FMO DATABASE

FMODB ID: QVYGY

Calculation Name: 3CMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CMI

Chain ID: A

ChEMBL ID:

UniProt ID: P40581

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1404256.089647
FMO2-HF: Nuclear repulsion	1347682.40943
FMO2-HF: Total energy	-56573.680217
FMO2-MP2: Total energy	-56740.428341

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:2:SER)

Summations of interaction energy for fragment #1(A: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.
-19.567	-9.588	8.037	-7.287	-10.728	0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.028

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	4	PHE	0	0.033	0.024	2.512	-2.344	1.526	1.719	-2.481	-3.107	0.014
4	A	5	TYR	0	0.016	-0.019	2.221	-11.112	-8.881	5.401	-2.748	-4.884	0.004
5	A	6	LYS	1	0.933	0.972	4.126	-0.346	0.051	0.006	-0.106	-0.297	0.000
6	A	7	LEU	0	-0.057	0.002	6.601	-0.342	-0.342	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.026	0.006	8.693	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	9	PRO	0	0.006	0.027	11.593	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.001	0.009	14.496	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.730	-0.883	17.980	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.943	0.973	19.234	0.014	0.014	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.904	0.944	22.520	0.011	0.011	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.018	0.005	22.657	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.026	-0.020	20.459	0.000	0.000	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.012	0.000	16.153	0.006	0.006	0.000	0.000	0.000	0.000
16	A	17	PHE	0	0.017	0.004	12.315	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.012	0.013	10.878	0.039	0.039	0.000	0.000	0.000	0.000
18	A	19	PHE	0	0.074	0.000	6.761	-0.130	-0.130	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.827	-0.898	6.329	-0.104	-0.104	0.000	0.000	0.000	0.000
20	A	21	GLN	0	-0.024	0.002	7.397	-0.210	-0.210	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.042	-0.026	7.102	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.854	0.918	5.876	-0.112	-0.112	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.031	0.023	7.099	0.242	0.242	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.814	0.902	8.609	0.356	0.356	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.033	0.034	8.810	-0.156	-0.156	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.031	-0.028	8.264	0.079	0.079	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.017	0.020	11.087	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.008	0.000	9.779	0.028	0.028	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.001	0.000	13.990	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	31	ASN	0	-0.004	0.006	17.622	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.000	-0.011	19.898	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.052	0.040	22.921	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.065	-0.038	26.466	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.912	0.951	27.749	0.011	0.011	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.015	0.001	30.619	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.059	0.028	32.978	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.002	0.003	29.000	0.000	0.000	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.019	0.003	29.306	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.022	0.008	30.144	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.070	0.037	25.942	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	42	TYR	0	0.021	0.005	24.547	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.974	0.984	25.772	0.020	0.020	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.753	-0.854	25.505	-0.040	-0.040	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.012	0.004	20.019	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.722	-0.834	22.110	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.028	-0.015	24.207	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.004	0.006	19.402	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.031	-0.027	17.887	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.834	0.901	20.716	0.035	0.035	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.855	0.934	23.336	0.058	0.058	0.000	0.000	0.000	0.000
51	A	52	TYR	0	0.019	-0.020	18.612	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.792	0.887	17.719	0.051	0.051	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.806	-0.891	17.502	-0.081	-0.081	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.898	-0.926	18.045	-0.082	-0.082	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.027	-0.011	14.457	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	57	PHE	0	-0.007	-0.017	13.422	-0.049	-0.049	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.012	-0.018	12.117	0.036	0.036	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.007	0.014	14.130	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.014	-0.006	11.862	0.011	0.011	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.025	0.011	15.207	0.002	0.002	0.000	0.000	0.000	0.000
61	A	62	PHE	0	0.037	0.001	13.231	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	PRO	0	-0.013	0.003	19.002	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	64	CYS	0	-0.043	-0.005	22.157	0.003	0.003	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.040	-0.009	24.165	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	66	GLN	0	-0.048	-0.040	23.274	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.008	0.011	22.663	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.028	0.026	28.342	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	87	GLY	0	-0.010	-0.016	28.214	0.000	0.000	0.000	0.000	0.000	0.000
69	A	88	VAL	0	-0.064	-0.020	23.353	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	89	THR	0	-0.058	-0.075	23.685	0.001	0.001	0.000	0.000	0.000	0.000
71	A	90	PHE	0	0.023	0.025	18.406	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	91	PRO	0	-0.004	-0.009	15.496	0.008	0.008	0.000	0.000	0.000	0.000
73	A	92	ILE	0	-0.041	-0.006	18.076	0.000	0.000	0.000	0.000	0.000	0.000
74	A	93	MET	0	-0.041	-0.008	15.905	0.007	0.007	0.000	0.000	0.000	0.000
75	A	94	LYS	1	0.966	0.976	19.082	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	95	LYS	1	0.802	0.898	20.672	0.004	0.004	0.000	0.000	0.000	0.000
77	A	96	ILE	0	0.021	0.021	17.094	0.000	0.000	0.000	0.000	0.000	0.000
78	A	97	ASP	-1	-0.823	-0.898	20.844	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	98	VAL	0	0.020	0.010	18.220	0.004	0.004	0.000	0.000	0.000	0.000
80	A	99	ASN	0	0.016	0.010	18.537	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	100	GLY	0	0.060	0.042	20.957	0.001	0.001	0.000	0.000	0.000	0.000
82	A	101	GLY	0	0.007	-0.005	21.562	0.000	0.000	0.000	0.000	0.000	0.000
83	A	102	ASN	0	0.000	0.002	22.207	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	103	GLU	-1	-0.873	-0.927	16.550	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	104	ASP	-1	-0.813	-0.917	14.618	0.068	0.068	0.000	0.000	0.000	0.000
86	A	105	PRO	0	0.014	-0.008	12.582	0.001	0.001	0.000	0.000	0.000	0.000
87	A	106	VAL	0	0.028	0.019	10.466	0.025	0.025	0.000	0.000	0.000	0.000
88	A	107	TYR	0	0.043	-0.001	10.912	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	108	LYS	1	0.959	0.992	12.951	0.011	0.011	0.000	0.000	0.000	0.000
90	A	109	PHE	0	0.040	0.023	4.211	0.048	0.140	-0.001	-0.014	-0.077	0.000
91	A	110	LEU	0	-0.003	0.010	8.581	-0.048	-0.048	0.000	0.000	0.000	0.000
92	A	111	LYS	1	0.792	0.882	10.271	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	112	SER	0	-0.112	-0.048	9.253	-0.019	-0.019	0.000	0.000	0.000	0.000
94	A	113	GLN	0	-0.032	-0.008	6.163	-0.057	-0.057	0.000	0.000	0.000	0.000
95	A	114	LYS	1	0.835	0.900	9.731	0.087	0.087	0.000	0.000	0.000	0.000
96	A	115	SER	0	-0.009	-0.019	12.970	0.009	0.009	0.000	0.000	0.000	0.000
97	A	116	GLY	0	0.016	0.020	16.467	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	117	MET	0	0.020	-0.002	19.536	0.000	0.000	0.000	0.000	0.000	0.000
99	A	118	LEU	0	0.029	0.021	20.834	0.002	0.002	0.000	0.000	0.000	0.000
100	A	119	GLY	0	0.016	0.019	23.454	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	120	LEU	0	0.008	-0.007	22.992	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	121	ARG	1	0.984	0.972	14.570	0.025	0.025	0.000	0.000	0.000	0.000
103	A	122	GLY	0	0.013	0.017	18.436	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	123	ILE	0	-0.043	-0.011	16.796	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	124	LYS	1	0.882	0.930	20.738	0.025	0.025	0.000	0.000	0.000	0.000
106	A	125	TRP	0	0.033	0.001	23.606	0.001	0.001	0.000	0.000	0.000	0.000
107	A	126	ASN	0	-0.048	-0.007	23.249	0.000	0.000	0.000	0.000	0.000	0.000
108	A	127	PHE	0	0.033	-0.004	21.974	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	128	GLU	-1	-0.779	-0.862	18.901	-0.033	-0.033	0.000	0.000	0.000	0.000
110	A	129	LYS	1	0.803	0.902	17.036	0.049	0.049	0.000	0.000	0.000	0.000
111	A	130	PHE	0	-0.004	-0.002	11.728	0.008	0.008	0.000	0.000	0.000	0.000
112	A	131	LEU	0	0.009	0.017	12.636	0.004	0.004	0.000	0.000	0.000	0.000
113	A	132	VAL	0	-0.051	-0.023	6.164	0.003	0.003	0.000	0.000	0.000	0.000
114	A	133	ASP	-1	-0.711	-0.837	7.163	-0.607	-0.607	0.000	0.000	0.000	0.000
115	A	134	LYS	1	0.848	0.957	6.781	-0.160	-0.160	0.000	0.000	0.000	0.000
116	A	135	LYS	1	0.835	0.906	5.584	0.119	0.119	0.000	0.000	0.000	0.000
117	A	136	GLY	0	-0.052	-0.015	2.277	-3.702	-1.850	0.501	-1.124	-1.229	-0.003
118	A	137	LYS	1	0.953	0.963	2.894	-1.063	0.487	0.412	-0.811	-1.151	-0.008
119	A	138	VAL	0	-0.010	-0.010	5.365	0.146	0.133	-0.001	-0.003	0.017	0.000
120	A	139	TYR	0	-0.025	-0.010	8.305	0.039	0.039	0.000	0.000	0.000	0.000
121	A	140	GLU	-1	-0.786	-0.873	11.325	-0.029	-0.029	0.000	0.000	0.000	0.000
122	A	141	ARG	1	0.688	0.821	13.677	0.024	0.024	0.000	0.000	0.000	0.000
123	A	142	TYR	0	0.059	0.021	15.768	0.002	0.002	0.000	0.000	0.000	0.000
124	A	143	SER	0	0.042	0.012	19.278	0.003	0.003	0.000	0.000	0.000	0.000
125	A	144	SER	0	0.004	-0.008	22.283	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	145	LEU	0	-0.006	-0.012	24.087	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	146	THR	0	0.006	0.014	22.379	0.000	0.000	0.000	0.000	0.000	0.000
128	A	147	LYS	1	0.899	0.937	24.109	0.029	0.029	0.000	0.000	0.000	0.000
129	A	148	PRO	0	0.001	-0.007	21.772	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	149	SER	0	-0.008	-0.020	22.303	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	150	SER	0	-0.005	-0.006	24.481	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	151	LEU	0	-0.034	-0.010	17.850	0.000	0.000	0.000	0.000	0.000	0.000
133	A	152	SER	0	-0.031	-0.031	19.745	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	153	GLU	-1	-0.838	-0.889	20.743	-0.064	-0.064	0.000	0.000	0.000	0.000
135	A	154	THR	0	-0.002	0.005	16.127	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	155	ILE	0	-0.030	-0.020	16.032	-0.027	-0.027	0.000	0.000	0.000	0.000
137	A	156	GLU	-1	-0.747	-0.844	16.576	-0.083	-0.083	0.000	0.000	0.000	0.000
138	A	157	GLU	-1	-0.861	-0.915	16.742	-0.089	-0.089	0.000	0.000	0.000	0.000
139	A	158	LEU	0	-0.045	-0.031	11.778	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	159	LEU	0	-0.063	-0.045	13.532	-0.037	-0.037	0.000	0.000	0.000	0.000
141	A	160	LYS	1	0.889	0.947	15.534	0.072	0.072	0.000	0.000	0.000	0.000
142	A	161	GLH	0	-0.038	-0.039	9.675	0.014	0.014	0.000	0.000	0.000	0.000
143	A	162	VAL	0	0.004	0.017	13.244	0.031	0.031	0.000	0.000	0.000	0.000

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