FMO DATABASE

FMODB ID: G8961

Calculation Name: 2C1D-B-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c | s-mercaptocysteine

Ligand 3-letter code: HEC | CSS

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C1D

Chain ID: B

ChEMBL ID:

UniProt ID: O33434

Base Structure: X-ray

Registration Date: 2025-10-03

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1077792.201958
FMO2-HF: Nuclear repulsion	1026959.426244
FMO2-HF: Total energy	-50832.775714
FMO2-MP2: Total energy	-50978.80919

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:21:CYS)

Summations of interaction energy for fragment #1(A:21:CYS)

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.
-9.557	-6.985	-0.011	-1.248	-1.313	0.001

Interaction energy analysis for fragmet #1(A:21:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.122 / q_NPA : -0.077

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	23	THR	0	0.002	0.016	3.704	-1.890	0.176	-0.028	-0.998	-1.040	0.002
20	A	40	THR	0	-0.009	-0.012	4.570	-2.227	-2.156	-0.001	-0.039	-0.031	0.000
21	A	41	GLY	0	-0.016	-0.002	3.496	-1.554	-1.119	0.018	-0.211	-0.242	-0.001
4	A	24	ALA	0	0.091	0.065	6.602	1.494	1.494	0.000	0.000	0.000	0.000
5	A	25	PRO	0	-0.020	-0.029	8.240	0.700	0.700	0.000	0.000	0.000	0.000
6	A	26	LYS	1	0.756	0.854	11.901	2.148	2.148	0.000	0.000	0.000	0.000
7	A	27	GLU	-1	-0.911	-0.947	7.687	-6.474	-6.474	0.000	0.000	0.000	0.000
8	A	28	VAL	0	-0.030	-0.001	11.294	0.055	0.055	0.000	0.000	0.000	0.000
9	A	29	VAL	0	-0.019	-0.009	12.971	0.354	0.354	0.000	0.000	0.000	0.000
10	A	30	TYR	0	-0.008	-0.011	15.408	0.050	0.050	0.000	0.000	0.000	0.000
11	A	31	VAL	0	-0.024	-0.018	18.385	0.057	0.057	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.933	-0.967	21.140	-0.725	-0.725	0.000	0.000	0.000	0.000
13	A	33	GLY	0	0.016	0.013	21.891	0.052	0.052	0.000	0.000	0.000	0.000
14	A	34	ALA	0	-0.052	-0.024	19.726	-0.052	-0.052	0.000	0.000	0.000	0.000
15	A	35	VAL	0	-0.008	-0.008	13.237	-0.083	-0.083	0.000	0.000	0.000	0.000
16	A	36	GLU	-1	-0.922	-0.984	15.147	-0.992	-0.992	0.000	0.000	0.000	0.000
17	A	37	ALA	0	-0.044	-0.012	9.709	0.123	0.123	0.000	0.000	0.000	0.000
18	A	38	SER	0	-0.002	-0.021	8.640	-0.242	-0.242	0.000	0.000	0.000	0.000
19	A	39	LEU	0	-0.014	-0.014	7.991	-0.735	-0.735	0.000	0.000	0.000	0.000
22	A	42	ALA	0	-0.047	-0.015	5.738	1.349	1.349	0.000	0.000	0.000	0.000
23	A	43	PRO	0	-0.011	-0.020	7.141	-0.527	-0.527	0.000	0.000	0.000	0.000
24	A	44	GLY	0	0.032	0.038	10.912	0.171	0.171	0.000	0.000	0.000	0.000
25	A	45	ASN	0	-0.008	-0.023	12.758	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	46	PRO	0	0.035	0.016	15.406	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	47	GLU	-1	-0.922	-0.961	18.766	0.412	0.412	0.000	0.000	0.000	0.000
28	A	48	GLU	-1	-0.788	-0.857	15.342	0.323	0.323	0.000	0.000	0.000	0.000
29	A	49	GLY	0	0.019	0.009	17.832	-0.095	-0.095	0.000	0.000	0.000	0.000
30	A	50	VAL	0	0.029	0.013	18.638	-0.069	-0.069	0.000	0.000	0.000	0.000
31	A	51	ARG	1	0.813	0.887	18.339	-0.281	-0.281	0.000	0.000	0.000	0.000
32	A	52	ILE	0	-0.036	0.000	15.770	-0.043	-0.043	0.000	0.000	0.000	0.000
33	A	53	MET	0	-0.013	-0.018	20.280	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	54	THR	0	-0.032	-0.030	22.891	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	55	THR	0	-0.035	-0.011	22.806	0.036	0.036	0.000	0.000	0.000	0.000
36	A	56	ASN	0	0.000	-0.021	24.307	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	57	ALA	0	-0.062	-0.031	23.729	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	58	LEU	0	-0.031	-0.007	18.425	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	59	GLY	0	0.060	0.028	21.184	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	60	ASN	0	-0.035	-0.017	21.704	0.006	0.006	0.000	0.000	0.000	0.000
41	A	61	CYS	0	-0.001	0.014	23.442	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	62	VAL	0	0.072	0.042	26.083	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	63	ALA	0	0.007	0.017	28.983	0.018	0.018	0.000	0.000	0.000	0.000
44	A	64	CYS	0	-0.124	-0.075	29.273	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	65	HIS	0	0.000	0.008	26.833	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	66	GLN	0	0.030	0.014	30.865	0.022	0.022	0.000	0.000	0.000	0.000
47	A	67	ILE	0	0.017	-0.010	26.472	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	68	GLY	0	-0.002	0.003	30.711	0.021	0.021	0.000	0.000	0.000	0.000
49	A	69	ALA	0	-0.008	-0.011	29.036	0.019	0.019	0.000	0.000	0.000	0.000
50	A	70	LEU	0	-0.069	-0.037	25.988	0.025	0.025	0.000	0.000	0.000	0.000
51	A	71	PRO	0	0.000	-0.001	30.617	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	72	ASP	-1	-0.927	-0.960	32.671	0.055	0.055	0.000	0.000	0.000	0.000
53	A	73	VAL	0	-0.070	-0.028	29.383	0.003	0.003	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.918	-0.963	32.737	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	75	PHE	0	-0.108	-0.065	34.467	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	76	PRO	0	0.014	0.029	33.009	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	77	GLY	0	0.001	-0.005	33.064	0.003	0.003	0.000	0.000	0.000	0.000
58	A	78	THR	0	-0.061	-0.046	34.354	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	79	ILE	0	-0.048	-0.014	33.040	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	80	ALA	0	-0.002	-0.003	31.418	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	81	PRO	0	-0.030	-0.023	32.452	0.019	0.019	0.000	0.000	0.000	0.000
62	A	82	PRO	0	0.023	0.015	31.425	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	83	LEU	0	-0.011	-0.007	25.128	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	84	ASP	-1	-0.759	-0.866	27.901	-0.137	-0.137	0.000	0.000	0.000	0.000
65	A	85	GLY	0	0.131	0.074	29.737	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	86	ALA	0	-0.058	-0.033	25.704	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	87	GLY	0	0.029	0.013	24.383	-0.048	-0.048	0.000	0.000	0.000	0.000
68	A	88	ASP	-1	-0.871	-0.935	25.271	-0.159	-0.159	0.000	0.000	0.000	0.000
69	A	89	ARG	1	0.746	0.873	28.182	0.262	0.262	0.000	0.000	0.000	0.000
70	A	90	TRP	0	-0.025	-0.005	23.693	-0.045	-0.045	0.000	0.000	0.000	0.000
71	A	91	THR	0	0.030	0.010	21.526	0.016	0.016	0.000	0.000	0.000	0.000
72	A	92	GLU	-1	-0.831	-0.909	14.739	-0.707	-0.707	0.000	0.000	0.000	0.000
73	A	93	ALA	0	0.046	0.039	16.871	-0.087	-0.087	0.000	0.000	0.000	0.000
74	A	94	GLN	0	0.038	0.020	17.926	-0.072	-0.072	0.000	0.000	0.000	0.000
75	A	95	LEU	0	-0.007	0.002	19.414	-0.043	-0.043	0.000	0.000	0.000	0.000
76	A	96	ARG	1	0.765	0.840	12.238	1.440	1.440	0.000	0.000	0.000	0.000
77	A	97	GLY	0	0.024	0.014	16.715	-0.134	-0.134	0.000	0.000	0.000	0.000
78	A	98	ILE	0	-0.021	-0.018	18.190	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	99	VAL	0	-0.009	-0.011	17.620	0.029	0.029	0.000	0.000	0.000	0.000
80	A	100	ALA	0	0.007	0.006	15.209	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	101	ASN	0	-0.003	-0.043	16.904	0.128	0.128	0.000	0.000	0.000	0.000
82	A	102	ALA	0	0.100	0.064	19.868	0.024	0.024	0.000	0.000	0.000	0.000
83	A	103	LYS	1	0.781	0.875	23.322	0.756	0.756	0.000	0.000	0.000	0.000
84	A	104	MET	0	-0.057	-0.013	20.025	0.043	0.043	0.000	0.000	0.000	0.000
85	A	105	THR	0	0.013	0.014	23.189	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	106	PHE	0	-0.057	-0.026	25.173	0.065	0.065	0.000	0.000	0.000	0.000
87	A	107	GLU	-1	-0.868	-0.936	28.183	-0.606	-0.606	0.000	0.000	0.000	0.000
88	A	108	GLY	0	-0.034	-0.022	29.124	0.042	0.042	0.000	0.000	0.000	0.000
89	A	109	THR	0	-0.043	-0.005	27.000	0.046	0.046	0.000	0.000	0.000	0.000
90	A	110	PHE	0	-0.001	-0.006	28.803	-0.037	-0.037	0.000	0.000	0.000	0.000
91	A	111	MET	0	0.012	0.026	22.969	0.008	0.008	0.000	0.000	0.000	0.000
92	A	112	PRO	0	0.005	0.007	23.439	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	113	ALA	0	-0.014	-0.004	19.717	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	114	PHE	0	0.010	0.007	17.978	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	115	TYR	0	-0.021	-0.027	8.384	0.178	0.178	0.000	0.000	0.000	0.000
96	A	116	LYS	1	0.891	0.963	15.025	0.864	0.864	0.000	0.000	0.000	0.000
97	A	117	VAL	0	0.019	0.005	13.911	0.070	0.070	0.000	0.000	0.000	0.000
98	A	118	ASP	-1	-0.838	-0.901	17.178	-1.413	-1.413	0.000	0.000	0.000	0.000
99	A	119	GLY	0	0.010	0.010	19.955	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	120	PHE	0	-0.053	-0.031	20.211	0.055	0.055	0.000	0.000	0.000	0.000
101	A	121	VAL	0	0.004	-0.008	25.303	0.028	0.028	0.000	0.000	0.000	0.000
102	A	122	ARG	1	0.881	0.936	29.001	0.416	0.416	0.000	0.000	0.000	0.000
103	A	123	PRO	0	0.063	0.052	24.096	0.033	0.033	0.000	0.000	0.000	0.000
104	A	124	GLY	0	0.037	0.022	25.537	0.038	0.038	0.000	0.000	0.000	0.000
105	A	125	ASP	-1	-0.854	-0.920	23.901	-0.477	-0.477	0.000	0.000	0.000	0.000
106	A	126	GLY	0	0.015	0.013	23.593	0.062	0.062	0.000	0.000	0.000	0.000
107	A	127	PHE	0	0.005	-0.007	24.403	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	128	SER	0	-0.063	-0.044	27.568	0.036	0.036	0.000	0.000	0.000	0.000
109	A	129	GLY	0	-0.010	-0.011	29.541	0.026	0.026	0.000	0.000	0.000	0.000
110	A	130	LYS	1	0.856	0.934	28.802	0.254	0.254	0.000	0.000	0.000	0.000
111	A	131	ALA	0	0.007	0.003	28.190	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	132	GLY	0	0.017	0.013	23.814	0.024	0.024	0.000	0.000	0.000	0.000
113	A	133	ALA	0	-0.042	-0.030	22.096	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	134	GLU	-1	-0.771	-0.882	20.148	-1.004	-1.004	0.000	0.000	0.000	0.000
115	A	135	PRO	0	-0.075	-0.037	15.573	0.047	0.047	0.000	0.000	0.000	0.000
116	A	136	LEU	0	-0.007	-0.010	17.227	0.037	0.037	0.000	0.000	0.000	0.000
117	A	137	ALA	0	-0.002	-0.001	14.730	-0.216	-0.216	0.000	0.000	0.000	0.000
118	A	138	PRO	0	-0.036	-0.008	12.175	0.126	0.126	0.000	0.000	0.000	0.000
119	A	139	ILE	0	-0.031	-0.012	15.498	0.115	0.115	0.000	0.000	0.000	0.000
120	A	140	LEU	0	-0.003	0.005	15.348	0.189	0.189	0.000	0.000	0.000	0.000
121	A	141	ASN	0	0.003	-0.009	10.349	-0.348	-0.348	0.000	0.000	0.000	0.000
122	A	142	ALA	0	0.087	0.028	7.592	0.282	0.282	0.000	0.000	0.000	0.000
123	A	143	GLN	0	-0.005	-0.018	8.025	0.053	0.053	0.000	0.000	0.000	0.000
124	A	144	GLN	0	0.032	0.010	9.573	0.020	0.020	0.000	0.000	0.000	0.000
125	A	145	ILE	0	0.013	0.013	12.358	0.127	0.127	0.000	0.000	0.000	0.000
126	A	146	GLU	-1	-0.697	-0.801	9.100	-1.619	-1.619	0.000	0.000	0.000	0.000
127	A	147	ASP	-1	-0.802	-0.901	12.465	0.498	0.498	0.000	0.000	0.000	0.000
128	A	148	VAL	0	-0.021	-0.019	14.614	0.075	0.075	0.000	0.000	0.000	0.000
129	A	149	VAL	0	-0.021	0.003	15.125	0.065	0.065	0.000	0.000	0.000	0.000
130	A	150	ALA	0	0.021	0.013	15.490	0.052	0.052	0.000	0.000	0.000	0.000
131	A	151	PHE	0	0.020	0.000	17.394	0.045	0.045	0.000	0.000	0.000	0.000
132	A	152	LEU	0	-0.002	0.007	19.966	0.015	0.015	0.000	0.000	0.000	0.000
133	A	153	VAL	0	0.009	0.001	18.956	0.009	0.009	0.000	0.000	0.000	0.000
134	A	154	THR	0	-0.090	-0.057	21.536	0.048	0.048	0.000	0.000	0.000	0.000
135	A	155	LEU	0	-0.052	-0.009	23.933	0.024	0.024	0.000	0.000	0.000	0.000
136	A	156	LYS	1	0.762	0.871	24.572	0.140	0.140	0.000	0.000	0.000	0.000
137	A	157	GLU	-2	-1.924	-1.944	29.009	-0.120	-0.120	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:CYS)