FMO DATABASE

FMODB ID: 3M74L

Calculation Name: 2C8S-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | calcium ion

Ligand 3-letter code: HEM | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C8S

Chain ID: A

ChEMBL ID:

UniProt ID: P14774

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1366030.642111
FMO2-HF: Nuclear repulsion	1307676.902955
FMO2-HF: Total energy	-58353.739155
FMO2-MP2: Total energy	-58521.001871

3D Structure Molmil

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:24:SER)

Summations of interaction energy for fragment #1(A:24: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.
-209.204	-210.493	19.928	-11.018	-7.62	-0.136

Interaction energy analysis for fragmet #1(A:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.751 / q_NPA : 0.856

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	26	GLY	0	-0.007	0.011	3.847	1.044	2.289	-0.015	-0.499	-0.731	0.000
4	A	27	LYS	1	0.940	0.973	5.341	31.457	31.492	-0.001	-0.003	-0.030	0.000
5	A	28	GLU	-1	-0.785	-0.881	1.858	-142.652	-145.256	19.945	-10.512	-6.829	-0.136
94	A	117	THR	0	-0.043	-0.058	4.543	3.148	3.183	-0.001	-0.004	-0.030	0.000
6	A	29	GLY	0	0.035	0.003	5.952	6.297	6.297	0.000	0.000	0.000	0.000
7	A	30	GLY	0	0.008	0.021	6.717	-1.884	-1.884	0.000	0.000	0.000	0.000
8	A	31	ARG	1	0.856	0.896	7.739	29.383	29.383	0.000	0.000	0.000	0.000
9	A	32	ASP	-1	-0.888	-0.939	10.553	-26.301	-26.301	0.000	0.000	0.000	0.000
10	A	33	THR	0	-0.014	-0.024	10.756	1.894	1.894	0.000	0.000	0.000	0.000
11	A	34	PRO	0	0.027	-0.003	13.494	0.933	0.933	0.000	0.000	0.000	0.000
12	A	35	ALA	0	0.040	0.038	15.181	1.049	1.049	0.000	0.000	0.000	0.000
13	A	36	VAL	0	0.008	0.011	11.800	0.875	0.875	0.000	0.000	0.000	0.000
14	A	37	LYS	1	0.846	0.908	15.236	15.523	15.523	0.000	0.000	0.000	0.000
15	A	38	LYS	1	0.895	0.934	17.993	13.598	13.598	0.000	0.000	0.000	0.000
16	A	39	PHE	0	-0.001	0.014	17.268	0.841	0.841	0.000	0.000	0.000	0.000
17	A	40	LEU	0	-0.016	-0.017	16.035	0.655	0.655	0.000	0.000	0.000	0.000
18	A	41	GLU	-1	-0.898	-0.923	20.130	-13.296	-13.296	0.000	0.000	0.000	0.000
19	A	42	THR	0	-0.089	-0.063	23.053	0.758	0.758	0.000	0.000	0.000	0.000
20	A	43	GLY	0	0.016	0.016	22.535	0.450	0.450	0.000	0.000	0.000	0.000
21	A	44	GLU	-1	-0.915	-0.944	22.856	-12.719	-12.719	0.000	0.000	0.000	0.000
22	A	45	ASN	0	-0.013	-0.022	18.133	-1.155	-1.155	0.000	0.000	0.000	0.000
23	A	46	LEU	0	-0.003	-0.011	19.158	0.369	0.369	0.000	0.000	0.000	0.000
24	A	47	TYR	0	-0.029	-0.055	13.080	0.671	0.671	0.000	0.000	0.000	0.000
25	A	48	ILE	0	-0.022	0.003	18.949	-0.087	-0.087	0.000	0.000	0.000	0.000
26	A	49	ASP	-1	-0.913	-0.962	22.150	-12.148	-12.148	0.000	0.000	0.000	0.000
27	A	50	ASP	-1	-0.772	-0.848	19.406	-16.319	-16.319	0.000	0.000	0.000	0.000
28	A	51	LYS	1	0.978	0.967	19.590	11.993	11.993	0.000	0.000	0.000	0.000
29	A	52	SER	0	-0.044	-0.027	16.648	-0.452	-0.452	0.000	0.000	0.000	0.000
30	A	53	CYS	0	-0.034	0.016	13.180	-1.899	-1.899	0.000	0.000	0.000	0.000
31	A	54	LEU	0	-0.005	0.003	15.530	-0.663	-0.663	0.000	0.000	0.000	0.000
32	A	55	ARG	1	0.903	0.968	16.244	17.790	17.790	0.000	0.000	0.000	0.000
33	A	56	ASN	0	-0.020	-0.017	11.585	0.179	0.179	0.000	0.000	0.000	0.000
34	A	57	GLY	0	0.034	0.008	12.929	-0.954	-0.954	0.000	0.000	0.000	0.000
35	A	58	GLU	-1	-0.947	-0.981	14.826	-15.455	-15.455	0.000	0.000	0.000	0.000
36	A	59	SER	0	-0.031	-0.023	12.591	0.388	0.388	0.000	0.000	0.000	0.000
37	A	60	LEU	0	-0.003	0.004	8.333	-0.394	-0.394	0.000	0.000	0.000	0.000
38	A	61	PHE	0	0.008	0.004	12.324	0.383	0.383	0.000	0.000	0.000	0.000
39	A	62	ALA	0	-0.017	-0.008	15.830	0.745	0.745	0.000	0.000	0.000	0.000
40	A	63	THR	0	-0.036	-0.015	12.069	0.151	0.151	0.000	0.000	0.000	0.000
41	A	64	SER	0	0.008	-0.001	11.529	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	65	CYS	0	-0.056	-0.017	14.118	0.550	0.550	0.000	0.000	0.000	0.000
43	A	66	SER	0	-0.042	-0.022	17.742	1.303	1.303	0.000	0.000	0.000	0.000
44	A	67	GLY	0	0.004	0.002	19.313	0.858	0.858	0.000	0.000	0.000	0.000
45	A	68	CYS	0	-0.026	-0.020	20.980	0.796	0.796	0.000	0.000	0.000	0.000
46	A	69	HIS	0	0.013	-0.013	21.069	0.371	0.371	0.000	0.000	0.000	0.000
47	A	70	GLY	0	0.027	0.039	23.585	0.426	0.426	0.000	0.000	0.000	0.000
48	A	71	HIS	0	-0.041	-0.038	22.153	-0.274	-0.274	0.000	0.000	0.000	0.000
49	A	72	LEU	0	-0.035	-0.036	22.407	-0.506	-0.506	0.000	0.000	0.000	0.000
50	A	73	ALA	0	0.011	0.013	22.806	0.242	0.242	0.000	0.000	0.000	0.000
51	A	74	GLU	-1	-0.790	-0.895	24.489	-11.782	-11.782	0.000	0.000	0.000	0.000
52	A	75	GLY	0	-0.002	0.015	26.603	0.430	0.430	0.000	0.000	0.000	0.000
53	A	76	LYS	1	0.860	0.912	24.920	12.026	12.026	0.000	0.000	0.000	0.000
54	A	77	LEU	0	-0.074	-0.026	24.706	0.368	0.368	0.000	0.000	0.000	0.000
55	A	78	GLY	0	0.005	0.010	25.548	0.208	0.208	0.000	0.000	0.000	0.000
56	A	79	PRO	0	-0.007	-0.011	26.494	0.175	0.175	0.000	0.000	0.000	0.000
57	A	80	GLY	0	0.060	0.037	26.547	-0.485	-0.485	0.000	0.000	0.000	0.000
58	A	81	LEU	0	-0.062	-0.039	22.221	-0.063	-0.063	0.000	0.000	0.000	0.000
59	A	82	ASN	0	0.028	0.024	25.939	0.027	0.027	0.000	0.000	0.000	0.000
60	A	83	ASP	-1	-0.844	-0.914	27.650	-9.832	-9.832	0.000	0.000	0.000	0.000
61	A	84	ASN	0	-0.047	-0.056	30.232	-0.297	-0.297	0.000	0.000	0.000	0.000
62	A	85	TYR	0	-0.049	-0.016	32.528	0.308	0.308	0.000	0.000	0.000	0.000
63	A	86	TRP	0	0.018	-0.005	24.802	-0.541	-0.541	0.000	0.000	0.000	0.000
64	A	87	THR	0	-0.009	-0.010	30.239	0.230	0.230	0.000	0.000	0.000	0.000
65	A	88	TYR	0	0.032	0.018	27.707	0.151	0.151	0.000	0.000	0.000	0.000
66	A	89	PRO	0	0.072	0.024	28.357	-0.467	-0.467	0.000	0.000	0.000	0.000
67	A	90	SER	0	0.028	0.037	26.231	-0.179	-0.179	0.000	0.000	0.000	0.000
68	A	91	ASN	0	0.017	0.032	23.561	-0.785	-0.785	0.000	0.000	0.000	0.000
69	A	92	THR	0	0.000	0.004	25.007	-0.291	-0.291	0.000	0.000	0.000	0.000
70	A	93	THR	0	0.017	-0.004	25.544	-0.076	-0.076	0.000	0.000	0.000	0.000
71	A	94	ASP	-1	-0.715	-0.863	20.279	-14.829	-14.829	0.000	0.000	0.000	0.000
72	A	95	VAL	0	0.003	0.004	20.268	-0.685	-0.685	0.000	0.000	0.000	0.000
73	A	96	GLY	0	0.002	0.008	21.243	-0.330	-0.330	0.000	0.000	0.000	0.000
74	A	97	LEU	0	-0.021	-0.010	18.844	-0.159	-0.159	0.000	0.000	0.000	0.000
75	A	98	PHE	0	-0.005	-0.005	13.797	-0.609	-0.609	0.000	0.000	0.000	0.000
76	A	99	ALA	0	-0.017	-0.011	17.525	-0.642	-0.642	0.000	0.000	0.000	0.000
77	A	100	THR	0	-0.020	-0.021	20.001	0.184	0.184	0.000	0.000	0.000	0.000
78	A	101	ILE	0	-0.021	-0.009	14.509	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	102	PHE	0	-0.039	-0.030	10.879	-0.366	-0.366	0.000	0.000	0.000	0.000
80	A	103	GLY	0	-0.018	-0.007	16.088	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	104	GLY	0	-0.010	0.001	19.060	0.765	0.765	0.000	0.000	0.000	0.000
82	A	105	ALA	0	-0.017	-0.012	17.906	0.403	0.403	0.000	0.000	0.000	0.000
83	A	106	ASN	0	-0.058	-0.020	19.741	0.377	0.377	0.000	0.000	0.000	0.000
84	A	107	GLY	0	0.045	0.039	22.933	0.501	0.501	0.000	0.000	0.000	0.000
85	A	108	MET	0	-0.044	-0.042	24.988	0.439	0.439	0.000	0.000	0.000	0.000
86	A	109	MET	0	-0.024	-0.013	24.310	0.392	0.392	0.000	0.000	0.000	0.000
87	A	110	GLY	0	0.017	0.021	24.114	-0.131	-0.131	0.000	0.000	0.000	0.000
88	A	111	PRO	0	-0.042	-0.017	21.382	-0.107	-0.107	0.000	0.000	0.000	0.000
89	A	112	HIS	0	0.014	0.015	18.134	-1.150	-1.150	0.000	0.000	0.000	0.000
90	A	113	ASN	0	-0.003	-0.018	14.582	0.610	0.610	0.000	0.000	0.000	0.000
91	A	114	GLU	-1	-0.826	-0.898	10.642	-26.610	-26.610	0.000	0.000	0.000	0.000
92	A	115	ASN	0	-0.065	-0.043	9.611	-1.286	-1.286	0.000	0.000	0.000	0.000
93	A	116	LEU	0	0.025	0.034	7.861	-3.733	-3.733	0.000	0.000	0.000	0.000
95	A	118	PRO	0	-0.014	-0.024	7.563	2.249	2.249	0.000	0.000	0.000	0.000
96	A	119	ASP	-1	-0.775	-0.835	8.999	-24.998	-24.998	0.000	0.000	0.000	0.000
97	A	120	GLU	-1	-0.752	-0.851	5.904	-47.128	-47.128	0.000	0.000	0.000	0.000
98	A	121	MET	0	-0.025	0.022	9.806	2.294	2.294	0.000	0.000	0.000	0.000
99	A	122	LEU	0	0.019	0.013	12.582	1.750	1.750	0.000	0.000	0.000	0.000
100	A	123	GLN	0	0.026	0.004	10.499	2.245	2.245	0.000	0.000	0.000	0.000
101	A	124	THR	0	0.007	-0.014	12.527	1.300	1.300	0.000	0.000	0.000	0.000
102	A	125	ILE	0	-0.057	-0.019	15.160	1.331	1.331	0.000	0.000	0.000	0.000
103	A	126	ALA	0	0.002	0.006	17.675	1.101	1.101	0.000	0.000	0.000	0.000
104	A	127	TRP	0	0.014	0.013	17.822	0.894	0.894	0.000	0.000	0.000	0.000
105	A	128	ILE	0	-0.001	-0.005	18.747	0.838	0.838	0.000	0.000	0.000	0.000
106	A	129	ARG	1	0.749	0.856	21.422	14.150	14.150	0.000	0.000	0.000	0.000
107	A	130	HIS	1	0.811	0.887	22.428	13.500	13.500	0.000	0.000	0.000	0.000
108	A	131	LEU	0	0.002	0.003	21.664	0.487	0.487	0.000	0.000	0.000	0.000
109	A	132	TYR	0	-0.056	-0.025	25.037	0.469	0.469	0.000	0.000	0.000	0.000
110	A	133	THR	0	-0.040	-0.031	27.952	0.297	0.297	0.000	0.000	0.000	0.000
111	A	134	GLY	0	0.040	0.034	31.515	0.354	0.354	0.000	0.000	0.000	0.000
112	A	135	PRO	0	0.003	0.004	33.737	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	136	LYS	1	0.865	0.934	34.104	9.009	9.009	0.000	0.000	0.000	0.000
114	A	137	GLN	0	-0.054	-0.025	34.359	-0.100	-0.100	0.000	0.000	0.000	0.000
115	A	138	ASP	-1	-0.796	-0.895	33.956	-8.859	-8.859	0.000	0.000	0.000	0.000
116	A	139	ALA	0	0.015	0.028	29.911	-0.262	-0.262	0.000	0.000	0.000	0.000
117	A	140	VAL	0	-0.078	-0.062	29.502	-0.027	-0.027	0.000	0.000	0.000	0.000
118	A	141	TRP	0	-0.003	0.013	25.054	0.002	0.002	0.000	0.000	0.000	0.000
119	A	142	LEU	0	-0.047	-0.001	26.236	-0.354	-0.354	0.000	0.000	0.000	0.000
120	A	143	ASN	0	0.051	0.023	28.514	0.453	0.453	0.000	0.000	0.000	0.000
121	A	144	ASP	-1	-0.849	-0.936	30.502	-9.063	-9.063	0.000	0.000	0.000	0.000
122	A	145	GLU	-1	-0.945	-0.985	31.272	-9.849	-9.849	0.000	0.000	0.000	0.000
123	A	146	GLN	0	0.086	0.042	25.577	0.218	0.218	0.000	0.000	0.000	0.000
124	A	147	LYS	1	0.891	0.953	30.219	9.964	9.964	0.000	0.000	0.000	0.000
125	A	148	LYS	1	0.853	0.923	32.934	9.044	9.044	0.000	0.000	0.000	0.000
126	A	149	ALA	0	0.001	-0.004	30.716	0.186	0.186	0.000	0.000	0.000	0.000
127	A	150	TYR	0	-0.033	-0.009	29.592	-0.072	-0.072	0.000	0.000	0.000	0.000
128	A	151	THR	0	-0.005	-0.006	30.765	0.575	0.575	0.000	0.000	0.000	0.000
129	A	152	PRO	0	-0.031	-0.005	30.631	-0.319	-0.319	0.000	0.000	0.000	0.000
130	A	153	TYR	0	0.082	0.057	24.949	0.297	0.297	0.000	0.000	0.000	0.000
131	A	154	LYS	1	0.804	0.884	29.143	10.117	10.117	0.000	0.000	0.000	0.000
132	A	155	GLN	0	0.068	0.033	27.599	-0.026	-0.026	0.000	0.000	0.000	0.000
133	A	156	GLY	0	-0.011	-0.006	27.593	0.382	0.382	0.000	0.000	0.000	0.000
134	A	157	GLU	-1	-0.883	-0.910	25.790	-12.112	-12.112	0.000	0.000	0.000	0.000
135	A	158	VAL	0	-0.036	-0.022	23.918	-0.476	-0.476	0.000	0.000	0.000	0.000
136	A	159	ILE	0	0.012	0.016	20.891	0.410	0.410	0.000	0.000	0.000	0.000
137	A	160	PRO	0	-0.021	-0.014	22.784	-0.272	-0.272	0.000	0.000	0.000	0.000
138	A	161	LYS	1	0.986	0.977	20.469	13.795	13.795	0.000	0.000	0.000	0.000
139	A	162	ASP	-1	-0.898	-0.945	20.040	-13.699	-13.699	0.000	0.000	0.000	0.000
140	A	163	ALA	0	-0.054	-0.018	20.855	-0.132	-0.132	0.000	0.000	0.000	0.000
141	A	164	LYS	1	0.909	0.944	17.694	16.633	16.633	0.000	0.000	0.000	0.000
142	A	165	GLY	0	-0.029	-0.020	18.690	0.877	0.877	0.000	0.000	0.000	0.000
143	A	166	GLN	0	-0.105	-0.078	17.305	-0.308	-0.308	0.000	0.000	0.000	0.000
144	A	168	LYS	1	0.939	0.977	9.838	29.531	29.531	0.000	0.000	0.000	0.000
145	A	169	PRO	0	-0.029	-0.005	11.604	-1.500	-1.500	0.000	0.000	0.000	0.000
146	A	170	LEU	0	-0.007	-0.008	7.364	-1.812	-1.812	0.000	0.000	0.000	0.000
147	A	171	ASP	-1	-0.940	-0.958	10.110	-21.960	-21.960	0.000	0.000	0.000	0.000
148	A	172	GLU	-2	-1.834	-1.927	12.922	-40.686	-40.686	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:SER)