FMO DATABASE

FMODB ID: ZV65N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1398332.276046
FMO2-HF: Nuclear repulsion	1341759.690795
FMO2-HF: Total energy	-56572.585252
FMO2-MP2: Total energy	-56739.282372

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.
-14.045	-3.541	3.503	-5.645	-8.36	0.009

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 : 0.036 / 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	A	4	PHE	0	0.051	0.028	2.641	-4.110	-0.021	0.901	-2.218	-2.772	0.013
4	A	5	TYR	0	0.012	-0.018	2.577	-6.025	-2.965	2.160	-1.827	-3.392	-0.001
5	A	6	LYS	1	0.933	0.973	4.740	0.902	1.172	-0.001	-0.040	-0.228	0.000
6	A	7	LEU	0	-0.036	0.012	6.941	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.031	0.011	9.104	0.009	0.009	0.000	0.000	0.000	0.000
8	A	9	PRO	0	-0.009	0.027	11.971	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.002	0.010	14.899	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.749	-0.892	18.365	0.011	0.011	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.940	0.954	19.550	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.881	0.937	22.837	0.008	0.008	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.014	-0.004	22.987	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.005	-0.012	20.981	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.016	0.016	16.571	0.015	0.015	0.000	0.000	0.000	0.000
16	A	17	PHE	0	0.041	0.015	12.879	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.000	0.010	11.443	0.053	0.053	0.000	0.000	0.000	0.000
18	A	19	PHE	0	0.050	-0.011	7.092	-0.054	-0.054	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.880	-0.942	7.016	-0.292	-0.292	0.000	0.000	0.000	0.000
20	A	21	GLN	0	-0.042	-0.012	8.084	-0.081	-0.081	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.073	-0.048	8.009	0.007	0.007	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.921	0.973	4.910	1.123	1.123	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.009	0.020	7.178	0.121	0.121	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.868	0.935	8.747	0.129	0.129	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.047	0.048	9.041	0.027	0.027	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.022	-0.018	9.162	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.022	0.020	11.592	0.043	0.043	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.003	-0.009	10.014	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.001	0.006	14.249	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.002	0.020	17.882	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.043	-0.034	19.935	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.026	0.017	23.081	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.027	-0.018	26.662	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.939	0.979	27.935	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.017	-0.003	30.633	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.035	0.021	33.064	0.000	0.000	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.036	0.015	29.378	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.010	-0.004	29.932	0.004	0.004	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.014	-0.002	30.657	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.053	0.024	26.463	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	42	TYR	0	0.053	0.010	25.136	0.005	0.005	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.956	0.979	26.520	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.816	-0.920	26.314	0.058	0.058	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.012	0.002	20.640	0.003	0.003	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.754	-0.853	22.766	0.042	0.042	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.029	-0.011	24.832	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.008	0.008	19.611	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.007	-0.009	18.253	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.881	0.929	21.364	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.929	0.984	23.540	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	52	TYR	0	0.005	-0.036	19.059	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.884	0.967	18.532	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.911	-0.967	18.351	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.922	-0.947	18.586	0.020	0.020	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.069	-0.025	14.959	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	57	PHE	0	-0.002	-0.017	13.807	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.002	-0.012	12.816	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.003	0.006	14.748	0.030	0.030	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.002	0.006	12.453	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.012	0.001	15.652	0.016	0.016	0.000	0.000	0.000	0.000
61	A	62	PHE	0	0.050	0.002	13.646	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	63	PRO	0	-0.011	0.013	19.203	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	CYS	0	-0.003	0.027	22.201	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.002	-0.030	24.179	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	GLN	0	0.038	0.003	23.386	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.016	0.011	22.951	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.003	0.011	28.664	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	87	GLY	0	-0.009	-0.016	28.552	0.000	0.000	0.000	0.000	0.000	0.000
69	A	88	VAL	0	-0.059	-0.015	23.550	0.000	0.000	0.000	0.000	0.000	0.000
70	A	89	THR	0	-0.072	-0.086	24.429	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	90	PHE	0	0.002	0.015	18.969	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	91	PRO	0	-0.001	-0.005	16.329	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	92	ILE	0	-0.022	0.005	18.602	0.016	0.016	0.000	0.000	0.000	0.000
74	A	93	MET	0	-0.039	-0.008	16.279	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	94	LYS	1	0.955	0.974	19.559	0.002	0.002	0.000	0.000	0.000	0.000
76	A	95	LYS	1	0.901	0.953	20.784	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	96	ILE	0	-0.020	0.005	17.488	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	97	ASP	-1	-0.903	-0.947	21.528	0.029	0.029	0.000	0.000	0.000	0.000
79	A	98	VAL	0	-0.002	-0.018	18.579	0.006	0.006	0.000	0.000	0.000	0.000
80	A	99	ASN	0	-0.015	-0.021	18.748	0.018	0.018	0.000	0.000	0.000	0.000
81	A	100	GLY	0	0.053	0.022	21.361	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	101	GLY	0	0.011	-0.005	21.575	0.001	0.001	0.000	0.000	0.000	0.000
83	A	102	ASN	0	0.017	0.016	22.229	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	103	GLU	-1	-0.930	-0.950	16.768	0.067	0.067	0.000	0.000	0.000	0.000
85	A	104	ASP	-1	-0.830	-0.928	15.134	0.064	0.064	0.000	0.000	0.000	0.000
86	A	105	PRO	0	0.033	0.000	12.986	0.024	0.024	0.000	0.000	0.000	0.000
87	A	106	VAL	0	0.021	0.020	10.885	0.033	0.033	0.000	0.000	0.000	0.000
88	A	107	TYR	0	0.038	-0.009	11.207	0.074	0.074	0.000	0.000	0.000	0.000
89	A	108	LYS	1	0.960	1.004	12.979	0.063	0.063	0.000	0.000	0.000	0.000
90	A	109	PHE	0	0.038	0.010	4.072	0.045	0.140	-0.001	-0.014	-0.081	0.000
91	A	110	LEU	0	0.008	0.019	8.741	0.037	0.037	0.000	0.000	0.000	0.000
92	A	111	LYS	1	0.825	0.923	10.421	-0.117	-0.117	0.000	0.000	0.000	0.000
93	A	112	SER	0	-0.132	-0.078	9.538	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	113	GLN	0	-0.023	0.005	6.619	0.048	0.048	0.000	0.000	0.000	0.000
95	A	114	LYS	1	0.941	0.974	9.852	-0.262	-0.262	0.000	0.000	0.000	0.000
96	A	115	SER	0	-0.010	-0.021	13.020	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	116	GLY	0	0.006	0.019	16.473	0.001	0.001	0.000	0.000	0.000	0.000
98	A	117	MET	0	0.028	0.004	19.490	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	118	LEU	0	0.018	0.018	20.761	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	119	GLY	0	0.006	0.009	23.324	0.004	0.004	0.000	0.000	0.000	0.000
101	A	120	LEU	0	-0.026	-0.024	22.828	0.003	0.003	0.000	0.000	0.000	0.000
102	A	121	ARG	1	1.045	1.022	14.651	-0.083	-0.083	0.000	0.000	0.000	0.000
103	A	122	GLY	0	-0.018	-0.002	18.594	0.014	0.014	0.000	0.000	0.000	0.000
104	A	123	ILE	0	-0.050	-0.016	16.944	0.003	0.003	0.000	0.000	0.000	0.000
105	A	124	LYS	1	0.957	0.973	20.855	-0.089	-0.089	0.000	0.000	0.000	0.000
106	A	125	TRP	0	0.038	0.006	23.750	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	126	ASN	0	-0.022	-0.002	23.459	0.011	0.011	0.000	0.000	0.000	0.000
108	A	127	PHE	0	0.017	-0.011	22.215	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	128	GLU	-1	-0.758	-0.858	18.854	0.115	0.115	0.000	0.000	0.000	0.000
110	A	129	LYS	1	0.836	0.913	17.272	-0.099	-0.099	0.000	0.000	0.000	0.000
111	A	130	PHE	0	0.008	0.014	11.894	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	131	LEU	0	0.025	0.025	12.902	0.012	0.012	0.000	0.000	0.000	0.000
113	A	132	VAL	0	-0.046	-0.028	6.461	0.053	0.053	0.000	0.000	0.000	0.000
114	A	133	ASP	-1	-0.796	-0.871	6.473	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	134	LYS	1	0.952	1.008	7.255	0.028	0.028	0.000	0.000	0.000	0.000
116	A	135	LYS	1	0.912	0.933	5.237	-0.268	-0.268	0.000	0.000	0.000	0.000
117	A	136	GLY	0	-0.015	-0.001	2.584	-5.799	-3.392	0.426	-1.401	-1.432	-0.002
118	A	137	LYS	1	0.905	0.952	3.632	0.365	0.952	0.019	-0.143	-0.463	-0.001
119	A	138	VAL	0	0.029	0.008	5.323	-0.089	-0.093	-0.001	-0.002	0.008	0.000
120	A	139	TYR	0	0.024	0.021	8.084	-0.061	-0.061	0.000	0.000	0.000	0.000
121	A	140	GLU	-1	-0.864	-0.931	11.278	0.152	0.152	0.000	0.000	0.000	0.000
122	A	141	ARG	1	0.655	0.815	13.909	-0.123	-0.123	0.000	0.000	0.000	0.000
123	A	142	TYR	0	0.061	0.020	15.684	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	143	SER	0	0.026	-0.003	19.188	0.001	0.001	0.000	0.000	0.000	0.000
125	A	144	SER	0	0.015	-0.005	22.197	0.002	0.002	0.000	0.000	0.000	0.000
126	A	145	LEU	0	-0.035	-0.021	24.140	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	146	THR	0	-0.030	0.014	22.609	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	147	LYS	1	0.955	0.967	24.018	-0.048	-0.048	0.000	0.000	0.000	0.000
129	A	148	PRO	0	0.011	-0.004	22.293	0.004	0.004	0.000	0.000	0.000	0.000
130	A	149	SER	0	0.025	0.019	22.670	0.004	0.004	0.000	0.000	0.000	0.000
131	A	150	SER	0	-0.032	-0.019	24.843	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	151	LEU	0	-0.014	-0.002	18.640	0.002	0.002	0.000	0.000	0.000	0.000
133	A	152	SER	0	-0.032	-0.008	19.996	0.006	0.006	0.000	0.000	0.000	0.000
134	A	153	GLU	-1	-0.850	-0.924	20.972	0.064	0.064	0.000	0.000	0.000	0.000
135	A	154	THR	0	-0.011	0.001	16.672	0.002	0.002	0.000	0.000	0.000	0.000
136	A	155	ILE	0	-0.049	-0.036	16.323	0.010	0.010	0.000	0.000	0.000	0.000
137	A	156	GLU	-1	-0.843	-0.901	16.774	0.050	0.050	0.000	0.000	0.000	0.000
138	A	157	GLU	-1	-0.939	-0.966	17.312	0.098	0.098	0.000	0.000	0.000	0.000
139	A	158	LEU	0	-0.048	-0.030	12.195	0.003	0.003	0.000	0.000	0.000	0.000
140	A	159	LEU	0	-0.063	-0.042	13.598	-0.017	-0.017	0.000	0.000	0.000	0.000
141	A	160	LYS	1	0.957	0.985	15.594	-0.067	-0.067	0.000	0.000	0.000	0.000
142	A	161	GLH	0	-0.085	-0.059	9.881	0.006	0.006	0.000	0.000	0.000	0.000
143	A	162	VAL	0	-0.013	0.002	13.115	-0.010	-0.010	0.000	0.000	0.000	0.000

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