FMO DATABASE

FMODB ID: G5VZ1

Calculation Name: 3CM1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CM1

Chain ID: A

ChEMBL ID:

UniProt ID: Q47N25

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1148558.593861
FMO2-HF: Nuclear repulsion	1095621.602176
FMO2-HF: Total energy	-52936.991685
FMO2-MP2: Total energy	-53092.5075

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(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.
-6.507	-3.885	9.816	-3.523	-8.914	-0.022

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 : -0.027 / q_NPA : -0.010

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	SER	0	-0.013	-0.013	3.236	-3.597	-1.574	0.066	-1.060	-1.029	-0.001
4	A	4	SER	0	0.128	0.064	5.540	0.463	0.463	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.021	0.048	6.364	0.288	0.288	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.072	-0.029	7.361	0.298	0.298	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.016	0.008	9.718	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.032	-0.008	12.537	0.091	0.091	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.023	-0.014	15.083	-0.059	-0.059	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.112	-0.035	18.756	0.041	0.041	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.907	-0.955	21.513	0.038	0.038	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.011	-0.002	24.301	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.028	0.003	26.896	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.006	-0.014	28.432	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.010	-0.015	32.075	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.026	0.027	34.733	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.058	-0.041	36.480	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.005	-0.013	38.840	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.007	-0.004	41.172	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.901	-0.932	44.072	0.024	0.024	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.881	0.940	42.546	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.007	0.016	44.654	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.025	-0.028	39.868	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.000	0.009	38.757	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.027	-0.004	36.624	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.008	-0.002	31.830	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.017	0.015	28.806	0.010	0.010	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.006	-0.003	26.588	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.965	0.989	21.931	0.061	0.061	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.003	-0.002	20.542	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.913	-0.968	17.369	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.005	-0.016	9.749	0.027	0.027	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.022	0.008	11.420	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.005	-0.001	5.855	0.090	0.090	0.000	0.000	0.000	0.000
35	A	35	ASH	0	-0.053	-0.077	7.242	-0.250	-0.250	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.887	-0.946	9.091	-0.375	-0.375	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.036	0.037	7.361	0.253	0.253	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.038	0.023	9.505	0.272	0.272	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.023	0.013	12.655	0.090	0.090	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.026	-0.014	14.543	0.052	0.052	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.883	0.963	14.232	0.229	0.229	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.003	-0.020	19.786	0.039	0.039	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.005	0.017	23.195	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.006	-0.008	25.950	0.020	0.020	0.000	0.000	0.000	0.000
45	A	45	HIS	1	0.942	0.963	29.334	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.010	-0.016	32.470	0.011	0.011	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.005	0.009	35.998	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.962	-0.976	35.765	0.011	0.011	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.934	-0.962	35.296	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.931	-0.976	31.712	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.069	-0.044	28.078	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.010	0.017	29.297	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.965	-1.004	21.945	-0.114	-0.114	0.000	0.000	0.000	0.000
54	A	54	TRP	0	-0.051	-0.026	24.773	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.049	0.020	17.540	0.011	0.011	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.027	-0.014	20.053	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.104	0.053	17.285	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.845	0.911	10.156	-0.540	-0.540	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.924	-0.978	16.696	0.157	0.157	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.080	0.052	18.088	0.021	0.021	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.018	-0.015	20.382	0.007	0.007	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.007	0.016	18.625	0.042	0.042	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.005	0.006	20.922	0.013	0.013	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.056	0.024	23.406	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.028	-0.006	22.489	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.096	-0.046	24.613	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.886	0.918	26.085	-0.190	-0.190	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.969	-0.984	28.268	0.065	0.065	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.042	0.022	24.932	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.014	-0.027	27.010	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.922	-0.950	21.718	-0.044	-0.044	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.019	-0.002	26.135	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.897	-0.948	28.579	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.013	0.004	25.257	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.946	0.973	28.179	-0.043	-0.043	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.002	-0.004	24.284	0.003	0.003	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.015	0.006	28.512	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.019	0.038	29.937	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.067	-0.036	31.507	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.036	-0.027	33.817	0.021	0.021	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.795	-0.894	36.382	0.093	0.093	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.008	0.003	38.252	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.941	0.954	36.764	-0.138	-0.138	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.930	-0.964	32.950	0.167	0.167	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.902	0.962	28.706	-0.192	-0.192	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.026	0.002	30.896	0.012	0.012	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.002	-0.005	26.716	0.003	0.003	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.060	-0.033	29.867	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.075	0.043	25.879	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.029	-0.013	29.707	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.034	0.039	30.236	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.031	-0.022	31.785	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.065	0.018	33.887	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.005	-0.006	36.657	0.005	0.005	0.000	0.000	0.000	0.000
95	A	95	PHE	0	-0.072	-0.036	39.294	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.013	0.025	40.304	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.030	-0.008	35.988	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.009	0.012	35.467	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.899	0.939	33.963	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.038	0.012	29.735	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	HIS	1	0.795	0.899	32.569	-0.087	-0.087	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.081	0.031	28.695	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	103	GLN	0	0.022	0.019	29.207	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.027	0.009	25.417	0.006	0.006	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.004	0.004	24.933	0.020	0.020	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.016	0.006	23.594	0.034	0.034	0.000	0.000	0.000	0.000
107	A	107	LEU	0	0.052	0.031	22.188	0.018	0.018	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.000	-0.007	20.565	0.023	0.023	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.971	-0.980	18.158	0.617	0.617	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.009	-0.004	17.157	0.081	0.081	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.029	0.006	16.087	0.048	0.048	0.000	0.000	0.000	0.000
112	A	112	HIS	0	-0.018	0.015	14.736	0.079	0.079	0.000	0.000	0.000	0.000
113	A	113	ARG	1	1.009	0.999	13.282	-0.409	-0.409	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.087	-0.039	11.432	0.163	0.163	0.000	0.000	0.000	0.000
115	A	115	TYR	0	-0.050	-0.071	10.147	0.093	0.093	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.985	-0.985	9.285	1.636	1.636	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.071	-0.023	6.644	0.829	0.829	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.020	0.007	5.249	1.053	1.053	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.025	0.017	6.299	-0.688	-0.688	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.021	-0.017	9.230	-0.224	-0.224	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.065	-0.034	11.061	0.116	0.116	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.018	-0.017	5.870	0.759	0.759	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.797	-0.903	5.256	-0.276	-0.276	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.017	-0.021	6.263	-0.498	-0.498	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.851	-0.907	2.301	-0.616	-0.362	2.138	-0.756	-1.636	-0.005
126	A	126	TYR	0	-0.006	-0.020	2.832	-2.842	-2.209	5.798	-1.440	-4.991	-0.015
127	A	127	ILE	0	-0.025	-0.003	4.272	0.525	0.572	0.000	-0.014	-0.033	0.000
128	A	128	ASP	-1	-0.904	-0.958	5.920	-1.258	-1.258	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.011	-0.002	2.381	-0.031	-0.366	1.814	-0.253	-1.225	-0.001
130	A	130	ASP	-1	-0.916	-0.963	6.617	-1.158	-1.158	0.000	0.000	0.000	0.000
131	A	131	ALA	0	-0.067	-0.031	9.515	0.259	0.259	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.873	-0.942	7.461	-1.743	-1.743	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.060	-0.012	8.780	0.207	0.207	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.018	-0.014	12.198	0.160	0.160	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-1.014	-1.003	13.706	-0.740	-0.740	0.000	0.000	0.000	0.000
136	A	136	HIS	0	-0.131	-0.076	13.079	0.112	0.112	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.096	-0.032	16.583	0.102	0.102	0.000	0.000	0.000	0.000

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