FMO DATABASE

FMODB ID: 9GR82

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1094694.65008
FMO2-HF: Nuclear repulsion	1037955.825598
FMO2-HF: Total energy	-56738.824482
FMO2-MP2: Total energy	-56898.391842

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.
-8.064	-3.5	7.462	-5.637	-6.388	-0.032

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 : -0.011 / 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

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	-0.909	-0.937	3.878	-1.549	0.292	-0.019	-0.969	-0.852	-0.001
4	M	5	LYS	1	0.851	0.897	5.607	1.893	1.893	0.000	0.000	0.000	0.000
5	M	6	GLU	-1	-0.764	-0.862	2.192	-6.053	-4.295	6.674	-4.241	-4.192	-0.030
6	M	7	TYR	0	-0.031	-0.020	4.095	0.001	0.196	0.001	-0.048	-0.147	0.000
7	M	8	VAL	0	0.014	0.021	5.885	0.439	0.439	0.000	0.000	0.000	0.000
8	M	9	GLU	-1	-0.802	-0.913	3.967	-4.377	-4.135	-0.001	-0.067	-0.174	0.000
9	M	10	MET	0	-0.081	-0.048	2.473	0.499	1.027	0.807	-0.312	-1.023	-0.001
10	M	11	LEU	0	-0.017	0.016	6.679	0.302	0.302	0.000	0.000	0.000	0.000
11	M	12	ASP	-1	-0.818	-0.925	9.993	-0.545	-0.545	0.000	0.000	0.000	0.000
12	M	13	ARG	1	0.898	0.973	8.506	0.374	0.374	0.000	0.000	0.000	0.000
13	M	14	LEU	0	-0.036	-0.012	11.384	0.116	0.116	0.000	0.000	0.000	0.000
14	M	15	TYR	0	-0.017	-0.026	13.329	0.110	0.110	0.000	0.000	0.000	0.000
15	M	16	SER	0	-0.019	-0.024	14.011	0.060	0.060	0.000	0.000	0.000	0.000
16	M	17	LYS	1	0.953	0.971	14.843	0.228	0.228	0.000	0.000	0.000	0.000
17	M	18	LEU	0	0.026	0.022	17.347	0.032	0.032	0.000	0.000	0.000	0.000
18	M	19	PRO	0	-0.026	-0.020	18.353	0.030	0.030	0.000	0.000	0.000	0.000
19	M	20	GLU	-1	-0.930	-0.942	21.050	-0.145	-0.145	0.000	0.000	0.000	0.000
20	M	21	LYS	1	0.881	0.922	23.258	0.130	0.130	0.000	0.000	0.000	0.000
21	M	22	GLY	0	-0.005	0.002	22.698	0.010	0.010	0.000	0.000	0.000	0.000
22	M	23	ARG	1	0.947	0.984	21.584	0.246	0.246	0.000	0.000	0.000	0.000
23	M	24	LYS	1	0.830	0.907	23.760	0.177	0.177	0.000	0.000	0.000	0.000
24	M	25	GLU	-1	-0.870	-0.931	26.298	-0.185	-0.185	0.000	0.000	0.000	0.000
25	M	26	GLY	0	0.016	0.002	29.655	-0.001	-0.001	0.000	0.000	0.000	0.000
26	M	27	THR	0	-0.033	-0.010	33.278	0.001	0.001	0.000	0.000	0.000	0.000
27	M	28	GLN	0	0.052	0.016	33.858	0.006	0.006	0.000	0.000	0.000	0.000
28	M	29	SER	0	-0.034	-0.015	36.750	0.004	0.004	0.000	0.000	0.000	0.000
29	M	30	LEU	0	0.020	0.021	39.075	0.003	0.003	0.000	0.000	0.000	0.000
30	M	31	PRO	0	0.008	0.016	41.055	0.003	0.003	0.000	0.000	0.000	0.000
31	M	32	ASN	0	-0.028	-0.028	42.962	0.002	0.002	0.000	0.000	0.000	0.000
32	M	33	MET	0	0.029	0.024	46.022	-0.002	-0.002	0.000	0.000	0.000	0.000
33	M	34	ILE	0	-0.003	-0.008	48.917	0.003	0.003	0.000	0.000	0.000	0.000
34	M	35	ILE	0	0.017	0.010	52.365	-0.001	-0.001	0.000	0.000	0.000	0.000
35	M	36	LEU	0	0.010	0.007	55.314	0.001	0.001	0.000	0.000	0.000	0.000
36	M	37	ASN	0	-0.026	-0.019	57.335	0.002	0.002	0.000	0.000	0.000	0.000
37	M	38	ILE	0	-0.028	-0.007	56.877	0.000	0.000	0.000	0.000	0.000	0.000
38	M	39	GLY	0	-0.006	-0.012	61.029	0.001	0.001	0.000	0.000	0.000	0.000
39	M	40	ASN	0	-0.023	-0.002	64.021	0.002	0.002	0.000	0.000	0.000	0.000
40	M	41	THR	0	0.056	0.021	63.506	0.001	0.001	0.000	0.000	0.000	0.000
41	M	42	THR	0	-0.012	0.006	61.074	-0.001	-0.001	0.000	0.000	0.000	0.000
42	M	43	ILE	0	-0.016	-0.009	59.292	0.001	0.001	0.000	0.000	0.000	0.000
43	M	44	ILE	0	-0.036	-0.010	52.646	-0.002	-0.002	0.000	0.000	0.000	0.000
44	M	45	ARG	1	0.894	0.935	50.993	0.046	0.046	0.000	0.000	0.000	0.000
45	M	46	ASN	0	0.049	0.015	53.358	0.001	0.001	0.000	0.000	0.000	0.000
46	M	47	PHE	0	-0.031	-0.015	50.416	-0.002	-0.002	0.000	0.000	0.000	0.000
47	M	48	ALA	0	0.027	0.011	50.956	-0.001	-0.001	0.000	0.000	0.000	0.000
48	M	49	GLU	-1	-0.872	-0.913	50.755	-0.036	-0.036	0.000	0.000	0.000	0.000
49	M	50	TYR	0	-0.035	-0.033	46.028	-0.003	-0.003	0.000	0.000	0.000	0.000
50	M	51	CYS	0	-0.017	-0.007	46.169	-0.002	-0.002	0.000	0.000	0.000	0.000
51	M	52	ASP	-1	-0.860	-0.932	44.940	-0.040	-0.040	0.000	0.000	0.000	0.000
52	M	53	ARG	1	0.844	0.923	40.873	0.062	0.062	0.000	0.000	0.000	0.000
53	M	54	ILE	0	-0.029	-0.012	38.841	-0.003	-0.003	0.000	0.000	0.000	0.000
54	M	55	ARG	1	0.933	0.967	39.566	0.042	0.042	0.000	0.000	0.000	0.000
55	M	56	ARG	1	0.841	0.929	39.274	0.054	0.054	0.000	0.000	0.000	0.000
56	M	57	GLU	-1	-0.784	-0.897	45.439	-0.036	-0.036	0.000	0.000	0.000	0.000
57	M	58	ASP	-1	-0.703	-0.849	48.513	-0.029	-0.029	0.000	0.000	0.000	0.000
58	M	59	LYS	1	0.855	0.918	50.818	0.026	0.026	0.000	0.000	0.000	0.000
59	M	60	ILE	0	-0.059	-0.006	44.174	0.000	0.000	0.000	0.000	0.000	0.000
60	M	61	CYS	0	0.017	-0.008	46.721	-0.001	-0.001	0.000	0.000	0.000	0.000
61	M	62	MET	0	0.002	0.039	48.540	0.000	0.000	0.000	0.000	0.000	0.000
62	M	63	LYS	1	0.954	0.966	51.628	0.031	0.031	0.000	0.000	0.000	0.000
63	M	64	TYR	0	-0.106	-0.078	47.198	-0.001	-0.001	0.000	0.000	0.000	0.000
64	M	65	LEU	0	0.073	0.028	50.062	0.000	0.000	0.000	0.000	0.000	0.000
65	M	66	LEU	0	-0.009	0.016	52.354	0.001	0.001	0.000	0.000	0.000	0.000
66	M	67	LYS	1	0.862	0.911	49.171	0.042	0.042	0.000	0.000	0.000	0.000
67	M	68	GLU	-1	-0.819	-0.871	49.233	-0.050	-0.050	0.000	0.000	0.000	0.000
68	M	69	LEU	0	-0.023	-0.012	53.564	0.000	0.000	0.000	0.000	0.000	0.000
69	M	70	ALA	0	-0.017	0.007	57.253	0.001	0.001	0.000	0.000	0.000	0.000
70	M	71	ALA	0	-0.031	-0.014	59.207	0.001	0.001	0.000	0.000	0.000	0.000
71	M	72	PRO	0	-0.028	-0.043	57.997	-0.001	-0.001	0.000	0.000	0.000	0.000
72	M	73	GLY	0	0.039	0.027	57.239	-0.001	-0.001	0.000	0.000	0.000	0.000
73	M	74	ASN	0	-0.009	-0.024	58.431	0.000	0.000	0.000	0.000	0.000	0.000
74	M	75	VAL	0	-0.020	-0.019	56.485	-0.001	-0.001	0.000	0.000	0.000	0.000
75	M	76	ASP	-1	-0.821	-0.918	58.509	-0.027	-0.027	0.000	0.000	0.000	0.000
76	M	77	ASP	-1	-0.945	-0.964	59.374	-0.025	-0.025	0.000	0.000	0.000	0.000
77	M	78	LYS	1	0.831	0.917	60.376	0.029	0.029	0.000	0.000	0.000	0.000
78	M	79	GLY	0	0.021	0.007	56.526	-0.001	-0.001	0.000	0.000	0.000	0.000
79	M	80	GLU	-1	-0.869	-0.936	56.122	-0.033	-0.033	0.000	0.000	0.000	0.000
80	M	81	LEU	0	-0.055	-0.001	53.731	0.001	0.001	0.000	0.000	0.000	0.000
81	M	82	VAL	0	0.040	0.012	57.364	-0.001	-0.001	0.000	0.000	0.000	0.000
82	M	83	ILE	0	-0.013	-0.017	54.816	0.000	0.000	0.000	0.000	0.000	0.000
83	M	84	GLN	0	0.054	0.049	59.343	-0.001	-0.001	0.000	0.000	0.000	0.000
84	M	85	GLY	0	-0.010	-0.025	59.653	0.001	0.001	0.000	0.000	0.000	0.000
85	M	86	LYS	1	0.862	0.912	60.700	0.029	0.029	0.000	0.000	0.000	0.000
86	M	87	PHE	0	0.046	0.026	57.835	0.000	0.000	0.000	0.000	0.000	0.000
87	M	88	SER	0	0.028	0.020	57.130	-0.002	-0.002	0.000	0.000	0.000	0.000
88	M	89	SER	0	0.016	0.003	55.455	0.000	0.000	0.000	0.000	0.000	0.000
89	M	90	GLN	0	0.022	-0.005	53.614	-0.002	-0.002	0.000	0.000	0.000	0.000
90	M	91	VAL	0	0.018	0.014	51.418	-0.002	-0.002	0.000	0.000	0.000	0.000
91	M	92	ILE	0	0.029	0.011	50.862	-0.001	-0.001	0.000	0.000	0.000	0.000
92	M	93	ASN	0	0.015	-0.015	46.872	0.001	0.001	0.000	0.000	0.000	0.000
93	M	94	THR	0	0.014	0.012	46.858	-0.002	-0.002	0.000	0.000	0.000	0.000
94	M	95	LEU	0	-0.028	-0.008	46.012	-0.003	-0.003	0.000	0.000	0.000	0.000
95	M	96	MET	0	-0.091	-0.029	46.044	0.000	0.000	0.000	0.000	0.000	0.000
96	M	97	GLU	-1	-0.811	-0.889	41.333	-0.076	-0.076	0.000	0.000	0.000	0.000
97	M	98	ARG	1	0.870	0.955	40.553	0.055	0.055	0.000	0.000	0.000	0.000
98	M	99	PHE	0	-0.051	-0.066	38.726	0.003	0.003	0.000	0.000	0.000	0.000
99	M	100	LEU	0	0.030	0.020	34.166	-0.001	-0.001	0.000	0.000	0.000	0.000
100	M	101	LYS	1	0.967	0.988	32.094	0.113	0.113	0.000	0.000	0.000	0.000
101	M	102	ALA	0	-0.006	-0.001	34.124	0.002	0.002	0.000	0.000	0.000	0.000
102	M	103	TYR	0	-0.045	-0.018	33.274	0.008	0.008	0.000	0.000	0.000	0.000
103	M	104	VAL	0	0.050	0.018	30.221	0.003	0.003	0.000	0.000	0.000	0.000
104	M	105	GLU	-1	-0.893	-0.926	27.664	-0.140	-0.140	0.000	0.000	0.000	0.000
105	M	106	CYS	0	-0.005	-0.003	29.928	0.002	0.002	0.000	0.000	0.000	0.000
106	M	107	SER	0	-0.008	-0.013	29.241	-0.005	-0.005	0.000	0.000	0.000	0.000
107	M	108	THR	0	-0.016	-0.010	26.298	0.005	0.005	0.000	0.000	0.000	0.000
108	M	109	CYS	0	-0.021	-0.023	27.037	0.006	0.006	0.000	0.000	0.000	0.000
109	M	110	LYS	1	0.819	0.873	25.449	0.133	0.133	0.000	0.000	0.000	0.000
110	M	111	SER	0	-0.046	-0.073	24.957	-0.001	-0.001	0.000	0.000	0.000	0.000
111	M	112	LEU	0	-0.057	-0.046	25.991	-0.013	-0.013	0.000	0.000	0.000	0.000
112	M	113	ASP	-1	-0.835	-0.905	28.237	-0.053	-0.053	0.000	0.000	0.000	0.000
113	M	114	THR	0	-0.028	-0.026	32.069	-0.001	-0.001	0.000	0.000	0.000	0.000
114	M	115	ILE	0	-0.015	0.015	33.818	-0.002	-0.002	0.000	0.000	0.000	0.000
115	M	116	LEU	0	-0.005	-0.002	36.254	0.005	0.005	0.000	0.000	0.000	0.000
116	M	117	LYS	1	0.894	0.929	38.606	0.030	0.030	0.000	0.000	0.000	0.000
117	M	118	LYS	1	0.887	0.923	39.630	0.024	0.024	0.000	0.000	0.000	0.000
118	M	119	GLU	-1	-0.814	-0.889	41.257	-0.022	-0.022	0.000	0.000	0.000	0.000
119	M	120	LYS	1	0.904	0.940	42.386	0.023	0.023	0.000	0.000	0.000	0.000
120	M	121	LYS	1	0.947	0.981	41.816	0.035	0.035	0.000	0.000	0.000	0.000
121	M	122	SER	0	-0.001	-0.004	38.522	0.001	0.001	0.000	0.000	0.000	0.000
122	M	123	TRP	0	0.035	0.021	35.600	0.003	0.003	0.000	0.000	0.000	0.000
123	M	124	TYR	0	-0.020	-0.023	34.098	-0.001	-0.001	0.000	0.000	0.000	0.000
124	M	125	ILE	0	0.015	0.017	31.833	-0.002	-0.002	0.000	0.000	0.000	0.000
125	M	126	VAL	0	0.024	0.015	26.986	-0.004	-0.004	0.000	0.000	0.000	0.000
126	M	127	CYM	-1	-0.767	-0.789	27.469	-0.071	-0.071	0.000	0.000	0.000	0.000
127	M	128	LEU	0	0.009	0.016	28.675	0.004	0.004	0.000	0.000	0.000	0.000
128	M	129	ALA	0	-0.001	-0.003	28.238	0.005	0.005	0.000	0.000	0.000	0.000
129	M	130	CYS	0	0.018	0.009	24.440	-0.002	-0.002	0.000	0.000	0.000	0.000
130	M	131	GLY	0	-0.038	-0.009	26.086	0.008	0.008	0.000	0.000	0.000	0.000
131	M	132	ALA	0	-0.022	-0.019	22.803	-0.006	-0.006	0.000	0.000	0.000	0.000
132	M	133	GLN	0	0.002	0.021	23.753	-0.007	-0.007	0.000	0.000	0.000	0.000
133	M	134	THR	0	0.015	-0.002	23.188	0.007	0.007	0.000	0.000	0.000	0.000
134	M	135	PRO	0	-0.013	-0.017	25.727	-0.005	-0.005	0.000	0.000	0.000	0.000
135	M	136	VAL	0	0.000	-0.006	28.391	-0.003	-0.003	0.000	0.000	0.000	0.000
136	M	137	LYS	1	1.012	1.010	31.106	0.007	0.007	0.000	0.000	0.000	0.000
137	M	138	PRO	0	-0.040	-0.019	32.877	-0.003	-0.003	0.000	0.000	0.000	0.000
138	M	139	LEU	0	0.009	0.020	27.048	-0.005	-0.005	0.000	0.000	0.000	0.000

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