921	50.712	-0.052	-0.052	0.000	0.000	0.000	0.000
49	M	50	TYR	0	-0.065	-0.047	45.416	-0.004	-0.004	0.000	0.000	0.000	0.000
50	M	51	CYS	0	0.009	-0.003	45.868	-0.004	-0.004	0.000	0.000	0.000	0.000
51	M	52	ASP	-1	-0.855	-0.919	44.967	-0.059	-0.059	0.000	0.000	0.000	0.000
52	M	53	ARG	1	0.872	0.938	39.821	0.088	0.088	0.000	0.000	0.000	0.000
53	M	54	ILE	0	-0.052	-0.034	38.547	-0.004	-0.004	0.000	0.000	0.000	0.000
54	M	55	ARG	1	0.933	0.961	39.744	0.066	0.066	0.000	0.000	0.000	0.000
55	M	56	ARG	1	0.849	0.946	39.097	0.081	0.081	0.000	0.000	0.000	0.000
56	M	57	GLU	-1	-0.828	-0.903	45.184	-0.053	-0.053	0.000	0.000	0.000	0.000
57	M	58	ASP	-1	-0.721	-0.875	48.207	-0.044	-0.044	0.000	0.000	0.000	0.000
58	M	59	LYS	1	0.884	0.926	50.897	0.040	0.040	0.000	0.000	0.000	0.000
59	M	60	ILE	0	-0.028	0.003	43.608	0.000	0.000	0.000	0.000	0.000	0.000
60	M	61	CYS	0	-0.041	-0.047	46.110	-0.001	-0.001	0.000	0.000	0.000	0.000
61	M	62	MET	0	0.037	0.048	48.126	0.000	0.000	0.000	0.000	0.000	0.000
62	M	63	LYS	1	0.959	0.977	51.650	0.044	0.044	0.000	0.000	0.000	0.000
63	M	64	TYR	0	-0.112	-0.066	46.675	-0.001	-0.001	0.000	0.000	0.000	0.000
64	M	65	LEU	0	0.074	0.026	49.822	-0.001	-0.001	0.000	0.000	0.000	0.000
65	M	66	LEU	0	-0.005	0.026	52.246	0.001	0.001	0.000	0.000	0.000	0.000
66	M	67	LYS	1	0.822	0.909	49.137	0.056	0.056	0.000	0.000	0.000	0.000
67	M	68	GLU	-1	-0.799	-0.879	48.837	-0.067	-0.067	0.000	0.000	0.000	0.000
68	M	69	LEU	0	-0.042	-0.018	53.319	0.000	0.000	0.000	0.000	0.000	0.000
69	M	70	ALA	0	0.022	0.011	57.087	0.001	0.001	0.000	0.000	0.000	0.000
70	M	71	ALA	0	-0.034	-0.004	59.513	0.001	0.001	0.000	0.000	0.000	0.000
71	M	72	PRO	0	0.009	-0.034	57.372	-0.002	-0.002	0.000	0.000	0.000	0.000
72	M	73	GLY	0	0.008	0.029	56.839	-0.001	-0.001	0.000	0.000	0.000	0.000
73	M	74	ASN	0	-0.025	-0.039	58.061	0.001	0.001	0.000	0.000	0.000	0.000
74	M	75	VAL	0	-0.007	-0.012	56.064	-0.001	-0.001	0.000	0.000	0.000	0.000
75	M	76	ASP	-1	-0.888	-0.939	58.246	-0.038	-0.038	0.000	0.000	0.000	0.000
76	M	77	ASP	-1	-0.922	-0.957	59.340	-0.036	-0.036	0.000	0.000	0.000	0.000
77	M	78	LYS	1	0.817	0.917	60.352	0.040	0.040	0.000	0.000	0.000	0.000
78	M	79	GLY	0	0.052	0.004	56.430	-0.001	-0.001	0.000	0.000	0.000	0.000
79	M	80	GLU	-1	-0.869	-0.929	55.774	-0.046	-0.046	0.000	0.000	0.000	0.000
80	M	81	LEU	0	-0.022	-0.001	53.488	0.001	0.001	0.000	0.000	0.000	0.000
81	M	82	VAL	0	0.056	0.013	57.029	-0.001	-0.001	0.000	0.000	0.000	0.000
82	M	83	ILE	0	-0.027	-0.013	54.413	0.001	0.001	0.000	0.000	0.000	0.000
83	M	84	GLN	0	0.057	0.028	58.988	0.000	0.000	0.000	0.000	0.000	0.000
84	M	85	GLY	0	-0.017	-0.008	59.571	0.001	0.001	0.000	0.000	0.000	0.000
85	M	86	LYS	1	0.876	0.919	60.601	0.039	0.039	0.000	0.000	0.000	0.000
86	M	87	PHE	0	0.046	0.024	57.275	0.000	0.000	0.000	0.000	0.000	0.000
87	M	88	SER	0	0.030	0.018	56.863	-0.002	-0.002	0.000	0.000	0.000	0.000
88	M	89	SER	0	0.004	-0.001	55.570	0.001	0.001	0.000	0.000	0.000	0.000
89	M	90	GLN	0	0.040	0.002	53.631	-0.002	-0.002	0.000	0.000	0.000	0.000
90	M	91	VAL	0	0.032	0.029	51.288	-0.003	-0.003	0.000	0.000	0.000	0.000
91	M	92	ILE	0	0.023	0.005	51.003	-0.001	-0.001	0.000	0.000	0.000	0.000
92	M	93	ASN	0	0.039	-0.014	47.368	-0.001	-0.001	0.000	0.000	0.000	0.000
93	M	94	THR	0	0.019	0.023	46.395	-0.002	-0.002	0.000	0.000	0.000	0.000
94	M	95	LEU	0	-0.025	-0.009	46.067	-0.003	-0.003	0.000	0.000	0.000	0.000
95	M	96	MET	0	-0.102	-0.026	45.684	-0.001	-0.001	0.000	0.000	0.000	0.000
96	M	97	GLU	-1	-0.809	-0.887	41.465	-0.101	-0.101	0.000	0.000	0.000	0.000
97	M	98	ARG	1	0.872	0.962	40.530	0.075	0.075	0.000	0.000	0.000	0.000
98	M	99	PHE	0	-0.026	-0.057	38.346	0.005	0.005	0.000	0.000	0.000	0.000
99	M	100	LEU	0	0.032	0.022	33.911	-0.001	-0.001	0.000	0.000	0.000	0.000
100	M	101	LYS	1	0.964	0.989	32.236	0.142	0.142	0.000	0.000	0.000	0.000
101	M	102	ALA	0	-0.006	-0.009	33.974	0.003	0.003	0.000	0.000	0.000	0.000
102	M	103	TYR	0	-0.022	-0.007	33.630	0.007	0.007	0.000	0.000	0.000	0.000
103	M	104	VAL	0	0.040	0.008	30.201	0.002	0.002	0.000	0.000	0.000	0.000
104	M	105	GLU	-1	-0.852	-0.896	27.270	-0.196	-0.196	0.000	0.000	0.000	0.000
105	M	106	CYS	0	-0.038	-0.021	29.163	0.008	0.008	0.000	0.000	0.000	0.000
106	M	107	SER	0	0.015	0.004	28.674	-0.008	-0.008	0.000	0.000	0.000	0.000
107	M	108	THR	0	-0.025	-0.006	25.950	0.007	0.007	0.000	0.000	0.000	0.000
108	M	109	CYS	0	-0.026	-0.010	26.203	-0.001	-0.001	0.000	0.000	0.000	0.000
109	M	110	LYS	1	0.841	0.894	25.433	0.195	0.195	0.000	0.000	0.000	0.000
110	M	111	SER	0	0.028	-0.002	24.937	0.005	0.005	0.000	0.000	0.000	0.000
111	M	112	LEU	0	-0.049	-0.023	25.426	-0.017	-0.017	0.000	0.000	0.000	0.000
112	M	113	ASP	-1	-0.845	-0.909	28.170	-0.092	-0.092	0.000	0.000	0.000	0.000
113	M	114	THR	0	-0.041	-0.029	31.872	0.000	0.000	0.000	0.000	0.000	0.000
114	M	115	ILE	0	0.019	0.028	33.731	-0.003	-0.003	0.000	0.000	0.000	0.000
115	M	116	LEU	0	-0.003	0.000	36.238	0.006	0.006	0.000	0.000	0.000	0.000
116	M	117	LYS	1	0.910	0.937	38.437	0.048	0.048	0.000	0.000	0.000	0.000
117	M	118	LYS	1	0.898	0.929	39.327	0.042	0.042	0.000	0.000	0.000	0.000
118	M	119	GLU	-1	-0.850	-0.909	41.062	-0.036	-0.036	0.000	0.000	0.000	0.000
119	M	120	LYS	1	0.902	0.952	43.037	0.038	0.038	0.000	0.000	0.000	0.000
120	M	121	LYS	1	0.961	0.989	41.782	0.047	0.047	0.000	0.000	0.000	0.000
121	M	122	SER	0	-0.001	-0.014	38.572	0.001	0.001	0.000	0.000	0.000	0.000
122	M	123	TRP	0	0.007	0.006	35.552	0.002	0.002	0.000	0.000	0.000	0.000
123	M	124	TYR	0	0.004	-0.016	34.318	0.000	0.000	0.000	0.000	0.000	0.000
124	M	125	ILE	0	-0.012	-0.001	31.776	-0.003	-0.003	0.000	0.000	0.000	0.000
125	M	126	VAL	0	0.018	0.035	26.746	-0.004	-0.004	0.000	0.000	0.000	0.000
126	M	127	CYM	-1	-0.813	-0.910	27.593	-0.113	-0.113	0.000	0.000	0.000	0.000
127	M	128	LEU	0	-0.061	-0.023	28.932	0.009	0.009	0.000	0.000	0.000	0.000
128	M	129	ALA	0	-0.009	-0.004	27.387	0.001	0.001	0.000	0.000	0.000	0.000
129	M	130	CYS	0	0.031	0.004	24.293	-0.001	-0.001	0.000	0.000	0.000	0.000
130	M	131	GLY	0	-0.038	-0.007	26.337	0.009	0.009	0.000	0.000	0.000	0.000
131	M	132	ALA	0	-0.026	-0.018	23.112	-0.007	-0.007	0.000	0.000	0.000	0.000
132	M	133	GLN	0	0.035	0.022	24.198	-0.016	-0.016	0.000	0.000	0.000	0.000
133	M	134	THR	0	0.007	-0.001	23.028	0.009	0.009	0.000	0.000	0.000	0.000
134	M	135	PRO	0	0.004	-0.003	25.664	-0.004	-0.004	0.000	0.000	0.000	0.000
135	M	136	VAL	0	-0.010	0.000	28.414	-0.004	-0.004	0.000	0.000	0.000	0.000
136	M	137	LYS	1	1.007	0.979	31.285	0.024	0.024	0.000	0.000	0.000	0.000
137	M	138	PRO	0	-0.055	-0.015	33.393	-0.004	-0.004	0.000	0.000	0.000	0.000
138	M	139	LEU	0	0.049	0.044	26.797	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(M:2:SER)