FMO DATABASE

FMODB ID: LZ229

Calculation Name: 3WFN-D-Xray372

Preferred Name: Calmodulin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3WFN

Chain ID: D

ChEMBL ID: CHEMBL3562176

UniProt ID: P0DP26

Base Structure: X-ray

Registration Date: 2023-09-20

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	154
LigandCharge	DLY=1,DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1344926.356686
FMO2-HF: Nuclear repulsion	1282368.17501
FMO2-HF: Total energy	-62558.181676
FMO2-MP2: Total energy	-62735.939861

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(D:-2:HIS)

Summations of interaction energy for fragment #1(D:-2:HIS)

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.
-9.477	-8.035	-0.002	-0.534	-0.905	0.002

Interaction energy analysis for fragmet #1(D:-2:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.035

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	D	0	HIS	0	0.017	0.009	3.832	1.838	3.177	-0.001	-0.505	-0.833	0.002
4	D	1	MET	0	-0.030	-0.016	6.721	-0.586	-0.586	0.000	0.000	0.000	0.000
5	D	2	ALA	0	0.047	0.008	8.911	-0.018	-0.018	0.000	0.000	0.000	0.000
6	D	3	ASP	-1	-0.837	-0.916	4.377	-8.397	-8.294	-0.001	-0.029	-0.072	0.000
7	D	4	GLN	0	-0.059	-0.024	7.504	0.554	0.554	0.000	0.000	0.000	0.000
8	D	5	LEU	0	-0.026	0.008	10.804	0.370	0.370	0.000	0.000	0.000	0.000
9	D	6	THR	0	0.011	0.000	11.714	-0.272	-0.272	0.000	0.000	0.000	0.000
10	D	7	GLU	-1	-0.940	-0.986	13.625	-1.215	-1.215	0.000	0.000	0.000	0.000
11	D	8	GLU	-1	-0.964	-0.986	14.392	-0.654	-0.654	0.000	0.000	0.000	0.000
12	D	9	GLN	0	0.081	0.044	15.904	-0.052	-0.052	0.000	0.000	0.000	0.000
13	D	10	ILE	0	-0.011	0.006	10.992	0.119	0.119	0.000	0.000	0.000	0.000
14	D	11	ALA	0	-0.015	-0.006	15.481	0.120	0.120	0.000	0.000	0.000	0.000
15	D	12	GLU	-1	-0.855	-0.927	18.353	-0.572	-0.572	0.000	0.000	0.000	0.000
16	D	13	PHE	0	0.014	-0.009	16.569	0.066	0.066	0.000	0.000	0.000	0.000
17	D	14	LYS	1	0.951	0.977	17.304	0.626	0.626	0.000	0.000	0.000	0.000
18	D	15	GLU	-1	-0.986	-0.972	19.565	-0.354	-0.354	0.000	0.000	0.000	0.000
19	D	16	ALA	0	-0.005	-0.013	22.849	0.052	0.052	0.000	0.000	0.000	0.000
20	D	17	PHE	0	-0.064	-0.034	20.787	0.034	0.034	0.000	0.000	0.000	0.000
21	D	18	SER	0	-0.026	-0.050	22.283	0.042	0.042	0.000	0.000	0.000	0.000
22	D	19	LEU	0	-0.051	0.001	24.514	0.041	0.041	0.000	0.000	0.000	0.000
23	D	20	PHE	0	-0.063	-0.037	27.765	0.013	0.013	0.000	0.000	0.000	0.000
24	D	21	ASP	-1	-0.808	-0.897	23.295	-0.171	-0.171	0.000	0.000	0.000	0.000
25	D	22	LYS	1	0.668	0.803	26.118	0.126	0.126	0.000	0.000	0.000	0.000
26	D	23	ASP	-1	-0.896	-0.940	23.711	-0.106	-0.106	0.000	0.000	0.000	0.000
27	D	24	GLY	0	-0.034	-0.019	23.200	0.007	0.007	0.000	0.000	0.000	0.000
28	D	25	ASP	-1	-0.906	-0.932	24.526	-0.037	-0.037	0.000	0.000	0.000	0.000
29	D	26	GLY	0	0.018	0.029	21.497	-0.017	-0.017	0.000	0.000	0.000	0.000
30	D	27	THR	0	-0.107	-0.076	20.820	-0.011	-0.011	0.000	0.000	0.000	0.000
31	D	28	ILE	0	0.071	0.062	22.971	0.002	0.002	0.000	0.000	0.000	0.000
32	D	29	THR	0	-0.027	-0.051	24.993	0.030	0.030	0.000	0.000	0.000	0.000
33	D	30	THR	0	0.034	0.016	25.891	-0.018	-0.018	0.000	0.000	0.000	0.000
34	D	31	LYS	1	0.794	0.882	27.887	0.080	0.080	0.000	0.000	0.000	0.000
35	D	32	GLU	-1	-0.804	-0.891	28.736	-0.118	-0.118	0.000	0.000	0.000	0.000
36	D	33	LEU	0	0.042	0.040	23.535	-0.016	-0.016	0.000	0.000	0.000	0.000
37	D	34	GLY	0	-0.017	-0.041	27.539	-0.009	-0.009	0.000	0.000	0.000	0.000
38	D	35	THR	0	-0.054	-0.017	28.181	0.010	0.010	0.000	0.000	0.000	0.000
39	D	36	VAL	0	0.021	0.040	24.544	-0.010	-0.010	0.000	0.000	0.000	0.000
40	D	37	MET	0	-0.038	-0.013	23.262	-0.022	-0.022	0.000	0.000	0.000	0.000
41	D	62	GLY	0	0.007	0.005	26.556	0.006	0.006	0.000	0.000	0.000	0.000
42	D	63	THR	0	-0.047	-0.047	23.609	-0.010	-0.010	0.000	0.000	0.000	0.000
43	D	64	ILE	0	-0.041	-0.014	20.041	0.022	0.022	0.000	0.000	0.000	0.000
44	D	65	ASP	-1	-0.804	-0.905	16.283	-0.112	-0.112	0.000	0.000	0.000	0.000
45	D	66	PHE	0	0.044	0.016	15.250	-0.054	-0.054	0.000	0.000	0.000	0.000
46	D	67	PRO	0	0.005	-0.004	11.848	-0.096	-0.096	0.000	0.000	0.000	0.000
47	D	68	GLU	-1	-0.863	-0.916	13.883	-0.062	-0.062	0.000	0.000	0.000	0.000
48	D	69	PHE	0	0.008	-0.003	16.075	-0.025	-0.025	0.000	0.000	0.000	0.000
49	D	70	LEU	0	0.006	0.002	12.665	-0.052	-0.052	0.000	0.000	0.000	0.000
50	D	71	THR	0	-0.051	-0.039	12.831	-0.107	-0.107	0.000	0.000	0.000	0.000
51	D	72	MET	0	-0.069	-0.024	14.625	0.019	0.019	0.000	0.000	0.000	0.000
52	D	73	MET	0	0.004	0.008	17.273	0.038	0.038	0.000	0.000	0.000	0.000
53	D	74	ALA	0	0.047	0.026	13.609	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	75	ARG	1	0.890	0.934	15.459	0.198	0.198	0.000	0.000	0.000	0.000
55	D	76	LYS	1	0.944	0.986	17.218	0.372	0.372	0.000	0.000	0.000	0.000
56	D	77	MET	0	-0.005	-0.004	16.970	0.036	0.036	0.000	0.000	0.000	0.000
57	D	78	LYS	1	0.912	0.968	12.957	0.858	0.858	0.000	0.000	0.000	0.000
58	D	79	ASP	-1	-0.944	-0.980	18.587	-0.258	-0.258	0.000	0.000	0.000	0.000
59	D	80	THR	0	-0.058	-0.040	21.971	0.051	0.051	0.000	0.000	0.000	0.000
60	D	81	ASP	-1	-0.850	-0.915	19.271	-0.670	-0.670	0.000	0.000	0.000	0.000
61	D	82	SER	0	-0.065	-0.042	21.510	0.044	0.044	0.000	0.000	0.000	0.000
62	D	83	GLU	-1	-0.860	-0.938	23.125	-0.208	-0.208	0.000	0.000	0.000	0.000
63	D	84	GLU	-1	-0.958	-0.975	25.803	-0.370	-0.370	0.000	0.000	0.000	0.000
64	D	85	GLU	-1	-0.893	-0.950	23.374	-0.406	-0.406	0.000	0.000	0.000	0.000
65	D	86	ILE	0	-0.041	-0.030	26.262	0.030	0.030	0.000	0.000	0.000	0.000
66	D	87	ARG	1	0.754	0.830	28.702	0.242	0.242	0.000	0.000	0.000	0.000
67	D	88	GLU	-1	-0.909	-0.944	29.267	-0.265	-0.265	0.000	0.000	0.000	0.000
68	D	89	ALA	0	-0.046	-0.024	29.397	0.015	0.015	0.000	0.000	0.000	0.000
69	D	90	PHE	0	0.002	-0.022	31.398	0.019	0.019	0.000	0.000	0.000	0.000
70	D	91	ARG	1	0.901	0.975	34.224	0.191	0.191	0.000	0.000	0.000	0.000
71	D	92	VAL	0	-0.018	0.000	32.899	0.011	0.011	0.000	0.000	0.000	0.000
72	D	93	PHE	0	-0.044	-0.031	33.432	0.011	0.011	0.000	0.000	0.000	0.000
73	D	94	ASP	-1	-0.794	-0.855	38.220	-0.131	-0.131	0.000	0.000	0.000	0.000
74	D	95	LYS	1	0.783	0.865	40.553	0.105	0.105	0.000	0.000	0.000	0.000
75	D	96	ASP	-1	-0.896	-0.950	43.209	-0.117	-0.117	0.000	0.000	0.000	0.000
76	D	97	GLY	0	-0.037	-0.018	41.603	-0.002	-0.002	0.000	0.000	0.000	0.000
77	D	98	ASN	0	-0.104	-0.059	42.629	-0.005	-0.005	0.000	0.000	0.000	0.000
78	D	99	GLY	0	0.032	0.014	40.650	0.003	0.003	0.000	0.000	0.000	0.000
79	D	100	TYR	0	-0.036	-0.023	41.395	0.002	0.002	0.000	0.000	0.000	0.000
80	D	101	ILE	0	-0.035	-0.006	38.426	-0.002	-0.002	0.000	0.000	0.000	0.000
81	D	102	SER	0	0.027	0.030	42.738	0.008	0.008	0.000	0.000	0.000	0.000
82	D	103	ALA	0	0.087	0.032	43.516	-0.003	-0.003	0.000	0.000	0.000	0.000
83	D	104	ALA	0	-0.030	-0.021	43.606	0.000	0.000	0.000	0.000	0.000	0.000
84	D	105	GLU	-1	-0.838	-0.907	41.933	-0.103	-0.103	0.000	0.000	0.000	0.000
85	D	106	LEU	0	0.058	0.024	36.912	-0.004	-0.004	0.000	0.000	0.000	0.000
86	D	107	ARG	1	0.887	0.912	39.294	0.039	0.039	0.000	0.000	0.000	0.000
87	D	108	HIS	0	-0.021	0.017	40.588	0.006	0.006	0.000	0.000	0.000	0.000
88	D	109	VAL	0	0.026	0.005	37.347	0.000	0.000	0.000	0.000	0.000	0.000
89	D	110	MET	0	-0.010	0.008	33.565	-0.005	-0.005	0.000	0.000	0.000	0.000
90	D	111	THR	0	0.001	-0.007	35.981	0.003	0.003	0.000	0.000	0.000	0.000
91	D	112	ASN	0	-0.104	-0.065	38.512	0.008	0.008	0.000	0.000	0.000	0.000
92	D	113	LEU	0	-0.034	0.000	34.879	-0.001	-0.001	0.000	0.000	0.000	0.000
93	D	114	GLY	0	0.027	0.017	31.438	0.005	0.005	0.000	0.000	0.000	0.000
94	D	115	GLU	-1	-0.898	-0.923	26.111	-0.135	-0.135	0.000	0.000	0.000	0.000
95	D	116	LYS	1	0.881	0.961	31.045	0.092	0.092	0.000	0.000	0.000	0.000
96	D	117	LEU	0	-0.004	0.003	32.619	0.009	0.009	0.000	0.000	0.000	0.000
97	D	118	THR	0	-0.043	-0.050	35.407	0.000	0.000	0.000	0.000	0.000	0.000
98	D	119	ASP	-1	-0.876	-0.949	37.857	-0.030	-0.030	0.000	0.000	0.000	0.000
99	D	120	GLU	-1	-0.900	-0.937	38.682	0.003	0.003	0.000	0.000	0.000	0.000
100	D	121	GLU	-1	-0.781	-0.856	32.876	-0.027	-0.027	0.000	0.000	0.000	0.000
101	D	122	VAL	0	0.003	-0.002	37.149	-0.007	-0.007	0.000	0.000	0.000	0.000
102	D	123	ASP	-1	-0.822	-0.886	38.971	-0.028	-0.028	0.000	0.000	0.000	0.000
103	D	124	GLU	-1	-0.816	-0.860	37.250	-0.007	-0.007	0.000	0.000	0.000	0.000
104	D	125	MET	0	-0.025	-0.005	34.315	-0.004	-0.004	0.000	0.000	0.000	0.000
105	D	126	ILE	0	-0.032	-0.024	38.220	-0.005	-0.005	0.000	0.000	0.000	0.000
106	D	127	ARG	1	0.750	0.840	39.578	0.014	0.014	0.000	0.000	0.000	0.000
107	D	128	GLU	-1	-0.792	-0.881	36.172	-0.028	-0.028	0.000	0.000	0.000	0.000
108	D	129	ALA	0	-0.016	0.001	40.134	-0.006	-0.006	0.000	0.000	0.000	0.000
109	D	130	ASP	-1	-1.001	-0.990	41.066	-0.049	-0.049	0.000	0.000	0.000	0.000
110	D	131	ILE	0	-0.072	-0.027	43.957	0.002	0.002	0.000	0.000	0.000	0.000
111	D	132	ASP	-1	-0.861	-0.925	46.260	-0.069	-0.069	0.000	0.000	0.000	0.000
112	D	133	GLY	0	-0.044	-0.018	49.375	0.002	0.002	0.000	0.000	0.000	0.000
113	D	134	DAS	-1	-0.865	-0.916	50.819	-0.039	-0.039	0.000	0.000	0.000	0.000
114	D	135	GLY	0	-0.093	-0.091	49.329	-0.001	-0.001	0.000	0.000	0.000	0.000
115	D	136	GLN	0	-0.091	-0.044	46.198	-0.007	-0.007	0.000	0.000	0.000	0.000
116	D	137	VAL	0	0.034	0.014	39.973	0.004	0.004	0.000	0.000	0.000	0.000
117	D	138	ASN	0	0.052	0.040	40.894	-0.015	-0.015	0.000	0.000	0.000	0.000
118	D	139	TYR	0	-0.026	-0.057	35.984	-0.002	-0.002	0.000	0.000	0.000	0.000
119	D	140	GLU	-1	-0.764	-0.828	35.184	-0.189	-0.189	0.000	0.000	0.000	0.000
120	D	141	GLU	-1	-0.906	-0.967	36.093	-0.098	-0.098	0.000	0.000	0.000	0.000
121	D	142	PHE	0	0.015	0.001	34.047	0.003	0.003	0.000	0.000	0.000	0.000
122	D	143	VAL	0	0.000	-0.008	30.782	0.003	0.003	0.000	0.000	0.000	0.000
123	D	144	GLN	0	-0.041	-0.041	32.121	0.008	0.008	0.000	0.000	0.000	0.000
124	D	145	MET	0	-0.061	0.001	33.445	0.009	0.009	0.000	0.000	0.000	0.000
125	D	146	MET	0	-0.005	0.025	30.265	0.012	0.012	0.000	0.000	0.000	0.000
126	D	147	THR	0	0.422	0.562	28.268	0.007	0.007	0.000	0.000	0.000	0.000
127	D	148	ALA	0	0.374	0.359	24.984	-0.020	-0.020	0.000	0.000	0.000	0.000
128	D	149	DLY	2	0.580	0.619	21.702	0.342	0.342	0.000	0.000	0.000	0.000
129	D	150	GLY	-1	0.099	0.018	23.330	-0.283	-0.283	0.000	0.000	0.000	0.000
130	D	151	GLY	0	-0.047	-0.146	23.755	0.001	0.001	0.000	0.000	0.000	0.000
131	D	152	GLY	0	-0.173	-0.142	25.700	0.030	0.030	0.000	0.000	0.000	0.000
132	D	153	GLY	0	-0.412	-0.441	29.405	0.027	0.027	0.000	0.000	0.000	0.000
133	D	154	GLY	0	0.028	0.024	31.360	-0.012	-0.012	0.000	0.000	0.000	0.000
134	D	155	GLU	-1	-0.867	-0.936	31.745	-0.192	-0.192	0.000	0.000	0.000	0.000
135	D	156	GLU	-1	-0.853	-0.900	31.191	-0.142	-0.142	0.000	0.000	0.000	0.000
136	D	157	VAL	0	0.021	0.034	25.848	0.000	0.000	0.000	0.000	0.000	0.000
137	D	158	SER	0	-0.037	-0.045	28.162	-0.013	-0.013	0.000	0.000	0.000	0.000
138	D	159	ALA	0	0.017	0.002	30.385	0.005	0.005	0.000	0.000	0.000	0.000
139	D	160	VAL	0	-0.043	0.010	25.802	0.013	0.013	0.000	0.000	0.000	0.000
140	D	161	VAL	0	-0.072	0.010	25.598	0.007	0.007	0.000	0.000	0.000	0.000
141	D	162	LEU	0	-0.002	0.004	27.173	0.010	0.010	0.000	0.000	0.000	0.000
142	D	163	GLN	0	0.006	-0.021	29.746	0.005	0.005	0.000	0.000	0.000	0.000
143	D	164	ARG	1	0.780	0.869	22.383	0.255	0.255	0.000	0.000	0.000	0.000
144	D	165	ALA	0	0.024	0.014	26.448	0.020	0.020	0.000	0.000	0.000	0.000
145	D	166	TYR	0	0.004	-0.024	27.329	0.020	0.020	0.000	0.000	0.000	0.000
146	D	167	ARG	1	0.754	0.832	28.121	0.074	0.074	0.000	0.000	0.000	0.000
147	D	168	GLY	0	-0.072	-0.031	26.054	0.025	0.025	0.000	0.000	0.000	0.000
148	D	169	HIS	0	-0.006	-0.014	26.695	0.018	0.018	0.000	0.000	0.000	0.000
149	D	170	LEU	0	0.015	0.005	29.622	0.019	0.019	0.000	0.000	0.000	0.000
150	D	171	ALA	0	-0.030	-0.012	26.512	0.019	0.019	0.000	0.000	0.000	0.000
151	D	172	ARG	1	0.848	0.922	25.392	0.091	0.091	0.000	0.000	0.000	0.000
152	D	173	ARG	1	0.820	0.898	28.440	0.013	0.013	0.000	0.000	0.000	0.000
153	D	174	GLY	0	-0.012	0.019	31.199	0.004	0.004	0.000	0.000	0.000	0.000
154	D	175	PHE	0	-0.098	-0.037	26.693	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:-2:HIS)