FMO DATABASE

FMODB ID: R89G8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1399709.420827
FMO2-HF: Nuclear repulsion	1343135.960948
FMO2-HF: Total energy	-56573.459879
FMO2-MP2: Total energy	-56740.200288

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.
-15.678	-4.694	3.498	-5.977	-8.505	0.006

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 : 0.047 / q_NPA : 0.022

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	0.042	0.026	2.612	-4.418	-0.265	1.034	-2.311	-2.876	0.015
4	A	5	TYR	0	0.027	-0.011	2.558	-6.317	-3.134	1.866	-1.811	-3.238	-0.002
5	A	6	LYS	1	0.933	0.975	4.412	0.798	1.075	-0.001	-0.045	-0.230	0.000
6	A	7	LEU	0	-0.040	0.009	7.069	-0.045	-0.045	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.025	0.005	9.136	0.001	0.001	0.000	0.000	0.000	0.000
8	A	9	PRO	0	-0.004	0.028	12.020	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.004	0.005	14.923	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.730	-0.894	18.458	0.005	0.005	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.943	0.972	19.570	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.895	0.946	22.921	0.017	0.017	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.016	-0.009	23.040	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.024	-0.014	21.154	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.019	0.013	16.561	0.013	0.013	0.000	0.000	0.000	0.000
16	A	17	PHE	0	0.032	0.012	12.801	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.017	0.013	11.462	0.046	0.046	0.000	0.000	0.000	0.000
18	A	19	PHE	0	0.052	-0.004	7.172	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.820	-0.903	7.112	-0.393	-0.393	0.000	0.000	0.000	0.000
20	A	21	GLN	0	-0.016	0.005	8.183	-0.101	-0.101	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.049	-0.036	8.101	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.844	0.925	5.557	0.756	0.756	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.015	0.019	7.136	0.175	0.175	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.832	0.917	8.693	0.273	0.273	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.040	0.041	8.940	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.029	-0.022	8.914	0.018	0.018	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.013	0.020	11.480	0.036	0.036	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.005	-0.008	10.089	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.005	0.004	14.232	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	31	ASN	0	-0.015	0.013	17.866	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.019	-0.031	19.925	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.031	0.021	23.073	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.029	-0.020	26.655	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.934	0.978	27.935	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.018	-0.001	30.627	0.002	0.002	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.036	0.020	33.058	0.000	0.000	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.033	0.009	29.440	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.006	-0.006	29.916	0.002	0.002	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.018	0.003	30.640	0.000	0.000	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.054	0.027	26.445	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	42	TYR	0	0.038	0.012	25.049	0.004	0.004	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.962	0.980	26.478	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.753	-0.857	26.070	0.028	0.028	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.017	0.003	20.632	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.733	-0.836	22.663	0.008	0.008	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.026	-0.009	24.739	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.001	0.006	19.455	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.012	-0.014	18.316	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.862	0.906	21.270	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.895	0.965	23.641	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	52	TYR	0	0.017	-0.026	18.987	0.000	0.000	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.812	0.914	18.451	0.014	0.014	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.849	-0.920	18.286	-0.039	-0.039	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.904	-0.939	18.528	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.060	-0.021	14.887	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	57	PHE	0	-0.009	-0.018	13.717	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.004	-0.013	12.731	0.003	0.003	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.001	0.005	14.653	0.020	0.020	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.003	0.007	12.479	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.015	0.002	15.647	0.015	0.015	0.000	0.000	0.000	0.000
61	A	62	PHE	0	0.046	0.001	13.531	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.001	0.020	19.203	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	CYS	0	-0.036	-0.002	22.193	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.003	-0.026	24.180	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	66	GLN	0	0.012	-0.004	23.373	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.014	0.012	22.949	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.019	0.016	28.672	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	87	GLY	0	-0.006	-0.015	28.527	0.000	0.000	0.000	0.000	0.000	0.000
69	A	88	VAL	0	-0.065	-0.018	23.528	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	89	THR	0	-0.056	-0.074	24.383	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	90	PHE	0	0.006	0.016	18.964	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	91	PRO	0	-0.001	-0.007	16.343	0.000	0.000	0.000	0.000	0.000	0.000
73	A	92	ILE	0	-0.024	0.003	18.602	0.014	0.014	0.000	0.000	0.000	0.000
74	A	93	MET	0	-0.045	-0.008	16.305	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	94	LYS	1	0.962	0.978	19.570	0.000	0.000	0.000	0.000	0.000	0.000
76	A	95	LYS	1	0.797	0.907	20.796	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	96	ILE	0	0.013	0.016	17.413	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	97	ASP	-1	-0.848	-0.918	21.565	0.026	0.026	0.000	0.000	0.000	0.000
79	A	98	VAL	0	0.031	0.006	18.527	0.006	0.006	0.000	0.000	0.000	0.000
80	A	99	ASN	0	-0.008	-0.013	18.756	0.017	0.017	0.000	0.000	0.000	0.000
81	A	100	GLY	0	0.069	0.031	21.368	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	101	GLY	0	0.017	-0.001	21.583	0.002	0.002	0.000	0.000	0.000	0.000
83	A	102	ASN	0	-0.001	0.003	22.287	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	103	GLU	-1	-0.919	-0.937	16.673	0.070	0.070	0.000	0.000	0.000	0.000
85	A	104	ASP	-1	-0.812	-0.917	15.047	0.077	0.077	0.000	0.000	0.000	0.000
86	A	105	PRO	0	0.034	-0.003	13.007	0.021	0.021	0.000	0.000	0.000	0.000
87	A	106	VAL	0	0.016	0.009	10.815	0.037	0.037	0.000	0.000	0.000	0.000
88	A	107	TYR	0	0.034	-0.011	11.218	0.063	0.063	0.000	0.000	0.000	0.000
89	A	108	LYS	1	0.955	0.998	13.069	0.014	0.014	0.000	0.000	0.000	0.000
90	A	109	PHE	0	0.019	0.006	4.276	0.066	0.145	-0.001	-0.010	-0.068	0.000
91	A	110	LEU	0	0.011	0.018	8.870	0.026	0.026	0.000	0.000	0.000	0.000
92	A	111	LYS	1	0.819	0.907	10.425	-0.115	-0.115	0.000	0.000	0.000	0.000
93	A	112	SER	0	-0.120	-0.059	9.386	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	113	GLN	0	-0.025	0.003	6.310	0.027	0.027	0.000	0.000	0.000	0.000
95	A	114	LYS	1	0.815	0.893	9.845	-0.168	-0.168	0.000	0.000	0.000	0.000
96	A	115	SER	0	-0.018	-0.037	13.014	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	116	GLY	0	0.003	0.015	16.467	0.000	0.000	0.000	0.000	0.000	0.000
98	A	117	MET	0	0.030	0.007	19.482	0.000	0.000	0.000	0.000	0.000	0.000
99	A	118	LEU	0	0.020	0.019	20.750	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	119	GLY	0	0.010	0.009	23.317	0.002	0.002	0.000	0.000	0.000	0.000
101	A	120	LEU	0	-0.018	-0.017	22.823	0.003	0.003	0.000	0.000	0.000	0.000
102	A	121	ARG	1	1.010	1.001	14.517	-0.088	-0.088	0.000	0.000	0.000	0.000
103	A	122	GLY	0	-0.003	0.004	18.594	0.011	0.011	0.000	0.000	0.000	0.000
104	A	123	ILE	0	-0.054	-0.024	16.938	0.002	0.002	0.000	0.000	0.000	0.000
105	A	124	LYS	1	0.952	0.973	20.859	-0.074	-0.074	0.000	0.000	0.000	0.000
106	A	125	TRP	0	0.041	0.010	23.758	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	126	ASN	0	-0.039	-0.012	23.466	0.009	0.009	0.000	0.000	0.000	0.000
108	A	127	PHE	0	0.027	-0.003	22.185	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	128	GLU	-1	-0.753	-0.849	19.131	0.087	0.087	0.000	0.000	0.000	0.000
110	A	129	LYS	1	0.830	0.918	17.284	-0.062	-0.062	0.000	0.000	0.000	0.000
111	A	130	PHE	0	0.010	0.011	11.906	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	131	LEU	0	0.021	0.026	12.884	0.010	0.010	0.000	0.000	0.000	0.000
113	A	132	VAL	0	-0.037	-0.025	6.389	0.036	0.036	0.000	0.000	0.000	0.000
114	A	133	ASP	-1	-0.739	-0.848	6.732	-0.438	-0.438	0.000	0.000	0.000	0.000
115	A	134	LYS	1	0.903	0.976	7.114	0.124	0.124	0.000	0.000	0.000	0.000
116	A	135	LYS	1	0.825	0.898	5.218	0.048	0.077	-0.001	-0.007	-0.021	0.000
117	A	136	GLY	0	-0.032	-0.008	2.430	-7.077	-4.352	0.582	-1.693	-1.614	-0.006
118	A	137	LYS	1	0.936	0.969	3.470	1.228	1.771	0.020	-0.098	-0.466	-0.001
119	A	138	VAL	0	0.010	-0.005	5.314	-0.041	-0.046	-0.001	-0.002	0.008	0.000
120	A	139	TYR	0	-0.020	-0.013	8.079	-0.042	-0.042	0.000	0.000	0.000	0.000
121	A	140	GLU	-1	-0.785	-0.880	11.270	0.114	0.114	0.000	0.000	0.000	0.000
122	A	141	ARG	1	0.681	0.833	13.907	-0.099	-0.099	0.000	0.000	0.000	0.000
123	A	142	TYR	0	0.047	0.013	15.682	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	143	SER	0	0.027	-0.002	19.187	0.003	0.003	0.000	0.000	0.000	0.000
125	A	144	SER	0	0.002	-0.010	22.198	0.000	0.000	0.000	0.000	0.000	0.000
126	A	145	LEU	0	-0.014	-0.011	24.144	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	146	THR	0	0.007	0.018	22.549	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	147	LYS	1	0.899	0.930	24.021	-0.025	-0.025	0.000	0.000	0.000	0.000
129	A	148	PRO	0	0.000	-0.010	22.155	0.002	0.002	0.000	0.000	0.000	0.000
130	A	149	SER	0	0.006	-0.014	22.524	0.000	0.000	0.000	0.000	0.000	0.000
131	A	150	SER	0	-0.022	-0.009	24.577	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	151	LEU	0	-0.027	-0.007	18.181	0.002	0.002	0.000	0.000	0.000	0.000
133	A	152	SER	0	0.001	0.008	19.837	0.001	0.001	0.000	0.000	0.000	0.000
134	A	153	GLU	-1	-0.881	-0.939	20.818	0.013	0.013	0.000	0.000	0.000	0.000
135	A	154	THR	0	-0.013	-0.004	16.497	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	155	ILE	0	-0.035	-0.027	16.178	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	156	GLU	-1	-0.780	-0.866	16.626	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	157	GLU	-1	-0.875	-0.922	17.015	0.027	0.027	0.000	0.000	0.000	0.000
139	A	158	LEU	0	-0.036	-0.023	12.021	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	159	LEU	0	-0.076	-0.049	13.459	-0.036	-0.036	0.000	0.000	0.000	0.000
141	A	160	LYS	1	0.896	0.945	15.465	-0.010	-0.010	0.000	0.000	0.000	0.000
142	A	161	GLH	0	-0.076	-0.053	9.730	0.018	0.018	0.000	0.000	0.000	0.000
143	A	162	VAL	0	0.036	0.033	13.058	-0.027	-0.027	0.000	0.000	0.000	0.000

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